Refactor: Replace mindpipe -> micone

Author: dileep-kishore

.pre-commit-config.yaml

@@ -4,5 +4,4 @@ repos:
     hooks:
     - id: black
       language_version: python3
-      args: [--py36]
       exclude: micone/pipelines/src

CONTRIBUTING.rst

@@ -15,7 +15,7 @@ Types of Contributions
 Report Bugs
 ~~~~~~~~~~~
 
-Report bugs at https://github.com/dileep-kishore/mindpipe/issues.
+Report bugs at https://github.com/dileep-kishore/micone/issues.
 
 If you are reporting a bug, please include:
 
@@ -45,7 +45,7 @@ articles, and such.
 Submit Feedback
 ~~~~~~~~~~~~~~~
 
-The best way to send feedback is to file an issue at https://github.com/dileep-kishore/mindpipe/issues.
+The best way to send feedback is to file an issue at https://github.com/dileep-kishore/micone/issues.
 
 If you are proposing a feature:
 
@@ -57,17 +57,17 @@ If you are proposing a feature:
 Get Started!
 ------------
 
-Ready to contribute? Here's how to set up `mindpipe` for local development.
+Ready to contribute? Here's how to set up `micone` for local development.
 
-1. Fork the `mindpipe` repo on GitHub.
+1. Fork the `micone` repo on GitHub.
 2. Clone your fork locally::
 
-    $ git clone [email protected]:your_name_here/mindpipe.git
+    $ git clone [email protected]:your_name_here/micone.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::
 
-    $ mkvirtualenv mindpipe
-    $ cd mindpipe/
+    $ mkvirtualenv micone
+    $ cd micone/
     $ python setup.py develop
 
 4. Create a branch for local development::
@@ -79,7 +79,7 @@ Ready to contribute? Here's how to set up `mindpipe` for local development.
 5. When you're done making changes, check that your changes pass flake8 and the
    tests, including testing other Python versions with tox::
 
-    $ flake8 mindpipe tests
+    $ flake8 micone tests
     $ python setup.py test or py.test
     $ tox
 
@@ -103,15 +103,15 @@ Before you submit a pull request, check that it meets these guidelines:
    your new functionality into a function with a docstring, and add the
    feature to the list in README.rst.
 3. The pull request should work for Python 2.7, 3.4, 3.5 and 3.6, and for PyPy. Check
-   https://travis-ci.org/dileep-kishore/mindpipe/pull_requests
+   https://travis-ci.org/dileep-kishore/micone/pull_requests
    and make sure that the tests pass for all supported Python versions.
 
 Tips
 ----
 
 To run a subset of tests::
 
-$ py.test tests.test_mindpipe
+$ py.test tests.test_micone
 
 
 Deploying

HISTORY.rst

@@ -20,7 +20,7 @@ Added
 - ``Pipeline`` class defines the pipeline and methods to run the pipeline
 - ``Environments`` class that creates, lists and loads conda environments
 - Logging functionality
-- CLI interface for mindpipe
+- CLI interface for micone
 
 
 0.4.2 (2018-10-08)
@@ -196,8 +196,8 @@ Added
 - First release and initial commits
 
 
-.. _[0.2.3]: https://github.com/dileep-kishore/mindpipe/compare/v0.2.2...v0.2.3
-.. _[0.2.2]: https://github.com/dileep-kishore/mindpipe/compare/v0.2.1...v0.2.2
-.. _[0.2.1]: https://github.com/dileep-kishore/mindpipe/compare/v0.2.0...v0.2.1
-.. _[0.2.0]: https://github.com/dileep-kishore/mindpipe/compare/v0.1.0...v0.2.0
+.. _[0.2.3]: https://github.com/dileep-kishore/micone/compare/v0.2.2...v0.2.3
+.. _[0.2.2]: https://github.com/dileep-kishore/micone/compare/v0.2.1...v0.2.2
+.. _[0.2.1]: https://github.com/dileep-kishore/micone/compare/v0.2.0...v0.2.1
+.. _[0.2.0]: https://github.com/dileep-kishore/micone/compare/v0.1.0...v0.2.0
 

MANIFEST.in

@@ -5,7 +5,7 @@ include LICENSE
 include README.rst
 
 recursive-include tests *
-recursive-include mindpipe *
+recursive-include micone *
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]
 

README.md

@@ -1,7 +1,7 @@
 MiCoNE - Microbial Co-occurrence Network Explorer
 =================================================
 
