.travis.yml

@@ -6,10 +6,12 @@ os:
   - linux
   - osx
 env:
-  - CONDA_PY=3.6 MAKE_DOC=TRUE
-  - CONDA_PY=3.5 MAKE_DOC=TRUE USE_CYTHON=TRUE
+  - CONDA_PY=3.7
+  - CONDA_PY=3.6
+  - CONDA_PY=3.5 USE_CYTHON=TRUE
 
 before_install:
+  - export MPLBACKEND='Agg'
   - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh; fi
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh; fi
   - bash miniconda.sh -b -p $HOME/miniconda
@@ -30,7 +32,7 @@ install:
 
 script:
   - WITH_COVERAGE=TRUE make test
-  - if [ ${MAKE_DOC} ]; then make -C doc clean html; fi
+  - make -C doc clean html
 
 after_success:
   - coveralls

CHANGELOG.md

 # scikit-bio changelog
 
+
+
+## Version 0.5.5 (2018-12-10)
+
+### Features
+
+* `skbio.stats.composition` now has methods to compute additive log-ratio transformation and inverse additive log-ratio transformation (`alr`, `alr_inv`) as well as a method to build a basis from a sequential binary partition (`sbp_basis`).
+
+### Backward-incompatible changes [stable]
+
+### Backward-incompatible changes [experimental]
+
+### Performance enhancements
+
+### Bug fixes
+
+### Deprecated functionality [stable]
+
+### Deprecated functionality [experimental]
+
+### Miscellaneous
+* Python 3.6 and 3.7 compatibility is now supported
+
+* A pytest runner is shipped with every installation ([#1633](https://github.com/biocore/scikit-bio/pull/1633))
+
+* The nosetest framework has been replaced in favor of pytest ([#1624](https://github.com/biocore/scikit-bio/pull/1624))
+
+* The numpy docs are deprecated in favor of [Napoleon](http://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html) ([#1629](https://github.com/biocore/scikit-bio/pull/1629))
+
+* This version is now compatible with NumPy >= 1.9.2 and Pandas >= 0.23. ([#1627](https://github.com/biocore/scikit-bio/pull/1627))
+
+
 ## Version 0.5.4 (2018-08-23)
 
 ### Features

CONTRIBUTING.md

@@ -184,11 +184,9 @@ The scikit-bio coding guidelines describe our [expectations for unit tests](http
 Tests can be executed by running ``make test`` from the base directory of the project or from within a Python or IPython session:
 
 ``` python
->>> import skbio
->>> skbio.test()
+>>> from skbio.test import pytestrunner
+>>> pytestrunner()
 # full test suite is executed
->>> skbio.io.test()
-# tests for the io module are executed
 ```
 
 Documentation guidelines

MANIFEST.in

@@ -24,3 +24,4 @@ global-exclude *.pyc
 global-exclude *.pyo
 global-exclude *.so
 global-exclude .*.swp
+global-exclude .coverage

Makefile

@@ -7,8 +7,7 @@
 # ----------------------------------------------------------------------------
 
 ifeq ($(WITH_COVERAGE), TRUE)
-	TEST_COMMAND = COVERAGE_FILE=../.coverage coverage run \
-	--rcfile ../.coveragerc -m skbio.test
+	TEST_COMMAND = coverage run --rcfile ../.coveragerc -m skbio.test; coverage report --rcfile ../.coveragerc
 else
 	TEST_COMMAND = python -m skbio.test
 endif
@@ -20,7 +19,7 @@ endif
 # simulate a user's install/test process this way to find package data that did
 # not install correctly (for example).
 test:
-	cd ci && $(TEST_COMMAND)
+	cd ci && $(TEST_COMMAND); cd -
 	flake8 skbio setup.py checklist.py
 	./checklist.py
 	check-manifest

ci/conda_requirements.txt

 pip
-# See note in setup.py install_requires about numpy version pin.
-numpy<1.14.0
+numpy
 scipy
 matplotlib
-pandas<0.23.0
-nose
+pandas
 pep8
 ipython
 pyflakes
@@ -12,3 +10,5 @@ flake8
 python-dateutil
 decorator
 scikit-learn
+pytest
+coverage

ci/pip_requirements.txt

@@ -5,6 +5,5 @@ lockfile
 CacheControl
 Sphinx
 sphinx-bootstrap-theme
-numpydoc < 0.8.0
 check-manifest
 hdmedians

debian/changelog

-python-skbio (0.5.4-1) UNRELEASED; urgency=medium
+python-skbio (0.5.5-1) unstable; urgency=medium
 
