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32 changes: 12 additions & 20 deletions .github/workflows/CI.yml
Original file line number Diff line number Diff line change
Expand Up @@ -366,29 +366,24 @@ jobs:
restore-keys: datasets-
enableCrossOsArchive: true

- uses: conda-incubator/setup-miniconda@d2e6a045a86077fb6cad6f5adf368e9076ddaa8d # corresponds to v3.1.0
- uses: mamba-org/setup-micromamba@v2
with:
auto-update-conda: true
python-version: ${{ matrix.python-version }}
mamba-version: "*"
channels: conda-forge
channel-priority: true
activate-environment: elephant
create-args: python=${{ matrix.python-version }}
environment-file: requirements/environment-tests.yml
conda-remove-defaults: true
init-shell: bash

- name: Install dependencies
shell: bash -el {0}
run: |
python --version
mamba install -c conda-forge pytest pytest-cov coveralls mpi4py openmpi
micromamba install -y -c conda-forge pytest pytest-cov coveralls mpi4py openmpi
pip install -e .

- name: List packages
shell: bash -el {0}
run: |
pip list
mamba list
micromamba list
python --version

- name: Test with pytest
Expand Down Expand Up @@ -438,23 +433,20 @@ 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@d2e6a045a86077fb6cad6f5adf368e9076ddaa8d # corresponds to v3.1.0
- uses: mamba-org/setup-micromamba@v2
with:
auto-update-conda: true
python-version: ${{ matrix.python-version }}
mamba-version: "*"
activate-environment: elephant
create-args: python=${{ matrix.python-version }}
environment-file: requirements/environment.yml
conda-remove-defaults: true
init-shell: bash

- name: Install dependencies
shell: bash -el {0} # enables conda incubator to activate environment
shell: bash -el {0}
run: |
sudo apt-get update
sudo apt install -y libopenmpi-dev openmpi-bin

mamba install -c conda-forge openmpi pandoc libstdcxx-ng # fix libstdc++.so.6: version for new scipy versions > 1.9.1
mamba env update --file requirements/environment-docs.yml --name elephant
micromamba install -y -c conda-forge openmpi pandoc libstdcxx-ng # fix libstdc++.so.6: version for new scipy versions > 1.9.1
micromamba env update --file requirements/environment-docs.yml --name elephant
python -m pip install --upgrade pip
pip install -e .[extras,tutorials,docs]
# run notebooks
Expand All @@ -464,7 +456,7 @@ jobs:
shell: bash -el {0}
run: |
pip list
mamba list
micromamba list
python --version

- name: make html
Expand Down
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