This is an automated email from the ASF dual-hosted git repository.
isjarana pushed a commit to branch main
in repository https://gitbox.apache.org/repos/asf/airavata-cerebrum.git
The following commit(s) were added to refs/heads/main by this push:
new 67d4ff0 merge previous repo
67d4ff0 is described below
commit 67d4ff0ec3434822ba9a4ae29b7f982c77d84183
Author: Isuru Ranawaka <[email protected]>
AuthorDate: Sun Dec 3 11:12:41 2023 -0500
merge previous repo
---
.gitignore | 160 ++++++
LICENSE | 201 ++++++++
cybershuttle/__init__.py | 0
cybershuttle/annotations/__init__.py | 0
cybershuttle/annotations/decorator.py | 138 +++++
requirements.txt | 2 +
resources/BMTK_v1_demo/BMTK_V1.ipynb | 561 +++++++++++++++++++++
.../Computing_Platform-analyis.drawio.png | Bin 0 -> 398056 bytes
resources/BMTK_v1_demo/model_simulation.png | Bin 0 -> 63138 bytes
resources/BMTK_v1_demo/neuro-apis.drawio.png | Bin 0 -> 61769 bytes
resources/BMTK_v1_demo/requirements.txt | 49 ++
resources/BMTK_v1_demo/settings.ini | 44 ++
resources/BMTK_v1_demo/workflow.drawio.png | Bin 0 -> 32846 bytes
setup.cfg | 0
setup.py | 29 ++
15 files changed, 1184 insertions(+)
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..68bc17f
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,160 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+# Usually these files are written by a python script from a template
+# before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+# For a library or package, you might want to ignore these files since the
code is
+# intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in
version control.
+# However, in case of collaboration, if having platform-specific
dependencies or dependencies
+# having no cross-platform support, pipenv may install dependencies that
don't work, or not
+# install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+# Similar to Pipfile.lock, it is generally recommended to include
poetry.lock in version control.
+# This is especially recommended for binary packages to ensure
reproducibility, and is more
+# commonly ignored for libraries.
+#
https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+# Similar to Pipfile.lock, it is generally recommended to include pdm.lock
in version control.
+#pdm.lock
+# pdm stores project-wide configurations in .pdm.toml, but it is recommended
to not include it
+# in version control.
+# https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and
github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+# JetBrains specific template is maintained in a separate JetBrains.gitignore
that can
+# be found at
https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+# and can be added to the global gitignore or merged into this file. For a
more nuclear
+# option (not recommended) you can uncomment the following to ignore the
entire idea folder.
+#.idea/
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..261eeb9
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,201 @@
+ Apache License
+ Version 2.0, January 2004
+ http://www.apache.org/licenses/
+
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+ 1. Definitions.
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diff --git a/cybershuttle/__init__.py b/cybershuttle/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/cybershuttle/annotations/__init__.py
b/cybershuttle/annotations/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/cybershuttle/annotations/decorator.py
b/cybershuttle/annotations/decorator.py
new file mode 100644
index 0000000..4c398d5
--- /dev/null
+++ b/cybershuttle/annotations/decorator.py
@@ -0,0 +1,138 @@
+import zipfile
+import os
+import random
+import string
+import shutil
+
+from airavata_sdk.clients.utils.experiment_handler_util import
ExperimentHandlerUtil
+from ipywidgets import widgets
+from IPython.display import display
+
+
+class CybershuttleHPCRun(object):
+
+ def __init__(self, output='./'):
+ configFile = "./settings.ini"
+ self.experiment_handler = ExperimentHandlerUtil(configFile)
+ self.output = output
+ self.input_path = ""
+ self.selected_compute_resource_name = ""
+ self.selected_queue_name = ""
+
+ def __call__(self, func):
+ def wrapper(*args, **kwargs):
+ # Capture the decorator arguments and function arguments here
+
+ self.input_path = kwargs['input']
+
+ # Call the decorated function
+ print("Executing user provided function...")
+ func(*args, **kwargs)
+ print("Function execution succeeded...")
+ self._select_compute_resources()
+
+ return wrapper
+
+ def _run_on_hpc(self, local_input_path, compute_resource_name, queue_name,
output_path):
+
+ allen_v1 = "allen_v1_" + self._generate_random_string(4)
+
+ print("Experiment name: ", allen_v1)
+ print("local_data_directory: ", local_input_path)
+ print("output_data_directory: ", output_path)
+ print("scheduled compute resource: ", compute_resource_name)
+ print("scheduled queue: ", queue_name)
+
+ file_mapping = self._create_BMTK_file_mapping(local_input_path)
+
+ print("Creating experiment ....")
