Tests in GH actions

bioexcel · Sep 7, 2023 · 6bcc269 · 6bcc269
1 parent e00c05f
commit 6bcc269
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Showing 2 changed files with 22 additions and 18 deletions.
diff --git a/.github/env.yaml b/.github/env.yaml
@@ -2,11 +2,10 @@ name: test_environment
 channels:
   - conda-forge
   - bioconda
-  - defaults
+  - anaconda
 dependencies:
-  - python >=3.7,<3.10
-  - biobb_common ==4.0.0
-  - pandas ==1.3.0
+  - biobb_common ==4.1.0
+  - pandas >=1.3.0
   - scikit-learn ==0.24.2
   - curves ==3.0.0
 
diff --git a/.github/workflows/linting_and_testing.yml b/.github/workflows/linting_and_testing.yml
@@ -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
@@ -35,30 +35,35 @@ 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
             pytest-html
             flake8
-            pillow
-            imagehash
             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
@@ -73,7 +78,7 @@ jobs:
           flake8 . --exclude=docs --ignore=C901,E226 --count --exit-zero --max-complexity=10 --max-line-length=9999 --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
 
@@ -84,7 +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
@@ -103,12 +108,12 @@ jobs:
           pytest biobb_dna/test/unitests/ --cov=biobb_dna/ --cov-report=xml --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
@@ -123,7 +128,7 @@ 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