fSTG-Toolkit 1.2.1__tar.gz → 1.4.0__tar.gz

{fstg_toolkit-1.2.1 → fstg_toolkit-1.4.0}/LICENSE

@@ -1,5 +1,7 @@
 
-CeCILL-B FREE SOFTWARE LICENSE AGREEMENT
+  CeCILL FREE SOFTWARE LICENSE AGREEMENT
+
+Version 2.1 dated 2013-06-21
 
 
     Notice
@@ -8,41 +10,39 @@ This Agreement is a Free Software license agreement that is the result
 of discussions between its authors in order to ensure compliance with
 the two main principles guiding its drafting:
 
-    * firstly, compliance with the principles governing the distribution
-      of Free Software: access to source code, broad rights granted to
-      users,
-    * secondly, the election of a governing law, French law, with which
-      it is conformant, both as regards the law of torts and
-      intellectual property law, and the protection that it offers to
-      both authors and holders of the economic rights over software.
+  * firstly, compliance with the principles governing the distribution
+    of Free Software: access to source code, broad rights granted to users,
+  * secondly, the election of a governing law, French law, with which it
+    is conformant, both as regards the law of torts and intellectual
+    property law, and the protection that it offers to both authors and
+    holders of the economic rights over software.
 
-The authors of the CeCILL-B (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre])
-license are: 
+The authors of the CeCILL (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre])
+license are:
 
-Commissariat à l'Energie Atomique - CEA, a public scientific, technical
-and industrial research establishment, having its principal place of
-business at 25 rue Leblanc, immeuble Le Ponant D, 75015 Paris, France.
+Commissariat à l'énergie atomique et aux énergies alternatives - CEA, a
+public scientific, technical and industrial research establishment,
+having its principal place of business at 25 rue Leblanc, immeuble Le
+Ponant D, 75015 Paris, France.
 
 Centre National de la Recherche Scientifique - CNRS, a public scientific
 and technological establishment, having its principal place of business
 at 3 rue Michel-Ange, 75794 Paris cedex 16, France.
 
 Institut National de Recherche en Informatique et en Automatique -
-INRIA, a public scientific and technological establishment, having its
+Inria, a public scientific and technological establishment, having its
 principal place of business at Domaine de Voluceau, Rocquencourt, BP
 105, 78153 Le Chesnay cedex, France.
 
 
     Preamble
 
-This Agreement is an open source software license intended to give users
-significant freedom to modify and redistribute the software licensed
-hereunder.
+The purpose of this Free Software license agreement is to grant users
+the right to modify and redistribute the software governed by this
+license within the framework of an open source distribution model.
 
-The exercising of this freedom is conditional upon a strong obligation
-of giving credits for everybody that distributes a software
-incorporating a software ruled by the current license so as all
-contributions to be properly identified and acknowledged.
+The exercising of this right is conditional upon certain obligations for
+users so as to preserve this status for all subsequent redistributions.
 
 In consideration of access to the source code and the rights to copy,
 modify and redistribute granted by the license, users are provided only
@@ -65,6 +65,10 @@ removed herefrom.
 This Agreement may apply to any or all software for which the holder of
 the economic rights decides to submit the use thereof to its provisions.
 
+Frequently asked questions can be found on the official website of the
+CeCILL licenses family (http://www.cecill.info/index.en.html) for any
+necessary clarification.
+
 
     Article 1 - DEFINITIONS
 
@@ -116,6 +120,15 @@ spaces, with one calling the other when they are run.
 Internal Module: means any or all Module, connected to the Software so
 that they both execute in the same address space.
 
+GNU GPL: means the GNU General Public License version 2 or any
+subsequent version, as published by the Free Software Foundation Inc.
+
+GNU Affero GPL: means the GNU Affero General Public License version 3 or
+any subsequent version, as published by the Free Software Foundation Inc.
+
+EUPL: means the European Union Public License version 1.1 or any
+subsequent version, as published by the European Commission.
+
 Parties: mean both the Licensee and the Licensor.
 
 These expressions may be used both in singular and plural form.
@@ -125,8 +138,8 @@ These expressions may be used both in singular and plural form.
 
 The purpose of the Agreement is the grant by the Licensor to the
 Licensee of a non-exclusive, transferable and worldwide license for the
-Software as set forth in Article 5 hereinafter for the whole term of the
-protection granted by the rights over said Software.
+Software as set forth in Article 5 <#scope> hereinafter for the whole
+term of the protection granted by the rights over said Software.
 
