Merge pull request #6 from jmenglund/develop

jmenglund · web-flow · commit 1f0e560062ac · 2016-08-08T12:57:41.000+02:00
Update docs and testing
diff --git a/.travis.yml b/.travis.yml
@@ -2,15 +2,17 @@ language: python
 
 python:
     - '2.7'
+    - '3.3'
     - '3.4'
+    - '3.5'
 
 # whitelist
 branches:
     only:
         - master
 
 script:
-    py.test --cov=pandascharm.py
+    py.test --cov=pandascharm.py --pep8
 
 after_success:
   - codecov
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -1,29 +1,45 @@
 Changelog
 =========
 
-0.1.0
+0.1.2
 -----
 
-Initial release.
-
-Includes the following functions:
+* Added Python versions for Travis-CI (3.3, 3.5)
+* Added ``pep8`` check to Travis-CI
+* Updates to *README.rst*
+    - Fixed issue with one example not working (``pc.to_charmatrix()``)
+    - Updated text in various places
+* Updates to *release-checklist.rst*
 
-* frame_as_categorical()
-* frame_as_object()
-* from_bioalignment()
-* from_charmatrix()
-* to_bioalignment()
-* to_charmatrix()
+Release date: 2016-08-08
 
-Release date: 2016-07-05
+`View commits <https://github.com/jmenglund/pandas-charm/compare/v0.1.1...v0.1.2>`_
 
 
 0.1.1
 -----
 
 * Simplified builds with Travis-CI.
 * DOI badge added to the top of *README.rst*.
-* Information on how to cite pandas-charm added to *README.rst*.
+* Information on how to cite ``pandas-charm`` added to *README.rst*.
 
 Release date: 2016-07-05
 
+`View commits <https://github.com/jmenglund/pandas-charm/compare/v0.1.0...v0.1.1>`_
+
+
+0.1.0
+-----
+
+Initial release.
+
+Includes the following functions:
+
+* ``frame_as_categorical()``
+* ``frame_as_object()``
+* ``from_bioalignment()``
+* ``from_charmatrix()``
+* ``to_bioalignment()``
+* ``to_charmatrix()``
+
+Release date: 2016-07-05
diff --git a/LICENSE.txt b/LICENSE.txt
@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2015 Markus Englund
+Copyright (c) 2016 Markus Englund
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
diff --git a/README.rst b/README.rst
@@ -1,41 +1,29 @@
 pandas-charm
 ============
 
-.. image:: https://travis-ci.org/jmenglund/pandas-charm.svg?branch=master
-    :target: https://travis-ci.org/jmenglund/pandas-charm
+|Build-Status| |Coverage-Status| |PyPI-Status| |License| |DOI-URI|
 
-.. image:: https://codecov.io/gh/jmenglund/pandas-charm/branch/master/graph/badge.svg
-    :target: https://codecov.io/gh/jmenglund/pandas-charm
-
-.. image:: https://img.shields.io/badge/license-MIT-blue.svg
-    :target: https://opensource.org/licenses/MIT
-
-.. image:: https://zenodo.org/badge/23107/jmenglund/pandas-charm.svg
-    :target: https://zenodo.org/badge/latestdoi/23107/jmenglund/pandas-charm
-
-|
-
-pandas-charm is a small Python package (or library) for getting character 
+``pandas-charm`` is a small Python package for getting character 
 matrices (alignments) into and out of `pandas <http://pandas.pydata.org>`_.
-The intention of the package is to make pandas interoperable with 
-other scientific packages that can be used for working with character 
-matrices, like for example `BioPython <http://biopython.org>`_ and 
-`Dendropy <http://dendropy.org>`_.
+Its purpose is to make pandas interoperable with other scientific 
+packages that can be used for dealing with character matrices, like for example 
+`BioPython <http://biopython.org>`_ and `Dendropy <http://dendropy.org>`_.
 
-With pandas-charm, it is currently possible to convert between the 
+With ``pandas-charm``, it is currently possible to convert between the 
 following objects:
 
 * BioPython MultipleSeqAlignment <-> pandas DataFrame
 * DendroPy CharacterMatrix <-> pandas DataFrame
 
-Source repository: `<https://github.com/jmenglund/pandas-charm>`_
+The code has been tested with Python 2.7, 3.3, 3.4 and 3.5.
 
