Merge pull request #131 from ChihweiLHBird/update_docs

Update document cover

CODE_OF_CONDUCT.md

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+# Code of Conduct
+
+## Our Pledge
+
+We ask that all contributors be
+- Respectful and patient.
+- Mindful and considerate.
+  - Consider that our actions affect others, including colleagues and the public.
+  - Be careful in the words that you choose!
+- Open with tools and dissemination efforts, and transparent in all communication.
+  - Our work, our tools, our discussions, and our findings should be open and accessible to all.
+  - Choose freely-available, open source tools, open access dissemination practices.
+  - Communicate over open channels.
+- Welcome new interactions, new views, new ideas, and new people.
+  - Disagreements will occur in a diverse scientific community.
+  - But they can be resolved constructively with no harmful behavior!
+
+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, sex characteristics, gender identity and expression,
+level of experience, education, socio-economic status, 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.
+
+## 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 SciUnit team leader at rick@scidash.org,
+or any member of the [SciUnit Executive Committee](COMMITTEE.md). All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and 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 https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see
+https://www.contributor-covenant.org/faq

COMMITTEE.md

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+# SciUnit Executive Committee
+
+The executive committee steers the SciUnit project and reviews regular reports prepared by the chairperson.
+Concerns about project governance or code of conduct violations may be confidentially shared with any member of the committee.
+
+| Name  | Title | Affiliation |
+|---|---|---|
+| Richard C. (Rick) Gerkin* | Associate Research Professor | School of Life Sciences, Arizona State Univ., USA |
+| Shailesh Appukuttan | Postdoctoral Researcher | CNRS, France |
+| Justas Birgiolas | Postdoctoral Fellow | Dept. of Psychology, Cornell University, USA |
+| Sharon M Crook | Professor | School of Mathematical and Statistical Sciences, Arizona State Univ., USA |
+| Andrew Davison | Senior Research Scientist, Group Leader, Neuroinformatics | CNRS, France |
+| Robin Gutzen | PhD Student | Research Centre Jülich, Germany |
+| Giovanni Idili | Chief Operating Officer | MetaCell, LLC, UK |
+| Cyrus Omar | Assistant Professor | Dept. of Computer Science, Univ. of Michigan, USA |
+
+*denotes current chairperson

CONTRIBUTING.md

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+# Contributing to SciUnit
+
+## Reporting issues
+
+When reporting issues please include as much detail as possible about your
+operating system, `sciunit` version, and python version. Whenever possible, please
+also include a brief, self-contained code example that demonstrates the problem.
+
+## Contributing code
+
+Thanks for your interest in contributing code to SciUnit!
+Our developers aim to adhere to Python Enhancement Proposals (PEP) standards to ensure that code is readable, usable, and maintainable.
+
++ If this is your first time contributing to a project on GitHub, please consider reading
+this [example guide](https://numpy.org/devdocs/dev/index.html) to contributing code provided by the developers of numpy.
++ If you have contributed to other projects on GitHub you may open a pull request directly against the `dev` branch.
+
+Either way, please be sure to provide informative commit messages
+and ensure that each commit contains code addressing only one development goal.
+
+Writing unit tests to cover new code is encouraged but not required.
+Your changes can be tested using the current set of units tests by executing `test.sh` in the root directory.

docs/README.md

@@ -1,16 +1,11 @@
-# Recipe for building the API docs from scratch:
-
-updating .rst files with sphinx-apidoc
-
-shell commands:
-```
-rm -rf source
-sphinx-apidoc -o "./source" "../sciunit"
-sphinx-quickstart
-```
-
-Copy conf.py from the oringinal sciunit repo. Then:
-
-```
-sphinx-build -b html ./source ./build
-```
+---
+title: 'New to SciUnit?'
+---
+
+-   Start with [Chapter
+    1](https://github.com/scidash/sciunit/blob/master/docs/chapter1.ipynb)
+    of the tutorial.
+-   View [our
+    slides](https://github.com/scidash/sciunit/blob/master/docs/workshop-tutorial.ipynb).
+-   Or run either of the above
+    [interactively](https://mybinder.org/v2/gh/scidash/sciunit/b491f545854040b5934b3898e7b9f7089089041f).

docs/source/README.md

@@ -0,0 +1,16 @@
+# Recipe for building the API docs from scratch:
+
+updating .rst files with sphinx-apidoc
+
+shell commands:
+```
+rm -rf source
+sphinx-apidoc -o "./source" "../sciunit"
+sphinx-quickstart
+```
+
+Copy conf.py from the oringinal sciunit repo. Then:
+
+```
+sphinx-build -b html ./source ./build
+```

docs/source/index.rst

@@ -1,5 +1,5 @@
 .. sciunit documentation master file, created by
-   sphinx-quickstart on Sat Dec 21 14:20:34 2019.
+   sphinx-quickstart on Thu Feb 13 13:47:10 2020.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
@@ -10,6 +10,93 @@ Welcome to sciunit's documentation!
    :maxdepth: 2
    :caption: Contents:
 
