fix

cbg-ethz · Nov 12, 2024 · c95f26c · c95f26c
1 parent 8b9b4ec
commit c95f26c
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Showing 2 changed files with 14 additions and 12 deletions.
diff --git a/.github/workflows/poetry-conda.yml b/.github/workflows/poetry-conda.yml
@@ -18,19 +18,24 @@ jobs:
         uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
-          channels: conda-forge
-
+          channels: conda-forge, bioconda
           environment-file: environment.yml
           activate-environment: myenv
 
-      #- name: Install Poetry
-      #  uses: snok/install-poetry@v1
-      #  with:
-      #    virtualenvs-create: true
-      #    virtualenvs-in-project: true
+      - name: Install Poetry
+        run: |
+          source $(conda info --base)/etc/profile.d/conda.sh
+          conda activate myenv
+          conda install -c conda-forge poetry
 
       - name: Install the module
-        run: poetry install --with dev --no-interaction
+        run: |
+          source $(conda info --base)/etc/profile.d/conda.sh
+          conda activate myenv
+          poetry install --with dev --no-interaction
 
       - name: Run unit tests
-        run: poetry run pytest
+        run: |
+          source $(conda info --base)/etc/profile.d/conda.sh
+          conda activate myenv
+          poetry run pytest
diff --git a/environment.yml b/environment.yml
@@ -6,6 +6,3 @@ channels:
 dependencies:
   - python=3.10
   - nextclade
-  - pip
-  - pip:
-    - poetry