capsul 2.3.2__tar.gz → 2.6.0__tar.gz

{capsul-2.3.2/capsul.egg-info → capsul-2.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: capsul
-Version: 2.3.2
+Version: 2.6.0
 Summary: CAPSUL
 Home-page: https://github.com/populse/capsul
 Author: Populse team
@@ -15,23 +15,34 @@ Classifier: Programming Language :: Python
 Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Utilities
 License-File: LICENSE
-Requires-Dist: traits>=4.0
-Requires-Dist: soma-base>=4.6.1
-Requires-Dist: soma-workflow>=2.9.0
-Requires-Dist: populse-db>=1.1.1
+Requires-Dist: traits>=4.6
+Requires-Dist: soma-base>=5.0
+Requires-Dist: soma-workflow>=3.2
+Requires-Dist: populse-db<3.0,>=2.2
 Requires-Dist: six>=1.13
 Requires-Dist: PyYAML
 Provides-Extra: doc
 Requires-Dist: sphinx>=1.0; extra == "doc"
-Requires-Dist: numpy>=1.3; extra == "doc"
+Requires-Dist: numpy>=1.17; extra == "doc"
 Provides-Extra: database
 Requires-Dist: populse_db; extra == "database"
 Provides-Extra: nipype
-Requires-Dist: numpy>=1.3; extra == "nipype"
-Requires-Dist: scipy>=0.7; extra == "nipype"
+Requires-Dist: numpy>=1.17; extra == "nipype"
+Requires-Dist: scipy>=1.5; extra == "nipype"
 Requires-Dist: nibabel>=1.0; extra == "nipype"
 Requires-Dist: networkx>=1.0; extra == "nipype"
-Requires-Dist: nipype==0.10.0; extra == "nipype"
+Requires-Dist: nipype>=1.8; extra == "nipype"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: home-page
+Dynamic: license
+Dynamic: license-file
+Dynamic: platform
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: summary
 
 
 ========

capsul-2.6.0/README.rst

@@ -0,0 +1,32 @@
+======
+CAPSUL
+======
+.. image:: https://github.com/populse/capsul/actions/workflows/doc.yml/badge.svg?branch=master
+    :target: https://github.com/populse/capsul/actions/workflows/doc.yml
+    :alt: Tests
+
+.. image:: https://img.shields.io/badge/license-CeCILL--B-informational
+    :target: https://github.com/populse/capsul/blob/master/LICENSE
+    :alt: License
+
+.. image:: https://img.shields.io/badge/python-3.9%2C%203.10%2C%203.11-informational
+    :target: http://github.com/populse/capsul
+    :alt: Python
+
+.. image:: https://img.shields.io/badge/platform-Linux%2C%20OSX%2C%20Windows-informational
+    :target: http://github.com/populse/capsul
+    :alt: Platforms
+
+Documentation
+=============
+
+  Visit CAPSUL (http://populse.github.io/capsul) main page for the docs of the git master branch.
+  
+  See the BrianVISA website (http://brainvisa.info/capsul/) for the docs of the released versions.
+
+Download
+========
+
+  CAPSUL is available on `pypi <https://pypi.org/project/capsul/>`_ to download:,
+  
+  or via the `BrainVISA distribution <http://brainvisa.info/web/download.html>`_.

{capsul-2.3.2 → capsul-2.6.0}/capsul/engine/__init__.py

@@ -540,7 +540,7 @@ def capsul_engine(database_location=None, require=None):
     Configuration is read from a dictionary stored in two database entries.
     The first entry has the key 'global_config' (i.e.
     database.json_value('global_config')), it contains the configuration
-    values that are shared by all processings engines. The secon entry is 
+    values that are shared by all processing engines. The second entry is
     computing_config`. It contains a dictionary with one item per computing
     resource where the key is the resource name and the value is configuration 
     values that are specific to this computing resource.

