reformat files using black

doc/conf.py

@@ -16,7 +16,7 @@
 import sys
 import os
 
-sys.path.append(os.path.join(os.path.dirname(os.path.abspath(__file__)), 'ext'))
+sys.path.append(os.path.join(os.path.dirname(os.path.abspath(__file__)), "ext"))
 
 
 # If extensions (or modules to document with autodoc) are in another directory,
@@ -27,44 +27,41 @@ sys.path.append(os.path.join(os.path.dirname(os.path.abspath(__file__)), 'ext'))
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
-#needs_sphinx = '1.0'
+# needs_sphinx = '1.0'
 
 # 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',
-    'nbsphinx',
-]
+extensions = ["sphinx.ext.autodoc", "nbsphinx"]
 
 # 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', '.md']
-#source_parsers = {".md": "recommonmark.parser.CommonMarkParser"}
+source_suffix = [".rst", ".md"]
+# source_parsers = {".md": "recommonmark.parser.CommonMarkParser"}
 
 # The encoding of source files.
-#source_encoding = 'utf-8-sig'
+# source_encoding = 'utf-8-sig'
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = 'est'
-copyright = '2016-2019, ESRF'
-author = 'ESRF'
+project = "est"
+copyright = "2016-2019, ESRF"
+author = "ESRF"
 
 # 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.
 #
 # The short X.Y version.
-version = '0.3'
+version = "0.3"
 # The full version, including alpha/beta/rc tags.
-release = '0.3'
+release = "0.3"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -75,37 +72,37 @@ 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 patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns = ['build']
+exclude_patterns = ["build"]
 
 # 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"
 
 # A list of ignored prefixes for module index sorting.
-#modindex_common_prefix = []
+# modindex_common_prefix = []
 
 # If true, keep warnings as "system message" paragraphs in the built documents.
-#keep_warnings = False
+# keep_warnings = False
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
@@ -115,22 +112,22 @@ todo_include_todos = False
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'nature'
+html_theme = "nature"
 
 # 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
 # documentation.
-#html_theme_options = {}
+# html_theme_options = {}
 
 # Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = []
+# html_theme_path = []
 
 # 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.
@@ -139,7 +136,7 @@ html_logo = "img/icon_medium.svg"
 # 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,
@@ -149,119 +146,110 @@ html_logo = "img/icon_medium.svg"
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied
 # directly to the root of the documentation.
-#html_extra_path = []
+# html_extra_path = []
 
 # 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_sidebars = {}
+# html_sidebars = {}
 
 # Additional templates that should be rendered to pages, maps page names to
 # template names.
-#html_additional_pages = {}
+# html_additional_pages = {}
 
 # If false, no module index is generated.
-#html_domain_indices = True
+# html_domain_indices = 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, links to the reST sources are added to the pages.
-#html_show_sourcelink = True
+# html_show_sourcelink = True
 
 # If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
-#html_show_sphinx = True
+# html_show_sphinx = True
 
 # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
-#html_show_copyright = True
+# html_show_copyright = 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 = ''
 
 # This is the file name suffix for HTML files (e.g. ".xhtml").
-#html_file_suffix = None
+# html_file_suffix = None
 
 # Language to be used for generating the HTML full-text search index.
 # Sphinx supports the following languages:
 #   'da', 'de', 'en', 'es', 'fi', 'fr', 'h', 'it', 'ja'
 #   'nl', 'no', 'pt', 'ro', 'r', 'sv', 'tr'
-#html_search_language = 'en'
+# html_search_language = 'en'
 
 # A dictionary with options for the search language support, empty by default.
 # Now only 'ja' uses this config value
-#html_search_options = {'type': 'default'}
+# html_search_options = {'type': 'default'}
 
 # The name of a javascript file (relative to the configuration directory) that
 # implements a search results scorer. If empty, the default will be used.
-#html_search_scorer = 'scorer.js'
+# html_search_scorer = 'scorer.js'
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'est'
+htmlhelp_basename = "est"
 
 # -- Options for LaTeX output ---------------------------------------------
 
 latex_elements = {
-# 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',
+    # 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',
 }
 