 
     Article 3 - ACCEPTANCE
@@ -135,18 +148,17 @@ protection granted by the rights over said Software.
 conditions of this Agreement upon the occurrence of the first of the
 following events:
 
-    * (i) loading the Software by any or all means, notably, by
-      downloading from a remote server, or by loading from a physical
-      medium;
-    * (ii) the first time the Licensee exercises any of the rights
-      granted hereunder.
+  * (i) loading the Software by any or all means, notably, by
+    downloading from a remote server, or by loading from a physical medium;
+  * (ii) the first time the Licensee exercises any of the rights granted
+    hereunder.
 
 3.2 One copy of the Agreement, containing a notice relating to the
 characteristics of the Software, to the limited warranty, and to the
 fact that its use is restricted to experienced users has been provided
 to the Licensee prior to its acceptance as set forth in Article 3.1
-hereinabove, and the Licensee hereby acknowledges that it has read and
-understood it.
+<#accepting> hereinabove, and the Licensee hereby acknowledges that it
+has read and understood it.
 
 
     Article 4 - EFFECTIVE DATE AND TERM
@@ -155,7 +167,7 @@ understood it.
       4.1 EFFECTIVE DATE
 
 The Agreement shall become effective on the date when it is accepted by
-the Licensee as set forth in Article 3.1.
+the Licensee as set forth in Article 3.1 <#accepting>.
 
 
       4.2 TERM
@@ -185,18 +197,18 @@ The Licensee is authorized to use the Software, without any limitation
 as to its fields of application, with it being hereinafter specified
 that this comprises:
 
-   1. permanent or temporary reproduction of all or part of the Software
-      by any or all means and in any or all form.
+ 1. permanent or temporary reproduction of all or part of the Software
+    by any or all means and in any or all form.
 
-   2. loading, displaying, running, or storing the Software on any or
-      all medium.
+ 2. loading, displaying, running, or storing the Software on any or all
+    medium.
 
-   3. entitlement to observe, study or test its operation so as to
-      determine the ideas and principles behind any or all constituent
-      elements of said Software. This shall apply when the Licensee
-      carries out any or all loading, displaying, running, transmission
-      or storage operation as regards the Software, that it is entitled
-      to carry out hereunder.
+ 3. entitlement to observe, study or test its operation so as to
+    determine the ideas and principles behind any or all constituent
+    elements of said Software. This shall apply when the Licensee
+    carries out any or all loading, displaying, running, transmission or
+    storage operation as regards the Software, that it is entitled to
+    carry out hereunder.
 
 
       5.2 ENTITLEMENT TO MAKE CONTRIBUTIONS
@@ -229,69 +241,62 @@ The Licensee is authorized to distribute true copies of the Software in
 Source Code or Object Code form, provided that said distribution
 complies with all the provisions of the Agreement and is accompanied by:
 
-   1. a copy of the Agreement,
+ 1. a copy of the Agreement,
 
-   2. a notice relating to the limitation of both the Licensor's
-      warranty and liability as set forth in Articles 8 and 9,
+ 2. a notice relating to the limitation of both the Licensor's warranty
+    and liability as set forth in Articles 8 and 9,
 
 and that, in the event that only the Object Code of the Software is
 redistributed, the Licensee allows effective access to the full Source
-Code of the Software at a minimum during the entire period of its
+Code of the Software for a period of at least three years from the
 distribution of the Software, it being understood that the additional
-cost of acquiring the Source Code shall not exceed the cost of
-transferring the data.
+acquisition cost of the Source Code shall not exceed the cost of the
+data transfer.
 
 
         5.3.2 DISTRIBUTION OF MODIFIED SOFTWARE
 
-If the Licensee makes any Contribution to the Software, the resulting
-Modified Software may be distributed under a license agreement other
-than this Agreement subject to compliance with the provisions of Article
-5.3.4.
-
-
-        5.3.3 DISTRIBUTION OF EXTERNAL MODULES
-
-When the Licensee has developed an External Module, the terms and
-conditions of this Agreement do not apply to said External Module, that
-may be distributed under a separate license agreement.
+When the Licensee makes a Contribution to the Software, the terms and
+conditions for the distribution of the resulting Modified Software
+become subject to all the provisions of this Agreement.
 
