Release 1.3.2

.gitignore

@@ -14,3 +14,4 @@ htmlcov
 .ipynb_checkpoints
 
 build
+_build

.travis.yml

@@ -9,6 +9,7 @@ install:
   - pip install six
   - pip install numpy
   - pip install pandas
+  - pip install -U mock
   - pip install coveralls
 script:
   - coverage run setup.py test

README.mkd

@@ -5,7 +5,9 @@
 
 # pyplink - Module to process Plink's binary files
 
-`PyPlink` is a Python module to read and write Plink's binary files.
+`PyPlink` is a Python module to read and write Plink's binary files. Short
+documentation available at
+[https://lemieuxl.github.io/pyplink/](https://lemieuxl.github.io/pyplink/).
 
 
 ## Dependencies
@@ -67,12 +69,11 @@ conda update pyplink -c http://statgen.org/wp-content/uploads/Softwares/pyplink
 
 To test the module, just perform the following command:
 
-```python
->>> import pyplink
->>> pyplink.test()
+```console
+$ python -m pyplink.tests
 .............................................
 ----------------------------------------------------------------------
-Ran 45 tests in 0.480s
+Ran 45 tests in 0.334s
 
 OK
 ```

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = pyplink
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/conf.py

@@ -0,0 +1,186 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+#
+# pyplink documentation build configuration file, created by
+# sphinx-quickstart on Fri Mar 10 09:00:31 2017.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+
+import os
+import sys
+sys.path.insert(0, os.path.abspath('..'))
+
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.githubpages',
+    'sphinx.ext.napoleon',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = 'pyplink'
+copyright = '2017, Louis-Philippe Lemieux Perreault'
+author = 'Louis-Philippe Lemieux Perreault'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+import pyplink
+version = ".".join(pyplink.__version__.split(".")[:-1])
+release = pyplink.__version__
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+
+
+# -- Options for HTML output ----------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'alabaster'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+
+html_theme_options = {
+    'github_user': 'lemieuxl',
+    'github_repo': 'pyplink',
+    'github_button': False,
+    'fixed_sidebar': True,
+}
+
+html_sidebars = {
+    '**': [
+        'about.html',
+        'navigation.html',
+        'relations.html',
+        'searchbox.html',
+        'donate.html',
+    ]
+}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'pyplinkdoc'
+
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, 'pyplink.tex', 'pyplink Documentation',
+     'Louis-Philippe Lemieux Perreault', 'manual'),
+]
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'pyplink', 'pyplink Documentation',
+     [author], 1)
+]
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'pyplink', 'pyplink Documentation',
+     author, 'pyplink', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {
+    'https://docs.python.org/3': None,
+    'numpy': ('http://docs.scipy.org/doc/numpy/', None),
+    'pandas': ('http://pandas.pydata.org/pandas-docs/stable/', None),
+}

docs/index.rst

@@ -0,0 +1,39 @@
+.. pyplink documentation master file, created by
+   sphinx-quickstart on Fri Mar 10 09:00:31 2017.
+
+pyplink
+========
+
+:py:mod:`pyplink` is a Python (2 and 3) binary Plink file parser and writer
+released under the MIT licence. The difference with existing parsers (and Plink
+itself) is that :py:mod:`pyplink` does not load the BED file in memory, making
+possible to work with extremely large files (*e.g.* 1000 Genomes Phase 3
+files).
+
+For more information on how to use :py:mod:`pyplink`, refer to the
+:doc:`API documentation <pyplink>`. Below is a snippet describing the most
+common usage of the module.
+
+
+.. code-block:: python
+
+    from pyplink import PyPlink
+
+    with PyPlink("plink_file_prefix") as bed:
+        # Getting the BIM and FAM
+        bim = bed.get_bim()
+        fam = bed.get_fam()
+
+        # Iterating over all loci
+        for loci_name, genotypes in bed:
+            pass
+
+        # Getting the genotypes of a single marker (numpy.ndarray)
+        genotypes = bed.get_geno_marker("rs12345")
+
+
+.. toctree::
+   :hidden:
+
+   installation
+   pyplink

docs/installation.rst

@@ -0,0 +1,30 @@
+
+Installation
+=============
+
+You can install :py:mod:`pyplink` using either ``pip`` or ``conda``.
+
+.. code-block:: bash
+
+   # Using pip
+   pip install pyplink
+
+
+.. code-block:: bash
+
+   # Using conda
+   conda config --add channels http://statgen.org/wp-content/uploads/Softwares/pyplink
+   conda install pyplink
+
+
+To test the installation, run ``python`` and execute the following commands.
+
+.. code-block:: python
+
+   >>> import pyplink
+   >>> pyplink.test()
+   .............................................
+   ----------------------------------------------------------------------
+   Ran 45 tests in 0.343s
+
+   OK

docs/pyplink.rst

@@ -0,0 +1,11 @@
+
+pyplink's API
+==============
+
+.. autoclass:: pyplink.PyPlink
+   :members:
+
+
+.. automodule:: pyplink
+   :members:
+

pyplink/__init__.py

@@ -25,7 +25,7 @@
 # THE SOFTWARE.
 
 
-from .pyplink import *
+from .pyplink import PyPlink
 
 try:
     from .version import pyplink_version as __version__
@@ -46,7 +46,7 @@ def test(verbosity=1):  # pragma: no cover
     """Executes all the tests for pyplink.
 
     Args:
-        verbosity (int): the verbosity level for unittest
+        verbosity (int): The verbosity level for :py:mod:`unittest`.
 
     Just set ``verbosity`` to an integer higher than ``1`` to have more
     information about the tests.