genmod 3.9__tar.gz → 3.10__tar.gz

genmod-3.10/.github/workflows/build_and_publish.yml

@@ -0,0 +1,63 @@
+name: Publish to PyPI
+
+on:
+ release:
+  types:
+   - created
+
+jobs:
+ pypi:
+    name: Build and publish to PyPI
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v3
+      - run: uv build
+      - run: uv publish --trusted-publishing always
+
+ docker-image-CI:
+   name: Docker Image CI
+   runs-on: ubuntu-latest
+   steps:
+
+    - name: Check out git repository
+      uses: actions/checkout@v4
+
+    - name: Login to Docker Hub
+      uses: docker/login-action@v3
+      with:
+        username: ${{ secrets.DOCKER_USERNAME }}
+        password: ${{ secrets.DOCKER_PASSWORD }}
+
+    - name: Set up Docker Buildx
+      id: buildx
+      uses: docker/setup-buildx-action@v3
+
+    - name: Publish server image (Dockerfile-server) to Registry
+      uses: docker/build-push-action@v6
+      with:
+        context: ./
+        file: ./Dockerfile
+        push: true
+        provenance: mode=max
+        sbom: true
+        tags: "clinicalgenomics/genmod:latest, clinicalgenomics/genmod:${{ github.event.release.tag_name }}"
+
+
+ deploy-docs:
+    name: Deploy Docs to GitHubIO
+    runs-on: ubuntu-latest
+    steps:
+     - name: Checkout repo
+       uses: actions/checkout@v4
+     - name: Setup environment for docs deployment
+       uses: actions/setup-python@v5
+       with:
+         python-version: 3.x
+     - name: Install mkdocs
+       run: pip install mkdocs mkdocs-material markdown-include
+     - name: Deploy documentation
+       run: mkdocs gh-deploy --force
+

genmod-3.10/.github/workflows/check_format.yml

@@ -0,0 +1,26 @@
+# Basic CI setup: Lint format with ruff
+name: Format-check
+
+on:
+  pull_request:
+    types: [ opened, synchronize, reopened, ready_for_review, labeled, unlabeled ]
+
+jobs:
+  lint-format:
+    name: Ruff includes and format
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Ruff check import sorting
+        uses: astral-sh/ruff-action@v3
+        with:
+          version: "latest"
+          args: "check --select I ."
+
+      - name: Ruff format diff
+        uses: astral-sh/ruff-action@v3
+        with:
+          version: "latest"
+          args: "format --diff ."
+

genmod-3.10/.github/workflows/keep_a_changelog.yml

@@ -0,0 +1,15 @@
+name: "Changelog Reminder"
+on:
+  pull_request:
+      types: [opened, synchronize, reopened, ready_for_review, labeled, unlabeled]
+
+jobs:
+  # Enforces the update of a changelog file on every pull request
+  changelog:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: dangoslen/changelog-enforcer@v3
+      with:
+        changeLogPath: 'CHANGELOG.md'
+        skipLabels: 'Skip-Changelog'

genmod-3.10/.github/workflows/lint.yml

@@ -0,0 +1,19 @@
+# Basic CI setup: Lint with ruff
+name: Lint
+
+on:
+  pull_request:
+    types: [ opened, synchronize, reopened, ready_for_review, labeled, unlabeled ]
+
+jobs:
+  lint:
+    name: Lint
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Ruff lint
+        uses: astral-sh/ruff-action@v3
+        with:
+          version: "latest"
+          args: "check ."

genmod-3.10/.github/workflows/test.yml

@@ -0,0 +1,24 @@
+name: Tests
+
+on:
+  pull_request:
+  #push:
+
+jobs:
+  run-tests:
+    timeout-minutes: 30
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v4
+        with:
+          ref: "${{github.event.inputs.branch_name}}"
+          fetch-depth: 0
+
+      - name: Run Tests
+        run: |
+          make test
+
+      - name: Run Packaging Test
+        run: |
+          make test_dist

genmod-3.10/.gitignore

@@ -0,0 +1,20 @@
+/data
+/res
+/doc
+/dist
+/build
+/pickles
+/local
+/publication
+/things
+/venv
+/.idea
+*.pyc
+.DS_Store
+*.egg-info
+*.tmproj
+*.ipynb
+*.tmp
+*.temp
+*.bak
+notes.mdsite/

genmod-3.10/.python-version

@@ -0,0 +1 @@
+3.13

genmod-3.10/.travis.yml

@@ -0,0 +1,16 @@
+# config file for automatic testing at travis-ci.org
+language: python
+
+python:
+    - "2.7"
+
+install:
+    # install test dependencies and package
+    - pip install pytest
+    - pip install .
+
+script:
+    - py.test
+
+notifications:
+    email: no