+ self.experiment_handler.launch_experiment(experiment_name=allen_v1,
+
description='allen_v1_experminent',
+
local_input_path=local_input_path,
+
input_file_mapping=file_mapping,
+
computation_resource_name=compute_resource_name,
+ queue_name=queue_name,
output_path=output_path)
+
+ zip_path = local_input_path + "/all_input.zip"
+ self._unzip_and_delete(zip_path)
+
+ def _create_BMTK_file_mapping(self, input_folder_path):
+ file_mapping = {}
+ self._create_zip(input_folder_path, "all_input.zip")
+ input_file_list = self._get_file_list(input_folder_path)
+ for x in input_file_list:
+ if x.endswith(".zip"):
+ file_mapping['Network Inputs'] = x
+ elif x.endswith(".json"):
+ file_mapping['Simulation Config File'] = x
+ return file_mapping
+
+ def _create_zip(self, folder_path, zip_file_name):
+ with zipfile.ZipFile(zip_file_name, 'w', zipfile.ZIP_DEFLATED) as zipf:
+ for root, _, files in os.walk(folder_path):
+ for file in files:
+ file_path = os.path.join(root, file)
+ zipf.write(file_path, arcname=os.path.relpath(file_path,
folder_path))
+
+ # Delete subfolders
+ for root, dirs, _ in os.walk(folder_path, topdown=False):
+ for dir in dirs:
+ dir_path = os.path.join(root, dir)
+ shutil.rmtree(dir_path)
+
+ # Move zip file to root folder
+ zip_file_path = os.path.join(folder_path, zip_file_name)
+ shutil.move(zip_file_name, zip_file_path)
+
+ def _get_file_list(self, folder_path):
+ file_list = []
+ for root, _, files in os.walk(folder_path):
+ for file in files:
+ file_list.append(file)
+ return file_list
+
+ def _generate_random_string(self, length):
+ characters = string.ascii_lowercase
+ random_string = ''.join(random.choice(characters) for _ in
range(length))
+ return random_string
+
+ def _select_compute_resources(self):
+ exp_conf = self.experiment_handler.experiment_conf
+ options = exp_conf.COMPUTE_HOST_DOMAIN.split(',')
+ print("select compute resource")
+ dropdown = widgets.Dropdown(
+ options=options,
+ value=options[0],
+ description='Select Compute Resources',
+ disabled=False,
+ )
+ dropdown.observe(self._select_compute_resources_queue, names="value")
+ display(dropdown)
+
+ def _select_compute_resources_queue(self, compute_resource):
+ selected_compute_resource = compute_resource.new
+ self.selected_compute_resource_name = selected_compute_resource
+
+ print("Select Compute Resources Queue ",
self.selected_compute_resource_name)
+
+ queues = self.experiment_handler.queue_names(selected_compute_resource)
+ queue = widgets.Dropdown(
+ options=queues,
+ value=queues[0],
+ description='Select Compute Resources Queue',
+ disabled=False,
+ )
+ queue.observe(self._on_select_compute_queue, names="value")
+ display(queue)
+
+ def _on_select_compute_queue(self, queue_name):
+ selected_queue_name = queue_name.new
+ self.selected_queue_name = selected_queue_name
+ print("selected compute resource queue ", self.selected_queue_name)
+ self._run_on_hpc(self.input_path, self.selected_compute_resource_name,
self.selected_queue_name,
+ output_path=self.output)
+
+ def _unzip_and_delete(self, zip_file_path):
+ with zipfile.ZipFile(zip_file_path, 'r') as zip_ref:
+ zip_ref.extractall(os.path.dirname(zip_file_path))
+ os.remove(zip_file_path)
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 0000000..64bfed7
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,2 @@
+airavata-python-sdk==1.1.6
+ipywidgets
\ No newline at end of file
diff --git a/resources/BMTK_v1_demo/BMTK_V1.ipynb
b/resources/BMTK_v1_demo/BMTK_V1.ipynb
new file mode 100644
index 0000000..962f6e0
--- /dev/null
+++ b/resources/BMTK_v1_demo/BMTK_V1.ipynb
@@ -0,0 +1,561 @@
+{
+ "cells": [
+ {
+ "cell_type": "code",
+ "execution_count": 26,
+ "metadata": {
+ "pycharm": {
+ "name": "#%%\n"
+ }
+ },
+ "outputs": [
+ {
+ "data": {
+ "image/png":
"iVBORw0KGgoAAAANSUhEUgAABFsAAAEmCAYAAAC9JJ+wAAAKxmlDQ1BJQ0MgUHJvZmlsZQAASImVlwdUU+kSgP97b3qhBSIgJfQmSCeAlNADKL3aCEkgocSYEJpdWVzBtSAixbKCiyIKrgWQtSAWbItiw4JukEVEWRcLNlTeBR5h973z3jtvcub8Xybzz8x/z/w5cwGgEjhicQasAkCmKEsSGejDiE9IZOAHAASwgAqMAZbDlYpZ4eGhAJWp9e/y/h7qjcpt6/FY//77fxVVHl/KBQAKRzmZJ+Vmonwc1WGuWJIFALIPtRvlZInH+TLK6hK0QJR7xjl1kofHOXmCMZgJn+hIX5Q1ASBQOBxJKgAUY9TOyOamonEofijbinhCEcrod+DJFXB4KKN5wazMzCXjLEfZPPkvcVL/FjNZEZPDSVXw5FkmhOAnlIozOHn/5+P435KZIZvKYYoqRSAJikRX
[...]
+ "text/plain": [
+ "<IPython.core.display.Image object>"
+ ]
+ },
+ "execution_count": 26,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "from IPython import display\n",
+ "display.Image(\"model_simulation.png\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 27,
+ "metadata": {
+ "pycharm": {
+ "name": "#%%\n"
+ }
+ },
+ "outputs": [
+ {
+ "data": {
+ "image/png":
"iVBORw0KGgoAAAANSUhEUgAAC4sAAAchCAYAAAAPGOG9AAAgAElEQVR4XuydCdxW47r/bxmLrUQIGaMMyazsU0KK0+5oMo8hU0WkiGMeEtqnkjnDJplrSzKmCBl2psy2Mk8RwiFs+//5rf958vS8a637Ws+z1nqf9+17fT59nLOfe93D9x7Xu37XdS/z73//+98OgwAEIAABCEAAAhCAAAQgAAEIQAACEIAABCAAAQhAAAIQgAAEIAABCEAAAhCAAAQgAAEIQAACEIAABCAAgXpFYBnE4vWqP2kMBCAAAQhAAAIQgAAEIAABCEAAAhCAAAQgAAEIQAACEIAABCAAAQhAAAIQgAAEIAABCEAAAhCAAAQgAIGAAGJxBgIEIAABCEAAAhCAAAQgAAEIQAACEIAABCAAAQhAAAIQgAAEIAABCEAAAhCAAAQgAAEIQAACEIAABCAAgXpIALF4PexUmgQB
[...]
