biocommons.python_package 0.0.8__tar.gz

biocommons_python_package-0.0.8/.deepsource.toml

@@ -0,0 +1,13 @@
+version = 1
+
+test_patterns = [
+  "tests/**"
+]
+
+[[analyzers]]
+name = "python"
+enabled = true
+runtime_version = "3.x.x"
+
+  [analyzers.meta]
+  max_line_length = 100

biocommons_python_package-0.0.8/.dockerignore

@@ -0,0 +1,33 @@
+# Bytecode files
+__pycache__/
+*.pyc
+*.pyo
+
+# Virtual environment
+venv/
+.venv/
+
+# Debug and log files
+*.log
+debug*.txt
+
+# Data and media
+data/
+media/
+
+# Temporary files and directories
+tmp/
+temp/
+*.swp
+
+# IDE and OS files
+.idea/
+.vscode/
+.DS_Store
+
+# Distribution files
+dist/
+build/
+*.egg-info/
+
+.env

biocommons_python_package-0.0.8/.github/CODEOWNERS

@@ -0,0 +1 @@
+* @biocommons/maintainers

biocommons_python_package-0.0.8/.github/actions/setup-python-env/action.yml

@@ -0,0 +1,31 @@
+name: "Setup Python Environment"
+description: "Set up Python environment for the given Python version"
+
+inputs:
+  python-version:
+    description: "Python version to use"
+    required: true
+    default: "3.13"
+  uv-version:
+    description: "uv version to use"
+    required: true
+    default: "0.7.14"
+
+runs:
+  using: "composite"
+  steps:
+    - uses: actions/setup-python@v5
+      with:
+        python-version: ${{ inputs.python-version }}
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6
+      with:
+        version: ${{ inputs.uv-version }}
+        python-version: ${{ inputs.python-version }}
+        enable-cache: 'true'
+        cache-suffix: ${{ matrix.python-version }}
+
+    - name: Install Python dependencies
+      run: uv sync --frozen
+      shell: bash

biocommons_python_package-0.0.8/.github/dependabot.yml

@@ -0,0 +1,19 @@
+version: 2
+updates:
+  - package-ecosystem: "uv"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    groups:
+      patch:
+        update-types:
+          - "patch"
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    groups:
+      patch:
+        update-types:
+          - "patch"

biocommons_python_package-0.0.8/.github/labels.yml

@@ -0,0 +1,3 @@
+# file must contain an array, which may be empty
+
+[]

biocommons_python_package-0.0.8/.github/workflows/dependabot-automerge.yml

@@ -0,0 +1,25 @@
+name: Dependabot auto-merge
+
+on: pull_request_target
+
+permissions:
+  contents: write
+  pull-requests: write
+
+jobs:
+  automerge:
+    if: github.actor == 'dependabot[bot]'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Get Dependabot metadata
+        id: metadata
+        uses: dependabot/fetch-metadata@v3
+        with:
+          github-token: "${{ secrets.GITHUB_TOKEN }}"
+
+      - name: Enable auto-merge for minor/patch updates
+        if: steps.metadata.outputs.update-type != 'version-update:semver-major'
+        run: gh pr merge --auto --merge "$PR_URL"
+        env:
+          PR_URL: ${{ github.event.pull_request.html_url }}
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}

biocommons_python_package-0.0.8/.github/workflows/labels.yml

@@ -0,0 +1,29 @@
+name: Sync labels
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - 'main'
+    paths:
+      - '.github/labels.yml'
+      - '.github/workflows/labels.yml'
+
+permissions:
+  issues: write
+
+jobs:
+  labels:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v7
+        with:
+          sparse-checkout: .github/labels.yml
+
+      - uses: EndBug/label-sync@v2
+        with:
+          config-file: |
+            https://raw.githubusercontent.com/biocommons/.github/main/etc/labels.yml
+            .github/labels.yml
+
+          delete-other-labels: false