   * New upstream version
+    Closes: #906156
   * Standards-Version: 4.2.1
   * Build-Depends: python3-hdmedians
+  * Secure URI in copyright format
+  * No override for dh_auto_test
+  * Test-Depends: python3-pytest
 
- -- Andreas Tille <tille@debian.org>  Tue, 28 Aug 2018 18:14:05 +0200
+ -- Andreas Tille <tille@debian.org>  Mon, 17 Dec 2018 12:03:10 +0100
 
 python-skbio (0.5.2-1) unstable; urgency=medium
 

debian/copyright

-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: scikit-bio
 Upstream-Contact: gregcaporaso@gmail.com
 Source: https://github.com/biocore/scikit-bio

debian/rules

@@ -18,9 +18,6 @@ override_dh_auto_build:
 		http_proxy='127.0.0.1:9' \
 		python3 `which sphinx-build` -b html -d doc/build/doctrees doc/source doc/build/html
 
-override_dh_auto_test:
-	dh_auto_test
-
 override_dh_auto_clean:
 	if [ "`find . -name "*.pyo"`" = "" ] ; then echo no need to clean up ; else dh_auto_clean; fi
 

debian/tests/control

 Tests: import-skbio testsuite
 Depends: python3-skbio,
          python3-httpretty,
+         python3-pytest
 Restrictions: allow-stderr

doc/README.md

@@ -11,7 +11,11 @@ Building the documentation
 --------------------------
 
 To build the documentation, you'll need a scikit-bio development environment
-set up. See [CONTRIBUTING.md](../CONTRIBUTING.md) for instructions.
+set up. See [CONTRIBUTING.md](../CONTRIBUTING.md) for instructions. In
+addition, you will also need to install Sphinx and the theme for the
+documentation, you can do that with:
+
+    pip install Sphinx sphinx-bootstrap-theme
 
 **Important:** The documentation will be built for whatever version of
 scikit-bio is *currently installed* on your system (i.e., the version imported

doc/source/_static/copybutton.js

-// originally taken from scikit-learn's Sphinx theme
 $(document).ready(function() {
     /* Add a [>>>] button on the top-right corner of code samples to hide
      * the >>> and ... prompts and the output and thus make the code
-     * copyable.
-     * Note: This JS snippet was taken from the official python.org
-     * documentation site.*/
+     * copyable. */
     var div = $('.highlight-python .highlight,' +
                 '.highlight-python3 .highlight,' +
-                '.highlight-pycon .highlight')
+                '.highlight-pycon .highlight,' +
+		'.highlight-default .highlight')
     var pre = div.find('pre');
 
     // get the styles from the current theme
@@ -22,7 +20,7 @@ $(document).ready(function() {
         'border-color': border_color, 'border-style': border_style,
         'border-width': border_width, 'color': border_color, 'text-size': '75%',
         'font-family': 'monospace', 'padding-left': '0.2em', 'padding-right': '0.2em',
-        'display': 'inline'
+        'border-radius': '0 3px 0 0'
     }
 
     // create and add the button to all the code blocks that contain >>>
@@ -32,31 +30,34 @@ $(document).ready(function() {
             var button = $('<span class="copybutton">&gt;&gt;&gt;</span>');
             button.css(button_styles)
             button.attr('title', hide_text);
+            button.data('hidden', 'false');
             jthis.prepend(button);
+        }
+        // tracebacks (.gt) contain bare text elements that need to be
+        // wrapped in a span to work with .nextUntil() (see later)
+        jthis.find('pre:has(.gt)').contents().filter(function() {
+            return ((this.nodeType == 3) && (this.data.trim().length > 0));
+        }).wrap('<span>');
+    });
 
