Merge pull request #78 from pyiron/github_actions

cleanup github actions

.github/workflows/black.yml

@@ -12,7 +12,7 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - uses: psf/black@stable
       with:
         options: "--check --diff"

.github/workflows/dependabot.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     if: (github.actor == 'dependabot[bot]')
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           ref: ${{ github.event.pull_request.head.ref }} # Check out the head of the actual branch, not the PR
           fetch-depth: 0 # otherwise, you will fail to push refs to dest repo

.github/workflows/deploy.yml

@@ -14,15 +14,14 @@ jobs:
     runs-on: ubuntu-latest
     environment:
       name: pypi
-      url: https://pypi.org/p/atomistics
+      url: https://pypi.org/p/${{ github.event.repository.name }}
     permissions:
       id-token: write
     steps:
-    - uses: actions/checkout@v2
-    - uses: actions/setup-python@v2
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v4
       with:
         python-version: "3.11"
-
     - name: Install dependencies
       run: >-
         python -m pip install --user --upgrade setuptools wheel

.github/workflows/format_black.yml

@@ -0,0 +1,33 @@
+# This workflow will checkout the branch of the PR, apply black formatting and commit the result to the PR. Does not work for forks.
+
+name: Format black
+
+on:
+  pull_request:
+    types: [labeled]
+
+jobs:
+  build:
+    if: contains(github.event.pull_request.labels.*.name, 'format_black' )
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        token: ${{ secrets.DEPENDABOT_WORKFLOW_TOKEN }}
+        ref: ${{ github.event.pull_request.head.ref }} # Check out the head of the actual branch, not the PR
+        fetch-depth: 0 # otherwise, you will fail to push refs to dest repo
+    - name: format black
+      uses: psf/black@stable
+      with:
+        options: ""
+        src: "./${{ github.event.repository.name }}"
+    - name: commit
+      run: |
+        git config --local user.email "[email protected]"
+        git config --local user.name "pyiron-runner"
+        git commit -m "Format black" -a
+    - name: push
+      uses: ad-m/github-push-action@master
+      with:
+        github_token: ${{ secrets.DEPENDABOT_WORKFLOW_TOKEN }}
+        branch: ${{ github.event.pull_request.head.ref }}

.github/workflows/minimal.yml

@@ -6,16 +6,11 @@ on:
   pull_request:
     branches: [ main ]
 
-env:
-  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-  CODACY_PROJECT_TOKEN: ${{ secrets.CODACY_PROJECT_TOKEN }}
-
 jobs:
   build:
-
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Setup Mambaforge
       uses: conda-incubator/setup-miniconda@v2
       with:
@@ -24,16 +19,11 @@ jobs:
         channels: conda-forge
         channel-priority: strict
         activate-environment: my-env
+        environment-file: .ci_support/environment.yml
         use-mamba: true
-    - name: Update environment
-      run: mamba env update -n my-env -f .ci_support/environment.yml
-    - name: Setup
-      shell: bash -l {0}
-      run: |
-        pip install --no-deps .
     - name: Test
       shell: bash -l {0}
       timeout-minutes: 30
       run: |
-        coverage run --omit atomistics/_version.py -m unittest discover tests
-        coverage combine
+        pip install --no-deps .
+        python -m unittest discover tests

.github/workflows/notebooks.yml

@@ -10,14 +10,13 @@ on:
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
-
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Merge Notebook environment
         run: |
-          python .ci_support/condamerge.py --base .ci_support/environment.yml --add .ci_support/environment-notebooks.yml > environment.yml
+          cp .ci_support/environment.yml environment.yml
+        tail --lines=+4 .ci_support/environment-abinit.yml >> environment.yml
       - name: Setup Mambaforge
         uses: conda-incubator/setup-miniconda@v2
         with:
@@ -26,13 +25,10 @@ jobs:
           channels: conda-forge
           channel-priority: strict
           activate-environment: my-env
+          environment-file: environment.yml
           use-mamba: true
-      - name: Update environment
-        run: mamba env update -n my-env -f environment.yml
-      - name: Setup
+      - name: Test
         shell: bash -l {0}
         run: |
           pip install --no-deps .
-      - name: Test
-        shell: bash -l {0}
-        run: ./.ci_support/build_notebooks.sh
+          ./.ci_support/build_notebooks.sh

.github/workflows/pypicheck.yml

@@ -10,11 +10,9 @@ on:
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
-
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Setup Mambaforge
       uses: conda-incubator/setup-miniconda@v2
       with:
@@ -23,9 +21,8 @@ jobs:
         channels: conda-forge
         channel-priority: strict
         activate-environment: my-env
+        environment-file: .ci_support/environment.yml
         use-mamba: true
-    - name: Update environment
-      run: mamba env update -n my-env -f .ci_support/environment.yml
     - name: Pip check
       shell: bash -l {0}
       run: |

.github/workflows/unittests.yml

@@ -6,13 +6,8 @@ on:
   pull_request:
     branches: [ main ]
 
