Merge pull request #104 from cadenmyers13/black

Edits made by running pre-commit

Author: sbillinge

.coveragerc

@@ -1,5 +1,5 @@
 [run]
-source = 
+source =
     src/diffpy/pdfmorph/
 [report]
 omit =

.flake8

@@ -0,0 +1,12 @@
+[flake8]
+exclude =
+    .git,
+    __pycache__,
+    build,
+    dist,
+    versioneer.py,
+    labpdfproc/_version.py,
+    doc/manual/source/conf.py
+max-line-length = 115
+# Ignore some style 'errors' produced while formatting by 'black'
+ignore = E203, W503

.github/workflows/docs.yml

@@ -25,7 +25,7 @@ jobs:
 
       - name: install requirements
         run: >-
-          conda install -n build -c conda-forge 
+          conda install -n build -c conda-forge
           --file requirements/build.txt
           --file requirements/run.txt
           --file requirements/docs.txt
@@ -42,4 +42,3 @@ jobs:
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: ./doc/manual/build/html
-

.isort.cfg

@@ -0,0 +1,4 @@
+[settings]
+line_length = 115
+multi_line_output = 3
+include_trailing_comma = True

.pre-commit-config.yaml

@@ -6,7 +6,9 @@ repos:
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer
+        exclude: '\.(rst|txt)$'
       - id: trailing-whitespace
+        exclude: '\.(rst|txt)$'
   - repo: https://github.com/ambv/black
     rev: 23.3.0
     hooks:

doc/manual/source/conf.py

@@ -13,65 +13,68 @@
 import sys
 from pathlib import Path
 
-sys.path.insert(0, str(Path('../../..').resolve()))
-sys.path.insert(0, str(Path('../../../src').resolve()))
+sys.path.insert(0, str(Path("../../..").resolve()))
+sys.path.insert(0, str(Path("../../../src").resolve()))
 
 
 # -- Project information -----------------------------------------------------
 
-project = 'PDFmorph'
-project_full = 'diffpy.pdfmorph'
-copyright = '2009-2019, Trustees of Columbia University in the City of New York, all rights reserved.'
-author = 'Chris Farrow, Christopher J. Wright, Pavol Juhás, Chia-Hao (Timothy) Liu, S. Matthew Román, Simon J.L. Billinge'
+project = "PDFmorph"
+project_full = "diffpy.pdfmorph"
+copyright = "2009-2019, Trustees of Columbia University in the City of New York, all rights reserved."
+author = "Chris Farrow, Christopher J. Wright, Pavol Juhás, Chia-Hao (Timothy) Liu, S. Matthew Román, Simon J.L. Billinge"
 
 # The full version, including alpha/beta/rc tags
 from importlib.metadata import version
+
 fullversion = version(project_full)
 # The short X.Y version.
-version = ''.join(fullversion.split('.post')[:1])
+version = "".join(fullversion.split(".post")[:1])
 # The full version, including alpha/beta/rc tags.
 release = fullversion
 
 # Get current date for copyright
 import time
-today = time.strftime('%B %d, %Y', time.localtime())
+
+today = time.strftime("%B %d, %Y", time.localtime())
 year = today.split()[-1]
-copyright = copyright.replace('%Y', year)
+copyright = copyright.replace("%Y", year)
 
 
 # -- General configuration ---------------------------------------------------
 
 # 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.napoleon', 
-	'sphinx.ext.todo',
-    'sphinx.ext.viewcode', 
-	'sphinx.ext.intersphinx',
-    'sphinx_rtd_theme',
-    'm2r',
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.todo",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.intersphinx",
+    "sphinx_rtd_theme",
+    "m2r",
 ]
 napoleon_google_docstring = False
 napoleon_use_param = False
 napoleon_use_ivar = False
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
-from jinja2 import Template, Environment, FileSystemLoader
+from jinja2 import Environment, FileSystemLoader, Template
 
-source_suffix = '.rst'
+source_suffix = ".rst"
 
-master_doc = 'index'
+master_doc = "index"
 
-language = 'en'
+language = "en"
 # 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 = ['Thumbs.db', '.DS_Store'] 
+exclude_patterns = ["Thumbs.db", ".DS_Store"]
 
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 todo_include_todos = True
 
@@ -80,7 +83,8 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 import sphinx_rtd_theme
-html_theme = 'sphinx_rtd_theme'
+
+html_theme = "sphinx_rtd_theme"
 html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 
 html_theme_options = {}
@@ -90,25 +94,29 @@
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = []
 
-htmlhelp_basename = 'PDFmorphdoc'
+htmlhelp_basename = "PDFmorphdoc"
 
 latex_documents = [
-	(master_doc, 'pdfmorph.tex', 'PDFmorph Documentation', 
-	'author', 'manual'),
+    (master_doc, "pdfmorph.tex", "PDFmorph Documentation", "author", "manual"),
 ]
 