+Source repository: `<https://github.com/jmenglund/pandas-charm>`_
 
-The name
---------
+------------------------------------------
 
-pandas-charm got its name from the pandas library plus an acronym for
-CHARacter Matrix.
+.. contents:: Table of contents
+   :backlinks: top
+   :local:
 
 
 Installation
@@ -49,7 +37,7 @@ hosted on `PyPI <https://pypi.python.org/>`_:
     $ pip install pandas-charm
 
 The project is hosted at https://github.com/jmenglund/pandas-charm and 
-can be installed using git:
+can also be installed using git:
 
 .. code-block::
 
@@ -58,25 +46,30 @@ can be installed using git:
     $ python setup.py install
 
 
+You may consider installing ``pandas-charm`` and its required Python packages 
+within a virtual environment in order to avoid cluttering your system's 
+Python path. See for example the environment management system 
+`conda <http://conda.pydata.org>`_ or the package 
+`virtualenv <https://virtualenv.pypa.io/en/latest/>`_.
+
+
 Running tests
 -------------
 
-After installing the pandas-charm, you may want to check that everything
-works as expected. Below is an example of how to run the tests with pytest. 
-The packages BioPython, DendroPy, pytest, coverage, and pytest-cov need 
-to be installed.
+Testing is carried out with `pytest <http://pytest.org>`_. Here is an 
+example on how to run the test suite and generating a coverage report:
 
 .. code-block::
 
-    $ cd pandas-charm
-    $ py.test -v --cov-report term-missing --cov pandascharm.py
+    $ pip install pytest pytest-cov pytest-pep8 dendropy biopython 
+    $ py.test -v --cov-report term-missing --cov pandascharm.py --pep8
 
 
 Usage
 -----
 
 Below are a few examples on how to use pandas-charm. The examples are 
-written with Python 3 code, but pandas-charm should work also with 
+written with Python 3 code, but ``pandas-charm`` should work also with 
 Python 2.7. You need to install BioPython and/or DendroPy manually 
 before you start:
 
@@ -86,8 +79,8 @@ before you start:
     $ pip install dendropy
 
 
-Converting a DendroPy CharacterMatrix to a pandas DataFrame
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+DendroPy CharacterMatrix to pandas DataFrame
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 .. code-block:: pycon
 
@@ -112,9 +105,9 @@ Converting a DendroPy CharacterMatrix to a pandas DataFrame
     3  A  A  A
     4  A  A  A
 
-As seen above, characters are stored as rows and sequences as 
-columns in the DataFrame. If you want rows to hold sequences, 
-it is easy to transpose the matrix in pandas:
+By default, characters are stored as rows and sequences as columns 
+in the DataFrame. If you want rows to hold sequences, just transpose 
+the matrix in pandas:
 
 .. code-block:: pycon
 
@@ -125,8 +118,8 @@ it is easy to transpose the matrix in pandas:
     t3  T  G  -  A  A
 
 
-Converting a pandas DataFrame to a Dendropy CharacterMatrix
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+pandas DataFrame to Dendropy CharacterMatrix
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 .. code-block:: pycon
 
@@ -145,16 +138,16 @@ Converting a pandas DataFrame to a Dendropy CharacterMatrix
     3  A  A  A
     4  A  A  A
     
-    >>> matrix = pc.to_charmatrix(df, type='dna')
+    >>> matrix = pc.to_charmatrix(df, data_type='dna')
     >>> print(matrix.as_string('phylip'))
     3 5
     t1  TCCAA
     t2  TGCAA
     t3  TG-AA
 
 
-Converting a BioPython MultipleSeqAlignment to a pandas DataFrame
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+BioPython MultipleSeqAlignment to pandas DataFrame
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 .. code-block:: pycon
 
@@ -180,8 +173,8 @@ Converting a BioPython MultipleSeqAlignment to a pandas DataFrame
     4  A  A  A
 
 
-Converting a pandas DataFrame to a BioPython MultipleSeqAlignment
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+pandas DataFrame to BioPython MultipleSeqAlignment
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 .. code-block:: pycon
 
@@ -208,11 +201,19 @@ Converting a pandas DataFrame to a BioPython MultipleSeqAlignment
     TG-AA t3
     
 
+
+The name
+--------
+
+``pandas-charm`` got its name from the pandas library plus an acronym for
+CHARacter Matrix.
+
+
 License
 -------
 
-pandas-charm is distributed under 
-`the MIT license <https://opensource.org/licenses/MIT>`_.
+``pandas-charm`` is distributed under the 
+`MIT license <https://opensource.org/licenses/MIT>`_.
 