+The Licensee is authorized to distribute the Modified Software, in
+source code or object code form, provided that said distribution
+complies with all the provisions of the Agreement and is accompanied by:
 
-        5.3.4 CREDITS
+ 1. a copy of the Agreement,
 
-Any Licensee who may distribute a Modified Software hereby expressly
-agrees to:
+ 2. a notice relating to the limitation of both the Licensor's warranty
+    and liability as set forth in Articles 8 and 9,
 
-   1. indicate in the related documentation that it is based on the
-      Software licensed hereunder, and reproduce the intellectual
-      property notice for the Software,
+and, in the event that only the object code of the Modified Software is
+redistributed,
 
-   2. ensure that written indications of the Software intended use,
-      intellectual property notice and license hereunder are included in
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+ 3. a note stating the conditions of effective access to the full source
+    code of the Modified Software for a period of at least three years
+    from the distribution of the Modified Software, it being understood
+    that the additional acquisition cost of the source code shall not
+    exceed the cost of the data transfer.
 
-   3. mention, on a freely accessible website describing the Modified
-      Software, at least throughout the distribution term thereof, that
-      it is based on the Software licensed hereunder, and reproduce the
-      Software intellectual property notice,
 
-   4. where it is distributed to a third party that may distribute a
-      Modified Software without having to make its source code
-      available, make its best efforts to ensure that said third party
-      agrees to comply with the obligations set forth in this Article .
+        5.3.3 DISTRIBUTION OF EXTERNAL MODULES
 
-If the Software, whether or not modified, is distributed with an
-External Module designed for use in connection with the Software, the
-Licensee shall submit said External Module to the foregoing obligations.
+When the Licensee has developed an External Module, the terms and
+conditions of this Agreement do not apply to said External Module, that
+may be distributed under a separate license agreement.
 
 
-        5.3.5 COMPATIBILITY WITH THE CeCILL AND CeCILL-C LICENSES
+        5.3.4 COMPATIBILITY WITH OTHER LICENSES
 
-Where a Modified Software contains a Contribution subject to the CeCILL
-license, the provisions set forth in Article 5.3.4 shall be optional.
+The Licensee can include a code that is subject to the provisions of one
+of the versions of the GNU GPL, GNU Affero GPL and/or EUPL in the
+Modified or unmodified Software, and distribute that entire code under
+the terms of the same version of the GNU GPL, GNU Affero GPL and/or EUPL.
 
-A Modified Software may be distributed under the CeCILL-C license. In
-such a case the provisions set forth in Article 5.3.4 shall be optional.
+The Licensee can include the Modified or unmodified Software in a code
+that is subject to the provisions of one of the versions of the GNU GPL,
+GNU Affero GPL and/or EUPL and distribute that entire code under the
+terms of the same version of the GNU GPL, GNU Affero GPL and/or EUPL.
 
 
     Article 6 - INTELLECTUAL PROPERTY
@@ -306,7 +311,7 @@ and no one shall be entitled to modify the terms and conditions for the
 distribution of said Initial Software.
 
 The Holder undertakes that the Initial Software will remain ruled at
-least by this Agreement, for the duration set forth in Article 4.2.
+least by this Agreement, for the duration set forth in Article 4.2 <#term>.
 
 
       6.2 OVER THE CONTRIBUTIONS
@@ -328,17 +333,17 @@ govern its distribution.
 
 The Licensee expressly undertakes:
 
-   1. not to remove, or modify, in any manner, the intellectual property
-      notices attached to the Software;
+ 1. not to remove, or modify, in any manner, the intellectual property
+    notices attached to the Software;
 
-   2. to reproduce said notices, in an identical manner, in the copies
-      of the Software modified or not.
+ 2. to reproduce said notices, in an identical manner, in the copies of
+    the Software modified or not.
 
 The Licensee undertakes not to directly or indirectly infringe the
-intellectual property rights of the Holder and/or Contributors on the
-Software and to take, where applicable, vis-à-vis its staff, any and all
-measures required to ensure respect of said intellectual property rights
-of the Holder and/or Contributors.
+intellectual property rights on the Software of the Holder and/or
+Contributors, and to take, where applicable, vis-à-vis its staff, any
+and all measures required to ensure respect of said intellectual
+property rights of the Holder and/or Contributors.
 
