2023-12-13: updates: pandas/2.1.4 ; SQLAlchemy/2.0.23
2023-12-12: removed: magic-impute, scprep. Old dependency blocking new installs & upgrades. magic-impute available in snapshot
2023-12-05: new: cellbender/0.3.0 ; jupyter-contrib-core/0.4.2 ; jupyter-contrib-nbextensions/0.7.0 ; jupyter-highlight-selected-word/0.2.0 ; jupyter-nbextensions-configurator/0.6.3
2023-12-05: updates: pip/23.3.1
2023-12-05: downgrades: mistune/0.8.4 ; nbconvert/6.5.4
2023-11-30: updates: cellrank/2.0.2 ; llvmlite/0.41.1 ; numba/0.58.1
2023-11-27: new: mageck/0.5.9.5
2023-11-22: new: TElocal/1.1.1
2023-11-22: updates: argparse/1.4.0
2023-11-21: new: anndata2ri/1.3.1
2023-11-20: new: rpy2/3.5.14
2023-11-15: new: TEtranscripts/2.2.3
2023-11-14: new: apricot-select/0.6.1 ; pomegranate/1.0.3
2023-11-10: updates: multivelo/0.1.3
2023-11-10: downgrades: ipywidgets/7.7.1 ; widgetsnbextension/3.6.6
2023-10-30: updates: pyscenic/0.12.2b0
2023-10-27: updates: packaging/23.2
2023-10-12: new: nd2/0.8.0 ; resource-backed-dask-array/0.1.0
2023-10-04: new: annotated-types/0.5.0 ; backoff/2.2.1 ; blessed/1.20.0 ; croniter/1.4.1 ; dateutils/0.6.12 ; deepdiff/6.5.0 ; fastapi/0.103.2 ; h11/0.14.0 ; inquirer/3.1.3 ; lightning/2.0.9.post0 ; lightning-cloud/0.5.39 ; lightning-utilities/0.9.0 ; ordered-set/4.1.0 ; pydantic_core/2.4.0 ; python-editor/1.0.4 ; python-multipart/0.0.6 ; pytorch-lightning/2.0.9.post0 ; readchar/4.0.5 ; scvi-tools/1.0.3 ; starlette/0.27.0 ; starsessions/1.3.0 ; uvicorn/0.23.2 ; websockets/11.0.3
2023-10-04: updates: anyio/3.7.1 ; ml-dtypes/0.3.1 ; numpyro/0.13.2 ; requests/2.31.0 ; typing_extensions/4.8.0
2023-10-04: downgrades: jax/0.4.17 ; jaxlib/0.4.17
about-time/4.2.1 ipaddress/1.0.23 pynndescent/0.5.10 absl-py/1.4.0 ipykernel/6.23.0 pynvml/11.5.0 adjustText/0.8 ipython/8.13.2 pyOpenSSL/23.1.1 aeppl/0.1.4 ipython-genutils/0.2.0 pypairix/0.3.7 aesara/2.9.0 ipywidgets/7.7.1 pyparsing/3.0.9 aiofiles/22.1.0 isal/1.1.0 PyPDF2/3.0.1 aiohttp/3.8.4 isodate/0.6.1 pyperclip/1.8.2 aiosignal/1.3.1 isoduration/20.11.0 PyQt5/5.15.9 aiosqlite/0.19.0 isort/5.12.0 PyQt5-Qt5/5.15.2 alabaster/0.7.13 iteround/1.0.4 PyQt5-sip/12.12.1 alembic/1.10.4 itsdangerous/2.1.2 PyQtWebEngine/5.15.6 alive-progress/3.1.2 jaraco.classes/3.2.3 PyQtWebEngine-Qt5/5.15.2 aniso8601/9.0.1 jax/0.4.17 pyranges/0.0.125 anndata/0.9.1 jaxlib/0.4.17 pyro-api/0.1.2 