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Posted to commits@airavata.apache.org by sm...@apache.org on 2026/06/01 15:37:34 UTC
(airavata-cerebrum) 01/01: Merge pull request #28 from srirampc/main
This is an automated email from the ASF dual-hosted git repository.
smarru pushed a commit to branch main
in repository https://gitbox.apache.org/repos/asf/airavata-cerebrum.git
commit af001750dae99e19113fcd9da54c76ba8c374c13
Merge: 04748ef ef4eab7
Author: Suresh Marru <sm...@apache.org>
AuthorDate: Mon Jun 1 11:37:20 2026 -0400
Merge pull request #28 from srirampc/main
Updates for packaging and examples
.flake8 | 11 +-
.gitignore | 9 +-
.gitmodules | 9 +
INSTALL.md | 61 -
README.md | 115 +-
Roadmap.md | 17 -
TODO.md | 19 +
.../cybershuttle/annotations/__init__.py | 0
.../cybershuttle/annotations/decorator.py | 138 -
airavata_cerebrum/dataset/__init__.py | 3 +-
airavata_cerebrum/dataset/abc_mouse.py | 77 +-
airavata_cerebrum/dataset/abm_celltypes.py | 42 +-
airavata_cerebrum/dataset/ai_synphys.py | 36 +-
airavata_cerebrum/dataset/bicn.py | 2 +-
airavata_cerebrum/dataset/me_features.py | 14 +-
airavata_cerebrum/model/builder.py | 52 +-
airavata_cerebrum/util/profile.py | 54 +-
environment.yml | 40 +-
examples/README.md | 113 +
{resources/notebooks => examples}/cybershuttle.yml | 0
examples/editor/README.md | 19 +
.../editor}/SonataEditorDemo.ipynb | 0
.../editor}/marimo_sonata_editor.py | 0
examples/env.sh | 31 +
examples/environment.yml | 25 +
.../notebooks => examples/sleep}/WGN-Sleep.ipynb | 0
.../sleep}/wbn_sleep/.gitignore | 0
.../sleep}/wbn_sleep/data_config.json | 0
.../sleep}/wbn_sleep/model.py | 0
.../sleep}/wbn_sleep/network_config.json | 0
.../sleep}/wbn_sleep/recipe/custom_mod.json | 0
.../sleep}/wbn_sleep/recipe/mriNetworkNew.json | 0
.../sleep}/wbn_sleep/recipe/recipe.json | 0
.../sleep}/wbn_sleep/recipe/recipe_template.json | 0
.../sleep}/wbn_sleep/recipe/test.json | 0
resources/DOC.md => examples/v1/README.md | 75 +-
.../v1}/V1-BMTK-Simulate.ipynb | 0
.../notebooks => examples/v1}/V1-CS-Notebook.ipynb | 0
.../notebooks => examples/v1}/V1-Notebook.ipynb | 6396 +-------------------
.../notebooks => examples/v1}/V1L4-Nest-Run.ipynb | 0
.../notebooks => examples/v1}/V1L4-Notebook.ipynb | 2 +-
.../v1}/archive/V1L4-Scratch.ipynb | 0
.../v1}/archive/atlas2cellprop.ipynb | 0
.../v1}/archive/bmtk_pointnet_run.py | 0
.../v1}/archive/merfish2model.ipynb | 0
.../notebooks => examples/v1}/archive/v1l4_view.py | 0
.../v1/bkg}/bkg_spikes_1kHz_10s.h5 | Bin
.../v1/bkg}/bkg_spikes_1kHz_3s.h5 | Bin
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.../v1/bkg}/bkg_spikes_full_10s.h5 | Bin
.../v1/bkg}/bkg_spikes_full_3s.h5 | Bin
.../bkg}/bkg_spikes_n1_fr1000_dt0.25_2.trial_0.h5 | Bin
.../v1/bkg}/bkg_spikes_regular_1s.h5 | Bin
.../v1/builds}/v1030/config.json | 10 +-
examples/v1/builds/v1030/full_path_config.json | 71 +
.../v1/builds/v1030/network/bkg_node_types.csv | 2 +
.../v1/builds/v1030}/network/bkg_nodes.h5 | Bin
.../v1/builds/v1030/network/bkg_v1_edge_types.csv | 170 +
examples/v1/builds/v1030/network/bkg_v1_edges.h5 | Bin 0 -> 979713 bytes
.../v1/builds/v1030/network/lgn_node_types.csv | 15 +
examples/v1/builds/v1030/network/lgn_nodes.h5 | Bin 0 -> 1202940 bytes
.../v1/builds/v1030/network/lgn_v1_edge_types.csv | 185 +
examples/v1/builds/v1030/network/lgn_v1_edges.h5 | Bin 0 -> 77939369 bytes
examples/v1/builds/v1030/network/v1_node_types.csv | 192 +
examples/v1/builds/v1030/network/v1_nodes.h5 | Bin 0 -> 842904 bytes
.../v1/builds/v1030/network/v1_v1_edge_types.csv | 2843 +++++++++
.../v1/builds/v1030}/network/v1_v1_edges.h5 | Bin 19081894 -> 19057795 bytes
.../v1/builds}/v1l4/config/config_bkg.json | 0
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.../v1/builds}/v1l4/network/bkg_nodes.h5 | Bin
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.../v1/builds}/v1r1/config.json | 6 +-
.../v1/builds}/v1r1/config_nest.json | 4 +-
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