IGNORE Reformatted code base with black

Author: s-weigand

docs/source/conf.py

@@ -15,18 +15,15 @@
 #
 import os
 import sys
-sys.path.insert(0, os.path.abspath('../..'))
+
+sys.path.insert(0, os.path.abspath("../.."))
 
 
 # -- Project information -----------------------------------------------------
 
-project = 'pyglotaran'
-copyright = u"2018, Joern Weissenborn, " \
-            u"Joris Snellenburg, " \
-            u"Ivo van Stokkum"
-author = u"Joern Weissenborn, " \
-         u"Joris Snellenburg, " \
-         u"Ivo van Stokkum"
+project = "pyglotaran"
+copyright = "2018, Joern Weissenborn, " "Joris Snellenburg, " "Ivo van Stokkum"
+author = "Joern Weissenborn, " "Joris Snellenburg, " "Ivo van Stokkum"
 
 # The version info for the project you're documenting, acts as replacement
 # for |version| and |release|, also used in various other places throughout
@@ -48,18 +45,18 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.autosummary',
-    'sphinx.ext.doctest',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.extlinks',
-    'sphinx.ext.imgmath',
-    'sphinx.ext.viewcode',
-    'sphinx.ext.napoleon',
-    'numpydoc',
-    'IPython.sphinxext.ipython_directive',
-    'IPython.sphinxext.ipython_console_highlighting',
-    'sphinx_copybutton',
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.doctest",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.extlinks",
+    "sphinx.ext.imgmath",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.napoleon",
+    "numpydoc",
+    "IPython.sphinxext.ipython_directive",
+    "IPython.sphinxext.ipython_console_highlighting",
+    "sphinx_copybutton",
 ]
 
 autoclass_content = "both"
@@ -72,18 +69,18 @@
 napoleon_use_ivar = True
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
-imgmath_image_format = 'svg'
+imgmath_image_format = "svg"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -98,17 +95,17 @@
 exclude_patterns = []
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 
 # -- Options for HTML output -------------------------------------------------
 
 # 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_options = {
-    'navigation_depth': -1,
+    "navigation_depth": -1,
 }
 html_favicon = "images/glotaran_favicon.png"
 html_logo = "images/glotaran.png"
@@ -140,7 +137,7 @@
 # -- Options for HTMLHelp output ---------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'pyglotarandoc'
+htmlhelp_basename = "pyglotarandoc"
 
 
 # -- Options for LaTeX output ------------------------------------------------
@@ -149,15 +146,12 @@
     # 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',
@@ -167,22 +161,21 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'pyglotaran.tex', 'pyglotaran Documentation',
-     u'Joris Snellenburg, '
-     u'Joern Weissenborn, '
-     u'Ivo van Stokkum',
-     'manual'),
+    (
+        master_doc,
+        "pyglotaran.tex",
+        "pyglotaran Documentation",
+        "Joris Snellenburg, " "Joern Weissenborn, " "Ivo van Stokkum",
+        "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, 'pyglotaran', 'pyglotaran Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "pyglotaran", "pyglotaran Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output ----------------------------------------------
@@ -191,10 +184,15 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'pyglotaran', 'pyglotaran Documentation',
-     author, 'pyglotaran',
-     'Global and target analysis software package based on Python',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "pyglotaran",
+        "pyglotaran Documentation",
+        author,
+        "pyglotaran",
+        "Global and target analysis software package based on Python",
+        "Miscellaneous",
+    ),
 ]
 
 
@@ -213,24 +211,24 @@
 # epub_uid = ''
 
 # A list of files that should not be packed into the epub file.
-epub_exclude_files = ['search.html']
+epub_exclude_files = ["search.html"]
 
