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Merge PR #370 (Add "Lint" GitHub action and fixed security issues)
This merge brings PR #370 (Add "Lint" GitHub actions and fixed security issues in other actions, by @yantosca) into the GCPy development stream. In PR #370 we have done the following: 1. Added the "lint-ci-workflows` GitHub action 2. Fixed various security issues in GitHub actions 3. Updated badges in README.md and docs/source/index.rst to show the results of GitHub actions. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
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‎.github/workflows/build-gcpy-environment-py312.yml‎

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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
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python-version: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.14"]
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steps:
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- name: Checkout the GCPy repository
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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persist-credentials: false
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- name: Create "gcpy_env" environment
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uses: mamba-org/setup-micromamba@v1
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with:
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cache-environment: false
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generate-run-shell: true
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post-cleanup: 'all'
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- name: Test if "import gcpy" works
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run: python -c "import gcpy"
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shell: micromamba-shell {0}
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- name: Test if we can create a plot
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run: python -m gcpy.examples.plotting.create_test_plot
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shell: micromamba-shell {0}

‎.github/workflows/build-gcpy-environment-py313.yml‎

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---
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#
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# GitHub action to build the GCPy production environment
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# (for Python 3.12) with micromamba
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# (for Python 3.13) with micromamba
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# See: https://github.com/marketplace/actions/setup-micromamba
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#
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name: build-gcpy-environment-py313
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
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python-version: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.14"]
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steps:
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- name: Checkout the GCPy repository
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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persist-credentials: false
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- name: Create "gcpy_env" environment
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uses: mamba-org/setup-micromamba@v1
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with:
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cache-environment: false
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generate-run-shell: true
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post-cleanup: 'all'
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- name: Test if "import gcpy" works
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run: python -c "import gcpy"
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shell: micromamba-shell {0}
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- name: Test if we can create a plot
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run: python -m gcpy.examples.plotting.create_test_plot
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shell: micromamba-shell {0}

‎.github/workflows/build-rtd-environment.yml‎

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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
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python-version: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.14"]
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steps:
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- name: Checkout the GCPy repository
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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persist-credentials: false
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- name: Create "rtd_env" environment
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uses: mamba-org/setup-micromamba@v1
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with:
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cache-environment: false
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generate-run-shell: true
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post-cleanup: 'all'
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- name: Get version numbers of packages
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run: |
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python --version

‎.github/workflows/codeql.yml‎

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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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persist-credentials: false
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# Initializes the CodeQL tools for scanning.
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- name: Initialize CodeQL

‎.github/workflows/lint-ci-workflows.yml‎

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# Workflow to run linting checks on source
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name: Lint
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# Controls when the workflow will run
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on:
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# Triggers the workflow on pushes to the "main", "dev", or "dev/** branches,
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# i.e., PR merges
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push:
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branches: [ "main", "dev", "dev/**" ]
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# Triggers the workflow on pushes to open pull requests with code changes
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pull_request:
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paths:
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- '.github/workflows/*.yml'
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# Allows you to run this workflow manually from the Actions tab
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# (usually leave it blank)
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workflow_dispatch:
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# Allow the jobs to read the secret GitHub token
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permissions:
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contents: read
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# Cancel jobs running if new commits are pushed
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concurrency:
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group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
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cancel-in-progress: true
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# Workflow run - one or more jobs that can run sequentially or in parallel
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jobs:
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# This workflow contains a single job called "lint"
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lint:
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# The type of runner that the job will run on
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runs-on: ubuntu-latest
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# Don't quit the Action at the first
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strategy:
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fail-fast: false
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# GitHub secret token
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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# Steps represent a sequence of tasks that will be
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# executed as part of the job
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steps:
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# Checks-out your repository under $GITHUB_WORKSPACE,
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# so your job can access it
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- name: Checkout code
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with:
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persist-credentials: false
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uses: actions/checkout@v4
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# Installs Python 3.x
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- name: Install Python
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uses: actions/setup-python@v5
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with:
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python-version: '3.x'
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# Installs Python packages
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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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python -m venv ci_venv
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. ci_venv/bin/activate
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pip install zizmor==0.9.2
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# Apply GitHub Actions linter, zizmor
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- name: zizmor
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if: always()
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run: |
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cd ${{ github.workspace }}
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. ci_venv/bin/activate
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zizmor .github/workflows/*.yml

