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eleanorfrajkaCopilot
eleanorfrajka
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[CLEANUP] Update workflows and environment (#69)
* Cleanup - update workflows and environment * Update readme and coding conventions docs * Linting * Update README.md Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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‎.claude/settings.local.json‎

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{
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"permissions": {
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"allow": [
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"Bash(find:*)"
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],
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"deny": [],
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"ask": []
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}
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}

‎.github/PULL_REQUEST_TEMPLATE.md‎

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**Checklist:**
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- [ ] I have followed the [coding conventions](https://amoccommunity.github.io/amocarray/conventions.html).
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- [ ] I have followed the [coding conventions](docs/source/conventions.md).
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- [ ] I have updated or added tests to cover my changes.
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- [ ] I have updated the documentation if needed.
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- [ ] I have run `pytest` to check that all tests pass.

‎.github/workflows/docs.yml‎

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- '**.py'
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- '**.ipynb'
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- '**.rst'
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- '**.md'
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jobs:
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build-docs:
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runs-on: ubuntu-latest
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permissions:
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contents: write
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contents: read
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steps:
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- name: checkout
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Checkout
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Setup Micromamba ${{ matrix.python-version }}
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uses: mamba-org/setup-micromamba@v2.0.1
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with:
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environment-name: TEST
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init-shell: bash
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create-args: >-
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python=3 pip
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--file requirements-dev.txt
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--channel conda-forge
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- name: Setup Micromamba
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uses: mamba-org/setup-micromamba@v2
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with:
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environment-file: environment.yml
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init-shell: bash
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condarc: |
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channels:
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- conda-forge
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channel_priority: strict
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cache-environment: true
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- name: Install seagliderOG1
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shell: bash -l {0}
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run: |
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python -m pip install -e . --no-deps --force-reinstall
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- name: Install package (editable)
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shell: bash -l {0}
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run: |
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micromamba run -n TEST python -m pip install --upgrade pip
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micromamba run -n TEST python -m pip install -e . --no-deps --force-reinstall
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- name: Build documentation
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shell: bash -l {0}
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run: |
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set -e
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jupyter nbconvert --to notebook --execute notebooks/demo.ipynb --output=demo-output.ipynb --ExecutePreprocessor.allow_errors=True
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mv notebooks/*output.ipynb docs/source/
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pushd docs
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make clean html
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popd
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- name: Build documentation
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shell: bash -l {0}
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run: |
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set -e
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micromamba run -n TEST jupyter nbconvert --to notebook --execute notebooks/demo.ipynb --output=demo-output.ipynb --ExecutePreprocessor.allow_errors=True
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mv notebooks/*output.ipynb docs/source/
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pushd docs
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micromamba run -n TEST make clean html
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popd

‎.github/workflows/docs_deploy.yml‎

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push:
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branches:
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- main
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# Optional: manual trigger
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workflow_dispatch:
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jobs:
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build-docs:
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deploy-docs:
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runs-on: ubuntu-latest
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permissions:
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contents: write
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steps:
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- name: Run a one-line script
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run: echo "The job was automatically triggered by a ${{ github.event_name }} event."
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- name: checkout
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Checkout
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Setup Micromamba ${{ matrix.python-version }}
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uses: mamba-org/setup-micromamba@v2.0.1
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with:
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environment-name: TEST
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init-shell: bash
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create-args: >-
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python=3 pip
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--file requirements-dev.txt
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--channel conda-forge
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- name: Setup Micromamba
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uses: mamba-org/setup-micromamba@v2
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with:
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environment-file: environment.yml
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init-shell: bash
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condarc: |
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channels:
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- conda-forge
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channel_priority: strict
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cache-environment: true
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- name: Install seagliderOG1
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shell: bash -l {0}
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run: |
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python -m pip install -e . --no-deps --force-reinstall
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- name: Install package (editable)
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shell: bash -l {0}
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run: |
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micromamba run -n TEST python -m pip install --upgrade pip
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micromamba run -n TEST python -m pip install -e . --no-deps --force-reinstall
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- name: Build documentation
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shell: bash -l {0}
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run: |
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set -e
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jupyter nbconvert --to notebook --execute notebooks/demo.ipynb --output=demo-output.ipynb --ExecutePreprocessor.allow_errors=True
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mv notebooks/*output.ipynb docs/source/
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pushd docs
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make clean html
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popd
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- name: Build documentation
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shell: bash -l {0}
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run: |
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set -e
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micromamba run -n TEST jupyter nbconvert --to notebook --execute notebooks/demo.ipynb --output=demo-output.ipynb --ExecutePreprocessor.allow_errors=True
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mv notebooks/*output.ipynb docs/source/
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pushd docs
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micromamba run -n TEST make clean html
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popd
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- name: Deploy
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uses: peaceiris/actions-gh-pages@v4
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: docs/build/html
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- name: Deploy to GitHub Pages
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uses: peaceiris/actions-gh-pages@v4
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: docs/build/html

‎.github/workflows/tests.yml‎

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- '**.ipynb'
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jobs:
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job_mytests:
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test:
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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, windows-latest, macos-latest]
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python-version: ["3.10", "3.12"]
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fail-fast: true
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defaults:
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run:
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shell: bash -l {0}
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steps:
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- name: Run a one-line script
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run: echo "The job was automatically triggered by a ${{ github.event_name }} event."
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- uses: actions/checkout@v4
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- name: Setup Micromamba Python ${{ matrix.python-version }}
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uses: mamba-org/setup-micromamba@v2
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with:
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environment-name: TEST
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init-shell: bash
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create-args: >-
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python=${{ matrix.python-version }} --file requirements-dev.txt --channel conda-forge
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env:
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MAMBA_NO_BANNER: true
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Check Package Installation
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run: |
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micromamba env list
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micromamba list
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python -m pip check
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- name: Setup Micromamba
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uses: mamba-org/setup-micromamba@v2
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with:
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environment-file: environment.yml
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init-shell: bash
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condarc: |
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channels:
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- conda-forge
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channel_priority: strict
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cache-environment: true
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create-args: >-
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python=${{ matrix.python-version }}
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- name: Check Package Installation
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shell: bash -l {0}
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run: |
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micromamba run -n TEST micromamba env list
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micromamba run -n TEST micromamba list
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micromamba run -n TEST python -m pip check
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- name: Install seagliderOG1
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run: |
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python -m pip install -e . --no-deps --force-reinstall
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- name: Install package (editable)
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shell: bash -l {0}
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run: |
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micromamba run -n TEST python -m pip install --upgrade pip
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micromamba run -n TEST python -m pip install -e . --no-deps --force-reinstall
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- name: Full Tests
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run: |
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python -m pytest --cov=seagliderOG1 --cov-report term-missing tests/
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- name: Run tests
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shell: bash -l {0}
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run: |
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micromamba run -n TEST python -m pytest --cov=seagliderOG1 --cov-report term-missing tests/

‎.gitignore‎

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# Claude Code files
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CLAUDE.md
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.claude/*.json

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