Fix CI

zavolanlab · Dec 22, 2024 · f1e00f5 · f1e00f5
1 parent e6961e7
commit f1e00f5
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Showing 3 changed files with 7 additions and 4 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -32,6 +32,7 @@ jobs:
           activate-environment: zarp
           environment-file: install/environment.yml
           auto-activate-base: false
+          conda-remove-defaults: true
 
       - name: Update zarp env with root. packages
         run: mamba env update -p $CONDA_PREFIX -f install/environment.root.yml
@@ -80,6 +81,7 @@ jobs:
           activate-environment: zarp
           environment-file: install/environment.yml
           auto-activate-base: false
+          conda-remove-defaults: true
 
       - name: Update zarp env with root. packages
         run: |
@@ -125,6 +127,7 @@ jobs:
           activate-environment: zarp
           environment-file: install/environment.yml
           auto-activate-base: false
+          conda-remove-defaults: true
 
       - name: Update zarp env with root. packages
         run: mamba env update -p $CONDA_PREFIX -f install/environment.root.yml
@@ -162,6 +165,7 @@ jobs:
           activate-environment: zarp
           environment-file: install/environment.yml
           auto-activate-base: false
+          conda-remove-defaults: true
 
       - name: Update zarp env with root. packages
         run: mamba env update -p $CONDA_PREFIX -f install/environment.root.yml
@@ -199,6 +203,7 @@ jobs:
           activate-environment: zarp
           environment-file: install/environment.yml
           auto-activate-base: false
+          conda-remove-defaults: true
 
       - name: Update zarp env with dev. packages
         run: mamba env update -p $CONDA_PREFIX -f install/environment.dev.yml

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -21,13 +21,14 @@ jobs:
         uses: conda-incubator/setup-miniconda@v3
         with:
           python-version: "3.10"
-          mamba-version: "*"
+          mamba-version: "1"
           channels: conda-forge
           channel-priority: true
           auto-update-conda: false
           activate-environment: zarp
           environment-file: install/environment.yml
           auto-activate-base: false
+          conda-remove-defaults: true
 
       - name: Update zarp env with root. packages
         run: mamba env update -p $CONDA_PREFIX -f install/environment.root.yml

diff --git a/tests/input_files/samples_docker.tsv b/tests/input_files/samples_docker.tsv