Python packages -- generated 2026-05-07
Reproducibility
Older versions may be available in historic snapshots (run module avail python-cbrg for history).
See python-cbrg for details.
Changes (last 90 days)
2026-04-29:
-
new:
alphafold-colabfold/2.3.13 colabfold/1.6.1 dm-haiku/0.0.16 immutabledict/4.3.1 importlib_metadata/8.7.1 jmp/0.0.4 OpenMM/8.5.1 OpenMM-CUDA-12/8.5.1 orjson/3.11.8 pdbfixer/1.12.0 py3Dmol/2.5.4 tensorflow_cpu/2.21.0 -
update:
dm-tree/0.1.10 numpy/2.2.5 opentelemetry-api/1.41.1 opentelemetry-exporter-prometheus/0.62b1 opentelemetry-sdk/1.41.1 opentelemetry-semantic-conventions/0.62b1 tangermeme/1.0.4 zipp/3.23.1 -
downgrade:
h5py/3.14.0
2026-04-23:
- new:
cattrs/26.1.0 pybiomart/0.2.0 requests-cache/1.3.1 url-normalize/2.2.1 - update:
attrs/26.1.0 liana/1.7.1 - removed:
hierdiff, tcrdist3- Requires fishersapi
2026-04-22:
-
new:
bed-reader/1.0.6 bgen-reader/4.0.8 bitsandbytes/0.49.2 cbgen/1.0.6 pybgen/0.7.1 pysnptools/0.5.13 quickdraws/0.1.5 rhe/1.0.0 -
update:
more-itertools/11.0.2 psutil/7.2.2 - removed:
fishersapi- Requires fisher that requires Numpy1
2026-04-21: update: ipy-slurm-exec/1.0.0
2026-04-17: new: captum/0.9.0 gseapy/1.1.13 papermill/2.7.0
2026-02-26: update: scvi-tools/1.4.2
2026-02-24: new: matplotlib-venn/1.1.2
2026-02-18: new: pyclustree/0.4.1
2026-02-17:
- new:
idtrack/0.0.5 PyMySQL/1.1.2 PySocks/1.7.1 - update:
urllib3/2.6.3
2026-02-10: new: doubletdetection/4.3.0.post1
2026-02-06:
- new:
pep8/1.7.1 zope.event/6.1 zope.interface/8.2 - update:
greenlet/3.3.1
Python packages
syntax: module / version ( latest snapshot )
about-time/4.2.1 nvidia-cusparse-cu11/11.7.4.91
absl-py/1.4.0 nvidia-cusparse-cu12/12.5.10.65
adjustText/0.8 /12.1.0.106 (202507)
aeppl/0.1.4 (202507) nvidia-cusparselt-cu12/0.7.1
aesara/2.9.0 (202507) nvidia-nccl-cu11/2.14.3
aiofiles/22.1.0 nvidia-nccl-cu12/2.27.3
aiohappyeyeballs/2.6.1 /2.20.5 (202507)
aiohttp/3.12.13 nvidia-nvjitlink-cu12/12.9.86
/3.8.4 (202507) /12.4.127 (202507)
aiohttp-cors/0.8.1 nvidia-nvtx-cu11/11.7.91
aiosignal/1.3.1 nvidia-nvtx-cu12/12.9.79
aiosqlite/0.19.0 /12.1.105 (202507)
airr/1.5.0 oauth2client/4.1.3
alabaster/0.7.13 oauthlib/3.2.2
alembic/1.10.4 olga/1.2.4
alive-progress/3.1.2 ome-types/0.6.2
alphafold-colabfold/2.3.13 ome-zarr/0.11.1
aniso8601/9.0.1 /0.9.0 (202510)