-            var show_output = false;
-            button.bind('click', function() {
-                if (show_output) {
-                    var button = $(this);
-                    button.parent().find('.go, .gp, .gt').show();
-                    button.next('pre').find('.gt').nextUntil('.gp, .go').css('visibility', 'visible');
-                    button.css('text-decoration', 'none');
-                    button.attr('title', hide_text);
-                    show_output = false;
-                } else {
+    // define the behavior of the button when it's clicked
+    $('.copybutton').click(function(e){
+        e.preventDefault();
         var button = $(this);
+        if (button.data('hidden') === 'false') {
+            // hide the code output
             button.parent().find('.go, .gp, .gt').hide();
             button.next('pre').find('.gt').nextUntil('.gp, .go').css('visibility', 'hidden');
             button.css('text-decoration', 'line-through');
             button.attr('title', show_text);
-                    show_output = true;
-                }
-            });
+            button.data('hidden', 'true');
+        } else {
+            // show the code output
+            button.parent().find('.go, .gp, .gt').show();
+            button.next('pre').find('.gt').nextUntil('.gp, .go').css('visibility', 'visible');
+            button.css('text-decoration', 'none');
+            button.attr('title', hide_text);
+            button.data('hidden', 'false');
         }
-        // tracebacks (.gt) contain bare text elements that need to be
-        // wrapped in a span to work with .nextUntil() (see later)
-        jthis.find('pre:has(.gt)').contents().filter(function() {
-            return ((this.nodeType == 3) && (this.data.trim().length > 0));
-        }).wrap('<span>');
     });
 });

doc/source/_templates/autosummary/class.rst

-{% extends "!autosummary/class.rst" %}
+{# This template was modified from autosummaries default format #}
+{{ fullname | escape | underline}}
 
-{# Taken from scipy's sphinx documentation setup (https://github.com/scipy/scipy/blob/master/doc/source/_templates/autosummary/class.rst). #}
-
-{% block methods %}
-{% if methods %}
-   .. HACK -- the point here is that we don't want this to appear in the output, but the autosummary should still generate the pages.
-      .. autosummary::
-         :toctree:
+{# We need a list of the built-ins that we implemented, not the default ones #}
+{% set built_in_methods = []  %}
 {% for item in all_methods %}
-         {# We want to build dunder methods if they exist, but not every kind of dunder. These are the dunders provided by default on `object` #}
-         {%- if not item.startswith('_') or (item not in ['__class__',
+   {% if (item not in ['__class__',
                         '__delattr__',
                         '__getattribute__',
                         '__init__',
                         '__dir__',
+                        '__format__',
                         '__new__',
                         '__reduce__',
                         '__reduce_ex__',
@@ -21,21 +17,41 @@
                         '__setattr__',
                         '__sizeof__',
                         '__subclasshook__'] and item.startswith('__')) %}
-         {{ name }}.{{ item }}
-         {%- endif -%}
-      {%- endfor %}
+      {{ built_in_methods.append(item) or '' }}
    {% endif %}
-{% endblock %}
+{% endfor %}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
 
-{% block attributes %}
    {% if attributes %}
-   .. HACK -- the point here is that we don't want this to appear in the output, but the autosummary should still generate the pages.
+   .. rubric:: Attributes
+
+   .. autosummary::
+   {% for item in attributes %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+
+   {% if built_in_methods %}
+   .. rubric:: Built-ins
+
+   .. autosummary::
+      :toctree:
+   {% for item in built_in_methods %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+
+   {% if methods %}
+   .. rubric:: Methods
+
    .. autosummary::
       :toctree:
-      {% for item in all_attributes %}
-         {%- if not item.startswith('_') %}
-         {{ name }}.{{ item }}
-         {%- endif -%}
+   {% for item in methods %}
+      {% if item != '__init__' %}
+      ~{{ name }}.{{ item }}
+      {% endif %}
    {%- endfor %}
    {% endif %}
-{% endblock %}

doc/source/conf.py

@@ -70,27 +70,8 @@ class NewAuto(autosummary.Autosummary):
 autosummary.Autosummary = NewAuto
 
