Repo cleanup

.editorconfig

@@ -0,0 +1,21 @@
+# http://editorconfig.org
+
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+trim_trailing_whitespace = true
+insert_final_newline = true
+charset = utf-8
+end_of_line = lf
+
+[*.bat]
+indent_style = tab
+end_of_line = crlf
+
+[LICENSE]
+insert_final_newline = false
+
+[Makefile]
+indent_style = tab

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,17 @@
+* Python version:
+* numpy version:
+* matplotlib version:
+* mpl-probscale version:
+* Operating System:
+
+### Description
+
+Describe what you were trying to get done.
+Tell us what happened, what went wrong, and what you expected to happen.
+
+### What I Did
+
+```
+Paste the command(s) you ran and the output.
+If there was a crash, please include the traceback here.
+```

.travis.yml

@@ -5,23 +5,23 @@ matrix:
     - python: 2.7
       env:
         - COVERAGE=false
-        - TESTERS="conda-forge pytest mock pytest-mpl coverage"
+        - EXTRATESTERS="mock"
         - ARGS="--verbose"
     - python: 3.4
       env:
         - COVERAGE=false
-        - TESTERS="conda-forge pytest pytest-mpl coverage"
+        - EXTRATESTERS=""
         - ARGS="--mpl --verbose"
     - python: 3.5
       env:
         - COVERAGE=false
-        - TESTERS="conda-forge pytest pytest-mpl coverage"
+        - EXTRATESTERS=""
         - ARGS="--mpl --verbose"
     - python: 3.5
       env:
         - COVERAGE=true
-        - TESTERS="conda-forge pytest pytest-mpl coverage"
-        - ARGS="--mpl --verbose"
+        - EXTRATESTERS=""
+        - ARGS="--mpl --verbose --pep8"
 
 before_install:
 
@@ -41,7 +41,7 @@ install:
 
   - conda create --yes -n test python=$TRAVIS_PYTHON_VERSION numpy matplotlib docopt requests pyyaml
   - source activate test
-  - conda install --yes --channel=${TESTERS}
+  - conda install --yes --channel=conda-forge pytest-mpl pytest-cov pytest-pep8 ${EXTRATESTERS}
   - if [ ${COVERAGE} = true ]; then conda install scipy --yes; fi
   - pip install codecov
   - pip install .

AUTHORS.rst

@@ -0,0 +1,13 @@
+=======
+Credits
+=======
+
+Development Lead
+----------------
+
+* Paul M. Hobson <[email protected]>
+
+Contributors
+------------
+
+* Pierre Haessig

CONTRIBUTING.rst

@@ -0,0 +1,149 @@
+.. highlight:: shell
+
+============
+Contributing
+============
+
+Contributions are welcome, and they are greatly appreciated! Every
+little bit helps, and credit will always be given.
+
+You can contribute in many ways:
+
+Types of Contributions
+----------------------
+
+Report Bugs
+~~~~~~~~~~~
+
+Report bugs at https://github.com/phobson/probscale/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.
+
+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
+~~~~~~~~~~~~~~~~~~~
+
+mpl-probscale could always use more documentation, whether as part of the
+official mpl-probscale docs, 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/phobson/probscale/issues.
+
+If you are proposing a feature:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible, to make it easier to implement.
+* Remember that this is a volunteer-driven project, and that contributions
+  are welcome :)
+
+Get Started!
+------------
+
+Ready to contribute? Here's how to set up `probscale` for local development.
+
+1. Fork the `probscale` repo on GitHub.
+2. Clone your fork locally::
+
+    $ git clone [email protected]:your_name_here/probscale.git
+
+3. Install your local copy into a conda environment. Assuming you have conda installed, this is how you set up your fork for local development::
+
+    $ conda config --add channels conda-forge
+    $ conda create --name=probscale python=3.5 numpy matplotlib pytest pytest-cov pytest-pep8 pytest-mpl
+    $ cd probscale/
+    $ pip install -e .
+
+4. Create a branch for local development::
+
+    $ git checkout -b name-of-your-bugfix-or-feature
+
+   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 with tox::
+
+    $ python check_probscale.py --mpl --pep8 --cov
+
+6. Commit your changes and push your branch to GitHub::
+
+    $ git add <files you want to stage>
+    $ git commit -m "Your detailed description of your changes."
+    $ git push origin name-of-your-bugfix-or-feature
+
+7. Submit a pull request through the GitHub website.
+
+Matplotlib has good info on working with `source code`_ using `git and GitHub`_.
+
+.. _source code: http://matplotlib.org/devel/coding_guide.html`
+.. _git and GitHub: http://matplotlib.org/devel/gitwash/development_workflow.html
+
+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, and add the
+   feature to the list in README.rst.
+3. The pull request should work for Python 3.4 and higher. Check
+   https://travis-ci.org/phobson/probscale/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_probscale
+
+
+Configuring Sublime Text 3 to run the tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+In Sublime, got to Tools -> Build System -> New Build System.
+Then add the following configuration and save as "probscale.sublime-build"::
+
+    {
+        "working_dir": "<path to the git repository>",
+        "cmd": "<full path of the python executable> check_probscale.py --verbose <other pytest options>",
+    }
+
+
+Configuring Atom to run the tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+In Atom, install the build_ package, create a new file called ".atom-build.yml" in the
+top level of the project directory, and add the following contents::
+
+    cmd: "<full path of the python executable>"
+    name: "probscale"
+    args:
+      - check_probscale.py
+      - --verbose
+      - <other pytest options ...>
+    cwd: <path to the git repository>
+    sh: false
+    keymap: ctrl-b
+    atomCommandName: namespace:testprobscale
+
+After this, hitting ctrl+b in either text editor will run the test suite.
+
+.. _build: https://atom.io/packages/build

