Merge branch 'main' into pr/36

.github/workflows/autoblack_pull_request.yml

@@ -0,0 +1,35 @@
+# GitHub Action that uses Black to reformat the Python code in an incoming pull request.
+# If all Python code in the pull request is complient with Black then this Action does nothing.
+# Othewrwise, Black is run and its changes are committed back to the incoming pull request.
+# https://github.com/cclauss/autoblack
+
+name: autoblack_pull_request
+on: [ pull_request ]
+jobs:
+  black-code:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          ref: ${{ github.head_ref }}
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+      - run: pip install black
+      - run: black --check .
+      - name: If needed, commit black changes to the pull request
+        if: failure()
+        run: |
+          printenv | grep GITHUB
+          git config --global user.name 'PMBio'
+          git config --global user.email 'PMBio@users.noreply.github.com'          
+          git remote set-url origin https://x-access-token:${{ secrets.GITHUB_TOKEN }}@github.com/$GITHUB_REPOSITORY
+          git remote -v
+          git branch
+          git status
+          black .
+          git status
+          echo ready to commit
+          git commit -am "fixup! Format Python code with psf/black pull_request"
+          echo ready to push
+          git push

.github/workflows/docs-tests.yml

@@ -0,0 +1,23 @@
+name: "Pull Request Docs Check"
+run-name: "Docs Check 📑📝"
+
+on:
+- pull_request
+
+jobs:
+  docs-build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: ammaraskar/sphinx-action@0.4
+      with:
+        docs-folder: "docs/"
+
+  docs-link-check:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: ammaraskar/sphinx-action@0.4
+      with:
+        docs-folder: "docs/"
+        build-command: "make linkcheck"

.github/workflows/github-actions.yml

@@ -14,7 +14,6 @@ jobs:
           directory: 'example'
           snakefile: 'pipelines/training_association_testing.snakefile'
           args: '-j 2 -n'
-          stagein: 'pip install -e ${{ github.workspace }}'
       - name: Link pretrained models
         run: cd ${{ github.workspace }}/example && ln -s ../pretrained_models
       - name: Association Testing Pretrained Smoke Test
@@ -70,3 +69,71 @@ jobs:
           python -m snakemake -j 2 --directory ${{ github.workspace }}/example \
           --snakefile ${{ github.workspace }}/pipelines/seed_gene_discovery.snakefile --show-failed-logs
         shell: micromamba-shell {0}
+
+
+  DeepRVAT-Preprocessing-Pipeline-Smoke-Tests:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository code
+        uses: actions/checkout@v3
+      - name: Preprocessing Smoke Test
+        uses: snakemake/snakemake-github-action@v1.24.0
+        with:
+          directory: 'example/preprocess'
+          snakefile: 'pipelines/preprocess.snakefile'
+          args: '-j 2 -n --configfile pipelines/config/deeprvat_preprocess_config.yaml'
+          stagein: 'touch example/preprocess/workdir/reference/GRCh38.primary_assembly.genome.fa'
+
+
+  DeepRVAT-Annotation-Pipeline-Smoke-Tests:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository code
+        uses: actions/checkout@v3
+      - name: Annotations Smoke Test
+        uses: snakemake/snakemake-github-action@v1.25.1
+        with:
+          directory: 'example/annotations'
+          snakefile: 'pipelines/annotations.snakefile'
+          args: '-j 2 -n --configfile pipelines/config/deeprvat_annotation_config.yaml'
+
+
+  DeepRVAT-Preprocessing-Pipeline-Tests:
+    runs-on: ubuntu-latest
+    needs: DeepRVAT-Preprocessing-Pipeline-Smoke-Tests
+    steps:
+
+      - name: Check out repository code
+        uses: actions/checkout@v3
+      - uses: mamba-org/setup-micromamba@v1.4.3
+        with:
+          environment-name: deeprvat-preprocess-gh-action
+          environment-file: ${{ github.workspace }}/deeprvat_preprocessing_env.yml
+          cache-environment: true
+          cache-downloads: true
+
+      - name: Install DeepRVAT
+        run: pip install -e ${{ github.workspace }}
+        shell: micromamba-shell {0}
+
+      - name: Cache Fasta file
+        id: cache-fasta
+        uses: actions/cache@v3
+        with:
+          path: example/preprocess/workdir/reference
+          key: ${{ runner.os }}-reference-fasta
+
+      - name: Download and unpack fasta data
+        if: steps.cache-fasta.outputs.cache-hit != 'true'
+        run: |
+          cd ${{ github.workspace }}/example/preprocess && \
+          wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_44/GRCh38.primary_assembly.genome.fa.gz \
+          -O workdir/reference/GRCh38.primary_assembly.genome.fa.gz \
+          && gzip -d workdir/reference/GRCh38.primary_assembly.genome.fa.gz
+
+      - name: Run preprocessing pipeline
+        run: |
+          python -m snakemake -j 2 --directory ${{ github.workspace }}/example/preprocess \
+          --snakefile ${{ github.workspace }}/pipelines/preprocess.snakefile \
+          --configfile ${{ github.workspace }}/pipelines/config/deeprvat_preprocess_config.yaml --show-failed-logs
+        shell: micromamba-shell {0}

.github/workflows/test-runner.yml

@@ -0,0 +1,25 @@
+name: DeepRVAT test runner
+run-name: DeepRVAT Tests 🧑🏼‍💻✅
+on: [ push ]
+
+jobs:
+  DeepRVAT-Tests-Runner:
+    runs-on: ubuntu-latest
+    steps:
+
+      - name: Check out repository code
+        uses: actions/checkout@v3
+      - uses: mamba-org/setup-micromamba@v1.4.3
+        with:
+          environment-name: deeprvat-preprocess-gh-action
+          environment-file: ${{ github.workspace }}/deeprvat_preprocessing_env.yml
+          cache-environment: true
+          cache-downloads: true
+
+      - name: Install DeepRVAT
+        run: pip install -e ${{ github.workspace }}
+        shell: micromamba-shell {0}
+
+      - name: Run pytest
+        run: pytest -v ${{ github.workspace }}/tests
+        shell: micromamba-shell {0}

.gitignore

@@ -0,0 +1,167 @@
+
+example/**/.snakemake/**
+example/**/.snakemake_*
+example/preprocess/workdir/reference/*.fa
+
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+.idea/
+/docs/apidocs/

.readthedocs.yaml

@@ -0,0 +1,20 @@
+# .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"
+
+sphinx:
+   configuration: docs/conf.py
+   fail_on_warning: true
+
+python:
+   install:
+   - requirements: docs/requirements.txt