Modernize repo

.github/workflows/create-release.yml

@@ -8,24 +8,6 @@ on:
 name: Create GitHub Release
 
 jobs:
-  build:
-    name: Create Release
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout code
-        uses: actions/checkout@v2
-      - name: Create Release
-        id: create_release
-        uses: actions/create-release@v1
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # This token is provided by Actions, you do not need to create your own token
-        with:
-          tag_name: ${{ github.ref }}
-          release_name: Release ${{ github.ref }}
-          body: |
-            See Changelog for details
-          draft: false
-          prerelease: false
   deploy:
     name: Push Release to PyPi
     runs-on: ubuntu-latest

.github/workflows/docs.yml

@@ -0,0 +1,109 @@
+name: Build, test, and publish documentation
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+# Required permissions for deploying to GitHub Pages
+permissions:
+  contents: write
+  pages: write
+
+jobs:
+  test:
+    name: Run tests and upload coverage
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.12]
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Cache pip
+        uses: actions/cache@v4
+        with:
+          path: ~/.cache/pip
+          key: "pip-${{ runner.os }}-py-${{ matrix.python-version }}-${{ hashFiles('**/requirements*.txt') }}"
+          restore-keys: |
+            pip-${{ runner.os }}-py-${{ matrix.python-version }}-
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools wheel
+          pip install -r docs/requirements.txt
+          pip install -e .
+          pip install pytest pytest-cov
+
+      - name: Run tests with coverage
+        run: |
+          pytest --cov=panoptes.data --cov-report=xml:coverage.xml --cov-report=html:htmlcov -q
+
+      - name: Upload coverage report (xml)
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-xml
+          path: coverage.xml
+
+      - name: Upload coverage HTML
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-html
+          path: htmlcov
+
+  build-docs:
+    name: Build and publish docs
+    needs: test
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.12]
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Cache pip
+        uses: actions/cache@v4
+        with:
+          path: ~/.cache/pip
+          key: "pip-${{ runner.os }}-py-${{ matrix.python-version }}-${{ hashFiles('**/requirements*.txt') }}"
+          restore-keys: |
+            pip-${{ runner.os }}-py-${{ matrix.python-version }}-
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools wheel
+          pip install -r docs/requirements.txt
+          pip install -e .
+
+      - name: Build docs
+        working-directory: docs
+        run: make html
+
+      - name: Upload HTML docs artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: docs-html
+          path: docs/_build/html
+
+      - name: Deploy to GitHub Pages
+        if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: docs/_build/html
+          publish_branch: gh-pages

.github/workflows/tests.yml

@@ -0,0 +1,52 @@
+name: Run tests
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  test:
+    name: Run test suite
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.12]
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Setup Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Cache pip
+        uses: actions/cache@v4
+        with:
+          path: ~/.cache/pip
+          key: "pip-${{ runner.os }}-py-${{ matrix.python-version }}-${{ hashFiles('**/requirements*.txt') }}"
+          restore-keys: |
+            pip-${{ runner.os }}-py-${{ matrix.python-version }}-
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools wheel
+          # Install broad dependencies used by the project/tests
+          if [ -f docs/requirements.txt ]; then pip install -r docs/requirements.txt; fi
+          # Install the package itself
+          pip install -e .
+          # Install test tools
+          pip install pytest pytest-cov
+
+      - name: Run tests with coverage
+        run: |
+          pytest --cov=panoptes.data --cov-report=xml:coverage.xml --cov-report=term-missing -q
+
+      - name: Upload coverage (xml)
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-xml
+          path: coverage.xml

.readthedocs.yaml

@@ -1,21 +1,13 @@
-# .readthedocs.yaml
-# Read the Docs configuration file
-# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
-
-# Required
 version: 2
 
-# Set the OS, Python version and other tools you might need
 build:
   os: ubuntu-22.04
   tools:
     python: "3.12"
 
-# Build documentation in the "docs/" directory with Sphinx
 sphinx:
   configuration: docs/conf.py
 
-# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
 python:
   install:
     - requirements: docs/requirements.txt

CHANGELOG.md

@@ -1,5 +1,41 @@
 # Changelog
 
+## UNRELEASED
+
+- Modernize the repo to use `pyproject.toml`.
+- Update docs.
+- Add basic tests.
+- Releases are created directly by GitHub Actions.
+
+## Version 0.2.0 (2024-10-08)
+
+- Print length of observations.
+- Only apply status filter if given.
+
+## Version 0.1.9 (2024-10-07)
+
+- Do better path matching for image url for new scheme.
+
+## Version 0.1.8 (2024-10-07)
+
+- Merge branch 'main' of github.com:panoptes/panoptes-data
+
+## Version 0.1.7 (2024-04-18)
+
+- Fix image_list for latest processing.
+
+## Version 0.1.6 (2024-04-18)
+
+- Change default bucket for downloading images and also make it a parameter.
+
+## Version 0.1.5 (2024-02-02)
+
+- Fixing release for pypi api tokens.
+
+## Version 0.1.4 (2024-02-02)
+
+- Add GitHub Actions PyPI release workflow.
+
 ## Version 0.1.3
 
 - Cleanup of images and observations.
@@ -44,7 +80,15 @@
 - Added basic cli interface for download images and metadata for observations.
 - Fixed install dependencies.
 