+ "text/plain": [
+ "<IPython.core.display.Image object>"
+ ]
+ },
+ "execution_count": 27,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "from IPython import display\n",
+ "display.Image(\"Computing_Platform-analyis.drawio.png\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 28,
+ "metadata": {
+ "pycharm": {
+ "name": "#%%\n"
+ }
+ },
+ "outputs": [
+ {
+ "data": {
+ "image/png":
"iVBORw0KGgoAAAANSUhEUgAAAY4AAAGTCAYAAAA/TPU5AAAAAXNSR0IArs4c6QAARZ90RVh0bXhmaWxlACUzQ214ZmlsZSUyMGhvc3QlM0QlMjJhcHAuZGlhZ3JhbXMubmV0JTIyJTIwbW9kaWZpZWQlM0QlMjIyMDIzLTA2LTIxVDE0JTNBMzUlM0EyNi44NTFaJTIyJTIwYWdlbnQlM0QlMjJNb3ppbGxhJTJGNS4wJTIwKE1hY2ludG9zaCUzQiUyMEludGVsJTIwTWFjJTIwT1MlMjBYJTIwMTBfMTVfNyklMjBBcHBsZVdlYktpdCUyRjUzNy4zNiUyMChLSFRNTCUyQyUyMGxpa2UlMjBHZWNrbyklMjBDaHJvbWUlMkYxMTQuMC4wLjAlMjBTYWZhcmklMkY1MzcuMzYlMjIlMjBldGFnJTNEJTIyLU5SU01DeG02QjBFQWhld01rMEwl
[...]
+ "text/plain": [
+ "<IPython.core.display.Image object>"
+ ]
+ },
+ "execution_count": 28,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "from IPython import display\n",
+ "display.Image(\"neuro-apis.drawio.png\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 29,
+ "metadata": {
+ "pycharm": {
+ "name": "#%%\n"
+ }
+ },
+ "outputs": [
+ {
+ "data": {
+ "image/png":
"iVBORw0KGgoAAAANSUhEUgAAAc0AAAEjCAYAAABQC1rvAAAAAXNSR0IArs4c6QAAGoh0RVh0bXhmaWxlACUzQ214ZmlsZSUyMGhvc3QlM0QlMjJhcHAuZGlhZ3JhbXMubmV0JTIyJTIwbW9kaWZpZWQlM0QlMjIyMDIzLTA2LTIxVDE1JTNBMzclM0EwNS42OTNaJTIyJTIwYWdlbnQlM0QlMjJNb3ppbGxhJTJGNS4wJTIwKE1hY2ludG9zaCUzQiUyMEludGVsJTIwTWFjJTIwT1MlMjBYJTIwMTBfMTVfNyklMjBBcHBsZVdlYktpdCUyRjUzNy4zNiUyMChLSFRNTCUyQyUyMGxpa2UlMjBHZWNrbyklMjBDaHJvbWUlMkYxMTQuMC4wLjAlMjBTYWZhcmklMkY1MzcuMzYlMjIlMjBldGFnJTNEJTIyYjFnaDZUWG1tTU9UTS16ZGVocjYl
[...]
+ "text/plain": [
+ "<IPython.core.display.Image object>"
+ ]
+ },
+ "execution_count": 29,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "from IPython import display\n",
+ "display.Image(\"workflow.drawio.png\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 30,
+ "metadata": {
+ "pycharm": {
+ "name": "#%%\n"
+ }
+ },
+ "outputs": [],
+ "source": [
+ "from cybershuttle.annotations.decorator import CybershuttleHPCRun\n",
+ "import pandas as pd\n",
+ "import numpy as np\n",
+ "import math\n",
+ "import json\n",
+ "import matplotlib.pyplot as plt\n",
+ "import h5py\n",
+ "import glob\n",
+ "import logging\n",
+ "import os\n",
+ "\n",
+ "\n",
+ "from bmtk.analyzer.spike_trains import plot_rates_boxplot, plot_rates,
plot_raster\n",
+ "from bmtk.utils import sonata\n",
+ "from bmtk.utils.reports import SpikeTrains\n",
+ "\n",
+ "logger =
logging.getLogger(\"airavata_sdk.clients.utils.experiment_handler_util\")\n",
+ "\n",
+ "logger.setLevel(logging.INFO)\n",
+ "logging.basicConfig(level=os.environ.get(\"LOGLEVEL\", \"INFO\"))"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 31,
+ "metadata": {
+ "pycharm": {
+ "name": "#%%\n"
+ }
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Click on Login URI
https://neuroscience.cybershuttle.org/auth/login-desktop/?show-code=true\n";,
+ "Copy paste the access token········\n"
+ ]
+ }
+ ],
+ "source": [
+ "@CybershuttleHPCRun(output=\"./output\")\n",
+ "def load_v1_network_validate_run(input='./inputs'):\n",
+ " net = sonata.File(\n",
+ " data_files=input+'/network/l4_nodes.h5',\n",
+ " data_type_files=input+'/network/l4_node_types.csv')\n",
+ " l4_nodes_df = net.nodes['l4'].to_dataframe(index_by_id=False)\n",
+ " l4_nodes_df[['layer', 'ei', 'model_name', 'dynamics_params',
'model_template', 'model_type','node_id']] \\\n",
+ " .groupby(['layer', 'ei', 'model_name', 'model_template',
'model_type', 'dynamics_params']) \\\n",
+ " .agg('count') \\\n",
+ " .rename(columns={'node_id':'node_count'})\n",
+ " l4_edges_df = pd.read_csv(input+'/network/l4_l4_edge_types.csv',
sep=' ').sort_values(['dynamics_params', 'target_query'])\n",
+ " print(l4_nodes_df)\n",
+ " with h5py.File(input+'/network/l4_l4_edges.h5', 'r') as h5:\n",
+ " edge_ids, edge_counts =
np.unique(h5['/edges/l4_to_l4/edge_type_id'][()], return_counts=True)\n",
+ " edge_counts_df = pd.DataFrame({'edge_type_id': edge_ids, 'counts':
edge_counts})\n",
+ " l4_edges_df = l4_edges_df.merge(edge_counts_df, how='left',
on='edge_type_id')\n",
+ "\n",
+ " l4_edges_df.set_index(['edge_type_id', 'target_query',
'source_query', 'dynamics_params'])\n",
+ " print(l4_edges_df)\n",
+ " print('Valid SONATA inputs:')\n",
+ " for spikes_file in glob.glob(input+'/inputs/spikes.*.h5'):\n",
+ " print('->', spikes_file)\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 32,
+ "metadata": {
+ "pycharm": {
+ "name": "#%%\n"
+ }
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Executing user provided function...\n",
+ " node_type_id node_id tuning_angle x y
z \\\n",
+ "0 100 0 0.000000 119.485001 384.989275
-56.577812 \n",
+ "1 100 1 3.050847 -73.669430 417.107342
166.282127 \n",
+ "2 100 2 6.101695 54.743024 403.567362
124.182278 \n",
+ "3 100 3 9.152542 14.297729 396.574152
48.710376 \n",
+ "4 100 4 12.203390 -129.647833 347.253059
-58.759062 \n",
+ "... ... ... ... ... ...
