From 4cafd6bf95700917ac21e17517ff8b077563c5b8 Mon Sep 17 00:00:00 2001 From: Claude Date: Thu, 5 Mar 2026 13:16:54 +0000 Subject: [PATCH 1/4] Migrate to modern Python tooling: pyproject.toml, uv, ruff, ty - Replace setup.py + requirements*.txt with a single pyproject.toml using hatchling as build backend - Add [tool.uv] dev-dependencies for uv-managed dev workflow - Add [tool.ruff] config for linting (E/W/F/I/UP/B/C4/SIM) and formatting (replaces any prior flake8/black/isort setup) - Add [tool.ty] config for static type checking with ty - Add [tool.pytest.ini_options] and [tool.coverage] sections - Update CI to use astral-sh/setup-uv and uv sync/run, upgrade actions/checkout to v4, add dedicated lint and typecheck jobs uv.lock will be generated automatically on first `uv sync`. https://claude.ai/code/session_01G13wzGLvmoog4E73fUairt --- .github/workflows/ci.yml | 63 ++++++++++++++----- pyproject.toml | 133 +++++++++++++++++++++++++++++++++++++++ requirements.txt | 10 --- requirements_test.txt | 10 --- setup.py | 51 --------------- 5 files changed, 180 insertions(+), 87 deletions(-) create mode 100644 pyproject.toml delete mode 100644 requirements.txt delete mode 100644 requirements_test.txt delete mode 100644 setup.py diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 1c7bf76..34c3f64 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,4 +1,5 @@ -name: codecov +name: CI + on: pull_request: branches-ignore: @@ -6,30 +7,60 @@ on: push: branches: - main + jobs: - run: + test: runs-on: ${{ matrix.os }} strategy: matrix: os: [ubuntu-latest, macos-latest] - python-version: ['3.13', '3.12', '3.11', '3.10', '3.9'] + python-version: ["3.13", "3.12", "3.11", "3.10", "3.9"] env: OS: ${{ matrix.os }} steps: - - name: Checkout - uses: actions/checkout@v1 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + - uses: actions/checkout@v4 + + - name: Install uv + uses: astral-sh/setup-uv@v5 with: - python-version: ${{ matrix.python-version }} - node-version: 16 + enable-cache: true + + - name: Set up Python ${{ matrix.python-version }} + run: uv python install ${{ matrix.python-version }} + - name: Install dependencies - run: | - pip install -r requirements.txt --use-pep517 - pip install -r requirements_test.txt --use-pep517 - python setup.py sdist bdist_wheel - pip install dist/*.whl + run: uv sync --python ${{ matrix.python-version }} + - name: Run tests and collect coverage - run: python -m pytest tests/ --cov=./ --cov-report=xml + run: uv run pytest + - name: Upload coverage to Codecov - uses: codecov/codecov-action@v3 + uses: codecov/codecov-action@v4 + + lint: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + + - name: Install uv + uses: astral-sh/setup-uv@v5 + + - name: Ruff lint + run: uvx ruff check . + + - name: Ruff format check + run: uvx ruff format --check . + + typecheck: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + + - name: Install uv + uses: astral-sh/setup-uv@v5 + + - name: Install ty + run: uv tool install ty + + - name: Run ty + run: uv run ty check obsidiantools diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..f159211 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,133 @@ +[build-system] +requires = ["hatchling"] +build-backend = "hatchling.build" + +[project] +name = "obsidiantools" +version = "0.11.0" +description = "Obsidian Tools - a Python interface for Obsidian.md vaults" +readme = "README.md" +license = { text = "BSD" } +authors = [{ name = "Mark Farragher" }] +keywords = [ + "obsidian", + "obsidian.md", + "knowledge", + "note-taking", + "notes", + "knowledge management", + "connected notes", +] +classifiers = [ + "Development Status :: 3 - Alpha", + "Intended Audience :: Education", + "Intended Audience :: Science/Research", + "Topic :: Text Processing :: Markup :: Markdown", + "Topic :: Office/Business", + "Topic :: Education", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", + "License :: OSI Approved :: BSD License", + "Operating System :: OS Independent", +] +requires-python = ">=3.9" +dependencies = [ + "markdown", + "pymdown-extensions", + "html2text", + "pandas", + "numpy", + "networkx", + "python-frontmatter", + "beautifulsoup4", + "bleach", + "lxml", +] + +[project.urls] +Source = "https://github.com/mfarragher/obsidiantools" + +[project.optional-dependencies] +dev = [ + "pytest", + "pytest-cov", + "pytest-mock", + "coverage", + "twine", +] + +# --------------------------------------------------------------------------- +# uv +# --------------------------------------------------------------------------- +[tool.uv] +dev-dependencies = [ + "pytest", + "pytest-cov", + "pytest-mock", + "coverage", + "twine", + "ruff", + "ty", +] + +# --------------------------------------------------------------------------- +# Ruff – linting & formatting +# --------------------------------------------------------------------------- +[tool.ruff] +target-version = "py39" +line-length = 88 + +[tool.ruff.lint] +select = [ + "E", # pycodestyle errors + "W", # pycodestyle warnings + "F", # Pyflakes + "I", # isort + "UP", # pyupgrade + "B", # flake8-bugbear + "C4", # flake8-comprehensions + "SIM", # flake8-simplify +] +ignore = [ + "E501", # line-too-long (formatter handles this) +] + +[tool.ruff.lint.isort] +known-first-party = ["obsidiantools"] + +[tool.ruff.format] +quote-style = "double" +indent-style = "space" + +# --------------------------------------------------------------------------- +# ty – static type checking +# --------------------------------------------------------------------------- +[tool.ty] +# Specify source root for type checking +src = ["obsidiantools"] + +[tool.ty.rules] +# Start with a permissive baseline; tighten over time +reportMissingTypeStubs = "warn" +reportUnknownVariableType = "warn" +reportUnknownMemberType = "warn" + +# --------------------------------------------------------------------------- +# pytest +# --------------------------------------------------------------------------- +[tool.pytest.ini_options] +testpaths = ["tests"] +addopts = "--cov=obsidiantools --cov-report=xml" + +# --------------------------------------------------------------------------- +# coverage +# --------------------------------------------------------------------------- +[tool.coverage.run] +source = ["obsidiantools"] +omit = ["tests/*"] + +[tool.coverage.report] +show_missing = true diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 6fe8252..0000000 --- a/requirements.txt +++ /dev/null @@ -1,10 +0,0 @@ -markdown -pymdown-extensions -html2text -pandas -numpy -networkx -python-frontmatter -beautifulsoup4 -bleach -lxml # front matter parsing diff --git a/requirements_test.txt b/requirements_test.txt deleted file mode 100644 index b96ac13..0000000 --- a/requirements_test.txt +++ /dev/null @@ -1,10 +0,0 @@ -setuptools -pytest -pytest-cov -pytest-mock -coverage -codecov -tox -twine -wheel -pandas>=1.5 diff --git a/setup.py b/setup.py deleted file mode 100644 index ba9c661..0000000 --- a/setup.py +++ /dev/null @@ -1,51 +0,0 @@ -import setuptools - -with open("README.md", "r", encoding="utf8") as f: - LONG_DESCRIPTION = f.read() - -PROJECT_URLS = {"Source": "https://github.com/mfarragher/obsidiantools"} -INSTALL_REQUIRES = [ - "markdown", - "pymdown-extensions", - "html2text", - "pandas", - "numpy", - "networkx", - "python-frontmatter", - "beautifulsoup4", - "bleach", - "lxml"] - -CLASSIFIERS = [ - "Development Status :: 3 - Alpha", - "Intended Audience :: Education", - "Intended Audience :: Science/Research", - "Topic :: Text Processing :: Markup :: Markdown", - "Topic :: Office/Business", - "Topic :: Education", - "Programming Language :: Python :: 3.11", - "Programming Language :: Python :: 3.10", - "Programming Language :: Python :: 3.9", - "License :: OSI Approved :: BSD License", - "Operating System :: OS Independent", -] - -setuptools.setup( - name="obsidiantools", - version="0.11.0", - author="Mark Farragher", - description="Obsidian Tools - a Python interface for Obsidian.md vaults", - long_description=LONG_DESCRIPTION, - long_description_content_type="text/markdown", - keywords=["obsidian", "obsidian.md", "knowledge", - "note-taking", "notes", - "knowledge management", - "connected notes"], - url="https://github.com/mfarragher/obsidiantools", - project_urls=PROJECT_URLS, - packages=setuptools.find_packages(exclude=("tests")), - python_requires=">=3.9", - install_requires=INSTALL_REQUIRES, - license="BSD", - classifiers=CLASSIFIERS -) From 42c7a6a1786db372a4f7b46f1a8fa5f537e93bad Mon Sep 17 00:00:00 2001 From: Claude Date: Thu, 5 Mar 2026 13:35:40 +0000 Subject: [PATCH 2/4] Apply ruff lint fixes and formatting across codebase - Fix F401: use explicit re-export syntax in __init__.py (as api, etc.) - Fix I001: sort all import blocks to isort standard - Fix C416/C404/C405: replace unnecessary comprehensions with simpler equivalents (dict(), list(), set literals) - Fix SIM118: remove .keys() in dict membership tests - Fix UP032: convert .format() calls to f-strings - Fix B006: replace mutable default arg with None sentinel in html_processing._remove_main_formatting - Fix B028: add stacklevel=2 to warnings.warn in api.py - Fix E722: replace bare except with except Exception in md_utils.py - Fix W291: suppress intentional trailing whitespace in test string literal via per-file-ignores in pyproject.toml - Run ruff format over all 23 files (consistent style) - Remove --cov flags from pytest addopts (added by CI, not hardcoded) https://claude.ai/code/session_01G13wzGLvmoog4E73fUairt --- obsidiantools/__init__.py | 10 +- obsidiantools/_constants.py | 83 +- obsidiantools/_io.py | 74 +- obsidiantools/api.py | 705 ++++++++-------- obsidiantools/canvas_utils.py | 68 +- obsidiantools/html_processing.py | 25 +- obsidiantools/md_utils.py | 254 +++--- obsidiantools/media_utils.py | 12 +- pyproject.toml | 5 +- tests/test_api_canvas.py | 1 - tests/test_api_md.py | 1 - tests/test_api_setup.py | 23 +- tests/test_api_vault_stub_attr_setters.py | 18 +- ...api_vault_stub_connect_attachments_true.py | 438 +++++----- ..._api_vault_stub_connect_defaults_canvas.py | 82 +- ...test_api_vault_stub_connect_defaults_md.py | 791 ++++++++++-------- tests/test_api_vault_stub_gather.py | 30 +- tests/test_canvas_utils_fpath_funcs.py | 8 +- tests/test_canvas_utils_vault_stub.py | 29 +- tests/test_html_processing.py | 10 +- tests/test_md_utils.py | 279 +++--- tests/test_md_utils_fpath_funcs.py | 19 +- tests/test_md_utils_vault_stub.py | 29 +- 23 files changed, 1595 insertions(+), 1399 deletions(-) diff --git a/obsidiantools/__init__.py b/obsidiantools/__init__.py index 7300a0e..a00d166 100644 --- a/obsidiantools/__init__.py +++ b/obsidiantools/__init__.py @@ -1,5 +1,5 @@ -from . import api -from . import md_utils -from . import html_processing -from . import canvas_utils -from . import media_utils +from . import api as api +from . import canvas_utils as canvas_utils +from . import html_processing as html_processing +from . import md_utils as md_utils +from . import media_utils as media_utils diff --git a/obsidiantools/_constants.py b/obsidiantools/_constants.py index a5dcff2..bcf8ce4 100644 --- a/obsidiantools/_constants.py +++ b/obsidiantools/_constants.py @@ -1,36 +1,77 @@ # WIKILINKS AND EMBEDDED FILES: regex that includes any aliases # group 0 captures embedded link; group 1 is everything inside [[]] -WIKILINK_REGEX = r'(!)?\[{2}([^\]\]]+)\]{2}' +WIKILINK_REGEX = r"(!)?\[{2}([^\]\]]+)\]{2}" # TAGS -TAG_INCLUDE_NESTED_REGEX = r'(?\)' -INLINE_LINK_VIA_MD_ONLY_REGEX = r'\[([^\]]+)\]\(([^)]+)\)' +INLINE_LINK_AFTER_HTML_PROC_REGEX = r"\[([^\]]+)\]\(<([^)]+)>\)" +INLINE_LINK_VIA_MD_ONLY_REGEX = r"\[([^\]]+)\]\(([^)]+)\)" # helpers: -WIKILINK_AS_STRING_REGEX = r'\[[^\]]+\]\([^)]+\)' -EMBEDDED_FILE_LINK_AS_STRING_REGEX = r'!?\[{2}([^\]\]]+)\]{2}' +WIKILINK_AS_STRING_REGEX = r"\[[^\]]+\]\([^)]+\)" +EMBEDDED_FILE_LINK_AS_STRING_REGEX = r"!?\[{2}([^\]\]]+)\]{2}" # Sets of extensions via https://help.obsidian.md/How+to/Embed+files : # NB: file.ext and file.EXT can exist in same folder -IMG_EXT_SET = {'.png', '.jpg', '.jpeg', '.gif', '.bmp', '.svg', - '.PNG', '.JPG', '.JPEG', '.GIF', '.BMP', '.SVG'} -AUDIO_EXT_SET = {'.mp3', '.webm', '.wav', '.m4a', '.ogg', '.3gp', '.flac', - '.MP3', '.WEBM', '.WAV', '.M4A', '.OGG', '.3GP', '.FLAC'} -VIDEO_EXT_SET = {'.mp4', '.webm', '.ogv', '.mov', '.mkv', - '.MP4', '.WEBM', '.OGV', '.MOV', '.MKV'} -PDF_EXT_SET = {'.pdf', - '.PDF'} +IMG_EXT_SET = { + ".png", + ".jpg", + ".jpeg", + ".gif", + ".bmp", + ".svg", + ".PNG", + ".JPG", + ".JPEG", + ".GIF", + ".BMP", + ".SVG", +} +AUDIO_EXT_SET = { + ".mp3", + ".webm", + ".wav", + ".m4a", + ".ogg", + ".3gp", + ".flac", + ".MP3", + ".WEBM", + ".WAV", + ".M4A", + ".OGG", + ".3GP", + ".FLAC", +} +VIDEO_EXT_SET = { + ".mp4", + ".webm", + ".ogv", + ".mov", + ".mkv", + ".MP4", + ".WEBM", + ".OGV", + ".MOV", + ".MKV", +} +PDF_EXT_SET = {".pdf", ".PDF"} # canvas files: -CANVAS_EXT_SET = {'.canvas', - '.CANVAS'} +CANVAS_EXT_SET = {".canvas", ".CANVAS"} # metadata df cols order: METADATA_DF_COLS_GENERIC_TYPE = [ - 'rel_filepath', 'abs_filepath', - 'file_exists', - 'n_backlinks', 'n_wikilinks', 'n_tags', 'n_embedded_files', - 'modified_time'] + "rel_filepath", + "abs_filepath", + "file_exists", + "n_backlinks", + "n_wikilinks", + "n_tags", + "n_embedded_files", + "modified_time", +] diff --git a/obsidiantools/_io.py b/obsidiantools/_io.py index ce86d95..e85f1e6 100644 --- a/obsidiantools/_io.py +++ b/obsidiantools/_io.py @@ -1,5 +1,6 @@ -from pathlib import Path from glob import glob +from pathlib import Path + import numpy as np @@ -18,16 +19,20 @@ def get_relpaths_from_dir(dir_path: Path, *, extension: str) -> list[Path]: Returns: list of Path objects """ - relpaths_list = [Path(p).relative_to(dir_path) - for p in glob(f"{dir_path}/**/*.{extension}", - recursive=True)] + relpaths_list = [ + Path(p).relative_to(dir_path) + for p in glob(f"{dir_path}/**/*.{extension}", recursive=True) + ] return relpaths_list -def get_relpaths_matching_subdirs(dir_path: Path, *, - extension: str, - include_subdirs: list = None, - include_root: bool = True) -> list[Path]: +def get_relpaths_matching_subdirs( + dir_path: Path, + *, + extension: str, + include_subdirs: list = None, + include_root: bool = True, +) -> list[Path]: """Get list of relative paths for {extension} files in a given directory, filtered to include specified subdirectories (with include_subdirs kwarg). The default arguments align with get_relpaths_from_dir @@ -61,34 +66,35 @@ def get_relpaths_matching_subdirs(dir_path: Path, *, # forward slash consistently here. if include_subdirs: - include_subdirs_final = [str(Path(i).as_posix()) - for i in include_subdirs] + include_subdirs_final = [str(Path(i).as_posix()) for i in include_subdirs] if not include_subdirs and include_root: - return get_relpaths_from_dir(dir_path, - extension=extension) + return get_relpaths_from_dir(dir_path, extension=extension) elif not include_subdirs and not include_root: - return [i for i in get_relpaths_from_dir(dir_path, - extension=extension) - if str(i.parent.as_posix()) != '.'] + return [ + i + for i in get_relpaths_from_dir(dir_path, extension=extension) + if str(i.parent.as_posix()) != "." + ] else: if include_root: - return [i for i in get_relpaths_from_dir(dir_path, - extension=extension) - if str(i.parent.as_posix()) - in include_subdirs_final + ['.']] + return [ + i + for i in get_relpaths_from_dir(dir_path, extension=extension) + if str(i.parent.as_posix()) in include_subdirs_final + ["."] + ] else: - return [i for i in get_relpaths_from_dir(dir_path, - extension=extension) - if str(i.parent.as_posix()) - in include_subdirs_final] + return [ + i + for i in get_relpaths_from_dir(dir_path, extension=extension) + if str(i.parent.as_posix()) in include_subdirs_final + ] -def _get_valid_filepaths_by_ext_set(dirpath: Path, *, - exts: set[str]): - all_files = [p.relative_to(dirpath) - for p in Path(dirpath).glob("**/*") - if p.suffix in exts] +def _get_valid_filepaths_by_ext_set(dirpath: Path, *, exts: set[str]): + all_files = [ + p.relative_to(dirpath) for p in Path(dirpath).glob("**/*") if p.suffix in exts + ] return all_files @@ -98,15 +104,13 @@ def _get_shortest_path_by_filename(relpaths_list: list[Path]) -> dict[str, Path] # get indices of dupe 'filename w/ ext': _, inverse_ix, counts = np.unique( - np.array(all_file_names_list), - return_inverse=True, - return_counts=True, - axis=0) + np.array(all_file_names_list), return_inverse=True, return_counts=True, axis=0 + ) dupe_names_ix = np.where(counts[inverse_ix] > 1)[0] # get shortest paths via mask: shortest_paths_arr = np.array(all_file_names_list, dtype=object) shortest_paths_arr[dupe_names_ix] = np.array( - [str(fpath) - for fpath in relpaths_list])[dupe_names_ix] - return {fn: path for fn, path in zip(shortest_paths_arr, relpaths_list)} + [str(fpath) for fpath in relpaths_list] + )[dupe_names_ix] + return dict(zip(shortest_paths_arr, relpaths_list)) diff --git a/obsidiantools/api.py b/obsidiantools/api.py index 5f02bde..31b51f1 100644 --- a/obsidiantools/api.py +++ b/obsidiantools/api.py @@ -1,39 +1,51 @@ import warnings +from collections import Counter +from itertools import chain +from pathlib import Path + import networkx as nx import numpy as np import pandas as pd -from collections import Counter -from pathlib import Path -from itertools import chain -# init -from .md_utils import (get_md_relpaths_matching_subdirs) -from .canvas_utils import (get_canvas_relpaths_matching_subdirs, - _get_all_valid_canvas_file_relpaths) -# connect -from .md_utils import (_get_md_front_matter_and_content, - _get_html_from_md_content, - _get_md_links_from_source_text, - _get_unique_md_links_from_source_text, - _get_unique_wikilinks_from_source_text, - _get_all_wikilinks_from_source_text, - _get_all_embedded_files_from_source_text, - get_tags, - _get_all_latex_from_html_content) from ._constants import METADATA_DF_COLS_GENERIC_TYPE from ._io import _get_shortest_path_by_filename -from .media_utils import _get_all_valid_media_file_relpaths -# gather: -from .md_utils import (get_source_text_from_html, - _get_readable_text_from_html) + # canvas: -from .canvas_utils import (get_canvas_content, - get_canvas_graph_detail) +from .canvas_utils import ( + _get_all_valid_canvas_file_relpaths, + get_canvas_content, + get_canvas_graph_detail, + get_canvas_relpaths_matching_subdirs, +) + +# init +# connect +# gather: +from .md_utils import ( + _get_all_embedded_files_from_source_text, + _get_all_latex_from_html_content, + _get_all_wikilinks_from_source_text, + _get_html_from_md_content, + _get_md_front_matter_and_content, + _get_md_links_from_source_text, + _get_readable_text_from_html, + _get_unique_md_links_from_source_text, + _get_unique_wikilinks_from_source_text, + get_md_relpaths_matching_subdirs, + get_source_text_from_html, + get_tags, +) +from .media_utils import _get_all_valid_media_file_relpaths class Vault: - def __init__(self, dirpath: Path, *, - include_subdirs: list[str] = None, include_root: bool = True): + def __init__( + self, + dirpath: Path, + *, + include_subdirs: list[str] = None, + include_root: bool = True, + ): """A Vault object lets you dig into your Obsidian vault, by giving you a toolkit for analysing its contents. Specify a dirpath to instantiate the class. This class is intended to support multiple @@ -132,18 +144,20 @@ def __init__(self, dirpath: Path, *, canvas_graph_detail_index """ if not isinstance(dirpath, Path): - raise TypeError("Specify a pathlib.Path for the dirpath argument (not other types like strings)") + raise TypeError( + "Specify a pathlib.Path for the dirpath argument (not other types like strings)" + ) # args: self._dirpath = dirpath self._attachments = None # connect() self._md_file_index = self._get_md_relpaths_by_name( - include_subdirs=include_subdirs, - include_root=include_root) + include_subdirs=include_subdirs, include_root=include_root + ) self._canvas_file_index = self._get_canvas_relpaths_by_name( - include_subdirs=include_subdirs, - include_root=include_root) + include_subdirs=include_subdirs, include_root=include_root + ) self._is_connected = False self._is_gathered = False @@ -443,25 +457,26 @@ def canvas_content_index(self, value) -> dict[str, str]: self._canvas_content_index = value @property - def canvas_graph_detail_index(self) -> \ - dict[str, tuple[nx.MultiDiGraph, - dict[str, tuple[int, int]], - dict[tuple[str, str], str]] - ]: + def canvas_graph_detail_index( + self, + ) -> dict[ + str, + tuple[nx.MultiDiGraph, dict[str, tuple[int, int]], dict[tuple[str, str], str]], + ]: """dict of tuple: 'shortest path when possible' filepath with canvas ext (k), to canvas graph detail tuple (v).""" return self._canvas_graph_detail_index @canvas_graph_detail_index.setter - def canvas_graph_detail_index(self, value) -> \ - dict[str, tuple[nx.MultiDiGraph, - dict[str, tuple[int, int]], - dict[tuple[str, str], str]] - ]: + def canvas_graph_detail_index( + self, value + ) -> dict[ + str, + tuple[nx.MultiDiGraph, dict[str, tuple[int, int]], dict[tuple[str, str], str]], + ]: self._canvas_graph_detail_index = value - def connect(self, *, show_nested_tags: bool = False, - attachments=False): + def connect(self, *, show_nested_tags: bool = False, attachments=False): """connect your notes together by representing the vault as a Networkx graph object, G. @@ -501,19 +516,17 @@ def connect(self, *, show_nested_tags: bool = False, # loop through md files: for f, relpath in self._md_file_index.items(): self._connect_update_based_on_new_relpath( - relpath, note=f, - show_nested_tags=show_nested_tags) + relpath, note=f, show_nested_tags=show_nested_tags + ) # canvas content: # loop through canvas files: self._canvas_content_index = {} self._canvas_graph_detail_index = {} for f, relpath in self._canvas_file_index.items(): - content_c = get_canvas_content( - self._dirpath / relpath) + content_c = get_canvas_content(self._dirpath / relpath) self._canvas_content_index[f] = content_c - G_c, pos_c, edge_labels_c = get_canvas_graph_detail( - content_c) + G_c, pos_c, edge_labels_c = get_canvas_graph_detail(content_c) self._canvas_graph_detail_index[f] = G_c, pos_c, edge_labels_c # set these up before graph is created: @@ -521,8 +534,7 @@ def connect(self, *, show_nested_tags: bool = False, self._set_media_file_attrs() # graph setup: - graph_data_dict = self.