anndata2ri/1.3.1 jdcal/1.4.1 pyro-ppl/1.8.4 annotated-types/0.5.0 jedi/0.17.2 pyrsistent/0.19.3 annoy/1.17.2 jeepney/0.8.0 pysam/0.21.0 anyio/3.7.1 jellyfish/0.11.2 pyscenic/0.12.2b0 appdirs/1.4.4 Jinja2/3.0.3 pysimdjson/5.0.2 apricot-select/0.6.1 jinja2-time/0.2.0 pysr/0.12.3 arboreto/0.1.6 jit-open/1.0.2 pystan/3.7.0 argcomplete/3.0.8 jmespath/1.0.1 pytensor/2.11.2 argh/0.28.1 joblib/1.2.0 pytest/7.3.1 argon2-cffi/21.3.0 json5/0.9.11 pytest-cov/4.0.0 argon2-cffi-bindings/21.2.0 jsonpointer/2.3 pytest-dependency/0.5.1 argparse/1.4.0 jsonschema/4.17.3 python-dateutil/2.8.2 arrow/1.2.3 julia/0.6.1 python-editor/1.0.4 arviz/0.15.1 jupyter/1.0.0 python-igraph/0.10.4 asciitree/0.3.3 jupyter-console/6.6.3 python-json-logger/2.0.7 astor/0.8.1 jupyter-contrib-core/0.4.2 python-jsonrpc-server/0.4.0 astroid/2.15.4 jupyter-contrib-nbextensions/0.7.0 python-language-server/0.36.2 asttokens/2.2.1 jupyter-events/0.6.3 python-Levenshtein/0.21.0 astunparse/1.6.3 jupyter-highlight-selected-word/0.2.0 python-lsp-black/1.2.1 async-generator/1.10 jupyter-nbextensions-configurator/0.6.3 python-lsp-jsonrpc/1.0.0 async-timeout/4.0.2 jupyter-telemetry/0.1.0 python-lsp-server/1.7.2 atomicwrites/1.4.1 jupyter-ydoc/0.2.4 python-magic/0.4.27 attmap/0.13.2 jupyter_client/8.2.0 python-multipart/0.0.6 attrs/23.1.0 jupyter_core/5.3.0 python-slugify/8.0.1 autopage/0.5.1 jupyter_server/2.5.0 python-utils/3.5.2 autopep8/2.0.2 jupyter_server_fileid/0.9.0 pytoolconfig/1.2.5 azure-common/1.1.28 jupyter_server_terminals/0.4.4 pytorch-ignite/0.4.12 azure-core/1.26.4 jupyter_server_ydoc/0.8.0 pytorch-lightning/2.0.9.post0 azure-identity/1.12.0 jupyterhub/4.0.0 pytz/2023.3 azure-mgmt-core/1.4.0 jupyterlab/3.6.3 pytz-deprecation-shim/0.1.0.post0 azure-mgmt-storage/21.0.0 jupyterlab-pygments/0.2.2 pyu2f/0.1.5 azure-storage-blob/12.16.0 jupyterlab-widgets/3.0.7 pyviz-comms/2.2.1 azure-storage-file-datalake/12.11.0 jupyterlab_server/2.22.1 PyWavelets/1.4.1 Babel/2.12.1 kb-python/0.27.3 pywin32-ctypes/0.2.0 backcall/0.2.0 keyring/23.13.1 pyxdg/0.28 backoff/2.2.1 kiwisolver/1.4.4 PyYAML/6.0 backports-abc/0.5 kneed/0.8.3 pyzmq/25.0.2 backspinpy/0.2.1 lazy-object-proxy/1.9.0 QDarkStyle/3.1 bambi/0.10.0 lazy_loader/0.2 qnorm/0.8.1 bcbio-gff/0.7.0 legacy-api-wrap/1.2 qstylizer/0.2.2 beautifulsoup4/4.12.2 leidenalg/0.9.1 QtAwesome/1.2.3 binaryornot/0.4.4 