TVB-3109 created pyproject.toml for tvb packages

tvb_contrib/pyproject.toml

@@ -0,0 +1,75 @@
+# -*- coding: utf-8 -*-
+#
+#
+#  TheVirtualBrain-Contributors Package. This package holds simulator extensions.
+#  See also http://www.thevirtualbrain.org
+#
+# (c) 2012-2024, Baycrest Centre for Geriatric Care ("Baycrest") and others
+#
+# This program is free software: you can redistribute it and/or modify it under the
+# terms of the GNU General Public License as published by the Free Software Foundation,
+# either version 3 of the License, or (at your option) any later version.
+# This program is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.  See the GNU General Public License for more details.
+# You should have received a copy of the GNU General Public License along with this
+# program.  If not, see <http://www.gnu.org/licenses/>.
+#
+#
+#   CITATION:
+# When using The Virtual Brain for scientific publications, please cite it as explained here:
+# https://www.thevirtualbrain.org/tvb/zwei/neuroscience-publications
+#
+#
+
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "tvb-contrib"
+version = "2.9.2"
+description = "A package with TVB contributed additions to the simulator, useful for scripting."
+readme = "README.rst"
+license = { file = "LICENSE" }
+authors = [
+    { name = "Stuart Knock" },
+    { name = "Dionysios Perdikis" },
+    { name = "Paula Sanz Leon" },
+    { name = "Bogdan Valean" },
+    { name = "Marmaduke Woodman" },
+    { name = "Michiel van der Vlag" },
+]
+maintainers = [
+    { name = "Codemart", email = "[email protected]" }
+]
+keywords = [
+    "brain",
+    "contrib",
+    "neuroscience",
+    "simulator",
+    "tvb",
+]
+dependencies = [
+    "lxml",
+    "pylems",
+    "scikit-learn",
+    "tvb-library",
+    "xarray",
+]
+
+[project.urls]
+Download = "https://github.com/the-virtual-brain/tvb-root"
+Homepage = "https://www.thevirtualbrain.org"
+
+[tool.hatch.version]
+path = "tvb/__init__.py"
+
+[tool.hatch.build.targets.sdist]
+include = [
+    "/tvb",
+]
+
+[tool.hatch.build.targets.wheel]
+packages = ["tvb"]

tvb_deprecated/README.rst

@@ -0,0 +1,129 @@
+THE VIRTUAL BRAIN SCIENTIFIC LIBRARY
+====================================
+
+The Virtual Brain Project (TVB Project) has the purpose of offering some
+modern tools to the Neurosciences community, for computing, simulating
+and analyzing functional and structural data of human brains.
+
+"TVB Scientific Library" is the most important scientific contribution
+of TVB Project, but only a part of our code. In order to use this TVB
+Python Library (modify/run/test), you are advised to follow the steps
+described here:
+http://docs.thevirtualbrain.com/manuals/ContributorsManual/ContributorsManual.html#contributors-manual
+
+The interaction with TVB source code is recommended for advanced users
+only, for which the concepts proposed by TVB are known and understood,
+and which also have some programming knowledge.
+
+"TVB Scientific Library" comes in two major forms for code-contributors:
+as a light-weight Python library, or plugged into TVB framework
+(including Web interface and Persistence of data layers). Depending on
+your needs and resources, you could use any of the two available options
+for contributing and testing new code.
+
+"TVB Scientific Library" is a light-weight, stand-alone Python library
+that contains all the needed packages in order to run simulations and
+analysis on data without the need for the entire TVB Framework. This
+implies that no storage will be provided so data from each session will
+be lost on close. You need to either persist it yourself in some manner
+or use the full TVBFramework where HDF5 / database storage is provided
+as default.
+
+For more details, check: http://www.thevirtualbrain.org/
+
+"TVB Scientific Library" contains the following packages: basic,
+datatypes, simulator and analyzers. The dependencies between these
+packages can be seen in tvb-package-diagram.jpg . Following is a short
+description of each of these packages:
+
+-  tvb.basic
+
+This package is the base of TVB and holds sub-packages that are used by
+most of the other packages like logging, global settings and the TVB
+traits package. You should rarely (if at all) need to change code in
+this package, and should know exactly what you are doing before
+attempting to change anything from here.
+
+-  tvb.datatypes
+
+The simulator and analyzers packages (as well as uploaders and
+visualizers in TVB Framework) will need to have a common "language" in
+order to work with the same data. In TVB architecture, that "common
+language" is represented by Data Types. TVB Data Types declarations are
+located in this package.
+
+-  tvb.simulator
+
+The Simulation Component is the most important component in The Virtual
+Brain solution, as it is the component responsible for all the
+scientific computation related to brain models and data.
+
+You can find various demos of using the simulator here:
+http://docs.thevirtualbrain.org/demos/Demos.html .
+
+-  tvb.analyzers
+
+Holds modules that can run various analysis of data resulted from the
+simulator. TVB is not strong in
+doing data analysis, we barely have a minimum set of analyzers for
+immediate needs.
+
+NOTE:
+
+To contribute to this repo, you are advised to first fork it under
+GitHub (through the web ui), and next clone that fork on your machine,
+and use it as you use any other git repository.
+
+Testing
+=======
+
+For testing the package, the `Pytest  <https://docs.pytest.org/>`_
+framework is used. Pytest can be installed using pip.
+
+Pytest will run all files in the current directory and its subdirectories
+of the form test_*.py or \*_test.py.
+More generally, it follows `standard test discovery rules
+<https://docs.pytest.org/en/latest/getting-started.html>`_
+
+The command for running our tests has two forms.
+Recommendation when working with a git clone of tvb-library::
+
+    cd [folder_where_tvb_library_is]
+    pytest tvb/test [--junitxml=path]
+
+The second alternative form of running TVB tests, when installing TVB from Pypi, is::
+
+    pip install -U tvb-library
+    pytest --pyargs tvb.tests.library
+
+
+Coverage
+--------
+
+A coverage report can be generated with::
+
+    pip install pytest-cov
+    cd [folder_where_tvb_library_is]
+    py.test --cov-config .coveragerc --cov=tvb tvb/tests/ --cov-branch --cov-report xml:[file_where_xml_will_be_generated]
+
+
+Further Resources
+=================
+
+-  For issue tracking we are using Jira: http://req.thevirtualbrain.org
+-  For API documentation and live demos, have a look here:
+   http://docs.thevirtualbrain.org
+-  A public mailing list for users of The Virtual Brain can be joined
+   and followed using: [email protected]
+-  Raw demo IPython Notebooks can be found under:
+   https://github.com/the-virtual-brain/tvb-root/tree/master/tvb_documentation/demos
+
+
+Acknowledgments
+===============
+This project has received funding from the European Union’s Horizon 2020 Framework Programme for Research and
+Innovation under the Specific Grant Agreement Nos. 785907 (Human Brain Project SGA2), 945539 (Human Brain Project SGA3)
+and VirtualBrainCloud 826421.
+
+This project has received funding from the European Union’s Horizon Europe Programme under the Specific Grant
+Agreement No. 101147319 (EBRAINS 2.0 Project).