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Merge pull request #690 from abhi-glitchhg/pyzenodo
Update TVB-1999-deo branch
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@@ -40,6 +40,7 @@ | |
install_requires=CONTRIB_DEPENDENCIES, | ||
description='A package with TVB contributed additions to the simulator, useful for scripting.', | ||
long_description=DESCRIPTION, | ||
long_description_content_type="text/x-rst", | ||
license="GPL-3.0-or-later", | ||
author=TEAM, | ||
author_email='[email protected]', | ||
|
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@@ -40,12 +40,18 @@ | |
install_requires=["tvb-library"], | ||
description='This namespace is only redirecting to tvb-library', | ||
long_description=DESCRIPTION, | ||
long_description_content_type="text/x-rst", | ||
license="GPL-3.0-or-later", | ||
author=TVB_TEAM, | ||
author_email='[email protected]', | ||
url='https://www.thevirtualbrain.org', | ||
download_url='https://github.com/the-virtual-brain/tvb-root', | ||
keywords='tvb brain simulator neuroscience human animal neuronal dynamics models delay' | ||
keywords='tvb brain simulator neuroscience human animal neuronal dynamics models delay', | ||
classifiers=["Development Status :: 6 - Mature", | ||
"Intended Audience :: Science/Research", | ||
"License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)", | ||
"Programming Language :: Python :: 3" | ||
] | ||
) | ||
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# Cleanup | ||
|
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117 changes: 0 additions & 117 deletions
117
tvb_documentation/demos/display_surface_local_connectivity.ipynb
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tvb_documentation/demos/figures/exploring_a_surface_mesh.png
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@@ -64,12 +64,19 @@ | |
'test': ["pytest", "pytest-benchmark", "pytest-mock", "BeautifulSoup4"]}, | ||
description='A package for performing whole brain simulations', | ||
long_description=DESCRIPTION, | ||
long_description_content_type="text/x-rst", | ||
license="GPL-3.0-or-later", | ||
author=TVB_TEAM, | ||
author_email='[email protected]', | ||
url='https://www.thevirtualbrain.org', | ||
download_url='https://github.com/the-virtual-brain/tvb-root', | ||
keywords='tvb brain simulator neuroscience human animal neuronal dynamics models delay') | ||
keywords='tvb brain simulator neuroscience human animal neuronal dynamics models delay', | ||
classifiers=["Development Status :: 6 - Mature", | ||
"Intended Audience :: Science/Research", | ||
"License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)", | ||
"Programming Language :: Python :: 3" | ||
] | ||
) | ||
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# Clean after install | ||
shutil.rmtree('tvb_framework.egg-info', True) |
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|
@@ -50,18 +50,19 @@ | |
version=VERSION, | ||
packages=setuptools.find_packages( | ||
exclude=['tvb.interfaces.web', 'tvb.interfaces.web.*', 'tvb.interfaces.command', | ||
'tvb.interfaces.command.*', 'tvb.tests', 'tvb.tests.*', 'tvb.interfaces.rest' | ||
'tvb.interfaces.command.*', 'tvb.tests', 'tvb.tests.*', 'tvb.interfaces.rest', | ||
'tvb.interfaces.rest.*', 'tvb.adapters', 'tvb.adapters.*', 'tvb.core', | ||
'tvb.core.*']), | ||
include_package_data=True, | ||
install_requires=TVB_INSTALL_REQUIREMENTS, | ||
extras_require={'test': ["pytest", "pytest-benchmark"]}, | ||
description='A helper package containing BIDS directory monitor module', | ||
long_description=DESCRIPTION, | ||
long_description_content_type="text/x-rst", | ||
license="GPL-3.0-or-later", | ||
author=TVB_TEAM, | ||
author_email='[email protected]', | ||
url='http://www.thevirtualbrain.org', | ||
url='https://www.thevirtualbrain.org', | ||
download_url='https://github.com/the-virtual-brain/tvb-root', | ||
keywords='tvb rest client brain simulator neuroscience human animal neuronal dynamics models delay') | ||
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|
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|
@@ -59,6 +59,7 @@ | |
'test': ["pytest", "pytest-benchmark"]}, | ||
description='A helper package for preparing and sending requests towards the TVB REST API', | ||
long_description=DESCRIPTION, | ||
long_description_content_type="text/x-rst", | ||
license="GPL-3.0-or-later", | ||
author=TVB_TEAM, | ||
author_email='[email protected]', | ||
|
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|
@@ -42,12 +42,11 @@ | |
LIBRARY_REQUIRED_PACKAGES = ["autopep8", "Deprecated", "docutils", "ipywidgets", "lxml", "mako>=1.1.4", "matplotlib", | ||
"networkx", "numba", "numexpr", "numpy", "pooch", "pylems", "scipy", "six"] | ||
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LIBRARY_REQUIRED_EXTRA = ["h5py", "pytest", "pytest-benchmark", "pytest-xdist", "tvb-gdist", "tvb-data"] | ||
LIBRARY_REQUIRED_EXTRA = ["h5py", "pytest", "pytest-benchmark", "pytest-xdist", "tvb-gdist", "tvb-data"] | ||
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with open(os.path.join(os.path.dirname(__file__), 'README.rst')) as fd: | ||
DESCRIPTION = fd.read() | ||
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setuptools.setup(name='tvb-library', | ||
version=LIBRARY_VERSION, | ||
