From f3483c88c98410612e2627985afa783ebbc2430d Mon Sep 17 00:00:00 2001 From: Harrison Deng Date: Mon, 17 Feb 2025 17:45:18 +0000 Subject: [PATCH] Separated CLI from engine bioconda update pipelines --- .gitignore | 178 ++++++++++++++++++++++++++++++++++++++ Jenkinsfile | 26 +++++- autobigs-engine/meta.yaml | 44 ---------- environment.yml | 2 - 4 files changed, 202 insertions(+), 48 deletions(-) create mode 100644 .gitignore delete mode 100644 autobigs-engine/meta.yaml diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..49413d7 --- /dev/null +++ b/.gitignore @@ -0,0 +1,178 @@ +# Created by https://www.toptal.com/developers/gitignore/api/python +# Edit at https://www.toptal.com/developers/gitignore?templates=python + +### Python ### +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# 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 + +# 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 + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ +cover/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +.pybuilder/ +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# 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 + +# 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 + +# 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 + +# 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 + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ + +# 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/ + +### Python Patch ### +# Poetry local configuration file - https://python-poetry.org/docs/configuration/#local-configuration +poetry.toml + +# ruff +.ruff_cache/ + +# LSP config files +pyrightconfig.json + +# End of https://www.toptal.com/developers/gitignore/api/python + +autobigs-engine \ No newline at end of file diff --git a/Jenkinsfile b/Jenkinsfile index ea9e9f4..f37ce23 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -11,11 +11,10 @@ pipeline { parallel { stage("recipes repo") { steps { - sh 'git clone https://github.com/RealYHD/bioconda-recipes.git' + sh 'git clone https://github.com/Syph-and-VPD-Lab/bioconda-recipes.git' dir('bioconda-recipes') { sh 'git pull' sh 'git pull origin update-autobigs-engine' - sh 'git pull origin update-autobigs-cli' } } } @@ -26,5 +25,28 @@ pipeline { } } } + stage("generate recipe") { + steps { + sh 'grayskull pypi autobigs.engine --maintainers "Harrison Deng"' + sh 'python scripts/adapt_names.py autobigs.engine' + } + } + stage("build") { + steps { + sh 'conda build autobigs-engine' + } + } + stage("commit") { + environment { + TOKEN = credentials('github.com') + } + steps { + dir('bioconda-recipes') { + sh 'cp -r ../autobigs-engine/* recipes/autobigs-engine/.' + sh 'git commit -a -m "Automatically updated autobigs-engine bioconda recipe to $(python ../scripts/package_latest_version.py autoBIGS.engine)."' + sh 'git push https://${TOKEN}@github.com/Syph-and-VPD-Lab/bioconda-recipes.git update-autobigs-engine' + } + } + } } } \ No newline at end of file diff --git a/autobigs-engine/meta.yaml b/autobigs-engine/meta.yaml deleted file mode 100644 index 75457f3..0000000 --- a/autobigs-engine/meta.yaml +++ /dev/null @@ -1,44 +0,0 @@ -{% set name = "autobigs.engine" %} -{% set version = "0.11.0" %} - -package: - name: {{ name|lower|replace(".", "-") }} - version: {{ version }} - -source: - url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/autobigs_engine-{{ version }}.tar.gz - sha256: d479b0bce5fcf2c3eb2e666b780b55d0c8a2c03293c9200db9eeac74e869f47b - -build: - noarch: python - script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation - number: 0 - -requirements: - host: - - python >=3.12 - - setuptools >=64 - - setuptools-scm >=8 - - pip - run: - - python >=3.12 - - biopython ==1.85 - - aiohttp ==3.11.* - -test: - imports: - - autobigs - commands: - - pip check - requires: - - pip - -about: - summary: A library to rapidly fetch fetch MLST profiles given sequences for various diseases. - dev_url: https://github.com/RealYHD/autoBIGS.engine - license: GPL-3.0 - license_file: LICENSE - -extra: - recipe-maintainers: - - RealYHD diff --git a/environment.yml b/environment.yml index a055fbd..6c84ae0 100644 --- a/environment.yml +++ b/environment.yml @@ -5,6 +5,4 @@ channels: dependencies: - conda-build - grayskull - - bioconda-utils - - python=3.10 - git \ No newline at end of file