... \n",
+ "2410 105 2410 353.513514 12.805991 358.970289
-167.841390 \n",
+ "2411 105 2411 355.135135 -43.409817 316.332169
134.711173 \n",
+ "2412 105 2412 356.756757 80.453753 324.341894
-2.457055 \n",
+ "2413 105 2413 358.378378 -138.086114 364.519788
11.219260 \n",
+ "2414 105 2414 360.000000 -72.441261 319.505839
-50.285325 \n",
+ "\n",
+ " dynamics_params layer model_type cell_line
\\\n",
+ "0 501282204_glif_lif_asc_config.json VisL4 point_neuron i4Sst
\n",
+ "1 501282204_glif_lif_asc_config.json VisL4 point_neuron i4Sst
\n",
+ "2 501282204_glif_lif_asc_config.json VisL4 point_neuron i4Sst
\n",
+ "3 501282204_glif_lif_asc_config.json VisL4 point_neuron i4Sst
\n",
+ "4 501282204_glif_lif_asc_config.json VisL4 point_neuron i4Sst
\n",
+ "... ... ... ... ...
\n",
+ "2410 478958894_glif_lif_asc_config.json VisL4 point_neuron i4Pvalb
\n",
+ "2411 478958894_glif_lif_asc_config.json VisL4 point_neuron i4Pvalb
\n",
+ "2412 478958894_glif_lif_asc_config.json VisL4 point_neuron i4Pvalb
\n",
+ "2413 478958894_glif_lif_asc_config.json VisL4 point_neuron i4Pvalb
\n",
+ "2414 478958894_glif_lif_asc_config.json VisL4 point_neuron i4Pvalb
\n",
+ "\n",
+ " model_template model_name ei \n",
+ "0 nest:glif_lif_asc_psc Sst_501282204 i \n",
+ "1 nest:glif_lif_asc_psc Sst_501282204 i \n",
+ "2 nest:glif_lif_asc_psc Sst_501282204 i \n",
+ "3 nest:glif_lif_asc_psc Sst_501282204 i \n",
+ "4 nest:glif_lif_asc_psc Sst_501282204 i \n",
+ "... ... ... .. \n",
+ "2410 nest:glif_lif_asc_psc Pvalb_478958894 i \n",
+ "2411 nest:glif_lif_asc_psc Pvalb_478958894 i \n",
+ "2412 nest:glif_lif_asc_psc Pvalb_478958894 i \n",
+ "2413 nest:glif_lif_asc_psc Pvalb_478958894 i \n",
+ "2414 nest:glif_lif_asc_psc Pvalb_478958894 i \n",
+ "\n",
+ "[2415 rows x 13 columns]\n",
+ " edge_type_id target_query source_query \\\n",
+ "0 107 cell_line=='e4Rorb' cell_line=='e4Rorb' \n",
+ "1 113 cell_line=='e4Rorb' cell_line=='e4Scnn1a' \n",
+ "2 125 cell_line=='e4Rorb' cell_line=='e4other' \n",
+ "3 108 cell_line=='e4Scnn1a' cell_line=='e4Rorb' \n",
+ "4 114 cell_line=='e4Scnn1a' cell_line=='e4Scnn1a' \n",
+ "5 126 cell_line=='e4Scnn1a' cell_line=='e4other' \n",
+ "6 110 cell_line=='e4other' cell_line=='e4Rorb' \n",
+ "7 116 cell_line=='e4other' cell_line=='e4Scnn1a' \n",
+ "8 128 cell_line=='e4other' cell_line=='e4other' \n",
+ "9 109 cell_line=='i4Htr3a' cell_line=='e4Rorb' \n",
+ "10 115 cell_line=='i4Htr3a' cell_line=='e4Scnn1a' \n",
+ "11 127 cell_line=='i4Htr3a' cell_line=='e4other' \n",
+ "12 111 cell_line=='i4Pvalb' cell_line=='e4Rorb' \n",
+ "13 117 cell_line=='i4Pvalb' cell_line=='e4Scnn1a' \n",
+ "14 129 cell_line=='i4Pvalb' cell_line=='e4other' \n",
+ "15 106 cell_line=='i4Sst' cell_line=='e4Rorb' \n",
+ "16 112 cell_line=='i4Sst' cell_line=='e4Scnn1a' \n",
+ "17 124 cell_line=='i4Sst' cell_line=='e4other' \n",
+ "18 101 cell_line=='e4Rorb' cell_line=='i4Sst' \n",
+ "19 119 cell_line=='e4Rorb' cell_line=='i4Htr3a' \n",
+ "20 131 cell_line=='e4Rorb' cell_line=='i4Pvalb' \n",
+ "21 102 cell_line=='e4Scnn1a' cell_line=='i4Sst' \n",
+ "22 120 cell_line=='e4Scnn1a' cell_line=='i4Htr3a' \n",
+ "23 132 cell_line=='e4Scnn1a' cell_line=='i4Pvalb' \n",
+ "24 104 cell_line=='e4other' cell_line=='i4Sst' \n",
+ "25 122 cell_line=='e4other' cell_line=='i4Htr3a' \n",
