Initial commit after CMS Cookiecutter creation, version 1.6

.codecov.yml

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+# Codecov configuration to make it a bit less noisy
+coverage:
+ status:
+ patch: false
+ project:
+ default:
+ threshold: 50%
+comment:
+ layout: "header"
+ require_changes: false
+ branches: null
+ behavior: default
+ flags: null
+ paths: null

.github/CONTRIBUTING.md

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+# How to contribute
+
+We welcome contributions from external contributors, and this document
+describes how to merge code changes into this gnina. 
+
+## Getting Started
+
+* Make sure you have a [GitHub account](https://github.com/signup/free).
+* [Fork](https://help.github.com/articles/fork-a-repo/) this repository on GitHub.
+* On your local machine,
+ [clone](https://help.github.com/articles/cloning-a-repository/) your fork of
+ the repository.
+
+## Making Changes
+
+* Add some really awesome code to your local fork. It's usually a [good
+ idea](http:https://blog.jasonmeridth.com/posts/do-not-issue-pull-requests-from-your-master-branch/)
+ to make changes on a
+ [branch](https://help.github.com/articles/creating-and-deleting-branches-within-your-repository/)
+ with the branch name relating to the feature you are going to add.
+* When you are ready for others to examine and comment on your new feature,
+ navigate to your fork of gnina on GitHub and open a [pull
+ request](https://help.github.com/articles/using-pull-requests/) (PR). Note that
+ after you launch a PR from one of your fork's branches, all
+ subsequent commits to that branch will be added to the open pull request
+ automatically. Each commit added to the PR will be validated for
+ mergability, compilation and test suite compliance; the results of these tests
+ will be visible on the PR page.
+* If you're providing a new feature, you must add test cases and documentation.
+* When the code is ready to go, make sure you run the test suite using pytest.
+* When you're ready to be considered for merging, check the "Ready to go"
+ box on the PR page to let the gnina devs know that the changes are complete.
+ The code will not be merged until this box is checked, the continuous
+ integration returns checkmarks,
+ and multiple core developers give "Approved" reviews.
+
+# Additional Resources
+
+* [General GitHub documentation](https://help.github.com/)
+* [PR best practices](http:https://codeinthehole.com/writing/pull-requests-and-other-good-practices-for-teams-using-github/)
+* [A guide to contributing to software packages](http:https://www.contribution-guide.org)
+* [Thinkful PR example](http:https://www.thinkful.com/learn/github-pull-request-tutorial/#Time-to-Submit-Your-First-PR)

.github/PULL_REQUEST_TEMPLATE.md

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+## Description
+Provide a brief description of the PR's purpose here.
+
+## Todos
+Notable points that this PR has either accomplished or will accomplish.
+ - [ ] TODO 1
+
+## Questions
+- [ ] Question1
+
+## Status
+- [ ] Ready to go

.github/workflows/CI.yaml

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+name: CI
+
+on:
+ # GitHub has started calling new repo's first branch "main" https://github.com/github/renaming
+ # Existing codes likely still have "master" as the primary branch
+ # Both are tracked here to keep legacy and new codes working
+ push:
+ branches:
+ - "master"
+ - "main"
+ pull_request:
+ branches:
+ - "master"
+ - "main"
+ schedule:
+ # Nightly tests run on master by default:
+ # Scheduled workflows run on the latest commit on the default or base branch.
+ # (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
+ - cron: "0 0 * * *"
+
+jobs:
+ test:
+ name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}
+ runs-on: ${{ matrix.os }}
+ strategy:
+ matrix:
+ os: [macOS-latest, ubuntu-latest, windows-latest]
+ python-version: [3.7, 3.8, 3.9]
+
+ steps:
+ - uses: actions/checkout@v1
+
+ - name: Additional info about the build
+ shell: bash
+ run: |
+ uname -a
+ df -h
+ ulimit -a
+
+
+ # More info on options: https://github.com/conda-incubator/setup-miniconda
+ - uses: conda-incubator/setup-miniconda@v2
+ with:
+ python-version: ${{ matrix.python-version }}
+ environment-file: devtools/conda-envs/test_env.yaml
+
+ channels: conda-forge,defaults
+
+ activate-environment: test
+ auto-update-conda: false
+ auto-activate-base: false
+ show-channel-urls: true
+
+ - name: Install package
+
+ # conda setup requires this special shell
+ shell: bash -l {0}
+ run: |
+ python -m pip install . --no-deps
+ conda list
+
+
+ - name: Run tests
+
+ # conda setup requires this special shell
+ shell: bash -l {0}
+
+ run: |
+ pytest -v --cov=gnina --cov-report=xml --color=yes gnina/tests/
+
+ - name: CodeCov
+ uses: codecov/codecov-action@v1
+ with:
+ file: ./coverage.xml
+ flags: unittests
+ name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# 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
+.pytest_cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# 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
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# profraw files from LLVM? Unclear exactly what triggers this
+# There are reports this comes from LLVM profiling, but also Xcode 9.
+*profraw

.lgtm.yml

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+# Configure LGTM for this package
+
+extraction:
+ python: # Configure Python
+ python_setup: # Configure the setup
+ version: 3 # Specify Version 3
+path_classifiers:
+ library:
+ - versioneer.py # Set Versioneer.py to an external "library" (3rd party code)
+ - devtools/*
+ generated:
+ - gnina/_version.py

CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age,
+body size, disability, ethnicity, gender identity and expression, level of
+experience, nationality, personal appearance, race, religion, or sexual
+identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+Moreover, project maintainers will strive to offer feedback and advice to
+ensure quality and consistency of contributions to the code. Contributions
+from outside the group of project maintainers are strongly welcomed but the
+final decision as to whether commits are merged into the codebase rests with
+the team of project maintainers.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an
+appointed representative at an online or offline event. Representation of a
+project may be further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at '[email protected]'. The project team will
+review and investigate all complaints, and will respond in a way that it deems
+appropriate to the circumstances. The project team is obligated to maintain
+confidentiality with regard to the reporter of an incident. Further details of
+specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 1.4, available at
+[http:https://contributor-covenant.org/version/1/4][version]
+
+[homepage]: http:https://contributor-covenant.org
+[version]: http:https://contributor-covenant.org/version/1/4/

LICENSE

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+
+MIT License
+
+Copyright (c) 2021 Rocco Meli
+
+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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+include LICENSE
+include MANIFEST.in
+include CODE_OF_CONDUCT.md
+include versioneer.py
+
+graft gnina
+global-exclude *.py[cod] __pycache__ *.so

README.md

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+gnina
+==============================
+[//]: # (Badges)
+[![GitHub Actions Build Status](https://github.com/REPLACE_WITH_OWNER_ACCOUNT/gnina/workflows/CI/badge.svg)](https://github.com/REPLACE_WITH_OWNER_ACCOUNT/gnina/actions?query=workflow%3ACI)
+[![codecov](https://codecov.io/gh/REPLACE_WITH_OWNER_ACCOUNT/gnina/branch/master/graph/badge.svg)](https://codecov.io/gh/REPLACE_WITH_OWNER_ACCOUNT/gnina/branch/master)
+
+
+PyTorch implementation of GNINA
+
+### Copyright
+
+Copyright (c) 2021, Rocco Meli
+
+
+#### Acknowledgements
+
+Project based on the 
+[Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.6.