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Posted to commits@airavata.apache.org by di...@apache.org on 2026/04/10 13:27:55 UTC
(airavata-cerebrum) branch main updated (8d6b77e -> 04748ef)
This is an automated email from the ASF dual-hosted git repository.
dimuthuupe pushed a change to branch main
in repository https://gitbox.apache.org/repos/asf/airavata-cerebrum.git
from 8d6b77e Fix build error
add ec1bde5 Fix build error
add 1234110 Merge branch 'apache:main' into main
add 9b00d80 added install instrucitons
add ea8f036 fix issues in pyproject
add d98803d update pyproject
add c3d38e8 update readme
add 07474c3 fix typos in INSTALL.md
add 2aa39ba update README
add 2beb433 Refactor and Update Tree Node dependencies
add 27684a7 added views for maps
add 9de2da6 Fix bugs in Property Map Layout
add 870e632 completed the network genration for the sleep whole brain network.
add f21a341 added image in WGN-Sleep
add 6798e8c Added an initial version of V1 model
add e2df27f Refactor code and add detailed type annotations
add d8bfd4f refactor conversion scripts
add aa36af9 Initial version of marimo-based tree
add 4e31976 Refactor tree view
add 3259ef6 Bug Fixes to make it work with a simpler architechture
add 5dba165 A version for marimo
add 630ab8d Update Marimo outputs
add 6fd3371 added tree view is marimo
add aa6c347 Fixed bugs in marimo tree view
add b797e46 Use integrated view for data to model
add 2ad219b Integrated recipe explorer
add 4184fbe Save to database
add 49c2714 Initial version of v1
add 59c9d16 Added recipe files for V1 model
add 9705bdb Use of AwiTree for ipython notebook
add 55f5215 Fix Bugs in Tree View
add 8777d67 Network Build Directory
add 187365a added Props from the original V1 model
add 431d17b Fix the connection models json
add 6e9c040 add background spike files
add 9c8f579 Move nodes and edges to the network directory
add 043cd1e update source database
add 2b05a10 Added marimo notebook for Mouse V1
add fbd7d88 update marimo
add e03ff95 Added pyarrow to environment
add 7200cf7 revise marimo output
add 5403341 Update V1 model
add ea4857f Use of pydantic models instead of traitlets
add ca2323f Added Init and Exec Params
add b596671 Fix bugs in models for query and transform operations
add d1e7525 Added ME Features; Update tree
add 35b77c6 Update V1L4
add f8d056e Fix syntax errors; Fix db writer for mef_features dataset
add db963d0 update mouse properties
add f66e7c8 Added Types for the parameters
add 52d2f12 Fixed errors in IterAttrFilter parameters
add 2b3f7a6 Added files/data/script for V1 model
add 4ec2ee8 Added recipe and mapping for all layers of V1
add 55951d4 allow list to have None as one of the inputs
add 6a75351 Working Notebooks
add e2382b7 Update V1 notebook
add 60f32f0 add synapse models for v1
add 3abeae3 added bkg inputs
add 1d41538 Added mouse V1
add e03bf02 added nest simulator
add 4d33b64 removed igraph
add 89635ef update pyproject and environment files
add 5500101 update README to add instructions
add 011f523 Added nodejs dependency
add d936ec9 Added a version of cybershuttle
add d7c9a03 fix tree error
add 616b50a fixed issues in cybershuttle.yml, add %cd to subdirectory as first command
add 89cc6eb Merge pull request #1 from cyber-shuttle/main
add 82360f9 update cybershuttle to remove nest
add c7dc33c Update cybershuttle yml
add 4f3d4c5 Fix errors in CS Notebook
