use mamba

KosinskiLab · Oct 30, 2024 · 690e91d · 690e91d
1 parent 8bf9580
commit 690e91d
Showing 1 changed file with 9 additions and 5 deletions.
diff --git a/.github/workflows/github_actions.yml b/.github/workflows/github_actions.yml
@@ -35,17 +35,21 @@ jobs:
           echo "$GITHUB_WORKSPACE/alphapulldown" >> $GITHUB_PATH
       - if: matrix.install-type == 'user'
         run: |
-          conda create -n AlphaPulldown -c omnia -c bioconda -c conda-forge python==${{ matrix.python-version }} openmm==8.0 pdbfixer==1.9 kalign2 hmmer hhsuite modelcif
+          conda install --solver=classic -y -c conda-forge conda-libmamba-solver libmamba libmambapy libarchive
+          mamba create -n AlphaPulldown -c omnia -c bioconda -c conda-forge python==${{ matrix.python-version }} \
+          openmm==8.0 pdbfixer==1.9 kalign2 hmmer hhsuite modelcif 
           eval "$(conda shell.bash hook)"
-          conda activate AlphaPulldown
+          mamba activate AlphaPulldown
           pip install alphapulldown==2.0.0b6
           pip install -U "jax[cuda12]"
-          conda install -c conda-forge biopython==1.81 importlib_metadata pytest # REMOVE AFTER UPDATING THE PYPI RELEASE VERSION!
+          mamba install -c conda-forge biopython==1.81 importlib_metadata pytest # REMOVE AFTER UPDATING THE PYPI RELEASE VERSION!
       - if: matrix.install-type == 'developer'
         run: |
-          conda create -n AlphaPulldown -c omnia -c bioconda -c conda-forge python==${{ matrix.python-version }} openmm==8.0 pdbfixer==1.9 kalign2 hmmer hhsuite modelcif
+          conda install --solver=classic -y -c conda-forge conda-libmamba-solver libmamba libmambapy libarchive
+          mamba create -n AlphaPulldown -c omnia -c bioconda -c conda-forge python==${{ matrix.python-version }} \
+          openmm==8.0 pdbfixer==1.9 kalign2 hmmer hhsuite modelcif 
           eval "$(conda shell.bash hook)"
-          conda activate AlphaPulldown
+          mamba activate AlphaPulldown
           pip install -e .
           pip install -U "jax[cuda12]"
           # export PYTHONPATH=$PWD/AlphaLink2:$PYTHONPATH