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#!/bin/sh | ||
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# Check that the env folder exists or create it | ||
if [ -d ~/envs ] | ||
then | ||
echo "Found existing envs folder" | ||
else | ||
echo "Did not find envs folder, creating" | ||
mkdir ~/envs | ||
fi | ||
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# Check if conda environment exists. if it does, remove it. | ||
if [ -d "~/envs/fedomics_python_$1" ] | ||
then | ||
echo "Found existing fedomics conda environment, removing" | ||
conda env remove --prefix "~/envs/fedomics_python_$1" -y | ||
fi | ||
conda init bash | ||
. ~/.bashrc | ||
# | ||
echo "Creating environment" | ||
yes | conda create --prefix "~/envs/fedomics_python_$1" python="$1" | ||
echo "Created env fedomics_python_$1" | ||
eval "$(conda shell.bash hook)" | ||
conda activate "~/envs/fedomics_python_$1" |
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#!/bin/sh | ||
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# Check if conda environment exists. if it does, remove it. | ||
if [ -d "~/envs/fedomics_python_$1" ] | ||
then | ||
echo "Found existing fedomics conda environment, removing" | ||
conda env remove --prefix "~/envs/fedomics_python_$1" -y | ||
fi |
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--- | ||
name: Bug report | ||
about: Create a report to help us improve | ||
title: "[BUG] " | ||
labels: bug | ||
assignees: '' | ||
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--- | ||
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**Describe the bug** | ||
A clear and concise description of what the bug is. | ||
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**To Reproduce** | ||
Provide snippets of code and steps on how to reproduce the behavior. | ||
Please also specify the version you are using. | ||
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**Expected behavior** | ||
A clear and concise description of what you expected to happen. | ||
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**Screenshots** | ||
If applicable, add screenshots to help explain your problem. | ||
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**Desktop (please complete the following information):** | ||
- OS: [e.g. iOS] | ||
- Version [e.g. 0.02] | ||
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**Additional context** | ||
Add any other context about the problem here. |
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--- | ||
name: Feature request | ||
about: Suggest an idea for this project | ||
title: '' | ||
labels: '' | ||
assignees: '' | ||
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--- | ||
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**Is your feature request related to a problem? Please describe.** | ||
A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] | ||
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**Describe the solution you'd like** | ||
A clear and concise description of what you want to happen. | ||
|
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**Describe alternatives you've considered** | ||
A clear and concise description of any alternative solutions or features you've considered. | ||
|
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**Additional context** | ||
Add any other context or screenshots about the feature request here. |
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<!-- | ||
Thanks for contributing a pull request! Please ensure you have taken a look at | ||
the contribution guidelines: https://pydeseq2.readthedocs.io/en/latest/usage/contributing.html | ||
Make sure that you have added unit tests if applicable. | ||
--> | ||
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#### Reference Issue or PRs | ||
<!-- | ||
If this PR is related to an existing issue or PR please reference it, eg: | ||
Fixes #1234. | ||
You can use github keywords as described: | ||
https://github.com/blog/1506-closing-issues-via-pull-requests | ||
--> | ||
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|
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#### What does your PR implement? Be specific. |
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name: Python dev | ||
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on: | ||
pull_request: | ||
push: | ||
branches: | ||
- main | ||
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jobs: | ||
testing: | ||
runs-on: ubuntu-latest | ||
strategy: | ||
matrix: | ||
python: ["3.10", "3.11", "3.12"] | ||
name: Testing Python ${{ matrix.python }} | ||
steps: | ||
- name: Checkout repository | ||
uses: actions/checkout@v4 | ||
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- name: Set up Python | ||
uses: actions/setup-python@v5 | ||
with: | ||
python-version: ${{ matrix.python }} | ||
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- name: Install Poetry | ||
run: | | ||
python --version | ||
pip install poetry==1.8.2 | ||
- name: Install dependencies | ||
run: | | ||
python --version | ||
poetry install --with testing | ||
- name: Download data | ||
run: | | ||
mkdir -p /opt/conda | ||
wget https://repo.anaconda.com/miniconda/Miniconda3-py39_24.5.0-0-Linux-x86_64.sh -O /opt/conda/miniconda.sh | ||
bash /opt/conda/miniconda.sh -b -p /opt/miniconda | ||
poetry run fedpydeseq2-download-data --only_luad --raw_data_output_path /home/runner/work/fed-pydeseq2-datasets/fed-pydeseq2-datasets/data/raw --conda_activate_path /opt/miniconda/bin/activate | ||
- name: Testing | ||
run: | | ||
poetry run pytest -v tests | ||
linting: | ||
runs-on: ubuntu-latest | ||
name: Test Linting | ||
steps: | ||
- uses: actions/checkout@v4 | ||
- name: Set up Python | ||
uses: actions/setup-python@v5 | ||
with: | ||
python-version: "3.11" | ||
- name: Install Poetry | ||
run: pip install poetry==1.8.2 | ||
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- name: Install dependencies | ||
run: | | ||
which python | ||
python --version | ||
poetry install --with linting | ||
- name: Pre-commit checks | ||
run: | | ||
poetry run pre-commit run --all-files --show-diff-on-failure |
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# Byte-compiled / optimized / DLL files | ||
__pycache__/ | ||
*.py[cod] | ||
*$py.class | ||
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# C extensions | ||
*.so | ||
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# Distribution / packaging | ||
