Merge pull request #118 from ealcobaca/release_0.4.1

Release 0.4.1

.gitignore

@@ -1,7 +1,3 @@
-# envs
-env3.7
-env3.6
-
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

Makefile

@@ -12,6 +12,9 @@ clean: ## Clean all undesired files such as .so, .pyc, build files and etc.
 	rm -rf docs/_build
 	rm -rf docs/source/generated
 	rm -rf docs/source/auto_examples
+	rm -rf .pytest_cache/
+	rm -rf .mypy_cache/
+	rm -rf pymfe.egg-info/ 
 	cd docs ; make clean_all
 
 cl: clean ## Shortcut to clean
@@ -59,3 +62,5 @@ h: help ## Shortcut to help
 
 format: ## format all the package using black
 	@black --line-length 79 pymfe/
+	@black --line-length 79 tests/
+	@black --line-length 79 docs/

README.md

@@ -3,6 +3,7 @@
 [![Documentation Status](https://readthedocs.org/projects/pymfe/badge/?version=latest)](https://pymfe.readthedocs.io/en/latest/?badge=latest)
 [![PythonVersion](https://img.shields.io/pypi/pyversions/pymfe.svg)](https://www.python.org/downloads/release/python-370/)
 [![Pypi](https://badge.fury.io/py/pymfe.svg)](https://badge.fury.io/py/pymfe)
+[![Black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
 # pymfe: Python Meta-Feature Extractor
 The pymfe (**py**thon **m**eta-**f**eature **e**xtractor) provides a

docs/source/conf.py

@@ -13,7 +13,7 @@
 # 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.
-sys.path.insert(0, os.path.abspath('../sphinxext'))
+sys.path.insert(0, os.path.abspath("../sphinxext"))
 from github_link import make_linkcode_resolve
 import sphinx_gallery
 
@@ -22,29 +22,30 @@
 # General information about the project.
 
 project = "pymfe"
-copyright = "2018-2020, Edesio Alcobaça, Felipe Siqueira"
+copyright = "2018-2021, Edesio Alcobaça, Felipe Siqueira"
 author = "Edesio Alcobaça, Felipe Siqueira"
 
 # The full version, including alpha/beta/rc tags.
 from pymfe import __version__
+
 version = release = __version__
 
 
 # -- General configuration ---------------------------------------------------
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # 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.autosummary',
-    'sphinx.ext.linkcode',
-    'sphinx.ext.intersphinx',
-    'sphinx_gallery.gen_gallery',
-    'numpydoc',
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.linkcode",
+    "sphinx.ext.intersphinx",
+    "sphinx_gallery.gen_gallery",
+    "numpydoc",
 ]
 
 # see: https://github.com/phn/pytpm/issues/3#issuecomment-12133978
@@ -53,34 +54,33 @@
 
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # If true, '()' will be appended to :func: etc. cross-reference text.
 add_function_parentheses = False
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['_build', '_templates']
+exclude_patterns = ["_build", "_templates"]
 # exclude_patterns = []
 
-autodoc_default_options = {'members': True, 'inherited-members': True}
+autodoc_default_options = {"members": True, "inherited-members": True}
 # autodoc_default_flags = ['members', 'inherited-members']
 
 # generate autosummary even if no references
 autosummary_generate = True
 
 
-
 # -- Options for HTML output -------------------------------------------------
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 # html_theme = 'sphinx_rtd_theme'
 
 # Add any paths that contain custom static files (such as style sheets) here,
@@ -91,33 +91,35 @@
 
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'pymfe-docs'
+htmlhelp_basename = "pymfe-docs"
 