 # 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
 
 # If true, show page references after internal links.
-#latex_show_pagerefs = False
+# latex_show_pagerefs = False
 
 # If true, show URL addresses after external links.
-#latex_show_urls = False
+# latex_show_urls = False
 
 # Documents to append as an appendix to all manuals.
-#latex_appendices = []
+# latex_appendices = []
 
 # If false, no module index is generated.
-#latex_domain_indices = True
+# latex_domain_indices = True
 
 
 # -- 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, 'est', 'est Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "est", "est Documentation", [author], 1)]
 
-htmlhelp_pages = [
-    (master_doc, 'est', 'est Add-on Documentation',
-     [author], 1)
-]
+htmlhelp_pages = [(master_doc, "est", "est Add-on Documentation", [author], 1)]
 
 # If true, show URL addresses after external links.
-#man_show_urls = False
+# man_show_urls = False
 
 
 # -- Options for Texinfo output -------------------------------------------
@@ -270,19 +258,25 @@ htmlhelp_pages = [
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-  (master_doc, 'est', 'est Documentation',
-   author, 'est', 'One line description of project.',
-   'Miscellaneous'),
+    (
+        master_doc,
+        "est",
+        "est Documentation",
+        author,
+        "est",
+        "One line description of project.",
+        "Miscellaneous",
+    )
 ]
 
 # Documents to append as an appendix to all manuals.
-#texinfo_appendices = []
+# texinfo_appendices = []
 
 # If false, no module index is generated.
-#texinfo_domain_indices = True
+# texinfo_domain_indices = True
 
 # How to display URL addresses: 'footnote', 'no', or 'inline'.
-#texinfo_show_urls = 'footnote'
+# texinfo_show_urls = 'footnote'
 
 # If true, do not generate a @detailmenu in the "Top" node's menu.
-#texinfo_no_detailmenu = False
+# texinfo_no_detailmenu = False

est/__main__.py

@@ -36,12 +36,15 @@ __date__ = "06/12/2019"
 
 
 import logging
+
 logging.basicConfig()
 
 import sys
 from silx.utils.launcher import Launcher
+
 try:
     import est._version
+
     import_version = True
 except ImportError:
     import_version = False
@@ -57,20 +60,21 @@ def main():
     :returns: The execution status
     """
     if import_version is False:
-        _version = '???'
+        _version = "???"
     else:
         _version = est._version.version
     launcher = Launcher(prog="est", version=_version)
-    launcher.add_command("canvas",
-                         module_name="est.app.canvas",
-                         description="open the orange-canvas")
-    launcher.add_command("process",
-                         module_name="est.app.process",
-                         description="process a workflow from a .xml.ows file"
-                                     "description")
-    launcher.add_command("test",
-                         module_name="est.app.test_",
-                         description="Launch est unittest")
+    launcher.add_command(
+        "canvas", module_name="est.app.canvas", description="open the orange-canvas"
+    )
+    launcher.add_command(
+        "process",
+        module_name="est.app.process",
+        description="process a workflow from a .xml.ows file" "description",
+    )
+    launcher.add_command(
+        "test", module_name="est.app.test_", description="Launch est unittest"
+    )
     status = launcher.execute(sys.argv)
     return status
 

est/app/canvas_launcher/__init__.py

-from .launcher import Launcher
\ No newline at end of file
+from .launcher import Launcher

est/app/canvas_launcher/launcher.py

@@ -20,9 +20,7 @@ class EstConfig(config.Config):
 
     @staticmethod
     def core_packages():
-        return super(EstConfig, EstConfig).core_packages() + [
-            "est-add-on",
-        ]
+        return super(EstConfig, EstConfig).core_packages() + ["est-add-on"]
 
