This is an automated email from the ASF dual-hosted git repository.
smarru pushed a change to branch main
in repository https://gitbox.apache.org/repos/asf/airavata-cerebrum.git
from c0adfb4 Merge pull request #23 from srirampc/main
add 57e7331 Added AISynPhys and other info
add f116807 update project dependencies
add 46b4616 Merge branch 'apache:main' into main
add 1a9e3e6 Refactor code and re-organize for general databases
add 8d2e931 refactor directory paths
add f88005e fix bugs with newer format
add ff01f06 fix bugs in V1 L4
add fe45c0b add views
add 1ba3444 update notebook for V1L4
add a04e1b3 organized the classes
add bd7358d update type traits; added logging
add c6d2faa added tree views based on trait types
add 6c645f2 move V1L4 notebook to notebooks folder
add af0a016 update notebooks
add ad74b1d added tree views of network structure
add 245ad6d added v1l4
add a526375 added nest test
add dbc1471 fix error nest run
add d874e39 added save for mousev1
add 02d3823 moved mousev1 info to the notebooks folder
add e00e8e6 updated notebook for location
add 787a490 added bkg noise for mouse v1
add 15453ae remove old cell models
add 3964f17 update cell models with the appropriate format
add 18b97b0 fix error in 'virtual' node
add a47f1ad use lif_asc converter
add c968c9e update measurements
add 08c5d27 added nest notebook
add 2ef61ed updated notebooks to latest version
add f67feef updated complete notebook
add 01abfb6 Update documentation in V1L4 Notebook
add aa174b8 update environment file
new b757e7a Merge pull request #24 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:
.flake8 | 6 +-
.gitignore | 4 +-
airavata_cerebrum/{atlas => }/README.md | 0
airavata_cerebrum/atlas/data/base.py | 292 -
airavata_cerebrum/atlas/log/logging.py | 4 -
airavata_cerebrum/atlas/model/builder.py | 153 -
airavata_cerebrum/atlas/model/mousev1.py | 73 -
airavata_cerebrum/atlas/model/structure.py | 160 -
airavata_cerebrum/atlas/operations/netops.py | 191 -
airavata_cerebrum/base.py | 49 +
.../{atlas/data => dataset}/__init__.py | 1 +
.../{atlas/data => dataset}/abc_mouse.py | 800 +-
.../{atlas/data => dataset}/abm_celltypes.py | 208 +-
airavata_cerebrum/dataset/ai_synphys.py | 172 +
airavata_cerebrum/{atlas/data => dataset}/bicn.py | 1 -
.../{atlas/data => dataset}/mouse_brain.py | 0
airavata_cerebrum/{atlas => model}/__init__.py | 0
airavata_cerebrum/model/builder.py | 45 +
airavata_cerebrum/model/desc.py | 132 +
airavata_cerebrum/model/structure.py | 764 +
.../{atlas/model => operations}/__init__.py | 0
airavata_cerebrum/operations/abc_mouse.py | 76 +
airavata_cerebrum/operations/abm_celltypes.py | 112 +
airavata_cerebrum/operations/ai_synphys.py | 42 +
airavata_cerebrum/operations/dict_filter.py | 122 +
airavata_cerebrum/operations/json_filter.py | 182 +
airavata_cerebrum/operations/netops.py | 44 +
airavata_cerebrum/operations/xform.py | 74 +
airavata_cerebrum/register.py | 102 +
airavata_cerebrum/util/__init__.py | 5 +
airavata_cerebrum/util/desc_config.py | 158 +
airavata_cerebrum/util/io.py | 48 +
.../{atlas/operations => view}/__init__.py | 0
airavata_cerebrum/view/tree.py | 462 +
airavata_cerebrum/workflow.py | 124 +
environment.yml => env_full.yml | 17 +-
env_minimal.yml | 26 -
environment.yml | 71 +-
pyproject.toml | 33 +-
pyrcfg.json | 5 -
resources/notebooks/V1L4-Nest-Run.ipynb | 210 +
resources/notebooks/V1L4-Notebook.ipynb | 13926 ++++
resources/notebooks/V1L4-Scratch.ipynb | 884 +
resources/notebooks/atlas2cellprop.ipynb | 1541 +-
resources/notebooks/bmtk_pointnet_run.py | 65 +
resources/notebooks/merfish2model.ipynb | 4 +-
resources/notebooks/mousev1/model.py | 642 +
resources/notebooks/mousev1/operations.py | 715 +
resources/notebooks/nest_run.py | 59 +
resources/notebooks/v1l4.py | 66 +
.../notebooks/v1l4/bkg/bkg_spikes_250Hz_3s.h5 | Bin 0 -> 133346 bytes
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