Initial commit

.gitignore

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+# 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/
+*.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/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# 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/
+
+# IDEA
+.idea

README.rst

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+pybel-git
+=========
+Git and continuous integration tools for PyBEL.

setup.cfg

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+##########################
+# Setup.py Configuration #
+##########################
+# Configuring setup()
+[metadata]
+name = pybel_git
+version = 0.0.1-dev
+author = Charles Tapley Hoyt
+author_email = [email protected]
+maintainer = Charles Tapley Hoyt
+maintainer_email = [email protected]
+classifiers =
+    Development Status :: 1 - Planning
+    Intended Audience :: Developers
+    Programming Language :: Python
+    Programming Language :: Python :: 3.7
+    Programming Language :: Python :: 3.6
+    Programming Language :: Python :: 3 :: Only
+    License :: OSI Approved :: MIT License
+license = MIT
+license_file = LICENSE
+description = PyBEL Git utilities
+long_description = file: README.rst
+keywords =
+    Biological Expression Language
+    Protein Protein Interaction Networks
+
+[options]
+install_requires =
+    pybel
+    click
+    easy-config
+    gitpython
+python_requires = >=3.6
+packages = find:
+package_dir =
+    = src
+zip-safe = false
+
+[options.entry_points]
+console_scripts =
+    pybel-git = pybel_git.cli:main
+
+[options.packages.find]
+where = src
+
+# configuring bdist_wheel
+[bdist_wheel]
+python-tag = py36

setup.py

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+# -*- coding: utf-8 -*-
+
+"""Setup module for PyBEL-Git."""
+
+import setuptools
+
+if __name__ == '__main__':
+    setuptools.setup()

src/pybel_git/__init__.py

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+# -*- coding: utf-8 -*-

src/pybel_git/__main__.py

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+# -*- coding: utf-8 -*-
+
+from .cli import main
+
+if __name__ == '__main__':
+    main()

src/pybel_git/cli.py

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+# -*- coding: utf-8 -*-
+
+"""Command line interface for PyBEL-Git."""
+
+import os
+import sys
+
+import click
+from git import Repo
+
+from pybel import Manager, from_path
+from pybel.cli import connection_option
+from .commands import get_changed
+
+EMOJI = '🔔'
+
+
+@click.group()
+def main():
+    """PyBEL Git utilities."""
+
+
+# TODO download pre-built cache?
+
+@main.command()
+@click.option('-d', '--directory', default=os.getcwd(), type=click.Path(file_okay=False, dir_okay=True),
+              help='Directory of git repository')
+@connection_option
+def ci(directory: str, connection: str):
+    """Run in continuous integration setting."""
+    click.echo(f'{EMOJI} checking directory: {directory}')
+
+    repo = Repo(directory)
+    head_commit = repo.git.rev_parse('HEAD')
+    click.echo(f'{EMOJI} head commit: {head_commit}')
+
+    file_names = get_changed(repo)
+    if not file_names:
+        sys.exit(0)
+
+    manager = Manager(connection=connection)
+    failures = []
+    for file_name in file_names:
+        click.echo(f'{EMOJI} file changed: {file_name}')
+        graph = from_path(file_name, manager=manager)
+        if graph.warnings:
+            failures.append(graph)
+
+    sys.exit(1 if failures else 0)

src/pybel_git/commands.py

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+# -*- coding: utf-8 -*-
+
+
+from typing import List
+
+from git import Repo
+
+
+def get_changed(repo: Repo) -> List[str]:
+    """Get a list of files that have changed in the last commit."""
+    head_commit = repo.git.rev_parse('HEAD')
+    output = repo.git.diff_tree('--no-commit-id', '--name-only', '-r', head_commit)
+
+    return [
+        name
+        for name in output.split('\n')
+        if name.endswith('.bel')
+    ]

src/pybel_git/config.py

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+# -*- coding: utf-8 -*-
+
+"""Configuration for PyBEL-Git."""
+
+import logging
+
+from easy_config import EasyConfig
+
+log = logging.getLogger(__name__)
+
+
+class PyBELGitConfig(EasyConfig):
+    """Configuration for PyBEL-Git."""
+    NAME = 'pybel_git'
+    FILES = []
+
+
+pybel_git_config = PyBELGitConfig.load()
+log.info('loaded pybel-git configuration: %s', pybel_git_config)