add f195a17 Added update
add a7a8867 Added None class as a placeholder
add cfb850c add option for None in view
add 9120751 added template
add 2f09f47 Refactor recipe code to separate the constants
add 284a821 update cybershuttle.yml file and data paths
add 3ca992c update cybershuttle yml
add c47db69 added an example for running in NEST
add 9f994b8 added notebook that is accidentally removed
add 9c18a42 Fixed the bkg properties
add f6fa755 Merge branch 'srirampc:main' into main
add 3ae0031 updated yml and notebook
add ae9ee84 Merge pull request #2 from cyber-shuttle/main
add 085324b Added LGN node
add 9ca9f27 Fix issues with adding lgn; Update synapse models
add 5aacae5 Re-organize data
add 7657aa8 Re-organize data
add ab88b09 Re-organize v1l4
add bff8aa5 Update for glif_psc
add 799454a remove tau_syn
add 44f0b54 Added Simulation Notebook
add 79343d5 Add plot for LGN
add 070c8d1 added an MPI version
add 3216ebd Added a parallel version
add 713dc3b Added Box plots
add 2da137d Cleanup notebooks
add a4104bc added README
add 51a32af Revise document title to 'Airavata Cerebrum'
add 2022b90 Clarify script descriptions in README.md
add 1a7c61a edit readme
add ec09c8d added an initial version of edge editor
add 09c1cae update demo file with static images
add 86b623b update notebook to make it visible in github
add 44d3288 update V1 notebook to make it visible
add 5a4e6bf update notebooks to make L4 notebook visible
add bb60ab4 Re-organize notebooks
add 03faf32 update V1 Notebook
add 5ac092b Update command-line scripts section in README
add 296b3e0 move simulate location
new 04748ef Merge pull request #26 from srirampc/main
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "add" were already present in the repository and have only
been added to this reference.
Summary of changes:
.gitignore | 1 +
INSTALL.md | 61 +
README.md | 81 +-
airavata_cerebrum/__init__.py | 14 +
airavata_cerebrum/base.py | 173 +-
airavata_cerebrum/const.py | 44 +
airavata_cerebrum/dataset/__init__.py | 48 +
airavata_cerebrum/dataset/abc_mouse.py | 440 +-
airavata_cerebrum/dataset/abm_celltypes.py | 385 +-
airavata_cerebrum/dataset/ai_synphys.py | 242 +-
airavata_cerebrum/dataset/me_features.py | 112 +
airavata_cerebrum/model/builder.py | 18 +-
airavata_cerebrum/model/desc.py | 132 -
airavata_cerebrum/model/structure.py | 737 +-
airavata_cerebrum/operations/__init__.py | 55 +
airavata_cerebrum/operations/abc_mouse.py | 135 +-
airavata_cerebrum/operations/abm_celltypes.py | 278 +-
airavata_cerebrum/operations/ai_synphys.py | 72 +-
airavata_cerebrum/operations/dict_filter.py | 162 +-
airavata_cerebrum/operations/json_filter.py | 180 +-
airavata_cerebrum/operations/me_features.py | 83 +
airavata_cerebrum/operations/netops.py | 17 +-
airavata_cerebrum/operations/xform.py | 139 +-
airavata_cerebrum/recipe.py | 309 +
airavata_cerebrum/register.py | 178 +-
airavata_cerebrum/{ => sonata}/__init__.py | 0
airavata_cerebrum/sonata/edge.py | 759 +
airavata_cerebrum/util/__init__.py | 48 +-
airavata_cerebrum/util/desc_config.py | 158 -
airavata_cerebrum/util/io.py | 46 +-
airavata_cerebrum/util/profile.py | 96 +
airavata_cerebrum/view/__init__.py | 330 +
airavata_cerebrum/view/motree.py | 718 +
airavata_cerebrum/view/tree.py | 952 +-
airavata_cerebrum/workflow.py | 129 +-
env_full.yml | 68 -
environment.yml | 61 +-
pyproject.toml | 47 +-
pyrightconfig.json | 12 +
