requirements.txt

#
# This file is autogenerated by pip-compile with python 3.9
# To update, run:
#
#    pip-compile --index-url=http://localhost:1895 requirements.in
#
# --index-url http://localhost:1895

ansiwrap==0.8.4
    # via papermill
appdirs==1.4.4
    # via black
argon2-cffi==20.1.0
    # via notebook
astunparse==1.6.3
    # via mdtraj
async-generator==1.10
    # via nbclient
attrs==21.2.0
    # via jsonschema
backcall==0.2.0
    # via ipython
beautifulsoup4==4.9.3
    # via
    #   -r requirements.in
    #   bioregistry
    #   bioversions
bel-resources==0.0.3
    # via pybel
biopython==1.71
    # via
    #   -r requirements.in
    #   mdanalysis
bioregistry==0.1.8
    # via
    #   bioversions
    #   pybel
    #   pyobo
bioversions==0.1.2
    # via pyobo
black==21.5b2
    # via papermill
bleach==3.3.0
    # via nbconvert
boto3==1.17.84
    # via protmapper
botocore==1.20.84
    # via
    #   boto3
    #   s3transfer
cachier==1.5.0
    # via
    #   bioversions
    #   pyobo
certifi==2021.5.30
    # via requests
cffi==1.14.5
    # via argon2-cffi
chardet==4.0.0
    # via requests
click==8.0.1
    # via
    #   bioregistry
    #   bioversions
    #   black
    #   click-default-group
    #   click-plugins
    #   drugbank-downloader
    #   more-click
    #   papermill
    #   pybel
    #   pyobo
    #   pystow
    #   zenodo-client
click-default-group==1.2.2
    # via bioversions
click-plugins==1.1.1
    # via pybel
colorama==0.4.4
    # via
    #   mendeleev
    #   rich
commonmark==0.9.1
    # via
    #   -r requirements.in
    #   rich
cycler==0.10.0
    # via matplotlib
dataclasses-json==0.5.3
    # via
    #   bioversions
    #   zenodo-client
decorator==4.4.2
    # via
    #   ipython
    #   networkx
defusedxml==0.7.1
    # via
    #   bioregistry
    #   nbconvert
drugbank-downloader==0.1.0
    # via pyobo
entrypoints==0.3
    # via
    #   nbconvert
    #   papermill
greenlet==1.1.0
    # via sqlalchemy
griddataformats==0.5.0
    # via mdanalysis
gsd==2.4.2
    # via mdanalysis
h5py==3.2.1
    # via pyscf
humanize==3.6.0
    # via
    #   pybel
    #   pyobo
idna==2.10
    # via requests
ipykernel==5.5.5
    # via
    #   ipywidgets
    #   jupyter
    #   jupyter-console
    #   notebook
    #   qtconsole
ipython==7.24.0
    # via
    #   ipykernel
    #   ipywidgets
    #   jupyter-console
ipython-genutils==0.2.0
    # via
    #   nbformat
    #   notebook
    #   qtconsole
    #   traitlets
ipywidgets==7.6.3
    # via
    #   jupyter
    #   nglview
isodate==0.6.0
    # via rdflib
jedi==0.18.0
    # via ipython
jinja2==3.0.1
    # via
    #   nbconvert
    #   notebook
jmespath==0.10.0
    # via
    #   boto3
    #   botocore
joblib==1.0.1
    # via
    #   mdanalysis
    #   scikit-learn
jsonschema==3.2.0
    # via
    #   nbformat
    #   pybel
jupyter==1.0.0
    # via -r requirements.in
jupyter-client==6.2.0
    # via
    #   ipykernel
    #   jupyter-console
    #   nbclient
    #   notebook
    #   qtconsole
jupyter-console==6.4.0
    # via jupyter
jupyter-core==4.7.1
    # via
    #   jupyter-client
    #   nbconvert
    #   nbformat
    #   notebook
    #   qtconsole