__get_graph_data_dict( - attachments=attachments) + graph_data_dict = self.__get_graph_data_dict(attachments=attachments) G = nx.MultiDiGraph(graph_data_dict) self._graph = G self._set_graph_related_attributes() @@ -537,79 +549,76 @@ def connect(self, *, show_nested_tags: bool = False, return self # fluent - def _connect_update_based_on_new_relpath(self, relpath: Path, *, - note: str, - show_nested_tags: bool): + def _connect_update_based_on_new_relpath( + self, relpath: Path, *, note: str, show_nested_tags: bool + ): """Individual file read & associated attrs update for the connect method.""" exclude_canvas = not self._attachments # MAIN file read: front_matter, content = _get_md_front_matter_and_content( - self._dirpath / relpath) + self._dirpath / relpath + ) html = _get_html_from_md_content(content) - src_txt = get_source_text_from_html( - html, remove_code=True) + src_txt = get_source_text_from_html(html, remove_code=True) # info from core text: - self._md_links_index[note] = ( - _get_md_links_from_source_text(src_txt)) - self._unique_md_links_index[note] = ( - _get_unique_md_links_from_source_text(src_txt)) + self._md_links_index[note] = _get_md_links_from_source_text(src_txt) + self._unique_md_links_index[note] = _get_unique_md_links_from_source_text( + src_txt + ) self._embedded_files_index[note] = ( - _get_all_embedded_files_from_source_text( - src_txt, remove_aliases=True) + _get_all_embedded_files_from_source_text(src_txt, remove_aliases=True) # (aliases are redundant for connect method) - ) - self._wikilinks_index[note] = ( - _get_all_wikilinks_from_source_text( - src_txt, remove_aliases=True, - exclude_canvas=exclude_canvas)) - self._unique_wikilinks_index[note] = ( - _get_unique_wikilinks_from_source_text( - src_txt, remove_aliases=True, - exclude_canvas=exclude_canvas)) + ) + self._wikilinks_index[note] = _get_all_wikilinks_from_source_text( + src_txt, remove_aliases=True, exclude_canvas=exclude_canvas + ) + self._unique_wikilinks_index[note] = _get_unique_wikilinks_from_source_text( + src_txt, remove_aliases=True, exclude_canvas=exclude_canvas + ) # info from html: - self._math_index[note] = (_get_all_latex_from_html_content( - html)) + self._math_index[note] = _get_all_latex_from_html_content(html) # split out front matter: self._front_matter_index[note] = front_matter # MORE file reads needed for extra info: self._tags_index[note] = get_tags( - self._dirpath / relpath, - show_nested=show_nested_tags) + self._dirpath / relpath, show_nested=show_nested_tags + ) def _set_media_file_attrs(self): - (embedded_files_by_short_path, - non_embedded_files_by_short_path, - nonexistent_files_by_short_path) = ( - self._get_media_file_dicts_tuple()) + ( + embedded_files_by_short_path, + non_embedded_files_by_short_path, + nonexistent_files_by_short_path, + ) = self._get_media_file_dicts_tuple() # only set media file index once: if not self._media_file_index: - files_ix = {**embedded_files_by_short_path, - **non_embedded_files_by_short_path} + files_ix = { + **embedded_files_by_short_path, + **non_embedded_files_by_short_path, + } self._media_file_index = files_ix # these attrs can be set again, once graph is created: - self._nonexistent_media_files = list( - nonexistent_files_by_short_path.keys()) - self._isolated_media_files = list( - non_embedded_files_by_short_path.keys()) + self._nonexistent_media_files = list(nonexistent_files_by_short_path.keys()) + self._isolated_media_files = list(non_embedded_files_by_short_path.keys()) def _set_canvas_file_attrs(self): - (linked_files_by_short_path, - non_linked_files_by_short_path, - nonexistent_files_by_short_path) = ( - self._get_canvas_file_dicts_tuple()) - - self._nonexistent_canvas_files = list( - nonexistent_files_by_short_path.keys()) - self._isolated_canvas_files = list( - non_linked_files_by_short_path.keys()) - - def _get_media_file_dicts_tuple(self) \ - -> tuple[dict[str, Path], dict[str, Path], dict[str, Path]]: + ( + linked_files_by_short_path, + non_linked_files_by_short_path, + nonexistent_files_by_short_path, + ) = self._get_canvas_file_dicts_tuple() + + self._nonexistent_canvas_files = list(nonexistent_files_by_short_path.keys()) + self._isolated_canvas_files = list(non_linked_files_by_short_path.keys()) + + def _get_media_file_dicts_tuple( + self, + ) -> tuple[dict[str, Path], dict[str, Path], dict[str, Path]]: """Return (existent files embedded, existent files not embedded, nonexistent files embedded). @@ -621,17 +630,19 @@ def _get_media_file_dicts_tuple(self) \ # detail on all embedded files AND ones that exist: all_files_embedded_in_notes = list( - chain.from_iterable(self._embedded_files_index.values())) - media_file_relpaths_existent = _get_all_valid_media_file_relpaths( - self._dirpath) + chain.from_iterable(self._embedded_files_index.values()) + ) + media_file_relpaths_existent = _get_all_valid_media_file_relpaths(self._dirpath) return self.__get_file_dicts_tuple( all_files_embedded_in_notes, links_index=self._embedded_files_index, existing_file_relpaths=media_file_relpaths_existent, - file_type='media') + file_type="media", + ) - def _get_canvas_file_dicts_tuple(self) \ - -> tuple[dict[str, Path], dict[str, Path], dict[str, Path]]: + def _get_canvas_file_dicts_tuple( + self, + ) -> tuple[dict[str, Path], dict[str, Path], dict[str, Path]]: """Return (existent files linked, existent files not linked, nonexistent files linked). @@ -643,96 +654,110 @@ def _get_canvas_file_dicts_tuple(self) \ # detail on all linked files AND ones that exist: all_files_linked_in_notes = list( - chain.from_iterable(self._wikilinks_index.values())) + chain.from_iterable(self._wikilinks_index.values()) + ) canvas_file_relpaths_existent = _get_all_valid_canvas_file_relpaths( - self._dirpath) + self._dirpath + ) return self.__get_file_dicts_tuple( all_files_linked_in_notes, links_index=self._wikilinks_index, existing_file_relpaths=canvas_file_relpaths_existent, - file_type='canvas') + file_type="canvas", + ) - def __get_file_dicts_tuple(self, linked_files_list: list[str], *, - links_index: dict[list[str]], - existing_file_relpaths: list[Path], - file_type: str): + def __get_file_dicts_tuple( + self, + linked_files_list: list[str], + *, + links_index: dict[list[str]], + existing_file_relpaths: list[Path], + file_type: str, + ): # get shortest path for each 'linked' file of chosen type; # check whether each exists - shortest_names_existent = _get_shortest_path_by_filename( - existing_file_relpaths) + shortest_names_existent = _get_shortest_path_by_filename(existing_file_relpaths) # for nonexistent files, don't want to catch other types: short_names_not_wanted_set = ( set(shortest_names_existent) .union(set(self._nonexistent_notes)) - .union(set(self._md_file_index))) - if file_type == 'canvas': + .union(set(self._md_file_index)) + ) + if file_type == "canvas": other_fpaths_not_wanted_set = _get_all_valid_media_file_relpaths( - self._dirpath) - elif file_type == 'media': + self._dirpath + ) + elif file_type == "media": other_fpaths_not_wanted_set = _get_all_valid_canvas_file_relpaths( - self._dirpath) + self._dirpath + ) else: raise ValueError('Value for type is either "canvas" or "media".') shortest_names_nonexistent = { - fn: Path(fn) for fn in chain(*links_index.values()) + fn: Path(fn) + for fn in chain(*links_index.values()) if fn not in short_names_not_wanted_set - and Path(fn) not in other_fpaths_not_wanted_set} - shortest_names = {**shortest_names_existent, - **shortest_names_nonexistent} + and Path(fn) not in other_fpaths_not_wanted_set + } + shortest_names = {**shortest_names_existent, **shortest_names_nonexistent} # SETS # existent files (either linked or not): - set_files_existent_linked = ( - set(shortest_names_existent) - .intersection(set(linked_files_list))) - set_files_existent_not_linked = ( - set(shortest_names_existent) - .difference(set_files_existent_linked)) - # nonexistent files: - set_files_nonexistent_linked = ( + set_files_existent_linked = set(shortest_names_existent).intersection( set(linked_files_list) - .intersection(set(shortest_names_nonexistent))) + ) + set_files_existent_not_linked = set(shortest_names_existent).difference( + set_files_existent_linked + ) + # nonexistent files: + set_files_nonexistent_linked = set(linked_files_list).intersection( + set(shortest_names_nonexistent) + ) # DICTS # existent files (either linked or not): linked_files_by_short_path = { short_path: rel_path for short_path, rel_path in shortest_names.items() - if short_path in set_files_existent_linked} + if short_path in set_files_existent_linked + } non_linked_files_by_short_path = { short_path: rel_path for short_path, rel_path in shortest_names.items() - if short_path in set_files_existent_not_linked} + if short_path in set_files_existent_not_linked + } # nonexistent files: nonexistent_files_by_short_path = { short_path: np.nan - for short_path in shortest_names_nonexistent.keys() - if short_path in set_files_nonexistent_linked} - - return (linked_files_by_short_path, - non_linked_files_by_short_path, - nonexistent_files_by_short_path) + for short_path in shortest_names_nonexistent + if short_path in set_files_nonexistent_linked + } + + return ( + linked_files_by_short_path, + non_linked_files_by_short_path, + nonexistent_files_by_short_path, + ) def _get_backlink_counts_for_media_files_only(self) -> dict[str, int]: dict_out = dict.fromkeys(self._media_file_index.keys(), 0) - dict_counts = dict( - Counter(list(chain(*self._embedded_files_index.values())))) + dict_counts = dict(Counter(list(chain(*self._embedded_files_index.values())))) # merge counts into dict_out: dict_out = {**dict_out, **dict_counts} return dict_out def _get_backlink_counts_for_canvas_files_only(self) -> dict[str, int]: if not self._attachments: - raise AttributeError('Set attachments=True in connect() to get backlink counts for canvas files.') + raise AttributeError( + "Set attachments=True in connect() to get backlink counts for canvas files." + ) dict_out = dict.fromkeys(self._canvas_file_index.keys(), 0) - dict_counts = dict( - Counter(list(chain(*self._wikilinks_index.values())))) + dict_counts = dict(Counter(list(chain(*self._wikilinks_index.values())))) # merge counts into dict_out: dict_out = {**dict_out, **dict_counts} return dict_out - def __get_graph_data_dict(self, *, attachments=False) -> \ - dict[str, list[str]]: + def __get_graph_data_dict(self, *, attachments=False) -> dict[str, list[str]]: """Get the dict {k: v} of the graph's data: where k is a note name and v is a list of the 'wikilinks' in a note. @@ -762,27 +787,32 @@ def __get_graph_data_dict(self, *, attachments=False) -> \ # attachments include 'media' files and canvas files: # i) use wikilinks & embedded file info for graph edges: d_out = { - n: (self._wikilinks_index.get(n, []) + n: ( + self._wikilinks_index.get(n, []) + self._embedded_files_index.get(n, []) + ) + for n in ( + set( + list(self._wikilinks_index.keys()) + + list(self._embedded_files_index.keys()) ) - for n in (set(list(self._wikilinks_index.keys()) - + list(self._embedded_files_index.keys()))) + ) } # ii) add isolated media files & canvas files as nodes: isolated_files_dict = { - short_path: [] for short_path - in [*self._isolated_media_files, - *self._isolated_canvas_files]} - d_out = {**d_out, - **isolated_files_dict} + short_path: [] + for short_path in [ + *self._isolated_media_files, + *self._isolated_canvas_files, + ] + } + d_out = {**d_out, **isolated_files_dict} return d_out def _set_graph_related_attributes(self): - self._backlinks_index = self._get_backlinks_index( - graph=self._graph) + self._backlinks_index = self._get_backlinks_index(graph=self._graph) self._nonexistent_notes = self._get_nonexistent_notes() - self._isolated_notes = self._get_isolated_notes( - graph=self._graph) + self._isolated_notes = self._get_isolated_notes(graph=self._graph) def gather(self, *, tags: list[str] = None): """gather the content of your notes so that all the plaintext is @@ -807,30 +837,25 @@ def gather(self, *, tags: list[str] = None): and produces a one-line string. """ for f, relpath in self._md_file_index.items(): - self._gather_update_based_on_new_relpath( - relpath, - note=f, tags=tags) + self._gather_update_based_on_new_relpath(relpath, note=f, tags=tags) self._is_gathered = True return self # fluent - def _gather_update_based_on_new_relpath(self, relpath: Path, *, - note: str, tags: list[str]): + def _gather_update_based_on_new_relpath( + self, relpath: Path, *, note: str, tags: list[str] + ): """Individual file read & associated attrs update for the gather method.""" # MAIN file read: - _, content = _get_md_front_matter_and_content( - self._dirpath / relpath) + _, content = _get_md_front_matter_and_content(self._dirpath / relpath) html = _get_html_from_md_content(content) # (also remove LaTeX for source text:) - src_txt = get_source_text_from_html( - html, remove_code=True, remove_math=True) + src_txt = get_source_text_from_html(html, remove_code=True, remove_math=True) # 'source' text will not remove any content, but 'readable' will: self._source_text_index[note] = src_txt - self._readable_text_index[note] = ( - _get_readable_text_from_html( - html, tags=tags)) + self._readable_text_index[note] = _get_readable_text_from_html(html, tags=tags) def get_backlinks(self, note_name: str) -> list[str]: """Get backlinks for a note (given its name). @@ -849,10 +874,10 @@ def get_backlinks(self, note_name: str) -> list[str]: list """ if not self._is_connected: - raise AttributeError('Connect notes before calling the function') + raise AttributeError("Connect notes before calling the function") if note_name not in self._graph.nodes: - raise ValueError('"{}" not found in graph.'.format(note_name)) + raise ValueError(f'"{note_name}" not found in graph.') else: return self._backlinks_index[note_name] @@ -867,10 +892,10 @@ def get_backlink_counts(self, note_name: str) -> dict[str, int]: dict of integers >= 1 """ if not self._is_connected: - raise AttributeError('Connect notes before calling the function') + raise AttributeError("Connect notes before calling the function") if note_name not in self._graph.nodes: - raise ValueError('"{}" not found in graph.'.format(note_name)) + raise ValueError(f'"{note_name}" not found in graph.') else: backlinks = self.get_backlinks(note_name) return dict(Counter(backlinks)) @@ -890,10 +915,12 @@ def get_wikilinks(self, file_name: str) -> list[str]: list """ if not self._is_connected: - raise AttributeError('Connect notes before calling the function') + raise AttributeError("Connect notes before calling the function") if file_name not in self._md_file_index: - raise ValueError('"{}" does not exist so it cannot have wikilinks.'.format(file_name)) + raise ValueError( + f'"{file_name}" does not exist so it cannot have wikilinks.' + ) else: return self._wikilinks_index[file_name] @@ -908,10 +935,10 @@ def get_wikilink_counts(self, note_name: str) -> dict[str, int]: dict of integers >= 1 """ if not self._is_connected: - raise AttributeError('Connect notes before calling the function') + raise AttributeError("Connect notes before calling the function") if note_name not in self._graph.nodes: - raise ValueError('"{}" not found in graph.'.format(note_name)) + raise ValueError(f'"{note_name}" not found in graph.') else: wikilinks = self.get_wikilinks(note_name) return dict(Counter(wikilinks)) @@ -931,10 +958,12 @@ def get_embedded_files(self, file_name: str) -> list[str]: list """ if not self._is_connected: - raise AttributeError('Connect notes before calling the function') + raise AttributeError("Connect notes before calling the function") if file_name not in self._md_file_index: - raise ValueError('"{}" does not exist so it cannot have embedded files.'.format(file_name)) + raise ValueError( + f'"{file_name}" does not exist so it cannot have embedded files.' + ) else: return self._embedded_files_index[file_name] @@ -953,10 +982,12 @@ def get_md_links(self, file_name: str) -> list[str]: list """ if not self._is_connected: - raise AttributeError('Connect notes before calling the function') + raise AttributeError("Connect notes before calling the function") if file_name not in self._md_file_index: - raise ValueError('"{}" does not exist so it cannot have md links.'.format(file_name)) + raise ValueError( + f'"{file_name}" does not exist so it cannot have md links.' + ) else: return self._md_links_index[file_name] @@ -975,9 +1006,11 @@ def get_front_matter(self, file_name: str) -> list[dict]: list """ if not self._is_connected: - raise AttributeError('Connect notes before calling the function') + raise AttributeError("Connect notes before calling the function") if file_name not in self._md_file_index: - raise ValueError('"{}" does not exist so it cannot have front matter.'.format(file_name)) + raise ValueError( + f'"{file_name}" does not exist so it cannot have front matter.' + ) else: return self._front_matter_index[file_name] @@ -998,9 +1031,9 @@ def get_tags(self, file_name: str) -> list[str]: list """ if not self._is_connected: - raise AttributeError('Connect notes before calling the function') + raise AttributeError("Connect notes before calling the function") if file_name not in self._md_file_index: - raise ValueError('"{}" does not exist so it cannot have tags.'