biocommons_python_package-0.0.8/.github/workflows/python-ci-cd.yml

@@ -0,0 +1,23 @@
+name: Python CI/CD
+
+on:
+  push:           # branch or tag push on *this* repo
+  pull_request:   # PR on *this or forked* repo
+
+jobs:
+  python-ci-cd:
+    name: Python CI/CD
+    # run on all pushes and on PRs from forks;
+    # i.e., skip PRs on this repo because their push already triggered CI
+    if: github.event_name == 'push' || github.event.pull_request.head.repo.full_name != github.repository
+    permissions:
+      contents: write   # for gh-pages docs deploy
+      id-token: write   # for Codecov OIDC
+    uses: biocommons/.github/.github/workflows/python-ci-cd.yml@main
+    with:
+      # tagged commits (tags) trigger publishing to PyPI and docs
+      publish: ${{ github.event_name == 'push' && startsWith(github.ref, 'refs/tags/') }}
+    secrets:
+      # org-level token; PyPI trusted publishing doesn't support reusable
+      # workflows yet: https://github.com/pypi/warehouse/issues/11096
+      pypi-token: ${{ secrets.UV_PUBLISH_TOKEN }}

biocommons_python_package-0.0.8/.github/workflows/stale.yml

@@ -0,0 +1,14 @@
+name: 'Close stale issues and PRs'
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '1 1 * * *'
+
+permissions:
+  contents: read
+  issues: write
+  pull-requests: write
+
+jobs:
+  stale:
+    uses: biocommons/.github/.github/workflows/stale.yml@main

biocommons_python_package-0.0.8/.github/workflows/validate-codecov-config.yml

@@ -0,0 +1,17 @@
+name: Validate Codecov Config
+
+on:
+  pull_request:
+    paths: [codecov.yaml]
+  push:
+    branches: [main]
+
+jobs:
+  validate-codecov-config:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+    steps:
+      - uses: actions/checkout@v7
+      - name: Validate codecov configuration
+        run: curl -sSL --fail-with-body --data-binary @codecov.yaml https://codecov.io/validate

biocommons_python_package-0.0.8/.gitignore

@@ -0,0 +1,116 @@
+*$py.class
+*.bak
+*.cover
+*.egg
+*.egg-info
+*.egg-info/
+*.enc
+*.log
+*.manifest
+*.mo
+*.orig
+*.pot
+*.py.cover
+*.py[codz]
+*.rej
+*.sage.py
+*.so
+*.spec
+*.sqlite3
+*.sqlite3-journal
+*~
+.DS_Store
+.Python
+.abstra/
+.cache
+.claude/
+.coverage
+.coverage.*
+.cursorignore
+.cursorindexingignore
+.dmypy.json
+.eggs/
+.env
+.envrc
+.hypothesis/
+.idea
+.installed.cfg
+.ipynb_checkpoints
+.keys
+.mypy_cache/
+.nox/
+.pdm-build/
+.pdm-python
+.pixi
+.pybuilder/
+.pypirc
+.pyre/
+.pytest_cache
+.pytest_cache/
+.python-version
+.pytype/
+.ropeproject
+.ruff_cache/
+.scrapy
+.spyderproject
+.spyproject
+.tags
+.tags.mk
+.tox/
+.venv
+.vscode
+.webassets-cache
+/site
+ENV/
+MANIFEST
+__marimo__/
+__pycache__/
+__pypackages__/
+archive
+bdist
+bioutils/_data/assemblies/pull
+build
+build/
+celerybeat-schedule
+celerybeat.pid
+cover/
+coverage.xml
+cython_debug/
+develop-eggs/
+dist/
+dmypy.json
+doc*/changelog/*/.tags
+doc*/changelog/*/.tags.mk
+doc/_build
+doc/build
+doc/changelog/*/.tags
+doc/changelog/*/.tags.mk
+doc/changelog/*/hg-git-remap.pl
+docs/_build/
+docs/source
+downloads/
+eggs/
+env.bak/
+env/
+htmlcov/
+instance/
+ipython_config.py
+lib/
+lib64/
+local_settings.py
+marimo/_lsp/
+marimo/_static/
+misc
+nosetests.xml
+parts/
+pip-delete-this-directory.txt
+pip-log.txt
+profile_default/
+sdist/
+share/python-wheels/
+target/
+tmp/
+var/
+venv.bak/
+venv/
+wheels/

