\n"
if description is not None:
- ad += spacer + "{0}\n".format(("\n" + spacer).join(
+ ad += spacer + "{}\n".format(("\n" + spacer).join(
self.rst2html(description).splitlines()))
ad += spacer + "
")
table.append("\n\n")
diff --git a/capsul/test/test_completion.py b/capsul/test/test_completion.py
index 21b06b9f6..a53db68a4 100644
--- a/capsul/test/test_completion.py
+++ b/capsul/test/test_completion.py
@@ -211,8 +211,8 @@ def test_pipeline_completion(self):
metadata.bids = input_metadata
metadata.generate_paths(pipeline)
- params = dict(
- (i, getattr(pipeline, i, undefined))
+ params = {
+ i: getattr(pipeline, i, undefined)
for i in (
"input",
"template",
@@ -223,7 +223,7 @@ def test_pipeline_completion(self):
"right_gw_classif",
"right_gw_mesh",
)
- )
+ }
expected = {
"input": "!{dataset.input.path}/rawdata/sub-aleksander/ses-m0/anat/sub-aleksander_ses-m0_T1w.nii",
diff --git a/capsul/test/test_fake_morphologist.py b/capsul/test/test_fake_morphologist.py
index 2b7ae91c2..59d72ce05 100644
--- a/capsul/test/test_fake_morphologist.py
+++ b/capsul/test/test_fake_morphologist.py
@@ -630,8 +630,8 @@ def test_path_generation(self):
pv.show()
app.exec_()
- params = dict(
- (i, getattr(morphologist, i, undefined))
+ params = {
+ i: getattr(morphologist, i, undefined)
for i in (
"PrepareSubject_Normalization_Normalization_AimsMIRegister_anatomical_template",
"imported_t1mri",
@@ -640,7 +640,7 @@ def test_path_generation(self):
"left_labelled_graph",
"right_labelled_graph",
)
- )
+ }
self.maxDiff = None
self.assertEqual(params, expected[normalization])
# for field in morphologist.fields():
diff --git a/capsul/test/test_tiny_morphologist.py b/capsul/test/test_tiny_morphologist.py
index e6be192a1..300da5b31 100644
--- a/capsul/test/test_tiny_morphologist.py
+++ b/capsul/test/test_tiny_morphologist.py
@@ -638,8 +638,8 @@ def test_tiny_path_generation(self):
},
)
metadata.generate_paths(tiny_morphologist)
- params = dict(
- (i, getattr(tiny_morphologist, i, undefined))
+ params = {
+ i: getattr(tiny_morphologist, i, undefined)
for i in (
"template",
"nobias",
@@ -647,7 +647,7 @@ def test_tiny_path_generation(self):
"right_hemisphere",
"left_hemisphere",
)
- )
+ }
self.maxDiff = 2000
self.assertEqual(params, expected[normalization])
diff --git a/capsul/ui/static/engine.html b/capsul/ui/static/engine.html
index 5aad13ec9..0e00e9b09 100644
--- a/capsul/ui/static/engine.html
+++ b/capsul/ui/static/engine.html
@@ -20,7 +20,7 @@
Engine
Executions
-
+
Label
Status
Waiting
diff --git a/completion.md b/completion.md
index 71de0a791..6f914ff24 100644
--- a/completion.md
+++ b/completion.md
@@ -9,13 +9,13 @@ The path generation system is designed to be **fully automatic**. Path generatio
Path generation is done using **metadata and metadata schema**. The metadata contains the values that are used to build various part of the path. For instance, the subject code is often used in path names as well as an extension defining the file type. These two values are included in the metadata. There is no single way to create a path given metadata. There are many possible layouts for path names using various metadata. For instance, BrainVISA has defined a path organisation layout. BIDS is another path organisation layout that is the actual standard for neuroimaging. Capsul can support many different systems; each one beign defined in a `MetadataSchema` class (see below).
-Metadata given to create a path name can have **various origins**. For instance, the extension of the file is most often dependent on the process. An image parameter uses an image extension (such as `.nii`) whereas a mesh parameter uses a mesh format (such as `.gii`). This kind of metatada, called **process metadata**, is **defined globally for a process**, usually by the process developer. On the other hand, metadata such a subject identifier depends on the usage context of the process. This kind of metadata is called **user metadata** because it is **given at runtime** as the result of a user action (manual, entry, database selection, etc.).