Levenshtein/0.21.0 qtconsole/5.4.3 biopython/1.81 lightning/2.0.9.post0 QtPy/2.3.1 biothings-client/0.3.0 lightning-cloud/0.5.39 rake-nltk/1.0.6 BitVector/3.5.0 lightning-utilities/0.9.0 rapidfuzz/3.0.0 black/23.3.0 lit/16.0.3 ratelimiter/1.2.0.post0 bleach/6.0.0 llvmlite/0.41.1 readchar/4.0.5 blessed/1.20.0 locket/1.0.0 readme-renderer/37.3 blosc2/2.0.0 Logbook/1.5.3 refgenconf/0.12.2 bokeh/2.4.3 logical-unification/0.4.6 refgenie/0.12.1 boltons/23.0.0 logmuse/0.2.7 regex/2023.5.5 boto/2.49.0 logomaker/0.8 reportlab/4.0.0 boto3/1.26.131 loguru/0.7.0 Represent/1.6.0.post0 botocore/1.29.131 loompy/3.0.7 requests/2.31.0 Brotli/1.0.9 looper/1.5.1 requests-oauthlib/1.3.1 BucketCache/0.12.1 louvain/0.8.0 requests-toolbelt/1.0.0 bulker/0.7.3 lxml/4.9.2 reretry/0.11.8 bustools/0.1.0.dev2 lz4/4.3.2 resource-backed-dask-array/0.1.0 bx-python/0.9.0 lzstring/1.0.4 retry/0.9.2 cached-property/1.5.2 MACS3/3.0.0b1 retry-decorator/1.1.1 cachetools/5.3.0 mageck/0.5.9.5 retrying/1.3.4 cellbender/0.3.0 Mako/1.2.4 rfc3339-validator/0.1.4 cellpose/2.2.1 mappy/2.26 rfc3986/2.0.0 cellrank/2.0.2 Markdown/3.4.3 rfc3986-validator/0.1.1 cellSNP/0.3.2 markdown-it-py/2.2.0 rich/13.3.5 certifi/2023.5.7 MarkupSafe/2.1.2 rich-click/1.6.1 certipy/0.1.3 marshmallow/3.19.0 RISparser/0.4.4 cffi/1.15.1 matplotlib/3.7.1 rlPyCairo/0.2.0 cftime/1.6.2 matplotlib-inline/0.1.6 rope/1.8.0 chardet/5.1.0 mccabe/0.7.0 rpy2/3.5.14 charset-normalizer/2.0.12 mdurl/0.1.2 rsa/4.7.2 chex/0.1.7 mgatk/0.6.7 RSeQC/5.0.1 click/8.1.3 miniKanren/1.0.3 Rtree/1.0.1 clikit/0.6.2 mistune/0.8.4 ruamel.yaml/0.17.26 cloudpickle/2.2.1 ml-collections/0.1.1 ruamel.yaml.clib/0.2.7 clust/1.18.0 ml-dtypes/0.3.1 s-gd2/1.8.1 cmake/3.26.3 mock/5.0.2 s3fs/0.4.2 cmd2/2.4.3 monotonic/1.6 s3transfer/0.6.1 colorama/0.4.6 MOODS-python/1.9.4.1 scandir/1.10.0 colorcet/3.0.1 more-itertools/9.1.0 scanorama/1.7.3 coloredlogs/15.0.1 mpmath/1.3.0 scanpy/1.9.3 colormath/3.0.0 msal/1.22.0 scikit-image/0.20.0 comm/0.1.3 msal-extensions/1.0.0 scikit-learn/1.2.2 commonmark/0.9.1 msgpack/1.0.5 scipy/1.10.1 ConfigArgParse/1.5.3 msgraph-core/0.2.2 SCons/4.5.2 configparser/5.3.0 msrest/0.7.1 scrublet/0.2.3 configs/3.0.3 mudata/0.2.2 scvelo/0.2.5 connection-pool/0.0.3 multidict/6.0.4 scvi-tools/1.0.3 cons/0.4.5 multipagetiff/3.0.9 seaborn/0.12.2 contextlib2/21.6.0 multipledispatch/0.6.0 