[CLEANUP] Update workflows and environment

.claude/settings.local.json

@@ -0,0 +1,9 @@
+{
+  "permissions": {
+    "allow": [
+      "Bash(find:*)"
+    ],
+    "deny": [],
+    "ask": []
+  }
+}

.github/PULL_REQUEST_TEMPLATE.md

@@ -25,7 +25,7 @@ Please describe your changes clearly and concisely.
 
 **Checklist:**
 
-- [ ] I have followed the [coding conventions](https://amoccommunity.github.io/amocarray/conventions.html).
+- [ ] I have followed the [coding conventions](docs/source/conventions.md).
 - [ ] I have updated or added tests to cover my changes.
 - [ ] I have updated the documentation if needed.
 - [ ] I have run `pytest` to check that all tests pass.

.github/workflows/docs.yml

@@ -6,40 +6,43 @@ on:
       - '**.py'
       - '**.ipynb'
       - '**.rst'
+      - '**.md'
 
 jobs:
   build-docs:
     runs-on: ubuntu-latest
     permissions:
-      contents: write
+      contents: read
 
     steps:
-    - name: checkout
-      uses: actions/checkout@v4
-      with:
-        fetch-depth: 0
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
 
-    - name: Setup Micromamba ${{ matrix.python-version }}
-      uses: mamba-org/setup-micromamba@v2.0.1
-      with:
-        environment-name: TEST
-        init-shell: bash
-        create-args: >-
-          python=3 pip
-          --file requirements-dev.txt
-          --channel conda-forge
+      - name: Setup Micromamba
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-file: environment.yml
+          init-shell: bash
+          condarc: |
+            channels:
+              - conda-forge
+            channel_priority: strict
+          cache-environment: true
 
-    - name: Install seagliderOG1
-      shell: bash -l {0}
-      run: |
-        python -m pip install -e . --no-deps --force-reinstall
+      - name: Install package (editable)
+        shell: bash -l {0}
+        run: |
+          micromamba run -n TEST python -m pip install --upgrade pip
+          micromamba run -n TEST python -m pip install -e . --no-deps --force-reinstall
 
-    - name: Build documentation
-      shell: bash -l {0}
-      run: |
-        set -e
-        jupyter nbconvert --to notebook --execute notebooks/demo.ipynb --output=demo-output.ipynb --ExecutePreprocessor.allow_errors=True
-        mv notebooks/*output.ipynb docs/source/
-        pushd docs
-        make clean html
-        popd
+      - name: Build documentation
+        shell: bash -l {0}
+        run: |
+          set -e
+          micromamba run -n TEST jupyter nbconvert --to notebook --execute notebooks/demo.ipynb --output=demo-output.ipynb --ExecutePreprocessor.allow_errors=True
+          mv notebooks/*output.ipynb docs/source/
+          pushd docs
+          micromamba run -n TEST make clean html
+          popd

.github/workflows/docs_deploy.yml

@@ -4,48 +4,50 @@ on:
   push:
     branches:
       - main
+  # Optional: manual trigger
+  workflow_dispatch:
 
 jobs:
-  build-docs:
+  deploy-docs:
     runs-on: ubuntu-latest
     permissions:
       contents: write
 
     steps:
-    - name: Run a one-line script
-      run: echo "The job was automatically triggered by a ${{ github.event_name }} event."
-    - name: checkout
-      uses: actions/checkout@v4
-      with:
-        fetch-depth: 0
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
 
-    - name: Setup Micromamba ${{ matrix.python-version }}
-      uses: mamba-org/setup-micromamba@v2.0.1
-      with:
-        environment-name: TEST
-        init-shell: bash
-        create-args: >-
-          python=3 pip
-          --file requirements-dev.txt
-          --channel conda-forge
+      - name: Setup Micromamba
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-file: environment.yml
+          init-shell: bash
+          condarc: |
+            channels:
+              - conda-forge
+            channel_priority: strict
+          cache-environment: true
 
-    - name: Install seagliderOG1
-      shell: bash -l {0}
-      run: |
-        python -m pip install -e . --no-deps --force-reinstall
+      - name: Install package (editable)
+        shell: bash -l {0}
+        run: |
+          micromamba run -n TEST python -m pip install --upgrade pip
+          micromamba run -n TEST python -m pip install -e . --no-deps --force-reinstall
 
-    - name: Build documentation
-      shell: bash -l {0}
-      run: |
-        set -e
-        jupyter nbconvert --to notebook --execute notebooks/demo.ipynb --output=demo-output.ipynb --ExecutePreprocessor.allow_errors=True
-        mv notebooks/*output.ipynb docs/source/
-        pushd docs
-        make clean html
-        popd
+      - name: Build documentation
+        shell: bash -l {0}
+        run: |
+          set -e
+          micromamba run -n TEST jupyter nbconvert --to notebook --execute notebooks/demo.ipynb --output=demo-output.ipynb --ExecutePreprocessor.allow_errors=True
+          mv notebooks/*output.ipynb docs/source/
+          pushd docs
+          micromamba run -n TEST make clean html
+          popd
 
-    - name: Deploy
-      uses: peaceiris/actions-gh-pages@v4
-      with:
-        github_token: ${{ secrets.GITHUB_TOKEN }}
-        publish_dir: docs/build/html
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: docs/build/html

.github/workflows/tests.yml

@@ -15,42 +15,45 @@ on:
       - '**.ipynb'
 
 jobs:
-  job_mytests:
+  test:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
         python-version: ["3.10", "3.12"]
       fail-fast: true
-    defaults:
-      run:
-        shell: bash -l {0}
-    steps:
-    - name: Run a one-line script
-      run: echo "The job was automatically triggered by a ${{ github.event_name }} event."
-    - uses: actions/checkout@v4
 
-    - name: Setup Micromamba Python ${{ matrix.python-version }}
-      uses: mamba-org/setup-micromamba@v2
-      with:
-        environment-name: TEST
-        init-shell: bash
-        create-args: >-
-          python=${{ matrix.python-version }} --file requirements-dev.txt --channel conda-forge
-      env:
-        MAMBA_NO_BANNER: true
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
 
-    - name: Check Package Installation
-      run: |
-        micromamba env list
-        micromamba list
-        python -m pip check
+      - name: Setup Micromamba
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-file: environment.yml
+          init-shell: bash
+          condarc: |
+            channels:
+              - conda-forge
+            channel_priority: strict
+          cache-environment: true
+          create-args: >-
+            python=${{ matrix.python-version }}
 
+      - name: Check Package Installation
+        shell: bash -l {0}
+        run: |
+          micromamba run -n TEST micromamba env list
+          micromamba run -n TEST micromamba list
+          micromamba run -n TEST python -m pip check
 
-    - name: Install seagliderOG1
-      run: |
-        python -m pip install -e . --no-deps --force-reinstall
+      - name: Install package (editable)
+        shell: bash -l {0}
+        run: |
+          micromamba run -n TEST python -m pip install --upgrade pip
+          micromamba run -n TEST python -m pip install -e . --no-deps --force-reinstall
 
-    - name: Full Tests
-      run: |
-        python -m pytest --cov=seagliderOG1 --cov-report term-missing  tests/
+      - name: Run tests
+        shell: bash -l {0}
+        run: |
+          micromamba run -n TEST python -m pytest --cov=seagliderOG1 --cov-report term-missing tests/

.gitignore

@@ -172,3 +172,4 @@ de421.bsp
 
 # Claude Code files
 CLAUDE.md
+.claude/*.json