TVB-3110: 3rd party dependencies licences

README.md

@@ -81,7 +81,7 @@ interact with TVB Web Graphical Interface.
 ### Testing
 
 For testing our packages, PyTest framework can be used. We also need a few more dependencies for tests specific, 
-which are listed in setup.py files.
+which are listed in pyproject.toml files.
 
 Pytest will run all files in the current directory and its subdirectories
 of the form test_*.py or *_test.py.
@@ -100,16 +100,16 @@ The command for running our tests has two forms:
   2. The second alternative form of running TVB tests, when installing TVB from Pypi, is:
 
             pip install -U tvb-framework
-            # install optional dependencies needed just for tests (search "extras_require" in tvb_framework/setup.py)
+            # install optional dependencies needed just for tests (search "extras_require" in tvb_framework/pyproject.toml)
             pip install pytest pytest-benchmark pytest-mock BeautifulSoup4
             pytest --pyargs tvb.tests.framework
 
             pip install -U tvb-library
-            # install optional dependencies (from variable LIBRARY_REQUIRED_EXTRA in tvb_library/setup.py)
+            # install optional dependencies (from variable LIBRARY_REQUIRED_EXTRA in tvb_library/pyproject.toml)
             pip install h5py pytest pytest-benchmark pytest-xdist tvb-gdist tvb-data
             pytest --pyargs tvb.tests.library
 
-- For all the tests to run correctly, the dependencies specified as LIBRARY_REQUIRED_EXTRA in [setup.py](https://github.com/the-virtual-brain/tvb-root/blob/master/tvb_library/setup.py) should be installed
+- For all the tests to run correctly, the dependencies specified as LIBRARY_REQUIRED_EXTRA in [pyproject.toml](https://github.com/the-virtual-brain/tvb-root/blob/master/tvb_library/pyproject.toml) should be installed
 - Make sure that tvb-data package is installed from [Zenodo](https://zenodo.org/record/10128131)
 
 ### Coverage

tvb_build/Jenkinsfile-TVBRun

@@ -30,7 +30,7 @@ pipeline {
                 unstash 'step1'
                 unzip zipFile: 'tvb_build/build/TVB_build_step1.zip', dir: 'tvb_build/docker/step1'
                 script {
-                    VERSION_TAG = sh(script: "curl -s 'https://raw.githubusercontent.com/the-virtual-brain/tvb-root/master/tvb_framework/setup.py' | grep VERSION | head -1 | tr -d 'VERSION = \"'", returnStdout: true). trim()
+                    VERSION_TAG = sh(script: "curl -s 'https://raw.githubusercontent.com/the-virtual-brain/tvb-root/master/tvb_framework/pyproject.toml' | awk '/\\[project\\]/ {found=1} found && /version/ {print; exit}' | tr -d '\"' | awk -F'=' '{print \$2}'", returnStdout: true).trim()
                     LAST_SHA = sh(script: "curl -s 'https://api.github.com/repos/the-virtual-brain/tvb-root/commits' | grep sha | head -1 | cut -d ':' -f2 | tr -d '\",'", returnStdout: true).trim()
 
                     def dockerContext = "tvb_build/docker"

tvb_build/docker/requirements_group

@@ -1,4 +1,5 @@
 numpy<2
+siibra
 cryptography
 sqlalchemy
 pyAesCrypt
@@ -49,7 +50,6 @@ lxml
 pylems
 docutils
 Pillow
-siibra
 bctpy
 kubernetes
 watchdog

tvb_build/tvb_build/third_party_licenses/build_licenses.py

@@ -78,6 +78,20 @@
                    \n\n\n"
 
 
+def parse_versions(str_versions: str):
+    versions = str_versions[1:-1].split(',')
+    parsed_versions = []
+    temp = ''
+    paren_level = 0
+    for version in versions:
+        paren_level += version.count('(') - version.count(')')
+        temp = temp + ',' + version if temp else version
+        if paren_level == 0:
+            parsed_versions.append(temp)
+            temp = ''
+    return parsed_versions
+
+
 def _invalid_version(expected, actual):
     """ 
     Check if current found version of 3rd party library is 
@@ -86,7 +100,7 @@ def _invalid_version(expected, actual):
     if actual.startswith(expected):
         return False
     if expected.startswith('['):
-        expected = expected[1:-1].split(',')
+        expected = parse_versions(expected)
         return actual not in expected
     return True
 
@@ -169,7 +183,7 @@ def generate_artefact(root_folder_to_introspect, excludes=None, actual_libs=None
     # Run stand-alone.
     all_libs = parser.read_default()
     to_exclude = []
-    for libname, libattr in all_libs.iteritems():
+    for libname, libattr in all_libs.items():
         if 'Desktop' in libattr["description"] or 'unused' in libattr['env']:
             to_exclude.append(libname)
         all_libs[libname] = libattr["version"]

tvb_build/tvb_build/third_party_licenses/license/LICENSE_PyExecJS.txt

@@ -0,0 +1,22 @@
+Copyright (c) 2012 Omoto Kenji
+Copyright (c) 2011 Sam Stephenson
+Copyright (c) 2011 Josh Peek
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

tvb_build/tvb_build/third_party_licenses/license/LICENSE_PyObjC.txt

@@ -1,7 +1,10 @@
-(This is the MIT license)
+(This is the MIT license, note that libffi-src is a separate product with its own license)
 
-Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+Copyright 2002, 2003 - Bill Bumgarner, Ronald Oussoren, Steve Majewski, Lele Gaifax, et.al.
+Copyright 2003-2024 - Ronald Oussoren
 
-The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+ Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
 
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

tvb_build/tvb_build/third_party_licenses/license/LICENSE_accessibility.txt

@@ -0,0 +1,15 @@
+This project is licensed under the ISC License, reproduced below.
+
+Copyright (c) 2013-2014, Aaron Jacobs <[email protected]>
+
+Permission to use, copy, modify, and/or distribute this software for any purpose
+with or without fee is hereby granted, provided that the above copyright notice
+and this permission notice appear in all copies.
+
+THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH
+REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,
+INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
+OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER
+TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF
+THIS SOFTWARE.