Create AP env locally with prefix

.github/workflows/github_actions.yml

@@ -18,9 +18,6 @@ jobs:
         python-version: ["3.10", "3.11"]
         install-type: ['user', 'developer']
 
-    env:
-      MAMBA_ROOT_PREFIX: $RUNNER_TEMP/mamba-root
-
     steps:
       - uses: webfactory/[email protected]
         with:
@@ -39,20 +36,20 @@ jobs:
       - if: matrix.install-type == 'user'
         run: |
           conda install -y -c conda-forge mamba
-          mamba create -n AlphaPulldown -c omnia -c bioconda -c conda-forge python==${{ matrix.python-version }} \
-          openmm==8.0 pdbfixer==1.9 kalign2 hmmer hhsuite modelcif 
+          mamba create -y -p ./AlphaPulldown -c omnia -c bioconda -c conda-forge python==3.10 \
+            openmm==8.0 pdbfixer==1.9 kalign2 hmmer hhsuite modelcif
           eval "$(conda shell.bash hook)"
-          conda activate AlphaPulldown
+          conda activate ./AlphaPulldown
           pip install alphapulldown
           pip install -U "jax[cuda12]"
       - if: matrix.install-type == 'developer'
         run: |
           conda install -y -c conda-forge mamba
-          mamba create -n AlphaPulldown -c omnia -c bioconda -c conda-forge python==${{ matrix.python-version }} \
-          openmm==8.0 pdbfixer==1.9 kalign2 hmmer hhsuite modelcif 
+          mamba create -y -p ./AlphaPulldown -c omnia -c bioconda -c conda-forge python==3.10 \
+            openmm==8.0 pdbfixer==1.9 kalign2 hmmer hhsuite modelcif
           eval "$(conda shell.bash hook)"
-          conda activate AlphaPulldown
-          pip install .
+          conda activate ./AlphaPulldown
+          pip install alphapulldown
           pip install -U "jax[cuda12]"
           # export PYTHONPATH=$PWD/AlphaLink2:$PYTHONPATH
           # install dependencies for AlphaLink backend