-man_pages = [
-	(master_doc, 'pdfmorph', 'PDFmorph Documentation', [author], 1)
-]
+man_pages = [(master_doc, "pdfmorph", "PDFmorph Documentation", [author], 1)]
 
 texinfo_documents = [
-	(master_doc, 'PDFmorph', 'PDFmorph Documentation', author,
-	'PDFmorph', 'One line description of project.', 'Miscellaneous'),
+    (
+        master_doc,
+        "PDFmorph",
+        "PDFmorph Documentation",
+        author,
+        "PDFmorph",
+        "One line description of project.",
+        "Miscellaneous",
+    ),
 ]
 
 epub_title = project
 epub_author = author
 epub_publisher = author
 epub_copyright = copyright
 
-epub_exclude_files = ['search.html']
+epub_exclude_files = ["search.html"]

run_tests.py

@@ -1,15 +1,16 @@
 #!/usr/bin/env python
 
 import sys
+
 import pytest
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     # show output results from every test function
-    args = ['-v']
+    args = ["-v"]
     # show the message output for skipped and expected failure tests
     if len(sys.argv) > 1:
         args.extend(sys.argv[1:])
-    print('pytest arguments: {}'.format(args))
+    print("pytest arguments: {}".format(args))
     # # compute coverage stats for xpdAcq
     # call pytest and exit with the return code from pytest so that
     # travis will fail correctly if tests fail

src/diffpy/pdfmorph/morphs/morphishape.py

@@ -15,7 +15,7 @@
 
 
 """class MorphISphere -- apply inverse spherical shape function
-class MorphISpheroid -- apply inverse spheroidal shape function 
+class MorphISpheroid -- apply inverse spheroidal shape function
 """
 
 

src/diffpy/pdfmorph/pdfmorph_io.py

@@ -48,7 +48,8 @@ def single_morph_output(
     morph_file
         Name of the morphed PDF file. Required when printing to a non-terminal file.
     param xy_out: list
-        List of the form [x_morph_out, y_morph_out]. x_morph_out is a List of r values and y_morph_out is a List of gr values.
+        List of the form [x_morph_out, y_morph_out]. x_morph_out is a List of r values and
+         y_morph_out is a List of gr values.
     verbose: bool
         Print additional details about the morph when True (default False).
     stdout_flag: bool

src/diffpy/pdfmorph/pdfmorphapp.py

@@ -64,8 +64,8 @@ def custom_error(self, msg):
         metavar="NAME",
         dest="slocation",
         help="""Save the manipulated PDF to a file named NAME. Use \'-\' for stdout.
-When --multiple is enabled, save each manipulated PDF as a file in a directory named NAME;
-you can specify names for each saved PDF file using --save-names-file.""",
+ When --multiple is enabled, save each manipulated PDF as a file in a directory named NAME;
+ you can specify names for each saved PDF file using --save-names-file.""",
     )
     parser.add_option(
         "-v",
@@ -87,31 +87,31 @@ def custom_error(self, msg):
         action="store_true",
         dest="addpearson",
         help="""Maximize agreement in the Pearson function as well as
-minimizing the residual.""",
+ minimizing the residual.""",
     )
 
     group = optparse.OptionGroup(
         parser,
         "Multiple Morphs",
         """This program can morph a PDF against multiple targets in one command.
-See -s and Plot Options for how saving and plotting functionality changes when performing multiple morphs.""",
+ See -s and Plot Options for how saving and plotting functionality changes when performing multiple morphs.""",
     )
     parser.add_option_group(group)
     group.add_option(
         "--multiple",
         dest="multiple",
         action="store_true",
         help=f"""Changes usage to \'{prog_short} [options] FILE DIRECTORY\'. FILE
-will be morphed with each file in DIRECTORY as target.
-Files in DIRECTORY are sorted by alphabetical order unless a field is
-specified by --sort-by.""",
+ will be morphed with each file in DIRECTORY as target.
+ Files in DIRECTORY are sorted by alphabetical order unless a field is
+ specified by --sort-by.""",
     )
     group.add_option(
         "--sort-by",
         metavar="FIELD",
         dest="field",
         help="""Used with --multiple to sort files in DIRECTORY by FIELD from lowest to highest.
-FIELD must be included in the header of all the PDF files.""",
+ FIELD must be included in the header of all the PDF files.""",
     )
     group.add_option(
         "--reverse",
@@ -124,39 +124,39 @@ def custom_error(self, msg):
         metavar="SERIALFILE",
         dest="serfile",
         help="""Look for FIELD in a serial file instead.
-Must specify name of serial file SERIALFILE.""",
+ Must specify name of serial file SERIALFILE.""",
     )
     group.add_option(
         "--save-names-file",
         metavar="NAMESFILE",
         dest="snamesfile",
         help=f"""Used when both -s and --multiple are enabled.
-Specify names for each manipulated PDF when saving (see -s) using a serial file
-NAMESFILE. The format of NAMESFILE should be as follows: each target PDF
-is an entry in NAMESFILE. For each entry, there should be a key {__save_morph_as__}
-whose value specifies the name to save the manipulated PDF as.
+ Specify names for each manipulated PDF when saving (see -s) using a serial file
+ NAMESFILE. The format of NAMESFILE should be as follows: each target PDF
+ is an entry in NAMESFILE. For each entry, there should be a key {__save_morph_as__}
+ whose value specifies the name to save the manipulated PDF as.
 (See sample names files in the PDFmorph tutorial).""",
     )
     group.add_option(
         "--plot-parameter",
         metavar="PLOTPARAM",
         dest="plotparam",
         help="""Used when both plotting and --multiple are enabled.
-Choose a PLOTPARAM to plot for each morph (i.e. adding --pp=Pearson means the program
-will display a plot of the Pearson correlation coefficient for each morph-target pair).
-PLOTPARAM is not case sensitive, so both Pearson and pearson indicate the same parameter.
-When PLOTPARAM is not specified, Rw values for each morph-target pair will be plotted.
-PLOTPARAM will be displayed as the vertical axis label for the plot.""",
+ Choose a PLOTPARAM to plot for each morph (i.e. adding --pp=Pearson means the program
+ will display a plot of the Pearson correlation coefficient for each morph-target pair).
+ PLOTPARAM is not case sensitive, so both Pearson and pearson indicate the same parameter.
+ When PLOTPARAM is not specified, Rw values for each morph-target pair will be plotted.
+ PLOTPARAM will be displayed as the vertical axis label for the plot.""",
     )
 
