Merge pull request #94 from KrishnaswamyLab/dev

scprep v1.0.3

.travis.yml

@@ -42,6 +42,7 @@
 
   script:
     - pip install -U .[test]
+    - if [ "$TRAVIS_PYTHON_VERSION" != "3.5" ]; then black . --check --diff; fi
     - python setup.py test
     - pip install -U .[doc]
     - cd doc; make html

CONTRIBUTING.md

@@ -20,6 +20,13 @@ up" on issues that others reported and that are relevant to you. It also helps
 us if you spread the word: reference the project from your blog and articles,
 link to it from your website, or simply star it in GitHub to say "I use it".
 
+Code Style and Testing
+----------------------
+
+`scprep` is maintained at close to 100% code coverage. Contributors are encouraged to write tests for their code, but if you do not know how to do so, please do not feel discouraged from contributing code! Others can always help you test your contribution.
+
+Code style is dictated by [`black`](https://pypi.org/project/black/#installation-and-usage). To automatically reformat your code when you run `git commit`, you can run `./autoblack.sh` in the root directory of this project to add a hook to your `git` repository.
+
 Code of Conduct
 ---------------
 
@@ -29,4 +36,4 @@ of the Python Software Foundation: https://www.python.org/psf/codeofconduct/.
 Attribution
 ---------------
 
-This `CONTRIBUTING.md` was adapted from [scikit-learn](https://github.com/scikit-learn/scikit-learn/blob/master/CONTRIBUTING.md).
+This `CONTRIBUTING.md` was adapted from [scikit-learn](https://github.com/scikit-learn/scikit-learn/blob/master/CONTRIBUTING.md).

autoblack.sh

@@ -0,0 +1,14 @@
+cat <<EOF >> .git/hooks/pre-commit
+#!/bin/sh
+
+set -e
+
+files=\$(git diff --staged --name-only --diff-filter=d -- "*.py")
+
+for file in \$files; do
+  black -q \$file
+  git add \$file
+done
+EOF
+chmod +x .git/hooks/pre-commit
+

doc/source/conf.py

@@ -22,14 +22,13 @@
 import glob
 import shutil
 
-root_dir = os.path.abspath(os.path.join(os.path.dirname(
-    __file__), '..', '..'))
+root_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", ".."))
 sys.path.insert(0, root_dir)
 # print(sys.path)
 
 # Copy ipython notebooks
 dest_dir = "examples"
-for file in glob.glob(os.path.join(root_dir, 'examples', '*.ipynb')):
+for file in glob.glob(os.path.join(root_dir, "examples", "*.ipynb")):
     print("Copy {} to {}".format(file, dest_dir))
     shutil.copy(file, dest_dir)
 
@@ -42,44 +41,45 @@
 # 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.napoleon',
-              'sphinx.ext.doctest',
-              'sphinx.ext.coverage',
-              'sphinx.ext.viewcode',
-              'nbsphinx',
-              'sphinx.ext.mathjax',
-              'autodocsumm',
-              'IPython.sphinxext.ipython_console_highlighting']
+extensions = [
+    "sphinx.ext.napoleon",
+    "sphinx.ext.doctest",
+    "sphinx.ext.coverage",
+    "sphinx.ext.viewcode",
+    "nbsphinx",
+    "sphinx.ext.mathjax",
+    "autodocsumm",
+    "IPython.sphinxext.ipython_console_highlighting",
+]
 
 autodoc_mock_imports = ["h5py", "tables", "rpy2", "fcsparser"]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['ytemplates']
+templates_path = ["ytemplates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = ['.rst', '.ipynb']
+source_suffix = [".rst", ".ipynb"]
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = 'scprep'
-copyright = '2018 Krishnaswamy Lab, Yale University'
-author = 'Scott Gigante, Jay Stanley, Daniel Burkhardt'
+project = "scprep"
+copyright = "2018 Krishnaswamy Lab, Yale University"
+author = "Scott Gigante, Jay Stanley, Daniel Burkhardt"
 
 # 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.
 #
-version_py = os.path.join(root_dir, 'scprep', 'version.py')
+version_py = os.path.join(root_dir, "scprep", "version.py")
 # The full version, including alpha/beta/rc tags.
-release = open(version_py).read().strip().split(
-    '=')[-1].replace('"', '').strip()
+release = open(version_py).read().strip().split("=")[-1].replace('"', "").strip()
 # The short X.Y version.
-version = release.split('-')[0]
+version = release.split("-")[0]
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -91,10 +91,10 @@
 # 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', '**.ipynb_checkpoints']
+exclude_patterns = ["_build", "**.ipynb_checkpoints"]
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
@@ -105,7 +105,7 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'default'
+html_theme = "default"
 