.format(file_name)) + raise ValueError(f'"{file_name}" does not exist so it cannot have tags.') else: return self._tags_index[file_name] @@ -1020,9 +1053,9 @@ def get_source_text(self, file_name: str) -> str: str """ if not self._is_gathered: - raise AttributeError('Gather notes before calling the function') + raise AttributeError("Gather notes before calling the function") if file_name not in self._md_file_index: - raise ValueError('"{}" does not exist so it cannot have text.'.format(file_name)) + raise ValueError(f'"{file_name}" does not exist so it cannot have text.') else: return self._source_text_index[file_name] @@ -1046,9 +1079,9 @@ def get_readable_text(self, file_name: str) -> str: str """ if not self._is_gathered: - raise AttributeError('Gather notes before calling the function') + raise AttributeError("Gather notes before calling the function") if file_name not in self._md_file_index: - raise ValueError('"{}" does not exist so it cannot have text.'.format(file_name)) + raise ValueError(f'"{file_name}" does not exist so it cannot have text.') else: return self._readable_text_index[file_name] @@ -1068,8 +1101,7 @@ def _get_canvas_relpaths(self, **kwargs) -> list[Path]: Returns: list """ - return get_canvas_relpaths_matching_subdirs(self._dirpath, - **kwargs) + return get_canvas_relpaths_matching_subdirs(self._dirpath, **kwargs) def __get_relpaths_by_name(self, *, extension, **kwargs) -> dict[str, Path]: """Return k,v pairs @@ -1081,14 +1113,12 @@ def __get_relpaths_by_name(self, *, extension, **kwargs) -> dict[str, Path]: """ # get note names (for k) and relpaths (for v): # keep or remove ext, based on how the file refs appear in wikilinks: - if extension == 'md': - relpaths_list = self._get_md_relpaths( - **kwargs) + if extension == "md": + relpaths_list = self._get_md_relpaths(**kwargs) # remove .md ext: all_file_names_list = [f.stem for f in relpaths_list] - if extension == 'canvas': - relpaths_list = self._get_canvas_relpaths( - **kwargs) + if extension == "canvas": + relpaths_list = self._get_canvas_relpaths(**kwargs) # keep .canvas ext: all_file_names_list = [f.name for f in relpaths_list] @@ -1097,39 +1127,35 @@ def __get_relpaths_by_name(self, *, extension, **kwargs) -> dict[str, Path]: np.array(all_file_names_list), return_inverse=True, return_counts=True, - axis=0) + axis=0, + ) dupe_names_ix = np.where(counts[inverse_ix] > 1)[0] # get shortest paths via mask: shortest_paths_arr = np.array(all_file_names_list, dtype=object) - if extension == 'md': + if extension == "md": shortest_paths_arr[dupe_names_ix] = np.array( - [str(fpath.with_suffix('')) - for fpath in relpaths_list])[dupe_names_ix] - if extension == 'canvas': + [str(fpath.with_suffix("")) for fpath in relpaths_list] + )[dupe_names_ix] + if extension == "canvas": shortest_paths_arr[dupe_names_ix] = np.array( - [str(fpath) - for fpath in relpaths_list])[dupe_names_ix] + [str(fpath) for fpath in relpaths_list] + )[dupe_names_ix] - dict_out = {n: p for n, p in zip(shortest_paths_arr, relpaths_list)} - return dict_out + return dict(zip(shortest_paths_arr, relpaths_list)) def _get_md_relpaths_by_name(self, **kwargs) -> dict[str, Path]: - return self.__get_relpaths_by_name(extension='md', - **kwargs) + return self.__get_relpaths_by_name(extension="md", **kwargs) def _get_canvas_relpaths_by_name(self, **kwargs) -> dict[str, Path]: - return self.__get_relpaths_by_name(extension='canvas', - **kwargs) + return self.__get_relpaths_by_name(extension="canvas", **kwargs) @staticmethod - def _get_backlinks_index(*, - graph: nx.MultiDiGraph) -> dict[str, list[str]]: + def _get_backlinks_index(*, graph: nx.MultiDiGraph) -> dict[str, list[str]]: """Return k,v pairs where k is the md note name and v is list of ALL backlinks found in k""" - return {n: [n[0] for n in list(graph.in_edges(n))] - for n in graph.nodes} + return {n: [n[0] for n in list(graph.in_edges(n))] for n in graph.nodes} def get_note_metadata(self) -> pd.DataFrame: """Structured dataset of metadata on the vault's notes. This @@ -1144,64 +1170,69 @@ def get_note_metadata(self) -> pd.DataFrame: pd.DataFrame """ if not self._is_connected: - raise AttributeError('Connect notes before calling the function') - - ix_list = list(set(self._backlinks_index.keys()) - .difference(set(self._media_file_index)) - .difference(set(self._nonexistent_media_files)) - .difference(set(self._canvas_file_index)) - ) - - df = (pd.DataFrame(index=ix_list, - columns=METADATA_DF_COLS_GENERIC_TYPE) - .rename(columns={'file_exists': 'note_exists'}) - .rename_axis('note')) - df = (df.pipe(self._create_note_metadata_columns) - .pipe(self._clean_up_note_metadata_dtypes) - ) + raise AttributeError("Connect notes before calling the function") + + ix_list = list( + set(self._backlinks_index.keys()) + .difference(set(self._media_file_index)) + .difference(set(self._nonexistent_media_files)) + .difference(set(self._canvas_file_index)) + ) + + df = ( + pd.DataFrame(index=ix_list, columns=METADATA_DF_COLS_GENERIC_TYPE) + .rename(columns={"file_exists": "note_exists"}) + .rename_axis("note") + ) + df = df.pipe(self._create_note_metadata_columns).pipe( + self._clean_up_note_metadata_dtypes + ) return df - def _create_note_metadata_columns(self, - df: pd.DataFrame) -> pd.DataFrame: + def _create_note_metadata_columns(self, df: pd.DataFrame) -> pd.DataFrame: """pipe func for mutating df""" - df['rel_filepath'] = [self._md_file_index.get(f, np.nan) - for f in df.index.tolist()] - df['abs_filepath'] = np.where(df['rel_filepath'].notna(), - [self._dirpath / str(f) - for f in df['rel_filepath'].tolist()], - np.nan) - df['note_exists'] = np.where(df['rel_filepath'].notna(), - True, False) - df['n_backlinks'] = [len(self.get_backlinks(f)) for f in df.index] - df['n_wikilinks'] = np.where(df['note_exists'], - [len(self._wikilinks_index.get(f, [])) - for f in df.index.tolist()], - np.nan) - df['n_tags'] = np.where(df['note_exists'], - [len(self._tags_index.get(f, [])) - for f in df.index.tolist()], - np.nan) - df['n_embedded_files'] = np.where(df['note_exists'], - [len(self._embedded_files_index.get( - f, [])) - for f in df.index.tolist()], - np.nan) - df['modified_time'] = pd.to_datetime( - [f.lstat().st_mtime if not pd.isna(f) - else pd.NaT - for f in df['abs_filepath'].tolist()], - unit='s' + df["rel_filepath"] = [ + self._md_file_index.get(f, np.nan) for f in df.index.tolist() + ] + df["abs_filepath"] = np.where( + df["rel_filepath"].notna(), + [self._dirpath / str(f) for f in df["rel_filepath"].tolist()], + np.nan, + ) + df["note_exists"] = np.where(df["rel_filepath"].notna(), True, False) + df["n_backlinks"] = [len(self.get_backlinks(f)) for f in df.index] + df["n_wikilinks"] = np.where( + df["note_exists"], + [len(self._wikilinks_index.get(f, [])) for f in df.index.tolist()], + np.nan, + ) + df["n_tags"] = np.where( + df["note_exists"], + [len(self._tags_index.get(f, [])) for f in df.index.tolist()], + np.nan, + ) + df["n_embedded_files"] = np.where( + df["note_exists"], + [len(self._embedded_files_index.get(f, [])) for f in df.index.tolist()], + np.nan, + ) + df["modified_time"] = pd.to_datetime( + [ + f.lstat().st_mtime if not pd.isna(f) else pd.NaT + for f in df["abs_filepath"].tolist() + ], + unit="s", ) return df - def _clean_up_note_metadata_dtypes(self, - df: pd.DataFrame) -> pd.DataFrame: + def _clean_up_note_metadata_dtypes(self, df: pd.DataFrame) -> pd.DataFrame: """pipe func for mutating df""" - df['rel_filepath'] = np.where(df['rel_filepath'].notna(), - [Path(str(f)) - for f in df['rel_filepath']], - np.nan) - df['n_wikilinks'] = df['n_wikilinks'].astype(float) # for consistency + df["rel_filepath"] = np.where( + df["rel_filepath"].notna(), + [Path(str(f)) for f in df["rel_filepath"]], + np.nan, + ) + df["n_wikilinks"] = df["n_wikilinks"].astype(float) # for consistency return df def get_media_file_metadata(self) -> pd.DataFrame: @@ -1226,35 +1257,37 @@ def get_media_file_metadata(self) -> pd.DataFrame: Returns: pd.DataFrame """ - ix_list = [*list(self._media_file_index.keys()), - *self._nonexistent_media_files] - df = (pd.DataFrame(index=ix_list, - columns=METADATA_DF_COLS_GENERIC_TYPE) - .rename_axis('file')) + ix_list = [*list(self._media_file_index.keys()), *self._nonexistent_media_files] + df = pd.DataFrame( + index=ix_list, columns=METADATA_DF_COLS_GENERIC_TYPE + ).rename_axis("file") if not ix_list: return df else: df = df.pipe(self._create_media_file_metadata_columns) return df - def _create_media_file_metadata_columns(self, - df: pd.DataFrame) -> pd.DataFrame: + def _create_media_file_metadata_columns(self, df: pd.DataFrame) -> pd.DataFrame: """pipe func for mutating df""" - df['rel_filepath'] = [self._media_file_index.get(f, np.nan) - for f in df.index.tolist()] - df['abs_filepath'] = np.where(df['rel_filepath'].notna(), - [self._dirpath / str(f) - for f in df['rel_filepath'].tolist()], - np.nan) - df['file_exists'] = pd.Series( - np.logical_not(df.index.isin(self._nonexistent_media_files)), - index=df.index) - df['n_backlinks'] = self._get_backlink_counts_for_media_files_only() - df['modified_time'] = pd.to_datetime( - [f.lstat().st_mtime if not pd.isna(f) - else pd.NaT - for f in df['abs_filepath'].tolist()], - unit='s') + df["rel_filepath"] = [ + self._media_file_index.get(f, np.nan) for f in df.index.tolist() + ] + df["abs_filepath"] = np.where( + df["rel_filepath"].notna(), + [self._dirpath / str(f) for f in df["rel_filepath"].tolist()], + np.nan, + ) + df["file_exists"] = pd.Series( + np.logical_not(df.index.isin(self._nonexistent_media_files)), index=df.index + ) + df["n_backlinks"] = self._get_backlink_counts_for_media_files_only() + df["modified_time"] = pd.to_datetime( + [ + f.lstat().st_mtime if not pd.isna(f) else pd.NaT + for f in df["abs_filepath"].tolist() + ], + unit="s", + ) return df def get_canvas_file_metadata(self) -> pd.DataFrame: @@ -1280,39 +1313,44 @@ def get_canvas_file_metadata(self) -> pd.DataFrame: Returns: pd.DataFrame """ - ix_list = [*list(self._canvas_file_index.keys()), - *self._nonexistent_canvas_files] - df = (pd.DataFrame(index=ix_list, - columns=METADATA_DF_COLS_GENERIC_TYPE) - .rename_axis('file')) + ix_list = [ + *list(self._canvas_file_index.keys()), + *self._nonexistent_canvas_files, + ] + df = pd.DataFrame( + index=ix_list, columns=METADATA_DF_COLS_GENERIC_TYPE + ).rename_axis("file") if not ix_list: return df else: df = df.pipe(self._create_canvas_file_metadata_columns) return df - def _create_canvas_file_metadata_columns(self, - df: pd.DataFrame) -> pd.DataFrame: + def _create_canvas_file_metadata_columns(self, df: pd.DataFrame) -> pd.DataFrame: """pipe func for mutating df""" - df['rel_filepath'] = [self._canvas_file_index.get(f, np.nan) - for f in df.index.tolist()] - df['abs_filepath'] = np.where(df['rel_filepath'].notna(), - [self._dirpath / str(f) - for f in df['rel_filepath'].tolist()], - np.nan) - df['file_exists'] = pd.Series( + df["rel_filepath"] = [ + self._canvas_file_index.get(f, np.nan) for f in df.index.tolist() + ] + df["abs_filepath"] = np.where( + df["rel_filepath"].notna(), + [self._dirpath / str(f) for f in df["rel_filepath"].tolist()], + np.nan, + ) + df["file_exists"] = pd.Series( np.logical_not(df.index.isin(self._nonexistent_canvas_files)), - index=df.index) + index=df.index, + ) if self._attachments: - df['n_backlinks'] = ( - self._get_backlink_counts_for_canvas_files_only()) + df["n_backlinks"] = self._get_backlink_counts_for_canvas_files_only() else: - df['n_backlinks'] = np.nan - df['modified_time'] = pd.to_datetime( - [f.lstat().st_mtime if not pd.isna(f) - else pd.NaT - for f in df['abs_filepath'].tolist()], - unit='s') + df["n_backlinks"] = np.nan + df["modified_time"] = pd.to_datetime( + [ + f.lstat().st_mtime if not pd.isna(f) else pd.NaT + for f in df["abs_filepath"].tolist() + ], + unit="s", + ) return df def get_all_file_metadata(self) -> pd.DataFrame: @@ -1338,23 +1376,24 @@ def get_all_file_metadata(self) -> pd.DataFrame: Returns: pd.DataFrame """ - df = (self.get_note_metadata() - .rename(columns={'note_exists': 'file_exists'})) - df['graph_category'] = np.where( - df['file_exists'], 'note', 'nonexistent') + df = self.get_note_metadata().rename(columns={"note_exists": "file_exists"}) + df["graph_category"] = np.where(df["file_exists"], "note", "nonexistent") if not self._attachments: - warnings.warn('Only notes (md files) were used to build the graph. Set attachments=True in the connect method to show all file metadata.') + warnings.warn( + "Only notes (md files) were used to build the graph. Set attachments=True in the connect method to show all file metadata.", + stacklevel=2, + ) else: df_media = self.get_media_file_metadata() - df_media['graph_category'] = np.where( - df_media['file_exists'], 'attachment', 'nonexistent') + df_media["graph_category"] = np.where( + df_media["file_exists"], "attachment", "nonexistent" + ) df_canvas = self.get_canvas_file_metadata() - df_canvas['graph_category'] = np.where( - df_canvas['file_exists'], 'attachment', 'nonexistent') + df_canvas["graph_category"] = np.where( + df_canvas["file_exists"], "attachment", "nonexistent" + ) - df = (pd.concat( - [df, df_media, df_canvas]) - .rename_axis('file')) + df = pd.concat([df, df_media, df_canvas]).rename_axis("file") return df def _get_nonexistent_notes(self) -> list[str]: @@ -1362,18 +1401,18 @@ def _get_nonexistent_notes(self) -> list[str]: The comparison is done with sets but the result is returned as a list.""" - return list(set(self._backlinks_index.keys()) - # anything remaining that isn't a file is a non-e note: - .difference(set(self._md_file_index)) - .difference(set(self._media_file_index)) - .difference(set(self._nonexistent_media_files)) - .difference(set(self._canvas_file_index))) - - def _get_isolated_notes(self, *, - graph: nx.MultiDiGraph) -> list[str]: + return list( + set(self._backlinks_index.keys()) + # anything remaining that isn't a file is a non-e note: + .difference(set(self._md_file_index)) + .difference(set(self._media_file_index)) + .difference(set(self._nonexistent_media_files)) + .difference(set(self._canvas_file_index)) + ) + + def _get_isolated_notes(self, *, graph: nx.MultiDiGraph) -> list[str]: """Get notes that are not connected to any other notes in the vault, i.e. they have 0 wikilinks and 0 backlinks. These notes are retrieved from the graph.""" - return [fn for fn in nx.isolates(graph) - if fn in self._md_file_index] + return [fn for fn in nx.isolates(graph) if fn in self._md_file_index] diff --git a/obsidiantools/canvas_utils.py b/obsidiantools/canvas_utils.py index c40d009..f5fb757 100644 --- a/obsidiantools/canvas_utils.py +++ b/obsidiantools/canvas_utils.py @@ -1,10 +1,14 @@ import json -import networkx as nx from pathlib import Path + +import networkx as nx + from ._constants import CANVAS_EXT_SET -from ._io import (get_relpaths_from_dir, - get_relpaths_matching_subdirs, - _get_valid_filepaths_by_ext_set) +from ._io import ( + _get_valid_filepaths_by_ext_set, + get_relpaths_from_dir, + get_relpaths_matching_subdirs, +) def get_canvas_relpaths_from_dir(dir_path: Path) -> list[Path]: @@ -21,12 +25,12 @@ def get_canvas_relpaths_from_dir(dir_path: Path) -> list[Path]: Returns: list of Path objects """ - return get_relpaths_from_dir(dir_path, extension='canvas') + return get_relpaths_from_dir(dir_path, extension="canvas") -def get_canvas_relpaths_matching_subdirs(dir_path: Path, *, - include_subdirs: list = None, - include_root: bool = True) -> list[Path]: +def get_canvas_relpaths_matching_subdirs( + dir_path: Path, *, include_subdirs: list = None, include_root: bool = True +) -> list[Path]: """Get list of relative paths for canvas files in a given directory, filtered to include specified subdirectories (with include_subdirs kwarg). The default arguments align with get_canvas_relpaths_from_dir @@ -56,15 +60,14 @@ def get_canvas_relpaths_matching_subdirs(dir_path: Path, *, """ return get_relpaths_matching_subdirs( dir_path, - extension='canvas', + extension="canvas", include_subdirs=include_subdirs, - include_root=include_root) + include_root=include_root, + ) def _get_all_valid_canvas_file_relpaths(dirpath): - return (_get_valid_filepaths_by_ext_set( - dirpath, - exts=CANVAS_EXT_SET)) + return _get_valid_filepaths_by_ext_set(dirpath, exts=CANVAS_EXT_SET) def get_canvas_content(filepath: Path) -> dict: @@ -76,15 +79,14 @@ def get_canvas_content(filepath: Path) -> dict: Returns: dict """ - with open(filepath, encoding='utf-8') as f: + with open(filepath, encoding="utf-8") as f: json_as_dict = json.load(f) return json_as_dict -def get_canvas_graph_detail(canvas_content: dict) -> \ - tuple[nx.MultiDiGraph, - dict[str, tuple[int, int]], - dict[tuple[str, str], str]]: +def get_canvas_graph_detail( + canvas_content: dict, +) -> tuple[nx.MultiDiGraph, dict[str, tuple[int, int]], dict[tuple[str, str], str]]: """Get the content from a canvas in a NetworkX graph. With all the detail that is returned, it is possible to recreate the layout of the material in the canvas. @@ -104,22 +106,28 @@ def get_canvas_graph_detail(canvas_content: dict) -> \ edge_labels: list of labels for each edge in graph """ G = nx.MultiDiGraph() - nodes_list = [i.get('id') for i in canvas_content['nodes'] - if i.get('type') != 'group'] + nodes_list = [ + i.get("id") for i in canvas_content["nodes"] if i.get("type") != "group" + ] G.add_nodes_from(nodes_list) - graph_edges_list = [(i.get('fromNode'), i.get('toNode')) - for i in canvas_content['edges'] - if i.get('type') != 'group'] + graph_edges_list = [ + (i.get("fromNode"), i.get("toNode")) + for i in canvas_content["edges"] + if i.get("type") != "group" + ] G.add_edges_from(graph_edges_list) # y co-ord needs to be flipped to reflect app(?): - pos = {i.get('id'): (i.get('x'), -i.get('y')) - for i in canvas_content['nodes'] - if i.get('type') != 'group'} - - edge_labels = dict([((i.get('fromNode'), i.get('toNode')), - f"{i.get('label', '')}") - for i in canvas_content['edges']]) + pos = { + i.get("id"): (i.get("x"), -i.get("y")) + for i in canvas_content["nodes"] + if i.get("type") != "group" + } + + edge_labels = { + (i.get("fromNode"), i.get("toNode")): f"{i.get('label', '')}" + for i in canvas_content["edges"] + } return G, pos, edge_labels diff --git a/obsidiantools/html_processing.py b/obsidiantools/html_processing.py index f04ad86..a8e43b4 100644 --- a/obsidiantools/html_processing.py +++ b/obsidiantools/html_processing.py @@ -1,6 +1,6 @@ -from html2text import HTML2Text import bleach from bs4 import BeautifulSoup +from html2text import HTML2Text def _get_html2text_obj_with_config() -> HTML2Text: @@ -27,54 +27,53 @@ def _get_plaintext_from_html(html: str) -> str: def _remove_code(html: str) -> str: # exclude 'code' tags from link output: - soup = BeautifulSoup(html, 'lxml') + soup = BeautifulSoup(html, "lxml") soup = _remove_code_via_soup(soup) html_str = str(soup) return html_str def _remove_code_via_soup(soup): - for s in soup.select('code'): + for s in soup.select("code"): s.extract() return soup def _remove_del_text(html: str) -> str: - soup = BeautifulSoup(html, 'lxml') + soup = BeautifulSoup(html, "lxml") soup = _remove_del_text_via_soup(soup) html_str = str(soup) return html_str def _remove_del_text_via_soup(soup): - for s in soup.select('del'): + for s in soup.select("del"): s.extract() return soup -def _remove_main_formatting( - html: str, *, - tags: list[str] = ['p', 'h1', 'h2', 'h3', 'h4', 'h5', 'h6']) -> str: +def _remove_main_formatting(html: str, *, tags: list[str] | None = None) -> str: + if tags is None: + tags = ["p", "h1", "h2", "h3", "h4", "h5", "h6"] return bleach.clean(html, tags=tags, strip=True) def _remove_latex(html: str) -> str: - soup = BeautifulSoup(html, 'lxml') + soup = BeautifulSoup(html, "lxml") soup = _remove_latex_via_soup(soup) html_str = str(soup) return html_str def _remove_latex_via_soup(soup): - for s in soup.select('span', {'class': 'MathJax_Preview'}): + for s in soup.select("span", {"class": "MathJax_Preview"}): s.extract() return soup def _get_all_latex_from_html_content(html: str) -> list[str]: - soup = BeautifulSoup(html, 