Refine I(Q,t) data

.github/workflows/ci-build.yml

@@ -7,62 +7,49 @@ env:
   ruff_version: 0.15.5
 
 jobs:
-  build:
-    name: Build docker container
-    runs-on: ubuntu-22.04
-    # if this is a dependabot PR, skip all this and do the Dependabot workflow instead
-    if: ${{ github.actor != 'dependabot[bot]' }}
-    steps:
-      - name: Checkout repo
-        uses: actions/checkout@v6
-      - name: fetch  # grabs master to compare if Docker build files changed
-        run: git fetch origin master
-
-      - name: Check and build container
-        env:
-          DOCKER_PASSWORD: ${{ secrets.DOCKER_PASSWORD }}
-          BRANCH: ${{ github.head_ref }}
-        run: source .github/scripts/build_container.sh
 
   tests:
-    name: Docker tests
-    needs: build # so it can use new docker image if docker image has changed
+    name: Tests
     runs-on: ubuntu-22.04
     strategy:
       fail-fast: true
       matrix:
         testset: ["not lammps and not dlpoly"]
     steps:
       - name: Setup Python
-        uses: actions/setup-python@v6
+        uses: actions/setup-python@v7
         with:
           python-version: '3.11.2'
           architecture: x64
       - name: Checkout repo
-        uses: actions/checkout@v3
-      - name: Pull Docker Image
-        env:
-          BRANCH: ${{ github.head_ref }}
-        run: |
-          BRANCH="${BRANCH//\//-}"
-          docker pull -q mdmc/mdmc:ci-$BRANCH || docker pull -q mdmc/mdmc:latest
-          echo "IMG_NAME=$(echo $(docker images --filter=reference='mdmc/mdmc:*' --format "{{.Repository}}:{{.Tag}}"))" >> $GITHUB_ENV
+        uses: actions/checkout@v7
+      - name: Install MDMC
+        run: pip install .[test,docs]
+      - name: Install packmol
+        run: sudo apt-get install libgfortran5 -y && pip install packmol
       - name: Run tests
-        env:
-          TESTSET: ${{ matrix.testset }}
-        run: |
-          docker run -t --mount type=bind,source="$(pwd)",target="$(pwd)" ${{ env.IMG_NAME }} python3 -m pytest -m "$TESTSET" -s $(pwd)/tests/;[ $? -eq 0 ]
-          exit 0
+        working-directory: tests
+        run: pytest
 
-      - name: Copy coverage
-        run: docker cp $(docker ps -lq):/home/coverage.xml coverage.xml || exit 0
-        continue-on-error: true
-
-      - name: Upload code coverage report
-        uses: codecov/codecov-action@v6
+  notebooks:
+    name: Notebook test
+    runs-on: ubuntu-22.04
+    steps:
+      - name: Checkout Repo
+        uses: actions/checkout@v7
+      - name: Setup Python
+        uses: actions/setup-python@v7
         with:
-          token: ${{ secrets.CODECOV_TOKEN }}
-        continue-on-error: true
+          python-version: '3.11.2'
+          architecture: x64
+      - name: Install Requirements
+        run: sudo apt-get install pandoc -y
+      - name: Install MDMC
+        run: pip install .[test,docs]
+      - name: Convert Notebooks
+        run: jupyter nbconvert --config doc/notebook-test-config.py
+      - name: Test Notebooks
+        run: pytest --nbmake --nbmake-timeout=300 -k '.nbconvert.ipynb'
 
   linting:
     name: Lint - ${{ matrix.type }}
@@ -73,7 +60,7 @@ jobs:
 
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
       - uses: astral-sh/ruff-action@v3
         with:
           src: MDMC
@@ -87,48 +74,19 @@ jobs:
 
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
       - uses: astral-sh/ruff-action@v3
         with:
           src: MDMC
           args: check --preview --select CPY
           version: ${{ env.ruff_version }}
 