 
 Citing
@@ -222,8 +223,24 @@ If you use results produced with this package in a scientific
 publication, please just mention the package name in the text and 
 cite the Zenodo DOI of this project:
 
-.. image:: https://zenodo.org/badge/23107/jmenglund/pandas-charm.svg
-    :target: https://zenodo.org/badge/latestdoi/23107/jmenglund/pandas-charm
+|DOI-URI|
 
 You can select a citation style from the dropdown menu in the 
-*"Cite as"* section on the Zenodo page.
+"Cite as" section on the Zenodo page.
+
+
+Author
+------
+
+Markus Englund, `orcid.org/0000-0003-1688-7112 <http://orcid.org/0000-0003-1688-7112>`_
+
+.. |Build-Status| image:: https://travis-ci.org/jmenglund/pandas-charm.svg?branch=master
+   :target: https://travis-ci.org/jmenglund/pandas-charm
+.. |Coverage-Status| image:: https://codecov.io/gh/jmenglund/pandas-charm/branch/master/graph/badge.svg
+   :target: https://codecov.io/gh/jmenglund/pandas-charm
+.. |PyPI-Status| image:: https://img.shields.io/pypi/v/pandas-charm.svg
+   :target: https://pypi.python.org/pypi/pandas-charm
+.. |License| image:: https://img.shields.io/pypi/l/pandas-charm.svg
+   :target: https://raw.githubusercontent.com/jmenglund/pandas-charm/master/LICENSE.txt
+.. |DOI-URI| image:: https://zenodo.org/badge/23107/jmenglund/pandas-charm.svg
+   :target: https://zenodo.org/badge/latestdoi/23107/jmenglund/pandas-charm
diff --git a/pandascharm.py b/pandascharm.py
@@ -6,7 +6,7 @@
 
 __authors__ = 'Markus Englund'
 __license__ = 'MIT'
-__version__ = '0.1.1'
+__version__ = '0.1.2'
 
 
 def frame_as_categorical(frame, include_categories=None):
@@ -97,15 +97,15 @@ def to_bioalignment(frame, alphabet='generic_alphabet'):
     if alphabet not in [
             'generic_alphabet', 'generic_dna',
             'generic_nucleotide', 'generic_protein', 'generic_rna']:
-        raise ValueError(  # pragma: no cover
+        raise ValueError(
             'Invalid BioPython alphabet: {}'
             .format(alphabet))
     try:
         import Bio.Alphabet
         from Bio.AlignIO import MultipleSeqAlignment
         from Bio.Seq import Seq
         from Bio.SeqRecord import SeqRecord
-    except ImportError as ex:  # pragma: no cover
+    except ImportError as ex:
         raise ImportError(
             '\'to_bioalignment\' requires BioPython.\n{ex}'.format(ex=str(ex)))
     alignment = MultipleSeqAlignment([])
@@ -131,7 +131,7 @@ def to_charmatrix(frame, data_type):
     """
     try:
         import dendropy
-    except ImportError as ex:  # pragma: no cover
+    except ImportError as ex:
         raise ImportError(
             '\'to_charmatrix\' requires DendroPy.\n{ex}'.format(ex=str(ex)))
     d = frame.apply(lambda x: ''.join(x), axis=0).to_dict()
diff --git a/release-checklist.rst b/release-checklist.rst
@@ -3,26 +3,30 @@ Release checklist
 
 Things to remember when making a new release of pandas-charm.
 
-#.  Changes should be made to some branch other than master (a pull request 
-    should then be created before making the release).
+#.  Changes should be made to some branch other than master (a pull request should then be created before making the release).
 
