Separated CLI from engine bioconda update pipelines

.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

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'
+                }
+            }
+        }
     }
 }

autobigs-engine/meta.yaml

@@ -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

environment.yml

@@ -5,6 +5,4 @@ channels:
 dependencies:
   - conda-build
   - grayskull
-  - bioconda-utils
-  - python=3.10
   - git