+Metadata given to create a path name can have **various origins**. For instance, the extension of the file is most often dependent on the process. An image parameter uses an image extension (such as `.nii`) whereas a mesh parameter uses a mesh format (such as `.gii`). This kind of metadata, called **process metadata**, is **defined globally for a process**, usually by the process developer. On the other hand, metadata such a subject identifier depends on the usage context of the process. This kind of metadata is called **user metadata** because it is **given at runtime** as the result of a user action (manual, entry, database selection, etc.).
-The path generation system must be able to deal with **several metadata schemas for a single process**. If not it woul mean that all process parameters must be in the same schema. This is the case if all input and output data are following the BIDS standard. However, in many cases a process will have to deal with several metadata schemas. For instance, there could be one schema for input data (i.e. BIDS), another schema for output data (for use cases not covered by BIDS) and other schemas for third party data (for instance template images in SPM software directory). To support several metadata schema, Capsul make a link between a dataset (i.e. a directory) and the metadata schema used throughout that directory using he `Dataset` class.
+The path generation system must be able to deal with **several metadata schemas for a single process**. If not it would mean that all process parameters must be in the same schema. This is the case if all input and output data are following the BIDS standard. However, in many cases a process will have to deal with several metadata schemas. For instance, there could be one schema for input data (i.e. BIDS), another schema for output data (for use cases not covered by BIDS) and other schemas for third party data (for instance template images in SPM software directory). To support several metadata schema, Capsul make a link between a dataset (i.e. a directory) and the metadata schema used throughout that directory using he `Dataset` class.
### Using path generation
-Path generation is done for all path parameters of a process. The following diagram illustrate the case of a process with one `input` parameter supposed to follow BIDS schema and one `output` parameter following another schema called BrainVISA. In oder to use path generation, the user must create a ̀ProcessMetadata` instance that allows to set user metadata for all schemas used by the process. These user metadata are combined with process metadata in order to generate values for all path parameters.
+Path generation is done for all path parameters of a process. The following diagram illustrate the case of a process with one `input` parameter supposed to follow BIDS schema and one `output` parameter following another schema called BrainVISA. In order to use path generation, the user must create a ̀ProcessMetadata` instance that allows to set user metadata for all schemas used by the process. These user metadata are combined with process metadata in order to generate values for all path parameters.
```mermaid
graph LR
diff --git a/doc/source/conf.py b/doc/source/conf.py
index 2b3a1a99b..3723aae88 100644
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -9,7 +9,6 @@
# All configuration values have a default; values that are commented out
# serve to show the default.
-from __future__ import print_function
import sys, os
import time
import shutil
@@ -126,9 +125,9 @@ def null(*args, **kwargs):
master_doc = 'index'
# General information about the project.
-project = u'CAPSUL'
+project = 'CAPSUL'
release_info['COPYRIGHT_YEAR'] = time.strftime('%Y')
-copyright = u'%(COPYRIGHT_YEAR)s, %(AUTHOR)s <%(AUTHOR_EMAIL)s>' % release_info
+copyright = '%(COPYRIGHT_YEAR)s, %(AUTHOR)s <%(AUTHOR_EMAIL)s>' % release_info
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
@@ -275,8 +274,8 @@ def null(*args, **kwargs):
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title, author, documentclass [howto/manual]).
latex_documents = [
- ('index', 'capsul.tex', u'CAPSUL Documentation',
- u'CATI', 'manual'),
+ ('index', 'capsul.tex', 'CAPSUL Documentation',
+ 'CATI', 'manual'),
]
autoclass_content = "both"
diff --git a/doc/source/installation.rst b/doc/source/installation.rst
index 8cce2a1ff..403569417 100644
--- a/doc/source/installation.rst
+++ b/doc/source/installation.rst
@@ -5,7 +5,7 @@
`CAPSUL` installation
=====================
-.. This tutorial will walk you through the process of intalling CAPSUL.
+.. This tutorial will walk you through the process of installing CAPSUL.
..