-env:
-  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-  CODACY_PROJECT_TOKEN: ${{ secrets.CODACY_PROJECT_TOKEN }}
-
 jobs:
   build:
-
     runs-on: ${{ matrix.operating-system }}
     strategy:
       matrix:
@@ -43,7 +38,16 @@ jobs:
           prefix: /usr/share/miniconda3/envs/my-env
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
+    - name: Setup environment (windows)
+      if: matrix.operating-system == 'windows-latest'
+      run: cp .ci_support/environment.yml environment.yml
+    - name: Setup environment (unix)
+      if: matrix.operating-system != 'windows-latest'
+      shell: bash -l {0}
+      run: |
+        cp .ci_support/environment.yml environment.yml
+        tail --lines=+4 .ci_support/environment-lammps.yml >> environment.yml
     - name: Setup Mambaforge
       uses: conda-incubator/setup-miniconda@v2
       with:
@@ -52,26 +56,13 @@ jobs:
         channels: conda-forge
         channel-priority: strict
         activate-environment: my-env
+        environment-file: environment.yml
         use-mamba: true
-    - name: Setup environment (windows)
-      if: matrix.operating-system == 'windows-latest'
-      run: cp .ci_support/environment.yml environment.yml
-    - name: Setup environment (unix)
-      if: matrix.operating-system != 'windows-latest'
-      shell: bash -l {0}
-      run: |
-        mamba install -y pyyaml
-        python .ci_support/condamerge.py --base .ci_support/environment.yml --add .ci_support/environment-lammps.yml > environment.yml
-    - name: Update environment
-      run: mamba env update -n my-env -f environment.yml
-    - name: Setup
-      shell: bash -l {0}
-      run: |
-        pip install --no-deps .
     - name: Test
       shell: bash -l {0}
       timeout-minutes: 30
       run: |
+        pip install --no-deps .
         coverage run --omit atomistics/_version.py -m unittest discover tests
         coverage combine
     - name: Coveralls

.github/workflows/unittests_abinit.yml

@@ -6,19 +6,15 @@ on:
   pull_request:
     branches: [ main ]
 
-env:
-  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-  CODACY_PROJECT_TOKEN: ${{ secrets.CODACY_PROJECT_TOKEN }}
-
 jobs:
   build:
-
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Merge Notebook environment
       run: |
-        python .ci_support/condamerge.py --base .ci_support/environment.yml --add .ci_support/environment-abinit.yml > environment.yml
+        cp .ci_support/environment.yml environment.yml
+        tail --lines=+4 .ci_support/environment-abinit.yml >> environment.yml
     - name: Setup Mambaforge
       uses: conda-incubator/setup-miniconda@v2
       with:
@@ -27,17 +23,14 @@ jobs:
         channels: conda-forge
         channel-priority: strict
         activate-environment: my-env
+        environment-file: environment.yml
         use-mamba: true
-    - name: Update environment
-      run: mamba env update -n my-env -f environment.yml
-    - name: Setup
-      shell: bash -l {0}
-      run: |
-        pip install --no-deps .
     - name: Test
       shell: bash -l {0}
       timeout-minutes: 30
-      run: python -m unittest tests/test_evcurve_abinit.py
+      run: |
+        pip install --no-deps .
+        python -m unittest tests/test_evcurve_abinit.py
       env:
         ABINIT_PP_PATH: '/usr/share/miniconda3/envs/my-env/share/abinit/LDA_FHI'
         ABI_PSPDIR: '/usr/share/miniconda3/envs/my-env/share/abinit/LDA_FHI'

.github/workflows/unittests_gpaw.yml

@@ -6,19 +6,15 @@ on:
   pull_request:
     branches: [ main ]
 
-env:
-  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-  CODACY_PROJECT_TOKEN: ${{ secrets.CODACY_PROJECT_TOKEN }}
-
 jobs:
   build:
-
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Merge Notebook environment
       run: |
-        python .ci_support/condamerge.py --base .ci_support/environment.yml --add .ci_support/environment-gpaw.yml > environment.yml
+        cp .ci_support/environment.yml environment.yml
+        tail --lines=+4 .ci_support/environment-abinit.yml >> environment.yml
     - name: Setup Mambaforge
       uses: conda-incubator/setup-miniconda@v2
       with:
@@ -27,17 +23,13 @@ jobs:
         channels: conda-forge
         channel-priority: strict
         activate-environment: my-env
+        environment-file: environment.yml
         use-mamba: true
-    - name: Update environment
-      run: mamba env update -n my-env -f environment.yml
-    - name: Setup
-      shell: bash -l {0}
-      run: |
-        pip install --no-deps .
     - name: Test
       shell: bash -l {0}
       timeout-minutes: 30
       run: |
+        pip install --no-deps .
         python -m unittest tests/test_evcurve_gpaw.py
         python -m unittest tests/test_elastic_gpaw.py
         python -m unittest tests/test_phonons_gpaw.py