 
     Article 7 - RELATED SERVICES
@@ -399,13 +404,13 @@ or properties.
 
 9.2 The Licensor hereby represents, in good faith, that it is entitled
 to grant all the rights over the Software (including in particular the
-rights set forth in Article 5).
+rights set forth in Article 5 <#scope>).
 
 9.3 The Licensee acknowledges that the Software is supplied "as is" by
 the Licensor without any other express or tacit warranty, other than
-that provided for in Article 9.2 and, in particular, without any warranty 
-as to its commercial value, its secured, safe, innovative or relevant 
-nature.
+that provided for in Article 9.2 <#good-faith> and, in particular,
+without any warranty as to its commercial value, its secured, safe,
+innovative or relevant nature.
 
 Specifically, the Licensor does not warrant that the Software is free
 from any error, that it will operate without interruption, that it will
@@ -420,7 +425,7 @@ arising out of any or all proceedings for infringement that may be
 instituted in respect of the use, modification and redistribution of the
 Software. Nevertheless, should such proceedings be instituted against
 the Licensee, the Licensor shall provide it with technical and legal
-assistance for its defense. Such technical and legal assistance shall be
+expertise for its defense. Such technical and legal expertise shall be
 decided on a case-by-case basis between the relevant Licensor and the
 Licensee pursuant to a memorandum of understanding. The Licensor
 disclaims any and all liability as regards the Licensee's use of the
@@ -497,7 +502,8 @@ address new issues encountered by Free Software.
 
 12.3 Any Software distributed under a given version of the Agreement may
 only be subsequently distributed under the same version of the Agreement
-or a subsequent version.
+or a subsequent version, subject to the provisions of Article 5.3.4
+<#compatibility>.
 
 
     Article 13 - GOVERNING LAW AND JURISDICTION
@@ -511,5 +517,3 @@ occurrence, and unless emergency proceedings are necessary, the
 disagreements or disputes shall be referred to the Paris Courts having
 jurisdiction, by the more diligent Party.
 
-
-Version 1.0 dated 2006-09-05.

{fstg_toolkit-1.2.1 → fstg_toolkit-1.4.0}/PKG-INFO

@@ -1,12 +1,12 @@
 Metadata-Version: 2.4
 Name: fSTG-Toolkit
-Version: 1.2.1
-Summary: Aan Open-Source Software for Spatio-Temporal Graph Analysis of fMRI data.
-License-Expression: CECILL-B
+Version: 1.4.0
+Summary: An Open-Source Software for Spatio-Temporal Graph Analysis of fMRI data.
+License-Expression: CECILL-2.1
 License-File: LICENSE
 Author: Julien PONTABRY
 Author-email: jpontabry@unistra.fr
-Requires-Python: >=3.12,<=3.13
+Requires-Python: >=3.12,<3.14
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
@@ -47,10 +47,12 @@ Description-Content-Type: text/markdown
 <div style="text-align: center">
 
 ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/fSTG-Toolkit)
-[![CI](https://github.com/julienpontabry/fstg_toolkit/actions/workflows/ci.yml/badge.svg?branch=main)](https://github.com/julienpontabry/fstg_toolkit/actions/workflows/ci.yml)
+[![CI](https://github.com/ICube-Medical-Image-Computing/fstg_toolkit/actions/workflows/ci.yml/badge.svg?branch=main)](https://github.com/ICube-Medical-Image-Computing/fstg_toolkit/actions/workflows/ci.yml)
+[![Coverage](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/julienpontabry/c923f99a7adf99424c8c17066285ed3d/raw/fstg_toolkit_coverage.json)](https://github.com/ICube-Medical-Image-Computing/fstg_toolkit/actions/workflows/ci.yml)
 ![PyPI - Version](https://img.shields.io/pypi/v/fSTG-Toolkit)
 ![PyPI - License](https://img.shields.io/pypi/l/fSTG-Toolkit)
-[![Read the Docs](https://img.shields.io/readthedocs/fSTG-Toolkit)](https://fstg-toolkit.readthedocs.io/)
+[![Read the Docs](https://img.shields.io/readthedocs/fstg-toolkit)](https://fstg-toolkit.readthedocs.io/)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.22093918.svg)](https://doi.org/10.5281/zenodo.22093918)
 