 # 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
@@ -116,13 +116,13 @@
 # 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 = ['ystatic']
+html_static_path = ["ystatic"]
 
 
 # -- Options for HTMLHelp output ------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'scprepdoc'
+htmlhelp_basename = "scprepdoc"
 
 
 # -- Options for LaTeX output ---------------------------------------------
@@ -131,15 +131,12 @@
     # 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',
@@ -149,19 +146,21 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'scprep.tex', 'scprep Documentation',
-     'Scott Gigante, Jay Stanley, Daniel Burkhardt', 'manual'),
+    (
+        master_doc,
+        "scprep.tex",
+        "scprep Documentation",
+        "Scott Gigante, Jay Stanley, Daniel Burkhardt",
+        "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, 'scprep', 'scprep Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "scprep", "scprep Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output -------------------------------------------
@@ -170,9 +169,15 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'scprep', 'scprep Documentation',
-     author, 'scprep', 'One line description of project.',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "scprep",
+        "scprep Documentation",
+        author,
+        "scprep",
+        "One line description of project.",
+        "Miscellaneous",
+    ),
 ]
 
 nbsphinx_execute = "always"

scprep/__init__.py

@@ -16,12 +16,16 @@
 import scprep.run
 
 import pandas as pd
-if int(pd.__version__.split('.')[1]) < 26:
+
+if int(pd.__version__.split(".")[1]) < 26:
+
     def fill_value(self):
         # Used in reindex_indexer
         try:
             return self.values.dtype.fill_value
         except AttributeError:
             return self.values.dtype.na_value
+
     from pandas.core.internals.blocks import ExtensionBlock
-    setattr(ExtensionBlock, 'fill_value', property(fill_value))
+
+    setattr(ExtensionBlock, "fill_value", property(fill_value))

scprep/_lazyload.py

@@ -6,39 +6,49 @@
 # each module loads submodules on initialization but is only imported
 # and loads methods/classes when these are accessed
 _importspec = {
-    'matplotlib': ['colors', 'pyplot', 'animation', 'cm',
-                   'axes', 'lines', 'ticker', 'transforms'],
-    'mpl_toolkits': ['mplot3d'],
-    'fcsparser': ['api'],
-    'rpy2': [{'robjects': ['numpy2ri', 'packages', 'vectors', 'conversion']},
-             'rinterface',
-             {'rinterface_lib': ['callbacks']}],
-    'h5py': [],
-    'tables': [],
-    'requests': [],
+    "matplotlib": [
+        "colors",
+        "pyplot",
+        "animation",
+        "cm",
+        "axes",
+        "lines",
+        "ticker",
+        "transforms",
+    ],
+    "mpl_toolkits": ["mplot3d"],
+    "fcsparser": ["api"],
+    "rpy2": [
+        {"robjects": ["numpy2ri", "packages", "vectors", "conversion"]},
+        "rinterface",
+        {"rinterface_lib": ["callbacks"]},
+    ],
+    "h5py": [],
+    "tables": [],
+    "requests": [],
 }
 
 
 class AliasModule(object):
-
     def __init__(self, name, members=None):
         # easy access to AliasModule members to avoid recursionerror
         super_setattr = super().__setattr__
         if members is None:
             members = []
-        builtin_members = ['__class__', '__doc__']
-        super_setattr('__module_name__', name)
+        builtin_members = ["__class__", "__doc__"]
+        super_setattr("__module_name__", name)
         # create submodules
         submodules = []
         for member in members:
             if isinstance(member, dict):
                 for submodule, submembers in member.items():
-                    super_setattr(submodule, AliasModule(
-                        "{}.{}".format(name, submodule), submembers))
+                    super_setattr(
+                        submodule,
+                        AliasModule("{}.{}".format(name, submodule), submembers),
+                    )
                     submodules.append(submodule)
             else:
-                super_setattr(member, AliasModule(
-                    "{}.{}".format(name, member)))
+                super_setattr(member, AliasModule("{}.{}".format(name, member)))
                 submodules.append(member)
         super_setattr("__submodules__", submodules)
         super_setattr("__builtin_members__", builtin_members)