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 eb91193 Merge pull request #14 from girip/main
add 1bbe32a added functions for building network
add e705789 update network construction
add bf261ac Merge branch 'apache:main' into main
add a7c4a59 update model
add 005b8fe add pyproject and re-organize
add ebbab51 update dependencies in pyproject
add dd0d86e fix bugs in abc_mouse
add 02245cd add index names on Y-axis for heatmap
add 6f548d9 fix local references in the notebook
add 99cb711 Merge branch 'apache:main' into main
add f055953 Merge branch 'apache:main' into main
add c6efae0 added functionality to access Allen Cell Types database
add d588795 added references
new 0018245 Merge pull request #13 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 | 3 +
.gitignore | 7 +
{atlas => airavata_cerebrum}/__init__.py | 0
airavata_cerebrum/atlas/README.md | 228 ++++
.../atlas}/__init__.py | 0
.../atlas/data}/__init__.py | 0
airavata_cerebrum/atlas/data/abc_mouse.py | 827 +++++++++++++
airavata_cerebrum/atlas/data/abm_celltypes.py | 332 ++++++
airavata_cerebrum/atlas/data/base.py | 137 +++
{atlas => airavata_cerebrum/atlas/data}/bicn.py | 0
.../atlas/data}/mouse_brain.py | 0
airavata_cerebrum/atlas/log/logging.py | 4 +
.../atlas/model}/__init__.py | 0
airavata_cerebrum/atlas/model/builder.py | 153 +++
airavata_cerebrum/atlas/model/regions.py | 172 +++
.../atlas/operations}/__init__.py | 0
airavata_cerebrum/atlas/operations/netops.py | 166 +++
.../cybershuttle}/__init__.py | 0
.../cybershuttle/annotations}/__init__.py | 0
.../cybershuttle}/annotations/decorator.py | 0
atlas/abc_mouse.py | 569 ---------
pyproject.toml | 52 +
.../notebooks}/atlas2cellprop.ipynb | 1230 ++++++++++----------
.../notebooks}/merfish2model.ipynb | 46 +-
scripts/build_network.py | 258 ++++
setup.py | 29 +-
tests/abm_ct.py | 16 +
tests/ct_workflow.json | 104 ++
28 files changed, 3064 insertions(+), 1269 deletions(-)
create mode 100644 .flake8
copy {atlas => airavata_cerebrum}/__init__.py (100%)
create mode 100644 airavata_cerebrum/atlas/README.md
rename {cybershuttle => airavata_cerebrum/atlas}/__init__.py (100%)
rename {cybershuttle/annotations => airavata_cerebrum/atlas/data}/__init__.py
(100%)
create mode 100644 airavata_cerebrum/atlas/data/abc_mouse.py
create mode 100644 airavata_cerebrum/atlas/data/abm_celltypes.py
create mode 100644 airavata_cerebrum/atlas/data/base.py
rename {atlas => airavata_cerebrum/atlas/data}/bicn.py (100%)
rename {atlas => airavata_cerebrum/atlas/data}/mouse_brain.py (100%)
create mode 100644 airavata_cerebrum/atlas/log/logging.py
copy {atlas => airavata_cerebrum/atlas/model}/__init__.py (100%)
create mode 100644 airavata_cerebrum/atlas/model/builder.py
create mode 100644 airavata_cerebrum/atlas/model/regions.py
copy {atlas => airavata_cerebrum/atlas/operations}/__init__.py (100%)
create mode 100644 airavata_cerebrum/atlas/operations/netops.py
copy {atlas => airavata_cerebrum/cybershuttle}/__init__.py (100%)
rename {atlas => airavata_cerebrum/cybershuttle/annotations}/__init__.py (100%)
rename {cybershuttle =>
airavata_cerebrum/cybershuttle}/annotations/decorator.py (100%)
delete mode 100644 atlas/abc_mouse.py
create mode 100644 pyproject.toml
rename {notebooks => resources/notebooks}/atlas2cellprop.ipynb (65%)
rename {notebooks => resources/notebooks}/merfish2model.ipynb (99%)
create mode 100644 scripts/build_network.py
create mode 100644 tests/abm_ct.py
create mode 100644 tests/ct_workflow.json