.Python | ||
build/ | ||
develop-eggs/ | ||
dist/ | ||
downloads/ | ||
eggs/ | ||
.eggs/ | ||
lib/ | ||
lib64/ | ||
parts/ | ||
sdist/ | ||
var/ | ||
wheels/ | ||
share/python-wheels/ | ||
*.egg-info/ | ||
.installed.cfg | ||
*.egg | ||
MANIFEST | ||
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# PyInstaller | ||
# Usually these files are written by a python script from a template | ||
# before PyInstaller builds the exe, so as to inject date/other infos into it. | ||
*.manifest | ||
*.spec | ||
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# Installer logs | ||
pip-log.txt | ||
pip-delete-this-directory.txt | ||
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# Unit test / coverage reports | ||
htmlcov/ | ||
.tox/ | ||
.nox/ | ||
.coverage | ||
.coverage.* | ||
.cache | ||
nosetests.xml | ||
coverage.xml | ||
*.cover | ||
*.py,cover | ||
.hypothesis/ | ||
.pytest_cache/ | ||
cover/ | ||
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# Translations | ||
*.mo | ||
*.pot | ||
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# Django stuff: | ||
*.log | ||
local_settings.py | ||
db.sqlite3 | ||
db.sqlite3-journal | ||
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# Flask stuff: | ||
instance/ | ||
.webassets-cache | ||
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# Scrapy stuff: | ||
.scrapy | ||
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# Sphinx documentation | ||
docs/_build/ | ||
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# PyBuilder | ||
.pybuilder/ | ||
target/ | ||
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# Jupyter Notebook | ||
.ipynb_checkpoints | ||
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# IPython | ||
profile_default/ | ||
ipython_config.py | ||
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# pyenv | ||
# For a library or package, you might want to ignore these files since the code is | ||
# intended to run in multiple environments; otherwise, check them in: | ||
# .python-version | ||
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# pipenv | ||
# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. | ||
# However, in case of collaboration, if having platform-specific dependencies or dependencies | ||
# having no cross-platform support, pipenv may install dependencies that don't work, or not | ||
# install all needed dependencies. | ||
#Pipfile.lock | ||
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# poetry | ||
# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. | ||
# This is especially recommended for binary packages to ensure reproducibility, and is more | ||
# commonly ignored for libraries. | ||
# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control | ||
#poetry.lock | ||
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# pdm | ||
# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. | ||
#pdm.lock | ||
# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it | ||
# in version control. | ||
# https://pdm.fming.dev/#use-with-ide | ||
.pdm.toml | ||
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm | ||
__pypackages__/ | ||
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# Celery stuff | ||
celerybeat-schedule | ||
celerybeat.pid | ||
|
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# SageMath parsed files | ||
*.sage.py | ||
|
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# Environments | ||
.env | ||
.venv | ||
env/ | ||
venv/ | ||
ENV/ | ||
env.bak/ | ||
venv.bak/ | ||
|
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# Spyder project settings | ||
.spyderproject | ||
.spyproject | ||
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# Rope project settings | ||
.ropeproject | ||
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# mkdocs documentation | ||
/site | ||
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# mypy | ||
.mypy_cache/ | ||
.dmypy.json | ||
dmypy.json | ||
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# Pyre type checker | ||
.pyre/ | ||
|
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# pytype static type analyzer | ||
.pytype/ | ||
|
||
# Cython debug symbols | ||
cython_debug/ | ||
|
||
# PyCharm | ||
# JetBrains specific template is maintained in a separate JetBrains.gitignore that can | ||
# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore | ||
# and can be added to the global gitignore or merged into this file. For a more nuclear | ||
# option (not recommended) you can uncomment the following to ignore the entire idea folder. | ||
.idea/ | ||
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# VSCode | ||
.vscode/ | ||
|
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# DS_Store | ||
.DS_Store | ||
|
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# Data | ||
data/centers_data/* | ||
data/pooled_data/* | ||
data/processed/* | ||
data/raw/tcga/* | ||
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fedpydeseq2_datasets/download_data/.snakemake/* | ||
fedpydeseq2_datasets/download_data/workflow/.snakemake | ||
fedpydeseq2_datasets/download_data/logs/ | ||
fedpydeseq2_datasets/download_data/results/ | ||
|
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!data/raw/tcga/centers.csv | ||
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*logs/ | ||
|
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data/* |
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default_language_version: | ||
python: python3.11 | ||
repos: | ||
- repo: https://github.com/sirosen/check-jsonschema | ||
rev: 0.27.0 | ||
hooks: | ||
- id: check-github-actions | ||
- id: check-github-workflows | ||
- repo: https://github.com/pre-commit/pre-commit-hooks | ||
rev: v4.4.0 | ||
hooks: | ||
- id: trailing-whitespace | ||
name: Trim trailing whitespace | ||
- id: end-of-file-fixer | ||
name: Fix end of files | ||
exclude: \.ipynb$ | ||
- repo: https://github.com/psf/black | ||
rev: 23.11.0 | ||
hooks: | ||
- id: black | ||
additional_dependencies: ["click==8.0.4"] | ||
args: # arguments to configure black | ||
- --line-length=88 | ||
- repo: https://github.com/astral-sh/ruff-pre-commit | ||
rev: v0.1.5 | ||
hooks: | ||
- id: ruff | ||
args: [--fix, --exit-non-zero-on-fix] | ||
- repo: https://github.com/pre-commit/mirrors-mypy | ||
rev: v1.7.0 | ||
hooks: | ||
- id: mypy | ||
exclude: ^(tests/|docs/source/conf.py|datasets/) |
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