gentroutils 0.1.5__tar.gz

gentroutils-0.1.5/.github/workflows/pr.yaml

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+name: Dev tests
+
+on:
+  pull_request:
+
+env:
+  PYTHON_VERSION_DEFAULT: "3.10.8"
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 1
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.10.8
+      - name: Install uv
+        uses: yezz123/setup-uv@v4
+      - name: Install rye
+        uses: eifinger/setup-rye@v4
+        with:
+          version: "latest"
+      - name: Sync dependencies
+        run: rye sync
+      - name: Run checks
+        run: rye run pre-commit run --all-files

gentroutils-0.1.5/.github/workflows/release.yaml

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+name: Release
+
+on:
+  push:
+    tags:
+      - "v*"
+
+env:
+  PYTHON_VERSION_DEFAULT: "3.10.8"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 1
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.10.8
+      - name: Install uv
+        uses: yezz123/setup-uv@v4
+      - name: Install rye
+        uses: eifinger/setup-rye@v4
+        with:
+          version: "latest"
+      - name: Sync dependencies
+        run: rye sync
+      - name: Build package
+        run: make build
+      - name: Store the distribution packages
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+  test-release:
+    needs: build
+    runs-on: ubuntu-latest
+    environment: TEST
+    permissions:
+      id-token: write # IMPORTANT: mandatory for trusted publishing
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+      - name: Publish distribution 📦 to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+          packages-dir: dist/
+
+  release:
+    needs: test-release
+    runs-on: ubuntu-latest
+    environment: PyPI
+    permissions:
+      id-token: write # IMPORTANT: mandatory for trusted publishing
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://upload.pypi.org/legacy/
+          packages-dir: dist/

gentroutils-0.1.5/.github/workflows/release_pr.yaml

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+name: Trigger Release
+
+"on":
+  schedule:
+    - cron: "0 11 * * 2"
+  workflow_dispatch:
+
+jobs:
+  pull-request:
+    runs-on: ubuntu-latest
+    environment: DEV
+    steps:
+      - uses: actions/create-github-app-token@v1
+        id: trigger-token
+        with:
+          app-id: ${{ vars.TRIGGER_WORKFLOW_GH_APP_ID}}
+          private-key: ${{ secrets.TRIGGER_WORKFLOW_GH_APP_KEY }}
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          repository: opentargets/gentropy
+          token: ${{ secrets.GITHUB_TOKEN }}
+          persist-credentials: false
+      - uses: actions/checkout@v3
+      - name: pull-request
+        uses: diillson/auto-pull-request@v1.0.1
+        with:
+          source_branch: "dev"
+          destination_branch: "main"
+          pr_title: "chore: trigger release process"
+          pr_body: ":warning: *This PR requires a MERGE COMMIT (Don't squash or rebase!)*"
+          pr_label: "auto-pr"
+          pr_draft: false
+          pr_allow_empty: true
+          github_token: ${{ secrets.GITHUB_TOKEN }}

gentroutils-0.1.5/.github/workflows/tag.yaml

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+name: Tag
+
+"on":
+  push:
+    branches: ["main"]
+
+concurrency:
+  group: deploy
+  # NOTE: prevent hickups with semantic-release
+  cancel-in-progress: false
+
+env:
+  PYTHON_VERSION_DEFAULT: "3.10.8"
+
+jobs:
+  tag:
+    # NOTE: only trigger the workflow when the commit is not from the GitHubActions bot (prevent self-triggering)
+    if: github.event.commits[0].author.name != 'github-actions'
+    runs-on: ubuntu-latest
+    concurrency: release
+    environment: DEV
+    permissions:
+      contents: write
+
+    steps:
+      # NOTE: commits using GITHUB_TOKEN does not trigger workflows and we want to trigger PiPY from tag
+      - uses: actions/create-github-app-token@v1
+        id: trigger-token
+        with:
+          app-id: ${{ vars.TRIGGER_WORKFLOW_GH_APP_ID}}
+          private-key: ${{ secrets.TRIGGER_WORKFLOW_GH_APP_KEY }}
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          repository: opentargets/gentroutils
+          token: ${{ secrets.GITHUB_TOKEN }}
+          persist-credentials: false
+          ref: main
+      - name: Python Semantic Release
+        id: semrelease
+        # v9.6.0 is required due to the python v3.12 in the newer version of semantic release action which
+        # breaks the poetry build command.
+        uses: python-semantic-release/python-semantic-release@v9.6.0
+        with:
+          github_token: ${{ steps.trigger-token.outputs.token }}
+
+      - name: Publish package to GitHub Release
+        uses: python-semantic-release/upload-to-gh-release@main
+        if: ${{ steps.semrelease.outputs.released }} == 'true'
+        with:
+          # NOTE: allow to start the workflow when push action on tag gets executed
+          # requires using GH_APP to authenitcate, otherwise push authorised with
+          # the GITHUB_TOKEN does not trigger the tag artifact workflow.
+          # see https://github.com/actions/create-github-app-token
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          tag: ${{ steps.semrelease.outputs.tag }}