.. * :ref:`Install an official release `. This
.. is the best approach for users who want a stable version.
diff --git a/doc/source/sphinxext/numpy_ext/docscrape.py b/doc/source/sphinxext/numpy_ext/docscrape.py
index 2b1719db5..9f17ffee8 100644
--- a/doc/source/sphinxext/numpy_ext/docscrape.py
+++ b/doc/source/sphinxext/numpy_ext/docscrape.py
@@ -1,7 +1,6 @@
"""Extract reference documentation from the NumPy source tree.
"""
-from __future__ import division, absolute_import, print_function
import inspect
import textwrap
@@ -12,7 +11,7 @@
import sys
-class Reader(object):
+class Reader:
"""A line-based string reader.
"""
@@ -86,7 +85,7 @@ def is_empty(self):
return not ''.join(self._str).strip()
-class NumpyDocString(object):
+class NumpyDocString:
def __init__(self, docstring, config={}):
docstring = textwrap.dedent(docstring).split('\n')
@@ -272,7 +271,7 @@ def _parse_summary(self):
while True:
summary = self._doc.read_to_next_empty_line()
summary_str = " ".join([s.strip() for s in summary]).strip()
- if re.compile('^([\w., ]+=)?\s*[\w\.]+\(.*\)$').match(summary_str):
+ if re.compile(r'^([\w., ]+=)?\s*[\w\.]+\(.*\)$').match(summary_str):
self['Signature'] = summary_str
if not self._is_at_section():
continue
@@ -314,7 +313,7 @@ def _str_indent(self, doc, indent=4):
def _str_signature(self):
if self['Signature']:
- return [self['Signature'].replace('*','\*')] + ['']
+ return [self['Signature'].replace('*',r'\*')] + ['']
else:
return ['']
@@ -336,7 +335,7 @@ def _str_param_list(self, name):
out += self._str_header(name)
for param,param_type,desc in self[name]:
if param_type:
- out += ['%s : %s' % (param, param_type)]
+ out += ['{} : {}'.format(param, param_type)]
else:
out += [param]
out += self._str_indent(desc)
@@ -358,9 +357,9 @@ def _str_see_also(self, func_role):
last_had_desc = True
for func, desc, role in self['See Also']:
if role:
- link = ':%s:`%s`' % (role, func)
+ link = ':{}:`{}`'.format(role, func)
elif func_role:
- link = ':%s:`%s`' % (func_role, func)
+ link = ':{}:`{}`'.format(func_role, func)
else:
link = "`%s`_" % func
if desc or last_had_desc:
@@ -383,7 +382,7 @@ def _str_index(self):
for section, references in idx.items():
if section == 'default':
continue
- out += [' :%s: %s' % (section, ', '.join(references))]
+ out += [' :{}: {}'.format(section, ', '.join(references))]
return out
def __str__(self, func_role=''):
@@ -439,8 +438,8 @@ def __init__(self, func, role='func', doc=None, config={}):
else:
argspec = inspect.getargspec(func)
argspec = inspect.formatargspec(*argspec)
- argspec = argspec.replace('*','\*')
- signature = '%s%s' % (func_name, argspec)
+ argspec = argspec.replace('*',r'\*')
+ signature = '{}{}'.format(func_name, argspec)
except TypeError as e:
signature = '%s()' % func_name
self['Signature'] = signature
@@ -457,7 +456,7 @@ def __str__(self):
out = ''
func, func_name = self.get_func()
- signature = self['Signature'].replace('*', '\*')
+ signature = self['Signature'].replace('*', r'\*')
roles = {'func': 'function',
'meth': 'method'}
@@ -465,10 +464,10 @@ def __str__(self):
if self._role:
if self._role not in roles:
print("Warning: invalid role %s" % self._role)
- out += '.. %s:: %s\n \n\n' % (roles.get(self._role,''),
+ out += '.. {}:: {}\n \n\n'.format(roles.get(self._role,''),
func_name)
- out += super(FunctionDoc, self).__str__(func_role=self._role)
+ out += super().__str__(func_role=self._role)
return out
@@ -519,7 +518,7 @@ def methods(self):
return [name for name,func in inspect.getmembers(self._cls)
if ((not name.startswith('_')
or name in self.extra_public_methods)
- and isinstance(func, collections.Callable))]
+ and isinstance(func, collections.abc.Callable))]
@property
def properties(self):