+ "26 134 cell_line=='e4other' cell_line=='i4Pvalb' \n",
+ "27 103 cell_line=='i4Htr3a' cell_line=='i4Sst' \n",
+ "28 121 cell_line=='i4Htr3a' cell_line=='i4Htr3a' \n",
+ "29 133 cell_line=='i4Htr3a' cell_line=='i4Pvalb' \n",
+ "30 105 cell_line=='i4Pvalb' cell_line=='i4Sst' \n",
+ "31 123 cell_line=='i4Pvalb' cell_line=='i4Htr3a' \n",
+ "32 135 cell_line=='i4Pvalb' cell_line=='i4Pvalb' \n",
+ "33 100 cell_line=='i4Sst' cell_line=='i4Sst' \n",
+ "34 118 cell_line=='i4Sst' cell_line=='i4Htr3a' \n",
+ "35 130 cell_line=='i4Sst' cell_line=='i4Pvalb' \n",
+ "\n",
+ " dynamics_params syn_weight delay weight_sigma
weight_function \\\n",
+ "0 e2e.json 5.154132 1.3 30.0
DirectionRule_EE \n",
+ "1 e2e.json 5.154132 1.3 30.0
DirectionRule_EE \n",
+ "2 e2e.json 5.154132 1.3 30.0
DirectionRule_EE \n",
+ "3 e2e.json 13.687266 1.3 30.0
DirectionRule_EE \n",
+ "4 e2e.json 13.687266 1.3 30.0
DirectionRule_EE \n",
+ "5 e2e.json 13.687266 1.3 30.0
DirectionRule_EE \n",
+ "6 e2e.json 5.443508 1.3 30.0
DirectionRule_EE \n",
+ "7 e2e.json 5.443508 1.3 30.0
DirectionRule_EE \n",
+ "8 e2e.json 5.443508 1.3 30.0
DirectionRule_EE \n",
+ "9 e2i.json 1.027934 1.5 90.0
DirectionRule_others \n",
+ "10 e2i.json 1.027934 1.5 90.0
DirectionRule_others \n",
+ "11 e2i.json 1.027934 1.5 90.0
DirectionRule_others \n",
+ "12 e2i.json 5.238083 1.2 90.0
DirectionRule_others \n",
+ "13 e2i.json 5.238083 1.2 90.0
DirectionRule_others \n",
+ "14 e2i.json 5.238083 1.2 90.0
DirectionRule_others \n",
+ "15 e2i.json 3.388120 1.5 90.0
DirectionRule_others \n",
+ "16 e2i.json 3.388120 1.5 90.0
DirectionRule_others \n",
+ "17 e2i.json 3.388120 1.5 90.0
DirectionRule_others \n",
+ "18 i2e.json -0.258945 1.5 90.0
DirectionRule_others \n",
+ "19 i2e.json -0.258945 1.5 90.0
DirectionRule_others \n",
+ "20 i2e.json -0.571464 0.9 90.0
DirectionRule_others \n",
+ "21 i2e.json -0.687651 1.5 90.0
DirectionRule_others \n",
+ "22 i2e.json -0.687651 1.5 90.0
DirectionRule_others \n",
+ "23 i2e.json -1.517574 0.9 90.0
DirectionRule_others \n",
+ "24 i2e.json -0.273483 1.5 90.0
DirectionRule_others \n",
+ "25 i2e.json -0.273483 1.5 90.0
DirectionRule_others \n",
+ "26 i2e.json -0.603548 0.9 90.0
DirectionRule_others \n",
+ "27 i2i.json -0.578256 1.5 50.0
DirectionRule_others \n",
+ "28 i2i.json -0.411452 1.5 50.0
DirectionRule_others \n",
+ "29 i2i.json -0.455933 1.2 50.0
DirectionRule_others \n",
+ "30 i2i.json -1.120146 1.5 50.0
DirectionRule_others \n",
+ "31 i2i.json -0.403253 1.5 50.0
DirectionRule_others \n",
+ "32 i2i.json -1.523399 1.6 50.0
DirectionRule_others \n",
+ "33 i2i.json -0.549796 1.5 50.0
DirectionRule_others \n",
+ "34 i2i.json -1.172899 1.5 50.0
DirectionRule_others \n",
+ "35 i2i.json -1.539430 1.2 50.0
DirectionRule_others \n",
+ "\n",
+ " model_template counts \n",
+ "0 static_synapse 26060 \n",
+ "1 static_synapse 29915 \n",
+ "2 static_synapse 32074 \n",
+ "3 static_synapse 29609 \n",
+ "4 static_synapse 34341 \n",
+ "5 static_synapse 36462 \n",
+ "6 static_synapse 32077 \n",
+ "7 static_synapse 36294 \n",
+ "8 static_synapse 38328 \n",
+ "9 static_synapse 5802 \n",
+ "10 static_synapse 6578 \n",
+ "11 static_synapse 7004 \n",
+ "12 static_synapse 13020 \n",
+ "13 static_synapse 15298 \n",
+ "14 static_synapse 16067 \n",
+ "15 static_synapse 11195 \n",
+ "16 static_synapse 12668 \n",
