Merge pull request #695 from opencobra/chore-configuration

update configuration

.editorconfig

@@ -8,7 +8,7 @@ indent_size = 4
 end_of_line = lf
 insert_final_newline = true
 trim_trailing_whitespace = true
-max_line_length = 80
+max_line_length = 88
 
 [*.{json,yml}]
 indent_size = 2

.gitattributes

@@ -0,0 +1 @@
+src/memote/_version.py export-subst

.github/CODE_OF_CONDUCT.md

@@ -0,0 +1,130 @@
+
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders 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, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+[midnighter@posteo.net](mailto:midnighter@posteo.net).
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.
+

.github/CONTRIBUTING.rst

@@ -1,6 +1,3 @@
-.. highlight:: shell
-.. _contributing:
-
 ============
 Contributing
 ============
@@ -11,37 +8,34 @@ little bit helps, and credit will always be given.
 You can contribute in many ways:
 
 Report Bugs
-~~~~~~~~~~~
+===========
 
 Report bugs at https://github.com/opencobra/memote/issues.
 
-If you are reporting a bug, please include:
-
-* Your operating system name and version.
-* Any details about your local setup that might be helpful in troubleshooting.
-* Detailed steps to reproduce the bug.
+If you are reporting a bug, please follow the template guidelines. The more 
+detailed your report, the easier and thus faster we can help you.
 
 Fix Bugs
-~~~~~~~~
+========
 
 Look through the GitHub issues for bugs. Anything tagged with "bug"
 and "help wanted" is open to whoever wants to implement it.
 
 Implement Features
-~~~~~~~~~~~~~~~~~~
+==================
 
 Look through the GitHub issues for features. Anything tagged with "enhancement"
 and "help wanted" is open to whoever wants to implement it.
 
 Write Documentation
-~~~~~~~~~~~~~~~~~~~
+===================
 
 memote could always use more documentation, whether as part of the
-official memote docs, in docstrings, or even on the web in blog posts,
+official documentation, in docstrings, or even on the web in blog posts,
 articles, and such.
 
 Submit Feedback
-~~~~~~~~~~~~~~~
+===============
 
 The best way to send feedback is to file an issue at
 https://github.com/opencobra/memote/issues.
@@ -54,53 +48,68 @@ If you are proposing a feature:
   are welcome :)
 
 Get Started!
-------------
+============
 
-Ready to contribute? Here's how to set up `memote` for local development.
+Ready to contribute? Here's how to set up memote for
+local development.
 
-1. Fork the `memote` repo on GitHub.
-2. Clone your fork locally::
+1. Fork the https://github.com/opencobra/memote
+   repository on GitHub.
+2. Clone your fork locally
 
-    git clone git@github.com:your_name_here/memote.git
+   .. code-block:: console
+   
+       git clone git@github.com:your_name_here/memote.git
 
-3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
+3. Install your local copy into a a Python virtual environment.
+   You can `read this guide to learn more
+   <https://realpython.com/python-virtual-environments-a-primer/>`_
+   about them and how to create one. Alternatively, particularly if you are a 
+   Windows or Mac user, you can also use
+   `Anaconda <https://docs.anaconda.com/anaconda/>`_. Assuming you have 
+   virtualenvwrapper installed, this is how you set up your fork for local development
 
-    mkvirtualenv memote
-    cd memote/
-    pip install -e .
+   .. code-block:: console
+   
+       mkvirtualenv my-env
+       cd memote/
+       pip install -e .[development]
 
-4. Create a branch for local development using ``fix`` or ``feat`` as a prefix::
+4. Create a branch for local development using the ``devel`` branch as a 
+   starting point. Use ``fix`` or ``feat`` as a prefix
 
-    git checkout -b fix-name-of-your-bugfix
+   .. code-block:: console
+   
+       git checkout devel
+       git checkout -b fix-name-of-your-bugfix
 
    Now you can make your changes locally.
 
-5. When you're done making changes, check that your changes pass flake8 and
-   the tests, including testing other Python versions. This is all included
-   with tox::
-
-    tox
+5. When you're done making changes, apply the quality assurance tools and check 
+   that your changes pass our test suite. This is all included with tox
 
-   You can run all tests in parallel using detox. To get tox and detox, just
-   pip install them into your virtualenv.
+   .. code-block:: console
+   
+       make qa
+       tox
 
 6. Commit your changes and push your branch to GitHub. Please use `semantic
-   commit messages <http://karma-runner.github.io/2.0/dev/git-commit-msg.html>`_::
+   commit messages <http://karma-runner.github.io/2.0/dev/git-commit-msg.html>`_.
 
-    git add .
-    git commit -m "fix: Your detailed description of your changes."
-    git push origin fix-name-of-your-bugfix
+   .. code-block:: console
+   
+       git add .
+       git commit -m "fix: Your summary of changes"
+       git push origin fix-name-of-your-bugfix
 
-7. Submit a pull request through the GitHub website.
+7. Open the link displayed in the message when pushing your new branch 
+   in order to submit a pull request.
 
 Pull Request Guidelines
------------------------
+=======================
 
 Before you submit a pull request, check that it meets these guidelines:
 
 1. The pull request should include tests.
 2. If the pull request adds functionality, the docs should be updated. Put
    your new functionality into a function with a docstring.
-3. The pull request should work for Python 2.7, 3.4, 3.5 and 3.6. Check
-   https://travis-ci.org/opencobra/memote/pull_requests
-   and make sure that the tests pass for all supported Python versions.

.github/ISSUE_TEMPLATE/01-bug-report.md

@@ -0,0 +1,49 @@
+---
+name: Bug report
+about: Report a bug to help improve this project
+---
+
+<!--
+
+Before you create a new problem report, please look through the list of existing open
+ and closed issues to see if there are similar ones.
+ 
+https://github.com/opencobra/memote/issues
+
+-->
+
+#### Problem description
+
+Please explain:
+* **what** you tried to achieve,
+* **how** you went about it (referring to the code sample), and
+* **why** the current behaviour is a problem and what output
+  you expected instead.
+
+#### Code Sample
+
+Create a [minimal, complete, verifiable example](https://stackoverflow.com/help/mcve).
+
+<!-- Paste your code between the ``` tickmarks below or link to a gist. -->
+```python
+```
+
+<!-- If there was a crash, please include the traceback between the ``` tickmarks below. -->
+```
+```
+
+### Context
+
+<!-- Please run the following code and paste the output between the ``` tickmarks below
+inside the details block.
+
+python -c "import memote;memote.show_versions()"
+
+-->
+
+<details>
+
+```
+```
+
+</details>