[Fix] CI docs runner conda (NeuralEnsemble#615)

* fix docs runner * activate env for steps install, list, and make html * remove conda update * add install for pandoc * change environment file * optimize macOS runner * update setup-miniconda t newer version * edit shell command * Revert "edit shell command" This reverts commit 03cd19d. * add comment * use mamba in CI runners * add channels * add channels * add proper python version * update to latest version * add python version * change python version * change mamba version * activate base * no auto update * revert changes * add update * change channel * openmpi install * don't pin channel * docs runner update * add libstd install * reverse to conda * update env * use openmpi * use conda for mpi4py * remove comment * remove env list for Conda runner --------- Co-authored-by: Moritz-Alexander-Kern <[email protected]>
INM-6 · Mar 25, 2024 · d046165 · d046165
1 parent 7112f84
commit d046165
Showing 1 changed file with 33 additions and 30 deletions.
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -139,10 +139,13 @@ jobs:
           path: ~/conda_pkgs_dir
           key: ${{ runner.os }}-conda-${{hashFiles('requirements/environment.yml') }}-${{ hashFiles('**/CI.yml') }}-${{ steps.date.outputs.date }}
 
-      - uses: conda-incubator/setup-miniconda@3b0f2504dd76ef23b6d31f291f4913fb60ab5ff3 # corresponds to v2.2.0
+      - uses: conda-incubator/setup-miniconda@030178870c779d9e5e1b4e563269f3aa69b04081 # corresponds to v3.0.3
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
+          mamba-version: "*"
+          channels: conda-forge,defaults
+          channel-priority: true
           activate-environment: elephant
           environment-file: requirements/environment-tests.yml
           auto-activate-base: false
@@ -152,17 +155,16 @@ jobs:
         shell: bash -l {0}
         run: |
           python --version
-          conda env list
-          conda install mpi4py openmpi
-          conda install pytest
-          conda install pytest-cov coveralls
+          mamba install mpi4py openmpi
+          mamba install pytest
+          mamba install pytest-cov coveralls
           pip install -e .[extras]
 
       - name: List packages
         shell: bash -l {0}
         run: |
           pip list
-          conda list
+          mamba list
           python --version
 
       - name: Test with pytest
@@ -310,7 +312,6 @@ jobs:
       matrix:
         # OS [ubuntu-latest, macos-latest, windows-latest]
         os: [ubuntu-latest]
-        python-version: [3.9]
 
       # do not cancel all in-progress jobs if any matrix job fails
       fail-fast: false
@@ -325,34 +326,34 @@ jobs:
 
           key: ${{ runner.os }}-pip-${{hashFiles('requirements/environment-tests.yml') }}-${{ hashFiles('**/CI.yml') }}-${{ steps.date.outputs.date }}
 
-      - uses: conda-incubator/setup-miniconda@3b0f2504dd76ef23b6d31f291f4913fb60ab5ff3 # corresponds to v2.2.0
+      - uses: conda-incubator/setup-miniconda@030178870c779d9e5e1b4e563269f3aa69b04081 # corresponds to v3.0.3
         with:
           auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
+          python-version: 3.11
+          mamba-version: "*"
+          channels: conda-forge,defaults
+          channel-priority: true
           activate-environment: elephant
           environment-file: requirements/environment-tests.yml
-          auto-activate-base: false
-          use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
 
       - name: Install dependencies
-        shell: bash -l {0}
+        shell: bash -el {0}
         run: |
           python --version
-          conda env list
           conda install mpi4py openmpi
-          conda install pytest
-          conda install pytest-cov coveralls
+          mamba install pytest
+          mamba install pytest-cov coveralls
           pip install -e .
 
       - name: List packages
-        shell: bash -l {0}
+        shell: bash -el {0}
         run: |
           pip list
-          conda list
+          mamba list
           python --version
 
       - name: Test with pytest
-        shell: bash -l {0}
+        shell: bash -el {0}
         run: |
           pytest --cov=elephant
 
@@ -379,11 +380,6 @@ jobs:
 
       - uses: actions/checkout@v3
 
-      - name: Add conda to system path
-        run: |
-          # $CONDA is an environment variable pointing to the root of the miniconda directory
-          echo $CONDA/bin >> $GITHUB_PATH
-
       - name: Cache pip
         uses: actions/cache@v3
         with:
@@ -392,15 +388,22 @@ jobs:
           key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements-docs.txt') }}-${{ hashFiles('**/requirements-tutorials.txt') }}-${{ hashFiles('**/environment-docs.yml') }}
            -${{ hashFiles('**/CI.yml') }}-${{ steps.date.outputs.date }}
 
+      - uses: conda-incubator/setup-miniconda@030178870c779d9e5e1b4e563269f3aa69b04081 # corresponds to v3.0.3
+        with:
+          auto-update-conda: true
+          python-version: 3.11
+          mamba-version: "*"
+          activate-environment: elephant
+          environment-file: requirements/environment.yml
+
       - name: Install dependencies
+        shell: bash -el {0} # enables conda incubator to activate environment
         run: |
-          conda config --add channels conda-forge # bugfix with scipy==1.8.1: libstdcxx-ng 12.1.0 required
           sudo apt-get update
           sudo apt install -y libopenmpi-dev openmpi-bin
-          conda update conda
+          
           conda install -c conda-forge openmpi pandoc libstdcxx-ng # fix libstdc++.so.6: version for new scipy versions > 1.9.1
-          conda env update --file requirements/environment-docs.yml --name base
-          activate base
+          mamba env update --file requirements/environment-docs.yml --name elephant
           python -m pip install --upgrade pip
           pip install -r requirements/requirements-docs.txt
           pip install -r requirements/requirements-tutorials.txt
@@ -409,15 +412,15 @@ jobs:
           sed -i -E "s/nbsphinx_execute *=.*/nbsphinx_execute = 'always'/g" doc/conf.py
 
       - name: List packages
+        shell: bash -el {0}
         run: |
-          activate base
           pip list
-          conda list
+          mamba list
           python --version
 
       - name: make html
+        shell: bash -el {0}
         run: |
-          activate base
           cd doc
           make html