SecretStorage/3.3.3 contourpy/1.0.7 multiprocess/0.70.14 semver/3.0.0 cookiecutter/2.1.1 multiprocessing-on-dill/3.5.0a4 Send2Trash/1.8.2 cooler/0.9.1 multiqc/1.14 session-info/1.0.0 coverage/7.2.5 multivelo/0.1.3 setuptools-scm/7.1.0 CPAT/3.0.4 mxnet-mkl/1.6.0 shortuuid/1.0.11 crashtest/0.3.1 mygene/3.2.2 simplegeneric/0.8.1 crcmod/1.7 mypy-extensions/1.0.0 simplejson/3.19.1 croniter/1.4.1 mysql-connector-python/8.0.33 sinfo/0.3.4 CrossMap/0.6.5 natsort/8.3.1 singledispatch/4.0.0 cryptography/40.0.2 nbclassic/1.0.0 sinto/0.9.0 ctxcore/0.2.0 nbclient/0.7.4 six/1.16.0 cutadapt/4.4 nbconvert/6.5.4 sklearn/0.0.post5 cycler/0.11.0 nbformat/5.8.0 smart-open/6.3.0 cykhash/2.0.1 ncls/0.0.66 smmap/5.0.0 Cython/0.29.34 nd2/0.8.0 smmap2/3.0.1 cytoolz/0.12.1 nest-asyncio/1.5.6 snakemake/7.25.3 cyvcf2/0.30.18 netCDF4/1.6.3 sniffio/1.3.0 dask/2023.4.1 networkx/3.1 snowballstemmer/2.2.0 dask-mpi/2022.4.0 ngs-tools/1.8.3 sorted-nearest/0.0.38 dateutils/0.6.12 nimfa/1.4.0 sortedcontainers/2.4.0 datrie/0.8.2 nltk/3.8.1 soupsieve/2.4.1 debugpy/1.6.7 norns/0.1.6 sparse/0.14.0 decorator/5.1.1 nose/1.3.7 spectra/0.0.11 deepdiff/6.5.0 notebook/6.5.4 Sphinx/7.0.0 deepTools/3.5.2 notebook_shim/0.2.3 sphinxcontrib-applehelp/1.0.4 deeptoolsintervals/0.1.9 numba/0.58.1 sphinxcontrib-devhelp/1.0.2 defusedxml/0.7.1 numcodecs/0.11.0 sphinxcontrib-htmlhelp/2.0.1 demuxEM/0.1.7 numexpr/2.8.4 sphinxcontrib-jsmath/1.0.1 deprecat/2.1.1 numpy/1.24.3 sphinxcontrib-qthelp/1.0.3 Deprecated/1.2.13 numpy-groupies/0.9.22 sphinxcontrib-serializinghtml/1.1.5 dict-trie/1.0.1 numpydoc/1.5.0 spyder/5.4.3 diff-match-patch/20230430 numpyro/0.13.2 spyder-kernels/2.4.3 dill/0.3.6 nvidia-cublas-cu11/11.10.3.66 SQLAlchemy/2.0.23 diskcache/5.6.1 nvidia-cuda-cupti-cu11/11.7.101 sqlitedict/2.1.0 Distance/0.1.3 nvidia-cuda-nvrtc-cu11/11.7.99 sqlmodel/0.0.14 distributed/2023.4.1 nvidia-cuda-runtime-cu11/11.7.99 ssh-audit/2.9.0 divvy/0.6.0 nvidia-cudnn-cu11/8.5.0.96 stack-data/0.6.2 dm-tree/0.1.8 nvidia-cufft-cu11/10.9.0.58 starlette/0.27.0 dnaio/0.10.0 nvidia-curand-cu11/10.2.10.91 starsessions/1.3.0 dnspython/2.3.0 nvidia-cusolver-cu11/11.4.0.1 statistics/1.0.3.5 docopt/0.6.2 nvidia-cusparse-cu11/11.7.4.91 statsmodels/0.14.0 docrep/0.3.2 nvidia-nccl-cu11/2.14.3 stdlib-list/0.8.0 docstring-to-markdown/0.12 nvidia-nvtx-cu11/11.7.91 stevedore/5.0.0 docutils/0.19 