     @staticmethod
     def application_icon():
@@ -31,16 +29,26 @@ class EstConfig(config.Config):
 
 class EstSplashScreen(qt.QSplashScreen):
     """SplashScreen to overwrite the one of Orange"""
-    def __init__(self, parent=None, pixmap=None, textRect=None,
-                 textFormat=qt.Qt.PlainText, **kwargs):
+
+    def __init__(
+        self,
+        parent=None,
+        pixmap=None,
+        textRect=None,
+        textFormat=qt.Qt.PlainText,
+        **kwargs
+    ):
         qt.QSplashScreen.__init__(self, parent, pixmap=pixmap, **kwargs)
 
     def showMessage(self, message, alignment=qt.Qt.AlignLeft, color=qt.Qt.black):
-        super().showMessage(version(), qt.Qt.AlignCenter | qt.Qt.AlignBottom, qt.QColor("#e68f17"))
+        super().showMessage(
+            version(), qt.Qt.AlignCenter | qt.Qt.AlignBottom, qt.QColor("#e68f17")
+        )
 
 
 class Launcher:
     """Proxy to orange-canvas"""
+
     def launch(self, argv):
         config.Config = EstConfig
         self.fix_application_dirs()
@@ -91,4 +99,5 @@ class Launcher:
 
     def main(self, argv):
         from Orange.canvas.__main__ import main
+
         main(argv)

est/app/canvas_launcher/splash.py

@@ -11,7 +11,7 @@ def splash_screen():
     note: QRect is used by orange to define a mask to display the message.
           In our case we overwrite the QSplashScreen so we don't need this.
     """
-    pixmap = icons.getQPixmap('est')
+    pixmap = icons.getQPixmap("est")
     return pixmap, qt.QRect(0, 0, 0, 0)
 
 
@@ -21,5 +21,5 @@ def getIcon():
     :return: application icon
     :rtype: QIcon
     """
-    pixmap = icons.getQPixmap('est')
+    pixmap = icons.getQPixmap("est")
     return qt.QIcon(pixmap)

est/app/process.py

@@ -2,8 +2,10 @@ import argparse
 import sys
 from ..pushworkflow.scheme.parser import scheme_load
 import logging
+
 try:
     import h5py
+
     has_h5py = True
 except:
     has_h5py = False
@@ -17,23 +19,24 @@ def exec_(scheme, input_=None, output_=None):
         if input_:
             # monkey patch the input file for start nodes if an input is given
             for node in scheme.nodes:
-                if node.properties and '_input_file_setting' in node.properties:
-                    node.properties['_input_file_setting'] = input_
+                if node.properties and "_input_file_setting" in node.properties:
+                    node.properties["_input_file_setting"] = input_
+
     manage_input()
 
     def manage_output():
         if output_:
             # monkey patch the input file for start nodes if an input is given
             for node in scheme.nodes:
-                if node.properties and '_output_file_setting' in node.properties:
-                    node.properties['_output_file_setting'] = output_
+                if node.properties and "_output_file_setting" in node.properties:
+                    node.properties["_output_file_setting"] = output_
 
     # TODO: if the input file contains configuration, then overwrite the node
     # properties...
     manage_output()
 
     if len(scheme._start_actor.listDownStreamActor) is 0:
-        _logger.warning('no downstream node defined')
+        _logger.warning("no downstream node defined")
         return None
     scheme._start_actor.trigger(input_)
     scheme._end_actor.join()
@@ -51,18 +54,27 @@ def getInputFrmHdf5(file_path):
 def main(argv):
     parser = argparse.ArgumentParser(description=__doc__)
     parser.add_argument(
-        'workflow_file',
-        help='Workflow file providing the workflow description (.ows, .xml)')
-    parser.add_argument("-i", dest="input_", default=None,
-                        help="Input of the workflow. require at most one "
-                             "instance of XASInputOW")
-    parser.add_argument("-o", dest="output_", default=None,
-                        help="Output file of the workflow. Require at most one "
-                             "instance of XASOutputOW")
+        "workflow_file",
+        help="Workflow file providing the workflow description (.ows, .xml)",
+    )
+    parser.add_argument(
+        "-i",
+        dest="input_",
+        default=None,
+        help="Input of the workflow. require at most one " "instance of XASInputOW",
+    )
+    parser.add_argument(
+        "-o",
+        dest="output_",
+        default=None,
+        help="Output file of the workflow. Require at most one "
+        "instance of XASOutputOW",
+    )
     options = parser.parse_args(argv[1:])
 
     scheme = scheme_load(_file=options.workflow_file)
     exec_(scheme, options.input_, options.output_)
 
