Troubleshoot CI (#1)

This update is fixing bugs in the CI configuration for GitHub Actions.
bioforensics · Jun 12, 2020 · 9b47894 · 9b47894
1 parent 931e51f
commit 9b47894
Showing 1 changed file with 19 additions and 4 deletions.
diff --git a/.github/workflows/cibuild.yml b/.github/workflows/cibuild.yml
@@ -21,15 +21,30 @@ jobs:
         uses: actions/setup-python@v1
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Install
+      - name: Environment setup
         run: |
           conda env create -f environment.yaml
+      - name: Taxonomy data download
+        run: |
+          mkdir ~/.taxonkit
+          pushd ~/.taxonkit
+          wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
+          tar -xzf taxdump.tar.gz
+          popd
+      - name: Install
+        run: |
+          source $(conda info --base)/etc/profile.d/conda.sh
           conda activate pytaxonkit
-          mkdir ~/.taxonkit && pushd ~/.taxonkit && wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz && tar -xzf taxdump.tar.gz && popd
           python -m pip install --upgrade pip
           pip install .
           make devenv
       - name: Style check
-        run: make style
+        run: |
+          source $(conda info --base)/etc/profile.d/conda.sh
+          conda activate pytaxonkit
+          make style
       - name: Test with pytest
-        run: make test
+        run: |
+          source $(conda info --base)/etc/profile.d/conda.sh
+          conda activate pytaxonkit
+          make test