TVB-3109 created pyproject.toml for tvb-library, tvb-framework, tvb-s…

…torage and tvb-contrib
the-virtual-brain · Nov 13, 2024 · 4989981 · 4989981
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diff --git a/tvb_contrib/pyproject.toml b/tvb_contrib/pyproject.toml
@@ -0,0 +1,72 @@
+# -*- 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",
+]
diff --git a/tvb_contrib/setup.py → tvb_contrib/setup_old.py b/tvb_contrib/setup.py → tvb_contrib/setup_old.py
diff --git a/tvb_framework/pyproject.toml b/tvb_framework/pyproject.toml
@@ -0,0 +1,134 @@
+# -*- coding: utf-8 -*-
+#
+#
+# TheVirtualBrain-Framework Package. This package holds all Data Management, and
+# Web-UI helpful to run brain-simulations. To use it, you also need to download
+# TheVirtualBrain-Scientific Package (for simulators). See content of the
+# documentation-folder for more details. 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-framework"
+version = "2.9.2"
+description = "A package for performing whole brain simulations"
+readme = "README.rst"
+license = { file = "LICENSE" }
+requires-python = ">=3.8"
+authors = [
+    { name = "Mihai Andrei" },
+    { name = "Lia Domide" },
+    { name = "Stuart Knock" },
+    { name = "Bogdan Neacsa" },
+    { name = "Paula Prodan" },
+    { name = "Paula Sansz Leon" },
+    { name = "Marmaduke Woodman" },
+]
+maintainers = [
+    { name = "Codemart", email = "[email protected]" }
+]
+keywords = [
+    "animal",
+    "brain",
+    "delay",
+    "dynamics",
+    "human",
+    "models",
+    "neuronal",
+    "neuroscience",
+    "simulator",
+    "tvb",
+]
+classifiers = [
+    "Development Status :: 6 - Mature",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+]
+dependencies = [
+    "alembic",
+    "bctpy",
+    "cherrypy",
+    "docutils",
+    "flask",
+    "flask-restx",
+    "formencode",
+    "gevent",
+    "h5py",
+    "Jinja2",
+    "matplotlib",
+    "nibabel",
+    "numpy<2.0",
+    "pandas",
+    "Pillow",
+    "psutil",
+    "python-keycloak",
+    "requests",
+    "requests-toolbelt>=0.10",
+    "scikit-learn",
+    "scipy",
+    "siibra",
+    "simplejson",
+    "six",
+    "sqlalchemy",
+    "tvb-data",
+    "tvb-gdist",
+    "tvb-library",
+    "tvb-storage",
+    "werkzeug",
+]
+
+[project.optional-dependencies]
+extra = [
+    "allensdk",
+]
+hpc = [
+    "elasticsearch",
+    "pyunicore",
+]
+postgres = [
+    "psycopg2",
+]
+test = [
+    "BeautifulSoup4",
+    "pytest",
+    "pytest-benchmark",
+    "pytest-mock",
+]
+
+[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",
+]
diff --git a/tvb_framework/setup.py → tvb_framework/setup_old.py b/tvb_framework/setup.py → tvb_framework/setup_old.py
diff --git a/tvb_library/pyproject.toml b/tvb_library/pyproject.toml
@@ -0,0 +1,107 @@
+# -*- coding: utf-8 -*-
+#
+#
+# TheVirtualBrain-Scientific Package. This package holds all simulators, and
+# analysers necessary to run brain-simulations. You can use it stand alone or
+# in conjunction with TheVirtualBrain-Framework Package. See content of the
+# documentation-folder for more details. 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-library"
+version = "2.9.2"
+dynamic = ["version"]
+description = "A package for performing whole brain simulations"
+readme = "README.rst"
+license = { file = "LICENSE" }
+requires-python = ">=3.8"
+authors = [
+    { name = "Marmaduke Woodman" },
+    { name = "Jan Fousek" },
+    { name = "Stuart Knock" },
+    { name = "Paula Sanz Leon" },
+    { name = "Viktor Jirsa" },
+]
+maintainers = [
+    { name = "Codemart", email = "[email protected]" }
+]
+keywords = [
+    "animal",
+    "brain",
+    "delay",
+    "dynamics",
+    "human",
+    "models",
+    "neuronal",
+    "neuroscience",
+    "simulator",
+    "tvb",
+]
+classifiers = [
+    "Development Status :: 6 - Mature",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+]
+dependencies = [
+    "autopep8",
+    "Deprecated",
+    "docutils",
+    "ipywidgets",
+    "mako>=1.1.4",
+    "matplotlib",
+    "networkx",
+    "numba",
+    "numexpr",
+    "numpy<2.0",
+    "scipy",
+    "six",
+]
+
+[project.optional-dependencies]
+test = [
+    "h5py",
+    "pytest",
+    "pytest-benchmark",
+    "pytest-xdist",
+    "tvb-data",
+    "tvb-gdist",
+]
+
+[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",
+]
diff --git a/tvb_library/setup.py → tvb_library/setup_old.py b/tvb_library/setup.py → tvb_library/setup_old.py
diff --git a/tvb_storage/pyproject.toml b/tvb_storage/pyproject.toml
@@ -0,0 +1,82 @@
+# -*- coding: utf-8 -*-
+#
+#
+# TheVirtualBrain-Framework Package. This package holds all Data Management, and
+# Web-UI helpful to run brain-simulations. To use it, you also need to download
+# TheVirtualBrain-Scientific Package (for simulators). See content of the
+# documentation-folder for more details. 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-storage"
+version = "2.9.2"
+description = "A package which handles the storage of TVB data"
+readme = "README.rst"
+license = "GPL-3.0-or-later"
+authors = [
+    { name = "Lia Domide" },
+    { name = "Paula Prodan" },
+    { name = "Bogdan Valean" },
+    { name = "Robert Vincze" },
+]
+maintainers = [
+    { name = "Codemart", email = "[email protected]" }
+]
+keywords = [
+    "brain",
+    "h5",
+    "storage",
+    "tvb",
+]
+dependencies = [
+    "cryptography",
+    "h5py",
+    "kubernetes",
+    "numpy",
+    "pyAesCrypt",
+    "requests",
+    "tvb-library",
+]
+
+[project.optional-dependencies]
+encrypt = [
+    "syncrypto",
+]
+test = [
+    "decorator",
+    "pytest",
+]
+
+[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",
+]
diff --git a/tvb_storage/setup.py → tvb_storage/setup_old.py b/tvb_storage/setup.py → tvb_storage/setup_old.py