requirements.txt

#
# This file is autogenerated by pip-compile with Python 3.11
# by the following command:
#
#    pip-compile --output-file=requirements.txt pyproject.toml
#
adjusttext==1.0.4
    # via
    #   pycistopic
    #   scenicplus (pyproject.toml)
aiohttp==3.9.3
    # via pyscenic
aiosignal==1.3.1
    # via
    #   aiohttp
    #   ray
anndata==0.10.5.post1
    # via
    #   mudata
    #   scanpy
    #   scenicplus (pyproject.toml)
annoy==1.17.3
    # via
    #   bbknn
    #   scanorama
    #   scenicplus (pyproject.toml)
    #   scrublet
appdirs==1.4.4
    # via
    #   bioservices
    #   snakemake
arboreto==0.1.6
    # via
    #   pyscenic
    #   scenicplus (pyproject.toml)
argparse-dataclass==2.0.0
    # via
    #   snakemake-interface-common
    #   snakemake-interface-executor-plugins
array-api-compat==1.5.1
    # via anndata
asttokens==2.4.1
    # via stack-data
attr==0.3.2
    # via scenicplus (pyproject.toml)
attrs==23.2.0
    # via
    #   aiohttp
    #   cattrs
    #   jsonschema
    #   pyscenic
    #   referencing
    #   requests-cache
    #   scenicplus (pyproject.toml)
bbknn==1.6.0
    # via
    #   pycistopic
    #   scenicplus (pyproject.toml)
beautifulsoup4==4.12.3
    # via
    #   bioservices
    #   bs4
    #   scenicplus (pyproject.toml)
bidict==0.23.1
    # via tmtoolkit
bioservices==1.11.2
    # via gseapy
blosc2==2.5.1
    # via tables
bokeh==3.4.0
    # via dask
boltons==23.1.1
    # via pyscenic
bs4==0.0.2
    # via
    #   pycistopic
    #   scenicplus (pyproject.toml)
cattrs==23.2.3
    # via requests-cache
certifi==2024.2.2
    # via requests
charset-normalizer==3.3.2
    # via requests
click==8.1.7
    # via
    #   dask
    #   distributed
    #   loompy
    #   loomxpy
    #   ray
cloudpickle==3.0.0
    # via
    #   dask
    #   distributed
    #   pyscenic
colorama==0.4.6
    # via easydev
colorlog==6.8.2
    # via
    #   bioservices
    #   easydev
conda-inject==1.3.1
    # via snakemake
configargparse==1.7
    # via
    #   snakemake
    #   snakemake-interface-common
connection-pool==0.0.3
    # via snakemake
contourpy==1.2.0
    # via
    #   bokeh
    #   matplotlib
ctxcore==0.2.0
    # via
    #   pycistarget
    #   pyscenic
    #   scenicplus (pyproject.toml)
cycler==0.12.1
    # via matplotlib
cython==0.29.37
    # via
    #   bbknn
    #   macs2
    #   pyranges
    #   scenicplus (pyproject.toml)
    #   scrublet
cytoolz==0.12.3
    # via
    #   ctxcore
    #   pyscenic
    #   scenicplus (pyproject.toml)
dask[array,complete,dataframe,diagnostics,distributed]==2024.2.1
    # via
    #   arboreto
    #   distributed
    #   pyscenic
    #   scenicplus (pyproject.toml)
dataclasses-json==0.6.4
    # via loomxpy
datrie==0.8.2
    # via snakemake
decorator==5.1.1
    # via ipython
dill==0.3.8
    # via
    #   multiprocessing-on-dill
    #   scenicplus (pyproject.toml)
distributed==2024.2.1
    # via
    #   arboreto
    #   dask
    #   pyscenic
docutils==0.20.1
    # via
    #   snakemake
    #   statistics
dpath==2.1.6
    # via
    #   snakemake
    #   yte
easydev==0.13.1
    # via bioservices
et-xmlfile==1.1.0
    # via openpyxl
executing==2.0.1
    # via stack-data
fastjsonschema==2.19.1
    # via nbformat
fbpca==1.0
    # via
    #   geosketch
    #   scanorama
filelock==3.13.1
    # via ray
fonttools==4.50.0
    # via matplotlib
frozendict==2.4.0
    # via
    #   ctxcore
    #   pyscenic
frozenlist==1.4.1
    # via
    #   aiohttp
    #   aiosignal