 
 # -- Extension configuration -------------------------------------------------
 
 # -- Options for intersphinx extension ---------------------------------------
 
 intersphinx_mapping = {
-    'numpy': ('http://docs.scipy.org/doc/numpy/', None),
-    'xarray': ('http://xarray.pydata.org/en/stable/', None),
-    'https://docs.python.org/': None
+    "numpy": ("http://docs.scipy.org/doc/numpy/", None),
+    "xarray": ("http://xarray.pydata.org/en/stable/", None),
+    "https://docs.python.org/": None,
 }
 
-ipython_savefig_dir = 'images/plot'
+ipython_savefig_dir = "images/plot"
 
 # -- Options for extlinks extension ---------------------------------------
 extlinks = {
-    'numpydoc': ('https://docs.scipy.org/doc/numpy/reference/generated/numpy.%s.html', 'numpy.'),
-    'scipydoc': ('https://docs.scipy.org/doc/scipy/reference/generated/scipy.%s.html', 'scipy.'),
-    'xarraydoc': ('https://xarray.pydata.org/en/stable/generated/xarray.%s.html', 'xarray.'),
+    "numpydoc": ("https://docs.scipy.org/doc/numpy/reference/generated/numpy.%s.html", "numpy."),
+    "scipydoc": ("https://docs.scipy.org/doc/scipy/reference/generated/scipy.%s.html", "scipy."),
+    "xarraydoc": ("https://xarray.pydata.org/en/stable/generated/xarray.%s.html", "xarray."),
 }

glotaran/__init__.py

@@ -2,7 +2,7 @@
 
 from . import model, parameter, io  # noqa: F401
 
-__version__ = '0.1.0'
+__version__ = "0.1.0"
 
 ParameterGroup = parameter.ParameterGroup
 
@@ -18,5 +18,5 @@
 
 import pkg_resources  # noqa: E402
 
-for entry_point in pkg_resources.iter_entry_points('glotaran.plugins'):
+for entry_point in pkg_resources.iter_entry_points("glotaran.plugins"):
     entry_point.load()

glotaran/analysis/matrix_calculation.py

@@ -3,8 +3,8 @@
 import numpy as np
 
 
-LabelAndMatrix = collections.namedtuple('LabelAndMatrix', 'clp_label matrix')
-LabelAndMatrixAndData = collections.namedtuple('LabelAndMatrixAndData', 'label_matrix data')
+LabelAndMatrix = collections.namedtuple("LabelAndMatrix", "clp_label matrix")
+LabelAndMatrixAndData = collections.namedtuple("LabelAndMatrixAndData", "label_matrix data")
 
 
 def calculate_index_independend_ungrouped_matrices(scheme, parameter):
@@ -16,24 +16,22 @@ def calculate_index_independend_ungrouped_matrices(scheme, parameter):
     constraint_labels_and_matrices = {}
     model = scheme.model
 
-    descriptors = {label: descriptor.fill(model, parameter)
-                   for label, descriptor in scheme.model.dataset.items()}
+    descriptors = {
+        label: descriptor.fill(model, parameter)
+        for label, descriptor in scheme.model.dataset.items()
+    }
 
     for label, descriptor in descriptors.items():
         axis = scheme.data[label].coords[model.matrix_dimension].values
-        clp_label, matrix = _calculate_matrix(
-            model.matrix,
-            descriptor,
-            axis,
-            {},
-        )
+        clp_label, matrix = _calculate_matrix(model.matrix, descriptor, axis, {},)
         clp_labels[label] = clp_label
         matrices[label] = matrix
 
         if callable(model.has_matrix_constraints_function):
             if model.has_matrix_constraints_function():
-                clp_label, matrix = \
-                    model.constrain_matrix_function(parameter, clp_label, matrix, None)
+                clp_label, matrix = model.constrain_matrix_function(
+                    parameter, clp_label, matrix, None
+                )
 
         constraint_labels_and_matrices[label] = LabelAndMatrix(clp_label, matrix)
     return clp_labels, matrices, constraint_labels_and_matrices
@@ -42,12 +40,16 @@ def calculate_index_independend_ungrouped_matrices(scheme, parameter):
 def calculate_index_independend_grouped_matrices(scheme, groups, parameter):
 
