Initial commit for sphinx documentation

.buildinfo

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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: c2505eda61830c7fd38f6e8ae0a85121
+tags: 645f666f9bcd5a90fca523b33c5a78b7

.gitattributes

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+
+ptm_pose/Resource_Files/ptm_coordinates.csv filter=lfs diff=lfs merge=lfs -text

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+#### Description
+A clear and concise description of what the issue is about.
+
+#### Screenshots
+![Downhill Windmills](http://i.giphy.com/KO8AG2EByqkFi.gif)
+
+#### Files
+A list of relevant files for this issue. This will help people navigate the project and offer some clues of where to start.
+
+#### To Reproduce
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+#### Expected behavior
+A clear and concise description of what you expected to happen.
+
+
+#### Tasks
+Include specific tasks in the order they need to be done in. Include links to specific lines of code where the task should happen at, if known
+- [ ] Task 1
+- [ ] Task 2
+- [ ] Task 3

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**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 [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+#### Tasks
+Include specific tasks in the order they need to be done in. Include links to specific lines of code where the task should happen at.
+- [ ] Task 1
+- [ ] Task 2
+- [ ] Task 3
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.gitignore

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+# package specific files
+ptm_pose/Resource_Files/translator.csv
+ptm_pose/Resource_Files/uniprot_to_gene_name.json
+ptm_pose/Resource_Files/nonconstitutive_ptm_list.txt
+ptm_pose/Resource_Files/background_annotations/
+Test_datasets/
+Testing.ipynb
+.pybiomart.sqlite
+
+#sql lite(pybiomart generates)
+*.sqllite
+
+# 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/
+pip-wheel-metadata/
+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/
+
+# 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
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.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
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__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/