-  notebooks:
-    name: Notebooks
-    runs-on: ubuntu-22.04
-    needs: build
-    steps:
-      - name: Checkout Repo
-        uses: actions/checkout@v6
-      - name: Setup Python
-        uses: actions/setup-python@v6
-        with:
-          python-version: '3.11.2'
-          architecture: x64
-      - name: Pull Docker Image
-        env:
-          BRANCH: ${{ github.head_ref }}
-        run: |
-          BRANCH="${BRANCH//\//-}"
-          docker pull -q mdmc/mdmc:ci-$BRANCH || docker pull -q mdmc/mdmc:latest
-          echo "IMG_NAME=$(echo $(docker images --filter=reference='mdmc/mdmc:*' --format "{{.Repository}}:{{.Tag}}"))" >> $GITHUB_ENV
-      - name: Create Docker Container
-        run: |
-          echo "CONTAINER_HASH=$(echo $(docker run -d -it --mount type=bind,source="$(pwd)",target="/home/mdmc_home" -w "/home/mdmc_home" ${{ env.IMG_NAME }}))" >> $GITHUB_ENV
-      - name: Install Requirements
-        run: docker exec ${{ env.CONTAINER_HASH }} /bin/bash -c "apt-get install pandoc -y && pip install .[docs]"
-      - name: Convert Notebooks
-        run: docker exec ${{ env.CONTAINER_HASH }} /bin/bash -c "jupyter nbconvert --config doc/notebook-test-config.py"
-      - name: Test Notebooks
-        run: docker exec ${{ env.CONTAINER_HASH }} /bin/bash -c "pytest --nbmake --nbmake-timeout=2000 -k '.nbconvert.ipynb'"
-
   type-checking:
     name: Mypy
     runs-on: ubuntu-22.04
     steps:
     - name: Checkout repo
-      uses: actions/checkout@v6
+      uses: actions/checkout@v7
     - name: apt get
       run: |
         sudo apt-get update

.github/workflows/ci-dependabot.yml

@@ -11,31 +11,17 @@ jobs:
     runs-on: ubuntu-22.04
     if: ${{ github.actor == 'dependabot[bot]' }}
     steps:
+    - name: Setup Python
+      uses: actions/setup-python@v7
+      with:
+        python-version: '3.11.2'
+        architecture: x64
     - name: Checkout repo
-      uses: actions/checkout@v4
-    - name: Build Docker container
-      env:
-        BRANCH: ${{ github.head_ref }}
-      run: |
-        BRANCH="${BRANCH//\//-}"
-        docker build -t mdmc/mdmc:ci-$BRANCH -f "$(pwd)"/build/Docker/Dockerfile.mdmc . || exit 1
+      uses: actions/checkout@v7
+    - name: Install MDMC
+      run: pip install .[test,docs]
     - name: Run tests
-      env:
-        BRANCH: ${{ github.head_ref }}
-      run: |
-        BRANCH="${BRANCH//\//-}"
-        docker run -t --mount type=bind,source="$(pwd)",target="$(pwd)" mdmc/mdmc:ci-$BRANCH python3 -m pytest -s "$(pwd)"/tests/; [ $? -eq 0 ]
+      working-directory: tests
+      run: pytest
     - name: Try to build documentation
-      env:
-        BRANCH: ${{ github.head_ref }}
-      run: |
-        BRANCH="${BRANCH//\//-}"
-        docker run -t --mount type=bind,source="$(pwd)",target="$(pwd)" mdmc/mdmc:ci-$BRANCH /bin/bash -c  "cd $(pwd) && apt-get update && apt-get install pandoc -y && pip3 install . && make -d -C $(pwd)/doc html"
-    - name: Push image
-      env:
-        BRANCH: ${{ github.head_ref }}
-        DOCKER_PASSWORD: ${{ secrets.DEPENDABOT_DOCKER }}
-      run: |
-        BRANCH="${BRANCH//\//-}"
-        echo "$DOCKER_PASSWORD" | docker login -u "mdmc" --password-stdin
-        docker push mdmc/mdmc:ci-$BRANCH
+      run: apt-get install pandoc -y && make -d -C doc html