jupyterlab-pygments==0.1.2
    # via nbconvert
jupyterlab-widgets==1.0.0
    # via
    #   ipywidgets
    #   nglview
kiwisolver==1.3.1
    # via matplotlib
lxml==4.6.3
    # via bioversions
markupsafe==2.0.1
    # via jinja2
marshmallow==3.12.1
    # via
    #   dataclasses-json
    #   marshmallow-enum
marshmallow-enum==1.5.1
    # via dataclasses-json
matplotlib==3.4.2
    # via
    #   -r requirements.in
    #   mdanalysis
matplotlib-inline==0.1.2
    # via ipython
mdanalysis==0.20.1
    # via -r requirements.in
mdtraj==1.9.5
    # via -r requirements.in
mendeleev==0.7.0
    # via -r requirements.in
mistune==0.8.4
    # via nbconvert
mmtf-python==1.1.2
    # via mdanalysis
mock==4.0.3
    # via mdanalysis
more-click==0.0.4
    # via
    #   bioregistry
    #   bioversions
    #   pyobo
    #   zenodo-client
more-itertools==8.8.0
    # via
    #   bioregistry
    #   pybel
    #   pyobo
mpmath==1.2.1
    # via sympy
msgpack==1.0.2
    # via mmtf-python
multisplitby==0.0.1
    # via bel-resources
mypy-extensions==0.4.3
    # via
    #   black
    #   typing-inspect
nbclient==0.5.3
    # via
    #   nbconvert
    #   papermill
nbconvert==6.0.7
    # via
    #   jupyter
    #   notebook
nbformat==5.1.3
    # via
    #   ipywidgets
    #   nbclient
    #   nbconvert
    #   notebook
    #   papermill
nest-asyncio==1.5.1
    # via
    #   jupyter-client
    #   nbclient
networkx==2.5.1
    # via
    #   mdanalysis
    #   obonet
    #   pybel
nglview==3.0.1
    # via -r requirements.in
notebook==6.4.0
    # via
    #   jupyter
    #   widgetsnbextension
numpy==1.20.3
    # via
    #   -r requirements.in
    #   biopython
    #   griddataformats
    #   gsd
    #   h5py
    #   matplotlib
    #   mdanalysis
    #   mdtraj
    #   mendeleev
    #   nglview
    #   pandas
    #   pyscf
    #   rdkit-pypi
    #   scikit-learn
    #   scipy
obonet==0.3.0
    # via pyobo
openai==0.6.4
    # via -r requirements.in
packaging==20.9
    # via bleach
pandas==1.2.4
    # via
    #   -r requirements.in
    #   mendeleev
    #   pybel
    #   pyobo
pandocfilters==1.4.3
    # via nbconvert
papermill==2.3.3
    # via -r requirements.in
parso==0.8.2
    # via jedi
pathspec==0.8.1
    # via black
pathtools==0.1.2
    # via cachier
pexpect==4.8.0
    # via ipython
pickleshare==0.7.5
    # via ipython
pillow==8.2.0
    # via matplotlib
portalocker==2.3.0
    # via cachier
prometheus-client==0.10.1
    # via notebook
prompt-toolkit==3.0.18
    # via
    #   ipython
    #   jupyter-console
protmapper==0.0.21
    # via pyobo
ptyprocess==0.7.0
    # via
    #   pexpect
    #   terminado
pybel==0.15.3
    # via -r requirements.in
pycparser==2.20
    # via cffi
pyfiglet==0.8.post1
    # via mendeleev
pygments==2.9.0
    # via
    #   ipython
    #   jupyter-console
    #   jupyterlab-pygments
    #   mendeleev
    #   nbconvert
    #   qtconsole
    #   rich
pyobo==0.4.0
    # via pybel
pyparsing==2.4.7
    # via
    #   matplotlib
    #   mdtraj
    #   packaging
    #   pybel
    #   rdflib
pyperclip==1.8.2
    # via -r requirements.in
pyrate-limiter==2.3.4
    # via -r requirements.in
pyrsistent==0.17.3
    # via jsonschema
