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requirements_local.txt
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requirements_local.txt
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# ephys for Python 3 with basic working environment
# Used by make_env.sh
# development utilities
black>=24.10.0
flake8==7.0.0
Pint>=0.24.4
isort>=5.13.2
mypy==1.13.0
sphinx==8.1.3
sphinx-automodapi
sphinx-rtd-theme
refurb==1.13.0
jupyterlab==3.4.4
# plotnine>=0.9.0
pyperclip
pytest==7.3.1
gitpython
Cython==3.0.11
dill==0.3.8
# efel>=3.0.93
# envisage==4.7.2
colorcet
colormaps==0.4.1
termcolor
jinja2==3.1.2
python-docx==1.1.0 # for writing Word docx files. Maybe used by associated programs
pyabf==2.3.8 # for reading axon binary files
meegkit==0.1.7 # some filtering and baseline adjustments translated from Python originally from Alain de Cheveigné
lmfit==1.2.2
obspy==1.4.0 # for resampling and filtering
matplotlib>=3.9.0
matplotlib-scalebar>=0.8.1
nose==1.3.7
numba==0.60.0 # ==0.50.1
numpy>=1.26, <= 2.1.0
pandas>=2.2.0
pandas_parallel_apply==2.2
pyarrow==15.0.0
openpyxl
XlsxWriter>=3.0
psutil==5.6.7
pyparsing==2.4.0
tables==3.9.2
pypdf2
pingouin==0.5.4
resampy==0.4.2
scipy>=1.14.0
statsmodels==0.14.1
scikit_posthocs==0.9.0
sympy
deepdiff
pyqt6
pyqt6-sip
pyqtgraph==0.13.7
pyqt6-webengine
seaborn>=0.13.2
tifffile==2024.06.18
# specific for Allen SDK:
ruamel.yaml<1,>=0.15
imageio>=2.34 # scikit image
networkx>=2.0 # scikit image
PyWavelets>=1.6.0 # scikit image
nest_asyncio==1.2.0 # allensdk 2.11.2
# jinja2<2.12.0,>=2.7.3 # allensdk2.11.2
hdmf==3.14.1
isodate==0.6.1
#========================
# nwbinspector==0.4.37
xlrd>=1.0.0
# required for 3d display in pyqtgraph
PyOpenGL>=3.1.5
# required for mayavi in neuronvis
# vtk>=9
tensorflow>=2.17.0
tensorflow-metal==1.1.0
#-e git+https://github.com/pbmanis/pyqtgraph.git@e3ac16b3a220f76b69bf26c295edf140e2e928b4#egg=pyqtgraph
#-e git+https://github.com/pbmanis/pylibrary.git#egg=pylibrary
-e /Users/pbmanis/Desktop/Python/pylibrary
-e /Users/pbmanis/Desktop/Python/MetaArray
-e /Users/pbmanis/Desktop/Python/nwbinspector
imreg_dft>=2.0
descartes
#mahotas
#-e git+https://github.com/pbmanis/montager.git@578ba75af12bb2321e377451f35921977656041a#egg=montage
-e /Users/pbmanis/Desktop/Python/montage