 import sphinx_bootstrap_theme
-import numpydoc
-
-@property
-def _extras(self):
-    # This will be accessed in a for-loop, so memoize to prevent quadratic
-    # behavior.
-    if not hasattr(self, '__memoized_extras'):
-        # We want every dunder that has a function type (not class slot),
-        # meaning we created the dunder, not Python.
-        # We don't ever care about __init__ and the user will see plenty of
-        # __repr__ calls, so why waste space.
-        self.__memoized_extras = [
-            a for a, v in inspect.getmembers(self._cls)
-            if type(v) == types.FunctionType and a.startswith('__')
-            and a not in ['__init__', '__repr__']
-        ]
-    return self.__memoized_extras
 
 # The extra_public_methods depends on what class we are looking at.
-numpydoc.docscrape.ClassDoc.extra_public_methods = _extras
-
 
 import skbio
 from skbio.util._decorator import classproperty
@@ -114,7 +95,8 @@ needs_sphinx = '1.6'
 extensions = [
     'sphinx.ext.autodoc',
     'sphinx.ext.mathjax',
-    'numpydoc',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.linkcode',
     'sphinx.ext.coverage',
     'sphinx.ext.doctest',
     'sphinx.ext.autosummary',
@@ -388,14 +370,6 @@ texinfo_documents = [
 # -- Options for autosummary ----------------------------------------------
 autosummary_generate = glob.glob('*.rst')
 
-# -- Options for numpydoc -------------------------------------------------
-# Generate plots for example sections
-numpydoc_use_plots = True
-# If we don't turn numpydoc's toctree generation off, Sphinx will warn about
-# the toctree referencing missing document(s). This appears to be related to
-# generating docs for classes with a __call__ method.
-numpydoc_class_members_toctree = False
-
 #------------------------------------------------------------------------------
 # Plot
 #------------------------------------------------------------------------------
@@ -453,16 +427,6 @@ intersphinx_mapping = {
 import inspect
 from os.path import relpath, dirname
 
-for name in ['sphinx.ext.linkcode', 'linkcode', 'numpydoc.linkcode']:
-    try:
-        __import__(name)
-        extensions.append(name)
-        break
-    except ImportError:
-        pass
-else:
-    print "NOTE: linkcode extension not found -- no links to source generated"
-
 def linkcode_resolve(domain, info):
     """
     Determine the URL corresponding to Python object
@@ -522,24 +486,17 @@ def linkcode_resolve(domain, info):
 # Link-checking on Travis sometimes times out.
 linkcheck_timeout = 30
 
-# This is so that our docs build.
+# You might see the following exception when building the documentation:
+# TypeError: 'abstractproperty' object is not iterable
 def _closure():
     def __get__(self, cls, owner):
         return self
 
     classproperty.__get__ = __get__
-
 _closure()
 
-def autodoc_skip_member(app, what, name, obj, skip, options):
-    if what == "method":
-        if isinstance(obj, classproperty):
-            return True
-    return skip
-
 # Add the 'copybutton' javascript, to hide/show the prompt in code
 # examples, originally taken from scikit-learn's doc/conf.py
 def setup(app):
     app.add_javascript('copybutton.js')
     app.add_stylesheet('style.css')
-    app.connect('autodoc-skip-member', autodoc_skip_member)

setup.cfg

-[nosetests]
-verbosity=0
-with-doctest=1
-doctest-tests=1
-doctest-extension=pyx
-ignore-files=DONT_IGNORE_ANYTHING