 #.  Update the release (version) numbers in *setup.py* and *pandascharm.py*.
 
 #.  Make desirable changes to the code.
 
-#.  Check coding style with pep8.
+#.  Run tests with coverage report and PEP8 check:
+
+    .. code-block::
+
+        $ py.test -v --cov-report term-missing --cov predsim.py --pep8
 
 #.  Update the documentation in *README.rst*.
 
 #.  Update *CHANGELOG.rst*.
 
 #.  Create pull request(s) with changes for the new release.
 
-#.  Create the release in GitHub.
+#.  Create the new release in GitHub.
 
-#.  Create distributions and upload the files to PyPI.
+#.  Create distributions and upload the files to `PyPI <https://pypi.python.org/pypi>`_.
 
     .. code-block::
 
         $ python setup.py bdist_wheel --universal
         $ python setup.py sdist
+ 
diff --git a/requirements.txt b/requirements.txt
@@ -1,6 +1,7 @@
 pandas>=0.16
 pytest>=2.8
 codecov
+pytest-pep8
 pytest-cov
 DendroPy>=4.0
 BioPython
diff --git a/setup.py b/setup.py
diff --git a/test_pandascharm.py b/test_pandascharm.py

-Original file line number
+Diff line change
 setup(
     name='pandas-charm',
 -    version='0.1.1',
 +    version='0.1.2',
     description=(
         'A small Python library for getting character matrices '
         '(alignments) into and out of pandas'),
         'Programming Language :: Python :: 2',
         'Programming Language :: Python :: 2.7',
         'Programming Language :: Python :: 3',
 -        'Programming Language :: Python :: 3.4'
 +        'Programming Language :: Python :: 3.3',
 +        'Programming Language :: Python :: 3.4',
 +        'Programming Language :: Python :: 3.5',
     ],
     keywords=['alignment', 'BioPython', 'DendroPy', 'pandas'],
+)
-Original file line number
+Diff line change
         assert_frame_equal(frame_as_object(self.frame_cat), self.frame_obj)
+-
 class TestCharmatrixConversion():
     dna_charmatrix_string = '3 5\nt1  TCCAA\nt2  TGCAA\nt3  TG-AA\n'
         't3': ['0', '2', '-', '1', '0']}, dtype='category')
     def test_from_charmatrix_dna(self):
 -        assert_frame_equal (
 +        assert_frame_equal(
             from_charmatrix(self.dna_charmatrix), self.dna_frame)
+-
++
     def test_from_charmatrix_dna_object(self):
 -        assert_frame_equal (
 +        assert_frame_equal(
             from_charmatrix(self.dna_charmatrix, categorical=False),
             frame_as_object(self.dna_frame))
             .as_string('phylip') == self.dna_charmatrix.as_string('phylip'))
     def test_from_charmatrix_rna(self):
 -        assert_frame_equal (
 +        assert_frame_equal(
             from_charmatrix(self.rna_charmatrix), self.rna_frame)
     def test_to_charmatrix_rna(self):
             .as_string('phylip') == self.rna_charmatrix.as_string('phylip'))
     def test_from_charmatrix_protein(self):
 -        assert_frame_equal (
 +        assert_frame_equal(
             from_charmatrix(self.protein_charmatrix), self.protein_frame)
     def test_to_charmatrix_protein(self):
             .as_string('phylip'))
     def test_from_charmatrix_standard(self):
 -        assert_frame_equal (
 +        assert_frame_equal(
             from_charmatrix(self.standard_charmatrix), self.standard_frame)
     def test_to_charmatrix_standard(self):
         't3': ['T', 'G', '-', 'A', 'A']}, dtype='category')
     def test_from_bioalignment_dna(self):
 -        assert_frame_equal (
 +        assert_frame_equal(
             from_bioalignment(self.dna_bioalignment), self.dna_frame)
     def test_to_bioalignment_dna(self):
         assert (
             to_bioalignment(self.dna_frame, alphabet='generic_dna')
             .format('phylip') == self.dna_bioalignment.format('phylip'))
++
 +    def test_invalid_alphabet(self):
 +        with pytest.raises(ValueError):
 +            to_bioalignment(self.dna_frame, alphabet='dna')