    #   ray
fsspec==2024.3.1
    # via
    #   dask
    #   pyscenic
future==1.0.0
    # via pybiomart
gensim==4.3.2
    # via
    #   pycistopic
    #   scenicplus (pyproject.toml)
geosketch==1.2
    # via scanorama
gevent==24.2.1
    # via grequests
gitdb==4.0.11
    # via gitpython
gitpython==3.1.42
    # via snakemake
globre==0.1.5
    # via tmtoolkit
greenlet==3.0.3
    # via gevent
grequests==0.7.0
    # via bioservices
gseapy==0.10.8
    # via scenicplus (pyproject.toml)
h5py==3.10.0
    # via
    #   anndata
    #   loompy
    #   mudata
    #   pycistarget
    #   scanpy
    #   scenicplus (pyproject.toml)
harmonypy==0.0.9
    # via
    #   pycistopic
    #   scenicplus (pyproject.toml)
humanfriendly==10.0
    # via snakemake
idna==3.6
    # via
    #   requests
    #   yarl
igraph==0.11.4
    # via
    #   leidenalg
    #   pycistopic
    #   scenicplus (pyproject.toml)
imageio==2.34.0
    # via
    #   scenicplus (pyproject.toml)
    #   scikit-image
immutables==0.20
    # via snakemake
importlib-metadata==7.0.1
    # via
    #   dask
    #   scenicplus (pyproject.toml)
importlib-resources==6.1.2
    # via scenicplus (pyproject.toml)
interlap==0.2.7
    # via pyscenic
intervaltree==3.1.0
    # via
    #   scanorama
    #   scenicplus (pyproject.toml)
ipython==8.22.2
    # via
    #   pycistarget
    #   pyvis
jedi==0.19.1
    # via ipython
jinja2==3.1.3
    # via
    #   bokeh
    #   dask
    #   distributed
    #   pyvis
    #   snakemake
joblib==1.3.2
    # via
    #   gseapy
    #   pynndescent
    #   scanpy
    #   scatac-fragment-tools
    #   scenicplus (pyproject.toml)
    #   scikit-learn
jsonpickle==3.0.3
    # via pyvis
jsonschema==4.21.1
    # via
    #   nbformat
    #   ray
    #   snakemake
jsonschema-specifications==2023.12.1
    # via jsonschema
jupyter-core==5.7.2
    # via nbformat
kaleido==0.2.1
    # via scenicplus (pyproject.toml)
kiwisolver==1.4.5
    # via matplotlib
lazy-loader==0.3
    # via scikit-image
lda==3.0.0
    # via
    #   pycistopic
    #   scenicplus (pyproject.toml)
leidenalg==0.10.2
    # via
    #   pycistopic
    #   scenicplus (pyproject.toml)
line-profiler==4.1.2
    # via easydev
llvmlite==0.42.0
    # via
    #   numba
    #   pynndescent
    #   pyscenic
locket==1.0.0
    # via
    #   distributed
    #   partd
loompy==3.0.7
    # via
    #   loomxpy
    #   pyscenic
loomxpy @ git+https://github.com/aertslab/LoomXpy@main
    # via
    #   pycistopic
    #   scenicplus (pyproject.toml)
lxml==5.1.0
    # via
    #   bioservices
    #   pycistopic
    #   scenicplus (pyproject.toml)
lz4==4.3.3
    # via dask
macs2==2.2.9.1
    # via
    #   pycistopic
    #   scenicplus (pyproject.toml)
markdown-it-py==3.0.0
    # via rich
markupsafe==2.1.5
    # via jinja2
marshmallow==3.21.1
    # via dataclasses-json
matplotlib==3.6.3
    # via
    #   adjusttext
    #   bioservices
    #   gseapy
    #   mizani
    #   plotnine
    #   pycistopic
    #   scanorama
    #   scanpy
    #   scenicplus (pyproject.toml)
    #   scrublet
    #   seaborn
    #   tmtoolkit
    #   tspex
matplotlib-inline==0.1.6
    # via ipython
mdurl==0.1.2
    # via markdown-it-py
mizani==0.9.3
    # via plotnine
msgpack==1.0.8
    # via
    #   blosc2
    #   distributed
    #   ray
mudata==0.2.3
    # via scenicplus (pyproject.toml)
multidict==6.0.5
    # via
    #   aiohttp
    #   yarl
multiprocessing-on-dill==3.5.0a4
    # via pyscenic
mypy-extensions==1.0.0
    # via typing-inspect
natsort==8.4.0
