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Remove conda (#294)
* Update README.md * Remove setup.py and setup.cfg * Add configuration files for pdm * Update .gitignore * Add requirements files * Update installation instructions to remove conda * Update README.md * Rename cleanup workflow for clarity * Update installation instructions in CONTRIBUTING.md * Refactor tox.ini: Update env_list and groups * Add PDM and Dependencies actions Update build-docs workflow Add cache-dependencies workflow Update cleanup-firebase workflow Update ci workflow Update analyze workflow Update analyze workflow * Update pyproject.toml dependencies and add pdm lock file * Update requirements files * Update dependency installation script * Activate environment after installing dependencies * Run workflows through pdm * Remove venv activation specific to linux * Update cml setup version * Update black version * Formatting changes * * Add command "clean" to pyproject.toml * Update makefile to move cleanup * Specify base python in tox.ini * Refactor tox.ini to add 'test' and 'lint' groups * Add Flake8 configuration to pyproject.toml for linting * Update dependencies and migrate from tox.ini to pyproject.toml * Update version bump command in CONTRIBUTING.md to use bumpver * bump version 1.0.8 -> 1.1.0 * Update flake8 ignore rules in CI workflow * bump version 1.1.0 -> 1.1.1 * Update docutils version and adjust Python requirements in lock files * Update version format to include 'v' prefix in __init__.py and pyproject.toml * Bump version to v1.1.1 This version includes performance improvements, bug fixes, and installation updates
1 parent ecb33a2 commit 22053fb

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-294
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‎.github/actions/dependencies/action.yml

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name: PDM & Dependencies
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description: Install PDM and dependencies
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runs:
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using: composite
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steps:
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- uses: ./.github/actions/pdm
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- name: Install dependencies
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shell: bash
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# --only-keep flag in case the environment is restored from a stale cache.
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run: |
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pdm sync -d --only-keep

‎.github/actions/pdm/action.yml

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name: PDM
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description: Install PDM
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runs:
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using: composite
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steps:
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- name: Set up PDM
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uses: pdm-project/setup-pdm@v4
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with:
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python-version: "3.9"
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# Cache all dependencies installed from pdm.lock
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cache: true

‎.github/workflows/analyze.yml

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os: [ubuntu-latest]
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steps:
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- uses: actions/[email protected]
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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cache: "pip"
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cache-dependency-path: setup.py
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- name: Install Dependencies
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run: |
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python -m pip install --upgrade pip
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pip install .[all]
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- uses: ./.github/actions/dependencies
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- name: Pack test recipe
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run: |
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pack -r cellpack/tests/recipes/v2/test_spheres.json -c cellpack/tests/packing-configs/test_config.json
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pdm run pack -r cellpack/tests/recipes/v2/test_spheres.json -c cellpack/tests/packing-configs/test_config.json
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- name: Modify JSON with PR sub_directory path
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run: |
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jq --arg branch_name "${{ github.ref_name }}" '.create_report.output_image_location |= "https://cellpack-results.s3.us-west-2.amazonaws.com/\($branch_name)/spheresSST/figures"' cellpack/tests/analysis-configs/PR_analysis_config.json > cellpack/tests/analysis-configs/PR_analysis_config_temp.json
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mv cellpack/tests/analysis-configs/PR_analysis_config_temp.json cellpack/tests/analysis-configs/PR_analysis_config.json
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- name: Run analysis code
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run: analyze -r cellpack/tests/recipes/v2/test_spheres.json -a cellpack/tests/analysis-configs/PR_analysis_config.json -p cellpack/tests/outputs/test_spheres/spheresSST
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run: pdm run analyze -r cellpack/tests/recipes/v2/test_spheres.json -a cellpack/tests/analysis-configs/PR_analysis_config.json -p cellpack/tests/outputs/test_spheres/spheresSST
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- name: Upload results
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uses: actions/upload-artifact@v3
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uses: actions/upload-artifact@v4
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with:
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name: results
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path: cellpack/tests/outputs/test_spheres/
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aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
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aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
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aws-region: us-west-2
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- uses: actions/download-artifact@v3
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- uses: actions/download-artifact@v4
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- name: Copy files to results bucket
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run: aws s3 cp ./results s3://cellpack-results/${{ github.ref_name }}/ --recursive --acl public-read
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- uses: iterative/setup-cml@v1
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- uses: iterative/setup-cml@v2
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- name: Update comment for dependabot
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if: ${{ github.actor == 'dependabot[bot]' }}
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env:

‎.github/workflows/build-docs.yml

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- uses: actions/[email protected]
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with:
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persist-credentials: false
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: 3.9
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cache: "pip"
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cache-dependency-path: setup.py
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- name: Install Dependencies
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run: |
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pip install --upgrade pip
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pip install .[dev]
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- uses: ./.github/actions/dependencies
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- name: Generate Docs
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run: |
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make gen-docs

‎.github/workflows/cache-dependencies.yml

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# The purpose of this workflow is to get more cache hits when other workflows build dependencies.
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# Github actions do not share caches between branches, except that all branches can pull results
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# from the default (main) branch. Therefore, this workflow runs on the main branch to keep the
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# latest dependencies cached for other branches to use.
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# Branches that change the dependencies will still get cache misses.
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name: Build and cache dependencies on main
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on:
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push:
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branches:
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- main
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jobs:
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dependencies:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: ./.github/actions/dependencies