 
 # intersphinx configuration
 intersphinx_mapping = {
-    'python': ('https://docs.python.org/{.major}'.format(
-        sys.version_info), None),
-    'numpy': ('https://docs.scipy.org/doc/numpy/', None),
-    'scipy': ('https://docs.scipy.org/doc/scipy/reference', None),
-    'matplotlib': ('https://matplotlib.org/', None),
-    'sklearn': ('http://scikit-learn.org/stable', None),
-    'pandas': ('https://pandas.pydata.org/pandas-docs/stable/', None),
-    'arff': ('https://pythonhosted.org/liac-arff/', None)
+    "python": (
+        "https://docs.python.org/{.major}".format(sys.version_info),
+        None,
+    ),
+    "numpy": ("https://docs.scipy.org/doc/numpy/", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy/reference", None),
+    "matplotlib": ("https://matplotlib.org/", None),
+    "sklearn": ("http://scikit-learn.org/stable", None),
+    "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
+    "arff": ("https://pythonhosted.org/liac-arff/", None),
 }
 
 # ------ sphinx gallery ----------------------------------------------------
 
 sphinx_gallery_conf = {
-    'doc_module': 'pymfe',
-    'backreferences_dir': os.path.join('generated'),
+    "doc_module": "pymfe",
+    "backreferences_dir": os.path.join("generated"),
     # path to your example scripts
-    'examples_dirs': '../../examples',
+    "examples_dirs": "../../examples",
     # path where to save gallery generated examples
-    'gallery_dirs': 'auto_examples',
-    'reference_url': {
+    "gallery_dirs": "auto_examples",
+    "reference_url": {
         # The module you locally document uses None
-        'pymfe': None,
+        "pymfe": None,
     },
     # 'thumbnail_size': (50, 50),
     # 'junit': '../test-results/sphinx-gallery/junit.xml',
@@ -128,17 +130,19 @@
 }
 
 
-
 # --- GitHun link -----------------------------------------------------------
 
 # The following is used by sphinx.ext.linkcode to provide links to github
-linkcode_resolve = make_linkcode_resolve('pymfe',
-                                         u'https://github.com/ealcobaca/'
-                                         'pymfe/blob/{revision}/'
-                                         '{package}/{path}#L{lineno}')
+linkcode_resolve = make_linkcode_resolve(
+    "pymfe",
+    u"https://github.com/ealcobaca/"
+    "pymfe/blob/{revision}/"
+    "{package}/{path}#L{lineno}",
+)
 # print(linkcode_resolve('py', {'module': 'pymfe.mfe', 'fullname': 'MFE'}))
 
 
 # run auto pages
 import os
-os.system('python pages/run.py')
+
+os.system("python pages/run.py")

docs/source/install.rst

@@ -8,11 +8,12 @@ The PyMFE package requires the following dependencies:
 
 * numpy
 * scipy
-* sklearn
-* pandas
+* scikit-learn
 * patsy
+* pandas
 * statsmodels
 * texttable
+* tqdm
 
 
 Install
@@ -43,8 +44,3 @@ You want to test/test-coverage the code before to install::
 
   $ make install-dev
   $ make test-cov
-
-Or::
-
-  $ make install-dev
-  $ pytest --cov=pymfe/ tests/

docs/source/pages/run.py

@@ -33,10 +33,12 @@
 
 def meta_features_description():
     """Automatically create the meta-feature description file."""
-    data, _ = MFE.metafeature_description(sort_by_group=True,
-                                          sort_by_mtf=True,
-                                          print_table=False,
-                                          include_references=True)
+    data, _ = MFE.metafeature_description(
+        sort_by_group=True,
+        sort_by_mtf=True,
+        print_table=False,
+        include_references=True,
+    )
 
     if not os.path.exists(AUTO_PAGES_PATH):
         os.makedirs(AUTO_PAGES_PATH)
@@ -45,13 +47,13 @@ def meta_features_description():
     del data[0]
     df = pd.DataFrame(data, columns=col)
 
-    df.to_csv(AUTO_PAGES_PATH+"/meta_features_description.csv", index=False)
+    df.to_csv(AUTO_PAGES_PATH + "/meta_features_description.csv", index=False)
 
     notes = NOTE_REL_SUB + "\n" + NOTE_OTHER_INFO
 
     table_str = TABLE_CONF
-    f = open(AUTO_PAGES_PATH+"/meta_features_description.rst", "w")
-    f.write(TITLE + '\n' + table_str + '\n' + notes)
+    f = open(AUTO_PAGES_PATH + "/meta_features_description.rst", "w")
+    f.write(TITLE + "\n" + table_str + "\n" + notes)
     f.close()
 
