diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md new file mode 100644 index 0000000..79a0356 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/bug_report.md @@ -0,0 +1,46 @@ +--- +name: Bug report +about: Create a report to help us improve +title: '' +labels: bug +assignees: '' + +--- + + + +**Describe the bug** +A clear and concise description of what the bug is. + +**To Reproduce** +Steps to reproduce the behavior: +1. Go to '...' +2. Click on '....' +3. Scroll down to '....' +4. See error + +**Expected behavior** +A clear and concise description of what you expected to happen. + +**Screenshots** +If applicable, add screenshots to help explain your problem. + +**Desktop (please complete the following information):** + - OS: [e.g. iOS] + - Browser [e.g. chrome, safari] + - Version [e.g. 22] + +**Smartphone (please complete the following information):** + - Device: [e.g. iPhone6] + - OS: [e.g. iOS8.1] + - Browser [e.g. stock browser, safari] + - Version [e.g. 22] + +**Additional context** +Add any other context about the problem here. diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md new file mode 100644 index 0000000..f691a88 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/feature_request.md @@ -0,0 +1,28 @@ +--- +name: Feature request +about: Suggest an idea for this project +title: '' +labels: enhancement +assignees: '' + +--- + + + +**Is your feature request related to a problem? Please describe.** +A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] + +**Describe the solution you'd like** +A clear and concise description of what you want to happen. + +**Describe alternatives you've considered** +A clear and concise description of any alternative solutions or features you've considered. + +**Additional context** +Add any other context or screenshots about the feature request here. diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 0000000..45e61f3 --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,9 @@ +# Please see the documentation for all configuration options: +# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates + +version: 2 +updates: + - package-ecosystem: "pip" + directory: "/" + schedule: + interval: "weekly" diff --git a/.github/workflows/automerge.yml b/.github/workflows/automerge.yml new file mode 100644 index 0000000..05c540d --- /dev/null +++ b/.github/workflows/automerge.yml @@ -0,0 +1,19 @@ +name: Dependabot auto-merge + +on: pull_request + +permissions: + contents: write + +jobs: + dependabot: + runs-on: ubuntu-latest + if: ${{ github.actor == 'dependabot[bot]' }} + steps: + - name: Enable auto-merge for Dependabot PRs + run: gh pr merge --auto --squash "$PR_URL" + env: + PR_URL: ${{github.event.pull_request.html_url}} + # GitHub provides this variable in the CI env. You don't + # need to add anything to the secrets vault. + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/conventional-prs.yml b/.github/workflows/conventional-prs.yml new file mode 100644 index 0000000..17c8812 --- /dev/null +++ b/.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 diff --git a/.github/workflows/docker-build.yml b/.github/workflows/docker-build.yml new file mode 100644 index 0000000..975b38b --- /dev/null +++ b/.github/workflows/docker-build.yml @@ -0,0 +1,61 @@ +on: + push: + branches: + - main + pull_request: + branches: + - main + +# This workflow is run as part of CI to test that they run through. +# +# The images are pushed to `ghcr.io` for each PR and branch. The ones for +# the releases are pushed in `release-please.yml`. +name: Docker Build + +env: + REGISTRY: ghcr.io + IMAGE_NAME: ${{ github.repository }} + +jobs: + Image-Build-Push: + runs-on: ubuntu-latest + permissions: + contents: read + packages: write + + steps: + - name: Checkout repository + uses: actions/checkout@v4 + with: + lfs: 'true' + + - name: Log in to the Container registry + uses: docker/login-action@v2 + with: + registry: ${{ env.REGISTRY }} + username: ${{ github.actor }} + password: ${{ secrets.GITHUB_TOKEN }} + + - name: Extract metadata (tags, labels) for Docker + id: meta + uses: docker/metadata-action@v4 + with: + images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }} + tags: | + type=ref,event=branch + type=ref,event=pr + + - name: Write "git describe --tags --dirty" to VERSION + run: | + git describe --tags --dirty | tee VERSION + + - name: Build and push Docker image + uses: docker/build-push-action@v4 + with: + context: . + file: utils/docker/Dockerfile + tags: ${{ steps.meta.outputs.tags }} + labels: ${{ steps.meta.outputs.labels }} + push: true + build-args: + version_file=VERSION diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml new file mode 100644 index 0000000..a5560df --- /dev/null +++ b/.github/workflows/main.yml @@ -0,0 +1,78 @@ +name: CI + +on: + push: + branches: + - main + pull_request: + +jobs: + cancel-previous: + runs-on: ubuntu-latest + if: github.ref != 'refs/heads/main' + steps: + - uses: khan/pull-request-workflow-cancel@1.0.0 + with: + workflows: "main.yml" + env: + GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}' + + linting: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + with: + lfs: 'true' + + - name: Set up Python 3.10 + uses: actions/setup-python@v4 + with: + python-version: "3.10" + cache: "pipenv" + cache-dependency-path: | + Pipfile.lock + + - name: Install pipenv and deps + run: | + python -m pip install --upgrade pipenv wheel + make deps + + - name: Lint source code + run: make lint + + testing: + runs-on: ubuntu-latest + strategy: + matrix: + python-version: + - '3.10' + - '3.11' + needs: linting + steps: + - uses: actions/checkout@v4 + with: + lfs: 'true' + + - name: Set up Python 3.10 + uses: actions/setup-python@v4 + with: + python-version: "3.10" + cache: "pipenv" + cache-dependency-path: | + Pipfile.lock + + - name: Install pipenv and deps + run: | + python -m pip install --upgrade pipenv wheel + make deps + + - name: Install dependencies + run: make deps + + - name: Run tests + run: make test + + - name: Upload coverage reports to Codecov + uses: codecov/codecov-action@v3 + env: + CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} diff --git a/.github/workflows/release-please.yml b/.github/workflows/release-please.yml new file mode 100644 index 0000000..e4b6ccc --- /dev/null +++ b/.github/workflows/release-please.yml @@ -0,0 +1,18 @@ +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: cada-prio + token: ${{ secrets.BOT_TOKEN }} diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..c2f3f75 --- /dev/null +++ b/.gitignore @@ -0,0 +1,223 @@ +# Coverage information. +.coverage +coverage.lcov + +# Version file +/VERSION + +# Environment variables +.env + +# Local favicon +/frontend/favicon.ico + +# Created by https://www.toptal.com/developers/gitignore/api/visualstudiocode,pycharm,vim,emacs +# Edit at https://www.toptal.com/developers/gitignore?templates=visualstudiocode,pycharm,vim,emacs + +### Emacs ### +# -*- mode: gitignore; -*- +*~ +\#*\# +/.emacs.desktop +/.emacs.desktop.lock +*.elc +auto-save-list +tramp +.\#* + +# Org-mode +.org-id-locations +*_archive + +# flymake-mode +*_flymake.* + +# eshell files +/eshell/history +/eshell/lastdir + +# elpa packages +/elpa/ + +# reftex files +*.rel + +# AUCTeX auto folder +/auto/ + +# cask packages +.cask/ +dist/ + +# Flycheck +flycheck_*.el + +# server auth directory +/server/ + +# projectiles files +.projectile + +# directory configuration +.dir-locals.el + +# network security +/network-security.data + + +### PyCharm ### +# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio, WebStorm and Rider +# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839 + +# User-specific stuff +.idea/**/workspace.xml +.idea/**/tasks.xml +.idea/**/usage.statistics.xml +.idea/**/dictionaries +.idea/**/shelf + +# AWS User-specific +.idea/**/aws.xml + +# Generated files +.idea/**/contentModel.xml + +# Sensitive or high-churn files +.idea/**/dataSources/ +.idea/**/dataSources.ids +.idea/**/dataSources.local.xml +.idea/**/sqlDataSources.xml +.idea/**/dynamic.xml +.idea/**/uiDesigner.xml +.idea/**/dbnavigator.xml + +# Gradle +.idea/**/gradle.xml +.idea/**/libraries + +# Gradle and Maven with auto-import +# When using Gradle or Maven with auto-import, you should exclude module files, +# since they will be recreated, and may cause churn. Uncomment if using +# auto-import. +# .idea/artifacts +# .idea/compiler.xml +# .idea/jarRepositories.xml +# .idea/modules.xml +# .idea/*.iml +# .idea/modules +# *.iml +# *.ipr + +# CMake +cmake-build-*/ + +# Mongo Explorer plugin +.idea/**/mongoSettings.xml + +# File-based project format +*.iws + +# IntelliJ +out/ + +# mpeltonen/sbt-idea plugin +.idea_modules/ + +# JIRA plugin +atlassian-ide-plugin.xml + +# Cursive Clojure plugin +.idea/replstate.xml + +# SonarLint plugin +.idea/sonarlint/ + +# Crashlytics plugin (for Android Studio and IntelliJ) +com_crashlytics_export_strings.xml +crashlytics.properties +crashlytics-build.properties +fabric.properties + +# Editor-based Rest Client +.idea/httpRequests + +# Android studio 3.1+ serialized cache file +.idea/caches/build_file_checksums.ser + +### PyCharm Patch ### +# Comment Reason: https://github.com/joeblau/gitignore.io/issues/186#issuecomment-215987721 + +# *.iml +# modules.xml +# .idea/misc.xml +# *.ipr + +# Sonarlint plugin +# https://plugins.jetbrains.com/plugin/7973-sonarlint +.idea/**/sonarlint/ + +# SonarQube Plugin +# https://plugins.jetbrains.com/plugin/7238-sonarqube-community-plugin +.idea/**/sonarIssues.xml + +# Markdown Navigator plugin +# https://plugins.jetbrains.com/plugin/7896-markdown-navigator-enhanced +.idea/**/markdown-navigator.xml +.idea/**/markdown-navigator-enh.xml +.idea/**/markdown-navigator/ + +# Cache file creation bug +# See https://youtrack.jetbrains.com/issue/JBR-2257 +.idea/$CACHE_FILE$ + +# CodeStream plugin +# https://plugins.jetbrains.com/plugin/12206-codestream +.idea/codestream.xml + +# General idea +.idea/* + +# Azure Toolkit for IntelliJ plugin +# https://plugins.jetbrains.com/plugin/8053-azure-toolkit-for-intellij +.idea/**/azureSettings.xml + +### Vim ### +# Swap +[._]*.s[a-v][a-z] +!*.svg # comment out if you don't need vector files +[._]*.sw[a-p] +[._]s[a-rt-v][a-z] +[._]ss[a-gi-z] +[._]sw[a-p] + +# Session +Session.vim +Sessionx.vim + +# Temporary +.netrwhist +# Auto-generated tag files +tags +# Persistent undo +[._]*.un~ + +### VisualStudioCode ### +.vscode/* +.vscode/settings.json +!.vscode/tasks.json +!.vscode/launch.json +!.vscode/extensions.json +!.vscode/*.code-snippets + +# Local History for Visual Studio Code +.history/ + +# Built Visual Studio Code Extensions +*.vsix + +### VisualStudioCode Patch ### +# Ignore all local history of files +.history +.ionide + +# End of https://www.toptal.com/developers/gitignore/api/visualstudiocode,pycharm,vim,emacs diff --git a/.python-version b/.python-version new file mode 100644 index 0000000..c8cfe39 --- /dev/null +++ b/.python-version @@ -0,0 +1 @@ +3.10 diff --git a/.readthedocs.yaml b/.readthedocs.yaml new file mode 100644 index 0000000..68fa9dd --- /dev/null +++ b/.readthedocs.yaml @@ -0,0 +1,32 @@ +# Read the Docs configuration file for Sphinx projects +# 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: "3.11" + + +# Build documentation in the "docs/" directory with Sphinx +sphinx: + configuration: docs/conf.py + + +# Optionally build your docs in additional formats such as PDF and ePub +formats: + - pdf + - epub + + +# Optional but recommended, declare the Python requirements required +# to build your documentation +# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html + +python: + install: + - requirements: requirements/test.txt diff --git a/AUTHORS.rst b/AUTHORS.rst new file mode 100644 index 0000000..e0a8348 --- /dev/null +++ b/AUTHORS.rst @@ -0,0 +1,13 @@ +======= +Credits +======= + +Development Lead +---------------- + +* Manuel Holtgrewe + +Contributors +------------ + +None yet. Why not be the first? diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 0000000..7c6184c --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,57 @@ +# Changelog + +## [0.5.0](https://www.github.com/bihealth/cada-prio/compare/v0.4.0...v0.5.0) (2023-09-18) + + +### Features + +* adding "tune run-optuna" command ([#23](https://www.github.com/bihealth/cada-prio/issues/23)) ([6cc753b](https://www.github.com/bihealth/cada-prio/commit/6cc753b3b4f92aa75d961c3cf314e097d174ede0)) +* re-useable implementation of "tune train-eval" ([#21](https://www.github.com/bihealth/cada-prio/issues/21)) ([c80c4bf](https://www.github.com/bihealth/cada-prio/commit/c80c4bf1d69ff83bcb84b949cf3383746580a12d)) + +## [0.4.0](https://www.github.com/bihealth/cada-prio/compare/v0.3.1...v0.4.0) (2023-09-14) + + +### Features + +* adding dump-graph to cli ([#18](https://www.github.com/bihealth/cada-prio/issues/18)) ([3aace31](https://www.github.com/bihealth/cada-prio/commit/3aace31166ddbd4357ae32283b6514a21404e0ef)) +* adding param-opt command with single parameter evaluation ([#20](https://www.github.com/bihealth/cada-prio/issues/20)) ([83141c6](https://www.github.com/bihealth/cada-prio/commit/83141c6c4afe6efffc51fcde1ebdc92b5b3d0fbf)) +* allow running with legacy model/graph data ([#16](https://www.github.com/bihealth/cada-prio/issues/16)) ([9d3cc7c](https://www.github.com/bihealth/cada-prio/commit/9d3cc7cea6efeac82b41fe11dfc9527ab4fe2913)) +* embedding parameters can be provided via CLI and contains seeds ([#19](https://www.github.com/bihealth/cada-prio/issues/19)) ([bbd5d86](https://www.github.com/bihealth/cada-prio/commit/bbd5d86e879db94240093c20145b1c4c45edc69e)) + +### [0.3.1](https://www.github.com/bihealth/cada-prio/compare/v0.3.0...v0.3.1) (2023-09-13) + + +### Bug Fixes + +* add missing line endings to hgnc_info.jsonl ([#13](https://www.github.com/bihealth/cada-prio/issues/13)) ([aa14b9b](https://www.github.com/bihealth/cada-prio/commit/aa14b9b948a0e9512c57567de2acaa65e9b132bc)) +* properly parsing comma-separated list on REST API ([#14](https://www.github.com/bihealth/cada-prio/issues/14)) ([97fdfee](https://www.github.com/bihealth/cada-prio/commit/97fdfeee118d2e4985ca71433617fd9c470d0b49)) + +## [0.3.0](https://www.github.com/bihealth/cada-prio/compare/v0.2.1...v0.3.0) (2023-09-11) + + +### Features + +* also adding gene-to-phen edges from HPO ([#9](https://www.github.com/bihealth/cada-prio/issues/9)) ([d5a8337](https://www.github.com/bihealth/cada-prio/commit/d5a833774b1488fb7e1f0650692aab2c3f753144)) + +### [0.2.1](https://www.github.com/bihealth/cada-prio/compare/v0.2.0...v0.2.1) (2023-09-08) + + +### Bug Fixes + +* removing spurious debug print statement ([#7](https://www.github.com/bihealth/cada-prio/issues/7)) ([98e7443](https://www.github.com/bihealth/cada-prio/commit/98e74433001872517a4904bbe85fd021cc4ad613)) + +## [0.2.0](https://www.github.com/bihealth/cada-prio/compare/v0.1.0...v0.2.0) (2023-09-08) + + +### Features + +* gene to phenotype links file can be gziped ([#5](https://www.github.com/bihealth/cada-prio/issues/5)) ([66c48bf](https://www.github.com/bihealth/cada-prio/commit/66c48bf98c8bd73f8227c7cbd5687b4e74577ef8)) + +## 0.1.0 (2023-09-07) + + +### Features + +* adding REST API server for prediction ([#4](https://www.github.com/bihealth/cada-prio/issues/4)) ([8bb7516](https://www.github.com/bihealth/cada-prio/commit/8bb75161097529932f371925fe860290098f0885)) +* initial training implementation ([#1](https://www.github.com/bihealth/cada-prio/issues/1)) ([10d3a7c](https://www.github.com/bihealth/cada-prio/commit/10d3a7cb356b50a89fd8b1226ad66932dd5542f3)) +* prioritization