{capsul-2.3.2 → capsul-2.6.0}/capsul/engine/module/__init__.py

@@ -4,4 +4,5 @@ default_modules = ['afni',
                    'ants',
                    'fsl',
                    'matlab',
+                   'mrtrix',
                    'spm']

{capsul-2.3.2 → capsul-2.6.0}/capsul/engine/module/attributes.py

@@ -4,18 +4,11 @@ Attributes completion config module
 
 '''
 
-from __future__ import absolute_import
-
-import os
-import six
 from capsul.attributes.attributes_factory import AttributesFactory
 from capsul.attributes.attributes_schema import AttributesSchema, \
     ProcessAttributes
 from capsul.attributes.completion_engine \
     import ProcessCompletionEngineFactory, PathCompletionEngineFactory
-from capsul.engine import settings
-import capsul.engine
-import os.path as osp
 from functools import partial
 import weakref
 
@@ -143,7 +136,7 @@ def edition_widget(engine, environment, config_id='attributes'):
         traits.List(traits.Str(), desc='attributes shchemas modules names'))
     controller.add_trait(
         'attributes_schemas',
-        traits.DictStrStr(desc='attributes shchemas names'))
+        traits.Dict(str, str, desc='attributes shchemas names'))
     controller.add_trait(
         'process_completion',
         traits.Str(desc='process completion model name'))

capsul-2.6.0/capsul/engine/module/mrtrix.py

@@ -0,0 +1,101 @@
+# -*- coding: utf-8 -*-
+from __future__ import absolute_import
+
+import os
+from capsul import engine
+import six
+
+
+def init_settings(capsul_engine):
+    with capsul_engine.settings as settings:
+        settings.ensure_module_fields('mrtrix',
+                                      [dict(name='directory',
+                                            type='string',
+                                            description='Directory where mrtrix is installed')
+                                       ])
+
+        # init a single config
+        config = settings.config('mrtrix', 'global')
+        if not config:
+            settings.new_config('mrtrix', 'global',
+                                {capsul_engine.settings.config_id_field:
+                                    'mrtrix'})
+
+
+def check_notably_invalid_config(conf):
+    '''
+    Checks if the given module config is obviously invalid, for instance
+    if a mandatory path is not filled
+
+    Returns
+    -------
+    invalid: list
+        list of invalid config keys
+    '''
+    invalid = []
+    for k in ('directory', ):
+        if getattr(conf, k, None) is None:
+            invalid.append(k)
+    return invalid
+
+
+def activate_configurations():
+    '''
+    Activate the mrtrix module (set env variables) from the global
+    configurations, in order to use them via
+    :mod:`capsul.in_context.mrtrix` functions
+    '''
+    conf = engine.configurations.get('capsul.engine.module.mrtrix', {})
+    mrtrix_dir = conf.get('directory')
+    if mrtrix_dir:
+        os.environ['MRTRIXPATH'] = six.ensure_str(mrtrix_dir)
+    elif 'MRTRIXPATH' in os.environ:
+        del os.environ['MRTRIXPATH']
+
+
+def edition_widget(engine, environment, config_id='mrtrix'):
+    ''' Edition GUI for mrtrix config - see
+    :class:`~capsul.qt_gui.widgets.settings_editor.SettingsEditor`
+    '''
+    from soma.qt_gui.controller_widget import ScrollControllerWidget
+    from soma.controller import Controller
+    import types
+    import traits.api as traits
+
+    def validate_config(widget):
+        widget.update_controller()
+        controller = widget.controller_widget.controller
+        with widget.engine.settings as session:
+            conf = session.config(config_id, widget.environment)
+            values = {'config_id': config_id}
+            for k in ['directory']:
+                value = getattr(controller, k)
+                if value is traits.Undefined:
+                    value = None
+                values[k] = value
+            if conf is None:
+                session.new_config(config_id, widget.environment, values)
+            else:
+                for k, value in values.items():
+                    if k == 'config_id':
+                        continue
+                    setattr(conf, k, values[k])
+
+    controller = Controller()
+
+    controller.add_trait('directory',
+                         traits.Directory(traits.Undefined,
+                                          desc='Directory where mrtrix is installed'))
+
+    conf = engine.settings.select_configurations(
+        environment, {'mrtrix': 'any'})
+    if conf:
+        fconf = conf.get('capsul.engine.module.mrtrix', {})
+        controller.directory = fconf.get('directory', traits.Undefined)
+
+    widget = ScrollControllerWidget(controller, live=True)
+    widget.engine = engine
+    widget.environment = environment
+    widget.accept = types.MethodType(validate_config, widget)
+
+    return widget