oauth2client/4.1.3 stopit/1.1.2 dpath/2.1.5 oauthlib/3.2.2 svgwrite/1.4.3 drmaa/0.7.9 olga/1.2.4 sympy/1.11.1 DukeDSClient/4.0.0 onnx/1.14.0 tables/3.8.0 dunamai/1.16.0 ont-fast5-api/4.1.1 tabulate/0.9.0 eido/0.2.2 ont-tombo/1.5.1 tadtool/0.84 entrypoints/0.4 opencv-python/4.7.0.72 tasklogger/1.2.0 et-xmlfile/1.1.0 opencv-python-headless/4.7.0.72 tbb/2021.9.0 ete3/3.1.3 openpyxl/3.1.2 tblib/1.7.0 etils/1.2.0 opt-einsum/3.3.0 TElocal/1.1.1 etuples/0.3.8 optax/0.1.5 tenacity/6.2.0 executing/1.2.0 optparse-pretty/0.1.1 tensorboard-data-server/0.7.0 fastapi/0.103.2 orbax-checkpoint/0.2.2 tensorboard-plugin-wit/1.8.1 fasteners/0.18 ordered-set/4.1.0 tensorboardX/2.6 fastjsonschema/2.16.3 oyaml/1.0 tensorstore/0.1.36 fastobo/0.12.2 packaging/23.2 termcolor/2.3.0 fastools/1.1.5 palettable/3.3.3 terminado/0.17.1 fastprogress/1.0.3 palmotif/0.4 testpath/0.6.0 fastremap/1.13.4 pamela/1.0.0 TEtranscripts/2.2.3 fbpca/1.0 pandas/2.1.4 text-unidecode/1.3 feather-format/0.4.1 pandocfilters/1.5.0 textdistance/4.5.0 filelock/3.12.0 panel/0.14.4 texttable/1.6.7 fisher/0.1.10 param/1.13.0 Theano/1.0.5 fishersapi/0.5 parasail/1.3.4 Theano-PyMC/1.1.2 flake8/6.0.0 parmap/1.6.0 thop/0.1.1-2209072238 Flask/2.2.5 parse/1.19.0 threadpoolctl/3.1.0 Flask-Compress/1.13 parso/0.7.1 three-merge/0.1.1 Flask-Cors/3.0.10 partd/1.4.0 throttler/1.2.2 Flask-RESTful/0.3.9 pastel/0.2.1 tifffile/2023.4.12 flask-server-timing/0.1.2 pathlib2/2.3.7.post1 tiledb/0.21.3 flask-talisman/1.0.0 pathspec/0.11.1 tinycss2/1.2.1 Flask-Testing/0.8.1 pathtools/0.1.2 tokenizers/0.13.3 flatbuffers/1.12 patsy/0.5.3 toml/0.10.2 flatten-dict/0.4.2 pbr/5.11.1 tomli/2.0.1 flax/0.6.10 pdf2image/1.16.3 tomlkit/0.11.8 fonttools/4.39.3 pegasusio/0.8.0 toolz/0.12.0 formulae/0.3.4 pephubclient/0.2.1 toposort/1.10 fqdn/1.5.1 peppy/0.35.7 torch/2.0.1 freetype-py/2.3.0 pexpect/4.8.0 torchmetrics/0.11.4 frozendict/2.3.8 PhenoGraph/1.5.7 torchvision/0.15.2 frozenlist/1.3.3 pickleshare/0.7.5 tornado/6.3.1 fsspec/2023.5.0 pika/1.3.2 tqdm/4.65.0 future/0.18.3 Pillow/9.5.0 traitlets/5.9.0 future-fstrings/1.2.0 pip/23.3.1 triton/2.0.0 gast/0.5.4 piper/0.13.2 twine/4.0.2 gcs-oauth2-boto-plugin/3.0 pipestat/0.5.2 typed-ast/1.5.4 genomepy/0.15.0 pkginfo/1.9.6 typer/0.9.0 geosketch/1.2 plac/1.3.5 typing_extensions/4.8.0 get_version/3.5.4 platformdirs/3.5.0 tzdata/2023.3 gffutils/0.11.1 