 </div>
 
@@ -130,3 +132,16 @@ Full usage documentation, tutorials, and API reference are available at **[fstg-
 
 ![Illustration of the dashboard.](docs/_static/images/illustration_web-viewer.png)
 
+
+## Community
+
+- **Questions about using the toolkit?** Ask in the [discussions](https://github.com/ICube-Medical-Image-Computing/fstg_toolkit/discussions), in the *Q&A* category.
+- **Found a bug?** Open an [issue](https://github.com/ICube-Medical-Image-Computing/fstg_toolkit/issues/new/choose) with the bug report form.
+- **Want to contribute?** Bug fixes, new features, and documentation improvements are welcome: see [CONTRIBUTING.md](CONTRIBUTING.md) for the development setup, the test suites, and the pull request process.
+
+Everyone taking part in the project is expected to follow the [Code of Conduct](CODE_OF_CONDUCT.md).
+
+## License
+
+The fSTG Toolkit is distributed under the CeCILL Free Software Agreement v2.1. See LICENSE for more information. The Multi-SPMiner sources bundled under `src/fstg_toolkit/spminer/` are an exception: see `src/fstg_toolkit/spminer/NOTICE.md` for their provenance and status.
+

{fstg_toolkit-1.2.1 → fstg_toolkit-1.4.0}/README.md

@@ -5,10 +5,12 @@
 <div style="text-align: center">
 
 ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/fSTG-Toolkit)
-[![CI](https://github.com/julienpontabry/fstg_toolkit/actions/workflows/ci.yml/badge.svg?branch=main)](https://github.com/julienpontabry/fstg_toolkit/actions/workflows/ci.yml)
+[![CI](https://github.com/ICube-Medical-Image-Computing/fstg_toolkit/actions/workflows/ci.yml/badge.svg?branch=main)](https://github.com/ICube-Medical-Image-Computing/fstg_toolkit/actions/workflows/ci.yml)
+[![Coverage](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/julienpontabry/c923f99a7adf99424c8c17066285ed3d/raw/fstg_toolkit_coverage.json)](https://github.com/ICube-Medical-Image-Computing/fstg_toolkit/actions/workflows/ci.yml)
 ![PyPI - Version](https://img.shields.io/pypi/v/fSTG-Toolkit)
 ![PyPI - License](https://img.shields.io/pypi/l/fSTG-Toolkit)
-[![Read the Docs](https://img.shields.io/readthedocs/fSTG-Toolkit)](https://fstg-toolkit.readthedocs.io/)
+[![Read the Docs](https://img.shields.io/readthedocs/fstg-toolkit)](https://fstg-toolkit.readthedocs.io/)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.22093918.svg)](https://doi.org/10.5281/zenodo.22093918)
 
 </div>
 
@@ -87,3 +89,16 @@ python -m fstg_toolkit graph build --help
 Full usage documentation, tutorials, and API reference are available at **[fstg-toolkit.readthedocs.io](https://fstg-toolkit.readthedocs.io/)**.
 
 ![Illustration of the dashboard.](docs/_static/images/illustration_web-viewer.png)
+
+
+## Community
+
+- **Questions about using the toolkit?** Ask in the [discussions](https://github.com/ICube-Medical-Image-Computing/fstg_toolkit/discussions), in the *Q&A* category.
+- **Found a bug?** Open an [issue](https://github.com/ICube-Medical-Image-Computing/fstg_toolkit/issues/new/choose) with the bug report form.
+- **Want to contribute?** Bug fixes, new features, and documentation improvements are welcome: see [CONTRIBUTING.md](CONTRIBUTING.md) for the development setup, the test suites, and the pull request process.
+
+Everyone taking part in the project is expected to follow the [Code of Conduct](CODE_OF_CONDUCT.md).
+
+## License
+
+The fSTG Toolkit is distributed under the CeCILL Free Software Agreement v2.1. See LICENSE for more information. The Multi-SPMiner sources bundled under `src/fstg_toolkit/spminer/` are an exception: see `src/fstg_toolkit/spminer/NOTICE.md` for their provenance and status.