anndata/0.12.6 omnipath/1.0.12
/0.9.1 (202510) /1.0.8 (202510)
anndata2ri/1.3.1 onnx/1.14.0
annotated-types/0.7.0 ont-fast5-api/4.1.1
/0.5.0 (202501) ont-tombo/1.5.1
annoy/1.17.2 opencensus/0.11.4
anyio/3.7.1 opencensus-context/0.1.3
/3.6.2 (202310) opencv-python/4.12.0.88
appdirs/1.4.4 /4.7.0.72 (202510)
apricot-select/0.6.1 opencv-python-headless/4.12.0.88
arboreto/0.1.6 /4.7.0.72 (202510)
argcomplete/3.0.8 OpenMM/8.5.1
argh/0.28.1 OpenMM-CUDA-12/8.5.1
argon2-cffi/21.3.0 openpyxl/3.1.2
argon2-cffi-bindings/21.2.0 openslide-python/1.4.2
argparse/1.4.0 (202407) opentelemetry-api/1.41.1
argparse-dataclass/2.0.0 /1.34.1 (202604)
array-api-compat/1.12.0 opentelemetry-exporter-prometheus/0.62b1
arrow/1.2.3 /0.55b1 (202604)
arviz/0.22.0 opentelemetry-proto/1.39.1
/0.15.1 (202510) /1.27.0 (202601)
asciitree/0.3.3 opentelemetry-sdk/1.41.1
astor/0.8.1 /1.34.1 (202604)
astroid/2.15.4 opentelemetry-semantic-conventions/0.62b1
asttokens/2.2.1 /0.55b1 (202604)
astunparse/1.6.3 opt-einsum/3.3.0
async-generator/1.10 optax/0.2.4
async-timeout/4.0.2 /0.1.5 (202501)
atomicwrites/1.4.1 optimistix/0.0.10
attmap/0.13.2 optparse-pretty/0.1.1
attrs/26.1.0 optree/0.18.0
/23.1.0 (202604) orbax-checkpoint/0.2.2
autopage/0.5.1 ordered-set/4.1.0
autopep8/2.0.2 orderly-set/5.5.0
azure-common/1.1.28 orjson/3.11.8
azure-core/1.26.4 ott-jax/0.5.0
azure-identity/1.12.0 /0.4.6 (202407)
azure-mgmt-core/1.4.0 overrides/7.7.0
azure-mgmt-storage/21.0.0 oyaml/1.0
azure-storage-blob/12.16.0 packaging/25.0
azure-storage-file-datalake/12.11.0 /24.2 (202510)
Babel/2.12.1 /23.2 (202501)
backcall/0.2.0 /23.1 (202310)
backoff/2.2.1 palettable/3.3.3
backports-abc/0.5 palmotif/0.4
backspinpy/0.2.1 pamela/1.0.0
bambi/0.16.0 pandas/2.3.3
/0.10.0 (202510) /2.1.4 (202501)
bbknn/1.6.0 /2.1.1 (202510)
bcbio-gff/0.7.0 /2.0.1 (202310)
bcrypt/4.1.3 pandas_plink/2.2.9
beautifulsoup4/4.12.2 pandocfilters/1.5.0
bed-reader/1.0.6 panel/1.8.3
bgen-reader/4.0.8 /0.14.4 (202510)
binaryornot/0.4.4 papermill/2.7.0
bioframe/0.8.0 param/2.2.1
/0.7.2 (202510) /1.13.0 (202510)
biomart/0.9.2 paramiko/3.4.0
biopython/1.85 parasail/1.3.4
/1.81 (202501) parmap/1.6.0
biothings-client/0.3.0 parse/1.19.0
bitarray/2.9.3 parso/0.7.1
bitsandbytes/0.49.2 partd/1.4.0
bitstring/4.2.3 pastel/0.2.1
