Re-enable mamba in CI (#3177)

Fixes #3048
MDAnalysis · Apr 21, 2021 · ec7d636 · ec7d636
1 parent b8911ec
commit ec7d636
Showing 1 changed file with 10 additions and 9 deletions.
diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml
@@ -80,6 +80,7 @@ jobs:
         echo "CXX=clang++" >> $GITHUB_ENV
         gfortran-9 -v
         echo "FC=gfortran-9" >> $GITHUB_ENV
+        echo "numprocs=3" >> $GITHUB_ENV
 
     - name: setup_linux
       if: startsWith(matrix.os, 'ubuntu')
@@ -92,17 +93,17 @@ jobs:
         echo "CXX=g++" >> $GITHUB_ENV
         gfortran -v
         echo "FC=gfortran" >> $GITHUB_ENV
+        echo "numprocs=2" >> $GITHUB_ENV
 
     - name: setup_miniconda
       uses: conda-incubator/setup-miniconda@v2
       with:
         python-version: ${{ matrix.python-version }}
         auto-update-conda: true
         channel-priority: flexible
-        channels: biobuilds, conda-forge
+        channels: conda-forge, biobuilds
         add-pip-as-python-dependency: true
-        # TODO: mamba causes pip to segfault, switch when fixed
-        #mamba-version: "*"
+        mamba-version: "*"
         architecture: x64
 
     - name: install_deps
@@ -114,7 +115,7 @@ jobs:
         # NOTE: set matrix.numpy to pin to a specific numpy version
         conda_deps="${{ matrix.numpy }} ${MDA_CONDA_${{ matrix.run_type }}_DEPS}"
         pip_deps=${MDA_PIP_${{ matrix.run_type }}_DEPS}
-        conda install ${conda_deps}
+        mamba install ${conda_deps}
         pip install ${pip_deps}
 
         # also install asv if required
@@ -158,7 +159,7 @@ jobs:
           PYTEST_FLAGS="${PYTEST_FLAGS} --cov=MDAnalysis --cov-report=xml"
         fi
         echo $PYTEST_FLAGS
-        pytest -n 2 testsuite/MDAnalysisTests $PYTEST_FLAGS
+        pytest -n $numprocs testsuite/MDAnalysisTests $PYTEST_FLAGS
 
     - name: run_asv
       if: contains(matrix.name, 'asv_check')
@@ -191,15 +192,16 @@ jobs:
         python-version: 3.7
         auto-update-conda: true
         channel-priority: flexible
-        channels: biobuilds, conda-forge
+        channels: conda-forge, biobuilds
         add-pip-as-python-dependency: true
         architecture: x64
+        mamba-version: "*"
 
     - name: install_deps
       run: |
         conda_deps="${{ env.MDA_CONDA_MIN_DEPS }} ${{ env.MDA_CONDA_EXTRA_DEPS}}"
         pip_deps="${{ env.MDA_PIP_MIN_DEPS}} ${{ env.MDA_PIP_EXTRA_DEPS }} sphinx==1.8.5 sphinx-sitemap sphinx_rtd_theme msmb_theme==1.2.0"
-        conda install ${conda_deps}
+        mamba install ${conda_deps}
         pip install ${pip_deps}
 
     - name: install_mda
@@ -280,7 +282,6 @@ jobs:
         channel-priority: flexible
         channels: conda-forge
         add-pip-as-python-dependency: true
-        mamba-version: "*"
         architecture: x64
 
     - name: install
@@ -311,7 +312,7 @@ jobs:
         channel-priority: flexible
         channels: conda-forge
         add-pip-as-python-dependency: true
-        mamba-version: "*"
+        # mamba not enabled as install longer than deps install
         architecture: x64
 
     - name: install_conda