Skip to content

Remove anaconda usage #492

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 2 commits into
base: master
Choose a base branch
from
Open

Remove anaconda usage #492

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
ded1c33
use micromamba and last macOS docker image
lldelisle Sep 29, 2025
356c327
limit bx-python version to make CI tests pass
lldelisle Sep 29, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
39 changes: 16 additions & 23 deletions azure-pipelines.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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"
Expand Down Expand Up @@ -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:
Expand All @@ -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

Expand Down
2 changes: 1 addition & 1 deletion requirements_CI.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down