Skip to content
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

Jump to bottom

switch to conda with libmamba #42

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

switch to conda with libmamba #42

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
a144c3e
switch to conda with libmamba
cdiener Nov 21, 2024
f8d655a
Merge branch 'main' into feature/conda
cdiener Nov 21, 2024
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
10 changes: 3 additions & 7 deletions .github/workflows/qiime_dev.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -23,10 +23,6 @@ jobs:
- uses: actions/checkout@v4
- name: Setup conda
uses: conda-incubator/setup-miniconda@v3
with:
miniforge-variant: Mambaforge
miniforge-version: latest
use-mamba: true
- shell: bash -l {0}
run: |
conda info
Expand All @@ -35,19 +31,19 @@ jobs:
shell: bash -l {0}
run: |
wget https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py38-${{matrix.os.short}}-conda.yml
mamba env create -n qiime2-dev --file qiime2-latest-py38-${{matrix.os.short}}-conda.yml
conda env create -n qiime2-dev --file qiime2-latest-py38-${{matrix.os.short}}-conda.yml
rm qiime2-latest-py38-${{matrix.os.short}}-conda.yml
- name: Install q2-micom
shell: bash -l {0}
run: |
conda activate qiime2-dev
mamba env update -n qiime2-dev -f q2-micom.yml
conda env update -n qiime2-dev -f q2-micom.yml
pip install -e .
- name: Install CPLEX
shell: bash -l {0}
run: |
conda activate qiime2-dev
mamba install -y -c ibmdecisionoptimization cplex
conda install -y -c ibmdecisionoptimization cplex
- name: Lint with flake8
shell: bash -l {0}
run: |
Expand Down
12 changes: 4 additions & 8 deletions .github/workflows/test_package.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -33,12 +33,8 @@ jobs:

steps:
- uses: actions/checkout@v4
- name: Setup Mambaforge
- name: Setup conda
uses: conda-incubator/setup-miniconda@v3
with:
miniforge-variant: Mambaforge
miniforge-version: latest
use-mamba: true
- shell: bash -l {0}
run: |
conda info
Expand All @@ -51,17 +47,17 @@ jobs:
- name: Install Qiime 2
shell: bash -l {0}
run: |
mamba env create -n qiime2-dev --file env.yml
conda env create -n qiime2-dev --file env.yml
- name: Install CPLEX
shell: bash -l {0}
run: |
conda activate qiime2-dev
mamba install -v -c ibmdecisionoptimization cplex
conda install -v -c ibmdecisionoptimization cplex
- name: Install q2-micom
shell: bash -l {0}
run: |
conda activate qiime2-dev
mamba env update -n qiime2-dev -f q2-micom.yml
conda env update -n qiime2-dev -f q2-micom.yml
pip install -e .
- name: Lint with flake8
shell: bash -l {0}
Expand Down
Loading