‎.github/workflows/publish-python.yml‎

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# This workflow will upload a Python Package using Twine when a release is created
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# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
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# This workflow will upload a Python Package using Twine when a
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# release is created. For more information see:
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# https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
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# This workflow uses actions that are not certified by GitHub.
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# They are provided by a third-party and are governed by
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# separate terms of service, privacy policy, and support
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# documentation.
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name: Upload GCPy to PyPI
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name: Publish GCPy to PyPI as geoschem-gcpy
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on:
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release:
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types: [published]
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permissions:
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contents: read
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deploy:
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permissions:
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id-token: write
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contents: read
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steps:
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- uses: actions/checkout@v4
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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.x'
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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 build
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- name: Build package
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run: python -m build
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- name: Publish package
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uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
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with:
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user: __token__
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password: ${{ secrets.PYPI_KEY }}
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- name: Checkout GCPy code
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uses: actions/checkout@v4
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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.x'
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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 build
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- name: Build GCPy
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run: python -m build
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# NOTE: We have defined https://github.com/geoschem/gcpy
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# as a Trusted Publisher for geoschem-gcpy at PyPI.org
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- name: Publish geoschem-gcpy
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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skip-existing: true

‎CHANGELOG.md‎

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### Added
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- Added `gcpy/profile/vtune_plot_hotspots.py` to plot a bargraph of hotspots from Intel VTune reports
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- Added ReadTheDocs documentation for plotting hotspots from Intel VTune reports
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- Added "Lint" GitHub Action to check other actions for security issues
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- Added `gcpy_environment_py314.ym1` to specify the GCPy environment packages with Python 3.14
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- Added GitHub action `build-gcpy-environment-py314.yml` to test building the GCPy environment with Python 3.14
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### Changed
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- Modified criteria for terminating read of log files in `benchmark_scrape_gcclassic_timers.py` to avoid being spoofed by output that is attached by Intel VTune
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- Moved `gprofng_text_to_data_units` to function `text_to_data_units` in `gcpy/plot/core.py` so that it can be used by `gprofng_functions` and `vtune_plot_hotspots`
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- Updated GitHub badges in `README.md` and `docs/source/index.rst`
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### Fixed
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- Fix grid area calculation scripts of `grid_area` in `gcpy/gcpy/cstools.py`
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- Fixed various security issues in GitHub Actions workflows
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## [1.6.2] - 2025-06-12
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### Added