gentroutils-0.1.5/.github/workflows/test.yaml

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+name: Tests
+
+on:
+  push:
+    branches: ["dev"]
+
+env:
+  PYTHON_VERSION_DEFAULT: "3.10.8"
+  SKIP: no-commit-to-branch
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 1
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.10.8
+      - name: Install uv
+        uses: yezz123/setup-uv@v4
+      - name: Install rye
+        uses: eifinger/setup-rye@v4
+        with:
+          version: "latest"
+      - name: Sync dependencies
+        run: rye sync
+      - name: Run checks
+        run: rye run pre-commit run --all-files

gentroutils-0.1.5/.gitignore

@@ -0,0 +1,17 @@
+# python generated files
+__pycache__/
+*.py[oc]
+build/
+dist/
+wheels/
+*.egg-info
+
+# venv
+.venv
+
+# covarage
+.coverage
+coverage.xml
+
+# interrogate
+interrogate_badge.svg

gentroutils-0.1.5/.pre-commit-config.yaml

@@ -0,0 +1,77 @@
+default_language_version:
+  python: python3.10
+ci:
+  autoupdate_commit_msg: "chore: pre-commit autoupdate"
+  autofix_commit_msg: "chore: pre-commit auto fixes [...]"
+repos:
+  - repo: local
+    hooks:
+      - id: check
+        name: check code
+        entry: make check
+        language: system
+        types: [python]
+        pass_filenames: false
+        stages: ["pre-commit"]
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: trailing-whitespace
+        stages: ["pre-commit"]
+      - id: end-of-file-fixer
+        stages: ["pre-commit"]
+        exclude: "CHANGELOG.md"
+      - id: debug-statements
+        stages: ["pre-commit"]
+      - id: check-merge-conflict
+        stages: ["pre-commit"]
+      - id: check-case-conflict
+        stages: ["pre-commit"]
+      - id: check-json
+        stages: ["pre-commit"]
+        exclude: (.vscode|.devcontainer)
+      - id: no-commit-to-branch
+        args:
+          - --branch=dev
+        stages: ["pre-commit"]
+      - id: check-toml
+        stages: ["pre-commit"]
+      - id: check-yaml
+        stages: ["pre-commit"]
+      - id: check-ast
+        stages: ["pre-commit"]
+      - id: debug-statements
+        stages: ["pre-commit"]
+      - id: check-docstring-first
+        stages: ["pre-commit"]
+
+
+  - repo: https://github.com/adrienverge/yamllint.git
+    rev: v1.35.1
+    hooks:
+      - id: yamllint
+        args: ["-d", "{rules: {line-length: {max: 200}}}"]
+        stages: ["pre-commit"]
+
+
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0
+    hooks:
+      - id: python-check-mock-methods
+        stages: ["pre-commit"]
+      - id: python-check-blanket-noqa
+        stages: ["pre-commit"]
+
+  - repo: https://github.com/alessandrojcm/commitlint-pre-commit-hook
+    rev: v9.16.0
+    hooks:
+      - id: commitlint
+        additional_dependencies: ["@commitlint/config-conventional@18.6.3"]
+        stages: [commit-msg]
+
+  - repo: https://github.com/lovesegfault/beautysh
+    rev: v6.2.1
+    hooks:
+      - id: beautysh
+        stages: ["pre-commit"]

