Release 0.50.0a1

.flake8

@@ -0,0 +1,3 @@
+[flake8]
+exclude = .git,__pycache__,docs/source/conf.py,old,build,dist
+max-line-length = 120

.github/workflows/black.yml

@@ -1,6 +1,8 @@
 name: Lint
 
-on: [pull_request]
+on:
+  pull_request:
+    branches: [ main ]
 
 jobs:
   lint:

.github/workflows/cli-coverage.yml

@@ -0,0 +1,40 @@
+name: test coverage
+
+on:
+  push:
+    branches: [master, dev]
+
+jobs:
+  cli-coverage-report:
+    strategy:
+      matrix:
+        python-version: [ "3.12" ]
+        os: [ ubuntu-latest ]
+        r: [ release ]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v5
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: Install test dependencies
+        run: if [ -f requirements/requirements-test.txt ]; then pip install -r requirements/requirements-test.txt; fi
+
+      - run: pip install .
+
+      - name: Run tests
+        run: coverage run -m pytest
+
+      - name: build coverage
+        run: coverage html -i
+
+      - run: smokeshow upload htmlcov
+        env:
+          SMOKESHOW_GITHUB_STATUS_DESCRIPTION: Coverage {coverage-percentage}
+          SMOKESHOW_GITHUB_COVERAGE_THRESHOLD: 80
+          SMOKESHOW_GITHUB_CONTEXT: coverage
+          SMOKESHOW_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          SMOKESHOW_GITHUB_PR_HEAD_SHA: ${{ github.event.pull_request.head.sha }}
+          SMOKESHOW_AUTH_KEY: ${{ secrets.SMOKESHOW_AUTH_KEY }}

.github/workflows/pytest-windows.yml

@@ -0,0 +1,35 @@
+name: Run pytests windows
+
+on:
+  push:
+    branches: [dev]
+  pull_request:
+    branches: [main, dev, peppy0_50]
+
+jobs:
+  pytest:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ["3.11"]
+        os: [windows-latest]
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install all dependencies
+      run: pip install -r requirements/requirements-all.txt
+
+    - name: Install test dependencies
+      run: pip install -r requirements/requirements-test.txt
+
+    - name: Install package
+      run: python -m pip install .
+
+    - name: Run pytest tests
+      run: pytest tests -v

.github/workflows/run-pytest.yml → .github/workflows/pytest.yml

@@ -4,7 +4,7 @@ on:
   push:
     branches: [dev]
   pull_request:
-    branches: [master, dev]
+    branches: [main, dev, peppy0_50]
 
 jobs:
   pytest:
@@ -15,15 +15,15 @@ jobs:
         os: [ubuntu-latest]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v5
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - name: Install dev dependencies
-      run: if [ -f requirements/requirements-dev.txt ]; then pip install -r requirements/requirements-dev.txt; fi
+    - name: Install all dependencies
+      run: if [ -f requirements/requirements-all.txt ]; then pip install -r requirements/requirements-all.txt; fi
 
     - name: Install test dependencies
       run: if [ -f requirements/requirements-test.txt ]; then pip install -r requirements/requirements-test.txt; fi
@@ -32,4 +32,4 @@ jobs:
       run: python -m pip install .
 
     - name: Run pytest tests
-      run: pytest tests -x -vv --cov=./ --cov-report=xml --remote-data
+      run: pytest tests -v

.github/workflows/python-publish.yml

@@ -1,6 +1,3 @@
-# This workflows will upload a Python Package using Twine when a release is created
-# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
-
 name: Upload Python Package
 
 on:
@@ -14,9 +11,7 @@ jobs:
     permissions:
       id-token: write
     steps:
-    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
     - name: Install dependencies
@@ -27,4 +22,4 @@ jobs:
       run: |
         python setup.py sdist bdist_wheel
     - name: Publish package distributions to PyPI
-      uses: pypa/gh-action-pypi-publish@release/v1
+      uses: pypa/gh-action-pypi-publish@release/v1

.gitignore

@@ -1,87 +1,9 @@
-# ignore test results
-tests/test/*
-
-# toy/experimental files
-*.tsv
-*.pkl
-
-# ignore eggs
-.eggs/
-
-# generic ignore list:
-*.lst
-
-# Compiled source
-*.com
-*.class
-*.dll
-*.exe
-*.o
 *.so
-*.pyc
-
-# Packages
-# it's better to unpack these files and commit the raw source
-# git has its own built in compression methods
-*.7z
-*.dmg
-*.gz
-*.iso
-*.jar
-*.rar
-*.tar
-*.zip
-
-# Logs and databases
-*.log
-*.sql
-*.sqlite
-
-# OS generated files
-.DS_Store
-.DS_Store?
-._*
-.Spotlight-V100
-.Trashes
-ehthumbs.db
-Thumbs.db
-
-# Gedit temporary files
-*~
-
-# libreoffice lock files:
-.~lock*
-
-# Default-named test output
-microtest/
-open_pipelines/
-
-# IDE-specific items
-.idea/
-.vscode/
-
-# pytest-related
-.cache/
-.coverage
-.pytest_cache/
-
-# Reserved files for comparison
-*RESERVE*
 
-# Build-related stuff
 build/
 dist/
-peppy.egg-info/
 
-.ipynb_checkpoints/
 
-# env stuff
-env/
 .env
 venv/
-.venv/
 
-# swap files
-.swp
-.swo
-.swn

.pre-commit-config.yaml

@@ -1,21 +1,2 @@
 repos:
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.0.1
     hooks:
-      - id: trailing-whitespace
-      - id: check-yaml
-      - id: end-of-file-fixer
-      - id: requirements-txt-fixer
-      - id: trailing-whitespace
-      - id: check-ast
-
-  - repo: https://github.com/PyCQA/isort
-    rev: 5.8.0
-    hooks:
-      - id: isort
-        args: ["--profile", "black"]
-
-  - repo: https://github.com/psf/black
-    rev: 21.5b2
-    hooks:
-      - id: black

LICENSE.txt

@@ -1,5 +1,3 @@
-Copyright 2017 Nathan Sheffield
-
 Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
 
 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

MANIFEST.in

@@ -1,3 +1,6 @@
-include LICENSE.txt
 include requirements/*
 include README.md
+include peppy/pephubclient/*
+include peppy/eido/*
+include peppy/pephubclient/pephub_oauth/*
+include peppy/pephubclient/modules/*

Makefile

@@ -0,0 +1,13 @@
+lint:
+	ruff format .
+
+run-coverage:
+	coverage run -m pytest
+
+html-report:
+	coverage html --omit="*/test*"
+
+open-coverage:
+	cd htmlcov && google-chrome index.html
+
+coverage: run-coverage html-report open-coverage

README.md

@@ -12,4 +12,4 @@ Links to complete documentation:
 * Complete documentation and API for the `peppy` python package is at [peppy.databio.org](https://peppy.databio.org).
 * Reference documentation for standard **PEP** format is at [pep.databio.org](https://pep.databio.org/).
 * Example PEPs for testing `peppy` are in the [example_peps repository](https://github.com/pepkit/example_peps).
-* The package [on PyPI](https://pypi.org/project/peppy/).
+* The package [on PyPI](https://pypi.org/project/peppy/).