prediction with model ([#3](https://www.github.com/bihealth/cada-prio/issues/3)) ([48d504c](https://www.github.com/bihealth/cada-prio/commit/48d504c0bc373e1ae312773fa70a5a2e04d8dbed)) diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst new file mode 100644 index 0000000..38e474c --- /dev/null +++ b/CONTRIBUTING.rst @@ -0,0 +1,105 @@ +.. highlight:: shell + +============ +Contributing +============ + +Contributions are welcome, and they are greatly appreciated! +Every little bit helps, and credit will always be given. + +You can contribute in many ways: + +---------------------- +Types of Contributions +---------------------- + +Report Bugs +=========== + +Report bugs at https://github.com/bihealth/cada-prio/issues. + +If you are reporting a bug, please include: + +* Your operating system name and version. +* Any details about your local setup that might be helpful in troubleshooting. +* Detailed steps to reproduce the bug. + +Fix Bugs +======== + +Look through the GitHub issues for bugs. +Anything tagged with "bug" and "help wanted" is open to whoever wants to implement it. + +Implement Features +================== + +Look through the GitHub issues for features. +Anything tagged with "enhancement" and "help wanted" is open to whoever wants to implement it. + +Write Documentation +=================== + +cada-prio could always use more documentation, whether as part of the official cada-prio docs, in docstrings, or even on the web in blog posts, articles, and such. + +Submit Feedback +=============== + +The best way to send feedback is to file an issue at https://github.com/bihealth/cada-prio/issues. + +If you are proposing a feature: + +* Explain in detail how it would work. +* Keep the scope as narrow as possible, to make it easier to implement. +* Remember that this is a volunteer-driven project, and that contributions are welcome :) + +------------ +Get Started! +------------ + +Ready to contribute? Here's how to set up `cada-prio` for local development. + +1. Fork the `cada-prio` repo on GitHub. +2. Clone your fork locally:: + + $ git clone git@github.com:bihealth/cada-prio.git + +3. Install your local copy into a virtualenv. + Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development:: + + $ mkvirtualenv cada-prio + $ cd cada-prio/ + $ python setup.py develop + +4. Create a branch for local development:: + + $ git checkout -b name-of-your-bugfix-or-feature + + Now you can make your changes locally. + +5. When you're done making changes, check that your changes pass flake8 and the + tests, including testing other Python versions with tox:: + + $ flake8 cada-prio tests + $ python setup.py test or pytest + $ tox + + To get flake8 and tox, just pip install them into your virtualenv. + +6. Commit your changes and push your branch to GitHub:: + + $ git add . + $ git commit -m "Your detailed description of your changes." + $ git push origin name-of-your-bugfix-or-feature + +7. Submit a pull request through the GitHub website. + +----------------------- +Pull Request Guidelines +----------------------- + +Before you submit a pull request, check that it meets these guidelines: + +1. The pull request should include tests. +2. If the pull request adds functionality, the docs should be updated. + Put your new functionality into a function with a docstring. +3. The pull request should work for Python 3.9 to 3.11. diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..26c59aa --- /dev/null +++ b/LICENSE @@ -0,0 +1,22 @@ +MIT License + +Copyright (c) 2023, Berlin Institute of Health + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. + diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..23d0de8 --- /dev/null +++ b/Makefile @@ -0,0 +1,72 @@ +DIRS_PYTHON := dotty # tests + +.PHONY: help +help: + @echo "Usage: make " + @echo + @echo "Targets:" + @echo " help This help (default target)" + @echo " deps Install all dependencies" + @echo " format Format source code" + @echo " lint Run lint checks" + @echo " test Run tests" + @echo " ci Install dependencies, run lints and tests" + @echo " serve Run the (development) server" + +.PHONY: deps +deps: + pipenv install --dev + +.PHONY: format +format: \ + format-isort \ + format-black + +.PHONY: format-isort +format-isort: + pipenv run isort --profile=black $(DIRS_PYTHON) + +.PHONY: format-black +format-black: + pipenv run black --line-length 100 $(DIRS_PYTHON) + +.PHONY: lint +lint: \ + lint-isort \ + lint-black \ + lint-flake8 \ + lint-mypy + +.PHONY: lint-isort +lint-isort: + pipenv run isort --profile=black --check-only --diff $(DIRS_PYTHON) + +.PHONY: lint-black +lint-black: + pipenv run black --check --line-length 100 --diff $(DIRS_PYTHON) + +.PHONY: lint-flake8 +flake8: + pipenv run flake8 --max-line-length 100 $(DIRS_PYTHON) + +.PHONY: lint-mypy +lint-mypy: + pipenv run mypy $(DIRS_PYTHON_NO_ALEMBIC) + +.PHONY: test +test: + pipenv run pytest \ + --cov-report term-missing \ + --cov-report lcov \ + --cov=app \ + tests/ + +.PHONY: ci +ci: \ + deps \ + lint \ + test + +.PHONY: serve +serve: + pipenv run uvicorn dotty.main:app --host 0.0.0.0 --port 8080 --reload --workers 8 diff --git a/Pipfile b/Pipfile new file mode 100644 index 0000000..49ce9d1 --- /dev/null +++ b/Pipfile @@ -0,0 +1,19 @@ +[[source]] +url = "https://pypi.org/simple" +verify_ssl = true +name = "pypi" + +[packages] +cdot = "*" +fastapi = "*" + +[dev-packages] +black = "*" +flake8 = "*" +mypy = "*" +pytest = "*" +pytest-coverage = "*" +isort = "*" + +[requires] +python_version = "3.10" diff --git a/Pipfile.lock b/Pipfile.lock new file mode 100644 index 0000000..f2860fc --- /dev/null +++ b/Pipfile.lock @@ -0,0 +1,650 @@ +{ + "_meta": { + "hash": { + "sha256": "d4452f62d64848a05d64e0ad2e000287f4a37cc11c0cd165c2cc94bf208b0ad0" + }, + "pipfile-spec": 6, + "requires": { + "python_version": "3.10" + }, + "sources": [ + { + "name": "pypi", + "url": "https://pypi.org/simple", + "verify_ssl": true + } + ] + }, + "default": { + "annotated-types": { + "hashes": [ + "sha256:47cdc3490d9ac1506ce92c7aaa76c579dc3509ff11e098fc867e5130ab7be802", + "sha256:58da39888f92c276ad970249761ebea80ba544b77acddaa1a4d6cf78287d45fd" + ], + "markers": "python_version >= '3.7'", + "version": "==0.5.0" + }, + "anyio": { + "hashes": [ + "sha256:44a3c9aba0f5defa43261a8b3efb97891f2bd7d804e0e1f56419befa1adfc780", + 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100644 index 0000000..760f573 --- /dev/null +++ b/README.md @@ -0,0 +1,51 @@ +[![CI](https://github.com/bihealth/dotty/actions/workflows/main.yml/badge.svg?branch=main)](https://github.com/bihealth/dotty/actions/workflows/main.yml) +[![codecov](https://codecov.io/gh/bihealth/dotty/graph/badge.svg?token=HIBwaG4eYM)](https://codecov.io/gh/bihealth/dotty) + +# CADA: The Next Generation + +This is a re-implementation of the [CADA](https://github.com/Chengyao-Peng/CADA) method for phenotype-similarity prioritization. + +- Free software: MIT license +- Documentation: https://dotty.readthedocs.io/en/latest/ +- Discussion Forum: https://github.com/bihealth/dotty/discussions +- Bug Reports: https://github.com/bihealth/dotty/issues + +## Running Hyperparameter Tuning + +Install with `tune` feature enabled: + +``` +pip install dotty[tune] +``` + +Run tuning, e.g., on the "classic" model. +Thanks to [optuna](https://optuna.org/), you can run this in parallel as long as the database is shared. +Each run will use 4 CPUs in the example below and perform 1 trial. + +``` +dotty tune run-optuna \ + sqlite:///local_data/cada-tune.sqlite \ + --path-hgnc-json data/classic/hgnc_complete_set.json \ + --path-hpo-genes-to-phenotype data/classic/genes_to_phenotype.all_source_all_freqs_etc.txt \ + --path-hpo-obo data/classic/hp.obo \ + --path-clinvar-phenotype-links data/classic/cases_train.jsonl \ + --path-validation-links data/classic/cases_validate.jsonl \ + --n-trials 1 \ + --cpus=4 +``` + +## Managing GitHub Project with Terraform + +``` +# export GITHUB_OWNER=bihealth +# export GITHUB_TOKEN=ghp_ + +# cd utils/terraform + +# terraform init +# terraform import github_repository.dotty dotty +# terraform validate +# terraform fmt +# terraform plan +# terraform apply +``` diff --git a/dotty/__init__.py b/dotty/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/dotty/main.py b/dotty/main.py new file mode 100644 index 0000000..48dfe51 --- /dev/null +++ b/dotty/main.py @@ -0,0 +1,22 @@ +import logging + +import pydantic +from fastapi import FastAPI + +logging.basicConfig(level=logging.DEBUG) + +logger = logging.getLogger(__name__) + +app = FastAPI( + title="dotty", +) + + +class Result(pydantic.BaseModel): + payload: str + + +@app.get("/", response_model=list[Result]) +async def index() -> list[Result]: + """Render the index.html page at the root URL""" + return [Result(payload="foo")] diff --git a/utils/docker/Dockerfile b/utils/docker/Dockerfile new file mode 100644 index 0000000..ee699a2 --- /dev/null +++ b/utils/docker/Dockerfile @@ -0,0 +1,56 @@ +# syntax=docker/dockerfile:1.3 + +# --------------------------------------------------------------------------- +# Base +# --------------------------------------------------------------------------- + +FROM python:3.10-slim AS base + +ENV LANG C.UTF-8 +ENV LC_ALL C.UTF-8 +ENV PYTHONDONTWRITEBYTECODE 1 +ENV PYTHONFAULTHANDLER 1 + +RUN apt-get update && apt-get install -y curl +RUN apt-get clean autoclean && \ + apt-get autoremove --yes && \ + rm -rf /var/lib/{apt,dpkg,cache,log}/ + + +# --------------------------------------------------------------------------- +# Dependencies +# --------------------------------------------------------------------------- + +FROM base AS deps + +RUN pip install pipenv +RUN apt-get update && apt-get install -y --no-install-recommends gcc + +COPY Pipfile . +COPY Pipfile.lock . +RUN PIPENV_VENV_IN_PROJECT=1 pipenv install --deploy + + +# --------------------------------------------------------------------------- +# Runtime +# --------------------------------------------------------------------------- + +FROM base AS runtime + +ARG version_file=utils/docker/empty-file-dont-remove + +COPY --from=deps /.venv /.venv +COPY utils/docker/entrypoint.sh /entrypoint.sh +RUN chmod +x /entrypoint.sh + +ENV PATH="/.venv/bin:$PATH" + +RUN useradd --create-home dotty +WORKDIR /home/dotty +USER dotty + +COPY ${version_file} /VERSION +COPY dotty/. ./dotty/. + +CMD ["/entrypoint.sh"] +EXPOSE 8080 diff --git a/utils/docker/build-docker.sh b/utils/docker/build-docker.sh new file mode 100755 index 0000000..a9aae3b --- /dev/null +++ b/utils/docker/build-docker.sh @@ -0,0 +1,22 @@ +#!/bin/bash + +# Utility script to start the Docker build process. + +set -x +set -euo pipefail + +GIT_DESCRIBE=$((git describe --tags || echo 0.0.0) | cut -d - -f 1) +GIT_TAG=${GIT_TAG-$GIT_DESCRIBE} +DOCKER_VERSION=$(echo $GIT_TAG | sed -e 's/^v//') + +ORG=bihealth +REPO=dotty + +git describe --tags --dirty >VERSION + +sudo docker build . \ + --build-arg version_file=VERSION \ + --file utils/docker/Dockerfile \ + --pull \ + -t ghcr.io/$ORG/$REPO:$DOCKER_VERSION \ + "$@" diff --git a/utils/docker/empty-file-dont-remove b/utils/docker/empty-file-dont-remove new file mode 100644 index 0000000..e69de29 diff --git a/utils/docker/entrypoint.sh b/utils/docker/entrypoint.sh new file mode 100755 index 0000000..abccdb2 --- /dev/null +++ b/utils/docker/entrypoint.sh @@ -0,0 +1,16 @@ +#!/usr/bin/bash + +set -x +set -euo pipefail + +# Interpreted environment variables. +# +# HTTP_HOST -- host to listen on +# default: 0.0.0.0 +# HTTP_PORT -- port +# default: 8080 + +HTTP_HOST=${HTTP_HOST-0.0.0.0} +HTTP_PORT=${HTTP_PORT-8080} + +uvicorn dotty.main:app --host $HTTP_HOST --port $HTTP_PORT