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Merged
fedorgrab merged 7 commits into from
Jul 1, 2026
Merged

Bump cellarium-ml version and update dependencies #219

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f0982a7
chore: bump cellarium-ml version to 0.0.10
fedorgrab Jun 26, 2026
3924523
chore: update gitignore to exclude venv-linux
fedorgrab Jun 26, 2026
fc5868c
chore: update torch dependencies
fedorgrab Jun 26, 2026
292525b
chore: update lightning dependencies
fedorgrab Jun 26, 2026
b084b4c
chore: update gitignore
fedorgrab Jun 26, 2026
065bc56
feat: add dummy values for batch_index_n for scVI
fedorgrab Jun 30, 2026
678eb07
feat: add `.detach().numpy()` in cellarium ml pipeline res
fedorgrab Jun 30, 2026
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5 changes: 4 additions & 1 deletion .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -105,6 +105,7 @@ celerybeat.pid
*.env
*.env.*
.venv
.venv-linux
env/
venv/
ENV/
Expand Down Expand Up @@ -134,4 +135,6 @@ dmypy.json
src/data/
.DS_Store
.idea/
.vscode/
.vscode/
.omp/
.omp-review/
5 changes: 4 additions & 1 deletion cellarium/cas_backend/apps/model_inference/services.py
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Expand Up @@ -82,12 +82,15 @@ def _create_cellarium_data_module(adata: anndata.AnnData) -> CellariumAnnDataDat

:return: CellariumAnnDataDataModule
"""
# This dummy value is only used by scVI and ignored by other models
adata.obs["_scvi_batch_index_n"] = 0
data_module = CellariumAnnDataDataModule(
dadc=adata,
batch_keys={
"x_ng": AnnDataField(attr="X", convert_fn=densify),
"var_names_g": AnnDataField(attr="var_names"),
"total_mrna_umis_n": AnnDataField(attr="obs", key="total_mrna_umis"),
"batch_index_n": AnnDataField(attr="obs", key="_scvi_batch_index_n"),
},
batch_size=len(adata),
shuffle=False,
Expand All @@ -111,7 +114,7 @@ def _get_output_from_model(self, model: models.CASModel, adata: anndata.AnnData)

cellarium_output_dict = cellarium_module(batch)

embeddings = cellarium_output_dict["x_ng"].numpy()
embeddings = cellarium_output_dict["x_ng"].detach().numpy()

obs_ids = adata.obs.index.tolist()
return embeddings, obs_ids
Expand Down
2 changes: 1 addition & 1 deletion cellarium/cas_backend/core/config.py
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ class AllEnvSettings(BaseSettings):
# General
GOOGLE_ACCOUNT_CREDENTIALS: dict = json.loads(os.environ.get("GOOGLE_SERVICE_ACCOUNT_CREDENTIALS", "{}"))
ENVIRONMENT: str = ENV_TYPE
APP_VERSION: str = "1.8.4"
APP_VERSION: str = "1.8.5"
APP_ROOT: str = REPO_ROOT
DEFAULT_FEATURE_SCHEMA: str = "refdata-gex-GRCh38-2020-A"
PROJECT_BUCKET_NAME: str | None = os.environ.get("PROJECT_BUCKET_NAME")
Expand Down
45 changes: 25 additions & 20 deletions deploy/requirements.txt.lock
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ asn1crypto==1.5.1 ; python_version >= "3.12" and python_version < "4.0"
attrs==26.1.0 ; python_version >= "3.12" and python_version < "4.0"
boltons==25.0.0 ; python_version >= "3.12" and python_version < "4.0"
braceexpand==0.1.7 ; python_version >= "3.12" and python_version < "4.0"
cellarium-ml==0.0.7 ; python_version >= "3.12" and python_version < "4.0"
cellarium-ml==0.0.10 ; python_version >= "3.12" and python_version < "4.0"
certifi==2026.2.25 ; python_version >= "3.12" and python_version < "4.0"
cffi==2.0.0 ; python_version >= "3.12" and python_version < "4.0"
charset-normalizer==3.4.7 ; python_version >= "3.12" and python_version < "4.0"
Expand Down Expand Up @@ -81,7 +81,7 @@ jsonschema==4.26.0 ; python_version >= "3.12" and python_version < "4.0"
kiwisolver==1.5.0 ; python_version >= "3.12" and python_version < "4.0"
legacy-api-wrap==1.5 ; python_version >= "3.12" and python_version < "4.0"
lightning-utilities==0.15.3 ; python_version >= "3.12" and python_version < "4.0"
