Merge pull request #589 from FAIRmat-NFDI/update-workflows

update CI/CD workflows

Author: lukaspie

.github/workflows/build_docs.yml

@@ -3,10 +3,7 @@ name: build_and_deploy_mkdocs
 on:
   push:
     branches:
-      - master  # Triggers deployment on push to the main branch
-
-env:
-  UV_SYSTEM_PYTHON: true
+      - master  # Triggers deployment on push to the master branch
 
 permissions:
    contents: write
@@ -27,10 +24,10 @@ jobs:
           git config user.name github-actions[bot]
           git config user.email 41898282+github-actions[bot]@users.noreply.github.com
 
-      - name: Set up Python
-        uses: actions/setup-python@v5
+      - name: Install uv and set the python version to 3.11
+        uses: astral-sh/setup-uv@v5
         with:
-          python-version: '3.x'
+          python-version: 3.11
 
       - name: Cache mkdocs-material environment
         uses: actions/cache@v3
@@ -42,7 +39,6 @@ jobs:
 
       - name: Install Dependencies
         run: |
-          curl -LsSf https://astral.sh/uv/install.sh | sh
           uv pip install --no-cache-dir ".[docs]"
 
       - name: Build and Deploy

.github/workflows/nomad-requirements.yml

@@ -13,7 +13,7 @@ on:
     #   - 'dev-requirements.txt'
 
 env:
-  UV_SYSTEM_PYTHON: true
+  python-version: 3.11
 
 jobs:
   validate_dependencies:
@@ -28,26 +28,21 @@ jobs:
         git clone --depth 1 --branch develop --recurse-submodules https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR.git nomad
         git submodule update --init --recursive --depth 1
 
-    - name: Replace pynxtools dependency in NOMAD pyproject.toml
+    - name: Add pynxtools dependency in NOMAD test_plugins.txt
       working-directory: ./nomad
       run: |
-        sed -i 's|pynxtools\[convert\]==[0-9]\+\(\.[0-9]\+\)\+\([0-9]\)|pynxtools\[convert\]@git+https://github.com/FAIRmat-NFDI/pynxtools.git@${{ github.head_ref || github.ref_name }} |' default_plugins.txt
-    - name: Set up Python
-      uses: actions/setup-python@v5
+        echo "" >> test_plugins.txt
+        echo "pynxtools[convert]@git+https://github.com/FAIRmat-NFDI/pynxtools.git@${{ github.head_ref || github.ref_name }}" >> test_plugins.txt
+    - name: Install uv and set the python version to ${{ env.python-version }}
+      uses: astral-sh/setup-uv@v5
       with:
-        python-version: '3.11'
-
-    - name: Install uv
-      run: |
-        curl -LsSf https://astral.sh/uv/install.sh | sh
-
+        python-version: ${{ env.python-version }}
     - name: Generate (dev-)requirements.txt from modified pyproject.toml
       working-directory: ./nomad
       run: |
-        uv pip compile --universal -p 3.11 --annotation-style=line --extra=infrastructure --extra=parsing --output-file=requirements.txt pyproject.toml
-        uv pip compile --universal -p 3.11 --annotation-style=line --extra=dev --extra=infrastructure --extra=parsing --output-file=requirements-dev.txt requirements.txt pyproject.toml
-        uv pip compile --universal -p 3.11 --annotation-style=line --output-file=requirements-plugins.txt --unsafe-package nomad-lab -c requirements-dev.txt default_plugins.txt
-
+        uv pip compile --universal -p ${{ env.python-version }} --annotation-style=line --extra=infrastructure --extra=parsing --output-file=requirements.txt pyproject.toml
+        uv pip compile --universal -p ${{ env.python-version }} --annotation-style=line --extra=dev --extra=infrastructure --extra=parsing --output-file=requirements-dev.txt requirements.txt pyproject.toml
+        uv pip compile --universal -p ${{ env.python-version }} --annotation-style=line --output-file=requirements-plugins.txt --unsafe-package nomad-lab -c requirements-dev.txt test_plugins.txt
     - name: Install NOMAD dependencies with pynxtools from current branch
       working-directory: ./nomad
       run: |

.github/workflows/plugin_test.yaml

@@ -10,7 +10,7 @@ on:
     branches: [master]
 
 env:
-  UV_SYSTEM_PYTHON: true
+  python-version: 3.11
 
 jobs:
   pytest:
@@ -49,18 +49,17 @@ jobs:
             tests_to_run: tests/.
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
           submodules: recursive
-      - name: Set up Python 3.11
-        uses: actions/setup-python@v5
+      - name: Install uv and set the python version to ${{ env.python-version }}
+        uses: astral-sh/setup-uv@v5
         with:
-          python-version: 3.11
+          python-version: ${{ env.python-version }}
       - name: Install dependencies
         run: |
-          curl -LsSf https://astral.sh/uv/install.sh | sh
-          uv pip install --system coverage coveralls
+          uv pip install coverage coveralls
       - name: Install package
         run: |
           uv pip install ".[dev]"

.github/workflows/publish.yml

@@ -5,7 +5,7 @@ on:
     types: [published]
 
 env:
-  UV_SYSTEM_PYTHON: true
+  python-version: 3.11
 
 jobs:
   deploy:
@@ -21,13 +21,12 @@ jobs:
       with:
         fetch-depth: 0
         submodules: recursive
-    - name: Set up Python
-      uses: actions/setup-python@v5
+    - name: Install uv and set the python version to ${{ env.python-version }}
+      uses: astral-sh/setup-uv@v5
       with:
-        python-version: "3.x"
+        python-version: ${{ env.python-version }}
     - name: Install dependencies
       run: |
-        curl -LsSf https://astral.sh/uv/install.sh | sh
         uv pip install build
     - name: Git tag version
       id: git_tag_version

.github/workflows/pylint.yml

@@ -3,28 +3,24 @@ name: linting
 on: [push]
 
 env:
-  UV_SYSTEM_PYTHON: true
+  python-version: 3.11
 
 jobs:
   linting:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v5
+      - name: Install uv and set the python version to ${{ env.python-version }}
+        uses: astral-sh/setup-uv@v5
         with:
-          python-version: "3.10"
+          python-version: ${{ env.python-version }}
       - name: Install dependencies
         run: |
           git submodule sync --recursive
           git submodule update --init --recursive --jobs=4
-          curl -LsSf https://astral.sh/uv/install.sh | sh
-      - name: Install package
+      - name: Install package and dev requirements
         run: |
-          uv pip install --no-deps .
-      - name: Install dev requirements
-        run: |
-          uv pip install -r dev-requirements.txt
+          uv pip install .[dev]
       - name: ruff check
         run: |
           ruff check src/pynxtools tests

.github/workflows/pytest.yml

@@ -48,4 +48,4 @@ jobs:
         env:
             GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
-            coveralls --service=github
+            coveralls --service=github