resources/BMTK_v1_demo/BMTK_V1.ipynb | 561 -
.../Computing_Platform-analyis.drawio.png | Bin 398056 -> 0 bytes
resources/BMTK_v1_demo/model_simulation.png | Bin 63138 -> 0 bytes
resources/BMTK_v1_demo/neuro-apis.drawio.png | Bin 61769 -> 0 bytes
resources/BMTK_v1_demo/requirements.txt | 49 -
resources/BMTK_v1_demo/settings.ini | 44 -
resources/BMTK_v1_demo/workflow.drawio.png | Bin 32846 -> 0 bytes
resources/DOC.md | 360 +
resources/README.md | 29 +
resources/notebooks/SonataEditorDemo.ipynb | 365 +
resources/notebooks/V1-BMTK-Simulate.ipynb | 541 +
resources/notebooks/V1-CS-Notebook.ipynb | 894 +
resources/notebooks/V1-Notebook.ipynb | 141489 ++++++++++
resources/notebooks/V1L4-Nest-Run.ipynb | 2 +-
resources/notebooks/V1L4-Notebook.ipynb | 1073 +-
resources/notebooks/WGN-Sleep.ipynb | 3552 +
.../notebooks/{ => archive}/V1L4-Scratch.ipynb | 0
.../notebooks/{ => archive}/atlas2cellprop.ipynb | 0
.../notebooks/{ => archive}/bmtk_pointnet_run.py | 0
.../notebooks/{ => archive}/merfish2model.ipynb | 2 +-
resources/notebooks/archive/v1l4_view.py | 22 +
resources/notebooks/build_setup/v1030k.yaml | 3 +
resources/notebooks/build_setup/v1060k.yaml | 3 +
resources/notebooks/build_setup/v1120k.yaml | 3 +
resources/notebooks/build_setup/v1test.yml | 3 +
resources/notebooks/build_setup/v1test2.yml | 3 +
resources/notebooks/build_setup/v1test2x.yml | 3 +
resources/notebooks/build_setup/v1test3.yml | 3 +
resources/notebooks/build_setup/v1test4.yml | 3 +
resources/notebooks/cybershuttle.yml | 65 +
resources/notebooks/img/Class-types.png | Bin 0 -> 43800 bytes
resources/notebooks/img/Data2Model.png | Bin 0 -> 152153 bytes
resources/notebooks/img/Inhib-Fraction.png | Bin 0 -> 3343 bytes
resources/notebooks/img/L4CustomMod.png | Bin 0 -> 38199 bytes
resources/notebooks/img/L4SourceData.png | Bin 0 -> 43004 bytes
resources/notebooks/img/L4SrcConnections.png | Bin 0 -> 15513 bytes
resources/notebooks/img/L4SrcLocations.png | Bin 0 -> 10808 bytes
resources/notebooks/img/Ratios.png | Bin 0 -> 17858 bytes
resources/notebooks/img/Recipe.png | Bin 0 -> 248800 bytes
resources/notebooks/img/SourceData.png | Bin 0 -> 264257 bytes
resources/notebooks/img/Workflow.png | Bin 0 -> 599284 bytes
resources/notebooks/img/structure.png | Bin 0 -> 95073 bytes
resources/notebooks/marimo_sonata_editor.py | 333 +
resources/notebooks/marimo_v1.py | 406 +
resources/notebooks/marimo_v1l4.py | 404 +
resources/notebooks/marimo_v1l4db.py | 91 +
.../notebooks/model_bkg/bkg_spikes_1kHz_10s.h5 | Bin 0 -> 1382911 bytes
.../notebooks/model_bkg/bkg_spikes_1kHz_3s.h5 | Bin 0 -> 444525 bytes
.../notebooks/model_bkg/bkg_spikes_250Hz_10s.h5 | Bin 0 -> 470799 bytes
.../{v1l4/bkg => model_bkg}/bkg_spikes_250Hz_3s.h5 | Bin
.../notebooks/model_bkg/bkg_spikes_full_10s.h5 | Bin 0 -> 708126 bytes
.../notebooks/model_bkg/bkg_spikes_full_3s.h5 | Bin 0 -> 346833 bytes
.../bkg_spikes_n1_fr1000_dt0.25_2.trial_0.h5 | Bin 0 -> 58792 bytes
.../notebooks/model_bkg/bkg_spikes_regular_1s.h5 | Bin 0 -> 4752 bytes
resources/notebooks/model_builds/v1030/config.json | 71 +
.../model_builds/v1030/full_path_config.json | 71 +
.../{ => model_builds}/v1l4/config/config_bkg.json | 0
.../{ => model_builds}/v1l4/config_nest.json | 8 +-
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resources/notebooks/model_builds/v1r1/config.json | 71 +
.../{v1l4 => model_builds/v1r1}/config_nest.json | 20 +-