BitVector/3.5.0 pathlib2/2.3.7.post1
black/23.3.0 pathspec/0.11.1
bleach/6.0.0 pathtools/0.1.2
blessed/1.20.0 patsy/1.0.2
blitzgsea/1.3.42 /0.5.3 (202510)
blosc2/3.11.0 pbr/5.11.1
/2.0.0 (202510) pdbfixer/1.12.0
bokeh/3.8.1 pdf2image/1.16.3
/2.4.3 (202510) pegasusio/0.8.0
boltons/23.0.0 pep8/1.7.1
boto/2.49.0 pephubclient/0.4.5
boto3/1.34.162 /0.2.1 (202510)
/1.26.131 (202501) peppy/0.40.8
botocore/1.34.162 /0.35.7 (202510)
/1.29.131 (202501) pertpy/0.7.0 (202407)
Brotli/1.0.9 pexpect/4.8.0
BucketCache/0.12.1 Pgenlib/0.93.0
bulker/0.7.3 /0.90.2 (202510)
bustools/0.1.0.dev2 PhenoGraph/1.5.7
bx-python/0.14.0 pickleshare/0.7.5
/0.9.0 (202510) pika/1.3.2
cached-property/1.5.2 Pillow/9.5.0
cachetools/5.3.0 pillow/12.0.0
captum/0.9.0 PIMS/0.7
cattrs/26.1.0 pip/25.3
cbgen/1.0.6 /25.0.1 (202510)
ccb-file-utils/0.1.1 /23.3.1 (202501)
/0.1.0 (202407) /23.1.2 (202310)
ccb-file-utils-dbg/0.1.0 pipdeptree/2.29.0
cell2location/0.1.5 piper/0.13.2
/0.1.4 (202510) pipestat/0.12.2
cellbender/0.3.0 (202404) /0.5.2 (202510)
cellphonedb/5.0.0 pkginfo/1.9.6
cellpose/4.0.6 plac/1.3.5
/2.2.1 (202507) platformdirs/4.2.2
cellrank/2.0.7 /3.5.0 (202407)
/2.0.2 (202510) Platypus-Opt/1.1.0
/1.5.1 (202310) plotly/5.24.1
cellSNP/0.3.2 /5.14.1 (202501)
celltypist/1.7.1 plotnine/0.15.1
certifi/2024.7.4 /0.12.4 (202510)
/2023.5.7 (202407) pluggy/1.0.0
certipy/0.1.3 ply/3.11
cffi/1.15.1 polars/1.25.2
cfgv/3.4.0 pomegranate/1.0.3
cftime/1.6.5 pooch/1.8.2
/1.6.2 (202510) portalocker/2.7.0
cgatcore/0.6.16 pre-commit/3.7.1
changeo/1.3.0 presto/0.7.2
chardet/5.1.0 prettytable/3.7.0
charset-normalizer/2.0.12 progress/1.6
chex/0.1.89 progressbar2/4.2.0
/0.1.86 (202501) progressbar33/2.4
/0.1.7 (202407) prometheus-client/0.16.0
click/8.1.3 prompt-toolkit/3.0.38
clikit/0.6.2 propcache/0.3.2
cloudpickle/3.1.2 proto-plus/1.26.1
/2.2.1 (202510) protobuf/6.33.4
clust/1.18.0 /3.20.3 (202601)
cmake/3.26.3 psutil/7.2.2
cmd2/2.4.3 /5.9.5 (202604)
cnmf/1.7.0 psycopg2-binary/2.9.9
colabfold/1.6.1 ptyprocess/0.7.0
colorama/0.4.6 PubChemPy/1.0.4
colorcet/3.0.1 PuLP/2.7.0
coloredlogs/15.0.1 pure-eval/0.2.2
colorful/0.5.7 pwseqdist/0.6
colormath/3.0.0 py/1.11.0
comm/0.1.3 py-cpuinfo/9.0.0
commonmark/0.9.1 py-spy/0.4.0
conda-inject/1.3.2 py2bit/0.3.0
ConfigArgParse/1.7.1 py3Dmol/2.5.4
/1.5.3 (202510) py4j/0.10.9.7