lightning==2.3.0 ; python_version >= "3.12" and python_version < "4.0"
lightning==2.5.2 ; python_version >= "3.12" and python_version < "4.0"
llvmlite==0.47.0 ; python_version >= "3.12" and python_version < "4.0"
mako==1.2.4 ; python_version >= "3.12" and python_version < "4.0"
markdown-it-py==4.0.0 ; python_version >= "3.12" and python_version < "4.0"
Expand All @@ -94,44 +94,46 @@ multidict==6.7.1 ; python_version >= "3.12" and python_version < "4.0"
natsort==8.4.0 ; python_version >= "3.12" and python_version < "4.0"
networkx==3.3 ; python_version >= "3.12" and python_version < "4.0"
numba==0.65.0 ; python_version >= "3.12" and python_version < "4.0"
numpy==2.4.4 ; python_version >= "3.12" and python_version < "4.0"
nvidia-cublas-cu12==12.1.3.1 ; python_version >= "3.12" and python_version < "4.0" and platform_system == "Linux" and platform_machine == "x86_64" and sys_platform == "darwin"
numpy==1.26.4 ; python_version >= "3.12" and python_version < "4.0"
nvidia-cublas-cu12==12.4.5.8 ; python_version >= "3.12" and python_version < "4.0" and sys_platform == "darwin" and platform_system == "Linux" and platform_machine == "x86_64"
nvidia-cublas-cu12==12.6.4.1 ; python_version >= "3.14" and python_version < "4.0" and sys_platform != "darwin" and sys_platform != "linux" and platform_system == "Linux" and platform_machine == "x86_64"
nvidia-cublas==13.1.0.3 ; python_version >= "3.12" and python_version < "3.14" and sys_platform != "darwin" and sys_platform != "linux" and platform_system == "Linux"
nvidia-cuda-cupti-cu12==12.1.105 ; python_version >= "3.12" and python_version < "4.0" and platform_system == "Linux" and platform_machine == "x86_64" and sys_platform == "darwin"
nvidia-cuda-cupti-cu12==12.4.127 ; python_version >= "3.12" and python_version < "4.0" and sys_platform == "darwin" and platform_system == "Linux" and platform_machine == "x86_64"
nvidia-cuda-cupti-cu12==12.6.80 ; python_version >= "3.14" and python_version < "4.0" and sys_platform != "darwin" and sys_platform != "linux" and platform_system == "Linux" and platform_machine == "x86_64"
nvidia-cuda-cupti==13.0.85 ; python_version >= "3.12" and python_version < "3.14" and sys_platform == "win32" and platform_system == "Linux"
nvidia-cuda-nvrtc-cu12==12.1.105 ; python_version >= "3.12" and python_version < "4.0" and platform_system == "Linux" and platform_machine == "x86_64" and sys_platform == "darwin"
nvidia-cuda-nvrtc-cu12==12.4.127 ; python_version >= "3.12" and python_version < "4.0" and sys_platform == "darwin" and platform_system == "Linux" and platform_machine == "x86_64"
nvidia-cuda-nvrtc-cu12==12.6.77 ; python_version >= "3.14" and python_version < "4.0" and sys_platform != "darwin" and sys_platform != "linux" and platform_system == "Linux" and platform_machine == "x86_64"
nvidia-cuda-nvrtc==13.0.88 ; python_version >= "3.12" and python_version < "3.14" and sys_platform == "win32" and platform_system == "Linux"
nvidia-cuda-runtime-cu12==12.1.105 ; python_version >= "3.12" and python_version < "4.0" and platform_system == "Linux" and platform_machine == "x86_64" and sys_platform == "darwin"
nvidia-cuda-runtime-cu12==12.4.127 ; python_version >= "3.12" and python_version < "4.0" and sys_platform == "darwin" and platform_system == "Linux" and platform_machine == "x86_64"
nvidia-cuda-runtime-cu12==12.6.77 ; python_version >= "3.14" and python_version < "4.0" and sys_platform != "darwin" and sys_platform != "linux" and platform_system == "Linux" and platform_machine == "x86_64"
nvidia-cuda-runtime==13.0.96 ; python_version >= "3.12" and python_version < "3.14" and sys_platform == "win32" and platform_system == "Linux"
nvidia-cudnn-cu12==9.1.0.70 ; python_version >= "3.12" and python_version < "4.0" and platform_system == "Linux" and platform_machine == "x86_64" and sys_platform == "darwin"