pyscf==1.7.6.post1
    # via -r requirements.in
pystow==0.1.6
    # via
    #   bioregistry
    #   bioversions
    #   drugbank-downloader
    #   pybel
    #   pyobo
    #   zenodo-client
python-dateutil==2.8.1
    # via
    #   botocore
    #   jupyter-client
    #   matplotlib
    #   pandas
pytz==2021.1
    # via pandas
pyyaml==5.4.1
    # via
    #   bioregistry
    #   bioversions
    #   papermill
    #   pyobo
pyzmq==22.1.0
    # via
    #   jupyter-client
    #   notebook
    #   qtconsole
qtconsole==5.1.0
    # via jupyter
qtpy==1.9.0
    # via qtconsole
ratelimit==2.2.1
    # via pybel
rdflib==5.0.0
    # via protmapper
rdkit-pypi==2021.3.2.2
    # via -r requirements.in
regex==2021.4.4
    # via black
requests==2.25.1
    # via
    #   bel-resources
    #   bioregistry
    #   bioversions
    #   openai
    #   papermill
    #   protmapper
    #   pybel
    #   pyobo
    #   pystow
    #   requests-file
    #   requests-ftp
    #   zenodo-client
requests-file==1.5.1
    # via
    #   bel-resources
    #   pybel
requests-ftp==0.3.1
    # via
    #   bioregistry
    #   bioversions
rich==10.2.2
    # via -r requirements.in
s3transfer==0.4.2
    # via boto3
scikit-learn==0.24.2
    # via -r requirements.in
scipy==1.6.3
    # via
    #   -r requirements.in
    #   griddataformats
    #   mdanalysis
    #   mdtraj
    #   pyscf
    #   scikit-learn
send2trash==1.5.0
    # via notebook
six==1.16.0
    # via
    #   argon2-cffi
    #   astunparse
    #   bleach
    #   cycler
    #   griddataformats
    #   isodate
    #   jsonschema
    #   mdanalysis
    #   mendeleev
    #   python-dateutil
    #   rdflib
    #   requests-file
    #   tenacity
soupsieve==2.2.1
    # via beautifulsoup4
sqlalchemy==1.4.17
    # via
    #   mendeleev
    #   pybel
stringcase==1.2.0
    # via dataclasses-json
sympy==1.8
    # via -r requirements.in
tabulate==0.8.9
    # via
    #   bioregistry
    #   bioversions
    #   pybel
    #   pyobo
tenacity==7.0.0
    # via papermill
terminado==0.10.0
    # via notebook
testpath==0.5.0
    # via nbconvert
textwrap3==0.9.2
    # via ansiwrap
threadpoolctl==2.1.0
    # via scikit-learn
toml==0.10.2
    # via black
tornado==6.1
    # via
    #   ipykernel
    #   jupyter-client
    #   notebook
    #   terminado
tqdm==4.61.0
    # via
    #   bioregistry
    #   bioversions
    #   openai
    #   papermill
    #   pybel
    #   pyobo
    #   pystow
traitlets==5.0.5
    # via
    #   ipykernel
    #   ipython
    #   ipywidgets
    #   jupyter-client
    #   jupyter-core
    #   matplotlib-inline
    #   nbclient
    #   nbconvert
    #   nbformat
    #   notebook
    #   qtconsole
typing-extensions==3.10.0.0
    # via typing-inspect
typing-inspect==0.6.0
    # via dataclasses-json
urllib3==1.26.5
    # via
    #   botocore
    #   requests
watchdog==2.1.2
    # via cachier
wcwidth==0.2.5
    # via prompt-toolkit
webencodings==0.5.1
    # via bleach
wheel==0.36.2
    # via astunparse
widgetsnbextension==3.5.1
    # via ipywidgets
zenodo-client==0.1.0
    # via pyobo
zipp==3.4.1
    # via -r requirements.in

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