Inital commit

LICENSE

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+MIT License
+
+Copyright (c) 2022 Harshad Hegde
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

MANIFEST.in

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+graft src
+graft tests
+prune scripts
+prune notebooks
+prune tests/.pytest_cache
+
+prune docs/build
+prune docs/source/api
+
+recursive-include docs/source *.py
+recursive-include docs/source *.rst
+recursive-include docs/source *.png
+
+global-exclude *.py[cod] __pycache__ *.so *.dylib .DS_Store *.gpickle
+
+include README.md LICENSE
+exclude tox.ini .flake8 .bumpversion.cfg .readthedocs.yml

README.md

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+<!--
+<p align="center">
+  <img src="https://github.com/hrshdhgd/onto-crawler/raw/main/docs/source/logo.png" height="150">
+</p>
+-->
+
+Crawl github for ontology related issues.
+
+## Getting Started
+
+Firstly, generate a personalized token as instructed [here](https://docs.github.com/en/[email protected]/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token) and save it in `src/onto_crawler/token.txt`
+
+Next, run:
+
+```shell
+$ poetry run ocrawl issues --label synonym
+```
+This should return a list of issue titles tagged with the label `synonym`. By default, we've chosen the [mondo repository](https://github.com/monarch-initiative/mondo). If you need to test it with another repository, add an option `-r` and follow it with the `organization/repository_name`. 
+
+### Command Line Interface
+
+The onto_crawler command line tool is automatically installed. It can
+be used from the shell with the `--help` flag to show all subcommands:
+
+```shell
+$ poetry run ocrawl --help
+```
+
+## Installation
+
+<!-- Uncomment this section after first release
+The most recent release can be installed from
+[PyPI](https://pypi.org/project/onto_crawler/) with:
+
+```bash
+$ pip install onto-crawler
+```
+-->
+
+The most recent code and data can be installed directly from GitHub with:
+
+```bash
+$ pip install git+https://github.com/hrshdhgd/onto-crawler.git
+```
+
+<!-- ## Contributing
+
+Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See
+[CONTRIBUTING.md](https://github.com/hrshdhgd/onto-crawler/blob/master/.github/CONTRIBUTING.md) for more information on getting involved. -->
+
+
+
+### License
+
+The code in this package is licensed under the MIT License.
+
+
+## For Developers
+
+<details>
+  <summary>See developer instructions</summary>
+
+
+The final section of the README is for if you want to get involved by making a code contribution.
+
+### Development Installation
+
+To install in development mode, use the following:
+
+```bash
+$ pip install poetry
+$ git clone git+https://github.com/hrshdhgd/onto-crawler.git
+$ cd onto-crawler
+$ poetry install
+```
+
+### Testing
+
+After cloning the repository and installing `tox` with `pip install tox`, the unit tests in the `tests/` folder can be
+run reproducibly with:
+
+```shell
+$ tox
+```
+
+Additionally, these tests are automatically re-run with each commit in a [GitHub Action](https://github.com/hrshdhgd/onto-crawler/actions?query=workflow%3ATests).
+
+
+### Making a Release
+
+> TODO
+</details>

docs/source/cli.rst

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+Command Line Interface
+======================
+onto_crawler automatically installs the command :code:`onto_crawler`. See
+:code:`onto_crawler --help` for usage details.
+
+.. click:: onto_crawler.cli:main
+   :prog: onto_crawler
+   :show-nested:

docs/source/conf.py

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+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+
+import os
+import re
+import sys
+from datetime import date
+
+sys.path.insert(0, os.path.abspath("../../src"))
+
+# -- Project information -----------------------------------------------------
+
+project = "onto_crawler"
+copyright = f"{date.today().year}, Harshad Hegde"
+author = "Harshad Hegde"
+
+# The full version, including alpha/beta/rc tags.
+release = "0.0.1-dev"
+
+# The short X.Y version.
+parsed_version = re.match(
+    "(?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(?:-(?P<release>[0-9A-Za-z-]+(?:\.[0-9A-Za-z-]+)*))?(?:\+(?P<build>[0-9A-Za-z-]+(?:\.[0-9A-Za-z-]+)*))?",
+    release,
+)
+version = parsed_version.expand("\g<major>.\g<minor>.\g<patch>")
+
+if parsed_version.group("release"):
+    tags.add("prerelease")
+
+# -- General configuration ---------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+add_module_names = False
+
+# A list of prefixes that are ignored when creating the module index. (new in Sphinx 0.6)
+modindex_common_prefix = ["onto_crawler."]
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    "sphinx.ext.autosummary",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.coverage",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.todo",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.viewcode",
+    "sphinx_autodoc_typehints",
+    "sphinx_automodapi.automodapi",
+    "sphinx_automodapi.smart_resolver",
+    # 'texext',
+]
+
+
+extensions.append("sphinx_click.ext")
+
+
+# generate autosummary pages
+autosummary_generate = True
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = ".rst"
+
+# The master toctree document.
+master_doc = "index"
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = "en"
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = "sphinx"
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "sphinx_rtd_theme"
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+# html_static_path = ['_static']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#
+if os.path.exists("logo.png"):
+    html_logo = "logo.png"
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = "doc"
+
+# -- Options for LaTeX output ------------------------------------------------
+
+# latex_elements = {
+#     The paper size ('letterpaper' or 'a4paper').
+#
+#     'papersize': 'letterpaper',
+#
+#     The font size ('10pt', '11pt' or '12pt').
+#
+#     'pointsize': '10pt',
+#
+#     Additional stuff for the LaTeX preamble.
+#
+#     'preamble': '',
+#
+#     Latex figure (float) alignment
+#
+#     'figure_align': 'htbp',
+# }
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+# latex_documents = [
+#     (
+#         master_doc,
+#         'onto_crawler.tex',
+#         ' Documentation',
+#         author,
+#         'manual',
+#     ),
+# ]
+
+# -- Options for manual page output ------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (
+        master_doc,
+        "onto_crawler",
+        " Documentation",
+        [author],
+        1,
+    ),
+]
+
+# -- Options for Texinfo output ----------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (
+        master_doc,
+        "onto_crawler",
+        " Documentation",
+        author,
+        "Harshad Hegde",
+        "Crawl github for ontology related issues.",
+        "Miscellaneous",
+    ),
+]
+
+# -- Options for Epub output -------------------------------------------------
+
+# Bibliographic Dublin Core info.
+# epub_title = project
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#
+# epub_identifier = ''
+
+# A unique identification for the text.
+#
+# epub_uid = ''
+
+# A list of files that should not be packed into the epub file.
+# epub_exclude_files = ['search.html']
+
+# -- Extension configuration -------------------------------------------------
+
+# -- Options for intersphinx extension ---------------------------------------
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {
+    "https://docs.python.org/3/": None,
+}
+
+autoclass_content = "both"
+
+# Don't sort alphabetically, explained at:
+# https://stackoverflow.com/questions/37209921/python-how-not-to-sort-sphinx-output-in-alphabetical-order
+autodoc_member_order = "bysource"