nvidia-cudnn-cu12==9.1.0.70 ; python_version >= "3.12" and python_version < "4.0" and sys_platform == "darwin" and platform_system == "Linux" and platform_machine == "x86_64"
nvidia-cudnn-cu12==9.5.1.17 ; python_version >= "3.14" and python_version < "4.0" and sys_platform != "darwin" and sys_platform != "linux" and platform_system == "Linux" and platform_machine == "x86_64"
nvidia-cudnn-cu13==9.19.0.56 ; python_version >= "3.12" and python_version < "3.14" and sys_platform != "darwin" and sys_platform != "linux" and platform_system == "Linux"
nvidia-cufft-cu12==11.0.2.54 ; python_version >= "3.12" and python_version < "4.0" and platform_system == "Linux" and platform_machine == "x86_64" and sys_platform == "darwin"
nvidia-cufft-cu12==11.2.1.3 ; python_version >= "3.12" and python_version < "4.0" and sys_platform == "darwin" and platform_system == "Linux" and platform_machine == "x86_64"
nvidia-cufft-cu12==11.3.0.4 ; python_version >= "3.14" and python_version < "4.0" and sys_platform != "darwin" and sys_platform != "linux" and platform_system == "Linux" and platform_machine == "x86_64"
nvidia-cufft==12.0.0.61 ; python_version >= "3.12" and python_version < "3.14" and sys_platform == "win32" and platform_system == "Linux"
nvidia-cufile-cu12==1.11.1.6 ; python_version >= "3.14" and python_version < "4.0" and sys_platform != "darwin" and sys_platform != "linux" and platform_system == "Linux" and platform_machine == "x86_64"
nvidia-curand-cu12==10.3.2.106 ; python_version >= "3.12" and python_version < "4.0" and platform_system == "Linux" and platform_machine == "x86_64" and sys_platform == "darwin"
nvidia-curand-cu12==10.3.5.147 ; python_version >= "3.12" and python_version < "4.0" and sys_platform == "darwin" and platform_system == "Linux" and platform_machine == "x86_64"
nvidia-curand-cu12==10.3.7.77 ; python_version >= "3.14" and python_version < "4.0" and sys_platform != "darwin" and sys_platform != "linux" and platform_system == "Linux" and platform_machine == "x86_64"
nvidia-curand==10.4.0.35 ; python_version >= "3.12" and python_version < "3.14" and sys_platform == "win32" and platform_system == "Linux"
nvidia-cusolver-cu12==11.4.5.107 ; python_version >= "3.12" and python_version < "4.0" and platform_system == "Linux" and platform_machine == "x86_64" and sys_platform == "darwin"
nvidia-cusolver-cu12==11.6.1.9 ; python_version >= "3.12" and python_version < "4.0" and sys_platform == "darwin" and platform_system == "Linux" and platform_machine == "x86_64"
nvidia-cusolver-cu12==11.7.1.2 ; python_version >= "3.14" and python_version < "4.0" and sys_platform != "darwin" and sys_platform != "linux" and platform_system == "Linux" and platform_machine == "x86_64"
nvidia-cusolver==12.0.4.66 ; python_version >= "3.12" and python_version < "3.14" and sys_platform == "win32" and platform_system == "Linux"
nvidia-cusparse-cu12==12.1.0.106 ; python_version >= "3.12" and python_version < "4.0" and platform_system == "Linux" and platform_machine == "x86_64" and sys_platform == "darwin"
nvidia-cusparse-cu12==12.3.1.170 ; python_version >= "3.12" and python_version < "4.0" and sys_platform == "darwin" and platform_system == "Linux" and platform_machine == "x86_64"
nvidia-cusparse-cu12==12.5.4.2 ; python_version >= "3.14" and python_version < "4.0" and sys_platform != "darwin" and sys_platform != "linux" and platform_system == "Linux" and platform_machine == "x86_64"
nvidia-cusparse==12.6.3.3 ; python_version >= "3.12" and python_version < "3.14" and sys_platform == "win32" and platform_system == "Linux"
nvidia-cusparselt-cu12==0.6.2 ; python_version >= "3.12" and python_version < "4.0" and sys_platform == "darwin" and platform_system == "Linux" and platform_machine == "x86_64"
