Format Python code with black and isort

.git-blame-ignore-revs

@@ -0,0 +1,2 @@
+# Format Python code with black and isort
+a100c005f0714ebca78ec7770f770d6522b3b870

.github/workflows/test.yaml

@@ -15,7 +15,7 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install flake8
-        run: pip install flake8 flake8-import-order
+        run: pip install flake8
       - name: Lint
         run: flake8 .
   test:

.isort.cfg

@@ -0,0 +1,11 @@
+[settings]
+force_alphabetical_sort_within_sections=true
+# Override force_grid_wrap value from profile=black, but black is still happy
+force_grid_wrap=2
+known_first_party=bx,bx_extras
+# Same line length as for black
+line_length=120
+no_lines_before=LOCALFOLDER
+profile=black
+reverse_relative=true
+skip_gitignore=true

doc/source/conf.py

@@ -23,23 +23,23 @@
 
 # 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.doctest', 'sphinx.ext.intersphinx']
+extensions = ["sphinx.ext.autodoc", "sphinx.ext.doctest", "sphinx.ext.intersphinx"]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['templates']
+templates_path = ["templates"]
 
 # The suffix of source filenames.
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The encoding of source files.
-#source_encoding = 'utf-8'
+# source_encoding = 'utf-8'
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = 'bx-python'
-copyright = '2017, James Taylor'
+project = "bx-python"
+copyright = "2017, James Taylor"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -53,37 +53,37 @@
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
-#language = None
+# language = None
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
-#today = ''
+# today = ''
 # Else, today_fmt is used as the format for a strftime call.
-#today_fmt = '%B %d, %Y'
+# today_fmt = '%B %d, %Y'
 
 # List of documents that shouldn't be included in the build.
-#unused_docs = []
+# unused_docs = []
 
 # List of directories, relative to source directory, that shouldn't be searched
 # for source files.
 exclude_trees = []
 
 # The reST default role (used for this markup: `text`) to use for all documents.
-#default_role = None
+# default_role = None
 
 # If true, '()' will be appended to :func: etc. cross-reference text.
-#add_function_parentheses = True
+# add_function_parentheses = True
 
 # If true, the current module name will be prepended to all description
 # unit titles (such as .. function::).
-#add_module_names = True
+# add_module_names = True
 
 # If true, sectionauthor and moduleauthor directives will be shown in the
 # output. They are ignored by default.
-#show_authors = False
+# show_authors = False
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 
 # Options for HTML output
@@ -92,40 +92,40 @@
 # The style sheet to use for HTML and HTML Help pages. A file of that name
 # must exist either in Sphinx' static/ path, or in one of the custom paths
 # given in html_static_path.
-html_style = 'base.css'
+html_style = "base.css"
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
-#html_title = None
+# html_title = None
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
-#html_short_title = None
+# html_short_title = None
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-#html_logo = None
+# html_logo = None
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
 # pixels large.
-#html_favicon = None
+# html_favicon = None
 
 # 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']
+html_static_path = ["static"]
 
 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.
-#html_last_updated_fmt = '%b %d, %Y'
+# html_last_updated_fmt = '%b %d, %Y'
 
 # If true, SmartyPants will be used to convert quotes and dashes to
 # typographically correct entities.
-#html_use_smartypants = True
+# html_use_smartypants = True
 
 # Custom sidebar templates, maps document names to template names.
-html_index = 'index.html'
-html_sidebars = {'index': 'indexsidebar.html'}
+html_index = "index.html"
+html_sidebars = {"index": "indexsidebar.html"}
 
 # Additional templates that should be rendered to pages, maps page names to
 # template names.
@@ -134,61 +134,61 @@
 ##}
 
 # If false, no module index is generated.
-#html_use_modindex = True
+# html_use_modindex = True
 
 # If false, no index is generated.
-#html_use_index = True
+# html_use_index = True
 
 # If true, the index is split into individual pages for each letter.
-#html_split_index = False
+# html_split_index = False
 
 # If true, the reST sources are included in the HTML build as _sources/<name>.
-#html_copy_source = True
+# html_copy_source = True
 
 # If true, an OpenSearch description file will be output, and all pages will
 # contain a <link> tag referring to it.  The value of this option must be the
 # base URL from which the finished HTML is served.
-#html_use_opensearch = ''
+# html_use_opensearch = ''
 
 # If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml").
-#html_file_suffix = ''
+# html_file_suffix = ''
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'bx-doc'
+htmlhelp_basename = "bx-doc"
 
 
 # Options for LaTeX output
 # ------------------------
 
 # The paper size ('letter' or 'a4').
-#latex_paper_size = 'letter'
+# latex_paper_size = 'letter'
 
 # The font size ('10pt', '11pt' or '12pt').
-#latex_font_size = '10pt'
+# latex_font_size = '10pt'
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, document class [howto/manual]).
-latex_documents = [(
-    'index', 'bx-python.tex', 'bx-python Documentation',
-    'James Taylor', 'manual'), ]
+latex_documents = [
+    ("index", "bx-python.tex", "bx-python Documentation", "James Taylor", "manual"),
+]
 
 # The name of an image file (relative to this directory) to place at the top of
 # the title page.
-#latex_logo = None
+# latex_logo = None
 
 # For "manual" documents, if this is true, then toplevel headings are parts,
 # not chapters.
-#latex_use_parts = False
+# latex_use_parts = False
 