diff --git a/doc/source/sphinxext/numpy_ext/docscrape_sphinx.py b/doc/source/sphinxext/numpy_ext/docscrape_sphinx.py
index cdc2a37d1..0b89f8475 100644
--- a/doc/source/sphinxext/numpy_ext/docscrape_sphinx.py
+++ b/doc/source/sphinxext/numpy_ext/docscrape_sphinx.py
@@ -1,5 +1,3 @@
-from __future__ import division, absolute_import, print_function
-
import sys, re, inspect, textwrap, pydoc
import sphinx
import collections
@@ -53,7 +51,7 @@ def _str_returns(self):
out += ['']
for param, param_type, desc in self['Returns']:
if param_type:
- out += self._str_indent(['**%s** : %s' % (param.strip(),
+ out += self._str_indent(['**{}** : {}'.format(param.strip(),
param_type)])
else:
out += self._str_indent([param.strip()])
@@ -70,7 +68,7 @@ def _str_param_list(self, name):
out += ['']
for param, param_type, desc in self[name]:
if param_type:
- out += self._str_indent(['**%s** : %s' % (param.strip(),
+ out += self._str_indent(['**{}** : {}'.format(param.strip(),
param_type)])
else:
out += self._str_indent(['**%s**' % param.strip()])
@@ -116,7 +114,7 @@ def _str_member_list(self, name):
if param_obj and (pydoc.getdoc(param_obj) or not desc):
# Referenced object has a docstring
- autosum += [" %s%s" % (prefix, param)]
+ autosum += [" {}{}".format(prefix, param)]
else:
others.append((param, param_type, desc))
@@ -134,7 +132,7 @@ def _str_member_list(self, name):
for param, param_type, desc in others:
desc = sixu(" ").join(x.strip() for x in desc).strip()
if param_type:
- desc = "(%s) %s" % (param_type, desc)
+ desc = "({}) {}".format(param_type, desc)
out += [fmt % (param.strip(), desc)]
out += [hdr]
out += ['']
@@ -153,7 +151,7 @@ def _str_section(self, name):
def _str_see_also(self, func_role):
out = []
if self['See Also']:
- see_also = super(SphinxDocString, self)._str_see_also(func_role)
+ see_also = super()._str_see_also(func_role)
out = ['.. seealso::', '']
out += self._str_indent(see_also[2:])
return out
@@ -178,7 +176,7 @@ def _str_index(self):
elif section == 'refguide':
out += [' single: %s' % (', '.join(references))]
else:
- out += [' %s: %s' % (section, ','.join(references))]
+ out += [' {}: {}'.format(section, ','.join(references))]
return out
def _str_references(self):
@@ -259,7 +257,7 @@ def get_doc_object(obj, what=None, doc=None, config={}):
what = 'class'
elif inspect.ismodule(obj):
what = 'module'
- elif isinstance(obj, collections.Callable):
+ elif isinstance(obj, collections.abc.Callable):
what = 'function'
else:
what = 'object'
diff --git a/doc/source/sphinxext/numpy_ext/numpydoc.py b/doc/source/sphinxext/numpy_ext/numpydoc.py
index 2bc2d1e91..0f71168aa 100644
--- a/doc/source/sphinxext/numpy_ext/numpydoc.py
+++ b/doc/source/sphinxext/numpy_ext/numpydoc.py
@@ -15,7 +15,6 @@
.. [1] https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt
"""
-from __future__ import division, absolute_import, print_function
import os, sys, re, pydoc
import sphinx
@@ -96,7 +95,7 @@ def mangle_signature(app, what, name, obj, options, sig, retann):
'initializes x; see ' in pydoc.getdoc(obj.__init__))):
return '', ''
- if not (isinstance(obj, collections.Callable) or hasattr(obj, '__argspec_is_invalid_')): return
+ if not (isinstance(obj, collections.abc.Callable) or hasattr(obj, '__argspec_is_invalid_')): return
if not hasattr(obj, '__doc__'): return
doc = SphinxDocString(pydoc.getdoc(obj))
@@ -130,11 +129,11 @@ def setup(app, get_doc_object_=get_doc_object):
from sphinx.domains.c import CDomain
from sphinx.domains.python import PythonDomain
-class ManglingDomainBase(object):
+class ManglingDomainBase:
directive_mangling_map = {}
def __init__(self, *a, **kw):
- super(ManglingDomainBase, self).__init__(*a, **kw)
+ super().__init__(*a, **kw)
self.wrap_mangling_directives()