+ "17 static_synapse 13479 \n",
+ "18 static_synapse 5559 \n",
+ "19 static_synapse 2907 \n",
+ "20 static_synapse 14115 \n",
+ "21 static_synapse 6451 \n",
+ "22 static_synapse 3283 \n",
+ "23 static_synapse 16103 \n",
+ "24 static_synapse 6640 \n",
+ "25 static_synapse 3573 \n",
+ "26 static_synapse 16844 \n",
+ "27 static_synapse 1953 \n",
+ "28 static_synapse 32 \n",
+ "29 static_synapse 952 \n",
+ "30 static_synapse 6944 \n",
+ "31 static_synapse 81 \n",
+ "32 static_synapse 6725 \n",
+ "33 static_synapse 414 \n",
+ "34 static_synapse 1547 \n",
+ "35 static_synapse 224 \n",
+ "Valid SONATA inputs:\n",
+ "-> ./inputs/inputs/spikes.gratings.45deg_2Hz.h5\n",
+ "-> ./inputs/inputs/spikes.gratings.45deg_4Hz.h5\n",
+ "-> ./inputs/inputs/spikes.gratings.90deg_4Hz.h5\n",
+ "-> ./inputs/inputs/spikes.gratings.0deg_2Hz.h5\n",
+ "-> ./inputs/inputs/spikes.gratings.90deg_2Hz.h5\n",
+ "-> ./inputs/inputs/spikes.gratings.0deg_4Hz.h5\n",
+ "Function execution succeeded...\n",
+ "select compute resource\n"
+ ]
+ },
+ {
+ "data": {
+ "application/vnd.jupyter.widget-view+json": {
+ "model_id": "d89d813f6a9540a6afbe541b019fa676",
+ "version_major": 2,
+ "version_minor": 0
+ },
+ "text/plain": [
+ "Dropdown(description='Select Compute Resources', options=('Bridges2',
'Expanse'), value='Bridges2')"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Select Compute Resources Queue Expanse\n"
+ ]
+ },
+ {
+ "data": {
+ "application/vnd.jupyter.widget-view+json": {
+ "model_id": "29b514f4e8104469a9fedd706c0859b6",
+ "version_major": 2,
+ "version_minor": 0
+ },
+ "text/plain": [
+ "Dropdown(description='Select Compute Resources Queue',
options=('compute', 'gpu', 'gpu-debug', 'gpu-shared', '…"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "selected compute resource queue shared\n",
+ "Experiment name: allen_v1_ybxt\n",
+ "local_data_directory: ./inputs\n",
+ "output_data_directory: ./output\n",
+ "scheduled compute resource: Expanse\n",
+ "scheduled queue: shared\n",
+ "Creating experiment ....\n"
+ ]
+ },
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:airavata_sdk.clients:creating experiment allen_v1_ybxt\n",
+ "INFO:airavata_sdk.clients:connnecting to file upload endpoint
gf4.ucs.indiana.edu : 9003\n",
+ "INFO:airavata_sdk.clients:Input files uploaded to
[email protected]/Default_Project/allen_v1_ybxt_2023_06_21_12_20_03/\n",
+ "INFO:airavata_sdk.clients:configuring inputs ......\n",
+ "INFO:airavata_sdk.clients:experiment launched id:
allen_v1_ybxt_6294f141-57a5-471f-a77a-5fd95a36a730\n",
+ "INFO:airavata_sdk.clients:For more information visit
https://neuroscience-cybershuttle.org/workspace/experiments/allen_v1_ybxt_6294f141-57a5-471f-a77a-5fd95a36a730\n";,
+ "INFO:airavata_sdk.clients:Initial state EXECUTING\n",
+ "INFO:airavata_sdk.clients:State EXECUTING\n",
+ "INFO:airavata_sdk.clients:State JOB_ACTIVE\n",
+ "INFO:airavata_sdk.clients:State JOB_ACTIVE\n",
+ "INFO:airavata_sdk.clients:State JOB_ACTIVE\n",
+ "INFO:airavata_sdk.clients:State COMPLETED\n",
+ "INFO:airavata_sdk.clients:Completed\n"
+ ]
+ }
+ ],
+ "source": [
+ "load_v1_network_validate_run(input='./inputs')"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 33,
+ "metadata": {
+ "pycharm": {
+ "name": "#%%\n"
+ }
+ },
+ "outputs": [],
+ "source": [
