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.github/CODE_OF_CONDUCT.md

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+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we pledge to respect all people who contribute through reporting issues, posting feature requests, updating documentation, submitting pull requests or patches, and other activities. We are committed to making participation in our projects and our community a harassment-free experience for everyone, regardless of level of experience, gender identity and expression, sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion.
+
+## 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.
+
+## 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 opening an issue or contacting one or more of the project maintainers. All complaints will be reviewed and investigated and will result in a response that is deemed necessary and appropriate to the circumstances. The project teams are 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 may be removed from the project team.
+
+## Attribution
+
+This Code of Conduct is adapted from the Contributor Covenant, version 1.4, available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html

.github/ISSUE_TEMPLATE.md

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+### Description of the issue:
+*Try to be as clear as possible: Is it something wrong/missing in the model? Is it a simulation issue? PLEASE DELETE THIS LINE.*
+
+
+#### Expected feature/value/output:
+*How the reaction/metabolite/gene/simulation result should look (cite literature if needed). PLEASE DELETE THIS LINE.*
+
+
+#### Current feature/value/output:
+*How the reaction/metabolite/gene/simulation actually looks in the `master` branch. PLEASE DELETE THIS LINE.*
+
+
+#### Reproducing these results:
+*Please attach any code used below (if it's python code replace the keyword "matlab" with "python". PLEASE DELETE THIS LINE.*
+```matlab
+
+```
+
+**I hereby confirm that I have:**
+- [ ] Tested my code with [all requirements](https://github.com/SysBioChalmers/yeast-GEM#required-software---user) for running the model
+- [ ] Done this analysis in the `master` branch of the repository
+- [ ] Checked that a similar issue does not exist already
+- [ ] If needed, asked first in the [Gitter chat room](https://gitter.im/SysBioChalmers/yeast-GEM) about the issue
+
+*Note: replace [ ] with [X] to check the box. PLEASE DELETE THIS LINE*

.github/PULL_REQUEST_TEMPLATE.md

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+### Main improvements in this PR:
+*Try to be as clear as possible: Is it fixing/adding something in the model? Is it an additional test/function/dataset? PLEASE DELETE THIS LINE.*
+
+**I hereby confirm that I have:**
+
+- [ ] Tested my code on my own computer for running the model
+- [ ] Selected `devel` as a target branch
+
+*Note: replace [ ] with [X] to check the box. PLEASE DELETE THIS LINE*

.gitignore

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+### Source https://github.com/github/gitignore/
+
+
+## R.gitignore
+# History files
+.Rhistory
+.Rapp.history
+
+# Session Data files
+.RData
+
+# User-specific files
+.Ruserdata
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# R Environment Variables
+.Renviron
+
+
+## Julia.gitignore
+# Files generated by invoking Julia with --code-coverage
+*.jl.cov
+*.jl.*.cov
+
+# Files generated by invoking Julia with --track-allocation
+*.jl.mem
+
+# System-specific files and directories generated by the BinaryProvider and BinDeps packages
+# They contain absolute paths specific to the host computer, and so should not be committed
+deps/deps.jl
+deps/build.log
+deps/downloads/
+deps/usr/
+deps/src/
+
+# Build artifacts for creating documentation generated by the Documenter package
+docs/build/
+docs/site/
+
+# File generated by Pkg, the package manager, based on a corresponding Project.toml
+# It records a fixed state of all packages used by the project. As such, it should not be
+# committed for packages, but should be committed for applications that require a static
+# environment.
+Manifest.toml
+
+
+## Python.gitignore
+# 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/
+
+
+## Java.gitignore
+
+# Compiled class file
+*.class
+
+# Log file
+*.log
+
+# BlueJ files
+*.ctxt
+
+# Mobile Tools for Java (J2ME)
+.mtj.tmp/
+
+# Package Files #
+*.jar
+*.war
+*.nar
+*.ear
+*.zip
+*.tar.gz
+*.rar
+
+# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
+hs_err_pid*
+
+
+### Source https://github.com/jupyter/notebook/blob/master/.gitignore
+MANIFEST
+build
+dist
+_build
+docs/man/*.gz
+docs/source/api/generated
+docs/source/config.rst
+docs/gh-pages
+notebook/i18n/*/LC_MESSAGES/*.mo
+notebook/i18n/*/LC_MESSAGES/nbjs.json
+notebook/static/components
+notebook/static/style/*.min.css*
+notebook/static/*/js/built/
+notebook/static/*/built/
+notebook/static/built/
+notebook/static/*/js/main.min.js*
+notebook/static/lab/*bundle.js
+node_modules
+*.py[co]
+__pycache__
+*.egg-info
+*~
+*.bak
+.ipynb_checkpoints
+.tox
+.DS_Store
+\#*#
+.#*
+.coverage
+.pytest_cache
+src
+
+*.swp
+*.map
+.idea/
+Read the Docs
+config.rst
+*.iml
+/.project
+/.pydevproject
+
+package-lock.json
+geckodriver.log
+*.iml
+
+
+### Source https://github.com/github/gitignore/blob/master/Global/MATLAB.gitignore
+# Windows default autosave extension
+*.asv
+
+# OSX / *nix default autosave extension
+*.m~
+
+# Compiled MEX binaries (all platforms)
+*.mex*
+
+# Packaged app and toolbox files
+*.mlappinstall
+*.mltbx
+
+# Generated helpsearch folders
+helpsearch*/
+
+# Simulink code generation folders
+slprj/
+sccprj/
+
+# Matlab code generation folders
+codegen/
+
+# Simulink autosave extension
+*.autosave
+
+# Simulink cache files
+*.slxc
+
+# Octave session info
+octave-workspace
+
+
+### Misc
+.DS_Store