configparser/5.3.0 pyabc/0.12.16
configs/3.0.3 pyarrow/16.1.0
connection-pool/0.0.3 /12.0.0 (202407)
cons/0.4.5 pyasn1/0.5.0
contextlib2/21.6.0 pyasn1-modules/0.3.0
contourpy/1.3.3 pybedtools/0.9.1
/1.0.7 (202510) pybgen/0.7.1
cookiecutter/2.1.1 pybigtools/0.2.4
cooler/0.9.1 pyBigWig/0.3.24
coverage/7.11.3 /0.3.22 (202510)
/7.2.5 (202510) pybiomart/0.2.0
CPAT/3.0.4 pybktree/1.1
crashtest/0.3.1 pycairo/1.23.0
crc32c/2.8 pyCirclize/1.9.1
crcmod/1.7 pyclustree/0.4.1
croniter/1.4.1 pycodestyle/2.10.0
CrossMap/0.6.5 pycparser/2.21
crypt4gh/1.7 pyct/0.5.0
cryptography/42.0.8 pycurl/7.45.3
/40.0.2 (202407) pydantic/2.12.4
ctxcore/0.2.0 /1.10.21 (202510)
cupy-cuda12x/13.5.1 /1.10.13 (202501)
custom-inherit/2.4.1 pydantic-extra-types/2.10.6
cutadapt/4.4 pydantic_core/2.41.5
cycler/0.11.0 /2.4.0 (202510)
cykhash/2.0.1 pyDeprecate/0.3.2
Cython/0.29.34 pydocstyle/6.3.0
cytoolz/0.12.1 pydot/4.0.1
cyvcf2/0.31.4 pyfaidx/0.7.2.1
/0.30.18 (202510) pyflakes/3.0.1
dask/2024.11.2 pygam/0.10.1
/2024.6.2 (202510) /0.9.0 (202510)
/2023.4.1 (202407) Pygments/2.15.1
dask-expr/1.1.19 pygpcca/1.0.4
/1.1.6 (202510) pygraphviz/1.14
dask-image/2024.5.3 PyGSP/0.5.1
dask-mpi/2022.4.0 pyinstrument/5.0.1
datasets/4.0.0 pyjaspar/3.0.0
datashader/0.16.2 PyJWT/2.7.0
dateutils/0.6.12 pylev/1.4.0
datrie/0.8.2 pylint/2.17.4
debugpy/1.6.7 pylint-venv/3.0.1
decontx-python/0.2.0 pyls-black/0.4.7
decorator/5.1.1 pyls-spyder/0.4.0
decoupler/2.1.2 pymc/5.26.1
/1.6.0 (202510) /5.3.1 (202510)
deepdiff/8.6.1 pymc3/3.11.4 (202407)
/6.5.0 (202510) pymongo/4.3.3
deepTools/3.5.6 PyMuPDF/1.22.2
/3.5.2 (202510) PyMySQL/1.1.2
/3.5.1 (202307) PyNaCl/1.5.0
deeptoolsintervals/0.1.9 pynndescent/0.5.13
defusedxml/0.7.1 /0.5.10 (202510)
demuxEM/0.1.7.post1 pynvml/11.5.0
/0.1.7 (202501) pyogrio/0.9.0
deprecat/2.1.1 Pyomo/6.7.3
Deprecated/1.2.13 pyOpenSSL/24.1.0
dict-trie/1.0.1 /23.1.1 (202407)
diff-match-patch/20230430 pypairix/0.3.7
diffrax/0.7.0 pyparsing/3.2.3
dill/0.3.6 /3.0.9 (202507)
diskcache/5.6.1 pypath-omnipath/0.16.16
Distance/0.1.3 pypath_common/0.2.4
distlib/0.3.8 PyPDF2/3.0.1
distributed/2024.11.2 pyperclip/1.8.2
/2024.6.2 (202510) pypng/0.20220715.0
/2023.4.1 (202407) pyproj/3.6.1
divvy/0.6.0 PyQt5/5.15.9
dm-haiku/0.0.16 PyQt5-Qt5/5.15.2
dm-tree/0.1.10 PyQt5-sip/12.12.1