‎README.md‎

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# GCPy: Python toolkit for GEOS-Chem
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<p>
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<a href="https://github.com/geoschem/gcpy/releases"><img src="https://img.shields.io/github/v/release/geoschem/gcpy?label=Latest%20Stable%20Release"></a>
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<a href="https://anaconda.org/conda-forge/geoschem-gcpy"> <img src="https://anaconda.org/conda-forge/geoschem-gcpy/badges/version.svg" /> </a>
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<a href="https://img.shields.io/pypi/v/geoschem-gcpy"><img alt="PyPI - Version" src="https://img.shields.io/pypi/v/geoschem-gcpy"></a>
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<a href="https://github.com/geoschem/gcpy/releases/"><img src="https://img.shields.io/github/release-date/geoschem/gcpy"></a>
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<a href="https://github.com/geoschem/gcpy/releases"><img src="https://img.shields.io/github/v/release/geoschem/gcpy?label=Latest%20Stable%20Release" alt="Latest release" /></a>
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<a href="https://anaconda.org/conda-forge/geoschem-gcpy"> <img src="https://anaconda.org/conda-forge/geoschem-gcpy/badges/version.svg" alt="Anaconda version" /> </a>
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<a href="https://img.shields.io/pypi/v/geoschem-gcpy"><img src="https://img.shields.io/pypi/v/geoschem-gcpy" alt="PyPI version" /></a>
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<a href="https://github.com/geoschem/gcpy/releases/"><img src="https://img.shields.io/github/release-date/geoschem/gcpy" alt="Release date" /></a>
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<a href="https://anaconda.org/conda-forge/geoschem-gcpy"> <img src="https://anaconda.org/conda-forge/geoschem-gcpy/badges/platforms.svg" alt="Platforms" /> </a>
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<br />
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<a href="https://anaconda.org/conda-forge/geoschem-gcpy"> <img src="https://anaconda.org/conda-forge/geoschem-gcpy/badges/platforms.svg" /> </a>
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<a href="https://doi.org/10.5281/zenodo.3689589"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.3689589.svg" alt="DOI"></a>
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<a href="https://github.com/geoschem/gcpy/blob/main/LICENSE.txt"><img src="https://img.shields.io/badge/License-MIT-blue.svg"></a>
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<a href="https://doi.org/10.5281/zenodo.3689589"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.3689589.svg" alt="DOI" /></a>
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<a href="https://github.com/geoschem/gcpy/blob/main/LICENSE.txt"><img src="https://img.shields.io/badge/License-MIT-blue.svg" alt="License" /></a>
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<a href="https://gcpy.readthedocs.io/en/latest/"><img src="https://img.shields.io/readthedocs/gcpy?label=ReadTheDocs" alt="ReadTheDocs" /></a>
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<a href="https://github.com/geoschem/gcpy/actions/workflows/build-gcpy-environment-py312.yml"><img src="https://github.com/geoschem/gcpy/actions/workflows/build-gcpy-environment-py312.yml/badge.svg" alt="build-gcpy-environment-py312" /></a>
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<br />
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<a href="https://gcpy.readthedocs.io/en/latest/"><img src="https://img.shields.io/readthedocs/gcpy?label=ReadTheDocs"></a>
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<a href="https://github.com/geoschem/gcpy/actions/workflows/build-gcpy-environment.yml"><img src="https://github.com/geoschem/gcpy/actions/workflows/build-gcpy-environment.yml/badge.svg"></a>
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<a href="https://anaconda.org/conda-forge/geoschem-gcpy"> <img src="https://anaconda.org/conda-forge/geoschem-gcpy/badges/downloads.svg" /> </a>
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<a href="https://github.com/geoschem/gcpy/actions/workflows/build-gcpy-environment-py313.yml"><img src="https://github.com/geoschem/gcpy/actions/workflows/build-gcpy-environment-py313.yml/badge.svg" alt="build-gcpy-environment-py313" /></a>
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<a href="https://github.com/geoschem/gcpy/actions/workflows/build-rtd-environment.yml"><img src="https://github.com/geoschem/gcpy/actions/workflows/build-rtd-environment.yml/badge.svg" alt="build-rtd-environment /></a>
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<a href="https://anaconda.org/conda-forge/geoschem-gcpy"><img src="https://anaconda.org/conda-forge/geoschem-gcpy/badges/downloads.svg" alt="Downloads" /> </a>
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**GCPy** is a Python-based toolkit containing useful functions for working specifically with the GEOS-Chem model of atmospheric chemistry and composition.

‎docs/environment_files/gcpy_environment_py313.yml‎

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# for GCPy, use this command:
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#
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# $ mamba env create -n gcpy_env --file=/path/to/gcpy/environment.yml
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#
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# NOTE: This combination of packages may produce a warning
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#
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# VersionWarning: ESMF installation version 8.8.0, ESMPy version 8.8.0b0
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#
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# that you can disable by adding this to your ~/.bashrc
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#
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# export PYTHONWARNINGS="ignore"
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# =====================================================================
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name: gcpy_env
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channels:

