fix: implementing release-please (#30)

.github/workflows/ci.yml

@@ -1,42 +1,107 @@
 name: CI
 
-on: [push, pull_request]
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches_ignore: []
 
 jobs:
-  build:
+  cancel-previous:
+    runs-on: ubuntu-latest
+    if: github.ref != 'refs/heads/main'
+    steps:
+      - uses: khan/pull-request-workflow-cancel@1.0.0
+        with:
+          workflows: "main.yml"
+        env:
+          GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}'
+
+  linting:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v1
+
+      - name: Install Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.8"
+
+      - name: Install dependencies
+        run: |
+            pip install -r requirements/test.txt
+            pip freeze
+
+      - name: Run linting tools
+        run: |
+          make lint
+
+      - name: Comment PR
+        if: github.event_name == 'pull_request' && failure()
+        uses: marocchino/sticky-pull-request-comment@v1.1.0
+        with:
+          message: |
+            - Please format your Python code with [black](https://black.readthedocs.io): `make black`
+            - Please organize your imports [isorts](https://isort.readthedocs.io): `make isort`
+            - Please ensure that your code passes [flake8](https://flake8.pycqa.org/en/latest/): `make flake8`
+
+            You can trigger all lints locally by running `make lint`
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
+  sphinx-docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v1
+
+      - name: Install Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.8"
+
+      - name: Install dependencies
+        run: |
+            pip install -r requirements/dev.txt
+            pip freeze
+
+      - name: Build documentation
+        run: |
+          cd docs
+          make html
+
+  testing:
     runs-on: ubuntu-latest
     strategy:
       matrix:
         python-version:
-          - "3.7"
           - "3.8"
           - "3.9"
           - "3.10"
-
+          - "3.11"
+    needs: linting
     steps:
-      - name: Install Python via conda.
-        uses: s-weigand/setup-conda@v1
+      - name: Install Python
+        uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
-          conda-channels: defaults,bioconda,conda-forge
+
       - name: Checkout repository
         uses: actions/checkout@v2
         with:
           lfs: true
-      - name: Install test dependencies via pip
-        run: pip install -r requirements/test.txt
+          fetch-depth: 0
+
+      - name: Install dependencies
+        run: pip install -r requirements/test.txt; pip install --ignore-installed py
+
       - name: Run tests
         run: pytest
+        env:
+          DIFF_MAIN: ${{ github.event_name == 'pull_request' }}
+          DIFF_LAST_COMMIT: ${{ github.ref == 'refs/heads/main' }}
+
       - name: Create text report
         run: coverage report
-      - name: Create XML report for codacy
-        run: coverage xml
-#      - name: Run codacy-coverage-reporter
-#        uses: codacy/codacy-coverage-reporter-action@master
-#        with:
-#          project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
-#          coverage-reports: coverage.xml
-#        if: ${{ matrix.python-version == '3.7' }}
-#      - name: Check style with flake8
-#        run: flake8 .
+
+      - name: Coveralls
+        uses: AndreMiras/coveralls-python-action@develop

.github/workflows/conventional-prs.yml

@@ -0,0 +1,18 @@
+name: PR
+on:
+  pull_request_target:
+    types:
+      - opened
+      - reopened
+      - edited
+      - synchronize
+
+jobs:
+  title-format:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: amannn/action-semantic-pull-request@v3.4.0
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          validateSingleCommit: true

.github/workflows/release-please.yml

@@ -0,0 +1,41 @@
+on:
+  push:
+    branches:
+      - main
+
+name: release-please
+
+jobs:
+  release-please:
+    runs-on: ubuntu-latest
+    steps:
+
+      - uses: GoogleCloudPlatform/release-please-action@v2
+        id: release
+        with:
+          release-type: python
+          package-name: biomedsheets
+
+      - uses: actions/checkout@v2
+        if: ${{ steps.release.outputs.release_created }}
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        if: ${{ steps.release.outputs.release_created }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.x'
+
+      - name: Build package
+        if: ${{ steps.release.outputs.release_created }}
+        run: |
+          python -m pip install --upgrade pip
+          python setup.py sdist
+
+      - name: Publish to PyPI
+        if: ${{ steps.release.outputs.release_created }}
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_TOKEN }}