gentroutils-0.1.5/.python-version

@@ -0,0 +1 @@
+3.10.14

gentroutils-0.1.5/CHANGELOG.md

@@ -0,0 +1,220 @@
+# CHANGELOG
+
+
+
+## v0.1.5 (2024-08-13)
+
+### Ci
+
+* ci: added needs flags to release jobs ([`3b84cdd`](https://github.com/opentargets/gentroutils/commit/3b84cdd3d4e158f172d29ccc27d033facd56e244))
+
+* ci: add pypi release ([`271abbf`](https://github.com/opentargets/gentroutils/commit/271abbfe125f44db11c078f6b3ff91e7748551de))
+
+### Unknown
+
+* Merge pull request #15 from opentargets/dev
+
+chore: trigger release process ([`5740867`](https://github.com/opentargets/gentroutils/commit/57408679669c3e2427df680478baecc7e2873aec))
+
+
+## v0.1.4 (2024-08-13)
+
+### Ci
+
+* ci: fix link to testpypi ([`aa19be5`](https://github.com/opentargets/gentroutils/commit/aa19be588dcf2e93e862efc9e3ab54e06c3e762e))
+
+### Unknown
+
+* Merge pull request #14 from opentargets/dev
+
+chore: trigger release process ([`bd68b60`](https://github.com/opentargets/gentroutils/commit/bd68b60c81230afe0fbbe49010ef2e130a12353b))
+
+
+## v0.1.3 (2024-08-13)
+
+### Ci
+
+* ci: fix link to testpypi ([`b14085d`](https://github.com/opentargets/gentroutils/commit/b14085dd05bbb85c3e9a49742f59ff9043c391b0))
+
+### Unknown
+
+* Merge pull request #13 from opentargets/dev
+
+chore: trigger release process ([`79c17d9`](https://github.com/opentargets/gentroutils/commit/79c17d95baf1e7f7cdc0be3137426332b89badc7))
+
+
+## v0.1.2 (2024-08-13)
+
+### Ci
+
+* ci: use original github token for testpypi ([`1e2e5af`](https://github.com/opentargets/gentroutils/commit/1e2e5af0aba88c4decf8a471d042b3f8c0487414))
+
+### Unknown
+
+* Merge pull request #12 from opentargets/dev
+
+chore: trigger release process ([`48c63ba`](https://github.com/opentargets/gentroutils/commit/48c63ba7ab4753ce8bd2767d53ba32d41257a087))
+
+
+## v0.1.1 (2024-08-13)
+
+### Ci
+
+* ci: prevent second job run and fix build ([`422b3fc`](https://github.com/opentargets/gentroutils/commit/422b3fc78dcc869c464e0e722be6619dc444de05))
+
+### Unknown
+
+* Merge pull request #11 from opentargets/dev
+
+chore: trigger release process ([`bf30b0d`](https://github.com/opentargets/gentroutils/commit/bf30b0d95b065166620e67c866bb99b067fc7538))
+
+
+## v0.1.0 (2024-08-13)
+
+### Build
+
+* build: precommit & interrogate ([`8ae6533`](https://github.com/opentargets/gentroutils/commit/8ae6533e757551fbe32d386725deeeb27def2ed7))
+
+* build: docstring linting ([`5feea17`](https://github.com/opentargets/gentroutils/commit/5feea17a28241dd7f4ecd43ebb7c4e34e0fd8301))
+
+* build: added deptry ([`179f196`](https://github.com/opentargets/gentroutils/commit/179f196e766185ba8a54a5292a2aedf80e45b4ab))
+
+* build: added mypy ([`ccf0750`](https://github.com/opentargets/gentroutils/commit/ccf07504df5350063ad0c3cdc1e38876a14f5507))
+
+* build: added pydoclint ([`633b3da`](https://github.com/opentargets/gentroutils/commit/633b3da1623c41da519c9ad5f0caf747648a051e))
+
+* build: ruff setup ([`daddc69`](https://github.com/opentargets/gentroutils/commit/daddc6949bb2d8e39783e2837a85a3b853825590))
+
+* build: dev setup make target ([`0dda8bd`](https://github.com/opentargets/gentroutils/commit/0dda8bdab571d925e2a42e66fa0dc7809b2da68f))
+
+### Chore
+
+* chore: licence badge ([`93708ba`](https://github.com/opentargets/gentroutils/commit/93708bad3bbc1d65cc0f87faad4cbe14856bbf93))
+
+* chore: badge ([`d92782b`](https://github.com/opentargets/gentroutils/commit/d92782b8ccced842e8fa853f00c298b432e759c8))
+
+* chore: added licence ([`bac9b9d`](https://github.com/opentargets/gentroutils/commit/bac9b9d20279ce08623571fa29bf43d8d63fab83))
+
+### Ci
+