biocommons_python_package-0.0.8/.mailmap

@@ -0,0 +1,13 @@
+# This file is used by Git to consolidate the users who used multiple accounts
+# I pick the account with the most modified files in git shortlog -sne
+Andreas Prlic <andreas.prlic@invitae.com> Andreas Prlic <36012160+andreas-invitae@users.noreply.github.com>
+Andreas Prlic <andreas.prlic@invitae.com> Andreas Prlic <andreas.prlic@gmail.com>
+Caitlin Gong <ccaitlingo@gmail.com> Caitlin Gong <clgong@vassar.edu>
+Katie Stahl <kathryn.stahl@nationwidechildrens.org> katie stahl <kathryn.stahl@nationwidechildrens.org>
+Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de> Manuel Holtgrewe <manuel.holtgrewe@bihealth.de>
+Meng <wangm0855@gmail.com> Meng Wang <wangm0855@gmail.com>
+Reece Hart <reecehart@gmail.com> Reece Hart <reece@biocmmons.org>
+Reece Hart <reecehart@gmail.com> Reece Hart <reece@biocommons.org>
+Reece Hart <reecehart@gmail.com> Reece Hart <reecehart@Reeces-MacBook-Pro.local>
+Reece Hart <reecehart@gmail.com> Reece Hart <reece@ip-192-168-0-13.us-west-2.compute.internal>
+Rudy Rico <rudy.rico@invitae.com> Rudolph Rico <rudy.rico@invitae.com>

biocommons_python_package-0.0.8/.pre-commit-config.yaml

@@ -0,0 +1,45 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: check-added-large-files
+        args: ["--maxkb=1500"]
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-json
+        exclude: ^.devcontainer/.*devcontainer.json
+      - id: check-shebang-scripts-are-executable
+      - id: check-symlinks
+      - id: check-toml
+      - id: check-yaml
+      - id: detect-aws-credentials
+        args: [ --allow-missing-credentials ]
+      - id: detect-private-key
+      - id: end-of-file-fixer
+      - id: fix-byte-order-marker
+      - id: mixed-line-ending
+        args: [--fix=lf]
+      - id: pretty-format-json
+        exclude: ^.devcontainer/.*devcontainer.json
+        args: [--autofix, --no-sort-keys]
+      - id: trailing-whitespace
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.17.0
+    hooks:
+      - id: ruff-check
+        args: [--fix, --exit-non-zero-on-fix]
+      - id: ruff-format
+
+  - repo: https://github.com/rhysd/actionlint
+    rev: v1.7.12
+    hooks:
+      - id: actionlint
+
+  - repo: local
+    hooks:
+      - id: canonicalize-gitignore
+        name: Sort unique .gitignore
+        entry: sh -c 'LC_ALL=C sort -u -o .gitignore .gitignore'
+        language: system
+        files: ^\.gitignore$

biocommons_python_package-0.0.8/CONTRIBUTING.md

@@ -0,0 +1,9 @@
+# CONTRIBUTING
+
+Thank you for your interest in contributing to the biocommons community!
+Contributions are welcome and greatly appreciated. There are many types of
+contributions and you don't need to be a developer!
+
+See https://biocommons.org/ for information about projects, how to connect with
+the community, and contribution guidelines.  We look forward to hearing from
+you!

biocommons_python_package-0.0.8/Dockerfile

@@ -0,0 +1,21 @@
+# Install uv
+FROM python:3.12-slim
+COPY --from=ghcr.io/astral-sh/uv:latest /uv /bin/uv
+
+# Change the working directory to the `app` directory
+WORKDIR /app
+
+# Copy the lockfile and `pyproject.toml` into the image
+COPY uv.lock /app/uv.lock
+COPY pyproject.toml /app/pyproject.toml
+
+# Install dependencies
+RUN uv sync --frozen --no-install-project
+
+# Copy the project into the image
+COPY . /app
+
+# Sync the project
+RUN uv sync --frozen
+
+CMD [ "python", "python_package/foo.py" ]