{fstg_toolkit-1.2.1 → fstg_toolkit-1.4.0}/pyproject.toml

@@ -1,14 +1,14 @@
 [project]
 name = "fSTG-Toolkit"
-version = "1.2.1"
-description = "Aan Open-Source Software for Spatio-Temporal Graph Analysis of fMRI data."
+version = "1.4.0"
+description = "An Open-Source Software for Spatio-Temporal Graph Analysis of fMRI data."
 authors = [
-    {name = "Julien PONTABRY",email = "jpontabry@unistra.fr"}
+    {name = "Julien PONTABRY", email = "jpontabry@unistra.fr"}
 ]
 readme = "README.md"
-license = "CECILL-B"
+license = "CECILL-2.1"
 license-files = ["LICENSE"]
-requires-python = ">=3.12,<=3.13"
+requires-python = ">=3.12,<3.14"
 dependencies = [
     "networkx (>=3.4.2,<4.0.0)",
     "pandas (>=2.2.3,<3.0.0)",
@@ -47,8 +47,27 @@ docs = [
     "sphinx-copybutton (>=0.5.2,<0.6.0)",
 ]
 
-[tool.setuptools.package-data]
-fstg_toolkit = ["logging.yml"]
+[tool.coverage.run]
+source = ["src/fstg_toolkit"]
+omit = [
+    "src/fstg_toolkit/app/*",
+    "src/fstg_toolkit/spminer/*",
+]
+relative_files = true
+
+[tool.coverage.report]
+show_missing = true
+# Code that cannot run unattended: matplotlib widgets driven by mouse and
+# keyboard events, commands starting a Dash server or requiring the Docker
+# based SPMiner service, and the screen probing behind figure sizing.
+exclude_also = [
+    "^class DynamicPlot",
+    "^class DynamicTimeCursor",
+    "^def __figure_screen_setup",
+    "^def frequent",
+    "^def show",
+    "^def serve",
+]
 
 [build-system]
 requires = ["poetry-core>=2.0.0,<3.0.0"]

{fstg_toolkit-1.2.1 → fstg_toolkit-1.4.0}/src/fstg_toolkit/__init__.py

@@ -5,9 +5,9 @@
 # to model, process and analyze the longitudinal reorganization of brain
 # connectivity data, as functional MRI for instance.
 #
-# This software is governed by the CeCILL-B license under French law and
+# This software is governed by the CeCILL license under French law and
 # abiding by the rules of distribution of free software. You can use,
-# modify and/or redistribute the software under the terms of the CeCILL-B
+# modify and/or redistribute the software under the terms of the CeCILL
 # license as circulated by CEA, CNRS and INRIA at the following URL
 # "http://www.cecill.info".
 #
@@ -29,7 +29,7 @@
 # same conditions as regards security.
 #
 # The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL-B license and that you accept its terms.
+# knowledge of the CeCILL license and that you accept its terms.
 
 from importlib.metadata import version
 

{fstg_toolkit-1.2.1 → fstg_toolkit-1.4.0}/src/fstg_toolkit/__main__.py

@@ -5,9 +5,9 @@
 # to model, process and analyze the longitudinal reorganization of brain
 # connectivity data, as functional MRI for instance.
 #
-# This software is governed by the CeCILL-B license under French law and
+# This software is governed by the CeCILL license under French law and
 # abiding by the rules of distribution of free software. You can use,
-# modify and/or redistribute the software under the terms of the CeCILL-B
+# modify and/or redistribute the software under the terms of the CeCILL
 # license as circulated by CEA, CNRS and INRIA at the following URL
 # "http://www.cecill.info".
 #
@@ -29,7 +29,7 @@
 # same conditions as regards security.
 #
 # The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL-B license and that you accept its terms.
+# knowledge of the CeCILL license and that you accept its terms.
 
 __help_epilog = []
 __graph_help_epilog = []
@@ -126,6 +126,24 @@ def __load_graph(filepath: Path) -> SpatioTemporalGraph:
     return loader.load_graph(areas, chosen)
 
 
+def __with_zip_suffix(filepath: Path) -> Path:
+    """Add the '.zip' extension to a path of archive, if it is missing.
+
+    Parameters
+    ----------
+    filepath : Path
+        The path of the archive to write.
+
+    Returns
+    -------
+    Path
+        The path ending with the '.zip' extension.
+    """
+    if filepath.suffix.lower() == '.zip':
+        return filepath
+    return filepath.with_name(f'{filepath.name}.zip')
+
+
 ## building and computing #####################################################
 
 
@@ -224,6 +242,7 @@ def build(areas_description_path: Path, correlation_matrices_path: Tuple[Path],
 