+* ci: fix repo name in checkout action for tag ([`c49ee91`](https://github.com/opentargets/gentroutils/commit/c49ee911455468650a4e7230543c9060739c9182))
+
+* ci: fix path to the semvar version ([`614f3a7`](https://github.com/opentargets/gentroutils/commit/614f3a753fb562264fb05189ee27c16a522cfcbc))
+
+* ci: trigger release from main branch ([`9447be8`](https://github.com/opentargets/gentroutils/commit/9447be8627108b7924bcad0750d7c53f2babb100))
+
+* ci: skip no-commit-to-branch on dev test ([`e214f6c`](https://github.com/opentargets/gentroutils/commit/e214f6c657eae9ed519cf552fc03639396cb2d45))
+
+* ci: added manual trigger for release trigger job ([`911ba3f`](https://github.com/opentargets/gentroutils/commit/911ba3f42a81055dd006c8f1020ffdb315357eac))
+
+* ci: improvements over dev branch tests" ([`4597b90`](https://github.com/opentargets/gentroutils/commit/4597b90227306822718c0364db8d8a336282cc95))
+
+* ci: fix trigger date ([`da168b7`](https://github.com/opentargets/gentroutils/commit/da168b7153a5b0eb03319e0a248a704604bb9cca))
+
+* ci: changed ga workflow names ([`caab806`](https://github.com/opentargets/gentroutils/commit/caab806457f36c84556422ef61eeed6a219e6bb6))
+
+* ci: release schedule test ([`eaa132e`](https://github.com/opentargets/gentroutils/commit/eaa132ea06694110b969bd4b079f96f32ae80078))
+
+* ci: release schedule test ([`c43d2ab`](https://github.com/opentargets/gentroutils/commit/c43d2ab659ddbc7ec2e22c2c1a07d136a725e4d5))
+
+* ci: changed how uv and rye are installed ([`e7c9e5e`](https://github.com/opentargets/gentroutils/commit/e7c9e5e2dec910aa9cef2b14b1d88d4e669c057a))
+
+* ci: ci test release ([`8c98b46`](https://github.com/opentargets/gentroutils/commit/8c98b46b40e5779eb789b3b510d0352dc45a34f0))
+
+* ci: pr yaml ([`c65f137`](https://github.com/opentargets/gentroutils/commit/c65f1379d45bd1f1437fa816fa6fb4e5ae5f4737))
+
+### Documentation
+
+* docs: added documentation over the cli ([`fff60a9`](https://github.com/opentargets/gentroutils/commit/fff60a91a933d075989803f570fea0c8d64ec50c))
+
+* docs: readme scheleton ([`c3c7887`](https://github.com/opentargets/gentroutils/commit/c3c7887f633e89fb153ffd2a8981442e6fb58b92))
+
+### Feature
+
+* feat: added DEV environment ([`6a44a9e`](https://github.com/opentargets/gentroutils/commit/6a44a9ede2a9b56a3f58873f458a1843abc3b422))
+
+* feat: local pre-commit execution without action ([`4345691`](https://github.com/opentargets/gentroutils/commit/4345691c7e3a352b72d5003fbfe5781d7d111c90))
+
+* feat: attempt to install rye with cargo ([`ce4fd37`](https://github.com/opentargets/gentroutils/commit/ce4fd37ed2483c353bc552e6d9e91b5f9883dc52))
+
+* feat: gwas curation update script ([`31716bf`](https://github.com/opentargets/gentroutils/commit/31716bf7a62c097e19305023f9023b7338e404ee))
+
+* feat: pytest setup and cli entrypoint ([`c107abd`](https://github.com/opentargets/gentroutils/commit/c107abd843efc6a60c6604e22ca5994fe46d3617))
+
+* feat: package setup ([`0c5d4c3`](https://github.com/opentargets/gentroutils/commit/0c5d4c3186ae6ddc18f46e0e76ad690e08c8ec56))
+
+### Fix
+
+* fix: fix dev branch test run ([`8430526`](https://github.com/opentargets/gentroutils/commit/8430526f911fbe91c58131056f091cbd11ef2e15))
+
+* fix: fix dev branch test run ([`967c0b8`](https://github.com/opentargets/gentroutils/commit/967c0b83d3e1c4f6e9c7c2d909fbb71674ec8871))
+
+* fix: run pre-commit by rye ([`7fbd06c`](https://github.com/opentargets/gentroutils/commit/7fbd06cbeb42563f6c2a66f768e490f554a7c07b))
+
+* fix: typo in package name ([`10584a5`](https://github.com/opentargets/gentroutils/commit/10584a56790cf4693bd47ee3e50672bc4bb78068))
