From ded1c33718f4884f4954b42c09dd5adc4acbea0b Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Mon, 29 Sep 2025 13:29:06 +0200 Subject: [PATCH 1/2] use micromamba and last macOS docker image --- azure-pipelines.yml | 39 ++++++++++++++++----------------------- 1 file changed, 16 insertions(+), 23 deletions(-) diff --git a/azure-pipelines.yml b/azure-pipelines.yml index 48d1e407..6dd5e149 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -8,7 +8,7 @@ stages: timeoutInMinutes: 0 pool: vmImage: 'Ubuntu-latest' - container: python:3.8 + container: python:3.12 steps: - bash: | echo "##vso[task.prependpath]$HOME/.local/bin" @@ -45,26 +45,23 @@ stages: steps: - bash: | - echo "##vso[task.prependpath]$CONDA/bin" - hash -r - displayName: Add conda to PATH + "${SHELL}" <(curl -L micro.mamba.pm/install.sh) + displayName: Install micromamba - bash: | - conda config --set always_yes yes --set changeps1 no - conda info -a cat requirements_CI.txt | awk -v v=$(matplotlib.version) -v vp=$(python.version) 'BEGIN{print "python =="vp}{if($0~/matplotlib/){$0="matplotlib =="v}; print}' > requirements_CI_updated.txt - conda create -n pygenometracks --yes -c conda-forge -c bioconda --file requirements_CI_updated.txt - source activate pygenometracks + micromamba create -n pygenometracks --yes -c conda-forge -c bioconda --file requirements_CI_updated.txt + micromamba activate pygenometracks python -m pip install . displayName: installing dependencies - script: | - source activate pygenometracks + eval "$(micromamba shell hook --shell bash)" + micromamba activate pygenometracks py.test pygenometracks --doctest-modules -n 4 displayName: pytest - - job: OSX timeoutInMinutes: 0 pool: - vmImage: 'macOS-11' + vmImage: 'macOS-latest' strategy: matrix: Python38LowMatplotlib: @@ -76,25 +73,21 @@ stages: Python39HighMatplotlib: python.version: '3.9' matplotlib.version: '3.5.1' - steps: - bash: | - echo "##vso[task.prependpath]$CONDA/bin" - hash -r - displayName: Add conda to PATH - # On Hosted macOS, the agent user doesn't have ownership of Miniconda's installation directory/ - # We need to take ownership if we want to update conda or install packages globally - - bash: sudo chown -R $USER $CONDA - displayName: Take ownership of conda installation + brew install micromamba + displayName: Install micromamba - bash: | - conda config --set always_yes yes --set changeps1 no - conda info -a + eval "$(micromamba shell hook --shell bash)" cat requirements_CI.txt | awk -v v=$(matplotlib.version) -v vp=$(python.version) 'BEGIN{print "python =="vp}{if($0~/matplotlib/){$0="matplotlib =="v}; print}' > requirements_CI_updated.txt - conda create -n pygenometracks --yes -c conda-forge -c bioconda --file requirements_CI_updated.txt + micromamba create -n pygenometracks --yes -c conda-forge -c bioconda --file requirements_CI_updated.txt + micromamba activate pygenometracks + echo $PATH python -m pip install . displayName: installing dependencies - script: | - source activate pygenometracks + eval "$(micromamba shell hook --shell bash)" + micromamba activate pygenometracks py.test pygenometracks --doctest-modules -n 4 displayName: pytest From 356c3275be1cc82d9a0b1ee2a3c812c3bb750a84 Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Mon, 29 Sep 2025 13:29:34 +0200 Subject: [PATCH 2/2] limit bx-python version to make CI tests pass --- requirements_CI.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_CI.txt b/requirements_CI.txt index c4b52cbf..6c016d20 100644 --- a/requirements_CI.txt +++ b/requirements_CI.txt @@ -8,7 +8,7 @@ pysam >=0.14 gffutils >=0.9 pybedtools >=0.8.1 tqdm >=4.20 -bx-python >=0.8.13 +bx-python >=0.8.13, <0.13.0 pyfaidx >=0.1.3 # Below are dependencies for tests pytest