biocommons_python_package-0.0.8/LICENSE.txt

@@ -0,0 +1,201 @@
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
+      copyright notice that is included in or attached to the work
+      (an example is provided in the Appendix below).
+
+      "Derivative Works" shall mean any work, whether in Source or Object
+      form, that is based on (or derived from) the Work and for which the
+      editorial revisions, annotations, elaborations, or other modifications
+      represent, as a whole, an original work of authorship. For the purposes
+      of this License, Derivative Works shall not include works that remain
+      separable from, or merely link (or bind by name) to the interfaces of,
+      the Work and Derivative Works thereof.
+
+      "Contribution" shall mean any work of authorship, including
+      the original version of the Work and any modifications or additions
+      to that Work or Derivative Works thereof, that is intentionally
+      submitted to Licensor for inclusion in the Work by the copyright owner
+      or by an individual or Legal Entity authorized to submit on behalf of
+      the copyright owner. For the purposes of this definition, "submitted"
+      means any form of electronic, verbal, or written communication sent
+      to the Licensor or its representatives, including but not limited to
+      communication on electronic mailing lists, source code control systems,
+      and issue tracking systems that are managed by, or on behalf of, the
+      Licensor for the purpose of discussing and improving the Work, but
+      excluding communication that is conspicuously marked or otherwise
+      designated in writing by the copyright owner as "Not a Contribution."
+
+      "Contributor" shall mean Licensor and any individual or Legal Entity
+      on behalf of whom a Contribution has been received by Licensor and
+      subsequently incorporated within the Work.
+
+   2. Grant of Copyright License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      copyright license to reproduce, prepare Derivative Works of,
+      publicly display, publicly perform, sublicense, and distribute the
+      Work and such Derivative Works in Source or Object form.
+
+   3. Grant of Patent License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      (except as stated in this section) patent license to make, have made,
+      use, offer to sell, sell, import, and otherwise transfer the Work,
+      where such license applies only to those patent claims licensable
+      by such Contributor that are necessarily infringed by their
+      Contribution(s) alone or by combination of their Contribution(s)
+      with the Work to which such Contribution(s) was submitted. If You
+      institute patent litigation against any entity (including a
+      cross-claim or counterclaim in a lawsuit) alleging that the Work
+      or a Contribution incorporated within the Work constitutes direct
+      or contributory patent infringement, then any patent licenses
+      granted to You under this License for that Work shall terminate
+      as of the date such litigation is filed.
+
+   4. Redistribution. You may reproduce and distribute copies of the
+      Work or Derivative Works thereof in any medium, with or without
+      modifications, and in Source or Object form, provided that You
+      meet the following conditions:
+
+      (a) You must give any other recipients of the Work or
+          Derivative Works a copy of this License; and
+
+      (b) You must cause any modified files to carry prominent notices
+          stating that You changed the files; and
+
+      (c) You must retain, in the Source form of any Derivative Works
+          that You distribute, all copyright, patent, trademark, and
+          attribution notices from the Source form of the Work,
+          excluding those notices that do not pertain to any part of
+          the Derivative Works; and
+
+      (d) If the Work includes a "NOTICE" text file as part of its
+          distribution, then any Derivative Works that You distribute must
+          include a readable copy of the attribution notices contained
+          within such NOTICE file, excluding those notices that do not
+          pertain to any part of the Derivative Works, in at least one
+          of the following places: within a NOTICE text file distributed
+          as part of the Derivative Works; within the Source form or
+          documentation, if provided along with the Derivative Works; or,
+          within a display generated by the Derivative Works, if and
+          wherever such third-party notices normally appear. The contents
+          of the NOTICE file are for informational purposes only and
+          do not modify the License. You may add Your own attribution
+          notices within Derivative Works that You distribute, alongside
+          or as an addendum to the NOTICE text from the Work, provided
+          that such additional attribution notices cannot be construed
+          as modifying the License.
+
+      You may add Your own copyright statement to Your modifications and
+      may provide additional or different license terms and conditions
+      for use, reproduction, or distribution of Your modifications, or
+      for any such Derivative Works as a whole, provided Your use,
+      reproduction, and distribution of the Work otherwise complies with
+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+      implied, including, without limitation, any warranties or conditions
+      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "{}"
+      replaced with your own identifying information. (Don't include
+      the brackets!)  The text should be enclosed in the appropriate
+      comment syntax for the file format. We also recommend that a
+      file or class name and description of purpose be included on the
+      same "printed page" as the copyright notice for easier
+      identification within third-party archives.
+
+   Copyright 2025 Contributors
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.