Remove biobuilds from the global list of channels

It brings an outdated version of libssh2, which links to non-existing libopenssl.so.1.0.0
MDAnalysis · Apr 4, 2021 · 08c4e9d · 08c4e9d
1 parent d8226cf
commit 08c4e9d
Showing 1 changed file with 12 additions and 3 deletions.
diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml
@@ -15,9 +15,12 @@ defaults:
 
 env:
   MDA_CONDA_MIN_DEPS: "pip pytest==6.1.2 mmtf-python biopython networkx cython matplotlib-base scipy griddataformats hypothesis gsd codecov"
-  MDA_CONDA_EXTRA_DEPS: "seaborn>=0.7.0 clustalw=2.1 netcdf4 scikit-learn joblib>=0.12 chemfiles>=0.9 tqdm>=4.43.0 tidynamics>=1.0.0 rdkit>=2020.03.1 h5py==2.10.0"
+  MDA_CONDA_EXTRA_DEPS: "seaborn>=0.7.0 netcdf4 scikit-learn joblib>=0.12 chemfiles>=0.9 tqdm>=4.43.0 tidynamics>=1.0.0 rdkit>=2020.03.1 h5py==2.10.0"
   MDA_PIP_MIN_DEPS: "coveralls coverage<5 pytest-cov pytest-xdist"
   MDA_PIP_EXTRA_DEPS: "duecredit parmed"
+  # Install clustalw separately since it needs a specific conda channel (biobuilds)
+  # which do not play nicely with conda-forge
+  MDA_CLUSTALW_DEP: "clustalw=2.1"
 
 jobs:
   main_tests:
@@ -98,7 +101,7 @@ jobs:
           python-version: ${{ matrix.python-version }}
           auto-update-conda: true
           channel-priority: flexible
-          channels: biobuilds, conda-forge
+          channels: conda-forge
           add-pip-as-python-dependency: true
           # TODO: mamba causes pip to segfault, switch when fixed
           #mamba-version: "*"
@@ -121,6 +124,10 @@ jobs:
             pip install asv
           fi
 
+          if [ ${{ matrix.run_type }} = "FULL" ]; then
+            conda install -c biobuilds $MDA_CLUSTALW_DEP
+          fi
+
       - name: check_setup
         run: |
           # Check OS and python setup
@@ -189,7 +196,7 @@ jobs:
           python-version: 3.7
           auto-update-conda: true
           channel-priority: flexible
-          channels: biobuilds, conda-forge
+          channels: conda-forge
           add-pip-as-python-dependency: true
           architecture: x64
 
@@ -200,6 +207,8 @@ jobs:
           conda install ${conda_deps}
           pip install ${pip_deps}
 
+          conda install -c biobuilds $MDA_CLUSTALW_DEP
+
       - name: install_mda
         run: |
           cd package && python setup.py develop