‎.github/workflows/ci.yml

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steps:
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- uses: actions/[email protected]
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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cache: "pip"
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cache-dependency-path: setup.py
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- name: Install Dependencies
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run: |
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python -m pip install --upgrade pip
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pip install .[all]
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- uses: ./.github/actions/dependencies
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- name: Test with pytest
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run: |
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pytest --cov cellpack/tests/
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pdm run pytest --cov cellpack/tests/
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- name: Upload codecov
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uses: codecov/codecov-action@v4
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if: ${{ !contains(github.event.head_commit.message, 'Bump version') }}
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steps:
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- uses: actions/[email protected]
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: 3.9
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cache: "pip"
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cache-dependency-path: setup.py
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- name: Install Dependencies
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run: |
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python -m pip install --upgrade pip
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pip install .[test]
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- uses: ./.github/actions/dependencies
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- name: Lint with flake8
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run: |
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flake8 cellpack --count --verbose --show-source --statistics --ignore=E501,E277,W503,E203
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pdm run flake8 cellpack --count --verbose --show-source --statistics --ignore=E203,E277,E402,E501,E721,W291,W503
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- name: Check with black
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run: |
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black --check cellpack
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pdm run black --check cellpack
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publish:
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if: success() && startsWith(github.ref, 'refs/tags/')
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steps:
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- uses: actions/[email protected]
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: 3.9
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cache: "pip"
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cache-dependency-path: setup.py
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- name: Install Dependencies
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run: |
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python -m pip install --upgrade pip
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pip install setuptools wheel
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- name: Build Package
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run: |
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python setup.py sdist bdist_wheel
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- uses: ./.github/actions/dependencies
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- name: Publish to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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run: pdm publish
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‎.github/workflows/cleanup.yml renamed to ‎.github/workflows/cleanup-aws.yml

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name: cleanup
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name: Cleanup AWS S3 Bucket
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on:
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pull_request:

‎.github/workflows/cleanup-firebase.yml

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os: [ubuntu-latest, windows-latest, macOS-latest]
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steps:
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- uses: actions/[email protected]
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install .[all]
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- uses: ./.github/actions/dependencies
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- name: Cleanup Firebase Metadata
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env:
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FIREBASE_TOKEN: ${{ secrets.FIREBASE_TOKEN }}
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FIREBASE_EMAIL: ${{ secrets.FIREBASE_EMAIL }}
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run: |
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python cellpack/bin/cleanup_tasks.py
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pdm run python cellpack/bin/cleanup_tasks.py

‎.github/workflows/make-requirements.yml

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name: Make requirements files
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on:
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workflow_dispatch:
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push:
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branches:
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- main
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paths:
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- "pdm.lock"
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jobs:
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make-requirements:
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: [ubuntu-latest, macOS-latest, windows-latest]
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steps:
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- uses: actions/checkout@v4
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- uses: ./.github/actions/pdm
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- name: Generate requirements.txt
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shell: bash
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run: |
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case "${{ matrix.os }}" in
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"ubuntu-latest")
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export PLATFORM="linux"
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;;
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"macOS-latest")
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export PLATFORM="macos"
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;;
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"windows-latest")
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export PLATFORM="windows"
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;;
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esac
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rm -rf requirements/*
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mkdir -p requirements/$PLATFORM
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pdm requirements requirements/$PLATFORM/requirements.txt
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- name: Get platform variable
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id: platform
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shell: bash
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run: |
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case "${{ matrix.os }}" in
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"ubuntu-latest")
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echo "::set-output name=platform::linux"
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;;
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"macOS-latest")
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echo "::set-output name=platform::macos"
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;;
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"windows-latest")
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echo "::set-output name=platform::windows"
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;;
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esac
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- name: Upload requirements files
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uses: actions/upload-artifact@v4
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with:
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name: ${{ steps.platform.outputs.platform }}-requirements
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path: requirements/${{ steps.platform.outputs.platform }}
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open-PR:
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needs: [make-requirements]
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Download linux requirements files
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uses: actions/download-artifact@v4
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with:
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name: linux-requirements
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path: requirements/linux
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- name: Download windows requirements files
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uses: actions/download-artifact@v4
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with:
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name: windows-requirements
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path: requirements/windows
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- name: Download macOS requirements files
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uses: actions/download-artifact@v4
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with:
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name: macos-requirements
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path: requirements/macos
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- name: Clean-up CRLF
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shell: bash
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run: find requirements -type f -exec sed -i 's/\r//g' {} \;
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- name: Get timestamp
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id: timestamp
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run: echo "::set-output name=timestamp::$(date +'%Y-%m-%d_%H-%M')"
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- name: Create Pull Request
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uses: peter-evans/create-pull-request@v5
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with:
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base: main
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title: admin/requirements-update_${{ steps.timestamp.outputs.timestamp }}
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body: Updating requirements.txt.
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Due to some [challenges](https://github.com/peter-evans/create-pull-request/blob/main/docs/concepts-guidelines.md#triggering-further-workflow-runs),
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with getting this PR to trigger the tests, please manually close and re-open this PR.
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branch: admin/requirements-update_${{ steps.timestamp.outputs.timestamp }}
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commit-message: Updating requirements.txt after change to `pdm.lock` was pushed to `main`
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delete-branch: true

‎.gitignore

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.ipynb_checkpoints
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*.ipynb
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# pyenv
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.python-version
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# celery beat schedule file
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celerybeat-schedule
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**/converted/*
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# credentials
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.creds
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.creds
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# pdm files
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.pdm-python

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