 # Additional stuff for the LaTeX preamble.
-#latex_preamble = ''
+# latex_preamble = ''
 
 # Documents to append as an appendix to all manuals.
-#latex_appendices = []
+# latex_appendices = []
 
 # If false, no module index is generated.
-#latex_use_modindex = True
+# latex_use_modindex = True
 
 
 # Example configuration for intersphinx: refer to the Python standard library.
-#intersphinx_mapping = {'http://docs.python.org/dev': None}
+# intersphinx_mapping = {'http://docs.python.org/dev': None}

lib/bx/__init__.py

@@ -1 +1 @@
-__version__ = '0.8.13'
+__version__ = "0.8.13"

lib/bx/_seqmapping.pyx

@@ -11,10 +11,12 @@ cdef extern from "Python.h":
     int PyObject_AsWriteBuffer(object, void **, Py_ssize_t *) except -1
     int PyBytes_AsStringAndSize(object, char **, Py_ssize_t *) except -1
 
-from numpy import zeros
-from math import floor
 import random
 import sys
+from math import floor
+
+from numpy import zeros
+
 
 cdef class CharToIntArrayMapping:
     """Mapping for converting strings to int arrays"""

lib/bx/align/_epo.pyx

@@ -1,8 +1,11 @@
 
 
-import logging, gzip
+import gzip
+import logging
 from collections import namedtuple
+
 import numpy
+
 cimport numpy
 
 log = logging.getLogger(__name__)

lib/bx/align/axt.py

@@ -9,7 +9,7 @@
 from bx.align import (
     Alignment,
     Component,
-    src_split
+    src_split,
 )
 
 # Tools for dealing with pairwise alignments in AXT format
@@ -31,7 +31,16 @@ def get(self, src, start, end):
 class Indexed:
     """Indexed access to a axt using overlap queries, requires an index file"""
 
-    def __init__(self, axt_filename, index_filename=None, keep_open=False, species1=None, species2=None, species_to_lengths=None, support_ids=False):
+    def __init__(
+        self,
+        axt_filename,
+        index_filename=None,
+        keep_open=False,
+        species1=None,
+        species2=None,
+        species_to_lengths=None,
+        support_ids=False,
+    ):
         if index_filename is None:
             index_filename = axt_filename + ".index"
         self.indexes = interval_index_file.Indexes(filename=index_filename)
@@ -44,7 +53,7 @@ def __init__(self, axt_filename, index_filename=None, keep_open=False, species1=
         if self.species2 is None:
             self.species2 = "species2"
         self.species_to_lengths = species_to_lengths
-        self.support_ids = support_ids            # for extra text at end of axt header lines
+        self.support_ids = support_ids  # for extra text at end of axt header lines
         if keep_open:
             self.f = open(axt_filename)
         else:
@@ -80,7 +89,7 @@ def __init__(self, file, species1=None, species2=None, species_to_lengths=None,
         if self.species2 is None:
             self.species2 = "species2"
         self.species_to_lengths = species_to_lengths
-        self.support_ids = support_ids            # for extra text at end of axt header lines
+        self.support_ids = support_ids  # for extra text at end of axt header lines
         self.attributes = {}
 
     def __next__(self):
@@ -108,7 +117,6 @@ def __next__(self):
 
 
 class Writer:
-
     def __init__(self, file, attributes=None):
         if attributes is None:
             attributes = {}
@@ -120,9 +128,7 @@ def __init__(self, file, attributes=None):
 
     def write(self, alignment):
         if len(alignment.components) != 2:
-            raise ValueError(
-                "%d-component alignment is not compatible with axt" %
-                len(alignment.components))
+            raise ValueError("%d-component alignment is not compatible with axt" % len(alignment.components))
         c1 = alignment.components[0]
         c2 = alignment.components[1]
 
@@ -137,10 +143,19 @@ def write(self, alignment):
             chr1, chr2 = c1.src, c2.src
 
         self.file.write(
-            "%d %s %d %d %s %d %d %s %s\n" %
-            (self.block, chr1, c1.start+1, c1.start+c1.size,
-             chr2, c2.start+1, c2.start+c2.size, c2.strand,
-             alignment.score))
+            "%d %s %d %d %s %d %d %s %s\n"
+            % (
+                self.block,
+                chr1,
+                c1.start + 1,
+                c1.start + c1.size,
+                chr2,
+                c2.start + 1,
+                c2.start + c2.size,
+                c2.strand,
+                alignment.score,
+            )
+        )
         self.file.write("%s\n" % c1.text)
         self.file.write("%s\n" % c2.text)
         self.file.write("\n")
@@ -149,6 +164,7 @@ def write(self, alignment):
     def close(self):
         self.file.close()
 
+
 # ---- Helper methods ---------------------------------------------------------
 
 # typical axt block:
@@ -183,8 +199,9 @@ def read_next_axt(file, species1, species2, species_to_lengths=None, support_ids
     component.src = fields[1]
     if species1 != "":
         component.src = species1 + "." + component.src
-    component.start = int(fields[2]) - 1  # (axt intervals are origin-1
-    end = int(fields[3])                  # and inclusive on both ends)
+    # axt intervals are origin-1 and inclusive on both ends
+    component.start = int(fields[2]) - 1
+    end = int(fields[3])
     component.size = end - component.start
     component.strand = "+"
     component.text = seq1.strip()
@@ -217,5 +234,5 @@ def readline(file, skip_blank=False):
         line = file.readline()
         if not line:
             return None
-        if line[0] != '#' and not (skip_blank and line.isspace()):
+        if line[0] != "#" and not (skip_blank and line.isspace()):
             return line