genmod-3.10/CHANGELOG.md

@@ -0,0 +1,49 @@
+# Change Log
+All notable changes to this project will be documented in this file.
+This project adheres to [Semantic Versioning](http://semver.org/).
+
+About changelog [here](https://keepachangelog.com/en/1.0.0/)
+
+Please add a new candidate release at the top after changing the latest one. Feel free to copy paste from the "squash and commit" box that gets generated when creating PRs
+
+Try to use the following format:
+
+## [3.10]
+### Changed
+- Use `uv` with `hatchling` to build and publish ([#104](https://github.com/Clinical-Genomics/genmod/issues/143))
+- Automation for Docker publish and mkdocs githubio ([#161](https://github.com/Clinical-Genomics/genmod/issues/161))
+### Fixed
+- The optional fields Source and Version are allowed in the VCF header([#106](https://github.com/Clinical-Genomics/genmod/pull/106))
+- Released the constraint on Python 3.8 (collections, pkg_resources to importlib, tests) ([#142](https://github.com/Clinical-Genomics/genmod/pull/142))
+- Update annotation examples ([#144](https://github.com/Clinical-Genomics/genmod/pull/144))
+- Updated documentation with warning about compounds only being scored within the first family in the VCF ([#151](https://github.com/Clinical-Genomics/genmod/pull/151))
+- Fixed sorting of variants ([#152](https://github.com/Clinical-Genomics/genmod/pull/152))
+- genmod annotate for mitochondrial variants when using the `chrM` notation ([#157](https://github.com/Clinical-Genomics/genmod/pull/157))
+- Fix linting issues ([#154](https://github.com/Clinical-Genomics/genmod/issues/154))
+- genmod models adds headers to VCF even if it contains no variants ([#160](https://github.com/Clinical-Genomics/genmod/pull/160)) 
+
+## [3.9]
+- Fixed wrong models when chromosome X was named `chrX` and not `X` ([#135](https://github.com/Clinical-Genomics/genmod/pull/135))
+- Added GitHub Actions workflows for automatic publishing to PyPI on release, and keep a changelog reminder ([#136](https://github.com/Clinical-Genomics/genmod/pull/136))
+- Optional user defined threshold and penalty for compound scoring ([#138](https://github.com/Clinical-Genomics/genmod/pull/138))
+- Update README with current github.io docs page ([#140](https://github.com/Clinical-Genomics/genmod/pull/140))
+
+## [3.8.3]
+- Fixed unstable compounds order in models output ([#134](https://github.com/Clinical-Genomics/genmod/pull/134))
+- Added `six` to requirements.txt and setup.py ([#134](https://github.com/Clinical-Genomics/genmod/pull/134))
+
+## [3.8.0]
+- Rank score normalisation
+
+## [3.7.4]
+
+### Fixed
+- OSError crashes due to socket address conflicts when using containers
+
+## [x.x.x]
+
+### Changed
+- Adds support for escaped characters in FORMAT description header strings
+
+### Fixed
+- Documentation about cli options `strict` and `phased`

genmod-3.10/CITATION.cff

@@ -0,0 +1,16 @@
+cff-version: 1.2.0
+message: If you use this software, please cite it using these metadata.
+title: genmod
+abstract: Tool for annotating patterns of genetic inheritance in Variant Call Format (VCF) files.
+authors:
+  - family-names: Magnusson
+    given-names: Måns
+    orcid: "https:// https://orcid.org/0000-0002-0001-1047"
+version: 3.7.3
+date-released: "2018-11-15"
+identifiers:
+  - description: Updates click dependency
+    type: doi
+    value: "10.5281/zenodo.3841142"
+license: MIT Licence
+repository-code: "https://github.com/Clinical-Genomics/genmod"

genmod-3.10/DEVELOPING.md

@@ -0,0 +1,19 @@
+# Developing
+
+## Host Requirements
+* Docker
+* package "build-essentials" for running Makefile
+
+## Run pytest
+There's support for pytest via Docker.
+
+Run the following to run pytest:
+
+```
+make test
+```
+
+## Running Genmod CLI
+```
+python3 -m genmod.commands.base
+```

genmod-3.10/Dockerfile

@@ -0,0 +1,17 @@
+###############################################
+# Dockerfile to build GeMod container image
+###############################################
+FROM ghcr.io/astral-sh/uv:python3.13-alpine
+
+RUN apk update & apk add build-base zlib-dev
+# Copy the project into the image
+ADD . /app
+
+# Sync the project into a new virtual environment, using the frozen lockfile
+WORKDIR /app
+RUN uv sync --frozen
+
+# Add the project venv to PATH to be able to run genmod without changing to the environment
+ENV PATH="/app/.venv/bin:$PATH"
+
+ENTRYPOINT ["genmod"]

genmod-3.10/Dockerfile.pytest

@@ -0,0 +1,9 @@
+# Dockerfile to run genmod pytest suite
+FROM ghcr.io/astral-sh/uv:python3.13-bookworm
+
+ADD . /app
+
+WORKDIR /app
+RUN uv sync --all-extras --dev
+
+ENTRYPOINT ["uv", "run", "pytest"]

{genmod-3.9 → genmod-3.10}/MANIFEST.in

@@ -1,5 +1,9 @@
+include CHANGELOG.md
+include LICENSE.txt
+include README.md
+
 recursive-include examples *.ped *.vcf *.gz *.tbi
 recursive-include genmod/annotations *.gz
 recursive-include genmod/configs *.ini
 recursive-exclude * __pycache__
-recursive-exclude * *.py[co]
+recursive-exclude * *.py[co]

genmod-3.10/Makefile

@@ -0,0 +1,24 @@
+.PHONY: *
+
+DOCKER=DOCKER_BUILDKIT=1 docker
+
+all:
+	# Nothing to be built
+
+docker-build:
+	$(DOCKER) build -t genmod/test --force-rm=true --rm=true -f Dockerfile.pytest .
+
+test: docker-build
+	$(DOCKER) run -i -l genmod-test genmod/test -v
+
+test_%: docker-build
+	$(DOCKER) run -i -l genmod-test genmod/test -v -k $@
+
+test_dist: docker-build
+	$(DOCKER) run -i -l genmod-test --entrypoint=bash genmod/test -c \
+		"uv build && \
+		pip3 install dist/genmod*.tar.gz && \
+		uv run genmod -v annotate --annotate-regions --genome-build 37 examples/test_vcf.vcf"
+
+docker-clean-images:
+	docker system prune