     The CSV file for the description of areas and regions should have the columns: `Id_Area`, `Name_Area`, and `Name_Region`.
     """
+    output = __with_zip_suffix(output)
 
     # prepare the data saver
     saver = DataSaver()
@@ -234,6 +253,9 @@ def build(areas_description_path: Path, correlation_matrices_path: Tuple[Path],
             matrices = {}
             for cm in correlation_matrices_path:
                 for name, matrix in __read_load_np(cm):
+                    if name in matrices:
+                        error_console.print(f"Warning: sequence '{name}' from '{cm.name}' "
+                                            f"replaces a previous sequence with the same name.")
                     matrices[name] = matrix
                 console.print(f"- red '{cm.name}'")
         console.print(f"Red {len(correlation_matrices_path)} files.")
@@ -638,9 +660,10 @@ GRAPH_SEQUENCE_DESCRIPTION = GraphSequenceDescription()
 
 
 @graph.group()
-@click.option('-o', '--output_path', type=click.Path(writable=True),
+@click.option('-o', '--output_path', type=click.Path(writable=True, path_type=Path),
               default="output", show_default="a file named 'output' in the current directory",
-              help="Path where to write the simulated output.")
+              help="Path where to write the simulated output. The extension is added if missing: "
+                   "'.zip' for patterns and sequences, '.npz' for correlations.")
 @click.pass_context
 def simulate(ctx: click.core.Context, output_path: Path):
     """Simulate a spatio-temporal graph."""
@@ -679,7 +702,7 @@ def pattern(ctx: click.core.Context, networks: List[List[Tuple[Tuple[int, int],
     pat = generate_pattern(networks_list=networks,
                            spatial_edges=spatial_edges,
                            temporal_edges=temporal_edges)
-    save_spatio_temporal_graph(pat, ctx.obj)
+    save_spatio_temporal_graph(pat, __with_zip_suffix(ctx.obj))
 
 
 @simulate.command()
@@ -697,7 +720,7 @@ def sequence(ctx: click.core.Context, patterns: Tuple[Path], sequence_descriptio
                       for i, filepath in enumerate(patterns)}
     simulator = SpatioTemporalGraphSimulator(**pattern_graphs)
     graph = simulator.simulate(*sequence_description)
-    save_spatio_temporal_graph(graph, ctx.obj)
+    save_spatio_temporal_graph(graph, __with_zip_suffix(ctx.obj))
 
 
 @simulate.command()
@@ -707,11 +730,16 @@ def sequence(ctx: click.core.Context, patterns: Tuple[Path], sequence_descriptio
               help="The correlation threshold when building graph from matrices.")
 @click.pass_context
 def correlations(ctx: click.core.Context, graph_path: Path, threshold: float):
-    """Simulate correlations matrices from a spatio-temporal graph."""
+    """Simulate correlations matrices from a spatio-temporal graph.
+
+    The sequence of matrices is saved under the name of the output file (without its
+    '.npz' extension), which is the name the command 'build' gives to its graph.
+    """
     graph = __load_graph(graph_path)
     simulator = CorrelationMatrixSequenceSimulator(graph, threshold=threshold)
     matrices = simulator.simulate()
-    np.savez_compressed(ctx.obj, simulated=matrices)
+    name = Path(ctx.obj).name.removesuffix('.npz')
+    np.savez_compressed(ctx.obj, **{name: matrices})
 
 
 ## showing ####################################################################

{fstg_toolkit-1.2.1 → fstg_toolkit-1.4.0}/src/fstg_toolkit/app/__init__.py

@@ -5,9 +5,9 @@
 # to model, process and analyze the longitudinal reorganization of brain
 # connectivity data, as functional MRI for instance.
 #
-# This software is governed by the CeCILL-B license under French law and
+# This software is governed by the CeCILL license under French law and
 # abiding by the rules of distribution of free software. You can use,
-# modify and/or redistribute the software under the terms of the CeCILL-B
+# modify and/or redistribute the software under the terms of the CeCILL
 # license as circulated by CEA, CNRS and INRIA at the following URL
 # "http://www.cecill.info".
 #
@@ -29,4 +29,4 @@
 # same conditions as regards security.
 #
 # The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL-B license and that you accept its terms.
+# knowledge of the CeCILL license and that you accept its terms.