{capsul-2.3.2 → capsul-2.6.0}/capsul/engine/module/nipype.py

@@ -18,7 +18,7 @@ def ensure_config_exists(engine):
 
 def init_settings(capsul_engine):
     with capsul_engine.settings as settings:
-        settings.ensure_module_fields('nipype',[])
+        settings.ensure_module_fields('nipype', [])
     pass
 
     ensure_config_exists(capsul_engine)
@@ -40,7 +40,7 @@ def activate_configurations():
     from capsul.in_context import nipype
 
     # activate optional dependencies first
-    for module in ('spm', 'fsl', 'freesurfer', 'afni', 'ants'):
+    for module in ('spm', 'fsl', 'freesurfer', 'afni', 'ants', 'mrtrix'):
         module_name = Settings.module_name(module)
         mod_conf = engine.configurations.get(module_name)
         if mod_conf:

{capsul-2.3.2 → capsul-2.6.0}/capsul/engine/module/somaworkflow.py

@@ -1,11 +1,8 @@
 # -*- coding: utf-8 -*-
-from __future__ import absolute_import
 
 from capsul import engine
 import traits.api as traits
 from traits.api import Undefined
-import os
-import six
 
 
 def init_settings(capsul_engine):
@@ -135,8 +132,8 @@ def edition_widget(engine, environment, config_id='any'):
     controller.add_trait('path_translations',
                          traits.Dict(
                             key_trait=traits.Directory,
-                            value_trait=traits.ListStr(['', ''], minlen=2,
-                                                       maxlen=2),
+                            value_trait=traits.List(str)(['', ''], minlen=2,
+                                                         maxlen=2),
                             value={}, output=False,
                             desc=''))
 

{capsul-2.3.2 → capsul-2.6.0}/capsul/engine/module/spm.py

@@ -169,9 +169,11 @@ def check_notably_invalid_config(conf):
         list of invalid config keys
     '''
     invalid = []
-    for k in ('directory', 'version'):
-        if getattr(conf, k, None) is None:
-            invalid.append(k)
+    #for k in ('directory', 'version'):
+    #    if getattr(conf, k, None) is None:
+    #        invalid.append(k)
+    if getattr(conf, 'directory', None) is None:
+        invalid.append('directory')
     return invalid
 
 

{capsul-2.3.2 → capsul-2.6.0}/capsul/engine/run.py

@@ -330,7 +330,9 @@ def dispose(engine, execution_id, conditional=False):
     '''
     keep = False
     if conditional:
-        if not engine.study_config.somaworkflow_keep_succeeded_workflows:
+        if engine.study_config.somaworkflow_keep_succeeded_workflows:
+            keep = True
+        else:
             keep = False
             if engine.study_config.somaworkflow_keep_failed_workflows:
                 # must see it it failed or not

{capsul-2.3.2 → capsul-2.6.0}/capsul/engine/settings.py

@@ -12,7 +12,7 @@ This module provides classes to store CapsulEngine settings for several executio
 
 To implement all these features, it was necessary to have a settings storage system providing a query language to express requirements such as ``spm.version >= 12``. Populse_db was thus chosen as the storage and query system for settings. Some of the settings API choices have been influenced by populse_db API.
 
-CapsulEngine settings are organized in modules. Each module defines and documents the schema of values that can be set for its configuration. Typically, a module is dedicated to a software. For instance the module for SPM accepts confiurations containing a version (a string), an install directory (a string), a standalone/matlab flag (a boolean), etc. This schema is used to record configuration documents for the module. There can be several configuration documents per module. Each document corresponds to a full configuration of the module (for instance a document for SPM 8 configuration and another for SPM 12, or one for SPM 12 standalone and another for SPM 12 with matlab).
+CapsulEngine settings are organized in modules. Each module defines and documents the schema of values that can be set for its configuration. Typically, a module is dedicated to a software. For instance the module for SPM accepts configurations containing a version (a string), an install directory (a string), a standalone/matlab flag (a boolean), etc. This schema is used to record configuration documents for the module. There can be several configuration documents per module. Each document corresponds to a full configuration of the module (for instance a document for SPM 8 configuration and another for SPM 12, or one for SPM 12 standalone and another for SPM 12 with matlab).
 