+## Version 0.0.3 (2022-06-24)
+
+- More cleanup of dependencies for release.
+
 ## Version 0.0.2
 
 - Observation search available via ``panoptes.data.search.search_observations``.
 - ``ObservationInfo`` for working with observation data and metadata.
+
+## Version 0.0.1 (2022-06-23)
+
+- Fixing setup.

README.md

@@ -14,20 +14,29 @@ pip install panoptes-data
 
 ## Examples
 
-> See example Jupyter Notebooks in the [`notebooks`](notebooks/) folder.
+See the example Jupyter Notebooks in the `notebooks/` directory.
 
 ### Finding observations
 
 ```py
->>> from panoptes.data.search import search_observations
->>> from panoptes.data.observations import ObservationInfo
+from panoptes.data.search import search_observations
+from panoptes.data.observations import ObservationInfo
 
->>> # Find some observations
->>> results = search_observations(by_name='M42')
+# Find some observations
+results = search_observations(by_name='M42')
 
->>> # Use last result entry to create ObservationInfo object.
->>> obs_info = ObservationInfo(meta=results.iloc[0])
->>> obs_info.meta
+# Use last result entry to create ObservationInfo object.
+obs_info = ObservationInfo(meta=results.iloc[0])
+print(obs_info.meta)
+
+# Create an ObservationInfo object directly from a sequence_id.
+obs_info = ObservationInfo('PAN001_14d3bd_20180113T052325')
+# But then there is no metadata:
+print(obs_info.meta)
+```
+
+```text
+Sample output (truncated):
 
 camera_id                                           14d3bd
 camera_lens_serial_number                        HA0028608
@@ -43,21 +52,14 @@ time                             2018-01-13 05:23:25+00:00
 total_exptime                                       3360.0
 unit_id                                             PAN001
 Name: 6121, dtype: object
-
->>> # Create an ObservationInfo object directly from a sequence_id.
->>> obs_info = ObservationInfo('PAN001_14d3bd_20180113T052325')
->>> # But then there is no metadata:
->>> obs_info.meta
-
-{}
 ```
 
 ### Downloading images
 
 The `ObservationInfo` object makes it easy to download the files:
 
 ```py
->>> obs_info.download_images()
+obs_info.download_images()
 ```
 
 ### Command-line tools
@@ -67,8 +69,12 @@ There is a simple command line tool that allows for both searching and downloadi
 #### Search for observations:
 
 ```bash
-$ panoptes-data search --name M42 --min-num-images 90
+panoptes-data search --name M42 --min-num-images 90
+```
+
+Example table output:
 
+```text
 | sequence_id                   | field_name   | unit_id   |   coordinates_mount_ra |   coordinates_mount_dec |   num_images |   exptime |   total_exptime | time                      |
 |:------------------------------|:-------------|:----------|-----------------------:|------------------------:|-------------:|----------:|----------------:|:--------------------------|
 | PAN022_977c86_20220108T090553 | M42          | PAN022    |                83.8221 |                -5.39111 |           95 |   90      |            8550 | 2022-01-08 09:05:53+00:00 |

docs/conf.py

@@ -8,8 +8,8 @@
 # serve to show the default.
 
 import os
-import sys
 import shutil
+import sys
 
 # -- Path setup --------------------------------------------------------------
 
@@ -52,7 +52,7 @@
 
     apidoc.main(args)
 except Exception as e:
-    print("Running `sphinx-apidoc` failed!\n{}".format(e))
+    print(f"Running `sphinx-apidoc` failed!\n{e}")
 
 # -- General configuration ---------------------------------------------------
 
@@ -105,7 +105,7 @@
 
 # General information about the project.
 project = "panoptes-data"
-copyright = "2023, Wilfred Tyler Gee"
+copyright = "2025, Wilfred Tyler Gee"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -165,6 +165,9 @@
 # If this is True, todo emits a warning for each TODO entries. The default is False.
 todo_emit_warnings = True
 
+# Mock heavy or optional imports so autodoc can generate docs without them.
+autodoc_mock_imports = ["pydantic", "pydantic_settings", "tqdm", "typer"]
+
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for