+ "def plot_tuning_angle_fr(input_path,spikes_path, fr_window=(500.0,
3000.0), avg_window=15):\n",
+ " dur_secs = (fr_window[1] - fr_window[0]) / 1000.0\n",
+ "\n",
+ " net = sonata.File(\n",
+ " data_files=input_path+'/network/l4_nodes.h5',\n",
+ " data_type_files=input_path+'/network/l4_node_types.csv'\n",
+ " )\n",
+ " nodes_df = net.nodes['l4'].to_dataframe(index_by_id=False)\n",
+ " nodes_df = nodes_df[['node_id', 'node_type_id', 'model_name',
'tuning_angle', 'model_type', 'layer', 'ei']]\n",
+ " \n",
+ " spikes = SpikeTrains.load(spikes_path)\n",
+ " spikes_df = spikes.to_dataframe(population='l4')\n",
+ "\n",
+ " fr_df =
spikes_df['node_ids'][spikes_df.timestamps.between(fr_window[0],fr_window[1])]
\\\n",
+ " .value_counts() \\\n",
+ " .rename_axis('node_id') \\\n",
+ " .reset_index(name='spike_counts')\n",
+ " \n",
+ " fr_df['firing_rates'] = fr_df['spike_counts'].values / dur_secs\n",
+ " fr_df['node_id'] = fr_df['node_id'].astype(np.uint64)\n",
+ " fr_df = fr_df.merge(nodes_df, how='right', on='node_id') \n",
+ " fr_df['spike_counts'] = fr_df['spike_counts'].fillna(0.0) \n",
+ " fr_df['firing_rates'] = fr_df['firing_rates'].fillna(0.0)\n",
+ " \n",
+ " def create_subplot(ax, grp_df, label):\n",
+ " ax.scatter(grp_df['tuning_angle'], grp_df['firing_rates'],
s=2)\n",
+ " \n",
+ " fr_avgs = pd.DataFrame({\n",
+ " 'tuning_rounded': np.floor(grp_df['tuning_angle']),\n",
+ " 'firing_rates': grp_df['firing_rates']\n",
+ " }).groupby('tuning_rounded').agg(np.mean)\n",
+ " \n",
+ " if avg_window and len(fr_avgs['firing_rates']) > avg_window:\n",
+ " tuning_even_spaced = pd.DataFrame({\n",
+ " 'tuning_rounded':np.arange(360)\n",
+ " })\n",
+ " fr_avgs=fr_avgs.merge(tuning_even_spaced, how='right',
on='tuning_rounded')\n",
+ " fr_avgs['firing_rates_avg'] =
fr_avgs['firing_rates'].rolling(avg_window, min_periods=1).mean()\n",
+ "\n",
+ " ax.plot(fr_avgs['firing_rates_avg'], c='r', linewidth=3,
label=label)\n",
+ " ax.legend(fontsize=10, loc='upper right')\n",
+ " ax.set_xlabel('Tuning Angle (deg)')\n",
+ " ax.set_ylabel('Firing Rate (Hz)')\n",
+ "\n",
+ " # plot excitatory cells by layer\n",
+ " nrows = 2\n",
+ " fig, axes = plt.subplots(nrows, 1, figsize=(10, 5))\n",
+ " for r, layer in enumerate(['VisL4']):\n",
+ " exc_df = fr_df[(fr_df['ei'] == 'e') & (fr_df['layer'] ==
layer)]\n",
+ " create_subplot(axes[r], exc_df, 'exc; {}'.format(layer))\n",
+ "\n",
+ " # plot inhibitory cells\n",
+ " inh_df = fr_df[fr_df['ei'] == 'i']\n",
+ " create_subplot(axes[r+1], inh_df, 'inh; ALL')\n",
+ "\n",
+ " for r in range(nrows):\n",
+ " if r != (nrows - 1):\n",
+ " axes[r].set_xticklabels([])\n",
+ " \n",
+ " plt.show()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 34,
+ "metadata": {
+ "pycharm": {
+ "name": "#%%\n"
+ }
+ },
+ "outputs": [
+ {
+ "data": {
+ "image/png":
"iVBORw0KGgoAAAANSUhEUgAAA1cAAAHACAYAAABOPpIiAAAAOXRFWHRTb2Z0d2FyZQBNYXRwbG90bGliIHZlcnNpb24zLjcuMSwgaHR0cHM6Ly9tYXRwbG90bGliLm9yZy/bCgiHAAAACXBIWXMAAA9hAAAPYQGoP6dpAADth0lEQVR4nOydd3gU1frHv1vSk00IkEoSQi+hNxGkK4oNVOwK2BuiiFexAirYUK9XEPVKsf1UEJErYKPXSK8SSgKhpEFIr7s7vz+W2czOTt2Snd28n+fJA7t75pz3vKfNmZn3OzqGYRgQBEEQBEEQBEEQbqH3tQEEQRAEQRAEQRCBAG2uCIIgCIIgCIIgPABtrgiCIAiCIAiCIDwAba4IgiAIgiAIgiA8AG2uCIIgCIIgCIIgPABtrgiCIAiCIAiCIDwAba4IgiAIgiAIgiA8AG2uCIIgCIIgCIIgPIDR1wZoEavV
[...]