+
 if __name__ == "__main__":
     main(sys.argv)

est/app/reprocessing.py

@@ -3,8 +3,10 @@ import sys
 import logging
 from est.core.types import XASObject
 from est.core.reprocessing import get_process_instance_frm_h5_desc
+
 try:
     import h5py
+
     has_h5py = True
 except:
     has_h5py = False
@@ -13,26 +15,29 @@ logging.basicConfig(level=logging.DEBUG)
 _logger = logging.getLogger(__name__)
 
 
-def exec_(h5_file, entry='scan1', spectra_path=None, energy_path=None,
-          configuration_path=None):
+def exec_(
+    h5_file, entry="scan1", spectra_path=None, energy_path=None, configuration_path=None
+):
 
     try:
-        xas_obj = XASObject.from_file(h5_file=h5_file,
-                                      entry=entry or 'scan1',
-                                      spectra_path=spectra_path or 'data/absorbed_beam',
-                                      energy_path=energy_path or 'data/energy',
-                                      configuration_path=configuration_path)
+        xas_obj = XASObject.from_file(
+            h5_file=h5_file,
+            entry=entry or "scan1",
+            spectra_path=spectra_path or "data/absorbed_beam",
+            energy_path=energy_path or "data/energy",
+            configuration_path=configuration_path,
+        )
         xas_obj.link_to_h5(h5_file=h5_file)
     except Exception as e:
         _logger.error(e)
         xas_obj = None
 
     if not xas_obj:
-        _logger.error('Unable to create an object from the given file and path')
+        _logger.error("Unable to create an object from the given file and path")
 
     xas_processes = xas_obj.get_process_flow()
     if len(xas_processes) == 0:
-        _logger.warning('no xas process found in the given h5 file')
+        _logger.warning("no xas process found in the given h5 file")
         return
     xas_obj.clean_process_flow()
     for i_process, process in xas_processes.items():
@@ -53,21 +58,39 @@ def getInputFrmHdf5(file_path):
 def main(argv):
     parser = argparse.ArgumentParser(description=__doc__)
     parser.add_argument(
-        'workflow_file',
-        help='Workflow file providing the workflow description (.h5)')
-    parser.add_argument("--spectra_path", dest="spectra_path", default=None,
-                        help="path to the spectra data")
-    parser.add_argument("--energy_path", dest="energy_path", default=None,
-                        help="path to the energy data")
-    parser.add_argument("--configuration_path", dest="configuration_path", default=None,
-                        help="path to the process configuration")
-    parser.add_argument("--entry", dest="entry to load",
-                        default=None,
-                        help="path to the process configuration")
+        "workflow_file", help="Workflow file providing the workflow description (.h5)"
+    )
+    parser.add_argument(
+        "--spectra_path",
+        dest="spectra_path",
+        default=None,
+        help="path to the spectra data",
+    )
+    parser.add_argument(
+        "--energy_path",
+        dest="energy_path",
+        default=None,
+        help="path to the energy data",
+    )
+    parser.add_argument(
+        "--configuration_path",
+        dest="configuration_path",
+        default=None,
+        help="path to the process configuration",
+    )
+    parser.add_argument(
+        "--entry",
+        dest="entry to load",
+        default=None,
+        help="path to the process configuration",
+    )
     options = parser.parse_args(argv[1:])
-    exec_(h5_file=options.workflow_file, spectra_path=options.spectra_path,
-          energy_path=options.energy_path,
-          configuration_path=options.configuration_path)
+    exec_(
+        h5_file=options.workflow_file,
+        spectra_path=options.spectra_path,
+        energy_path=options.energy_path,
+        configuration_path=options.configuration_path,
+    )
 
 
 if __name__ == "__main__":

est/app/test/test_exec.py

@@ -34,6 +34,7 @@ from est.core.utils import DownloadDataset
 from ...pushworkflow.scheme.parser import scheme_load
 from ..process import exec_