.../v1r1/v1/network/bkg_node_types.csv | 2 +
.../v1r1/v1}/network/bkg_nodes.h5 | Bin
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delete mode 100644 airavata_cerebrum/model/desc.py
create mode 100644 airavata_cerebrum/operations/me_features.py
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(airavata-cerebrum) 01/01: Merge pull request #26 from srirampc/main
Posted by di...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
dimuthuupe pushed a commit to branch main
in repository https://gitbox.apache.org/repos/asf/airavata-cerebrum.git
commit 04748ef559d000b8d028c67161fcc82fd598bd3b
Merge: 8d6b77e 296b3e0
Author: Dimuthu Wannipurage <di...@gmail.com>
AuthorDate: Fri Apr 10 09:27:23 2026 -0400
Merge pull request #26 from srirampc/main
Fix installation Issues
.gitignore | 1 +
INSTALL.md | 61 +
README.md | 81 +-
airavata_cerebrum/__init__.py | 14 +
airavata_cerebrum/base.py | 173 +-
airavata_cerebrum/const.py | 44 +
airavata_cerebrum/dataset/__init__.py | 48 +
airavata_cerebrum/dataset/abc_mouse.py | 440 +-
airavata_cerebrum/dataset/abm_celltypes.py | 385 +-
airavata_cerebrum/dataset/ai_synphys.py | 242 +-
airavata_cerebrum/dataset/me_features.py | 112 +
airavata_cerebrum/model/builder.py | 18 +-
airavata_cerebrum/model/desc.py | 132 -
airavata_cerebrum/model/structure.py | 737 +-
airavata_cerebrum/operations/__init__.py | 55 +
airavata_cerebrum/operations/abc_mouse.py | 135 +-
airavata_cerebrum/operations/abm_celltypes.py | 278 +-
airavata_cerebrum/operations/ai_synphys.py | 72 +-
airavata_cerebrum/operations/dict_filter.py | 162 +-
airavata_cerebrum/operations/json_filter.py | 180 +-
airavata_cerebrum/operations/me_features.py | 83 +
airavata_cerebrum/operations/netops.py | 17 +-
airavata_cerebrum/operations/xform.py | 139 +-
airavata_cerebrum/recipe.py | 309 +
airavata_cerebrum/register.py | 178 +-
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airavata_cerebrum/view/motree.py | 718 +
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environment.yml | 61 +-
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resources/notebooks/tools/extract_images.py | 65 +
resources/notebooks/v1_plots.py | 34 +
resources/notebooks/v1l4.py | 66 -
.../notebooks/v1l4/network/bkg_node_types.csv | 2 -
.../notebooks/v1l4/network/bkg_v1l4_edge_types.csv | 50 -
resources/notebooks/v1l4/network/bkg_v1l4_edges.h5 | Bin 228506 -> 0 bytes
.../notebooks/v1l4/network/v1l4_node_types.csv | 62 -
resources/notebooks/v1l4/network/v1l4_nodes.h5 | Bin 216336 -> 0 bytes
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.../notebooks/v1l4/network/v1l4_v1l4_edges.h5 | Bin 1883102 -> 0 bytes
resources/notebooks/v1l4_build_cli.py | 69 +
resources/notebooks/v1l4_view.py | 27 -
resources/notebooks/wbn_sleep/.gitignore | 5 +
resources/notebooks/wbn_sleep/data_config.json | 11 +
resources/notebooks/wbn_sleep/model.py | 57 +
resources/notebooks/wbn_sleep/network_config.json | 1896 +
.../notebooks/wbn_sleep/recipe/custom_mod.json | 2715 +
.../notebooks/wbn_sleep/recipe/mriNetworkNew.json | 1793 +
resources/notebooks/wbn_sleep/recipe/recipe.json | 83 +
.../recipe/recipe_template.json} | 0
resources/notebooks/wbn_sleep/recipe/test.json | 2329 +
resources/scripts/v1_bkg_spike_generation.py | 121 +
resources/scripts/v1l4_nest_notebook.py | 38 +-
1661 files changed, 660337 insertions(+), 105528 deletions(-)