+
+* fix: ensure pip is installed for pre-commit action ([`7d74378`](https://github.com/opentargets/gentroutils/commit/7d74378a45c307b9ae64cd6dfd707948113b5e7d))
+
+* fix: debug v2 ([`332e0d5`](https://github.com/opentargets/gentroutils/commit/332e0d58dee315c9aa5f57f20464d1097c41cb59))
+
+* fix: debug ci ([`cd0c7ed`](https://github.com/opentargets/gentroutils/commit/cd0c7eda865af9df5bf1ab65dfa405b3a13e605c))
+
+* fix: add cargo to rc file ([`7e1340f`](https://github.com/opentargets/gentroutils/commit/7e1340f1fb4aa57092f149db0e9400d18a4a0cca))
+
+* fix: moved ci file ([`c2626a2`](https://github.com/opentargets/gentroutils/commit/c2626a2479217e1e0e4a36470503d3a1f19f3021))
+
+* fix: remove local log file ([`b2a80fc`](https://github.com/opentargets/gentroutils/commit/b2a80fceceeb34832ddc271c28c8de9363e3b745))
+
+### Unknown
+
+* Merge pull request #10 from opentargets/dev
+
+chore: trigger release process ([`0369439`](https://github.com/opentargets/gentroutils/commit/03694399a0f1f412950c81eb6a68e46af1be383d))
+
+* Merge branch 'main' into dev ([`6d40028`](https://github.com/opentargets/gentroutils/commit/6d400282725abf414dba86f2d4cfda3b2a317c75))
+
+* Merge pull request #9 from opentargets/dev
+
+chore: trigger release process ([`59321a9`](https://github.com/opentargets/gentroutils/commit/59321a90ab91ea4d9d605db7ded429df932fa2e9))
+
+* Merge pull request #8 from opentargets/dev
+
+chore: trigger release process ([`d767f55`](https://github.com/opentargets/gentroutils/commit/d767f55bf5d5b895915415b54699d2a54d83fb5d))
+
+* Merge pull request #7 from opentargets/dev
+
+chore: trigger release process ([`e0eea67`](https://github.com/opentargets/gentroutils/commit/e0eea67f21a0b1e1c72be8b5b2d139029a5f7f51))
+
+* Merge branch 'main' into dev ([`9669a40`](https://github.com/opentargets/gentroutils/commit/9669a405838289e8869c9f861e03134a65cf6825))
+
+* Merge pull request #6 from opentargets/dev
+
+chore: trigger release process ([`80475d0`](https://github.com/opentargets/gentroutils/commit/80475d0f727c93f67cb190537e16104752f1b9b2))
+
+* Merge pull request #5 from opentargets/new-branch
+
+ci: fix trigger date ([`f0550ea`](https://github.com/opentargets/gentroutils/commit/f0550eac15663684cbfe61725c7f669d0a54f7e8))
+
+* Merge branch 'dev' into new-branch ([`7079a77`](https://github.com/opentargets/gentroutils/commit/7079a7730972409ccd844d53b11b504a8d7740a0))
+
+* Merge pull request #4 from opentargets/new-branch
+
+ci: changed ga workflow names ([`e8d9650`](https://github.com/opentargets/gentroutils/commit/e8d96501481b76c6b0704de73e54c8b6977af12a))
+
+* Merge branch 'dev' into new-branch ([`75ec3da`](https://github.com/opentargets/gentroutils/commit/75ec3da21cb2ba1ef5e2d4101503f2769ff46562))
+
+* Merge pull request #3 from opentargets/new-branch
+
+ci: release schedule test ([`70389bb`](https://github.com/opentargets/gentroutils/commit/70389bb666079c15dbb84ebc0acf1cb9fdec1ee5))
+
+* Merge branch 'dev' into new-branch ([`0fa0ec6`](https://github.com/opentargets/gentroutils/commit/0fa0ec66a129d53f40f7acbe74d15044303efaba))
+
+* Merge pull request #2 from opentargets/new-branch
+
+ci: release schedule test ([`10ba02a`](https://github.com/opentargets/gentroutils/commit/10ba02afd97595a9148a7e07bdfaaa5bb194f4b0))
+
+* Merge branch 'dev' into new-branch ([`5f8e943`](https://github.com/opentargets/gentroutils/commit/5f8e9438c7f88c6d54c591d8e7ce3899efcf7a7d))
+
+* Merge pull request #1 from opentargets/new-branch
+
+ci: ci test release ([`1e07aa5`](https://github.com/opentargets/gentroutils/commit/1e07aa5cd4860c1c6c996b953a836f19028580db))