docs/authors.rst

@@ -0,0 +1 @@
+.. include:: ../AUTHORS.rst

docs/contributing.rst

@@ -0,0 +1 @@
+.. include:: ../CONTRIBUTING.rst

docs/installation.rst

@@ -0,0 +1,51 @@
+.. highlight:: shell
+
+============
+Installation
+============
+
+
+Stable release
+--------------
+
+To install mpl-probscale, run this command in your terminal:
+
+.. code-block:: console
+
+    $ pip install probscale
+
+This is the preferred method to install mpl-probscale, as it will always install the most recent stable release.
+
+If you don't have `pip`_ installed, this `Python installation guide`_ can guide
+you through the process.
+
+.. _pip: https://pip.pypa.io
+.. _Python installation guide: http://docs.python-guide.org/en/latest/starting/installation/
+
+
+From sources
+------------
+
+The sources for mpl-probscale can be downloaded from the `Github repo`_.
+
+You can either clone the public repository:
+
+.. code-block:: console
+
+    $ git clone git://github.com/phobson/probscale
+
+Or download the `tarball`_:
+
+.. code-block:: console
+
+    $ curl  -OL https://github.com/phobson/probscale/tarball/master
+
+Once you have a copy of the source, you can install it with:
+
+.. code-block:: console
+
+    $ pip install .
+
+
+.. _Github repo: https://github.com/phobson/probscale
+.. _tarball: https://github.com/phobson/probscale/tarball/master

docs/readme.rst

@@ -0,0 +1 @@
+.. include:: ../README.md

probscale/tests/__init__.py

@@ -4,7 +4,8 @@
 
 import probscale
 
+
 def test(*args):
     options = [resource_filename('probscale', 'tests')]
     options.extend(list(args))
-    return pytest.main(options)
+    return pytest.main(options)

probscale/tests/helpers.py

@@ -0,0 +1,12 @@
+from functools import wraps
+
+import numpy
+
+
+def seed(func):
+    """ Decorator to seed the RNG before any function. """
+    @wraps(func)
+    def wrapper(*args, **kwargs):
+        numpy.random.seed(0)
+        return func(*args, **kwargs)
+    return wrapper

probscale/tests/test_formatters.py

@@ -6,7 +6,10 @@
 from probscale import formatters
 
 
-@pytest.mark.parametrize("fmtr", [formatters.PctFormatter, formatters.ProbFormatter])
+@pytest.mark.parametrize("fmtr", [
+    formatters.PctFormatter,
+    formatters.ProbFormatter
+])
 def test_base_class_of_formatter(fmtr):
     assert issubclass(fmtr, formatters._FormatterMixin)
 

probscale/tests/test_probscale.py

@@ -58,9 +58,9 @@ def test_minimal_norm__approx_inv_erf(mn, mn_input):
 
 def test_minimal_norm_ppf(mn, mn_input):
     known_ppf = numpy.array([
-        -0.43715354,  0.6495236 , -1.49851307,  0.93847570,
+        -0.43715354,  0.64952360, -1.49851307,  0.93847570,
         -0.36648929, -1.34693863,  0.68713129, -0.40701088,
-         0.71275076,  0.40701088, -0.70952297,  1.34075503,
+        +0.71275076,  0.40701088, -0.70952297,  1.34075503,
     ])
     diff = mn.ppf(mn_input) - known_ppf
     assert numpy.all(numpy.abs(diff) < 0.001)

probscale/tests/test_transforms.py

@@ -8,7 +8,10 @@
 
 
 def test__mask_out_of_bounds():
-    known = numpy.array([numpy.nan, numpy.nan, 0.1, 0.5, 0.9, numpy.nan, numpy.nan])
+    known = numpy.array([
+        numpy.nan, numpy.nan, 0.1, 0.5,
+        0.9, numpy.nan, numpy.nan
+    ])
     x = [-0.1, 0, 0.1, 0.5, 0.9, 1.0, 1.1]
     result = transforms._mask_out_of_bounds(x)
     nptest.assert_array_equal(known, result)
@@ -22,7 +25,6 @@ def test__clip_out_of_bounds():
     assert numpy.all(diff < 0.0001)
 
 
-
 @pytest.fixture
 def prob_trans():
     cls = transforms.ProbTransform
@@ -80,13 +82,19 @@ def test_transform_inverted(trans, inver_cls):
     assert trans.out_of_bounds == t_inv.out_of_bounds
 
 
-@pytest.mark.parametrize('cls', [transforms.ProbTransform, transforms.QuantileTransform])
+@pytest.mark.parametrize('cls', [
+    transforms.ProbTransform,
+    transforms.QuantileTransform
+])
 def test_bad_out_of_bounds(cls):
     with pytest.raises(ValueError):
         cls(_minimal_norm, out_of_bounds='junk')
 
 
-@pytest.mark.parametrize('cls', [transforms.ProbTransform, transforms.QuantileTransform])
+@pytest.mark.parametrize('cls', [
+    transforms.ProbTransform,
+    transforms.QuantileTransform
+])
 @pytest.mark.parametrize(('method', 'func'), [
     ('clip', transforms._clip_out_of_bounds),
     ('mask', transforms._mask_out_of_bounds),