     # We just need to create groups from the ungrouped matrices
-    clp_labels, matrices, constraint_labels_and_matrices = \
-        calculate_index_independend_ungrouped_matrices(scheme, parameter)
+    (
+        clp_labels,
+        matrices,
+        constraint_labels_and_matrices,
+    ) = calculate_index_independend_ungrouped_matrices(scheme, parameter)
     for label, group in groups.items():
         if label not in matrices:
-            constraint_labels_and_matrices[label] = \
-                _combine_matrices([constraint_labels_and_matrices[label] for label in group])
+            constraint_labels_and_matrices[label] = _combine_matrices(
+                [constraint_labels_and_matrices[label] for label in group]
+            )
 
     return clp_labels, matrices, constraint_labels_and_matrices
 
@@ -59,20 +61,18 @@ def create_index_dependend_ungrouped_matrix_jobs(scheme, bag, parameter):
     matrices = {}
     constraint_labels_and_matrices = {}
 
-    descriptors = {label: descriptor.fill(model, parameter)
-                   for label, descriptor in scheme.model.dataset.items()}
+    descriptors = {
+        label: descriptor.fill(model, parameter)
+        for label, descriptor in scheme.model.dataset.items()
+    }
     for label, problem in bag.items():
         descriptor = descriptors[label]
         clp_labels[label] = []
         matrices[label] = []
         constraint_labels_and_matrices[label] = []
         for index in problem.global_axis:
             clp, matrix = dask.delayed(_calculate_matrix, nout=2)(
-                model.matrix,
-                descriptor,
-                problem.matrix_axis,
-                {},
-                index=index,
+                model.matrix, descriptor, problem.matrix_axis, {}, index=index,
             )
             clp_labels[label].append(clp)
             matrices[label].append(matrix)
@@ -91,17 +91,18 @@ def create_index_dependend_grouped_matrix_jobs(scheme, bag, parameter):
 
     model = scheme.model
 
-    descriptors = {label: descriptor.fill(model, parameter)
-                   for label, descriptor in scheme.model.dataset.items()}
+    descriptors = {
+        label: descriptor.fill(model, parameter)
+        for label, descriptor in scheme.model.dataset.items()
+    }
 
     def calculate_group(group):
-        results = [_calculate_matrix(
-            model.matrix,
-            descriptors[problem.dataset],
-            problem.axis,
-            {},
-            index=problem.index
-        ) for problem in group.descriptor]
+        results = [
+            _calculate_matrix(
+                model.matrix, descriptors[problem.dataset], problem.axis, {}, index=problem.index
+            )
+            for problem in group.descriptor
+        ]
         return results, group.descriptor[0].index
 
     def get_clp(result):
@@ -127,13 +128,13 @@ def constrain_and_combine_matrices(result):
 
 def _calculate_matrix(matrix_function, dataset_descriptor, axis, extra, index=None):
     args = {
-        'dataset_descriptor': dataset_descriptor,
-        'axis': axis,
+        "dataset_descriptor": dataset_descriptor,
+        "axis": axis,
     }
     for k, v in extra:
         args[k] = v
     if index is not None:
-        args['index'] = index
+        args["index"] = index
     clp_label, matrix = matrix_function(**args)
     if dataset_descriptor.scale is not None:
         matrix *= dataset_descriptor.scale

glotaran/analysis/nnls.py

@@ -6,8 +6,9 @@
 from scipy.optimize import nnls
 
 
-def residual_nnls(matrix: np.ndarray, data: np.ndarray) \
-        -> typing.Tuple[typing.List[str], np.ndarray]:
+def residual_nnls(
+    matrix: np.ndarray, data: np.ndarray
+) -> typing.Tuple[typing.List[str], np.ndarray]:
     """Calculates the conditionaly linear parameters and residual with the non-negative
     least-squares method.