 

docs/sphinxext/github_link.py

@@ -7,16 +7,16 @@
 import sys
 from functools import partial
 
-REVISION_CMD = 'git rev-parse --short HEAD'
+REVISION_CMD = "git rev-parse --short HEAD"
 
 
 def _get_git_revision():
     try:
         revision = subprocess.check_output(REVISION_CMD.split()).strip()
     except (subprocess.CalledProcessError, OSError):
-        print('Failed to execute git to get revision')
+        print("Failed to execute git to get revision")
         return None
-    return revision.decode('utf-8')
+    return revision.decode("utf-8")
 
 
 def _linkcode_resolve(domain, info, package, url_fmt, revision):
@@ -34,17 +34,17 @@ def _linkcode_resolve(domain, info, package, url_fmt, revision):
 
     if revision is None:
         return
-    if domain not in ('py', 'pyx'):
+    if domain not in ("py", "pyx"):
         return
-    if not info.get('module') or not info.get('fullname'):
+    if not info.get("module") or not info.get("fullname"):
         return
 
-    class_name = info['fullname'].split('.')[0]
+    class_name = info["fullname"].split(".")[0]
     if type(class_name) != str:
         # Python 2 only
-        class_name = class_name.encode('utf-8')
-    module = __import__(info['module'], fromlist=[class_name])
-    obj = attrgetter(info['fullname'])(module)
+        class_name = class_name.encode("utf-8")
+    module = __import__(info["module"], fromlist=[class_name])
+    obj = attrgetter(info["fullname"])(module)
 
     try:
         fn = inspect.getsourcefile(obj)
@@ -58,14 +58,16 @@ def _linkcode_resolve(domain, info, package, url_fmt, revision):
     if not fn:
         return
 
-    fn = os.path.relpath(fn,
-                         start=os.path.dirname(__import__(package).__file__))
+    fn = os.path.relpath(
+        fn, start=os.path.dirname(__import__(package).__file__)
+    )
     try:
         lineno = inspect.getsourcelines(obj)[1]
     except Exception:
-        lineno = ''
-    return url_fmt.format(revision=revision, package=package,
-                          path=fn, lineno=lineno)
+        lineno = ""
+    return url_fmt.format(
+        revision=revision, package=package, path=fn, lineno=lineno
+    )
 
 
 def make_linkcode_resolve(package, url_fmt):
@@ -77,5 +79,6 @@ def make_linkcode_resolve(package, url_fmt):
                                    '{path}#L{lineno}')
     """
     revision = _get_git_revision()
-    return partial(_linkcode_resolve, revision=revision, package=package,
-                   url_fmt=url_fmt)
+    return partial(
+        _linkcode_resolve, revision=revision, package=package, url_fmt=url_fmt
+    )

examples/01_introductory_examples/plot_pymfe_specific.py

@@ -25,7 +25,7 @@
 #
 # Extracting three information theoretical measures.
 
-mfe = MFE(features=["attr_ent", "joint_ent"],
+mfe = MFE(groups="all", features=["attr_ent", "joint_ent"],
           summary=["median", "min", "max"])
 mfe.fit(X, y)
 ft = mfe.extract()
@@ -38,7 +38,7 @@
 #
 # Extracting two statistical measures.
 
-mfe = MFE(features=["can_cor", "cor", "iq_range"],
+mfe = MFE(groups="all", features=["can_cor", "cor", "iq_range"],
           summary=["median", "min", "max"])
 mfe.fit(X, y)
 ft = mfe.extract()
@@ -51,7 +51,7 @@
 #
 # Extracting five measures.
 
-mfe = MFE(features=["attr_ent", "joint_ent", "can_cor", "cor", "iq_range"],
+mfe = MFE(groups="all", features=["attr_ent", "joint_ent", "can_cor", "cor", "iq_range"],
           summary=["median", "min", "max"])
 mfe.fit(X, y)
 ft = mfe.extract()