'html.parser') + soup = BeautifulSoup(html, "html.parser") - s_content = soup.find_all('span', {'class': 'MathJax_Preview'}, - string=True) + s_content = soup.find_all("span", {"class": "MathJax_Preview"}, string=True) latex_found_list = [i.string for i in s_content] return latex_found_list diff --git a/obsidiantools/md_utils.py b/obsidiantools/md_utils.py index c99a52e..f74c48d 100644 --- a/obsidiantools/md_utils.py +++ b/obsidiantools/md_utils.py @@ -1,23 +1,29 @@ import re -import yaml from pathlib import Path -from bs4 import BeautifulSoup -import markdown + import frontmatter -from ._constants import (WIKILINK_REGEX, - TAG_MAIN_ONLY_REGEX, TAG_INCLUDE_NESTED_REGEX, - WIKILINK_AS_STRING_REGEX, - EMBEDDED_FILE_LINK_AS_STRING_REGEX, - INLINE_LINK_AFTER_HTML_PROC_REGEX, - INLINE_LINK_VIA_MD_ONLY_REGEX) -from ._io import (get_relpaths_from_dir, - get_relpaths_matching_subdirs) -from .html_processing import (_get_plaintext_from_html, - _remove_code_via_soup, - _remove_latex_via_soup, - _remove_del_text_via_soup, - _remove_main_formatting, - _get_all_latex_from_html_content) +import markdown +import yaml +from bs4 import BeautifulSoup + +from ._constants import ( + EMBEDDED_FILE_LINK_AS_STRING_REGEX, + INLINE_LINK_AFTER_HTML_PROC_REGEX, + INLINE_LINK_VIA_MD_ONLY_REGEX, + TAG_INCLUDE_NESTED_REGEX, + TAG_MAIN_ONLY_REGEX, + WIKILINK_AS_STRING_REGEX, + WIKILINK_REGEX, +) +from ._io import get_relpaths_from_dir, get_relpaths_matching_subdirs +from .html_processing import ( + _get_all_latex_from_html_content, + _get_plaintext_from_html, + _remove_code_via_soup, + _remove_del_text_via_soup, + _remove_latex_via_soup, + _remove_main_formatting, +) def get_md_relpaths_from_dir(dir_path: Path) -> list[Path]: @@ -34,12 +40,12 @@ def get_md_relpaths_from_dir(dir_path: Path) -> list[Path]: Returns: list of Path objects """ - return get_relpaths_from_dir(dir_path, extension='md') + return get_relpaths_from_dir(dir_path, extension="md") -def get_md_relpaths_matching_subdirs(dir_path: Path, *, - include_subdirs: list = None, - include_root: bool = True) -> list[Path]: +def get_md_relpaths_matching_subdirs( + dir_path: Path, *, include_subdirs: list = None, include_root: bool = True +) -> list[Path]: """Get list of relative paths for markdown files in a given directory, filtered to include specified subdirectories (with include_subdirs kwarg). The default arguments align with get_md_relpaths_from_dir @@ -69,13 +75,13 @@ def get_md_relpaths_matching_subdirs(dir_path: Path, *, """ return get_relpaths_matching_subdirs( dir_path, - extension='md', + extension="md", include_subdirs=include_subdirs, - include_root=include_root) + include_root=include_root, + ) -def get_wikilinks(filepath: Path, *, - exclude_canvas: bool = True) -> list[str]: +def get_wikilinks(filepath: Path, *, exclude_canvas: bool = True) -> list[str]: """Get ALL wikilinks from a md file. The links' order of appearance in the file IS preserved in the output. @@ -99,8 +105,8 @@ def get_wikilinks(filepath: Path, *, src_txt = get_source_text_from_md_file(filepath, remove_code=True) wikilinks = _get_all_wikilinks_from_source_text( - src_txt, remove_aliases=True, - exclude_canvas=exclude_canvas) + src_txt, remove_aliases=True, exclude_canvas=exclude_canvas + ) return wikilinks @@ -123,13 +129,11 @@ def get_embedded_files(filepath: Path) -> list[str]: """ src_txt = get_source_text_from_md_file(filepath, remove_code=True) - files = _get_all_embedded_files_from_source_text( - src_txt, remove_aliases=True) + files = _get_all_embedded_files_from_source_text(src_txt, remove_aliases=True) return files -def get_unique_wikilinks(filepath: Path, *, - exclude_canvas: bool = True) -> list[str]: +def get_unique_wikilinks(filepath: Path, *, exclude_canvas: bool = True) -> list[str]: """Get UNIQUE wikilinks from a md file. The links' order of appearance in the file IS preserved in the output. @@ -151,8 +155,8 @@ def get_unique_wikilinks(filepath: Path, *, src_txt = get_source_text_from_md_file(filepath, remove_code=True) wikilinks = _get_unique_wikilinks_from_source_text( - src_txt, remove_aliases=True, - exclude_canvas=exclude_canvas) + src_txt, remove_aliases=True, exclude_canvas=exclude_canvas + ) return wikilinks @@ -237,18 +241,21 @@ def get_tags(filepath: Path, *, show_nested: bool = False) -> list[str]: """ # get text from source file, but remove any '\#' and code: src_txt = get_source_text_from_md_file( - filepath, remove_code=True, - str_transform_func=_transform_md_file_string_for_tag_parsing) + filepath, + remove_code=True, + str_transform_func=_transform_md_file_string_for_tag_parsing, + ) # remove wikilinks so that '#' headers are not caught: src_txt = _remove_wikilinks_from_source_text(src_txt) tags = _get_tags_from_source_text(src_txt, show_nested=show_nested) return tags -def _get_md_front_matter_and_content(filepath: Path, *, - str_transform_func=None) -> tuple[dict, str]: +def _get_md_front_matter_and_content( + filepath: Path, *, str_transform_func=None +) -> tuple[dict, str]: """parse md file into front matter and note content""" - with open(filepath, encoding='utf-8') as f: + with open(filepath, encoding="utf-8") as f: try: file_string = f.read() if str_transform_func: @@ -264,16 +271,15 @@ def _get_md_front_matter_and_content(filepath: Path, *, # handle template {{}} chars in front matter: except yaml.constructor.ConstructorError: file_string_esc = file_string.translate( - str.maketrans({"{": r"\{", - "}": r"\}"})) + str.maketrans({"{": r"\{", "}": r"\}"}) + ) return frontmatter.parse(file_string_esc) # any others: - except: + except Exception: return {}, file_string -def _get_html_from_md_file(filepath: Path, *, - str_transform_func=None) -> str: +def _get_html_from_md_file(filepath: Path, *, str_transform_func=None) -> str: """md file -> html (without front matter). pymarkdown extensions are used and configured to reflect the Obsidian @@ -281,33 +287,37 @@ def _get_html_from_md_file(filepath: Path, *, to parse math, md_mermaid for mermaid diagram support, etc. """ _, md_content = _get_md_front_matter_and_content( - filepath, - str_transform_func=str_transform_func) + filepath, str_transform_func=str_transform_func + ) html = _get_html_from_md_content(md_content) return html def _get_html_from_md_content(md_content: str) -> str: """md content -> html (without front matter)""" - html = markdown.markdown(md_content, output_format='html', - extensions=['pymdownx.arithmatex', - 'pymdownx.superfences', - 'pymdownx.mark', - 'pymdownx.tilde', - 'pymdownx.saneheaders', - 'footnotes', - 'sane_lists', - 'tables'], - extension_configs={'pymdownx.tilde': - {'subscript': False}}) + html = markdown.markdown( + md_content, + output_format="html", + extensions=[ + "pymdownx.arithmatex", + "pymdownx.superfences", + "pymdownx.mark", + "pymdownx.tilde", + "pymdownx.saneheaders", + "footnotes", + "sane_lists", + "tables", + ], + extension_configs={"pymdownx.tilde": {"subscript": False}}, + ) return html -def get_source_text_from_html(html: str, *, - remove_code: bool = False, - remove_math: bool = False) -> str: +def get_source_text_from_html( + html: str, *, remove_code: bool = False, remove_math: bool = False +) -> str: """html (without front matter) -> ASCII plaintext""" - soup = BeautifulSoup(html, 'lxml') + soup = BeautifulSoup(html, "lxml") if remove_code: soup = _remove_code_via_soup(soup) if remove_math: @@ -316,33 +326,31 @@ def get_source_text_from_html(html: str, *, return _get_plaintext_from_html(new_str) -def get_source_text_from_md_file(filepath: Path, *, - remove_code: bool = False, - remove_math: bool = False, - str_transform_func=None) -> str: +def get_source_text_from_md_file( + filepath: Path, + *, + remove_code: bool = False, + remove_math: bool = False, + str_transform_func=None, +) -> str: """md file -> html (without front matter) -> ASCII plaintext""" # strip out front matter (if any): - html = _get_html_from_md_file( - filepath, - str_transform_func=str_transform_func) + html = _get_html_from_md_file(filepath, str_transform_func=str_transform_func) - return get_source_text_from_html(html, remove_code=remove_code, - remove_math=remove_math) + return get_source_text_from_html( + html, remove_code=remove_code, remove_math=remove_math + ) -def get_readable_text_from_md_file(filepath: Path, *, - tags: list[str] = None) -> str: +def get_readable_text_from_md_file(filepath: Path, *, tags: list[str] = None) -> str: """md file -> html -> plaintext with major formatting removed.""" # strip out front matter (if any): - html = _get_html_from_md_file( - filepath) - html = _get_readable_text_from_html( - html, tags=tags) + html = _get_html_from_md_file(filepath) + html = _get_readable_text_from_html(html, tags=tags) return html -def _get_readable_text_from_html(html: str, *, - tags: list[str] = None) -> str: +def _get_readable_text_from_html(html: str, *, tags: list[str] = None) -> str: # -str or regex- # wikilinks and md links as text: html = _replace_md_links_with_their_text(html) @@ -351,7 +359,7 @@ def _get_readable_text_from_html(html: str, *, # -bs4- # remove code and remove major formatting on text: - soup = BeautifulSoup(html, 'lxml') + soup = BeautifulSoup(html, "lxml") soup = _remove_code_via_soup(soup) soup = _remove_latex_via_soup(soup) soup = _remove_del_text_via_soup(soup) @@ -373,56 +381,61 @@ def _get_all_wikilinks_and_embedded_files(src_txt: str) -> list[str]: return link_matches_list -def _remove_aliases_from_wikilink_regex_matches(link_matches_list: list[str]) -> list[str]: - return [(i.replace('\\', '') - .split("|")[0].rstrip() # catch alias/alt-text - .split('#', 1)[0]) # catch links to headers - for i in link_matches_list] +def _remove_aliases_from_wikilink_regex_matches( + link_matches_list: list[str], +) -> list[str]: + return [ + ( + i.replace("\\", "") + .split("|")[0] + .rstrip() # catch alias/alt-text + .split("#", 1)[0] + ) # catch links to headers + for i in link_matches_list + ] -def _get_all_wikilinks_from_source_text(src_txt: str, *, - remove_aliases: bool = True, - exclude_canvas: bool = True) -> list[str]: +def _get_all_wikilinks_from_source_text( + src_txt: str, *, remove_aliases: bool = True, exclude_canvas: bool = True +) -> list[str]: matches_list = _get_all_wikilinks_and_embedded_files(src_txt) - link_matches_list = [g[1] for g in matches_list - if g[0] == ''] + link_matches_list = [g[1] for g in matches_list if g[0] == ""] if remove_aliases: link_matches_list = _remove_aliases_from_wikilink_regex_matches( - link_matches_list) + link_matches_list + ) # remove .md: - link_matches_list = [name.removesuffix('.md') - for name in link_matches_list] + link_matches_list = [name.removesuffix(".md") for name in link_matches_list] if exclude_canvas: - link_matches_list = [n for n in link_matches_list - if not n.endswith('.canvas')] + link_matches_list = [n for n in link_matches_list if not n.endswith(".canvas")] return link_matches_list -def _get_all_embedded_files_from_source_text(src_txt: str, *, - remove_aliases: bool = True) -> list[str]: +def _get_all_embedded_files_from_source_text( + src_txt: str, *, remove_aliases: bool = True +) -> list[str]: matches_list = _get_all_wikilinks_and_embedded_files(src_txt) - embedded_files_sublist = [g[1] for g in matches_list - if g[0] == '!'] + embedded_files_sublist = [g[1] for g in matches_list if g[0] == "!"] if remove_aliases: embedded_files_sublist = _remove_aliases_from_wikilink_regex_matches( - embedded_files_sublist) + embedded_files_sublist + ) return embedded_files_sublist def _get_all_latex_from_md_file(filepath: Path) -> list[str]: - return _get_all_latex_from_html_content( - _get_html_from_md_file(filepath)) + return _get_all_latex_from_html_content(_get_html_from_md_file(filepath)) -def _get_unique_wikilinks_from_source_text(src_txt: str, *, - remove_aliases: bool = True, - exclude_canvas: bool = True) -> list[str]: +def _get_unique_wikilinks_from_source_text( + src_txt: str, *, remove_aliases: bool = True, exclude_canvas: bool = True +) -> list[str]: wikilinks = _get_all_wikilinks_from_source_text( - src_txt, remove_aliases=remove_aliases, - exclude_canvas=exclude_canvas) + src_txt, remove_aliases=remove_aliases, exclude_canvas=exclude_canvas + ) return list(dict.fromkeys(wikilinks)) @@ -434,22 +447,20 @@ def _get_all_md_link_info_from_source_text(src_txt: str) -> list[tuple[str]]: def _get_unique_md_links_from_source_text(src_txt: str) -> list[str]: - links_detail = _get_all_md_link_info_from_source_text( - src_txt) + links_detail = _get_all_md_link_info_from_source_text(src_txt) links_list = [link for _, link in links_detail] return list(dict.fromkeys(links_list)) def _remove_wikilinks_from_source_text(src_txt: str) -> str: - return re.sub(WIKILINK_REGEX, '', src_txt) + return re.sub(WIKILINK_REGEX, "", src_txt) def _transform_md_file_string_for_tag_parsing(txt: str) -> str: - return txt.replace('\\#', '') + return txt.replace("\\#", "") -def _get_tags_from_source_text(src_txt: str, *, - show_nested: bool = False) -> list[str]: +def _get_tags_from_source_text(src_txt: str, *, show_nested: bool = False) -> list[str]: if not show_nested: pattern = re.compile(TAG_MAIN_ONLY_REGEX) else: @@ -460,15 +471,18 @@ def _get_tags_from_source_text(src_txt: str, *, def _replace_wikilinks_with_their_text(src_txt: str) -> str: # get list of wikilinks as strings: - links_list = _get_all_wikilinks_from_source_text( - src_txt, remove_aliases=False) + links_list = _get_all_wikilinks_from_source_text(src_txt, remove_aliases=False) # get links in their text format: - readable_text_list = [(i.replace('\\', '') - # get wikilinks w/o alias, otherwise alias: - .split("|")[-1] - .strip()) - for i in links_list] + readable_text_list = [ + ( + i.replace("\\", "") + # get wikilinks w/o alias, otherwise alias: + .split("|")[-1] + .strip() + ) + for i in links_list + ] # loop over txt content to replace "[[...]]" wikilinks w/ readable text: out_str = src_txt @@ -502,10 +516,10 @@ def _remove_embedded_file_links_from_text(src_txt: str) -> str: # get list of embedded file links as strings: links_list = re.findall(EMBEDDED_FILE_LINK_AS_STRING_REGEX, src_txt) # add in the ![[...]] chars: - links_list = ["".join(['![[', i, ']]']) for i in links_list] + links_list = ["".join(["![[", i, "]]"]) for i in links_list] # remove from text: out_str = src_txt for i in links_list: - out_str = out_str.replace(i, '') + out_str = out_str.replace(i, "") return out_str diff --git a/obsidiantools/media_utils.py b/obsidiantools/media_utils.py index 63fa54f..f6c27b4 100644 --- a/obsidiantools/media_utils.py +++ b/obsidiantools/media_utils.py @@ -1,12 +1,8 @@ -from pathlib import Path -import numpy as np -from ._constants import (IMG_EXT_SET, AUDIO_EXT_SET, - VIDEO_EXT_SET, PDF_EXT_SET) +from ._constants import AUDIO_EXT_SET, IMG_EXT_SET, PDF_EXT_SET, VIDEO_EXT_SET from ._io import _get_valid_filepaths_by_ext_set def _get_all_valid_media_file_relpaths(dirpath): - return (_get_valid_filepaths_by_ext_set( - dirpath, - exts=(IMG_EXT_SET | AUDIO_EXT_SET - | VIDEO_EXT_SET | PDF_EXT_SET))) + return _get_valid_filepaths_by_ext_set( + dirpath, exts=(IMG_EXT_SET | AUDIO_EXT_SET | VIDEO_EXT_SET | PDF_EXT_SET) + ) diff --git a/pyproject.toml b/pyproject.toml index f159211..20ea001 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -95,6 +95,10 @@ ignore = [ "E501", # line-too-long (formatter handles this) ] +[tool.ruff.lint.per-file-ignores] +# Trailing whitespace is intentional inside expected-value string literals +"tests/test_md_utils.py" = ["W291"] + [tool.ruff.lint.isort] known-first-party = ["obsidiantools"] @@ -120,7 +124,6 @@ reportUnknownMemberType = "warn" # --------------------------------------------------------------------------- [tool.pytest.ini_options] testpaths = ["tests"] -addopts = "--cov=obsidiantools --cov-report=xml" # --------------------------------------------------------------------------- # coverage diff --git a/tests/test_api_canvas.py b/tests/test_api_canvas.py index b468c03..0bd4f47 100644 --- a/tests/test_api_canvas.py +++ b/tests/test_api_canvas.py @@ -1,6 +1,5 @@ import pytest - from obsidiantools.api import Vault diff --git a/tests/test_api_md.py b/tests/test_api_md.py index 742b0ce..c308b9c 100644 --- a/tests/test_api_md.py +++ b/tests/test_api_md.py @@ -1,6 +1,5 @@ import pytest - from obsidiantools.api import Vault diff --git a/tests/test_api_setup.py b/tests/test_api_setup.py index cc14155..7cb726f 100644 --- a/tests/test_api_setup.py +++ b/tests/test_api_setup.py @@ -1,6 +1,5 @@ -import pytest import networkx as nx - +import pytest from obsidiantools.api import Vault @@ -44,7 +43,7 @@ def test_vault_instantiation_needs_directory(): def test_type_error_is_raised_for_string_dirpath(): - actual_vault_dirpath = 'home/digital-garden' + actual_vault_dirpath = "home/digital-garden" with pytest.raises(TypeError): Vault(actual_vault_dirpath) @@ -73,22 +72,22 @@ def test_connect(mock_initial_vault): def test_functions_to_fail_for_unconnected_vault(mock_initial_vault): # catch functions that require attributes set via connect method with pytest.raises(AttributeError): - mock_initial_vault.get_backlinks('A note that would not exist') + mock_initial_vault.get_backlinks("A note that would not exist") with pytest.raises(AttributeError): - mock_initial_vault.get_backlink_counts('A note that would not exist') + mock_initial_vault.get_backlink_counts("A note that would not exist") with pytest.raises(AttributeError): - mock_initial_vault.get_wikilinks('A note that would not exist') + mock_initial_vault.get_wikilinks("A note that would not exist") with pytest.raises(AttributeError): - mock_initial_vault.get_wikilink_counts('A note that would not exist') + mock_initial_vault.get_wikilink_counts("A note that would not exist") with pytest.raises(AttributeError): - mock_initial_vault.get_tags('A note that would not exist') + mock_initial_vault.get_tags("A note that would not exist") with pytest.raises(AttributeError): - mock_initial_vault.get_embedded_files('A note that would not exist') + mock_initial_vault.get_embedded_files("A note that would not exist") with pytest.raises(AttributeError): - mock_initial_vault.get_math_index('A note that would not exist') + mock_initial_vault.get_math_index("A note that would not exist") with pytest.raises(AttributeError): - mock_initial_vault.get_front_matter('A note that would not exist') + mock_initial_vault.get_front_matter("A note that would not exist") with pytest.raises(AttributeError): - mock_initial_vault.get_md_links('A note that would not exist') + mock_initial_vault.get_md_links("A note that would not exist") with pytest.raises(AttributeError): mock_initial_vault.get_note_metadata() diff --git a/tests/test_api_vault_stub_attr_setters.py b/tests/test_api_vault_stub_attr_setters.py index f941134..e4adc89 100644 --- a/tests/test_api_vault_stub_attr_setters.py +++ b/tests/test_api_vault_stub_attr_setters.py @@ -1,7 +1,7 @@ -import pytest from pathlib import Path -import networkx as nx +import networkx as nx +import pytest from obsidiantools.api import Vault @@ -11,15 +11,15 @@ @pytest.fixture def actual_connected_vault(): - return Vault(WKD / 'tests/vault-stub').connect().gather() + return Vault(WKD / "tests/vault-stub").connect().gather() def test_attr_setters_main_setup(actual_connected_vault): actual_connected_vault.md_file_index = {} assert actual_connected_vault.md_file_index == {} - actual_connected_vault.canvas_file_index = {'New.canvas': ''} - assert actual_connected_vault.canvas_file_index == {'New.canvas': ''} + actual_connected_vault.canvas_file_index = {"New.canvas": ""} + assert actual_connected_vault.canvas_file_index == {"New.canvas": ""} def test_attr_setters_md_connect_related(actual_connected_vault): @@ -86,11 +86,11 @@ def test_attr_setters_md_connect_related(actual_connected_vault): def test_attr_setters_md_gather_related(actual_connected_vault): - actual_connected_vault.source_text_index = {'Isolated note': '`new text`'} - assert actual_connected_vault.source_text_index == {'Isolated note': '`new text`'} + actual_connected_vault.source_text_index = {"Isolated note": "`new text`"} + assert actual_connected_vault.source_text_index == {"Isolated note": "`new text`"} - actual_connected_vault.readable_text_index = {'Isolated note': 'Test'} - assert actual_connected_vault.readable_text_index == {'Isolated note': 'Test'} + actual_connected_vault.readable_text_index = {"Isolated note": "Test"} + assert actual_connected_vault.readable_text_index == {"Isolated note": "Test"} def test_attr_setters_canvas_connect_related(actual_connected_vault): diff --git a/tests/test_api_vault_stub_connect_attachments_true.py b/tests/test_api_vault_stub_connect_attachments_true.py index 173fb70..4cc8494 100644 --- a/tests/test_api_vault_stub_connect_attachments_true.py +++ b/tests/test_api_vault_stub_connect_attachments_true.py @@ -1,10 +1,10 @@ -import pytest +from pathlib import Path + import numpy as np import pandas as pd -from pathlib import Path +import pytest from pandas.testing import assert_series_equal - from obsidiantools.api import Vault # NOTE: run the tests from the project dir. @@ -13,160 +13,170 @@ @pytest.fixture def actual_connected_vault(): - return (Vault(WKD / 'tests/vault-stub') - .connect(attachments=True)) + return Vault(WKD / "tests/vault-stub").connect(attachments=True) @pytest.fixture def expected_note_metadata_dict(): return { - 'rel_filepath': {'Sussudio': Path('Sussudio.md'), - 'Isolated note': Path('Isolated note.md'), - 'Brevissimus moenia': Path('lipsum/Brevissimus moenia.md'), - 'Ne fuit': Path('lipsum/Ne fuit.md'), - 'Alimenta': Path('lipsum/Alimenta.md'), - 'Vulnera ubera': Path('lipsum/Vulnera ubera.md'), - 'lipsum/Isolated note': Path('lipsum/Isolated note.md'), - 'Causam mihi': Path('lipsum/Causam mihi.md'), - 'American Psycho (film)': np.nan, - 'Tarpeia': np.nan, - 'Caelum': np.nan, - 'Vita': np.nan, - 'Aras Teucras': np.nan, - 'Manus': np.nan, - 'Bacchus': np.nan, - 'Amor': np.nan, - 'Virtus': np.nan, - 'Tydides': np.nan, - 'Dives': np.nan, - 'Aetna': np.nan}, + "rel_filepath": { + "Sussudio": Path("Sussudio.md"), + "Isolated note": Path("Isolated note.md"), + "Brevissimus moenia": Path("lipsum/Brevissimus moenia.md"), + "Ne fuit": Path("lipsum/Ne fuit.md"), + "Alimenta": Path("lipsum/Alimenta.md"), + "Vulnera ubera": Path("lipsum/Vulnera ubera.md"), + "lipsum/Isolated note": Path("lipsum/Isolated note.md"), + "Causam mihi": Path("lipsum/Causam mihi.md"), + "American Psycho (film)": np.nan, + "Tarpeia": np.nan, + "Caelum": np.nan, + "Vita": np.nan, + "Aras Teucras": np.nan, + "Manus": np.nan, + "Bacchus": np.nan, + "Amor": np.nan, + "Virtus": np.nan, + "Tydides": np.nan, + "Dives": np.nan, + "Aetna": np.nan, + }, # abs_filepath would be here - 'note_exists': {'Sussudio': True, - 'Isolated note': True, - 'Brevissimus moenia': True, - 'Ne fuit': True, - 'Alimenta': True, - 'Vulnera ubera': True, - 'lipsum/Isolated note': True, - 'Causam mihi': True, - 'American Psycho (film)': False, - 'Tarpeia': False, - 'Caelum': False, - 'Vita': False, - 'Aras Teucras': False, - 'Manus': False, - 'Bacchus': False, - 'Amor': False, - 'Virtus': False, - 'Tydides': False, - 'Dives': False, - 'Aetna': False}, - 'n_backlinks': {'Sussudio': 0, - 'Isolated note': 0, - 'Brevissimus moenia': 1, - 'Ne fuit': 2, - 'Alimenta': 0, - 'Vulnera ubera': 0, - 'lipsum/Isolated note': 0, - 'Causam mihi': 1, - 'American Psycho (film)': 1, - 'Tarpeia': 3, - 'Caelum': 3, - 'Vita': 3, - 'Aras Teucras': 1, - 'Manus': 3, - 'Bacchus': 5, - 'Amor': 2, - 'Virtus': 1, - 'Tydides': 1, - 'Dives': 1, - 'Aetna': 1}, - 'n_wikilinks': {'Sussudio': 1.0, - 'Isolated note': 0.0, - 'Brevissimus moenia': 3.0, - 'Ne fuit': 6.0, - 'Alimenta': 12.0, - 'Vulnera ubera': 3.0, - 'lipsum/Isolated note': 0.0, - 'Causam mihi': 4.0, - 'American Psycho (film)': np.nan, - 'Tarpeia': np.nan, - 'Caelum': np.nan, - 'Vita': np.nan, - 'Aras Teucras': np.nan, - 'Manus': np.nan, - 'Bacchus': np.nan, - 'Amor': np.nan, - 'Virtus': np.nan, - 'Tydides': np.nan, - 'Dives': np.nan, - 'Aetna': np.nan}, - 'n_tags': {'Sussudio': 5.0, - 'Isolated note': 0.0, - 'Brevissimus moenia': 0.0, - 'Ne fuit': 0.0, - 'Alimenta': 0.0, - 'Vulnera ubera': 0.0, - 'lipsum/Isolated note': 0.0, - 'Causam mihi': 0.0, - 'American Psycho (film)': np.nan, - 'Tarpeia': np.nan, - 'Caelum': np.nan, - 'Vita': np.nan, - 'Aras Teucras': np.nan, - 'Manus': np.nan, - 'Bacchus': np.nan, - 'Amor': np.nan, - 'Virtus': np.nan, - 'Tydides': np.nan, - 'Dives': np.nan, - 'Aetna': np.nan}, - 'n_embedded_files': {'Isolated note': 0.0, - 'Sussudio': 2.0, - 'Brevissimus moenia': 0.0, - 'Ne fuit': 0.0, - 'Alimenta': 0.0, - 'Vulnera ubera': 0.0, - 'lipsum/Isolated note': 0.0, - 'Causam mihi': 0.0, - 'American Psycho (film)': np.nan, - 'Tarpeia': np.nan, - 'Caelum': np.nan, - 'Vita': np.nan, - 'Aras Teucras': np.nan, - 'Manus': np.nan, - 'Bacchus': np.nan, - 'Amor': np.nan, - 'Virtus': np.nan, - 'Tydides': np.nan, - 'Dives': np.nan, - 'Aetna': np.nan} + "note_exists": { + "Sussudio": True, + "Isolated note": True, + "Brevissimus moenia": True, + "Ne fuit": True, + "Alimenta": True, + "Vulnera ubera": True, + "lipsum/Isolated note": True, + "Causam mihi": True, + "American Psycho (film)": False, + "Tarpeia": False, + "Caelum": False, + "Vita": False, + "Aras Teucras": False, + "Manus": False, + "Bacchus": False, + "Amor": False, + "Virtus": False, + "Tydides": False, + "Dives": False, + "Aetna": False, + }, + "n_backlinks": { + "Sussudio": 0, + "Isolated note": 0, + "Brevissimus moenia": 1, + "Ne fuit": 2, + "Alimenta": 0, + "Vulnera ubera": 0, + "lipsum/Isolated note": 0, + "Causam mihi": 1, + "American Psycho (film)": 1, + "Tarpeia": 3, + "Caelum": 3, + "Vita": 3, + "Aras Teucras": 1, + "Manus": 3, + "Bacchus": 5, + "Amor": 2, + "Virtus": 1, + "Tydides": 1, + "Dives": 1, + "Aetna": 1, + }, + "n_wikilinks": { + "Sussudio": 1.0, + "Isolated note": 0.0, + "Brevissimus moenia": 3.0, + "Ne fuit": 6.0, + "Alimenta": 12.0, + "Vulnera ubera": 3.0, + "lipsum/Isolated note": 0.0, + "Causam mihi": 4.0, + "American Psycho (film)": np.nan, + "Tarpeia": np.nan, + "Caelum": np.nan, + "Vita": np.nan, + "Aras Teucras": np.nan, + "Manus": np.nan, + "Bacchus": np.nan, + "Amor": np.nan, + "Virtus": np.nan, + "Tydides": np.nan, + "Dives": np.nan, + "Aetna": np.nan, + }, + "n_tags": { + "Sussudio": 5.0, + "Isolated note": 0.0, + "Brevissimus moenia": 0.0, + "Ne fuit": 0.0, + "Alimenta": 0.0, + "Vulnera ubera": 0.0, + "lipsum/Isolated note": 0.0, + "Causam mihi": 0.0, + "American Psycho (film)": np.nan, + "Tarpeia": np.nan, + "Caelum": np.nan, + "Vita": np.nan, + "Aras Teucras": np.nan, + "Manus": np.nan, + "Bacchus": np.nan, + "Amor": np.nan, + "Virtus": np.nan, + "Tydides": np.nan, + "Dives": np.nan, + "Aetna": np.nan, + }, + "n_embedded_files": { + "Isolated note": 0.0, + "Sussudio": 2.0, + "Brevissimus moenia": 0.0, + "Ne fuit": 0.0, + "Alimenta": 0.0, + "Vulnera ubera": 0.0, + "lipsum/Isolated note": 0.0, + "Causam mihi": 0.0, + "American Psycho (film)": np.nan, + "Tarpeia": np.nan, + "Caelum": np.nan, + "Vita": np.nan, + "Aras Teucras": np.nan, + "Manus": np.nan, + "Bacchus": np.nan, + "Amor": np.nan, + "Virtus": np.nan, + "Tydides": np.nan, + "Dives": np.nan, + "Aetna": np.nan, + }, } @pytest.fixture def expected_media_file_metadata_dict(): return { - 'rel_filepath': {'1999.flac': np.nan, - 'Sussudio.mp3': np.nan}, + "rel_filepath": {"1999.flac": np.nan, "Sussudio.mp3": np.nan}, # abs_filepath would be here - 'file_exists': {'1999.flac': False, - 'Sussudio.mp3': False}, - 'n_backlinks': {'1999.flac': 1, - 'Sussudio.mp3': 1}, + "file_exists": {"1999.flac": False, "Sussudio.mp3": False}, + "n_backlinks": {"1999.flac": 1, "Sussudio.mp3": 1}, } @pytest.fixture def expected_embedded_files_index(): - return {'Isolated note': [], - 'lipsum/Isolated note': [], - 'Sussudio': ['Sussudio.mp3', '1999.flac'], - 'Brevissimus moenia': [], - 'Ne fuit': [], - 'Alimenta': [], - 'Vulnera ubera': [], - 'Causam mihi': []} + return { + "Isolated note": [], + "lipsum/Isolated note": [], + "Sussudio": ["Sussudio.mp3", "1999.flac"], + "Brevissimus moenia": [], + "Ne fuit": [], + "Alimenta": [], + "Vulnera ubera": [], + "Causam mihi": [], + } @pytest.fixture @@ -187,76 +197,76 @@ def actual_canvas_file_metadata_df(actual_connected_vault): def test_get_metadata_cols(actual_note_metadata_df): assert isinstance(actual_note_metadata_df, pd.DataFrame) - expected_cols = ['rel_filepath', 'abs_filepath', - 'note_exists', - 'n_backlinks', 'n_wikilinks', - 'n_tags', - 'n_embedded_files', - 'modified_time'] + expected_cols = [ + "rel_filepath", + "abs_filepath", + "note_exists", + "n_backlinks", + "n_wikilinks", + "n_tags", + "n_embedded_files", + "modified_time", + ] assert actual_note_metadata_df.columns.tolist() == expected_cols def test_get_metadata_dtypes(actual_note_metadata_df): - assert actual_note_metadata_df['rel_filepath'].dtype == 'object' - assert actual_note_metadata_df['abs_filepath'].dtype == 'object' - assert actual_note_metadata_df['note_exists'].dtype == 'bool' - assert actual_note_metadata_df['n_backlinks'].dtype == 'int' - assert actual_note_metadata_df['n_wikilinks'].dtype == 'float' - assert actual_note_metadata_df['n_tags'].dtype == 'float' - assert actual_note_metadata_df['n_embedded_files'].dtype == 'float' - assert actual_note_metadata_df['modified_time'].dtype == 'datetime64[ns]' + assert actual_note_metadata_df["rel_filepath"].dtype == "object" + assert actual_note_metadata_df["abs_filepath"].dtype == "object" + assert actual_note_metadata_df["note_exists"].dtype == "bool" + assert actual_note_metadata_df["n_backlinks"].dtype == "int" + assert actual_note_metadata_df["n_wikilinks"].dtype == "float" + assert actual_note_metadata_df["n_tags"].dtype == "float" + assert actual_note_metadata_df["n_embedded_files"].dtype == "float" + assert actual_note_metadata_df["modified_time"].dtype == "datetime64[ns]" -def test_get_metadata_backlinks(actual_note_metadata_df, - expected_note_metadata_dict): - TEST_COL = 'n_backlinks' +def test_get_metadata_backlinks(actual_note_metadata_df, expected_note_metadata_dict): + TEST_COL = "n_backlinks" actual_series = actual_note_metadata_df[TEST_COL] - expected_series = (pd.Series(expected_note_metadata_dict.get(TEST_COL), - name=TEST_COL) - .rename_axis('note')) - assert_series_equal(actual_series, expected_series, - check_like=True) + expected_series = pd.Series( + expected_note_metadata_dict.get(TEST_COL), name=TEST_COL + ).rename_axis("note") + assert_series_equal(actual_series, expected_series, check_like=True) def test_backlink_and_wikilink_totals_not_equal_for_test_vault(actual_note_metadata_df): # every wikilink is another note's backlink # INEQUALITY is expected when canvas files are INCLUDED in wikilinks list # for this vault - assert (actual_note_metadata_df['n_backlinks'].sum() - != actual_note_metadata_df['n_wikilinks'].sum()) + assert ( + actual_note_metadata_df["n_backlinks"].sum() + != actual_note_metadata_df["n_wikilinks"].sum() + ) def test_backlink_counts(actual_connected_vault): expected_bl_count_subset = { - 'Sussudio': {}, - 'Alimenta': {}, - 'Tarpeia': {'Brevissimus moenia': 1, - 'Alimenta': 1, - 'Vulnera ubera': 1}, - 'Ne fuit': {'Alimenta': 1, - 'Causam mihi': 1}, - 'Bacchus': {'Ne fuit': 1, - 'Alimenta': 4}, - '1999.flac': {'Sussudio': 1}, - 'Sussudio.mp3': {'Sussudio': 1} + "Sussudio": {}, + "Alimenta": {}, + "Tarpeia": {"Brevissimus moenia": 1, "Alimenta": 1, "Vulnera ubera": 1}, + "Ne fuit": {"Alimenta": 1, "Causam mihi": 1}, + "Bacchus": {"Ne fuit": 1, "Alimenta": 4}, + "1999.flac": {"Sussudio": 1}, + "Sussudio.mp3": {"Sussudio": 1}, } for k in list(expected_bl_count_subset.keys()): - assert (actual_connected_vault.get_backlink_counts(k) - == expected_bl_count_subset.get(k)) + assert actual_connected_vault.get_backlink_counts( + k + ) == expected_bl_count_subset.get(k) with pytest.raises(ValueError): actual_connected_vault.get_backlink_counts("Note that isn't in vault at all") def test_isolated_notes(actual_connected_vault): - expected_isol_notes = ['Isolated note', 'lipsum/Isolated note'] + expected_isol_notes = ["Isolated note", "lipsum/Isolated note"] assert isinstance(actual_connected_vault.isolated_notes, list) - assert (set(actual_connected_vault.isolated_notes) - == set(expected_isol_notes)) + assert set(actual_connected_vault.isolated_notes) == set(expected_isol_notes) # isolated notes can't have backlinks for n in actual_connected_vault.isolated_notes: @@ -270,12 +280,12 @@ def test_get_canvas_file_dicts_tuple(actual_connected_vault): # (linked_files_by_short_path, # non_linked_files_by_short_path, # nonexistent_files_by_short_path) - actual_tuple = (actual_connected_vault. - _get_canvas_file_dicts_tuple()) + actual_tuple = actual_connected_vault._get_canvas_file_dicts_tuple() expected_tuple = ( - {'Crazy wall 2.canvas': Path('Crazy wall 2.canvas')}, - {'Crazy wall.canvas': Path('Crazy wall.canvas')}, - {}) + {"Crazy wall 2.canvas": Path("Crazy wall 2.canvas")}, + {"Crazy wall.canvas": Path("Crazy wall.canvas")}, + {}, + ) assert actual_tuple == expected_tuple @@ -283,52 +293,54 @@ def test_get_media_file_dicts_tuple(actual_connected_vault): # (embedded_files_by_short_path, # non_embedded_files_by_short_path, # nonexistent_files_by_short_path) - actual_tuple = (actual_connected_vault. - _get_media_file_dicts_tuple()) - expected_tuple = ( - {}, - {}, - {'Sussudio.mp3': np.nan, '1999.flac': np.nan}) + actual_tuple = actual_connected_vault._get_media_file_dicts_tuple() + expected_tuple = ({}, {}, {"Sussudio.mp3": np.nan, "1999.flac": np.nan}) assert actual_tuple == expected_tuple -def test_nonexistent_canvas_files(actual_connected_vault, - actual_canvas_file_metadata_df): +def test_nonexistent_canvas_files( + actual_connected_vault, actual_canvas_file_metadata_df +): expected_non_e_files = [] assert isinstance(actual_connected_vault.nonexistent_canvas_files, list) - assert (set(actual_connected_vault.nonexistent_canvas_files) - == set(expected_non_e_files)) - assert (set(actual_canvas_file_metadata_df.loc[~actual_canvas_file_metadata_df['file_exists'], :] - .index.tolist()) - == set(expected_non_e_files)) + assert set(actual_connected_vault.nonexistent_canvas_files) == set( + expected_non_e_files + ) + assert set( + actual_canvas_file_metadata_df.loc[ + ~actual_canvas_file_metadata_df["file_exists"], : + ].index.tolist() + ) == set(expected_non_e_files) def test_nonexistent_media_files(actual_connected_vault, actual_media_file_metadata_df): - expected_non_e_files = ['1999.flac', 'Sussudio.mp3'] + expected_non_e_files = ["1999.flac", "Sussudio.mp3"] assert isinstance(actual_connected_vault.nonexistent_media_files, list) - assert (set(actual_connected_vault.nonexistent_media_files) - == set(expected_non_e_files)) - assert (set(actual_media_file_metadata_df.loc[~actual_media_file_metadata_df['file_exists'], :] - .index.tolist()) - == set(expected_non_e_files)) + assert set(actual_connected_vault.nonexistent_media_files) == set( + expected_non_e_files + ) + assert set( + actual_media_file_metadata_df.loc[ + ~actual_media_file_metadata_df["file_exists"], : + ].index.tolist() + ) == set(expected_non_e_files) def test_isolated_canvas_files(actual_connected_vault): - expected_isol_files = ['Crazy wall.canvas'] + expected_isol_files = ["Crazy wall.canvas"] assert isinstance(actual_connected_vault.isolated_canvas_files, list) - assert (set(actual_connected_vault.isolated_canvas_files) - == set(expected_isol_files)) + assert set(actual_connected_vault.isolated_canvas_files) == set(expected_isol_files) def test_n_backlinks_not_null_in_canvas_file_metadata(actual_connected_vault): df_canvas = actual_connected_vault.get_canvas_file_metadata() - assert df_canvas['n_backlinks'].isna().mean() == 0 + assert df_canvas["n_backlinks"].isna().mean() == 0 def test_all_file_metadata_df(actual_connected_vault): @@ -339,12 +351,12 @@ def test_all_file_metadata_df(actual_connected_vault): actual_canvas_df = actual_connected_vault.get_canvas_file_metadata() # check all dataframes concatenated successfully: - assert len(actual_all_df) == (len(actual_notes_df) - + len(actual_media_df) - + len(actual_canvas_df)) + assert len(actual_all_df) == ( + len(actual_notes_df) + len(actual_media_df) + len(actual_canvas_df) + ) # check that media files are included in graph under attachments=True, # with equality involving graph edges: - assert (actual_all_df['n_backlinks'].sum() - == (actual_all_df['n_wikilinks'].sum() - + actual_all_df['n_embedded_files'].sum())) + assert actual_all_df["n_backlinks"].sum() == ( + actual_all_df["n_wikilinks"].sum() + actual_all_df["n_embedded_files"].sum() + ) diff --git a/tests/test_api_vault_stub_connect_defaults_canvas.py b/tests/test_api_vault_stub_connect_defaults_canvas.py index cb6310a..007fcf8 100644 --- a/tests/test_api_vault_stub_connect_defaults_canvas.py +++ b/tests/test_api_vault_stub_connect_defaults_canvas.py @@ -1,7 +1,7 @@ -import pytest -import networkx as nx from pathlib import Path +import networkx as nx +import pytest from obsidiantools.api import Vault @@ -11,61 +11,62 @@ @pytest.fixture def expected_canvas_file_index(): - return {'Crazy wall.canvas': Path('Crazy wall.canvas'), - 'Crazy wall 2.canvas': Path('Crazy wall 2.canvas')} + return { + "Crazy wall.canvas": Path("Crazy wall.canvas"), + "Crazy wall 2.canvas": Path("Crazy wall 2.canvas"), + } @pytest.fixture def actual_connected_vault(): - return Vault(WKD / 'tests/vault-stub').connect() + return Vault(WKD / "tests/vault-stub").connect() -def test_canvas_file_index(actual_connected_vault, - expected_canvas_file_index): - assert (actual_connected_vault.canvas_file_index - == expected_canvas_file_index) +def test_canvas_file_index(actual_connected_vault, expected_canvas_file_index): + assert actual_connected_vault.canvas_file_index == expected_canvas_file_index def test_canvas_content_index(actual_connected_vault): - actual_crazy_wall_2_content = ( - actual_connected_vault.canvas_content_index - .get('Crazy wall 2.canvas')) - actual_crazy_wall_2_text = (actual_crazy_wall_2_content - .get('nodes')[0].get('text')) + actual_crazy_wall_2_content = actual_connected_vault.canvas_content_index.get( + "Crazy wall 2.canvas" + ) + actual_crazy_wall_2_text = actual_crazy_wall_2_content.get("nodes")[0].get("text") expected_crazy_wall_2_text = "Now we're getting meta..." assert actual_crazy_wall_2_text == expected_crazy_wall_2_text def test_canvas_graph_detail_index_graph(actual_connected_vault): actual_crazy_wall_graph_detail = ( - actual_connected_vault.canvas_graph_detail_index - .get('Crazy wall.canvas')) + actual_connected_vault.canvas_graph_detail_index.get("Crazy wall.canvas") + ) G, _, _ = actual_crazy_wall_graph_detail # check nodes in overall graph: - expected_nodes = ['0fb63a211244ab98', - '5b04fb9cabc4b282', - '8f032f9a663e27b5', - 'd3f112f83760095a', - 'c168506f5b075d91', - '9d13d42f967553bf', - '2919b72bf3df3791'] - actual_nodes = [i for i in G.nodes()] + expected_nodes = [ + "0fb63a211244ab98", + "5b04fb9cabc4b282", + "8f032f9a663e27b5", + "d3f112f83760095a", + "c168506f5b075d91", + "9d13d42f967553bf", + "2919b72bf3df3791", + ] + actual_nodes = list(G.nodes()) assert actual_nodes == expected_nodes # expect group node not in graph: - assert not set(['a10aaf054261706d']).issubset(set(actual_nodes)) + assert not {"a10aaf054261706d"}.issubset(set(actual_nodes)) # isolated nodes: - actual_isolated_nodes = [cv for cv in nx.isolates(G)] - expected_isolated_nodes = ['0fb63a211244ab98', '2919b72bf3df3791'] + actual_isolated_nodes = list(nx.isolates(G)) + expected_isolated_nodes = ["0fb63a211244ab98", "2919b72bf3df3791"] assert actual_isolated_nodes == expected_isolated_nodes # check main node's connections: actual_in_degree = {n[0]: n[1] for n in G.in_degree} actual_out_degree = {n[0]: n[1] for n in G.out_degree} - assert actual_in_degree.get('c168506f5b075d91') == 2 - assert actual_out_degree.get('c168506f5b075d91') == 1 + assert actual_in_degree.get("c168506f5b075d91") == 2 + assert actual_out_degree.get("c168506f5b075d91") == 1 # edge count: actual_n_edges = G.number_of_edges() @@ -74,29 +75,30 @@ def test_canvas_graph_detail_index_graph(actual_connected_vault): def test_canvas_graph_detail_index_graph_other_attributes(actual_connected_vault): actual_crazy_wall_graph_detail = ( - actual_connected_vault.canvas_graph_detail_index - .get('Crazy wall.canvas')) + actual_connected_vault.canvas_graph_detail_index.get("Crazy wall.canvas") + ) _, pos, edge_labels = actual_crazy_wall_graph_detail # check pos: - assert pos.get('2919b72bf3df3791') == (-1363, 812) + assert pos.get("2919b72bf3df3791") == (-1363, 812) actual_x_locs = {c: pos[0] for (c, pos) in pos.items()} - assert max(actual_x_locs, key=actual_x_locs.get) == 'c168506f5b075d91' - assert min(actual_x_locs, key=actual_x_locs.get) == '2919b72bf3df3791' + assert max(actual_x_locs, key=actual_x_locs.get) == "c168506f5b075d91" + assert min(actual_x_locs, key=actual_x_locs.get) == "2919b72bf3df3791" actual_y_locs = {c: pos[1] for (c, pos) in pos.items()} - assert max(actual_y_locs, key=actual_y_locs.get) == '0fb63a211244ab98' - assert min(actual_y_locs, key=actual_y_locs.get) == '5b04fb9cabc4b282' + assert max(actual_y_locs, key=actual_y_locs.get) == "0fb63a211244ab98" + assert min(actual_y_locs, key=actual_y_locs.get) == "5b04fb9cabc4b282" # check edge_labels: actual_non_blank_edge_labels = { - pair: label for pair, label in edge_labels.items() - if label != ''} + pair: label for pair, label in edge_labels.items() if label != "" + } expected_non_blank_edge_labels = { - ('d3f112f83760095a', 'c168506f5b075d91'): 'inspires?'