     # Manipulations
     group = optparse.OptionGroup(
         parser,
         "Manipulations",
         """These options select the manipulations that are to be applied to
-the PDF from FILE1. The passed values will be refined unless specifically
-excluded with the -a or -x options. If no option is specified, the PDFs from FILE1 and FILE2 will
-be plotted without any manipulations.""",
+ the PDF from FILE1. The passed values will be refined unless specifically
+ excluded with the -a or -x options. If no option is specified, the PDFs from FILE1 and FILE2 will
+ be plotted without any manipulations.""",
     )
     parser.add_option_group(group)
     group.add_option(
@@ -173,7 +173,7 @@ def custom_error(self, msg):
         dest="exclude",
         metavar="MANIP",
         help="""Exclude a manipulation from refinement by name. This can
-appear multiple times.""",
+ appear multiple times.""",
     )
     group.add_option("--scale", type="float", metavar="SCALE", help="Apply scale factor SCALE.")
     group.add_option(
@@ -193,7 +193,7 @@ def custom_error(self, msg):
         type="float",
         dest="baselineslope",
         help="""Slope of the baseline. This is used when applying the smear
-factor. It will be estimated if not provided.""",
+ factor. It will be estimated if not provided.""",
     )
     group.add_option(
         "--qdamp",
@@ -206,36 +206,42 @@ def custom_error(self, msg):
         type="float",
         metavar="RADIUS",
         help="""Apply characteristic function of sphere with radius RADIUS.
-If PRADIUS is also specified, instead apply characteristic function of spheroid with equatorial radius RADIUS and polar radius PRADIUS.""",
+ If PRADIUS is also specified, instead apply characteristic function of spheroid with equatorial
+ radius RADIUS and polar radius PRADIUS.""",
     )
     group.add_option(
         "--pradius",
         type="float",
         metavar="PRADIUS",
         help="""Apply characteristic function of spheroid with equatorial
-radius RADIUS and polar radius PRADIUS. If only PRADIUS is specified, instead apply characteristic function of sphere with radius PRADIUS.""",
+ radius RADIUS and polar radius PRADIUS. If only PRADIUS is specified, instead apply
+ characteristic function of sphere with radius PRADIUS.""",
     )
     group.add_option(
         "--iradius",
         type="float",
         metavar="IRADIUS",
-        help="""Apply inverse characteristic function of sphere with radius IRADIUS.  If IPRADIUS is also specified, instead apply inverse characteristic function of spheroid with equatorial radius IRADIUS and polar radius IPRADIUS.""",
+        help="""Apply inverse characteristic function of sphere with radius IRADIUS.
+         If IPRADIUS is also specified, instead apply inverse characteristic function of spheroid
+         with equatorial radius IRADIUS and polar radius IPRADIUS.""",
     )
     group.add_option(
         "--ipradius",
         type="float",
         metavar="IPRADIUS",
-        help="""Apply inverse characteristic function of spheroid with equatorial radius IRADIUS and polar radius IPRADIUS. If only IPRADIUS is specified, instead apply inverse characteristic function of sphere with radius IPRADIUS.""",
+        help="""Apply inverse characteristic function of spheroid with equatorial radius IRADIUS
+         and polar radius IPRADIUS. If only IPRADIUS is specified, instead apply inverse characteristic
+         function of sphere with radius IPRADIUS.""",
     )
 
     # Plot Options
     group = optparse.OptionGroup(
         parser,
         "Plot Options",
         """These options control plotting.
-The manipulated and target PDFs will be plotted against each other with a
-difference curve below. When --multiple is enabled, the value of a parameter (specified by
---plot-parameter) will be plotted instead.""",
+ The manipulated and target PDFs will be plotted against each other with a
+ difference curve below. When --multiple is enabled, the value of a parameter (specified by
+ --plot-parameter) will be plotted instead.""",
     )
     parser.add_option_group(group)
     group.add_option(