Fix CI

.github/workflows/gh-ci-cron.yaml

@@ -20,16 +20,16 @@ defaults:
 
 jobs:
   gen_matrix:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     outputs:
       matrix: ${{ steps.get-mdakits.outputs.matrix }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - id: get-python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v6
         with:
-          python-version: "3.12"
+          python-version: "3.13"
 
       - id: get-mdakits
         run: |
@@ -43,9 +43,9 @@ jobs:
       python-min: ${{ steps.get-compatible-python.outputs.oldest-python }}
 
     steps:
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v6
         with:
-          python-version: "3.12"
+          python-version: "3.13"
 
       - id: get-compatible-python
         uses: MDAnalysis/mdanalysis-compatible-python@main
@@ -54,14 +54,14 @@ jobs:
 
   mdakit-ci:
     needs: [gen_matrix, env_config]
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
         mdakit: ${{fromJSON(needs.gen_matrix.outputs.matrix)}}
         jobstep: ['latest', 'develop']
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - id: get-base-python-deps
         name: get-base-python-deps
@@ -79,11 +79,10 @@ jobs:
 
       - id: install-conda-env
         name: install-conda-env
-        uses: conda-incubator/setup-miniconda@v3
+        uses: conda-incubator/setup-miniconda@v4
         with:
           python-version: ${{ env.PYVER }}
           add-pip-as-python-dependency: true
-          architecture: x64
           use-mamba: true
           miniforge-version: latest
           channels: conda-forge
@@ -153,7 +152,7 @@ jobs:
 
       - id: upload-artifacts
         name: upload-artifacts
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: cron-statuses-${{ matrix.mdakit }}-${{ matrix.jobstep }}
           path: ${{ matrix.mdakit }}-${{ matrix.jobstep }}-statuses.json
@@ -163,16 +162,16 @@ jobs:
   process_results:
     if: ${{ always() }}
     needs: mdakit-ci
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     permissions:
       contents: write
       pull-requests: write 
       packages: none
       issues: write
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@v8
         with:
           path: json-statuses/
 
@@ -191,7 +190,7 @@ jobs:
         env:
           GITHUB_TOKEN:  ${{ github.token }}
 
-      - uses: stefanzweifel/git-auto-commit-action@v4
+      - uses: stefanzweifel/git-auto-commit-action@v7
         with:
           commit_message: commit changes to status files
           skip_dirty_check: false
@@ -200,22 +199,22 @@ jobs:
   deploy_docs:
     if: ${{ always() }}
     needs: process_results
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - name: setup_micromamba
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v3
         with:
           environment-file: docs/requirements.yaml
           environment-name: MDAKitRegistry-docs
           create-args: >-
-            python=3.9
+            python=3.12
             pip
       - name: build_docs
         run: |
           cd docs && sphinx-build -b html source build
       - name: deploy docs
-        uses: peaceiris/actions-gh-pages@v3
+        uses: peaceiris/actions-gh-pages@v4
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: ./docs/build

.github/workflows/gh-ci.yaml

@@ -16,20 +16,20 @@ defaults:
 
 jobs:
   gen_matrix:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     outputs:
       matrix: ${{ steps.get-changed-mdakits.outputs.matrix }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - id: get-python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v6
         with:
-          python-version: 3.9
+          python-version: 3.13
 
       - id: files
         name: get changed filed
-        uses: masesgroup/retrieve-changed-files@v3
+        uses: masesgroup/retrieve-changed-files@v4
         with:
           format: 'json'
       - id: get-changed-mdakits
@@ -46,9 +46,9 @@ jobs:
       python-stable: ${{ steps.get-compatible-python.outputs.stable-python }}
       python-min: ${{ steps.get-compatible-python.outputs.oldest-python }}
     steps:
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v6
         with:
-          python-version: "3.12"
+          python-version: "3.13"
 
       - id: get-compatible-python
         uses: MDAnalysis/mdanalysis-compatible-python@main
@@ -57,19 +57,19 @@ jobs:
 
   mdakit-ci:
     needs: [gen_matrix, env_config]
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
         mdakit: ${{fromJSON(needs.gen_matrix.outputs.matrix)}}
         jobstep: ['latest', 'develop']
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - id: get-base-python-deps
         name: get-base-python-deps
         run: |
-          pip install requests setuptools packaging pyyaml pydantic PyGithub
+          python -m pip install requests setuptools packaging pyyaml pydantic PyGithub
 
       - id: check-set-python-bounds
         name: check-set-python-bounds
@@ -82,11 +82,10 @@ jobs:
 
       - id: install-conda-env
         name: install-conda-env
-        uses: conda-incubator/setup-miniconda@v3
+        uses: conda-incubator/setup-miniconda@v4
         with:
           python-version: ${{ env.PYVER }}
           add-pip-as-python-dependency: true
-          architecture: x64
           use-mamba: true
           miniforge-version: latest
           channels: conda-forge
@@ -98,7 +97,7 @@ jobs:
         name: install-conda-base-deps
         run: |
           mamba install requests setuptools packaging pyyaml pydantic
-          pip install PyGithub
+          python -m pip install PyGithub
 
       - id: install-mdakit
         name: install-mdakit
@@ -119,8 +118,8 @@ jobs:
         continue-on-error: false
         run: |
           install=$(python utils/get_testdeps.py --mdakit ${{matrix.mdakit}})
-          echo "install tests:${install}"
-          eval ${install}
+          echo "test installs: ${install}"
+          eval "${install}"
 
       - id: install-mdanalysis
         name: install-mdanalysis

utils/get_install.py

@@ -53,4 +53,4 @@
     args = parser.parse_args()
     kit = MDAKit(f"mdakits/{args.mdakit}")
     instructions = kit.get_install(f"{args.itype}")
-    print(instructions)
+    print(instructions.lower())

utils/get_testdeps.py

@@ -46,4 +46,4 @@
     args = parser.parse_args()
     kit = MDAKit(f"mdakits/{args.mdakit}")
     instructions = kit.get_test_deps()
-    print(instructions)
+    print(instructions.lower())