Tests in GH actions

.github/env.yaml

@@ -4,8 +4,7 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - python >=3.7,<3.10
-  - biobb_common ==4.0.0
+  - biobb_common ==4.1.0
   - mdanalysis >=2.0.0
-  - biobb_structure_checking ==3.13.0
+  - biobb_structure_checking ==3.13.4
   - cmip ==2.7.0

.github/workflows/linting_and_testing.yaml

@@ -19,7 +19,7 @@ jobs:
     strategy:
       matrix:
         os: [self-hosted]
-        python-version: ["3.7", "3.8", "3.9"]
+        python-version: ["3.8", "3.9", "3.10"]
     runs-on: ${{ matrix.os }}
     steps:
       - name: Check out repository code
@@ -35,11 +35,18 @@ jobs:
         run: |
           ls ${{ github.workspace }}
 
+      - name: Remove all micromamba installations
+        run: |
+          rm -rf /home/user/.bash_profile /home/user/.conda /home/user/micromamba /home/user/micromamba-bin 2>/dev/null
+          touch /home/user/.bash_profile
+
       - name: provision-with-micromamba
-        uses: mamba-org/provision-with-micromamba@main
+        uses: mamba-org/setup-micromamba@v1
         with:
+          generate-run-shell: true
+          post-cleanup: all
           environment-file: .github/env.yaml
-          extra-specs: |
+          create-args: >-
             python=${{ matrix.python-version }}
             pytest
             pytest-cov
@@ -48,15 +55,15 @@ jobs:
             pip
 
       - name: Install genbadge from pip
-        shell: bash -l {0}  # necessary for conda env to be active
+        shell: micromamba-shell {0}  # necessary for conda env to be active
         run: pip install genbadge[all]
 
       - name: List installed package versions
-        shell: bash -l {0}  # necessary for conda env to be active
+        shell: micromamba-shell {0}  # necessary for conda env to be active
         run: micromamba list
 
       - name: Lint with flake8
-        shell: bash -l {0}  # necessary for conda env to be active
+        shell: micromamba-shell {0}  # necessary for conda env to be active
         run: |
           # F Codes: https://flake8.pycqa.org/en/latest/user/error-codes.html
           # E Code: https://pycodestyle.pycqa.org/en/latest/intro.html#error-codes
@@ -71,7 +78,7 @@ jobs:
           flake8 . --exclude=docs --ignore=C901,E226 --count --exit-zero --max-complexity=10 --max-line-length=999 --statistics --format=html --htmldir=./reports/flake8/ --tee --output-file=./reports/flake8/flake8stats.txt
 
       - name: Generate Flake8 badge
-        shell: bash -l {0}  # necessary for conda env to be active
+        shell: micromamba-shell {0}  # necessary for conda env to be active
         run: |
           genbadge flake8 --name "Flake8" --input-file ./reports/flake8/flake8stats.txt  --output-file ./reports/flake8/flake8badge.svg
 
@@ -82,7 +89,7 @@ jobs:
           path: './biobb_common'
 
       - name: Run tests
-        shell: bash -l {0}  # necessary for conda env to be active
+        shell: micromamba-shell {0}  # necessary for conda env to be active
         run: |
           # Ignoring docker and singularity tests
           export PYTHONPATH=.:./biobb_common:$PYTHONPATH
@@ -94,12 +101,12 @@ jobs:
           pytest biobb_cmip/test/unitests/ --cov=biobb_cmip/ --cov-report=xml --ignore-glob=*container.py --ignore-glob=*docker.py --ignore-glob=*singularity.py --junit-xml=./reports/junit/junit.xml --html=./reports/junit/report.html
 
       - name: Generate Tests badge
-        shell: bash -l {0}  # necessary for conda env to be active
+        shell: micromamba-shell {0}  # necessary for conda env to be active
         run: |
           genbadge tests --name "Tests" --input-file ./reports/junit/junit.xml  --output-file ./reports/junit/testsbadge.svg
 
       - name: Generate Coverage badge
-        shell: bash -l {0}  # necessary for conda env to be active
+        shell: micromamba-shell {0}  # necessary for conda env to be active
         run: |
           # Create directory for flake8 reports
           mkdir -p ./reports/coverage
@@ -114,7 +121,7 @@ jobs:
         with:
           folder: ./reports
 
-      - name: Restore .bash_profile
-        run: cp ~/.bash_profile_orig ~/.bash_profile
+      # - name: Restore .bash_profile
+      #   run: cp ~/.bash_profile_orig ~/.bash_profile
 
 

.readthedocs.yaml

@@ -11,7 +11,7 @@ sphinx:
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-   version: "3.7"
+   version: "3.8"
    install:
       - requirements: biobb_cmip/docs/source/requirements.txt
       - method: pip

biobb_cmip/docs/source/requirements.txt

@@ -1 +1 @@
-docutils==0.17.1
+# docutils==0.17.1