 Settings cannot be used directly to configure the execution of a software. It is necessary to first select a single configuration document for each module. This configurations selection step is done by the :meth:`Settings.select_configurations` method.
 
@@ -413,7 +413,7 @@ class SettingsSession:
     def remove_config(self, module, environment, config_id):
         '''
         Removes a configuration (document in the database) for a given module /
-        environment, idenfified by its `Settings.config_id_field` value.
+        environment, identified by its `Settings.config_id_field` value.
         '''
         collection = self.collection_name(module)
         id = '%s-%s' % (config_id, environment)
@@ -450,7 +450,7 @@ class SettingsSession:
 
     def config(self, module, environment, selection=None, any=True):
         '''
-        Selects configurations (like in :meth:`congigs`) and ensures at most
+        Selects configurations (like in :meth:`configs`) and ensures at most
         one one is selected
 
         Parameters
@@ -504,7 +504,7 @@ class SettingsSession:
                 environments.update([r[0] for r in res])
         return environments
 
-class SettingsConfig(object):
+class SettingsConfig:
     def __init__(self, populse_session, collection, id, environment,
                  notifiers=[]):
         super(SettingsConfig, self).__setattr__('_dbs', populse_session)

{capsul-2.3.2 → capsul-2.6.0}/capsul/engine/test/test_capsul_engine.py

@@ -1,6 +1,4 @@
 # -*- coding: utf-8 -*-
-from __future__ import print_function
-from __future__ import absolute_import
 
 import gc
 import unittest
@@ -19,11 +17,7 @@ from soma_workflow import configuration as swconfig
 from traits.api import File
 
 
-which = getattr(shutil, 'which', None)
-if which is None:
-    # python2 doesn't have shutil.which
-    import distutils.spawn
-    which = distutils.spawn.find_executable
+which = shutil.which
 
 
 def setUpModule():
@@ -97,24 +91,34 @@ def tearDownModule():
 
 def check_nipype_spm():
     # look for hardcoded paths, I have no other way at hand...
-    spm_standalone_paths = ['/usr/local/spm12-standalone',
-                            '/volatile/local/spm12-standalone',
-                            '/drf/local/spm12-standalone',
-                            '/i2bm/local/spm12-standalone']
+    spm_standalone_paths = []
+    mcr_path = None
+    spm_exe = which('spm12')
+    if spm_exe:
+        # installed as in neurospin
+        with open(spm_exe) as f:
+            for l in f.readlines():
+                if l.startswith('SPM_HOME='):
+                    spm_path = l.split('=', 1)[1].strip()
+                    spm_path = os.path.expandvars(spm_path).strip()
+                    spm_standalone_paths.append(spm_path)
+                elif l.startswith('MCR_HOME='):
+                    mcr_path = l.split('=', 1)[1].strip()
+                    mcr_path = os.path.expandvars(mcr_path).strip()
+    if not spm_standalone_paths and 'CONDA_PREFIX' in os.environ:
+        spm_standalone_paths.append(
+            os.path.join(os.getenv('CONDA_PREFIX'), 'share/spm12-standalone'))
+
+    spm_standalone_paths += ['/usr/local/spm12-standalone',
+                             '/volatile/local/spm12-standalone',
+                             '/drf/local/spm12-standalone',
+                             '/i2bm/local/spm12-standalone']
     spm_standalone_path = [p for p in spm_standalone_paths if os.path.isdir(p)]
     if not spm_standalone_path:
         return None
     spm_standalone_path = spm_standalone_path[0]
-    mcr_path = None
     mcr = glob.glob(osp.join(spm_standalone_path, 'mcr', 'v*'))
     if not mcr or len(mcr) != 1:
-        spm_exe = which('spm12')
-        if spm_exe:
-            # installed as in neurospin
-            with open(spm_exe) as f:
-                for l in f.readlines():
-                    if l.startswith('MCR_HOME='):
-                        mcr_path = l.split('=', 1)[1]
         if not mcr_path:
             mcr_paths = ['/usr/local/matlab/MATLAB_Runtime',
                          '/volatile/local/spm12-standalone/mcr',
@@ -184,6 +188,14 @@ class TestCapsulEngine(unittest.TestCase):
             settings.new_config('ants', 'global', {'directory': '/there',
                                                    cif: '235'})
 