/0.1.8 (202604) PyQtWebEngine/5.15.6
dna-features-viewer/3.1.3 PyQtWebEngine-Qt5/5.15.2
dnaio/0.10.0 pyranges/0.0.125
dnspython/2.3.0 pyreadr/0.5.0
docker-pycreds/0.4.0 pyro-api/0.1.2
docopt/0.6.2 pyro-ppl/1.9.1
docrep/0.3.2 /1.8.4 (202510)
docstring-inheritance/2.2.2 pyrsistent/0.19.3
docstring-to-markdown/0.12 pysam/0.21.0
docutils/0.19 pyscenic/0.12.1
donfig/0.8.1.post1 /0.12.2b0 (202510)
doubletdetection/4.3.0.post1 PySCIPOpt/5.4.1
dpath/2.2.0 pysftp/0.2.9
/2.1.5 (202510) pysimdjson/5.0.2
drmaa/0.7.9 pysnptools/0.5.13
drugz/1.1.0.2 PySocks/1.7.1
DukeDSClient/4.0.0 pysr/0.12.3 (202407)
dunamai/1.16.0 pystan/3.10.0
eido/0.2.2 /3.7.0 (202510)
einops/0.8.1 pytensor/2.35.1
einops-exts/0.0.4 /2.11.2 (202510)
entrypoints/0.4 pytest/7.3.1
equinox/0.11.12 (202604) pytest-cov/4.0.0
/0.11.4 (202407) pytest-dependency/0.5.1
et-xmlfile/1.1.0 python-circos/0.3.0
ete3/3.1.3 python-dateutil/2.8.2
etils/1.12.2 python-dotenv/1.1.1
/1.2.0 (202501) python-editor/1.0.4
etuples/0.3.8 python-igraph/1.0.0
executing/1.2.0 /0.10.4 (202510)
face/20.1.1 python-json-logger/2.0.7
faiss-cpu/1.9.0.post1 (202510) python-jsonrpc-server/0.4.0
faiss-gpu-cu12/1.13.0 python-language-server/0.36.2
fastapi/0.103.2 python-Levenshtein/0.21.0
fasteners/0.18 python-lsp-black/1.2.1
fastjsonschema/2.16.3 python-lsp-jsonrpc/1.0.0
fastobo/0.12.2 python-lsp-server/1.7.2
fastools/1.1.5 python-magic/0.4.27
fastprogress/1.0.3 python-multipart/0.0.6
fastremap/1.17.7 python-slugify/8.0.1
/1.13.4 (202510) python-utils/3.5.2
fastrlock/0.8.3 pytoolconfig/1.2.5
fbpca/1.0 pytorch-ignite/0.4.12
feather-format/0.4.1 pytorch-lightning/2.5.3
filelock/3.15.4 /2.0.9.post0 (202507)
/3.12.0 (202407) pytz/2023.3
fill_voids/2.1.1 pytz-deprecation-shim/0.1.0.post0
/2.1.0 (202510) pyu2f/0.1.5
fisher/0.1.10 (202510) pyvips/3.0.0
fishersapi/0.5 (202604) pyviz-comms/2.2.1
flake8/6.0.0 PyWavelets/1.9.0
Flask/2.2.5 /1.4.1 (202510)
Flask-Compress/1.13 pywin32-ctypes/0.2.0
Flask-Cors/3.0.10 pyxdg/0.28
Flask-RESTful/0.3.9 PyYAML/6.0
flask-server-timing/0.1.2 pyzmq/25.0.2
flask-talisman/1.0.0 QDarkStyle/3.1
Flask-Testing/0.8.1 qnorm/0.8.1
flatbuffers/25.12.19 qstylizer/0.2.2
/1.12 (202601) QtAwesome/1.2.3
flatten-dict/0.4.2 qtconsole/5.4.3
flax/0.8.5 qtl/0.1.10
/0.6.10 (202407) /0.1.8 (202510)
FlowIO/1.4.0 QtPy/2.3.1