nvidia-cusparselt-cu12==0.6.3 ; python_version >= "3.14" and python_version < "4.0" and sys_platform != "darwin" and sys_platform != "linux" and platform_system == "Linux" and platform_machine == "x86_64"
nvidia-cusparselt-cu13==0.8.0 ; python_version >= "3.12" and python_version < "3.14" and sys_platform != "darwin" and sys_platform != "linux" and platform_system == "Linux"
nvidia-nccl-cu12==2.20.5 ; python_version >= "3.12" and python_version < "4.0" and platform_system == "Linux" and platform_machine == "x86_64" and sys_platform == "darwin"
nvidia-nccl-cu12==2.21.5 ; python_version >= "3.12" and python_version < "4.0" and sys_platform == "darwin" and platform_system == "Linux" and platform_machine == "x86_64"
nvidia-nccl-cu12==2.26.2 ; python_version >= "3.14" and python_version < "4.0" and sys_platform != "darwin" and sys_platform != "linux" and platform_system == "Linux" and platform_machine == "x86_64"
nvidia-nccl-cu13==2.28.9 ; python_version >= "3.12" and python_version < "3.14" and sys_platform != "darwin" and sys_platform != "linux" and platform_system == "Linux"
nvidia-nvjitlink-cu12==12.6.85 ; python_version >= "3.12" and python_version < "4.0" and platform_system == "Linux" and platform_machine == "x86_64" and (sys_platform == "darwin" or python_version >= "3.14") and sys_platform != "linux"
nvidia-nvjitlink-cu12==12.4.127 ; python_version >= "3.12" and python_version < "4.0" and sys_platform == "darwin" and platform_system == "Linux" and platform_machine == "x86_64"
nvidia-nvjitlink-cu12==12.6.85 ; python_version >= "3.14" and python_version < "4.0" and sys_platform != "darwin" and sys_platform != "linux" and platform_system == "Linux" and platform_machine == "x86_64"
nvidia-nvjitlink==13.0.88 ; python_version >= "3.12" and python_version < "3.14" and sys_platform == "win32" and platform_system == "Linux"
nvidia-nvshmem-cu13==3.4.5 ; python_version >= "3.12" and python_version < "3.14" and sys_platform != "darwin" and sys_platform != "linux" and platform_system == "Linux"
nvidia-nvtx-cu12==12.1.105 ; python_version >= "3.12" and python_version < "4.0" and platform_system == "Linux" and platform_machine == "x86_64" and sys_platform == "darwin"
nvidia-nvtx-cu12==12.4.127 ; python_version >= "3.12" and python_version < "4.0" and sys_platform == "darwin" and platform_system == "Linux" and platform_machine == "x86_64"
nvidia-nvtx-cu12==12.6.77 ; python_version >= "3.14" and python_version < "4.0" and sys_platform != "darwin" and sys_platform != "linux" and platform_system == "Linux" and platform_machine == "x86_64"
nvidia-nvtx==13.0.85 ; python_version >= "3.12" and python_version < "3.14" and sys_platform == "win32" and platform_system == "Linux"
oauthlib==3.3.1 ; python_version >= "3.12" and python_version < "4.0"
Expand Down Expand Up @@ -176,6 +178,7 @@ rpds-py==0.30.0 ; python_version >= "3.12" and python_version < "4.0"
safetensors==0.7.0 ; python_version >= "3.12" and python_version < "4.0"
scanpy==1.11.5 ; python_version >= "3.12" and python_version < "4.0"
scikit-learn==1.8.0 ; python_version >= "3.12" and python_version < "4.0"
scikit-misc==0.5.1 ; python_version >= "3.12" and python_version < "4.0"
scipy==1.17.1 ; python_version >= "3.12" and python_version < "4.0"
scramp==1.4.8 ; python_version >= "3.12" and python_version < "4.0"
seaborn==0.13.2 ; python_version >= "3.12" and python_version < "4.0"
Expand All @@ -194,7 +197,8 @@ starkbank-ecdsa==2.2.0 ; python_version >= "3.12" and python_version < "4.0"
starlette-context==0.3.6 ; python_version >= "3.12" and python_version < "4.0"
starlette==0.41.2 ; python_version >= "3.12" and python_version < "4.0"
statsmodels==0.14.6 ; python_version >= "3.12" and python_version < "4.0"
sympy==1.14.0 ; python_version >= "3.12" and python_version < "4.0"
sympy==1.13.1 ; python_version >= "3.12" and python_version < "4.0" and (sys_platform == "darwin" or sys_platform == "linux")