+            # Create a global mrtrix configuration
+            config = settings.config('mrtrix', 'global')
+            if config:
+                settings.remove_config('mrtrix', 'global',
+                                       getattr(config, cif))
+            settings.new_config('mrtrix', 'global', {'directory': '/there',
+                                                     cif: '400'})
+
             # Create two global SPM configurations
             settings.new_config('spm', 'global', {'version': '8',
                                                   'standalone': True,
@@ -202,7 +214,8 @@ class TestCapsulEngine(unittest.TestCase):
                                         'capsul.engine.module.matlab': 'ALL',
                                         'capsul.engine.module.spm': 'ALL',
                                         'capsul.engine.module.afni': 'ALL',
-                                        'capsul.engine.module.ants': 'ALL'}},
+                                        'capsul.engine.module.ants': 'ALL',
+                                        'capsul.engine.module.mrtrix': 'ALL'}},
              'capsul.engine.module.fsl': {'config_environment': 'global',
                                           'directory': '/there',
                                           cif: '5'},
@@ -212,6 +225,9 @@ class TestCapsulEngine(unittest.TestCase):
              'capsul.engine.module.ants': {
                  'config_environment': 'global', 'directory': '/there',
                  cif: '235'},
+             'capsul.engine.module.mrtrix': {
+                 'config_environment': 'global', 'directory': '/there',
+                 cif: '400'},
              'capsul.engine.module.spm': {'config_environment': 'my_machine',
                                           'version': '20',
                                           'standalone': True,
@@ -246,6 +262,15 @@ class TestCapsulEngine(unittest.TestCase):
              'capsul_engine':
                  {'uses': {'capsul.engine.module.ants': 'any'}}})
 
+        self.assertEqual(
+            self.ce.settings.select_configurations('global',
+                                                   uses={'mrtrix': 'any'}),
+            {'capsul.engine.module.mrtrix':
+                {'config_environment': 'global', 'directory': '/there',
+                 cif: '400'},
+             'capsul_engine':
+                 {'uses': {'capsul.engine.module.mrtrix': 'any'}}})
+
         self.assertEqual(
             self.ce.settings.select_configurations('global',
                                                    uses={'spm': 'any'}),