fonttools/4.39.3 quickdraws/0.1.5
formulae/0.5.4 rake-nltk/1.0.6
/0.3.4 (202510) rapidfuzz/3.0.0
fqdn/1.5.1 ratelimiter/1.2.0.post0 (202407)
freetype-py/2.3.0 ray/2.47.1
frozendict/2.3.8 rdata/0.11.2
frozenlist/1.3.3 readchar/4.0.5
fsspec/2023.5.0 readfcs/2.0.1
future/0.18.3 readme-renderer/37.3
future-fstrings/1.2.0 redis/6.2.0
gast/0.5.4 referencing/0.35.1
gcs-oauth2-boto-plugin/3.0 refgenconf/0.12.2
genomepy/0.15.0 refgenie/0.12.1
geopandas/1.0.1 regex/2023.5.5
geosketch/1.2 reportlab/4.0.0
get_version/3.5.4 reportseff/2.7.7
gffutils/0.11.1 Represent/1.6.0.post0
gitdb/4.0.10 requests/2.32.5
gitdb2/4.0.2 /2.31.0 (202507)
GitPython/3.1.31 /2.26.0 (202310)
glom/23.5.0 requests-cache/1.3.1
GMM-Demux/0.2.2.3 requests-oauthlib/1.3.1
/0.2.1.3 (202410) requests-toolbelt/1.0.0
google-api-core/2.25.1 reretry/0.11.8
google-apitools/0.5.32 resource-backed-dask-array/0.1.0
google-auth/2.17.3 retry/0.9.2
google-auth-oauthlib/1.0.0 retry-decorator/1.1.1
google-pasta/0.2.0 retrying/1.3.4
google-reauth/0.1.1 rfc3339-validator/0.1.4
googleapis-common-protos/1.70.0 rfc3986/2.0.0
grapheme/0.6.0 rfc3986-validator/0.1.1
graphlite/1.0.5 rhe/1.0.0
graphtools/1.5.3 rich/13.9.4
graphviz/0.8.4 /13.3.5 (202501)
greenlet/3.3.1 rich-click/1.6.1
/2.0.2 (202601) RISparser/0.4.4
grpcio/1.54.0 rlPyCairo/0.2.0
gseapy/1.1.13 roifile/2025.5.10
gsutil/5.23 rope/1.8.0
gunicorn/20.1.0 rpds-py/0.18.1
h11/0.14.0 rpy2/3.5.14
h5netcdf/1.1.0 rsa/4.7.2
h5py/3.14.0 RSeQC/5.0.1
/3.15.1 (202604) Rtree/1.0.1
/3.8.0 (202510) ruamel.yaml/0.17.26
harmonypy/0.0.10 ruamel.yaml.clib/0.2.7
hdf5plugin/4.4.0 ruffus/2.8.4
HeapDict/1.0.1 rustworkx/0.16.0
helpdev/0.7.1 s-gd2/1.8.1 (202507)
henipipe/2.4.7 s3fs/0.4.2
hf-xet/1.1.8 s3transfer/0.10.4
hic2cool/0.8.3 /0.6.1 (202501)
HiCMatrix/17.2 safetensors/0.6.2
/15 (202407) scandir/1.10.0
hierdiff/0.9 (202604) scanorama/1.7.3
hmmlearn/0.3.3 scanpy/1.11.5
/0.3.0 (202410) /1.11.1 (202510)
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lineax/0.0.7 (202604) tensorflow_cpu/2.21.0
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lit/16.0.3 tensorstore/0.1.78
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mock/5.0.2 twine/4.0.2
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nose/1.3.7 wheel/0.40.0
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