requirements.txt

## How to set up a Python runtime environment for the Whole Cell Model.
## (See docs/create-pyenv.md for more details, esp. for Sherlock.)
## (See docs/dev-tools.md for prerequisites such as installing command line
## tools, additional SDK headers, and add pyenv init to your shell.)
#
## Install these packages using your local package manager such as homebrew on macOS:
#   brew install pyenv pyenv-virtualenv pyenv-virtualenvwrapper
#   brew install glpk openssl readline swig suite-sparse xz
#
## Whole Cell Model requires OpenBLAS 0.3.7+ or equivalent. Installing numpy and
## scipy binary wheels now embed a recent enough OpenBLAS release by default.
##
## If OpenBLAS uses multiple threads, it will produce slightly different results
## and usually runs significantly slower, esp. when called from multiple
## processes. See wholecell/tests/utils/test_blas.py .
## To fix that, set the environment variable:
#   export OPENBLAS_NUM_THREADS=1
#
## Install the required version of Python via pyenv, and remember to enable it as
## a shared library:
#   PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install 3.11.3
#
## Create the "wcEcoli3" python virtual environment based on that Python version,
## and select it for your project directory:
#   cd ~/dev/wcEcoli
#   pyenv virtualenv 3.11.3 wcEcoli3 && pyenv local wcEcoli3
#
## Upgrade this virtual environment's pip installer:
#   pip install --upgrade pip
#
## Install numpy (if it's the first time) then all the packages listed in this file (see
## docs/create-pyenv.md about whether to create a `~/.numpy-site.cfg` file and add
## `--no-binary numpy` to these `pip install` steps):
## [When updating the numpy version here also update it below, in Dockerfile, and in docs/*.]
#   pip install numpy==1.26.3  # or add: --no-binary numpy
#   pip install --upgrade -r requirements.txt && pyenv rehash
#
## Optionally, do some quick checks:
#   python -c "import numpy as np; np.show_config()"
#   runscripts/debug/numpy_benchmark.py
#   python -c "import scipy; scipy.__config__.show()"
#   python -c "import aesara; print(aesara.config.blas.ldflags)"
#   python runscripts/debug/summarize_environment.py
#   OPENBLAS_NUM_THREADS=1 python -m wholecell.tests.utils.test_library_performance
#
## Build the Cython code:
#   make clean compile

# Installers
pip>=23.1
setuptools==73.0.1  # setuptools>=74.0.0 breaks aesara (via distutils changes?)
virtualenv>=20.21.0
virtualenv-clone>=0.5.7
virtualenvwrapper>=4.8.4
wheel>=0.40.0

# Direct dependendencies.
#
# NOTE: *** When updating the numpy==______ version, also update
#           cloud/docker/runtime/Dockerfile and the instructions. ***
#
# bokeh==1.4.0 is the last version compatible with Python 2. Now irrelevant.
#
# FireWorks requires pymongo.
# dnspython enables pymongo to access server clusters (mongodb+srv:// URIs).
# pymongo[ocsp] adds dependencies for Sherlock to access Atlas server clusters.
# pytest-cov is for `pytest --cov`.
numpy==1.26.3
scipy==1.11.4

aesara==2.9.3
biopython==1.81
bokeh==3.1.1
borealis-fireworks==0.12.0
cvxpy==1.3.2
Cython==0.29.35
dash==2.9.3
dnspython==2.3.0
Equation==1.2.1
FireWorks==2.0.3
future==0.18.3
ipdb==0.13.13
ipython==8.13.2
line-profiler==4.0.3
numba==0.58.1
matplotlib==3.7.1
mock==5.0.2
mypy==1.3.0
pandas==2.0.1
Pillow==10.1.0
plotly==5.14.1
pymongo[ocsp]==4.3.3
pytest==7.3.1
pytest-cov==4.1.0
PyYAML==6.0.1  # not compatible with Cython 3 until they replace distutils use
requests==2.29.0  # update to 2.30 when docker is ready for urllib3 2.0
ruamel.yaml==0.17.26
stochastic-arrow==1.0.0
swiglpk==5.0.8
sympy==1.12
Unum==4.2.1

## Added by `mypy --install-types`:
types-mock==5.0.0.6
types-PyYAML==6.0.12.9
types-requests==2.30.0.0
types-urllib3==1.26.25.13

## Added by pymongo[ocsp]:
attrs==23.1.0
cffi==1.15.1
cryptography==40.0.2
pycparser==2.21
pyOpenSSL==23.1.1
service-identity==21.1.0

## Added by pip freeze:
appnope==0.1.3
asttokens==2.2.1
backcall==0.2.0
blinker==1.6.2
cachetools==5.3.0
certifi==2023.5.7
charset-normalizer==3.1.0
click==8.1.3
cons==0.4.5
contourpy==1.0.7
coverage==7.3.2
cycler==0.11.0
dash-core-components==2.0.0
dash-html-components==2.0.0
dash-table==5.0.0
decorator==5.1.1
distlib==0.3.6
docker==6.1.2
ecos==2.0.12
etuples==0.3.8
executing==1.2.0
filelock==3.12.0
Flask==2.3.2
flask-paginate==2022.1.8
fonttools==4.39.4
google-api-core==2.11.0
google-auth==2.18.0
google-cloud-appengine-logging==1.3.0
google-cloud-audit-log==0.2.5
google-cloud-core==2.3.2
google-cloud-logging==3.5.0
google-cloud-storage==2.9.0
google-crc32c==1.5.0
google-resumable-media==2.5.0
googleapis-common-protos==1.59.0
grpc-google-iam-v1==0.12.6
grpcio==1.54.2
grpcio-status==1.54.2
gunicorn==20.1.0
idna==3.4
iniconfig==2.0.0
itsdangerous==2.1.2
jedi==0.18.2
Jinja2==3.1.2
kiwisolver==1.4.4
llvmlite==0.41.1
logical-unification==0.4.6
MarkupSafe==2.1.2
matplotlib-inline==0.1.6
miniKanren==1.0.3
monty==2023.5.8
mpmath==1.3.0
multipledispatch==0.6.0
mypy-extensions==1.0.0
osqp==0.6.2.post9
packaging==23.1
parso==0.8.3
pbr==5.11.1
pexpect==4.8.0
pickleshare==0.7.5
platformdirs==3.5.1
pluggy==1.0.0
prompt-toolkit==3.0.38
proto-plus==1.22.2
protobuf==4.23.0
ptyprocess==0.7.0
pure-eval==0.2.2
pyasn1==0.5.0
pyasn1-modules==0.3.0
Pygments==2.15.1
pyparsing==3.0.9
python-dateutil==2.8.2
pytz==2023.3
qdldl==0.1.7
rsa==4.9
ruamel.yaml.clib==0.2.7
scs==3.2.3
six==1.16.0
stack-data==0.6.2
stevedore==5.0.0
tabulate==0.9.0
tenacity==8.2.2
toolz==0.12.0
tornado==6.3.2
tqdm==4.65.0
traitlets==5.9.0
typing_extensions==4.5.0
tzdata==2023.3
urllib3<2
wcwidth==0.2.6
websocket-client==1.5.1
Werkzeug==2.3.4
xyzservices==2023.2.0