‎docs/source/index.rst‎

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.. raw:: html
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<p>
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<a href="https://github.com/geoschem/gcpy/releases"><img src="https://img.shields.io/github/v/release/geoschem/gcpy?label=Latest%20Stable%20Release"></a>
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<a href="https://anaconda.org/conda-forge/geoschem-gcpy"> <img src="https://anaconda.org/conda-forge/geoschem-gcpy/badges/version.svg" /> </a>
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<a href="https://img.shields.io/pypi/v/geoschem-gcpy"><img alt="PyPI - Version" src="https://img.shields.io/pypi/v/geoschem-gcpy"></a>
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<a href="https://github.com/geoschem/gcpy/releases/"><img src="https://img.shields.io/github/release-date/geoschem/gcpy"></a>
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<br />
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<a href="https://anaconda.org/conda-forge/geoschem-gcpy"> <img src="https://anaconda.org/conda-forge/geoschem-gcpy/badges/platforms.svg" /> </a>
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<a href="https://doi.org/10.5281/zenodo.3689589"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.3689589.svg" alt="DOI"></a>
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<a href="https://github.com/geoschem/gcpy/blob/main/LICENSE.txt"><img src="https://img.shields.io/badge/License-MIT-blue.svg"></a>
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<br />
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<a href="https://gcpy.readthedocs.io/en/latest/"><img src="https://img.shields.io/readthedocs/gcpy?label=ReadTheDocs"></a>
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<a href="https://github.com/geoschem/gcpy/actions/workflows/build-gcpy-environment.yml"><img src="https://github.com/geoschem/gcpy/actions/workflows/build-gcpy-environment.yml/badge.svg"></a>
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<a href="https://anaconda.org/conda-forge/geoschem-gcpy"> <img src="https://anaconda.org/conda-forge/geoschem-gcpy/badges/downloads.svg" /> </a>
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<a href="https://github.com/geoschem/gcpy/releases"><img src="https://img.shields.io/github/v/release/geoschem/gcpy?label=Latest%20Stable%20Release" alt="Latest release" /></a>
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<a href="https://anaconda.org/conda-forge/geoschem-gcpy"> <img src="https://anaconda.org/conda-forge/geoschem-gcpy/badges/version.svg" alt="Anaconda version" /> </a>
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<a href="https://img.shields.io/pypi/v/geoschem-gcpy"><img src="https://img.shields.io/pypi/v/geoschem-gcpy" alt="PyPI version" /></a>
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<a href="https://github.com/geoschem/gcpy/releases/"><img src="https://img.shields.io/github/release-date/geoschem/gcpy" alt="Release date" /></a>
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<a href="https://anaconda.org/conda-forge/geoschem-gcpy"> <img src="https://anaconda.org/conda-forge/geoschem-gcpy/badges/platforms.svg" alt="Platforms" /> </a>
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<br />
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<a href="https://doi.org/10.5281/zenodo.3689589"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.3689589.svg" alt="DOI" /></a>
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<a href="https://github.com/geoschem/gcpy/blob/main/LICENSE.txt"><img src="https://img.shields.io/badge/License-MIT-blue.svg" alt="License" /></a>
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<a href="https://gcpy.readthedocs.io/en/latest/"><img src="https://img.shields.io/readthedocs/gcpy?label=ReadTheDocs" alt="ReadTheDocs" /></a>
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<a href="https://github.com/geoschem/gcpy/actions/workflows/build-gcpy-environment-py312.yml"><img src="https://github.com/geoschem/gcpy/actions/workflows/build-gcpy-environment-py312.yml/badge.svg" alt="build-gcpy-environment-py312" /></a>
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<br />
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<a href="https://github.com/geoschem/gcpy/actions/workflows/build-gcpy-environment-py313.yml"><img src="https://github.com/geoschem/gcpy/actions/workflows/build-gcpy-environment-py313.yml/badge.svg" alt="build-gcpy-environment-py313" /></a>
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<a href="https://github.com/geoschem/gcpy/actions/workflows/build-rtd-environment.yml"><img src="https://github.com/geoschem/gcpy/actions/workflows/build-rtd-environment.yml/badge.svg" alt="build-rtd-environment /></a>
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<a href="https://anaconda.org/conda-forge/geoschem-gcpy"><img src="https://anaconda.org/conda-forge/geoschem-gcpy/badges/downloads.svg" alt="Downloads" /> </a>
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</p>
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Welcome to the GCPy ReadTheDocs documentation! This site provides documentation

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