# The Python packages of the lab's deeplearning image, as pip constraints for a project's CI.
#
# Image:    /mnt/data/containers/deeplearning_v2026-09-15.sqsh (slinky pins it; CoreWeave keeps the same dated names)
# System:   Ubuntu 24.04.5, CUDA 13.0.2 (driver 580.95.05), cuDNN 9.20, NCCL 2.29
# Python:   3.12, /opt/conda/bin/python3, first on the job's PATH
#
# Copy this file into the project as ci/constraints.txt and install with the image's Python:
#   pip install -c ci/constraints.txt --extra-index-url https://download.pytorch.org/whl/cpu <the project's dependencies>
# torch==2.13.0 here admits the CPU wheel, 2.13.0+cpu.
#
# Read 2026-10-10 on slinky's login node, without a job, from the image's dist-info directories:
#   unsquashfs -l <image> | grep -oE "opt/conda/lib/python3.12/site-packages/[^/]+\.dist-info$" \
#     | sed -E "s|.*/||; s|\.dist-info$||; s|-|==|"
abnumber==0.4.4
absl_py==2.5.0
abstar==0.8.0
abutils==0.6.0
accelerate==1.15.0
aiofiles==25.1.0
aiohappyeyeballs==2.7.1
aiohttp==3.14.3
aiosignal==1.4.0
altair==6.3.0
anarci==2026.2.13.2
anarcii==2.0.8
anndata==0.13.3.post0
annotated_doc==0.0.5
annotated_types==0.8.0
annoy==1.17.3
anyio==4.15.1
archspec==0.2.5
array_api_compat==1.15.0
asttokens==3.0.2
attrs==26.1.0
backports_zstd==1.7.0
baltic==0.3.0
bbknn==1.6.0
bcrypt==5.0.0
beautifulsoup4==4.15.0
biopython==1.88
black==26.5.1
blosc2==4.13.1
bokeh==3.10.0
boltons==26.2.0
bottleneck==1.6.0
brotli==1.2.0
build==1.6.0
cached_property==2.0.1
certifi==2026.7.22
cffi==2.1.1
charset_normalizer==3.5.1
chex==0.1.92
click==8.5.0
cloudpickle==3.1.2
colorama==0.4.6
comm==0.2.3
conda==26.7.2
conda_index==0.13.0
conda_libmamba_solver==26.7.0
conda_lockfiles==0.2.1
conda_package_handling==2.6.0
conda_package_streaming==0.13.0
conda_pypi==0.12.0
conda_rattler_solver==0.1.1
conda_self==0.2.1
contourpy==1.4.0
cryptography==50.0.1
cuda_bindings==13.4.1
cuda_pathfinder==1.8.1
cuda_toolkit==13.0.3.0
cycler==0.12.1
cython==3.3.0
dask==2026.8.0
datasets==5.0.1
deepspeed==0.19.6
diffusers==0.40.0
dill==0.4.1
distro==1.9.0
dm_tree==0.1.10
dnachisel==3.2.16
dnspython==2.8.0
docopt==0.6.2
donfig==0.8.1.post1
doubletdetection==4.3.0.post1
duckdb==1.5.5
einops==0.8.2
equinox==0.13.8
ete3==3.1.3
etils==1.14.0
et_xmlfile==2.0.0
evaluate==0.4.6
executing==2.2.1
fastapi==0.141.1
fastcluster==1.3.0
fast_array_utils==1.5
fbpca==1.0
filelock==3.32.6
flametree==0.2.1
flash_attn==2.8.3.post1
flax==0.12.9
fonttools==4.65.0
formulaic==1.2.2
frozendict==2.4.7
frozenlist==1.8.0
fsspec==2026.6.0
gemmi==0.7.5
geosketch==1.3
googleapis_common_protos==1.75.3
google_crc32c==1.8.0
gradio==6.27.0
gradio_client==2.7.0
greenlet==3.5.6
groovy==0.1.2
h11==0.16.0
h2==4.4.1
h5py==3.16.0
harmonypy==2.0.0
hf_gradio==0.4.1
hf_xet==1.6.0
hjson==3.1.0
hpack==4.2.0
httpcore==1.0.9
httpx==0.28.1
huggingface_hub==1.31.0
humanize==4.16.0
hyperframe==6.1.0
idna==3.19
igraph==1.0.0
ihm==2.11
imageio==2.37.4
importlib_metadata==9.0.1
iniconfig==2.3.0
installer==1.0.1
interface_meta==2.0.1
intervaltree==3.2.1
invoke==3.0.3
ipympl==0.10.0
ipython==9.17.1
ipython_pygments_lexers==1.1.1
ipywidgets==8.1.9
jax==0.11.1
jaxlib==0.11.1
jaxtyping==0.3.11
jax_cuda13_pjrt==0.11.1
jax_cuda13_plugin==0.11.1
jedi==0.20.0
jinja2==3.1.6
joblib==1.6.0
jsonschema==4.26.0
jsonschema_specifications==2025.9.1
jupyterlab_widgets==3.0.17
keras==3.15.1
kiwisolver==1.5.1
lazy_loader==0.5
legacy_api_wrap==1.5
leidenalg==0.12.0
levenshtein==0.27.5
libmambapy==2.9.0
lightning==2.6.6
lightning_utilities==0.15.3
llvmlite==0.49.0
locket==1.0.0
logomaker==0.8.7
loompy==3.0.8
markdown_it_py==4.2.0
markupsafe==3.0.3
matplotlib==3.11.2