    # via
    #   anndata
    #   pyranges
    #   pyrle
    #   scanpy
nbformat==5.10.3
    # via snakemake
ncls==0.0.68
    # via
    #   pyranges
    #   scenicplus (pyproject.toml)
ndindex==1.8
    # via blosc2
networkx==3.2.1
    # via
    #   pyscenic
    #   pyvis
    #   scanpy
    #   scenicplus (pyproject.toml)
    #   scikit-image
numba==0.59.0
    # via
    #   ctxcore
    #   loompy
    #   pynndescent
    #   pyscenic
    #   scanpy
    #   scatac-fragment-tools
    #   scenicplus (pyproject.toml)
    #   scrublet
    #   umap-learn
numexpr==2.9.0
    # via
    #   pyscenic
    #   scenicplus (pyproject.toml)
    #   tables
numpy==1.26.4
    # via
    #   adjusttext
    #   anndata
    #   arboreto
    #   bbknn
    #   blosc2
    #   bokeh
    #   contourpy
    #   ctxcore
    #   dask
    #   gensim
    #   geosketch
    #   gseapy
    #   h5py
    #   harmonypy
    #   imageio
    #   lda
    #   loompy
    #   loomxpy
    #   macs2
    #   matplotlib
    #   mizani
    #   mudata
    #   ncls
    #   numba
    #   numexpr
    #   numpy-groupies
    #   pandas
    #   patsy
    #   plotnine
    #   pyarrow
    #   pybedtools
    #   pybigtools
    #   pycistarget
    #   pycistopic
    #   pygam
    #   pyrle
    #   pyscenic
    #   scanorama
    #   scanpy
    #   scatac-fragment-tools
    #   scenicplus (pyproject.toml)
    #   scikit-image
    #   scikit-learn
    #   scipy
    #   scrublet
    #   seaborn
    #   sorted-nearest
    #   statsmodels
    #   tables
    #   tifffile
    #   tmtoolkit
    #   tspex
    #   umap-learn
numpy-groupies==0.10.2
    # via
    #   loompy
    #   scenicplus (pyproject.toml)
openpyxl==3.1.2
    # via tmtoolkit
packaging==24.0
    # via
    #   anndata
    #   bokeh
    #   dask
    #   distributed
    #   marshmallow
    #   matplotlib
    #   plotly
    #   ray
    #   scanpy
    #   scikit-image
    #   snakemake
    #   statsmodels
    #   tables
pandas==1.5.0
    # via
    #   anndata
    #   arboreto
    #   bbknn
    #   bioservices
    #   bokeh
    #   ctxcore
    #   dask
    #   gseapy
    #   harmonypy
    #   loomxpy
    #   mizani
    #   mudata
    #   plotnine
    #   pybiomart
    #   pycistarget
    #   pycistopic
    #   pyranges
    #   pyrle
    #   pyscenic
    #   scanpy
    #   scenicplus (pyproject.toml)
    #   scrublet
    #   seaborn
    #   statsmodels
    #   tmtoolkit
    #   tspex
parso==0.8.3
    # via jedi
partd==1.4.1
    # via dask
patsy==0.5.6
    # via
    #   plotnine
    #   scanpy
    #   statsmodels
pexpect==4.9.0
    # via
    #   easydev
    #   ipython
pillow==10.2.0
    # via
    #   bokeh
    #   imageio
    #   matplotlib
    #   scikit-image
plac==1.4.3
    # via yte
platformdirs==4.2.0
    # via
    #   easydev
    #   jupyter-core
    #   requests-cache
plotly==5.19.0
    # via scenicplus (pyproject.toml)
plotnine==0.12.4
    # via scenicplus (pyproject.toml)
polars==0.20.13
    # via
    #   pycistopic
    #   scatac-fragment-tools
    #   scenicplus (pyproject.toml)
progressbar2==4.4.2
    # via pygam
prompt-toolkit==3.0.43
    # via ipython
protobuf==5.26.0
    # via ray
psutil==5.9.8
    # via
    #   distributed
    #   snakemake
ptyprocess==0.7.0
    # via pexpect
pulp==2.8.0
    # via snakemake
pure-eval==0.2.2
    # via stack-data
py-cpuinfo==9.0.0
    # via
    #   blosc2
    #   tables
pyarrow==15.0.0
    # via
    #   ctxcore
    #   dask
    #   pycistopic
    #   scatac-fragment-tools