} + ("d3f112f83760095a", "c168506f5b075d91"): "inspires?" + } assert actual_non_blank_edge_labels == expected_non_blank_edge_labels def test_n_backlinks_null_in_canvas_file_metadata(actual_connected_vault): df_canvas = actual_connected_vault.get_canvas_file_metadata() - assert df_canvas['n_backlinks'].isna().mean() == 1 + assert df_canvas["n_backlinks"].isna().mean() == 1 diff --git a/tests/test_api_vault_stub_connect_defaults_md.py b/tests/test_api_vault_stub_connect_defaults_md.py index 22b41d8..13fc057 100644 --- a/tests/test_api_vault_stub_connect_defaults_md.py +++ b/tests/test_api_vault_stub_connect_defaults_md.py @@ -1,13 +1,12 @@ -import pytest -import numpy as np -import pandas as pd from pathlib import Path -from pandas.testing import (assert_series_equal, - assert_frame_equal) +import numpy as np +import pandas as pd +import pytest +from pandas.testing import assert_frame_equal, assert_series_equal -from obsidiantools.api import Vault from obsidiantools._constants import METADATA_DF_COLS_GENERIC_TYPE +from obsidiantools.api import Vault # NOTE: run the tests from the project dir. WKD = Path().cwd() @@ -16,217 +15,249 @@ @pytest.fixture def expected_metadata_dict(): return { - 'rel_filepath': {'Sussudio': Path('Sussudio.md'), - 'Isolated note': Path('Isolated note.md'), - 'Brevissimus moenia': Path('lipsum/Brevissimus moenia.md'), - 'Ne fuit': Path('lipsum/Ne fuit.md'), - 'Alimenta': Path('lipsum/Alimenta.md'), - 'Vulnera ubera': Path('lipsum/Vulnera ubera.md'), - 'lipsum/Isolated note': Path('lipsum/Isolated note.md'), - 'Causam mihi': Path('lipsum/Causam mihi.md'), - 'American Psycho (film)': np.nan, - 'Tarpeia': np.nan, - 'Caelum': np.nan, - 'Vita': np.nan, - 'Aras Teucras': np.nan, - 'Manus': np.nan, - 'Bacchus': np.nan, - 'Amor': np.nan, - 'Virtus': np.nan, - 'Tydides': np.nan, - 'Dives': np.nan, - 'Aetna': np.nan}, + "rel_filepath": { + "Sussudio": Path("Sussudio.md"), + "Isolated note": Path("Isolated note.md"), + "Brevissimus moenia": Path("lipsum/Brevissimus moenia.md"), + "Ne fuit": Path("lipsum/Ne fuit.md"), + "Alimenta": Path("lipsum/Alimenta.md"), + "Vulnera ubera": Path("lipsum/Vulnera ubera.md"), + "lipsum/Isolated note": Path("lipsum/Isolated note.md"), + "Causam mihi": Path("lipsum/Causam mihi.md"), + "American Psycho (film)": np.nan, + "Tarpeia": np.nan, + "Caelum": np.nan, + "Vita": np.nan, + "Aras Teucras": np.nan, + "Manus": np.nan, + "Bacchus": np.nan, + "Amor": np.nan, + "Virtus": np.nan, + "Tydides": np.nan, + "Dives": np.nan, + "Aetna": np.nan, + }, # abs_filepath would be here - 'note_exists': {'Sussudio': True, - 'Isolated note': True, - 'Brevissimus moenia': True, - 'Ne fuit': True, - 'Alimenta': True, - 'Vulnera ubera': True, - 'lipsum/Isolated note': True, - 'Causam mihi': True, - 'American Psycho (film)': False, - 'Tarpeia': False, - 'Caelum': False, - 'Vita': False, - 'Aras Teucras': False, - 'Manus': False, - 'Bacchus': False, - 'Amor': False, - 'Virtus': False, - 'Tydides': False, - 'Dives': False, - 'Aetna': False}, - 'n_backlinks': {'Sussudio': 0, - 'Isolated note': 0, - 'Brevissimus moenia': 1, - 'Ne fuit': 2, - 'Alimenta': 0, - 'Vulnera ubera': 0, - 'lipsum/Isolated note': 0, - 'Causam mihi': 1, - 'American Psycho (film)': 1, - 'Tarpeia': 3, - 'Caelum': 3, - 'Vita': 3, - 'Aras Teucras': 1, - 'Manus': 3, - 'Bacchus': 5, - 'Amor': 2, - 'Virtus': 1, - 'Tydides': 1, - 'Dives': 1, - 'Aetna': 1}, - 'n_wikilinks': {'Sussudio': 1.0, - 'Isolated note': 0.0, - 'Brevissimus moenia': 3.0, - 'Ne fuit': 6.0, - 'Alimenta': 12.0, - 'Vulnera ubera': 3.0, - 'lipsum/Isolated note': 0.0, - 'Causam mihi': 4.0, - 'American Psycho (film)': np.nan, - 'Tarpeia': np.nan, - 'Caelum': np.nan, - 'Vita': np.nan, - 'Aras Teucras': np.nan, - 'Manus': np.nan, - 'Bacchus': np.nan, - 'Amor': np.nan, - 'Virtus': np.nan, - 'Tydides': np.nan, - 'Dives': np.nan, - 'Aetna': np.nan}, - 'n_tags': {'Sussudio': 5.0, - 'Isolated note': 0.0, - 'Brevissimus moenia': 0.0, - 'Ne fuit': 0.0, - 'Alimenta': 0.0, - 'Vulnera ubera': 0.0, - 'lipsum/Isolated note': 0.0, - 'Causam mihi': 0.0, - 'American Psycho (film)': np.nan, - 'Tarpeia': np.nan, - 'Caelum': np.nan, - 'Vita': np.nan, - 'Aras Teucras': np.nan, - 'Manus': np.nan, - 'Bacchus': np.nan, - 'Amor': np.nan, - 'Virtus': np.nan, - 'Tydides': np.nan, - 'Dives': np.nan, - 'Aetna': np.nan}, - 'n_embedded_files': {'Isolated note': 0.0, - 'Sussudio': 2.0, - 'Brevissimus moenia': 0.0, - 'Ne fuit': 0.0, - 'Alimenta': 0.0, - 'Vulnera ubera': 0.0, - 'lipsum/Isolated note': 0.0, - 'Causam mihi': 0.0, - 'American Psycho (film)': np.nan, - 'Tarpeia': np.nan, - 'Caelum': np.nan, - 'Vita': np.nan, - 'Aras Teucras': np.nan, - 'Manus': np.nan, - 'Bacchus': np.nan, - 'Amor': np.nan, - 'Virtus': np.nan, - 'Tydides': np.nan, - 'Dives': np.nan, - 'Aetna': np.nan} + "note_exists": { + "Sussudio": True, + "Isolated note": True, + "Brevissimus moenia": True, + "Ne fuit": True, + "Alimenta": True, + "Vulnera ubera": True, + "lipsum/Isolated note": True, + "Causam mihi": True, + "American Psycho (film)": False, + "Tarpeia": False, + "Caelum": False, + "Vita": False, + "Aras Teucras": False, + "Manus": False, + "Bacchus": False, + "Amor": False, + "Virtus": False, + "Tydides": False, + "Dives": False, + "Aetna": False, + }, + "n_backlinks": { + "Sussudio": 0, + "Isolated note": 0, + "Brevissimus moenia": 1, + "Ne fuit": 2, + "Alimenta": 0, + "Vulnera ubera": 0, + "lipsum/Isolated note": 0, + "Causam mihi": 1, + "American Psycho (film)": 1, + "Tarpeia": 3, + "Caelum": 3, + "Vita": 3, + "Aras Teucras": 1, + "Manus": 3, + "Bacchus": 5, + "Amor": 2, + "Virtus": 1, + "Tydides": 1, + "Dives": 1, + "Aetna": 1, + }, + "n_wikilinks": { + "Sussudio": 1.0, + "Isolated note": 0.0, + "Brevissimus moenia": 3.0, + "Ne fuit": 6.0, + "Alimenta": 12.0, + "Vulnera ubera": 3.0, + "lipsum/Isolated note": 0.0, + "Causam mihi": 4.0, + "American Psycho (film)": np.nan, + "Tarpeia": np.nan, + "Caelum": np.nan, + "Vita": np.nan, + "Aras Teucras": np.nan, + "Manus": np.nan, + "Bacchus": np.nan, + "Amor": np.nan, + "Virtus": np.nan, + "Tydides": np.nan, + "Dives": np.nan, + "Aetna": np.nan, + }, + "n_tags": { + "Sussudio": 5.0, + "Isolated note": 0.0, + "Brevissimus moenia": 0.0, + "Ne fuit": 0.0, + "Alimenta": 0.0, + "Vulnera ubera": 0.0, + "lipsum/Isolated note": 0.0, + "Causam mihi": 0.0, + "American Psycho (film)": np.nan, + "Tarpeia": np.nan, + "Caelum": np.nan, + "Vita": np.nan, + "Aras Teucras": np.nan, + "Manus": np.nan, + "Bacchus": np.nan, + "Amor": np.nan, + "Virtus": np.nan, + "Tydides": np.nan, + "Dives": np.nan, + "Aetna": np.nan, + }, + "n_embedded_files": { + "Isolated note": 0.0, + "Sussudio": 2.0, + "Brevissimus moenia": 0.0, + "Ne fuit": 0.0, + "Alimenta": 0.0, + "Vulnera ubera": 0.0, + "lipsum/Isolated note": 0.0, + "Causam mihi": 0.0, + "American Psycho (film)": np.nan, + "Tarpeia": np.nan, + "Caelum": np.nan, + "Vita": np.nan, + "Aras Teucras": np.nan, + "Manus": np.nan, + "Bacchus": np.nan, + "Amor": np.nan, + "Virtus": np.nan, + "Tydides": np.nan, + "Dives": np.nan, + "Aetna": np.nan, + }, } @pytest.fixture def expected_embedded_files_index(): - return {'Isolated note': [], - 'lipsum/Isolated note': [], - 'Sussudio': ['Sussudio.mp3', '1999.flac'], - 'Brevissimus moenia': [], - 'Ne fuit': [], - 'Alimenta': [], - 'Vulnera ubera': [], - 'Causam mihi': []} + return { + "Isolated note": [], + "lipsum/Isolated note": [], + "Sussudio": ["Sussudio.mp3", "1999.flac"], + "Brevissimus moenia": [], + "Ne fuit": [], + "Alimenta": [], + "Vulnera ubera": [], + "Causam mihi": [], + } @pytest.fixture def expected_front_matter_index(): - return {'Isolated note': {}, - 'lipsum/Isolated note': {}, - 'Sussudio': {'title': 'Sussudio', - 'artist': 'Phil Collins', - 'category': 'music', - 'year': 1985, - 'url': 'https://www.discogs.com/Phil-Collins-Sussudio/master/106239', - 'references': [[['American Psycho (film)']], 'Polka Party!'], - 'chart_peaks': [{'US': 1}, {'UK': 12}]}, - 'Brevissimus moenia': {}, - 'Ne fuit': {}, - 'Alimenta': {}, - 'Vulnera ubera': {}, - 'Causam mihi': {'title': 'Causam mihi', - 'author': 'Ovid', - 'category': 'literature', - 'year': 8, - 'language': 'la', - 'description': '\\{\\{description\\}\\}'}} + return { + "Isolated note": {}, + "lipsum/Isolated note": {}, + "Sussudio": { + "title": "Sussudio", + "artist": "Phil Collins", + "category": "music", + "year": 1985, + "url": "https://www.discogs.com/Phil-Collins-Sussudio/master/106239", + "references": [[["American Psycho (film)"]], "Polka Party!"], + "chart_peaks": [{"US": 1}, {"UK": 12}], + }, + "Brevissimus moenia": {}, + "Ne fuit": {}, + "Alimenta": {}, + "Vulnera ubera": {}, + "Causam mihi": { + "title": "Causam mihi", + "author": "Ovid", + "category": "literature", + "year": 8, + "language": "la", + "description": "\\{\\{description\\}\\}", + }, + } @pytest.fixture def expected_md_links_index(): - return {'Isolated note': [], - 'lipsum/Isolated note': [], - 'Sussudio': [], - 'Brevissimus moenia': ['http://www.alii.io/', - 'http://fronti.com/tumiseris.html'], - 'Ne fuit': ['http://vires.io/', - 'http://excoquitprotinus.net/quae.html', - 'http://medullis-me.net/novat', - 'http://sedibus.io/levemmonstra'], - 'Alimenta': ['http://fugitaer.net/dignus', - 'http://www.a-iuveni.com/', - 'http://cibos.net/venulus-redito.html', - 'http://et-pronus.com/', - 'http://iuppiter.net/'], - 'Vulnera ubera': [], - 'Causam mihi': []} + return { + "Isolated note": [], + "lipsum/Isolated note": [], + "Sussudio": [], + "Brevissimus moenia": [ + "http://www.alii.io/", + "http://fronti.com/tumiseris.html", + ], + "Ne fuit": [ + "http://vires.io/", + "http://excoquitprotinus.net/quae.html", + "http://medullis-me.net/novat", + "http://sedibus.io/levemmonstra", + ], + "Alimenta": [ + "http://fugitaer.net/dignus", + "http://www.a-iuveni.com/", + "http://cibos.net/venulus-redito.html", + "http://et-pronus.com/", + "http://iuppiter.net/", + ], + "Vulnera ubera": [], + "Causam mihi": [], + } @pytest.fixture def expected_tags_main_only_index(): - return {'Isolated note': [], - 'lipsum/Isolated note': [], - 'Sussudio': ['y1982', 'y_1982', 'y-1982', 'y1982', 'y2000'], - 'Brevissimus moenia': [], - 'Ne fuit': [], - 'Alimenta': [], - 'Vulnera ubera': [], - 'Causam mihi': []} + return { + "Isolated note": [], + "lipsum/Isolated note": [], + "Sussudio": ["y1982", "y_1982", "y-1982", "y1982", "y2000"], + "Brevissimus moenia": [], + "Ne fuit": [], + "Alimenta": [], + "Vulnera ubera": [], + "Causam mihi": [], + } @pytest.fixture def expected_math_index(): - return {'Isolated note': [], - 'lipsum/Isolated note': [], - 'Sussudio': [], - 'Brevissimus moenia': [], - 'Ne fuit': [], - 'Alimenta': [], - 'Vulnera ubera': [], - 'Causam mihi': []} + return { + "Isolated note": [], + "lipsum/Isolated note": [], + "Sussudio": [], + "Brevissimus moenia": [], + "Ne fuit": [], + "Alimenta": [], + "Vulnera ubera": [], + "Causam mihi": [], + } @pytest.fixture def actual_connected_vault(): - return Vault(WKD / 'tests/vault-stub').connect() + return Vault(WKD / "tests/vault-stub").connect() @pytest.fixture def actual_connected_vault_md_files_only(): - return Vault(WKD / 'tests/vault-stub/lipsum').connect() + return Vault(WKD / "tests/vault-stub/lipsum").connect() @pytest.fixture @@ -237,92 +268,88 @@ def actual_metadata_df(actual_connected_vault): def test_get_metadata_cols(actual_metadata_df): assert isinstance(actual_metadata_df, pd.DataFrame) - expected_cols = ['rel_filepath', 'abs_filepath', - 'note_exists', - 'n_backlinks', 'n_wikilinks', - 'n_tags', - 'n_embedded_files', - 'modified_time'] + expected_cols = [ + "rel_filepath", + "abs_filepath", + "note_exists", + "n_backlinks", + "n_wikilinks", + "n_tags", + "n_embedded_files", + "modified_time", + ] assert actual_metadata_df.columns.tolist() == expected_cols def test_get_metadata_dtypes(actual_metadata_df): - assert actual_metadata_df['rel_filepath'].dtype == 'object' - assert actual_metadata_df['abs_filepath'].dtype == 'object' - assert actual_metadata_df['note_exists'].dtype == 'bool' - assert actual_metadata_df['n_backlinks'].dtype == 'int' - assert actual_metadata_df['n_wikilinks'].dtype == 'float' - assert actual_metadata_df['n_tags'].dtype == 'float' - assert actual_metadata_df['n_embedded_files'].dtype == 'float' - assert actual_metadata_df['modified_time'].dtype == 'datetime64[ns]' + assert actual_metadata_df["rel_filepath"].dtype == "object" + assert actual_metadata_df["abs_filepath"].dtype == "object" + assert actual_metadata_df["note_exists"].dtype == "bool" + assert actual_metadata_df["n_backlinks"].dtype == "int" + assert actual_metadata_df["n_wikilinks"].dtype == "float" + assert actual_metadata_df["n_tags"].dtype == "float" + assert actual_metadata_df["n_embedded_files"].dtype == "float" + assert actual_metadata_df["modified_time"].dtype == "datetime64[ns]" -def test_get_metadata_rel_filepath(actual_metadata_df, - expected_metadata_dict): - TEST_COL = 'rel_filepath' +def test_get_metadata_rel_filepath(actual_metadata_df, expected_metadata_dict): + TEST_COL = "rel_filepath" actual_series = actual_metadata_df[TEST_COL] - expected_series = (pd.Series(expected_metadata_dict.get(TEST_COL), - name=TEST_COL) - .rename_axis('note')) - assert_series_equal(actual_series, expected_series, - check_like=True) + expected_series = pd.Series( + expected_metadata_dict.get(TEST_COL), name=TEST_COL + ).rename_axis("note") + assert_series_equal(actual_series, expected_series, check_like=True) -def test_get_metadata_note_exists(actual_metadata_df, - expected_metadata_dict): - TEST_COL = 'note_exists' +def test_get_metadata_note_exists(actual_metadata_df, expected_metadata_dict): + TEST_COL = "note_exists" actual_series = actual_metadata_df[TEST_COL] - expected_series = (pd.Series(expected_metadata_dict.get(TEST_COL), - name=TEST_COL) - .rename_axis('note')) - assert_series_equal(actual_series, expected_series, - check_like=True) + expected_series = pd.Series( + expected_metadata_dict.get(TEST_COL), name=TEST_COL + ).rename_axis("note") + assert_series_equal(actual_series, expected_series, check_like=True) -def test_get_metadata_wikilinks(actual_metadata_df, - expected_metadata_dict): - TEST_COL = 'n_wikilinks' +def test_get_metadata_wikilinks(actual_metadata_df, expected_metadata_dict): + TEST_COL = "n_wikilinks" actual_series = actual_metadata_df[TEST_COL] - expected_series = (pd.Series(expected_metadata_dict.get(TEST_COL), - name=TEST_COL) - .rename_axis('note')) - assert_series_equal(actual_series, expected_series, - check_like=True) + expected_series = pd.Series( + expected_metadata_dict.get(TEST_COL), name=TEST_COL + ).rename_axis("note") + assert_series_equal(actual_series, expected_series, check_like=True) -def test_get_metadata_backlinks(actual_metadata_df, - expected_metadata_dict): - TEST_COL = 'n_backlinks' +def test_get_metadata_backlinks(actual_metadata_df, expected_metadata_dict): + TEST_COL = "n_backlinks" actual_series = actual_metadata_df[TEST_COL] - expected_series = (pd.Series(expected_metadata_dict.get(TEST_COL), - name=TEST_COL) - .rename_axis('note')) - assert_series_equal(actual_series, expected_series, - check_like=True) + expected_series = pd.Series( + expected_metadata_dict.get(TEST_COL), name=TEST_COL + ).rename_axis("note") + assert_series_equal(actual_series, expected_series, check_like=True) -def test_get_metadata_tags(actual_metadata_df, - expected_metadata_dict): - TEST_COL = 'n_tags' +def test_get_metadata_tags(actual_metadata_df, expected_metadata_dict): + TEST_COL = "n_tags" actual_series = actual_metadata_df[TEST_COL] - expected_series = (pd.Series(expected_metadata_dict.get(TEST_COL), - name=TEST_COL) - .rename_axis('note')) - assert_series_equal(actual_series, expected_series, - check_like=True) + expected_series = pd.Series( + expected_metadata_dict.get(TEST_COL), name=TEST_COL + ).rename_axis("note") + assert_series_equal(actual_series, expected_series, check_like=True) def test_backlink_and_wikilink_totals_equal(actual_metadata_df): # every wikilink is another note's backlink # equality is expected when canvas files are excluded from wikilinks list # for ANY VAULT under the defaults - assert (actual_metadata_df['n_backlinks'].sum() - == actual_metadata_df['n_wikilinks'].sum()) + assert ( + actual_metadata_df["n_backlinks"].sum() + == actual_metadata_df["n_wikilinks"].sum() + ) def test_backlink_individual_notes(actual_connected_vault): @@ -331,10 +358,10 @@ def test_backlink_individual_notes(actual_connected_vault): assert isinstance(actual_bl_ix, dict) expected_bl_subset = { - 'Sussudio': [], - 'Alimenta': [], - 'Tarpeia': ['Brevissimus moenia', 'Alimenta', 'Vulnera ubera'], - 'Ne fuit': ['Alimenta', 'Causam mihi'] + "Sussudio": [], + "Alimenta": [], + "Tarpeia": ["Brevissimus moenia", "Alimenta", "Vulnera ubera"], + "Ne fuit": ["Alimenta", "Causam mihi"], } for k in list(expected_bl_subset.keys()): @@ -344,29 +371,25 @@ def test_backlink_individual_notes(actual_connected_vault): actual_connected_vault.get_backlinks("Note that isn't in vault at all") # check that every note is in the backlinks_index - graph_nodes = [n for n in actual_connected_vault.graph.nodes] - assert (len(actual_bl_ix) - == (actual_connected_vault.graph.number_of_nodes())) + graph_nodes = list(actual_connected_vault.graph.nodes) + assert len(actual_bl_ix) == (actual_connected_vault.graph.number_of_nodes()) for k in list(expected_bl_subset.keys()): assert k in graph_nodes def test_backlink_counts(actual_connected_vault): expected_bl_count_subset = { - 'Sussudio': {}, - 'Alimenta': {}, - 'Tarpeia': {'Brevissimus moenia': 1, - 'Alimenta': 1, - 'Vulnera ubera': 1}, - 'Ne fuit': {'Alimenta': 1, - 'Causam mihi': 1}, - 'Bacchus': {'Ne fuit': 1, - 'Alimenta': 4} + "Sussudio": {}, + "Alimenta": {}, + "Tarpeia": {"Brevissimus moenia": 1, "Alimenta": 1, "Vulnera ubera": 1}, + "Ne fuit": {"Alimenta": 1, "Causam mihi": 1}, + "Bacchus": {"Ne fuit": 1, "Alimenta": 4}, } for k in list(expected_bl_count_subset.keys()): - assert (actual_connected_vault.get_backlink_counts(k) - == expected_bl_count_subset.get(k)) + assert actual_connected_vault.get_backlink_counts( + k + ) == expected_bl_count_subset.get(k) with pytest.raises(ValueError): actual_connected_vault.get_backlink_counts("Note that isn't in vault at all") @@ -374,38 +397,36 @@ def test_backlink_counts(actual_connected_vault): def test_wikilink_counts(actual_connected_vault): expected_wl_count_subset = { - 'Sussudio': {'American Psycho (film)': 1}, - 'Isolated note': {}, - 'Vulnera ubera': {'Caelum': 1, - 'Tarpeia': 1, - 'Vita': 1}, - 'Ne fuit': {'Aras Teucras': 1, - 'Manus': 1, - 'Bacchus': 1, - 'Amor': 1, - 'Caelum': 1, - 'Causam mihi': 1}, - 'Causam mihi': {'Dives': 1, - 'Manus': 1, - 'Ne fuit': 1, - 'Aetna': 1}, - 'Brevissimus moenia': {'Tarpeia': 1, - 'Caelum': 1, - 'Vita': 1}, - 'Alimenta': {'Manus': 1, - 'Bacchus': 4, - 'Amor': 1, - 'Ne fuit': 1, - 'Virtus': 1, - 'Brevissimus moenia': 1, - 'Tarpeia': 1, - 'Tydides': 1, - 'Vita': 1} + "Sussudio": {"American Psycho (film)": 1}, + "Isolated note": {}, + "Vulnera ubera": {"Caelum": 1, "Tarpeia": 1, "Vita": 1}, + "Ne fuit": { + "Aras Teucras": 1, + "Manus": 1, + "Bacchus": 1, + "Amor": 1, + "Caelum": 1, + "Causam mihi": 1, + }, + "Causam mihi": {"Dives": 1, "Manus": 1, "Ne fuit": 1, "Aetna": 1}, + "Brevissimus moenia": {"Tarpeia": 1, "Caelum": 1, "Vita": 1}, + "Alimenta": { + "Manus": 1, + "Bacchus": 4, + "Amor": 1, + "Ne fuit": 1, + "Virtus": 1, + "Brevissimus moenia": 1, + "Tarpeia": 1, + "Tydides": 1, + "Vita": 1, + }, } for k in list(expected_wl_count_subset.keys()): - assert (actual_connected_vault.get_wikilink_counts(k) - == expected_wl_count_subset.get(k)) + assert actual_connected_vault.get_wikilink_counts( + k + ) == expected_wl_count_subset.get(k) with pytest.raises(ValueError): actual_connected_vault.get_wikilink_counts("Note that isn't in vault at all") @@ -418,29 +439,46 @@ def test_wikilink_individual_notes(actual_connected_vault): # these notes exist expected_wl_subset = { - 'Sussudio': ['American Psycho (film)'], - 'Alimenta': ['Manus', 'Bacchus', 'Amor', 'Ne fuit', 'Virtus', - 'Brevissimus moenia', 'Tarpeia', 'Tydides', 'Vita', - 'Bacchus', 'Bacchus', 'Bacchus'], - 'Ne fuit': ['Aras Teucras', 'Manus', 'Bacchus', - 'Amor', 'Caelum', 'Causam mihi'] + "Sussudio": ["American Psycho (film)"], + "Alimenta": [ + "Manus", + "Bacchus", + "Amor", + "Ne fuit", + "Virtus", + "Brevissimus moenia", + "Tarpeia", + "Tydides", + "Vita", + "Bacchus", + "Bacchus", + "Bacchus", + ], + "Ne fuit": [ + "Aras Teucras", + "Manus", + "Bacchus", + "Amor", + "Caelum", + "Causam mihi", + ], } - assert (actual_connected_vault.get_wikilinks('Alimenta') - == expected_wl_subset.get('Alimenta')) + assert actual_connected_vault.get_wikilinks("Alimenta") == expected_wl_subset.get( + "Alimenta" + ) for k in list(expected_wl_subset.keys()): # list - sequence the links appear in notes assert expected_wl_subset.get(k) == actual_wl_ix.get(k) with pytest.raises(ValueError): - actual_connected_vault.get_wikilinks('Tarpeia') + actual_connected_vault.get_wikilinks("Tarpeia") # check that every existing note (file) has wikilink info assert len(actual_wl_ix) == len(actual_connected_vault.md_file_index) for k in list(actual_wl_ix.keys()): - assert isinstance(actual_connected_vault.md_file_index.get(k), - Path) + assert isinstance(actual_connected_vault.md_file_index.get(k), Path) def test_unique_wikilinks(actual_connected_vault): @@ -450,39 +488,61 @@ def test_unique_wikilinks(actual_connected_vault): # these notes exist expected_u_wl_subset = { - 'Sussudio': ['American Psycho (film)'], - 'Alimenta': ['Manus', 'Bacchus', 'Amor', 'Ne fuit', 'Virtus', - 'Brevissimus moenia', 'Tarpeia', 'Tydides', 'Vita'], - 'Ne fuit': ['Aras Teucras', 'Manus', 'Bacchus', - 'Amor', 'Caelum', 'Causam mihi'] + "Sussudio": ["American Psycho (film)"], + "Alimenta": [ + "Manus", + "Bacchus", + "Amor", + "Ne fuit", + "Virtus", + "Brevissimus moenia", + "Tarpeia", + "Tydides", + "Vita", + ], + "Ne fuit": [ + "Aras Teucras", + "Manus", + "Bacchus", + "Amor", + "Caelum", + "Causam mihi", + ], } - assert (actual_u_wl_ix.get('Alimenta') - == expected_u_wl_subset.get('Alimenta')) + assert actual_u_wl_ix.get("Alimenta") == expected_u_wl_subset.get("Alimenta") def test_nonexistent_notes(actual_connected_vault, actual_metadata_df): - expected_non_e_notes = ['Tarpeia', 'Caelum', 'Vita', 'Aras Teucras', - 'Manus', 'Bacchus', 'Amor', 'Virtus', - 'Tydides', 'Dives', 'Aetna', - 'American Psycho (film)'] + expected_non_e_notes = [ + "Tarpeia", + "Caelum", + "Vita", + "Aras Teucras", + "Manus", + "Bacchus", + "Amor", + "Virtus", + "Tydides", + "Dives", + "Aetna", + "American Psycho (film)", + ] assert isinstance(actual_connected_vault.nonexistent_notes, list) - assert (set(actual_connected_vault.nonexistent_notes) - == set(expected_non_e_notes)) - assert (set(actual_metadata_df.loc[~actual_metadata_df['note_exists'], :] - .index.tolist()) - == set(expected_non_e_notes)) + assert set(actual_connected_vault.nonexistent_notes) == set(expected_non_e_notes) + assert set( + actual_metadata_df.loc[~actual_metadata_df["note_exists"], :].index.tolist() + ) == set(expected_non_e_notes) def test_isolated_notes(actual_connected_vault): - expected_isol_notes = ['Isolated note', 'lipsum/Isolated note'] + expected_isol_notes = ["Isolated note", "lipsum/Isolated note"] assert isinstance(actual_connected_vault.isolated_notes, list) - assert (set(actual_connected_vault.isolated_notes) - == set(expected_isol_notes)) + assert set(actual_connected_vault.isolated_notes) == set(expected_isol_notes) # isolated notes can't have backlinks for n in actual_connected_vault.isolated_notes: @@ -492,8 +552,7 @@ def test_isolated_notes(actual_connected_vault): assert actual_connected_vault.get_wikilinks(n) == [] -def test_front_matter_index( - actual_connected_vault, expected_front_matter_index): +def test_front_matter_index(actual_connected_vault, expected_front_matter_index): assert isinstance(actual_connected_vault.front_matter_index, dict) actual_front_matter_index = actual_connected_vault.front_matter_index @@ -501,27 +560,29 @@ def test_front_matter_index( def test_front_matter_sussudio(actual_connected_vault): - expected_fm = {'title': 'Sussudio', - 'artist': 'Phil Collins', - 'category': 'music', - 'year': 1985, - 'url': 'https://www.discogs.com/Phil-Collins-Sussudio/master/106239', - 'references': [[['American Psycho (film)']], 'Polka Party!'], - 'chart_peaks': [{'US': 1}, {'UK': 12}]} - - actual_fm = actual_connected_vault.get_front_matter('Sussudio') + expected_fm = { + "title": "Sussudio", + "artist": "Phil Collins", + "category": "music", + "year": 1985, + "url": "https://www.discogs.com/Phil-Collins-Sussudio/master/106239", + "references": [[["American Psycho (film)"]], "Polka Party!"], + "chart_peaks": [{"US": 1}, {"UK": 12}], + } + + actual_fm = actual_connected_vault.get_front_matter("Sussudio") assert actual_fm == expected_fm def test_front_matter_constructorerror(actual_connected_vault): - actual_fm = actual_connected_vault.get_front_matter('Causam mihi') - assert actual_fm['description'] == '\\{\\{description\\}\\}' + actual_fm = actual_connected_vault.get_front_matter("Causam mihi") + assert actual_fm["description"] == "\\{\\{description\\}\\}" def test_embedded_files_sussudio(actual_connected_vault): - expected_files = ['Sussudio.mp3', '1999.flac'] + expected_files = ["Sussudio.mp3", "1999.flac"] - actual_files = actual_connected_vault.get_embedded_files('Sussudio') + actual_files = actual_connected_vault.get_embedded_files("Sussudio") assert actual_files == expected_files @@ -532,77 +593,72 @@ def test_nodes_gte_files(actual_connected_vault): assert act_n_len >= act_f_len -def test_embedded_files_index( - actual_connected_vault, expected_embedded_files_index): +def test_embedded_files_index(actual_connected_vault, expected_embedded_files_index): actual_files_ix = actual_connected_vault.embedded_files_index assert actual_files_ix == expected_embedded_files_index -def test_math_index( - actual_connected_vault, expected_math_index): +def test_math_index(actual_connected_vault, expected_math_index): actual_math_index = actual_connected_vault.math_index assert actual_math_index == expected_math_index -def test_md_links_index( - actual_connected_vault, expected_md_links_index): +def test_md_links_index(actual_connected_vault, expected_md_links_index): actual_md_links_ix = actual_connected_vault.md_links_index assert actual_md_links_ix == expected_md_links_index -def test_tags_index( - actual_connected_vault, expected_tags_main_only_index): +def test_tags_index(actual_connected_vault, expected_tags_main_only_index): actual_tags_ix = actual_connected_vault.tags_index assert actual_tags_ix == expected_tags_main_only_index -def test_unique_md_links( - actual_connected_vault, expected_md_links_index): - actual_u_md_links_ix = (actual_connected_vault. - _unique_md_links_index) +def test_unique_md_links(actual_connected_vault, expected_md_links_index): + actual_u_md_links_ix = actual_connected_vault._unique_md_links_index # all notes in stub have unique md links: assert actual_u_md_links_ix == expected_md_links_index def test_md_links_individual_notes(actual_connected_vault): - actual_md_links = actual_connected_vault.get_md_links('Ne fuit') - expected_md_links = ['http://vires.io/', - 'http://excoquitprotinus.net/quae.html', - 'http://medullis-me.net/novat', - 'http://sedibus.io/levemmonstra'] + actual_md_links = actual_connected_vault.get_md_links("Ne fuit") + expected_md_links = [ + "http://vires.io/", + "http://excoquitprotinus.net/quae.html", + "http://medullis-me.net/novat", + "http://sedibus.io/levemmonstra", + ] assert actual_md_links == expected_md_links def test_tags_individual_notes(actual_connected_vault): - actual_md_links = actual_connected_vault.get_tags('Ne fuit') + actual_md_links = actual_connected_vault.get_tags("Ne fuit") expected_md_links = [] assert actual_md_links == expected_md_links def test_md_links_not_existing(actual_connected_vault): with pytest.raises(ValueError): - actual_connected_vault.get_md_links('Tarpeia') + actual_connected_vault.get_md_links("Tarpeia") def test_tags_not_existing(actual_connected_vault): with pytest.raises(ValueError): - actual_connected_vault.get_tags('Tarpeia') + actual_connected_vault.get_tags("Tarpeia") def test_front_matter_not_existing(actual_connected_vault): with pytest.raises(ValueError): - actual_connected_vault.get_front_matter('Tarpeia') + actual_connected_vault.get_front_matter("Tarpeia") def test_embedded_notes_not_existing(actual_connected_vault): with pytest.raises(ValueError): - actual_connected_vault.get_embedded_files('Tarpeia') + actual_connected_vault.get_embedded_files("Tarpeia") def test_media_file_metadata_df_empty(actual_connected_vault_md_files_only): # use the lipsum dir as the 'vault' dir (md only) - df_media = (actual_connected_vault_md_files_only - .get_media_file_metadata()) + df_media = actual_connected_vault_md_files_only.get_media_file_metadata() assert len(df_media) == 0 @@ -613,8 +669,7 @@ def test_media_file_metadata_df_empty(actual_connected_vault_md_files_only): def test_canvas_file_metadata_df_empty(actual_connected_vault_md_files_only): # use the lipsum dir as the 'vault' dir (md only) - df_media = (actual_connected_vault_md_files_only - .get_canvas_file_metadata()) + df_media = actual_connected_vault_md_files_only.get_canvas_file_metadata() assert len(df_media) == 0 @@ -631,16 +686,14 @@ def test_all_file_metadata_df(actual_connected_vault): # check that notes metadata was only used: assert_frame_equal( - actual_all_df.drop(columns=['graph_category']), - actual_note_df.rename(columns={'note_exists': 'file_exists'})) + actual_all_df.drop(columns=["graph_category"]), + actual_note_df.rename(columns={"note_exists": "file_exists"}), + ) # check that only notes are used for backlinks: - assert (actual_all_df['n_backlinks'].sum() - == (actual_all_df['n_wikilinks'].sum())) + assert actual_all_df["n_backlinks"].sum() == (actual_all_df["n_wikilinks"].sum()) -def test_internal_canvas_backlink_counts_func_errors( - actual_connected_vault): +def test_internal_canvas_backlink_counts_func_errors(actual_connected_vault): with pytest.raises(AttributeError): - (actual_connected_vault. - _get_backlink_counts_for_canvas_files_only()) + (actual_connected_vault._get_backlink_counts_for_canvas_files_only()) diff --git a/tests/test_api_vault_stub_gather.py b/tests/test_api_vault_stub_gather.py index 7adda27..1482c0c 100644 --- a/tests/test_api_vault_stub_gather.py +++ b/tests/test_api_vault_stub_gather.py @@ -1,6 +1,6 @@ -import pytest from pathlib import Path +import pytest from obsidiantools.api import Vault @@ -10,7 +10,7 @@ @pytest.fixture def actual_unconnected_vault(): - return Vault(WKD / 'tests/vault-stub') + return Vault(WKD / "tests/vault-stub") @pytest.fixture @@ -31,33 +31,31 @@ def test_vault_not_connected(actual_unconnected_vault): def test_vault_not_gathered(actual_unconnected_vault): with pytest.raises(AttributeError): - actual_unconnected_vault.get_source_text('Isolated note') + actual_unconnected_vault.get_source_text("Isolated note") with pytest.raises(AttributeError): - actual_unconnected_vault.get_readable_text('Isolated note') + actual_unconnected_vault.get_readable_text("Isolated note") def test_text_not_existing(actual_gathered_vault_defaults): assert actual_gathered_vault_defaults.is_gathered with pytest.raises(ValueError): - actual_gathered_vault_defaults.get_source_text('Tarpeia') + actual_gathered_vault_defaults.get_source_text("Tarpeia") with pytest.raises(ValueError): - actual_gathered_vault_defaults.get_readable_text('Tarpeia') + actual_gathered_vault_defaults.get_readable_text("Tarpeia") def test_source_text_existing_file(actual_gathered_vault_defaults): - actual_in_text = (actual_gathered_vault_defaults - .get_source_text('Isolated note')) - expected_start = '# Isolated note' - expected_end = 'an isolated note ~~an orphan~~.\n' + actual_in_text = actual_gathered_vault_defaults.get_source_text("Isolated note") + expected_start = "# Isolated note" + expected_end = "an isolated note ~~an orphan~~.\n" assert actual_in_text.startswith(expected_start) assert actual_in_text.endswith(expected_end) def test_readable_text_existing_file(actual_gathered_vault_defaults): - actual_in_text = (actual_gathered_vault_defaults - .get_readable_text('Sussudio')) - expected_start = '# Sussudio' - expected_end = '\\- #hash_char_not_tag\n' + actual_in_text = actual_gathered_vault_defaults.get_readable_text("Sussudio") + expected_start = "# Sussudio" + expected_end = "\\- #hash_char_not_tag\n" assert actual_in_text.startswith(expected_start) assert actual_in_text.endswith(expected_end) @@ -70,7 +68,7 @@ def test_isolated_note_md_text(actual_gathered_vault_defaults): assert actual_gathered_vault_defaults.is_gathered - actual_text = actual_gathered_vault_defaults.get_source_text('Isolated note') + actual_text = actual_gathered_vault_defaults.get_source_text("Isolated note") assert actual_text == expected_text @@ -107,5 +105,5 @@ def test_sussudio_readable_text(actual_gathered_vault_defaults): However these shouldn't be recognised as tags: \- (#y1985 ) \- #1985 \- American Psycho (film)#Patrick Bateman \- #hash_char_not_tag """ - actual_text = actual_gathered_vault_defaults.get_readable_text('Sussudio') + actual_text = actual_gathered_vault_defaults.get_readable_text("Sussudio") assert actual_text == expected_text diff --git a/tests/test_canvas_utils_fpath_funcs.py b/tests/test_canvas_utils_fpath_funcs.py index a674f99..f317217 100644 --- a/tests/test_canvas_utils_fpath_funcs.py +++ b/tests/test_canvas_utils_fpath_funcs.py @@ -1,14 +1,14 @@ from pathlib import Path -import pytest +import pytest -from obsidiantools.canvas_utils import (get_canvas_relpaths_from_dir) +from obsidiantools.canvas_utils import get_canvas_relpaths_from_dir @pytest.fixture def mocker_md_file(mocker): mocked_output = mocker.mock_open() - mocker.patch('builtins.open', mocked_output) + mocker.patch("builtins.open", mocked_output) return mocked_output @@ -19,4 +19,4 @@ def test_get_canvas_relpaths_from_dir(tmp_path): assert isinstance(actual_relpaths, list) for p in actual_relpaths: assert isinstance(p, Path) - assert p.suffix == 'canvas' + assert p.suffix == "canvas" diff --git a/tests/test_canvas_utils_vault_stub.py b/tests/test_canvas_utils_vault_stub.py index bb28b25..41d4238 100644 --- a/tests/test_canvas_utils_vault_stub.py +++ b/tests/test_canvas_utils_vault_stub.py @@ -1,39 +1,38 @@ -import pytest from pathlib import Path +import pytest from obsidiantools.canvas_utils import get_canvas_relpaths_matching_subdirs - # NOTE: run the tests from the project dir. WKD = Path().cwd() @pytest.fixture def actual_vault_path(): - return WKD / 'tests/vault-stub' + return WKD / "tests/vault-stub" def test_get_canvas_relpaths_matching_subdirs(actual_vault_path): actual_w_root = get_canvas_relpaths_matching_subdirs( - actual_vault_path, include_root=True) + actual_vault_path, include_root=True + ) # not including files directly in vault root: actual_wo_root = get_canvas_relpaths_matching_subdirs( - actual_vault_path, include_root=False) - expected_in_root = [Path('Crazy wall.canvas'), - Path('Crazy wall 2.canvas')] - assert (set(actual_w_root).difference(actual_wo_root) - == set(expected_in_root)) + actual_vault_path, include_root=False + ) + expected_in_root = [Path("Crazy wall.canvas"), Path("Crazy wall 2.canvas")] + assert set(actual_w_root).difference(actual_wo_root) == set(expected_in_root) # same result but via the other kwarg: actual_w_lipsum_only = get_canvas_relpaths_matching_subdirs( - actual_vault_path, include_subdirs=['lipsum']) - assert (set(actual_w_lipsum_only).difference(actual_wo_root) - == set(expected_in_root)) + actual_vault_path, include_subdirs=["lipsum"] + ) + assert set(actual_w_lipsum_only).difference(actual_wo_root) == set(expected_in_root) # both kwargs not default: actual_w_lipsum_only = get_canvas_relpaths_matching_subdirs( - actual_vault_path, include_subdirs=['lipsum'], include_root=False) - assert (set(actual_w_lipsum_only).difference(actual_wo_root) - == set()) + actual_vault_path, include_subdirs=["lipsum"], include_root=False + ) + assert set(actual_w_lipsum_only).difference(actual_wo_root) == set() diff --git a/tests/test_html_processing.py b/tests/test_html_processing.py index 4fec610..b15ffc4 100644 --- a/tests/test_html_processing.py +++ b/tests/test_html_processing.py @@ -1,8 +1,6 @@ from pathlib import Path -from obsidiantools.html_processing import (_remove_code, - _remove_del_text, - _remove_latex) +from obsidiantools.html_processing import _remove_code, _remove_del_text, _remove_latex from obsidiantools.md_utils import _get_html_from_md_file # NOTE: run the tests from the project dir. @@ -10,7 +8,7 @@ def test_remove_code(): - fpath = Path('.') / 'tests/general/wikilinks_exclude-code.md' + fpath = Path(".") / "tests/general/wikilinks_exclude-code.md" actual_html = _get_html_from_md_file(fpath) actual_proc_html = _remove_code(actual_html) @@ -24,7 +22,7 @@ def test_remove_code(): def test_remove_del_text(): - fpath = Path('.') / 'tests/general/readable-text_all-deleted.md' + fpath = Path(".") / "tests/general/readable-text_all-deleted.md" actual_html = _get_html_from_md_file(fpath) actual_proc_html = _remove_del_text(actual_html) @@ -35,7 +33,7 @@ def test_remove_del_text(): def test_remove_latex_in_note_with_highly_formatted_text(): - fpath = Path('.') / 'tests/general/latex.md' + fpath = Path(".") / "tests/general/latex.md" actual_html = _get_html_from_md_file(fpath) actual_proc_html = _remove_latex(actual_html) diff --git a/tests/test_md_utils.py b/tests/test_md_utils.py index b926080..c67f233 100644 --- a/tests/test_md_utils.py +++ b/tests/test_md_utils.py @@ -1,24 +1,27 @@ -import pytest from pathlib import Path -from obsidiantools.md_utils import (_get_all_wikilinks_from_source_text, - _get_all_embedded_files_from_source_text, - _get_unique_wikilinks_from_source_text, - _get_all_md_link_info_from_source_text, - _get_unique_md_links_from_source_text, - get_unique_md_links, - _get_html_from_md_file, - get_source_text_from_md_file, - _transform_md_file_string_for_tag_parsing, - get_wikilinks, - get_embedded_files, - get_front_matter, - get_tags, - _remove_wikilinks_from_source_text, - _replace_wikilinks_with_their_text, - _replace_md_links_with_their_text, - get_readable_text_from_md_file) -from obsidiantools.html_processing import (_get_all_latex_from_html_content) +import pytest + +from obsidiantools.html_processing import _get_all_latex_from_html_content +from obsidiantools.md_utils import ( + _get_all_embedded_files_from_source_text, + _get_all_md_link_info_from_source_text, + _get_all_wikilinks_from_source_text, + _get_html_from_md_file, + _get_unique_md_links_from_source_text, + _get_unique_wikilinks_from_source_text, + _remove_wikilinks_from_source_text, + _replace_md_links_with_their_text, + _replace_wikilinks_with_their_text, + _transform_md_file_string_for_tag_parsing, + get_embedded_files, + get_front_matter, + get_readable_text_from_md_file, + get_source_text_from_md_file, + get_tags, + get_unique_md_links, + get_wikilinks, +) @pytest.fixture @@ -71,78 +74,94 @@ def txt_md_links_stub(): @pytest.fixture def txt_sussudio_stub(): - text = _get_html_from_md_file('tests/vault-stub/Sussudio.md') + text = _get_html_from_md_file("tests/vault-stub/Sussudio.md") return text @pytest.fixture def txt_wikilink_extraction_stub(): - with open('tests/general/wikilinks_extraction.md') as f: + with open("tests/general/wikilinks_extraction.md") as f: in_str = f.read() return in_str @pytest.fixture def txt_md_link_extraction_stub(): - with open('tests/general/md-links_extraction.md') as f: + with open("tests/general/md-links_extraction.md") as f: in_str = f.read() return in_str def test_get_all_wikilinks_from_source_text(html_wikilinks_stub): actual_results = _get_all_wikilinks_from_source_text(html_wikilinks_stub) - expected_results = ['Shopping list', 'Bananas', 'Banana splits', - 'Apples', - 'Flour', 'Flower', - 'Bananas', - 'Durians', - 'Apples', 'Bananas', 'Protein shakes'] + expected_results = [ + "Shopping list", + "Bananas", + "Banana splits", + "Apples", + "Flour", + "Flower", + "Bananas", + "Durians", + "Apples", + "Bananas", + "Protein shakes", + ] assert actual_results == expected_results def test_get_all_wikilinks_from_source_text_keep_aliases(html_wikilinks_stub): actual_results = _get_all_wikilinks_from_source_text( - html_wikilinks_stub, remove_aliases=False) - expected_results = ['Shopping list | shopping list', - 'Bananas', 'Banana splits', - 'Apples', - 'Flour', 'Flower | flower', - 'Bananas | BANANAS', - 'Durians', - 'Apples|Freshly squeezed apple juice', - 'Bananas|Banana smoothie', - 'Protein shakes#Protein powder|Vanilla whey protein'] + html_wikilinks_stub, remove_aliases=False + ) + expected_results = [ + "Shopping list | shopping list", + "Bananas", + "Banana splits", + "Apples", + "Flour", + "Flower | flower", + "Bananas | BANANAS", + "Durians", + "Apples|Freshly squeezed apple juice", + "Bananas|Banana smoothie", + "Protein shakes#Protein powder|Vanilla whey protein", + ] assert actual_results == expected_results def test_get_all_embedded_files_from_source_text(html_wikilinks_stub): - actual_results = _get_all_embedded_files_from_source_text( - html_wikilinks_stub) - expected_results = ['Egg.jpg', 'Easter egg.png', 'Egg.jpg'] + actual_results = _get_all_embedded_files_from_source_text(html_wikilinks_stub) + expected_results = ["Egg.jpg", "Easter egg.png", "Egg.jpg"] assert actual_results == expected_results -def test_get_all_embedded_files_from_source_text_keep_aliases( - html_wikilinks_stub): +def test_get_all_embedded_files_from_source_text_keep_aliases(html_wikilinks_stub): actual_results = _get_all_embedded_files_from_source_text( - html_wikilinks_stub, remove_aliases=False) - expected_results = ['Egg.jpg', 'Easter egg.png', 'Egg.jpg | 125'] + html_wikilinks_stub, remove_aliases=False + ) + expected_results = ["Egg.jpg", "Easter egg.png", "Egg.jpg | 125"] assert actual_results == expected_results def test_get_unique_wikilinks_from_html_content(html_wikilinks_stub): actual_results = _get_unique_wikilinks_from_source_text( - html_wikilinks_stub, remove_aliases=True) - expected_results = ['Shopping list', - 'Bananas', 'Banana splits', - 'Apples', - 'Flour', 'Flower', - 'Durians', - 'Protein shakes'] + html_wikilinks_stub, remove_aliases=True + ) + expected_results = [ + "Shopping list", + "Bananas", + "Banana splits", + "Apples", + "Flour", + "Flower", + "Durians", + "Protein shakes", + ] assert actual_results == expected_results assert isinstance(expected_results, list) @@ -154,20 +173,27 @@ def test_get_unique_wikilinks_from_html_content_has_unique_links(html_wikilinks_ def test_get_all_md_link_info(txt_md_links_stub): - expected_links = [('The Times 03/Jan/2009 Chancellor on brink of second bailout for banks', - 'https://www.thetimes.co.uk/article/chancellor-alistair-darling-on-brink-of-second-bailout-for-banks-n9l382mn62h'), - ("Chancellor Alistair Darling on brink of second bailout for banks", - 'https://www.thetimes.co.uk/article/chancellor-alistair-darling-on-brink-of-second-bailout-for-banks-n9l382mn62h'), - ('ADA', 'https://cardano.org/') - ] + expected_links = [ + ( + "The Times 03/Jan/2009 Chancellor on brink of second bailout for banks", + "https://www.thetimes.co.uk/article/chancellor-alistair-darling-on-brink-of-second-bailout-for-banks-n9l382mn62h", + ), + ( + "Chancellor Alistair Darling on brink of second bailout for banks", + "https://www.thetimes.co.uk/article/chancellor-alistair-darling-on-brink-of-second-bailout-for-banks-n9l382mn62h", + ), + ("ADA", "https://cardano.org/"), + ] actual_links = _get_all_md_link_info_from_source_text(txt_md_links_stub) assert actual_links == expected_links def test_get_unique_md_links_has_order_preserved(txt_md_links_stub): - expected_links = ['https://www.thetimes.co.uk/article/chancellor-alistair-darling-on-brink-of-second-bailout-for-banks-n9l382mn62h', - 'https://cardano.org/'] + expected_links = [ + "https://www.thetimes.co.uk/article/chancellor-alistair-darling-on-brink-of-second-bailout-for-banks-n9l382mn62h", + "https://cardano.org/", + ] actual_links = _get_unique_md_links_from_source_text(txt_md_links_stub) assert actual_links == expected_links @@ -180,39 +206,39 @@ def test_get_unique_md_links_has_unique_links(txt_md_links_stub): def test_pretend_wikilink_not_extracted_from_front_matter(txt_sussudio_stub): actual_links = _get_unique_wikilinks_from_source_text(txt_sussudio_stub) - assert not set(['Polka Party!']).issubset(set(actual_links)) + assert not {"Polka Party!"}.issubset(set(actual_links)) def test_sussudio_front_matter(): - expected_metadata = {'title': 'Sussudio', - 'artist': 'Phil Collins', - 'category': 'music', - 'year': 1985, - 'url': 'https://www.discogs.com/Phil-Collins-Sussudio/master/106239', - 'references': [[['American Psycho (film)']], 'Polka Party!'], - 'chart_peaks': [{'US': 1}, {'UK': 12}]} - actual_metadata = get_front_matter( - Path('.') / 'tests/vault-stub/Sussudio.md') + expected_metadata = { + "title": "Sussudio", + "artist": "Phil Collins", + "category": "music", + "year": 1985, + "url": "https://www.discogs.com/Phil-Collins-Sussudio/master/106239", + "references": [[["American Psycho (film)"]], "Polka Party!"], + "chart_peaks": [{"US": 1}, {"UK": 12}], + } + actual_metadata = get_front_matter(Path(".") / "tests/vault-stub/Sussudio.md") assert actual_metadata == expected_metadata def test_ne_fuit_front_matter(): expected_metadata = {} - actual_metadata = get_front_matter( - Path('.') / 'tests/vault-stub/lipsum/Ne fuit.md') + actual_metadata = get_front_matter(Path(".") / "tests/vault-stub/lipsum/Ne fuit.md") assert actual_metadata == expected_metadata def test_front_matter_only_parsing(): - fm_only_files = Path('.').glob('tests/general/frontmatter-only*.md') + fm_only_files = Path(".").glob("tests/general/frontmatter-only*.md") for f in fm_only_files: actual_txt = get_source_text_from_md_file(f) - expected_txt = '\n' + expected_txt = "\n" assert actual_txt == expected_txt def test_separators_not_front_matter_parsing(): - files = Path('.').glob('tests/general/not-frontmatter*.md') + files = Path(".").glob("tests/general/not-frontmatter*.md") for f in files: actual_output = get_front_matter(f) expected_output = {} @@ -220,7 +246,7 @@ def test_separators_not_front_matter_parsing(): def test_handle_invalid_front_matter(): - files = Path('.').glob('tests/general/invalid-frontmatter*.md') + files = Path(".").glob("tests/general/invalid-frontmatter*.md") for f in files: actual_output = get_front_matter(f) expected_output = {} @@ -228,10 +254,10 @@ def test_handle_invalid_front_matter(): def test_front_matter_parse_double_curly(): - fpath = Path('.') / 'tests/general/frontmatter_parse-double-curly.md' + fpath = Path(".") / "tests/general/frontmatter_parse-double-curly.md" actual_txt = get_source_text_from_md_file(fpath) - expected_txt = '\n' + expected_txt = "\n" assert actual_txt == expected_txt @@ -245,119 +271,124 @@ def test_hash_char_parsing_func(): def test_sussudio_tags_with_nesting_not_shown(): - actual_tags = get_tags( - Path('.') / 'tests/vault-stub/Sussudio.md') - expected_tags = ['y1982', 'y_1982', 'y-1982', - 'y1982', 'y2000'] + actual_tags = get_tags(Path(".") / "tests/vault-stub/Sussudio.md") + expected_tags = ["y1982", "y_1982", "y-1982", "y1982", "y2000"] assert actual_tags == expected_tags def test_sussudio_tags_with_nesting_shown(): - actual_tags = get_tags( - Path('.') / 'tests/vault-stub/Sussudio.md', show_nested=True) - expected_tags = ['y1982', 'y_1982', 'y-1982', - 'y1982/sep', 'y2000/party-over/oops/out-of-time'] + actual_tags = get_tags(Path(".") / "tests/vault-stub/Sussudio.md", show_nested=True) + expected_tags = [ + "y1982", + "y_1982", + "y-1982", + "y1982/sep", + "y2000/party-over/oops/out-of-time", + ] assert actual_tags == expected_tags def test_embedded_files_alias_scaling(): actual_embedded_images = get_embedded_files( - Path('.') / 'tests/general/embedded-images_in-table.md') - expected_embedded_images = ['test-image_1_before.png', - 'test-image_1_after.png', - 'test-image_2_before.png', - 'test-image_2_after.png'] + Path(".") / "tests/general/embedded-images_in-table.md" + ) + expected_embedded_images = [ + "test-image_1_before.png", + "test-image_1_after.png", + "test-image_2_before.png", + "test-image_2_after.png", + ] assert actual_embedded_images == expected_embedded_images def test_wikilinks_code_block(): - actual_links = get_wikilinks( - Path('.') / 'tests/general/wikilinks_exclude-code.md') + actual_links = get_wikilinks(Path(".") / "tests/general/wikilinks_exclude-code.md") expected_links = [] assert actual_links == expected_links def test_latex(): - html = _get_html_from_md_file(Path('.') / 'tests/general/latex.md') + html = _get_html_from_md_file(Path(".") / "tests/general/latex.md") actual_latex_list = _get_all_latex_from_html_content(html) - expected_latex_list = ['\\beta', '\\beta', - '\\hat{\\beta}_{GEE} \\xrightarrow{D} N(\\beta_{0}, \\Sigma(\\beta_{0}))', - '\\beta', - 'U_{GEE}(\\beta, \\alpha, \\phi) = \\sum_{i=1}^{n} D_{i}^T~V_{i}(\\alpha; \\phi)^{-1} (y_{i} - \\mu_{i}) = 0 \\tag{1} \\label{eq1}', - '\\eqref{eq1}'] + expected_latex_list = [ + "\\beta", + "\\beta", + "\\hat{\\beta}_{GEE} \\xrightarrow{D} N(\\beta_{0}, \\Sigma(\\beta_{0}))", + "\\beta", + "U_{GEE}(\\beta, \\alpha, \\phi) = \\sum_{i=1}^{n} D_{i}^T~V_{i}(\\alpha; \\phi)^{-1} (y_{i} - \\mu_{i}) = 0 \\tag{1} \\label{eq1}", + "\\eqref{eq1}", + ] assert actual_latex_list == expected_latex_list def test_remove_wikilinks(txt_wikilink_extraction_stub): - out_str = _remove_wikilinks_from_source_text( - txt_wikilink_extraction_stub) + out_str = _remove_wikilinks_from_source_text(txt_wikilink_extraction_stub) expected_str = "\n" * 6 assert out_str == expected_str def test_wikilinks_as_readable_text(txt_wikilink_extraction_stub): - out_str = _replace_wikilinks_with_their_text( - txt_wikilink_extraction_stub) + out_str = _replace_wikilinks_with_their_text(txt_wikilink_extraction_stub) expected_str = "\n".join(["A", "B", "see", "dee", "ee", "A"]) + "\n" assert out_str == expected_str def test_md_links_as_readable_text(txt_md_link_extraction_stub): - out_str = _replace_md_links_with_their_text( - txt_md_link_extraction_stub) + out_str = _replace_md_links_with_their_text(txt_md_link_extraction_stub) - expected_str = ( - """Obsidian.md homepage + expected_str = """Obsidian.md homepage Github homepage https://obsidian.md Github homepage -""") +""" assert out_str == expected_str def test_unique_md_links(): actual_links = get_unique_md_links( - Path('.') / 'tests/general/md-links_extraction.md') - expected_links = ['http://obsidian.md', 'https://github.com'] + Path(".") / "tests/general/md-links_extraction.md" + ) + expected_links = ["http://obsidian.md", "https://github.com"] assert actual_links == expected_links def test_readable_text_from_latex_md_stub_default_tags(): - actual_str = get_readable_text_from_md_file( - Path('.') / 'tests/general/latex.md') - expected_str = '# Note with LaTeX\n\n## GEE \n\nRegression coefficients estimated through GEE are asymptotically normal: \n\nThe underscore chars above need to be caught through MathJax - capture subscripts rather than emphasis in the parsing.\n\n## GEE estimation\n\nA few eqs more using deeper LaTeX functionality:\n\nEquations for GEE are solved for the regression parameters using: \n\nTaking the expectation of the equation system in ...\n' + actual_str = get_readable_text_from_md_file(Path(".") / "tests/general/latex.md") + expected_str = "# Note with LaTeX\n\n## GEE \n\nRegression coefficients estimated through GEE are asymptotically normal: \n\nThe underscore chars above need to be caught through MathJax - capture subscripts rather than emphasis in the parsing.\n\n## GEE estimation\n\nA few eqs more using deeper LaTeX functionality:\n\nEquations for GEE are solved for the regression parameters using: \n\nTaking the expectation of the equation system in ...\n" assert actual_str == expected_str def test_readable_text_from_latex_md_stub_allow_no_tags(): actual_str = get_readable_text_from_md_file( - Path('.') / 'tests/general/latex.md', tags=[]) - expected_str = 'Note with LaTeX GEE Regression coefficients estimated through GEE are asymptotically normal: The underscore chars above need to be caught through MathJax - capture subscripts rather than emphasis in the parsing. GEE estimation A few eqs more using deeper LaTeX functionality: Equations for GEE are solved for the regression parameters using: Taking the expectation of the equation system in ...\n' + Path(".") / "tests/general/latex.md", tags=[] + ) + expected_str = "Note with LaTeX GEE Regression coefficients estimated through GEE are asymptotically normal: The underscore chars above need to be caught through MathJax - capture subscripts rather than emphasis in the parsing. GEE estimation A few eqs more using deeper LaTeX functionality: Equations for GEE are solved for the regression parameters using: Taking the expectation of the equation system in ...\n" assert actual_str == expected_str def test_readable_text_strikethrough_is_deleted(): actual_str = get_readable_text_from_md_file( - Path('.') / 'tests/general/readable-text_all-deleted.md') - expected_str = '\n' + Path(".") / "tests/general/readable-text_all-deleted.md" + ) + expected_str = "\n" assert actual_str == expected_str def test_readable_text_embedded_files_are_removed(): actual_str = get_readable_text_from_md_file( - Path('.') / 'tests/general/embedded-files_in-body.md') - expected_str = '\n' + Path(".") / "tests/general/embedded-files_in-body.md" + ) + expected_str = "\n" assert actual_str == expected_str def test_source_text_has_text_after_problematic_latex(): - expected_str = ( - """# Generalised estimating equations + expected_str = """# Generalised estimating equations **Generalised estimating equations (GEE)** are ... @@ -378,10 +409,10 @@ def test_source_text_has_text_after_problematic_latex(): ### Another subheading Text that shouldn't disappear. -""") +""" actual_str = get_source_text_from_md_file( - Path('.') / 'tests/general/source-text_handle-latex.md', - remove_math=True) + Path(".") / "tests/general/source-text_handle-latex.md", remove_math=True + ) assert actual_str == expected_str diff --git a/tests/test_md_utils_fpath_funcs.py b/tests/test_md_utils_fpath_funcs.py index 9797b3d..7034a4a 100644 --- a/tests/test_md_utils_fpath_funcs.py +++ b/tests/test_md_utils_fpath_funcs.py @@ -1,18 +1,21 @@ from pathlib import Path + import pytest -from obsidiantools.md_utils import (_get_html_from_md_file, - get_source_text_from_md_file) -from obsidiantools.md_utils import (get_md_relpaths_from_dir, - get_md_links, - get_unique_wikilinks, - get_wikilinks) +from obsidiantools.md_utils import ( + _get_html_from_md_file, + get_md_links, + get_md_relpaths_from_dir, + get_source_text_from_md_file, + get_unique_wikilinks, + get_wikilinks, +) @pytest.fixture def mocker_md_file(mocker): mocked_output = mocker.mock_open() - mocker.patch('builtins.open', mocked_output) + mocker.patch("builtins.open", mocked_output) return mocked_output @@ -23,7 +26,7 @@ def test_get_md_relpaths_from_dir(tmp_path): assert isinstance(actual_relpaths, list) for p in actual_relpaths: assert isinstance(p, Path) - assert p.suffix == 'md' + assert p.suffix == "md" def test_get_html_from_md_file(mocker_md_file): diff --git a/tests/test_md_utils_vault_stub.py b/tests/test_md_utils_vault_stub.py index 0534d69..b8c8cf1 100644 --- a/tests/test_md_utils_vault_stub.py +++ b/tests/test_md_utils_vault_stub.py @@ -1,39 +1,38 @@ -import pytest from pathlib import Path +import pytest from obsidiantools.md_utils import get_md_relpaths_matching_subdirs - # NOTE: run the tests from the project dir. WKD = Path().cwd() @pytest.fixture def actual_vault_path(): - return WKD / 'tests/vault-stub' + return WKD / "tests/vault-stub" def test_get_md_relpaths_matching_subdirs(actual_vault_path): actual_w_root = get_md_relpaths_matching_subdirs( - actual_vault_path, include_root=True) + actual_vault_path, include_root=True + ) # not including files directly in vault root: actual_wo_root = get_md_relpaths_matching_subdirs( - actual_vault_path, include_root=False) - expected_in_root = [Path('Sussudio.md'), - Path('Isolated note.md')] - assert (set(actual_w_root).difference(actual_wo_root) - == set(expected_in_root)) + actual_vault_path, include_root=False + ) + expected_in_root = [Path("Sussudio.md"), Path("Isolated note.md")] + assert set(actual_w_root).difference(actual_wo_root) == set(expected_in_root) # same result but via the other kwarg: actual_w_lipsum_only = get_md_relpaths_matching_subdirs( - actual_vault_path, include_subdirs=['lipsum']) - assert (set(actual_w_lipsum_only).difference(actual_wo_root) - == set(expected_in_root)) + actual_vault_path, include_subdirs=["lipsum"] + ) + assert set(actual_w_lipsum_only).difference(actual_wo_root) == set(expected_in_root) # both kwargs not default: actual_w_lipsum_only = get_md_relpaths_matching_subdirs( - actual_vault_path, include_subdirs=['lipsum'], include_root=False) - assert (set(actual_w_lipsum_only).difference(actual_wo_root) - == set()) + actual_vault_path, include_subdirs=["lipsum"], include_root=False + ) + assert set(actual_w_lipsum_only).difference(actual_wo_root) == set() From 8b31f1961641bda160716bd0f44f6b7df0da0f89 Mon Sep 17 00:00:00 2001 From: JavierGOrdonnez Date: Mon, 9 Mar 2026 19:23:25 +0100 Subject: [PATCH 3/4] [FEAT] add uv-lock --- .gitignore | 1 + uv.lock | 1981 ++++++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 1982 insertions(+) create mode 100644 uv.lock diff --git a/.gitignore b/.gitignore index a34e460..e9fe51a 100644 --- a/.gitignore 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