packages=setuptools.find_packages(), | ||
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@@ -56,12 +55,19 @@ | |
extras_require={"test": LIBRARY_REQUIRED_EXTRA}, | ||
description='A package for performing whole brain simulations', | ||
long_description=DESCRIPTION, | ||
long_description_content_type="text/x-rst", | ||
license="GPL-3.0-or-later", | ||
author=LIBRARY_TEAM, | ||
author_email='[email protected]', | ||
url='https://www.thevirtualbrain.org', | ||
download_url='https://github.com/the-virtual-brain/tvb-root', | ||
keywords='tvb brain simulator neuroscience human animal neuronal dynamics models delay') | ||
keywords='tvb brain simulator neuroscience human animal neuronal dynamics models delay', | ||
classifiers=["Development Status :: 6 - Mature", | ||
"Intended Audience :: Science/Research", | ||
"License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)", | ||
"Programming Language :: Python :: 3" | ||
] | ||
) | ||
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# Cleanup after EGG install. These are created by running setup.py in the source tree | ||
shutil.rmtree('tvb_library.egg-info', True) |
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Original file line number | Diff line number | Diff line change |
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@@ -28,7 +28,6 @@ | |
.. moduleauthor:: Abhijit Deo <[email protected]> | ||
""" | ||
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import os | ||
import requests | ||
import json | ||
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@@ -77,7 +76,7 @@ def __init__(self, version : str= "2.7", extract_dir : str = None): | |
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self.rec = Record(self._read_cached_response()[self.version]) | ||
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def _fetch_data(self, file_name): | ||
def fetch_data(self, file_name:str)->str: | ||
""" | ||
Function to fetch the file having `file_name` as name of the file. The function checks if the dataset is downloaded or not. If not, function downloads the dataset and then extracts/unzip the file. | ||
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@@ -89,7 +88,10 @@ def _fetch_data(self, file_name): | |
returns: str | ||
path of the extracted/Unzipped file. | ||
""" | ||
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if Path(file_name).is_absolute(): | ||
self.log.warning("Given `file_name` is an absolute path. No operations are done. The `file_name` is returned as it is") | ||
return file_name | ||
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extract_dir = self.extract_dir | ||
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try: | ||
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@@ -128,35 +130,20 @@ def _fetch_data(self, file_name): | |
file_name should be one of the following paths: {self.files_in_zip_dict[file_name]}""") | ||
raise NameError(f"file name should be one of the {self.files_in_zip_dict[file_name]}, but got {file_name}") | ||
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def describe(self): | ||
def describe(self)-> str: | ||
""" | ||
Returns the project description mentioned on the zenodo website. | ||
""" | ||
return self.rec.describe() | ||
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def get_recordid(self): | ||
def get_recordid(self) -> str: | ||
""" | ||
returns record id of the dataset | ||
""" | ||
return self.recid | ||
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def fetch_all_data(self): | ||
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if self.files_in_zip_dict == None: | ||
self._download(path = self.cached_dir, fname=f"tvb_data_{self.version}.zip") | ||
self.files_in_zip_dict = self._read_zipfile_structure(self.rec.file_loc['tvb_data.zip']) | ||
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for file_paths in self.files_in_zip_dict.values(): | ||
for file_path in file_paths: | ||
self.fetch_data(file_path) | ||
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if self.extract_dir.is_absolute(): | ||
return str(self.extract_dir) | ||
return str(Path.cwd()/self.extract_dir) | ||
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def delete_data(self): | ||
def delete_data(self)->None: | ||
""" | ||
Deletes the `tvb_data` folder in the `self.extract_dir` directory. | ||
""" | ||
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@@ -218,3 +205,20 @@ def _read_cached_response(self): | |
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responses = dict(responses) | ||
return responses | ||
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def _read_zipfile_structure(self, file_path): | ||
""" | ||
Reads the zipfile structure and returns the dictionary containing file_names as keys and list of relative paths having same file name. | ||
""" | ||
with ZipFile(file_path) as zf: | ||
file_names_in_zip = zf.namelist() | ||
zf.close() | ||
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file_names_dict = {} | ||
for i in file_names_in_zip: | ||
if str(Path(i).name) not in file_names_dict.keys(): | ||
file_names_dict[str(Path(i).name)] = [i] | ||
else: | ||
file_names_dict[str(Path(i).name)].append(i) | ||
return file_names_dict | ||
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