    #   scenicplus (pyproject.toml)
pyarrow-hotfix==0.6
    # via
    #   dask
    #   scenicplus (pyproject.toml)
pybedtools==0.9.1
    # via scenicplus (pyproject.toml)
pybigtools==0.1.2
    # via
    #   scatac-fragment-tools
    #   scenicplus (pyproject.toml)
pybigwig==0.3.22
    # via
    #   scatac-fragment-tools
    #   scenicplus (pyproject.toml)
pybiomart==0.2.0
    # via
    #   pycistopic
    #   scenicplus (pyproject.toml)
pycistarget @ git+https://github.com/aertslab/pycistarget
    # via scenicplus (pyproject.toml)
pycistopic @ git+https://github.com/aertslab/pycisTopic
    # via scenicplus (pyproject.toml)
pyfasta==0.5.2
    # via scenicplus (pyproject.toml)
pygam==0.9.0
    # via scenicplus (pyproject.toml)
pygments==2.17.2
    # via
    #   ipython
    #   rich
pynndescent==0.5.11
    # via
    #   bbknn
    #   umap-learn
pyparsing==3.1.2
    # via matplotlib
pyranges==0.0.111
    # via
    #   pycistarget
    #   pycistopic
    #   scenicplus (pyproject.toml)
pyrle==0.0.39
    # via
    #   pyranges
    #   scenicplus (pyproject.toml)
pysam==0.22.0
    # via
    #   pybedtools
    #   scenicplus (pyproject.toml)
pyscenic @ git+https://github.com/aertslab/pySCENIC@master
    # via
    #   loomxpy
    #   pycistopic
    #   scenicplus (pyproject.toml)
python-dateutil==2.9.0.post0
    # via
    #   matplotlib
    #   pandas
python-utils==3.8.2
    # via progressbar2
pytz==2024.1
    # via pandas
pyvis==0.3.2
    # via scenicplus (pyproject.toml)
pyyaml==6.0.1
    # via
    #   bokeh
    #   conda-inject
    #   ctxcore
    #   dask
    #   distributed
    #   pyscenic
    #   ray
    #   snakemake
    #   yte
ray==2.9.3
    # via
    #   pycistopic
    #   scenicplus (pyproject.toml)
referencing==0.34.0
    # via
    #   jsonschema
    #   jsonschema-specifications
requests==2.31.0
    # via
    #   bioservices
    #   grequests
    #   gseapy
    #   pybiomart
    #   pyscenic
    #   ray
    #   requests-cache
    #   scenicplus (pyproject.toml)
    #   snakemake
requests-cache==1.2.0
    # via
    #   bioservices
    #   pybiomart
    #   scenicplus (pyproject.toml)
reretry==0.11.8
    # via
    #   snakemake
    #   snakemake-interface-storage-plugins
rich==13.7.1
    # via rich-argparse
rich-argparse==1.4.0
    # via scatac-fragment-tools
rpds-py==0.18.0
    # via
    #   jsonschema
    #   referencing
scanorama==1.7.4
    # via
    #   pycistopic
    #   scenicplus (pyproject.toml)
scanpy==1.8.2
    # via
    #   pycistopic
    #   scenicplus (pyproject.toml)
scatac-fragment-tools==0.1.0
    # via
    #   pycistopic
    #   scenicplus (pyproject.toml)
scikit-image==0.22.0
    # via
    #   scenicplus (pyproject.toml)
    #   scrublet
scikit-learn==1.3.2
    # via
    #   arboreto
    #   bbknn
    #   geosketch
    #   harmonypy
    #   loomxpy
    #   pycistarget
    #   pycistopic
    #   pynndescent
    #   pyscenic
    #   scanorama
    #   scanpy
    #   scenicplus (pyproject.toml)
    #   scrublet
    #   umap-learn
scipy==1.12.0
    # via
    #   adjusttext
    #   anndata
    #   arboreto
    #   bbknn
    #   gensim
    #   gseapy
    #   harmonypy
    #   loompy
    #   mizani
    #   plotnine
    #   pygam
    #   pynndescent
    #   pyscenic
    #   scanorama
    #   scanpy
    #   scenicplus (pyproject.toml)
    #   scikit-image
    #   scikit-learn
    #   scrublet
    #   statsmodels
    #   tmtoolkit
    #   umap-learn
scrublet==0.2.3
    # via
    #   pycistopic
    #   scenicplus (pyproject.toml)