Platypus-Opt/1.1.0 tzlocal/4.3 gitdb/4.0.10 plotly/5.14.1 ubiquerg/0.6.3 gitdb2/4.0.2 pluggy/1.0.0 ujson/5.7.0 GitPython/3.1.31 pomegranate/1.0.3 umap-learn/0.5.3 GMM-Demux/0.2.1.3 portalocker/2.7.0 umi-tools/1.1.4 google-apitools/0.5.32 prettytable/3.7.0 Unidecode/1.3.6 google-auth/2.17.3 progress/1.6 uri-template/1.2.0 google-auth-oauthlib/1.0.0 progressbar2/4.2.0 urllib3/1.26.7 google-pasta/0.2.0 progressbar33/2.4 uropa/4.0.2 google-reauth/0.1.1 prometheus-client/0.16.0 uvicorn/0.23.2 grapheme/0.6.0 prompt-toolkit/3.0.38 velocyto/0.17.17 graphlite/1.0.5 protobuf/3.20.3 vendorize/0.3.0 graphtools/1.5.3 psutil/5.9.5 vireoSNP/0.5.8 graphviz/0.8.4 psycopg2-binary/2.9.9 Wand/0.6.11 greenlet/2.0.2 ptyprocess/0.7.0 watchdog/3.0.0 grpcio/1.54.0 PuLP/2.7.0 wcwidth/0.2.6 gsutil/5.23 pure-eval/0.2.2 webargs/8.2.0 gunicorn/20.1.0 pwseqdist/0.6 webcolors/1.13 h11/0.14.0 py/1.11.0 webencodings/0.5.1 h5netcdf/1.1.0 py-cpuinfo/9.0.0 websocket-client/1.5.1 h5py/3.8.0 py2bit/0.3.0 websockets/11.0.3 HeapDict/1.0.1 py4j/0.10.9.7 Werkzeug/2.3.4 helpdev/0.7.1 pyarrow/12.0.0 wget/3.2 henipipe/2.4.7 pyasn1/0.5.0 whatthepatch/1.0.5 hic2cool/0.8.3 pyasn1-modules/0.3.0 wheel/0.40.0 HiCMatrix/15 pyBigWig/0.3.22 widgetsnbextension/3.6.6 hierdiff/0.9 pybktree/1.1 wincertstore/0.2 hmmlearn/0.3.0 pycairo/1.23.0 wrapt/1.15.0 holoviews/1.16.0 pycodestyle/2.10.0 wurlitzer/3.0.3 html5lib/1.1 pycparser/2.21 xarray/2023.4.2 HTSeq/2.0.2 pyct/0.5.0 xarray-einstats/0.5.1 htsget/0.2.5 pydantic/1.10.13 xdg/6.0.0 httplib2/0.20.4 pydantic_core/2.4.0 xgboost/1.7.5 httpstan/4.10.0 pyDeprecate/0.3.2 xlrd/2.0.1 humanfriendly/10.0 pydocstyle/6.3.0 XlsxWriter/3.1.0 humanize/4.6.0 pyfaidx/0.7.2.1 xmltodict/0.13.0 hyperopt/0.2.7 pyflakes/3.0.1 xopen/1.7.0 idna/3.4 pygam/0.9.0 xtiff/0.7.9 idr/0.0.1 Pygments/2.15.1 xxhash/3.2.0 igraph/0.10.4 pygpcca/1.0.4 xyzservices/2023.2.0 imagecodecs/2023.3.16 PyGSP/0.5.1 y-py/0.5.9 imageio/2.28.1 PyJWT/2.7.0 yacman/0.9.2 imagesize/1.4.1 pylev/1.4.0 yapf/0.32.0 imctools/2.1.8 pylint/2.17.4 yarl/1.9.2 importlib-metadata/6.6.0 pylint-venv/3.0.1 ypy-websocket/0.8.2 importlib-resources/5.12.0 pyls-black/0.4.7 yte/1.5.1 inflection/0.5.1 pyls-spyder/0.4.0 zarr/2.14.2 iniconfig/2.0.0 pymc/5.3.1 zict/3.0.0 inquirer/3.1.3 pymc3/3.11.4 zipp/3.15.0 interlap/0.2.7 pymongo/4.3.3 zmq/0.0.0 intervaltree/3.1.0 PyMuPDF/1.22.2