capsul-2.6.0/capsul/in_context/freesurfer.py

@@ -0,0 +1,143 @@
+# -*- coding: utf-8 -*-
+'''
+Specific subprocess-like functions to call Freesurfer taking into account
+configuration stored in the activated configuration.
+'''
+
+from __future__ import absolute_import
+
+import os
+import os.path as osp
+import soma.subprocess
+from soma.utils.env import parse_env_lines
+from capsul import engine
+import pipes
+import six
+
+'''
+If this variable is set, it contains FS runtime env variables,
+allowing to run directly freesurfer commands from this process.
+'''
+freesurfer_runtime_env = None
+
+
+def freesurfer_command_with_environment(command, use_runtime_env=True):
+    '''
+    Given a Freesurfer command where first element is a command name without
+    any path or prefix (e.g. "recon-all"). Returns the appropriate command to
+    call taking into account the Freesurfer configuration stored in the
+    activated configuration.
+
+    Using :func`freesurfer_env` is an alternative to this.
+    '''
+
+    if use_runtime_env and freesurfer_runtime_env:
+        c0 = list(osp.split(command[0]))
+        c0 = osp.join(*c0)
+        cmd = [c0] + command[1:]
+        return cmd
+
+    fconf = engine.configurations.get('capsul.engine.module.freesurfer')
+
+    if fconf:
+        freesurfer_script = fconf.get('setup')
+
+        if freesurfer_script is not None and os.path.isfile(freesurfer_script):
+            freesurfer_dir = os.path.dirname(freesurfer_script)
+
+        else:
+            freesurfer_dir = None
+
+    else:
+        freesurfer_dir = os.environ.get('FREESURFER_HOME')
+
+        if freesurfer_dir is not None:
+            freesurfer_script = os.path.join(freesurfer_dir,
+                                             'SetUpFreeSurfer.sh')
+
+            if not os.path.isfile(freesurfer_script):
+                freesurfer_script = None
+
+        else:
+            freesurfer_script = None
+
+    if freesurfer_dir is not None and freesurfer_script is not None:
+        shell = os.environ.get('SHELL', '/bin/sh')
+
+        if shell.endswith('csh'):
+            cmd = [shell, '-c',
+                   'setenv FREESURFER_HOME "{0}"; source {1}; exec {2} '.format(
+                       freesurfer_dir, freesurfer_script, command[0]) + \
+                   ' '.join("'%s'" % i.replace("'", "\\'") for i in command[1:])]
+
+        else:
+            cmd = [shell, '-c',
+                   'export FREESURFER_HOME="{0}"; source {1}; exec {2} '.format(
+                       freesurfer_dir, freesurfer_script, command[0]) + \
+                   ' '.join("'%s'" % i.replace("'", "\\'") for i in command[1:])]
+
+    return cmd
+
+
+def freesurfer_env():
+    '''
+    get Freesurfer env variables by running the setup script in a separate bash
+    process
+    '''
+    global freesurfer_runtime_env
+
+    if freesurfer_runtime_env is not None:
+        return freesurfer_runtime_env
+
+    kwargs = {}
+    cmd = freesurfer_command_with_environment(['env'], use_runtime_env=False)
+    new_env = soma.subprocess.check_output(cmd, **kwargs).decode(
+        'utf-8').strip()
+    new_env = parse_env_lines(new_env)
+    env = {}
+
+    for l in new_env:
+        name, val = l.strip().split('=', 1)
+        name = six.ensure_str(name)
+        val = six.ensure_str(val)
+
+        if name not in ('_', 'SHLVL') and (name not in os.environ
+                                           or os.environ[name] != val):
+            env[name] = val
+
+    # cache dict
+    freesurfer_runtime_env = env
+    return env
+
+
+class FreesurferPopen(soma.subprocess.Popen):
+    '''
+    Equivalent to Python subprocess.Popen for Freesurfer commands
+    '''
+    def __init__(self, command, **kwargs):
+        cmd = freesurfer_command_with_environment(command)
+        super(FreesurferPopen, self).__init__(cmd, **kwargs)
+
+
+def freesurfer_call(command, **kwargs):
+    '''
+    Equivalent to Python subprocess.call for Freesurfer commands
+    '''
+    cmd = freesurfer_command_with_environment(command)
+    return soma.subprocess.call(cmd, **kwargs)
+
+
+def freesurfer_check_call(command, **kwargs):
+    '''
+    Equivalent to Python subprocess.check_call for Freesurfer commands
+    '''
+    cmd = freesurfer_command_with_environment(command)
+    return soma.subprocess.call(cmd, **kwargs)
+
+
+def freesurfer_check_output(command, **kwargs):
+    '''
+    Equivalent to Python subprocess.check_output for Freesurfer commands
+    '''
+    cmd = freesurfer_command_with_environment(command)
+    return soma.subprocess.check_output(cmd, **kwargs)

{capsul-2.3.2 → capsul-2.6.0}/capsul/in_context/fsl.py

@@ -12,7 +12,7 @@ with statement). For instance::
    with ce:
        fsl_check_call(['bet', '/somewhere/myimage.nii'])
 
-For calling FSL command with this module, the first arguent of
+For calling FSL command with this module, the first argument of
 command line must be the FSL executable without any path nor prefix. 
 Prefix are used in Neurodebian install. For instance on Ubuntu 16.04 
 Neurodebian FSL commands are prefixed with "fsl5.0-".