setup.py

@@ -42,6 +42,8 @@ classes = """
     Programming Language :: Python :: 3 :: Only
     Programming Language :: Python :: 3.4
     Programming Language :: Python :: 3.5
+    Programming Language :: Python :: 3.6
+    Programming Language :: Python :: 3.7
     Operating System :: Unix
     Operating System :: POSIX
     Operating System :: MacOS :: MacOS X
@@ -106,7 +108,7 @@ setup(name='scikit-bio',
       packages=find_packages(),
       ext_modules=extensions,
       include_dirs=[np.get_include()],
-      setup_requires=['nose >= 1.3.7'],
+      tests_require=['pytest', 'coverage'],
       install_requires=[
           'lockfile >= 0.10.2',  # req'd for our usage of CacheControl
           'CacheControl >= 0.11.5',
@@ -114,19 +116,12 @@ setup(name='scikit-bio',
           'IPython >= 3.2.0',
           'matplotlib >= 1.4.3',
           'natsort >= 4.0.3',
-          # numpy array repr changed in 1.14.0 to use less whitespace, which
-          # breaks the doctests. The doctests can't be updated to match the new
-          # arrray repr because we still support Python 3.4, which doesn't have
-          # a numpy 1.14.0 conda package on `defaults` or `conda-forge`
-          # channels.
-          'numpy >= 1.9.2, < 1.14.0',
-          'pandas >= 0.19.2, < 0.23.0',
+          'numpy >= 1.9.2',
+          'pandas >= 0.23',
           'scipy >= 0.15.1',
-          'nose >= 1.3.7',
           'hdmedians >= 0.13',
           'scikit-learn >= 0.19.1'
       ],
-      test_suite='nose.collector',
       classifiers=classifiers,
       package_data={
           'skbio.diversity.alpha.tests': ['data/qiime-191-tt/*'],

skbio/__init__.py

@@ -7,8 +7,6 @@
 # ----------------------------------------------------------------------------
 
 
-from skbio.util import TestRunner
-
 # Add skbio.io to sys.modules to prevent cycles in our imports
 import skbio.io  # noqa
 # imports included for convenience
@@ -26,7 +24,7 @@ __all__ = ['Sequence', 'DNA', 'RNA', 'Protein', 'GeneticCode',
            'TreeNode', 'nj', 'read', 'write', 'OrdinationResults']
 
 __credits__ = "https://github.com/biocore/scikit-bio/graphs/contributors"
-__version__ = "0.5.4"
+__version__ = "0.5.5"
 
 mottos = [
     # 03/15/2014
@@ -78,8 +76,3 @@ if __doc__ is None:
     __doc__ = title + art
 else:
     __doc__ = title + art + __doc__
-
-test = TestRunner(__file__).test
-
-if __name__ == '__main__':
-    test()

skbio/alignment/__init__.py

@@ -200,8 +200,6 @@ ACGTGCCTA-GGTACGCAAG
 # The full license is in the file COPYING.txt, distributed with this software.
 # ----------------------------------------------------------------------------
 
-from skbio.util import TestRunner
-
 from ._tabular_msa import TabularMSA
 from ._pairwise import (
     local_pairwise_align_nucleotide, local_pairwise_align_protein,
@@ -217,5 +215,3 @@ __all__ = ['TabularMSA', 'StripedSmithWaterman', 'AlignmentStructure',
            'global_pairwise_align_nucleotide', 'global_pairwise_align_protein',
            'local_pairwise_align', 'local_pairwise_align_nucleotide',
            'local_pairwise_align_protein', 'make_identity_substitution_matrix']
-
-test = TestRunner(__file__).test

skbio/alignment/_indexing.py

@@ -7,6 +7,7 @@
 # ----------------------------------------------------------------------------
 
 from abc import ABCMeta, abstractmethod
+import collections
 
 import numpy as np
 import pandas as pd
@@ -159,6 +160,8 @@ class TabularMSALoc(_Indexing):
         complete_key = False
         partial_key = False
         duplicated_key = False
+        if not isinstance(indexable, collections.Hashable):
+            return False
         if axis == 0 and self._has_fancy_index():
             try:
                 if type(indexable) is tuple:
@@ -168,7 +171,10 @@ class TabularMSALoc(_Indexing):
             except TypeError:  # Unhashable type, no biggie
                 pass
         if index.has_duplicates:
-            duplicated_key = indexable in index.get_duplicates()
+            # for a given Index object index,
+            # index[index.duplicated()].unique() is pandas' recommended
+            # replacement for index.get_duplicates(), per the pandas 0.23 docs
+            duplicated_key = indexable in index[index.duplicated()].unique()
         return (not duplicated_key and
                 ((np.isscalar(indexable) and not partial_key) or complete_key))