-[![Build Status](https://travis-ci.com/dileep-kishore/mindpipe.svg?token=qCMKydrUTvcJ87J6czex&branch=master)](https://travis-ci.com/dileep-kishore/mindpipe)
+[![Build Status](https://travis-ci.com/dileep-kishore/micone.svg?token=qCMKydrUTvcJ87J6czex&branch=master)](https://travis-ci.com/dileep-kishore/micone)
 [![CodeFactor](https://www.codefactor.io/repository/github/segrelab/micone/badge)](https://www.codefactor.io/repository/github/segrelab/micone)
 [![Updates](https://pyup.io/repos/github/segrelab/MiCoNE/shield.svg)](https://pyup.io/repos/github/segrelab/MiCoNE/)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)

README.rst

@@ -3,19 +3,19 @@ Microbial Interaction Database Pipeline
 =======================================
 
 
-.. image:: https://img.shields.io/pypi/v/mindpipe.svg
-        :target: https://pypi.python.org/pypi/mindpipe
+.. image:: https://img.shields.io/pypi/v/micone.svg
+        :target: https://pypi.python.org/pypi/micone
 
-.. image:: https://img.shields.io/travis/dileep-kishore/mindpipe.svg
-        :target: https://travis-ci.org/dileep-kishore/mindpipe
+.. image:: https://img.shields.io/travis/dileep-kishore/micone.svg
+        :target: https://travis-ci.org/dileep-kishore/micone
 
-.. image:: https://readthedocs.org/projects/mindpipe/badge/?version=latest
-        :target: https://mindpipe.readthedocs.io/en/latest/?badge=latest
+.. image:: https://readthedocs.org/projects/micone/badge/?version=latest
+        :target: https://micone.readthedocs.io/en/latest/?badge=latest
         :alt: Documentation Status
 
 
-.. image:: https://pyup.io/repos/github/dileep-kishore/mindpipe/shield.svg
-     :target: https://pyup.io/repos/github/dileep-kishore/mindpipe/
+.. image:: https://pyup.io/repos/github/dileep-kishore/micone/shield.svg
+     :target: https://pyup.io/repos/github/dileep-kishore/micone/
      :alt: Updates
 
 
@@ -24,7 +24,7 @@ The pipeline that powers the Microbial Interaction Network Database
 
 
 * Free software: MIT license
-* Documentation: https://mindpipe.readthedocs.io.
+* Documentation: https://micone.readthedocs.io.
 
 
 Features

docs/Makefile

@@ -4,7 +4,7 @@
 # You can set these variables from the command line.
 SPHINXOPTS    =
 SPHINXBUILD   = python -msphinx
-SPHINXPROJ    = mindpipe
+SPHINXPROJ    = micone
 SOURCEDIR     = .
 BUILDDIR      = _build
 

docs/make.bat

@@ -9,7 +9,7 @@ if "%SPHINXBUILD%" == "" (
 )
 set SOURCEDIR=.
 set BUILDDIR=_build
-set SPHINXPROJ=mindpipe
+set SPHINXPROJ=micone
 
 if "%1" == "" goto help
 

docs/micone.rst

@@ -27,10 +27,10 @@ micone.cli module
    :undoc-members:
    :show-inheritance:
 
-micone.mindpipe module
+micone.micone module
 ----------------------
 
-.. automodule:: micone.mindpipe
+.. automodule:: micone.micone
    :members:
    :undoc-members:
    :show-inheritance:

docs/readme.rst

@@ -70,8 +70,8 @@ This package was created with
 `audreyr/cookiecutter-pypackage <https://github.com/audreyr/cookiecutter-pypackage>`__
 project template.
 
-.. |Build Status| image:: https://travis-ci.com/dileep-kishore/mindpipe.svg?token=qCMKydrUTvcJ87J6czex&branch=master
-   :target: https://travis-ci.com/dileep-kishore/mindpipe
+.. |Build Status| image:: https://travis-ci.com/dileep-kishore/micone.svg?token=qCMKydrUTvcJ87J6czex&branch=master
+   :target: https://travis-ci.com/dileep-kishore/micone
 .. |CodeFactor| image:: https://www.codefactor.io/repository/github/segrelab/micone/badge
    :target: https://www.codefactor.io/repository/github/segrelab/micone
 .. |Updates| image:: https://pyup.io/repos/github/segrelab/MiCoNE/shield.svg