+.. figure:: https://raw.githubusercontent.com/scidash/assets/master/logos/SciUnit/sci-unit-square-small.png
+    :align: center
+=======================================================================================
+
+Concept
+-------
+
+`The conference
+paper <https://github.com/cyrus-/papers/raw/master/sciunit-icse14/sciunit-icse14.pdf>`__
+
+Documentation
+-------------
+
+`Chapter
+1 <https://github.com/scidash/sciunit/blob/master/docs/chapter1.ipynb>`__
+/ `Chapter
+2 <https://github.com/scidash/sciunit/blob/master/docs/chapter2.ipynb>`__
+/ `Chapter
+3 <https://github.com/scidash/sciunit/blob/master/docs/chapter3.ipynb>`__
+/
+
+Basic Usage
+-----------
+
+.. code:: python
+
+    my_model = MyModel(**my_args) # Instantiate a class that wraps your model of interest.  
+    my_test = MyTest(**my_params) # Instantiate a test that you write.  
+    score = my_test.judge() # Runs the test and return a rich score containing test results and more.  
+
+Domain-specific libraries and information
+-----------------------------------------
+
+`NeuronUnit <https://github.com/scidash/neuronunit>`__ for neuron and
+ion channel physiology See others
+`here <https://github.com/scidash/sciunit/network/dependents?dependent_type=REPOSITORY>`__
+
+Mailing List
+------------
+
+There is a `mailing
+list <https://groups.google.com/forum/?fromgroups#!forum/sciunit>`__ for
+announcements and discussion. Please join it if you are at all
+interested!
+
+Contributors
+------------
+
+-  `Rick Gerkin <http://rick.gerk.in>`__, Arizona State University
+   (School of Life Science)
+-  `Cyrus Omar <http://cs.cmu.edu/~comar>`__, Carnegie Mellon University
+   (Dept. of Computer Science)
+
+Reproducible Research ID
+------------------------
+
+RRID:\ `SCR\_014528 <https://scicrunch.org/resources/Any/record/nlx_144509-1/3faed1d9-6579-5da6-b4b4-75a5077656bb/search?q=sciunit&l=sciunit>`__
+
+License
+-------
+
+SciUnit is released under the permissive `MIT
+license <https://opensource.org/licenses/MIT>`__, requiring only
+attribution in derivative works. See the LICENSE file for terms.
+
+.. |Travis| image:: https://travis-ci.org/scidash/sciunit.svg?branch=master
+   :target: https://travis-ci.org/scidash/sciunit
+.. |Travis| image:: https://travis-ci.org/scidash/sciunit.svg?branch=dev
+   :target: https://travis-ci.org/scidash/sciunit
+.. |RTFD| image:: https://readthedocs.org/projects/sciunit/badge/?version=master
+   :target: http://sciunit.readthedocs.io/en/latest/?badge=master
+.. |RTFD| image:: https://readthedocs.org/projects/sciunit/badge/?version=dev
+   :target: http://sciunit.readthedocs.io/en/latest/?badge=dev
+.. |Binder| image:: https://mybinder.org/badge.svg
+   :target: https://mybinder.org/v2/gh/scidash/sciunit/master?filepath=docs%2Fchapter1.ipynb
+.. |Coveralls| image:: https://coveralls.io/repos/github/scidash/sciunit/badge.svg?branch=master
+   :target: https://coveralls.io/github/scidash/sciunit?branch=master
+.. |Coveralls| image:: https://coveralls.io/repos/github/scidash/sciunit/badge.svg?branch=dev
+   :target: https://coveralls.io/github/scidash/sciunit?branch=dev
+.. |Requirements| image:: https://requires.io/github/scidash/sciunit/requirements.svg?branch=master
+   :target: https://requires.io/github/scidash/sciunit/requirements/?branch=master
+.. |Requirements| image:: https://requires.io/github/scidash/sciunit/requirements.svg?branch=dev
+   :target: https://requires.io/github/scidash/sciunit/requirements/?branch=dev
+.. |Docker Build Status| image:: https://img.shields.io/docker/build/scidash/sciunit.svg
+   :target: https://hub.docker.com/r/scidash/sciunit/builds/
+.. |Repos using Sciunit| image:: https://img.shields.io/librariesio/dependent-repos/pypi/sciunit.svg
+   :target: https://github.com/scidash/sciunit/network/dependents?dependent_type=REPOSITORY
 
 
 Indices and tables

docs/source/sciunit.unit_test.rst

@@ -4,6 +4,22 @@ sciunit.unit\_test package
 Submodules
 ----------
 
+sciunit.unit\_test.active module
+--------------------------------
+
+.. automodule:: sciunit.unit_test.active
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+sciunit.unit\_test.backend\_tests module
+----------------------------------------
+
+.. automodule:: sciunit.unit_test.backend_tests
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 sciunit.unit\_test.base module
 ------------------------------
 

sciunit/version.py

@@ -1 +1 @@
-__version__ = '0.2.1.1'
+__version__ = '0.2.2'