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‎.editorconfig

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# http://editorconfig.org
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root = true
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[*]
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indent_style = space
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indent_size = 4
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trim_trailing_whitespace = true
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insert_final_newline = true
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charset = utf-8
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end_of_line = lf
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[*.bat]
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indent_style = tab
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end_of_line = crlf
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[LICENSE]
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insert_final_newline = false
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[Makefile]
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indent_style = tab

‎.github/ISSUE_TEMPLATE.md

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* Fimpy version:
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* Python version:
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* Operating System:
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### Description
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Describe what you were trying to get done.
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Tell us what happened, what went wrong, and what you expected to happen.
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### What I Did
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```
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Paste the command(s) you ran and the output.
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If there was a crash, please include the traceback here.
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```

‎.gitignore

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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# C extensions
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*.so
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# Distribution / packaging
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.Python
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env/
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*.cover
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.hypothesis/
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.pytest_cache/
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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local_settings.py
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# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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target/
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# Jupyter Notebook
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.ipynb_checkpoints
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# pyenv
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.python-version
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# celery beat schedule file
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celerybeat-schedule
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# SageMath parsed files
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*.sage.py
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# dotenv
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.env
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# virtualenv
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.venv
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venv/
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ENV/
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# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# mkdocs documentation
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/site
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# mypy
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.mypy_cache/
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# IDE settings
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.vscode/
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# Idea
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.idea/

‎.travis.yml

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# Config file for automatic testing at travis-ci.com
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language: python
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python:
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- 3.8
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- 3.7
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- 3.6
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# Command to install dependencies, e.g. pip install -r requirements.txt --use-mirrors
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install:
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- pip install -U tox-travis
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script:
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- tox
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after_success:
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- pip install codecov
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- codecov
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- pip install Sphinx==3.0.3
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- pip install sphinx_rtd_theme==0.4.3
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- pip install .
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- cd docs
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- sphinx-apidoc ../split_dataset -o ./
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- make html
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- cd ..
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# Assuming you have installed the travis-ci CLI tool, after you
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# create the Github repo and add it to Travis, run the
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# following command to finish PyPI deployment setup:
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# $ travis encrypt --add deploy.password
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deploy:
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- provider: pages
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skip_cleanup: true
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keep_history: true
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github_token:
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secure: "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"
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on:
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tags: true
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branch: master
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python: 3.8
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local-dir: docs/_build/html
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committer-from-gh: true
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- provider: pypi
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skip_cleanup: true
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distributions: sdist bdist_wheel
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user: __token__
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password:
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secure: 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on:
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tags: true
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branch: master
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python: 3.8
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skip_existing: true

‎AUTHORS.rst

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=======
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Credits
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=======
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Development Lead
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----------------
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* Luigi Petrucco & Vilim Stih @portugueslab <[email protected]>
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Contributors
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------------
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None yet. Why not be the first?

‎CONTRIBUTING.rst

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.. highlight:: shell
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============
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Contributing
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============
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Contributions are welcome, and they are greatly appreciated! Every little bit
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helps, and credit will always be given.
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You can contribute in many ways:
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Types of Contributions
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----------------------
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Report Bugs
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~~~~~~~~~~~
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Report bugs at https://github.com/portugueslab/fimpy/issues.
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If you are reporting a bug, please include:
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* Your operating system name and version.
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* Any details about your local setup that might be helpful in troubleshooting.
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* Detailed steps to reproduce the bug.
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Fix Bugs
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~~~~~~~~
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Look through the GitHub issues for bugs. Anything tagged with "bug" and "help
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wanted" is open to whoever wants to implement it.
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Implement Features
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~~~~~~~~~~~~~~~~~~
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Look through the GitHub issues for features. Anything tagged with "enhancement"
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and "help wanted" is open to whoever wants to implement it.
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Write Documentation
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~~~~~~~~~~~~~~~~~~~
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Fimpy could always use more documentation, whether as part of the
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official Fimpy docs, in docstrings, or even on the web in blog posts,
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articles, and such.
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Submit Feedback
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~~~~~~~~~~~~~~~
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The best way to send feedback is to file an issue at https://github.com/portugueslab/fimpy/issues.
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If you are proposing a feature:
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* Explain in detail how it would work.
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* Keep the scope as narrow as possible, to make it easier to implement.
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* Remember that this is a volunteer-driven project, and that contributions
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are welcome :)
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Get Started!
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------------
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Ready to contribute? Here's how to set up `fimpy` for local development.
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1. Fork the `fimpy` repo on GitHub.
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2. Clone your fork locally::
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$ git clone [email protected]:your_name_here/fimpy.git
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3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
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$ mkvirtualenv fimpy
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$ cd fimpy/
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$ python setup.py develop
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4. Create a branch for local development::
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$ git checkout -b name-of-your-bugfix-or-feature
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Now you can make your changes locally.
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#### Formatting
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Fimpy uses [Black](https://github.com/python/black) to ensure a consistent
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code style. Please run `black ./ -l 79 --target-version py37` before making
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any commits. To prevent any errors, it is easier to add a formatting check
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as a [pre-commit hook](https://www.atlassian.com/git/tutorials/git-hooks).
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E.g. on linux by adding this to your `.git/hooks/pre-commit`:
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black ./ -l 79 --target-version py37 --check || exit 1
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6. Commit your changes and push your branch to GitHub::
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$ git add .
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$ git commit -m "Your detailed description of your changes."
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$ git push origin name-of-your-bugfix-or-feature
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7. Submit a pull request through the GitHub website.
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Pull Request Guidelines
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-----------------------
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Before you submit a pull request, check that it meets these guidelines:
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1. The pull request should include tests.
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2. If the pull request adds functionality, the docs should be updated. Put
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your new functionality into a function with a docstring, and add the
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feature to the list in README.rst.
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3. The pull request should work for Python 3.6, 3.7 and 3.8, and for PyPy. Check
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https://travis-ci.com/portugueslab/fimpy/pull_requests
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and make sure that the tests pass for all supported Python versions.
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Tips
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----
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To run a subset of tests::
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$ pytest tests.test_fimpy
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Deploying
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---------
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A reminder for the maintainers on how to deploy.
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Make sure all your changes are committed (including an entry in HISTORY.rst).
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Then run::
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$ bump2version patch # possible: major / minor / patch
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$ git push
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$ git push --tags
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Travis will then deploy to PyPI if tests pass.

‎HISTORY.rst

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=======
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History
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=======
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0.1.0 (2020-05-07)
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------------------
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* First release on PyPI.

‎LICENSE

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GNU GENERAL PUBLIC LICENSE
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Version 3, 29 June 2007
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A python package for parallelizable processing of fluorescent imaging data
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Copyright (C) 2020 Luigi Petrucco & Vilim Stih @portugueslab
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This program is free software: you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation, either version 3 of the License, or
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(at your option) any later version.
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This program is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU General Public License for more details.
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You should have received a copy of the GNU General Public License
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along with this program. If not, see <http://www.gnu.org/licenses/>.
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Also add information on how to contact you by electronic and paper mail.
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You should also get your employer (if you work as a programmer) or school,
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if any, to sign a "copyright disclaimer" for the program, if necessary.
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For more information on this, and how to apply and follow the GNU GPL, see
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<http://www.gnu.org/licenses/>.
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The GNU General Public License does not permit incorporating your program
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into proprietary programs. If your program is a subroutine library, you
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may consider it more useful to permit linking proprietary applications with
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the library. If this is what you want to do, use the GNU Lesser General
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Public License instead of this License. But first, please read
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<http://www.gnu.org/philosophy/why-not-lgpl.html>.
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