matplotlib_inline==0.2.2
mdurl==0.1.2
menuinst==2.5.2
ml_collections==1.1.0
ml_dtypes==0.6.0
mnemonic==0.21
modelcif==1.8
mpmath==1.3.0
msgpack==1.2.2
multidict==6.8.0
multiprocess==0.70.19
mypy_extensions==1.1.0
namex==0.1.0
narwhals==2.26.0
natsort==8.4.0
ndindex==1.10.1
networkx==3.6.1
ninja==1.13.2
numba==0.67.0
numcodecs==0.16.5
numexpr==2.14.2
numpy==2.5.3
numpy_groupies==0.11.3
nvidia_cublas==13.1.1.3
nvidia_cuda_crt==13.4.59
nvidia_cuda_cupti==13.0.85
nvidia_cuda_nvcc==13.4.59
nvidia_cuda_nvrtc==13.0.88
nvidia_cuda_runtime==13.0.96
nvidia_cudnn_cu13==9.20.0.48
nvidia_cufft==12.0.0.61
nvidia_cufile==1.15.1.6
nvidia_curand==10.4.0.35
nvidia_cusolver==12.0.4.66
nvidia_cusparse==12.6.3.3
nvidia_cusparselt_cu13==0.8.1
nvidia_nccl_cu13==2.29.7
nvidia_nvjitlink==13.4.52
nvidia_nvshmem_cu13==3.4.5
nvidia_nvtx==13.0.85
nvidia_nvvm==13.4.59
openmm==8.6.1
openmm_cuda_13==8.6.1
openpyxl==3.1.5
opentelemetry_api==1.44.0
opentelemetry_exporter_otlp_proto_common==1.44.0
opentelemetry_exporter_otlp_proto_http==1.44.0
opentelemetry_proto==1.44.0
opentelemetry_sdk==1.44.0
opentelemetry_semantic_conventions==0.65b0
optax==0.2.8
optimum==2.3.0
optree==0.20.0
opt_einsum==3.4.0
orbax_checkpoint==0.12.4
orjson==3.12.0
packaging==26.3
pandas==3.0.5
paramiko==5.0.0
parasail==1.3.4
parso==0.8.7
partd==1.4.2
pathspec==1.1.1
patsy==1.0.3
pdbfixer==1.12.0
peft==0.21.0
pexpect==4.9.0
PhenoGraph==1.5.7
pillow==12.3.0
pip==26.2.1
platformdirs==4.11.8
plottable==0.1.5
pluggy==1.6.0
polars==1.44.2
polars_runtime_32==1.44.2
prettytable==3.18.0
proglog==0.1.12
prometheus_client==0.26.0
prompt_toolkit==3.0.53
propcache==0.5.2
protobuf==7.36.1
psutil==7.2.2
ptyprocess==0.7.0
pure_eval==0.2.4
pyarrow==25.0.1
pycosat==0.6.6
pycparser==3.0
pydantic==2.13.5
pydantic_core==2.46.5
pydantic_settings==2.15.0
pydub==0.25.1
pyfamsa==0.6.2
pyfastx==2.3.1
pygments==2.21.0
pymongo==4.18.1
pynacl==1.6.2
pynndescent==0.6.0
pypalettes==0.2.1
pyparsing==3.3.2
pyproject_hooks==1.2.0
PySocks==1.7.1
pytest==9.1.1
python_circos==0.3.0
python_codon_tables==0.1.18
python_dateutil==2.9.0.post0
python_dotenv==1.2.3
python_levenshtein==0.27.5
python_magic==0.4.27
python_multipart==0.0.32
pytokens==0.4.1
pytorch_lightning==2.6.6
pytz==2026.3.post1
pyyaml==6.0.3
py_cpuinfo==9.0.0
py_rattler==0.25.0
rapidfuzz==3.14.6
referencing==0.37.0
regex==2026.9.10
requests==2.34.2
rich==15.0.0
rpds_py==2026.6.3
ruamel_yaml==0.19.1
ruamel_yaml_clib==0.2.15
s3cmd==2.4.0
safehttpx==0.1.7
safetensors==0.8.0
sample_sheet==0.13.0
scab==0.2.4
scanorama==1.7.4
scanpy==1.12.4
scikit_image==0.26.0
scikit_learn==1.9.1
scipy==1.18.1
scoring_matrices==0.3.4
scrublet==0.2.3
scvelo==0.3.4
scverse_misc==0.1.6
seaborn==0.13.2
semantic_version==2.10.0
session_info2==0.4.2
shellingham==1.5.4
simplejson==4.1.2
six==1.17.0
smart_open==8.0.1
sniffio==1.3.1
sortedcontainers==2.4.0
soupsieve==2.9.2
sqlalchemy==2.0.53
stack_data==0.6.3
starlette==1.6.0
statsmodels==0.15.0
sympy==1.14.0
tables==3.11.1
tabulate==0.10.0
tensorstore==0.1.85
terminaltables==3.1.10
texttable==1.7.0
threadpoolctl==3.7.0
tifffile==2026.9.15
tokenizers==0.23.2
tomli==2.4.1
tomli_w==1.2.0
tomlkit==0.14.0
toolz==1.1.0
torch==2.13.0
torchmetrics==1.9.0
tornado==6.5.10
tqdm==4.70.1
traitlets==5.16.1
transformers==5.17.0
treescope==0.1.10
triton==3.7.1
truststore==0.10.4
typer==0.27.2
typing_extensions==4.16.0
typing_inspection==0.4.4
umap_learn==0.5.12
unearth==0.18.3
urllib3==2.7.0
uv==0.12.15
uvicorn==0.53.0
uvloop==0.22.1
wadler_lindig==0.1.7
wandb==0.30.0
wcwidth==0.8.3
wheel==0.48.0
widgetsnbextension==4.0.16
wrapt==2.4.1
xxhash==4.0.1
xyzservices==2026.9.1
yarl==1.24.5
zarr==3.3.0
zipp==4.1.0