+ "text/plain": [
+ "<Figure size 1000x500 with 2 Axes>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+
"plot_tuning_angle_fr('./inputs','./output/allen_v1_ybxt_2023_06_21_12_20_03/ARCHIVE/output_feedforward/spikes.h5')"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {
+ "pycharm": {
+ "name": "#%%\n"
+ }
+ },
+ "outputs": [],
+ "source": []
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "venv",
+ "language": "python",
+ "name": "venv"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.8.3"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}
\ No newline at end of file
diff --git a/resources/BMTK_v1_demo/Computing_Platform-analyis.drawio.png
b/resources/BMTK_v1_demo/Computing_Platform-analyis.drawio.png
new file mode 100644
index 0000000..f138ae1
Binary files /dev/null and
b/resources/BMTK_v1_demo/Computing_Platform-analyis.drawio.png differ
diff --git a/resources/BMTK_v1_demo/model_simulation.png
b/resources/BMTK_v1_demo/model_simulation.png
new file mode 100644
index 0000000..7cfaba2
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diff --git a/resources/BMTK_v1_demo/neuro-apis.drawio.png
b/resources/BMTK_v1_demo/neuro-apis.drawio.png
new file mode 100644
index 0000000..90b0dfb
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diff --git a/resources/BMTK_v1_demo/requirements.txt
b/resources/BMTK_v1_demo/requirements.txt
new file mode 100644
index 0000000..5c537c2
--- /dev/null
+++ b/resources/BMTK_v1_demo/requirements.txt
@@ -0,0 +1,49 @@
+airavata-python-sdk==1.1.6
+attrs==23.1.0
+bcrypt==4.0.1
+bmtk==1.0.7
+certifi==2023.5.7
+cffi==1.15.1
+charset-normalizer==3.1.0
+contourpy==1.1.0
+cryptography==41.0.1
+cycler==0.11.0
+fonttools==4.40.0
+h5py==3.8.0
+idna==3.4
+imageio==2.31.1
+jsonschema==4.17.3
+kiwisolver==1.4.4
+lazy_loader==0.2
+matplotlib==3.7.1
+mpmath==1.3.0
+nest==0.4.1
+networkx==3.1
+numpy==1.24.3
+oauthlib==3.2.2
+packaging==23.1
+pandas==2.0.2
+paramiko==3.2.0
+Pillow==9.5.0
+pycparser==2.21
+PyJWT==2.7.0
+PyNaCl==1.5.0
+pyparsing==3.0.9
+pyrsistent==0.19.3
+python-dateutil==2.8.2
+pytz==2023.3
+PyWavelets==1.4.1
+requests==2.31.0
+requests-oauthlib==1.3.1
+scikit-image==0.21.0
+scipy==1.10.1
+scp==0.14.5
+six==1.16.0
+sympy==1.12
+thrift==0.16.0
+thrift-connector==0.24
+tifffile==2023.4.12
+tqdm==4.65.0
+tzdata==2023.3
+urllib3==2.0.3
+
diff --git a/resources/BMTK_v1_demo/settings.ini
b/resources/BMTK_v1_demo/settings.ini
new file mode 100644
index 0000000..9df5953
--- /dev/null
+++ b/resources/BMTK_v1_demo/settings.ini
@@ -0,0 +1,44 @@
+[APIServer]
+API_HOST = 156.56.104.12
+API_PORT = 9930
+API_SECURE = True
+[Gateway]
+GATEWAY_ID = neuroscience-cybershuttle
+GATEWAY_DATA_STORE_RESOURCE_ID =
"gf4.ucs.indiana.edu_61552681-96f0-462a-a36c-a62a010bffc6",
+GATEWAY_DATA_STORE_DIR =
/var/www/portals/gateway-user-data/neuroscience-cybershuttle/
+GATEWAY_DATA_STORE_HOSTNAME = gf4.ucs.indiana.edu
+FILE_UPLOAD_TEMP_DIR =
/var/www/portals/gateway-user-data/neuroscience-cybershuttle/tmp/
+[ProfileServer]
+PROFILE_SERVICE_HOST = 156.56.104.12
+PROFILE_SERVICE_PORT = 8962
+PROFILE_SERVICE_SECURE = False
+[SharingServer]
+SHARING_API_HOST = 156.56.104.12
+SHARING_API_PORT = 7878
+SHARING_API_SECURE = False
+[CredentialStoreServer]
+CREDENTIAL_STORE_API_HOST = 156.56.104.12
+CREDENTIAL_STORE_API_PORT = 8960
+CREDENTIAL_STORE_API_SECURE = True
+[Thrift]
+THRIFT_CLIENT_POOL_KEEPALIVE = 5
+[KeycloakServer]
+CLIENT_ID = CHANGE_ME
+CLIENT_SECRET = CHANGE_ME
+TOKEN_URL =
https://iam.scigap.org/auth/realms/neuroscience-cybershuttle/protocol/openid-connect/token
+USER_INFO_URL =
https://iam.scigap.org/auth/realms/neuroscience-cybershuttle/protocol/openid-connect/userinfo
+VERIFY_SSL = False
+CERTIFICATE_FILE_PATH = PATH_TO_CERTIFICATE
+LOGIN_DESKTOP_URI =
https://neuroscience.cybershuttle.org/auth/login-desktop/?show-code=true
+[ExperimentConf]
+APPLICATION_NAME = BMTK_V1_L4
+PROJECT_NAME = Default Project
+COMPUTE_HOST_DOMAIN = Bridges2,Expanse
+GROUP_RESOURCE_PROFILE_NAME = Allen GRP
+STORAGE_RESOURCE_HOST = gf4.ucs.indiana.edu
+SFTP_PORT = 9003
+NODE_COUNT = 1
+TOTAL_CPU_COUNT = 1
+WALL_TIME_LIMIT = 30
+QUEUE_NAME = shared
+MONITOR_STATUS = True
diff --git a/resources/BMTK_v1_demo/workflow.drawio.png
b/resources/BMTK_v1_demo/workflow.drawio.png
new file mode 100644
index 0000000..2e1a7ea
Binary files /dev/null and b/resources/BMTK_v1_demo/workflow.drawio.png differ
diff --git a/setup.cfg b/setup.cfg
new file mode 100644
index 0000000..e69de29
diff --git a/setup.py b/setup.py
new file mode 100644
index 0000000..f0909d6
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,29 @@
+import os
+
+from setuptools import setup, find_packages
+
+
+def read(fname):
+ with open(os.path.join(os.path.dirname(__file__), fname)) as f:
+ return f.read()
+
+from pathlib import Path
+
+this_directory = Path(__file__).parent
+long_description = (this_directory / "README.md").read_text()
+
+setup(
+ name='cybershuttle-neuro-lib',
+ long_description_content_type="text/markdown",
+ version='0.0.1',
+ packages=find_packages(),
+ package_data={'': ['*.pem','*.md']},
+ include_package_data=True,
+ url='https://neuroscience.cybershuttle.org/',
+ license='Apache License 2.0',
+ author='Cybershuttle Developers',
+ author_email='[email protected]',
+ install_requires=['airavata-python-sdk==1.1.6', 'ipywidgets'],
+ description='Cybershuttle neuroscience libraries',
+ long_description=long_description,
+)
\ No newline at end of file
