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workflow
ewoksapps
est
Commits
99baef6b
Commit
99baef6b
authored
Aug 21, 2020
by
payno
Committed by
payno
Dec 03, 2020
Browse files
reformat files using black
parent
0566a1d8
Changes
96
Hide whitespace changes
Inline
Side-by-side
doc/conf.py
View file @
99baef6b
...
...
@@ -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
View file @
99baef6b
...
...
@@ -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
View file @
99baef6b
from
.launcher
import
Launcher
\ No newline at end of file
from
.launcher
import
Launcher
est/app/canvas_launcher/launcher.py
View file @
99baef6b
...
...
@@ -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
View file @
99baef6b
...
...
@@ -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
View file @
99baef6b
...
...
@@ -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
View file @
99baef6b
...
...
@@ -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
View file @
99baef6b
...
...
@@ -34,6 +34,7 @@ from est.core.utils import DownloadDataset
from
...pushworkflow.scheme.parser
import
scheme_load
from
..process
import
exec_