seaborn==0.13.2
    # via
    #   pycistopic
    #   scanpy
    #   scenicplus (pyproject.toml)
sinfo==0.3.4
    # via scanpy
six==1.16.0
    # via
    #   asttokens
    #   patsy
    #   pybedtools
    #   python-dateutil
    #   url-normalize
smart-open==6.4.0
    # via
    #   gensim
    #   snakemake
smmap==5.0.1
    # via gitdb
snakemake==8.5.5
    # via scenicplus (pyproject.toml)
snakemake-interface-common==1.17.1
    # via
    #   scenicplus (pyproject.toml)
    #   snakemake
    #   snakemake-interface-executor-plugins
    #   snakemake-interface-report-plugins
    #   snakemake-interface-storage-plugins
snakemake-interface-executor-plugins==8.2.0
    # via
    #   scenicplus (pyproject.toml)
    #   snakemake
snakemake-interface-report-plugins==1.0.0
    # via
    #   scenicplus (pyproject.toml)
    #   snakemake
snakemake-interface-storage-plugins==3.1.1
    # via
    #   scenicplus (pyproject.toml)
    #   snakemake
sorted-nearest==0.0.39
    # via pyranges
sortedcontainers==2.4.0
    # via
    #   distributed
    #   intervaltree
soupsieve==2.5
    # via beautifulsoup4
stack-data==0.6.3
    # via ipython
statistics==1.0.3.5
    # via scenicplus (pyproject.toml)
statsmodels==0.14.1
    # via
    #   plotnine
    #   pycistopic
    #   scanpy
    #   scenicplus (pyproject.toml)
stdlib-list==0.10.0
    # via sinfo
stopit==1.1.2
    # via snakemake
suds-community==1.1.2
    # via bioservices
tables==3.9.2
    # via scanpy
tabulate==0.9.0
    # via
    #   pyranges
    #   pyrle
    #   snakemake
tblib==3.0.0
    # via distributed
tenacity==8.2.3
    # via plotly
texttable==1.7.0
    # via igraph
threadpoolctl==3.4.0
    # via scikit-learn
throttler==1.2.2
    # via
    #   snakemake
    #   snakemake-interface-executor-plugins
    #   snakemake-interface-storage-plugins
tifffile==2024.2.12
    # via scikit-image
tmtoolkit==0.12.0
    # via
    #   pycistopic
    #   scenicplus (pyproject.toml)
toolz==0.12.1
    # via
    #   cytoolz
    #   dask
    #   distributed
    #   partd
toposort==1.10
    # via snakemake
tornado==6.4
    # via
    #   bokeh
    #   distributed
tqdm==4.66.2
    # via
    #   bioservices
    #   ctxcore
    #   pyscenic
    #   scanpy
    #   scenicplus (pyproject.toml)
    #   umap-learn
traitlets==5.14.2
    # via
    #   ipython
    #   jupyter-core
    #   matplotlib-inline
    #   nbformat
tspex==0.6.3
    # via scenicplus (pyproject.toml)
typing==3.7.4.3
    # via scenicplus (pyproject.toml)
typing-extensions==4.10.0
    # via
    #   python-utils
    #   typing-inspect
typing-inspect==0.9.0
    # via dataclasses-json
umap-learn==0.5.5
    # via
    #   bbknn
    #   pyscenic
    #   scanpy
    #   scenicplus (pyproject.toml)
    #   scrublet
url-normalize==1.4.3
    # via requests-cache
urllib3==2.2.1
    # via
    #   distributed
    #   requests
    #   requests-cache
wcwidth==0.2.13
    # via prompt-toolkit
wheel==0.43.0
    # via tmtoolkit
wrapt==1.16.0
    # via
    #   bioservices
    #   snakemake
    #   snakemake-interface-storage-plugins
xlrd==2.0.1
    # via
    #   tmtoolkit
    #   tspex
xmltodict==0.13.0
    # via bioservices
xyzservices==2023.10.1
    # via bokeh
yarl==1.9.4
    # via aiohttp
yte==1.5.4
    # via snakemake
zict==3.0.0
    # via distributed
zipp==3.18.1
    # via importlib-metadata
zope-event==5.0
    # via gevent
zope-interface==6.2
    # via gevent

# The following packages are considered to be unsafe in a requirements file:
# setuptools