def wrap_mangling_directives(self):
diff --git a/doc/source/status.rst b/doc/source/status.rst
index 413f2cfae..347755b88 100644
--- a/doc/source/status.rst
+++ b/doc/source/status.rst
@@ -19,7 +19,7 @@ Pipeline execution:
* sequential execution: |OK|
* via Soma-Workflow: |OK|
Switch nodes: |OK|
-Iteraton nodes: |OK|
+Iteration nodes: |OK|
StudyConfig: |OK|
Workflow transformation: |OK|
Attributes and parameters completion: |OK|
diff --git a/doc/source/user_guide_tree/advanced_usage.rst b/doc/source/user_guide_tree/advanced_usage.rst
index 6a5d28d33..d61e46d44 100644
--- a/doc/source/user_guide_tree/advanced_usage.rst
+++ b/doc/source/user_guide_tree/advanced_usage.rst
@@ -8,7 +8,7 @@ Parameters completion
Completion in Capsul v3
=======================
-This is not a doc yet, I write down thnigs that I seem to understand at the time I read them in the code.
+This is not a doc yet, I write down things that I seem to understand at the time I read them in the code.
Process parameters completion for filenames is working using attributes (or "metadata" assigned to a process or to its parameters. For instance a given data organization may organize data by study, center, subject, ... These study, center, subject elements can be seen as attributes.
@@ -49,7 +49,7 @@ It defines metadata for a given schema name (like ``shared``), and the way to bu
If a process uses several datasets with different schemas for different parameters (for instance input, output, shared datasets), several :class:`~capsul.dataset.ProcessSchema` subclasses may be declared for the same process class.
-As the used shema is specified in the :class:`~capsul.dataset.ProcessSchema` subclass declaration, several subclasses may be declared for the same process parameters with different schemas. The schema selection will be done, for each dataset, at the time of data selection.
+As the used schema is specified in the :class:`~capsul.dataset.ProcessSchema` subclass declaration, several subclasses may be declared for the same process parameters with different schemas. The schema selection will be done, for each dataset, at the time of data selection.
* set this in the Capsul config::
diff --git a/doc/source/user_guide_tree/xml_spec.rst b/doc/source/user_guide_tree/xml_spec.rst
index 60bddeb00..f0c993127 100644
--- a/doc/source/user_guide_tree/xml_spec.rst
+++ b/doc/source/user_guide_tree/xml_spec.rst
@@ -192,7 +192,7 @@ define the XML string associated to the function. Here is an example :
@xml_process('''
-
+
@@ -211,7 +211,7 @@ Example :
'''
-
+
@@ -230,7 +230,7 @@ Processes examples
+ doc="Method for thresolding."/>
@@ -357,7 +357,7 @@ Attributes:
- **name**: node name in the pipeline (as in process elements)
- **switch\_value** (optional): value of the "switch" parameter: name
of the active input
-- **enabed** (optional): as in process elements
+- **enabled** (optional): as in process elements
Children:
@@ -392,7 +392,7 @@ temporary values inside the pipeline if they are left undefined.
Attributes:
- **name**: node name in the pipeline (as in process elements)
-- **enabed** (optional): as in process elements
+- **enabled** (optional): as in process elements
Children:
diff --git a/readme.md b/readme.md
index c76e7afe5..0b0f28af7 100644
--- a/readme.md
+++ b/readme.md
@@ -24,7 +24,7 @@ The simplest is to use a [casa-distro](https://github.com/brainvisa/casa-distro>
singularity run -B capsul3:/casa/setup casa-dev-5.3-6.sif distro=opensource
```
-* change the `bv_maker.cfg` file for a ligher one, which switches to the expected branches:
+* change the `bv_maker.cfg` file for a lighter one, which switches to the expected branches:
```
cat > capsul3/conf/bv_maker.cfg << EOF
[ source \$CASA_SRC ]