sympy==1.14.0 ; python_version >= "3.12" and python_version < "4.0" and sys_platform != "darwin" and sys_platform != "linux"
tblib==3.2.2 ; python_version >= "3.12" and python_version < "4.0"
tenacity==8.2.3 ; python_version >= "3.12" and python_version < "4.0"
threadpoolctl==3.6.0 ; python_version >= "3.12" and python_version < "4.0"
Expand All @@ -204,13 +208,13 @@ tiledb==0.36.1 ; python_version >= "3.12" and python_version < "4.0"
tiledbsoma==2.3.0 ; python_version >= "3.12" and python_version < "4.0"
tokenizers==0.22.2 ; python_version >= "3.12" and python_version < "4.0"
torch==2.11.0 ; python_version >= "3.12" and python_version < "3.14" and sys_platform != "darwin" and sys_platform != "linux"
torch==2.4.1 ; python_version >= "3.12" and python_version < "4.0" and sys_platform == "darwin"
torch==2.4.1+cpu ; python_version >= "3.12" and python_version < "4.0" and sys_platform == "linux"
torch==2.6.0 ; python_version >= "3.12" and python_version < "4.0" and (sys_platform == "darwin" or sys_platform == "linux") and (sys_platform == "darwin" or platform_machine == "aarch64")
torch==2.6.0+cpu ; python_version >= "3.12" and python_version < "4.0" and sys_platform == "linux" and platform_machine != "aarch64"
torch==2.7.1 ; python_version >= "3.14" and python_version < "4.0" and sys_platform != "darwin" and sys_platform != "linux"
torchmetrics==1.9.0 ; python_version >= "3.12" and python_version < "4.0"
tqdm==4.67.3 ; python_version >= "3.12" and python_version < "4.0"
transformers==5.5.4 ; python_version >= "3.12" and python_version < "4.0"
triton==3.0.0 ; python_version == "3.12" and platform_system == "Linux" and platform_machine == "x86_64" and sys_platform == "darwin"
triton==3.2.0 ; python_version >= "3.12" and python_version < "4.0" and sys_platform == "darwin" and platform_system == "Linux" and platform_machine == "x86_64"
triton==3.3.1 ; python_version >= "3.14" and python_version < "4.0" and sys_platform != "darwin" and sys_platform != "linux" and platform_system == "Linux" and platform_machine == "x86_64"
triton==3.6.0 ; python_version >= "3.12" and python_version < "3.14" and sys_platform != "darwin" and sys_platform != "linux" and platform_system == "Linux"
typer==0.24.1 ; python_version >= "3.12" and python_version < "4.0"
Expand All @@ -221,11 +225,12 @@ umap-learn==0.5.12 ; python_version >= "3.12" and python_version < "4.0"
uritemplate==4.2.0 ; python_version >= "3.12" and python_version < "4.0"
urllib3==2.5.0 ; python_version >= "3.12" and python_version < "4.0"
uvicorn==0.29.0 ; python_version >= "3.12" and python_version < "4.0"
uvloop==0.22.1 ; python_version >= "3.12" and python_version < "4.0" and platform_python_implementation != "PyPy" and sys_platform != "win32" and sys_platform != "cygwin"
uvloop==0.22.1 ; python_version >= "3.12" and python_version < "4.0" and platform_python_implementation != "PyPy" and (sys_platform != "win32" and sys_platform != "cygwin" or sys_platform == "darwin" or sys_platform == "linux") and (sys_platform != "win32" and sys_platform != "cygwin" and sys_platform != "linux" or sys_platform == "darwin" or sys_platform == "linux" or platform_machine != "aarch64")
watchfiles==1.1.1 ; python_version >= "3.12" and python_version < "4.0"
websockets==16.0 ; python_version >= "3.12" and python_version < "4.0"
werkzeug==3.0.6 ; python_version >= "3.12" and python_version < "4.0"
wrapt==2.1.2 ; python_version >= "3.12" and python_version < "4.0"
wtforms==3.1.2 ; python_version >= "3.12" and python_version < "4.0"
yarl==1.23.0 ; python_version >= "3.12" and python_version < "4.0"
zipp==3.23.1 ; python_version >= "3.12" and python_version < "4.0"
zuko==1.6.0 ; python_version >= "3.12" and python_version < "4.0"
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