CHANGELOG.md

@@ -0,0 +1,140 @@
+# BioMed Sheets Changelog
+
+## v0.11.5
+
+-   Fixing consistency check for Duo Cases (#26).
+
+## v0.11.4
+
+-   Fixing issues with ResourceAdapter (#21).
+
+## v0.11.3
+
+-   Fixing warnings in the tests (#19).
+
+## v0.11.2
+
+-   Updating/modernizing dependencies.
+
+## v0.11.1
+
+-   Adding property to shortcut sheets that indicates available kwargs.
+
+## v0.11.0
+
+-   Adding custom option to join pedigrees by fields such as `familyId`.
+
+## v0.10.0
+
+-   Adding functionality for filtering pedigrees.
+
+## v0.9.1
+
+-   Fixing sorting bug.
+
+## v0.9.0
+
+-   Sorting donors for picking the index in germline sample sheets.
+
+## v0.8.1
+
+-   Fixing mapping of `Unknown` values.
+
+## v0.8.0
+
+-   Changed behaviour in case of no affected donor has library. In this
+    case, the first donor becomes the index. Consequently, the index
+    must have an NGS library.
+
+## v0.7.1
+
+-   Removing superflous print.
+
+## v0.7.0
+
+-   Allowing to specify `bioSample` and `testSample` in germline TSV
+    files.
+-   Fixing some tests.
+
+## v0.6.2
+
+-   Proper merging with recent `ruamel.yaml` updates.
+
+## v0.6.1
+
+-   Interpreting `#` in TSV files in more locations.
+
+## v0.6.0
+
+-   Allowing to comment out lines in TSV files by prefixing them with
+    `#`.
+
+## v0.5.6
+
+-   Fixing bug in computing index (for real).
+
+## v0.5.5
+
+-   Fixing bug in computing index.
+
+## v0.5.4
+
+-   Fixing `setup.py` to work with pip v10.t
+
+## v0.5.3
+
+-   Fixing packaging to use base and not test dependencies.
+
+## v0.5.2
+
+-   Removing some hard (transitive) dependencies.
+
+## v0.5.1
+
+-   Fixing manifest so the package contains the JSON file.
+
+## v0.5
+
+-   Allow cancer sheets for use in germline calling.
+-   Only warn if index has no NGS library, no error.
+
+## v0.4
+
+-   Fixin TSV I/O.
+-   Bumping ruamel.yaml version.
+-   Fixing cancer sheet iteration.
+-   Allowing cancer-only samples in cance case sheets.
+-   Fixing `float`-related bug.
+-   Fixing bug in reference resolving (+tests)
+
+## v0.3.1
+
+-   Fixing `setup.py` to work with pip v10.
+
+## v0.3
+
+-   Adding possibility for generic TSV sample sheets.
+-   Many updates to make documentation more clear.
+-   Various updates, fixing Codacy issues.
+-   Adding routines for writing out PED file from germline sample
+    sheets.
+
+## v0.2
+
+-   Auto-deployment to pypi
+-   Fixing shortcuts to father/mother during cohort loading
+-   Cleanup code (according to Flake 8)
+-   Adding more tests, replacing examples by TSV files
+-   Removing protein pools
+-   Adding Sphinx-based ocumentation
+-   Restructuring requirements txt files
+-   Configurable entity name generation. This allows to use secondary id
+    only for naming, e.g.
+-   Fixing `requirements*.txt` files for always using SSH
+-   Fixing sample naming for germline sample sheets
+-   Adding versioneer integration
+
+## v0.1.1
+
+-   First actual release, versioning done using versioneer
+-   Everything is new!