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# Scientific Python Binder for NSLS-II | ||
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Run this on Binder (free public cloud resources) using this link: | ||
This defines the container image run on https://jupyter.nsls2.bnl.gov. | ||
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[![Binder](http://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/NSLS-II/scipy-binder/main) | ||
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Or run it on the NSLS-II JupyterHub at SDCC by visiting | ||
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https://jupyter.sdcc.bnl.gov/jupyterhub/nsls/ | ||
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and choosing "scientific-python". | ||
Note that this only includes the Jupyter _server_ environment, which includes | ||
various Jupyter server extensions. It does not include the Jupyter _kernels_ | ||
where the user code is executed. Those are managed separately in | ||
[nsls2-conda-envs/nsls2-collection-tiled](https://github.com/nsls2-conda-envs/nsls2-collection-tiled) | ||
and mounted into the container under `/nsls2/conda/`. |
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channels: | ||
- conda-forge | ||
dependencies: | ||
- amostra # pinnned down | ||
- area-detector-handlers # pinned up | ||
- arvpyf # same | ||
- atsas-pipelines # missing | ||
- blosc # secondary | ||
- bokeh # missing | ||
- boto3 # same | ||
- botorch # same | ||
- bottleneck # missing | ||
- chxtools # same | ||
- csxtools>=0.1.14 # pinned further up | ||
- dask # same | ||
- dask-image # missing | ||
- dask-jobqueue # missing | ||
- dask-labextension # SERVER | ||
- dask-ml # missing | ||
- dask-xgboost # missing | ||
- databroker>=2.0.0b23 # pinned further up | ||
- edrixs>=0.0.8 # unpinned | ||
- eiger-io # same | ||
- fabio # same | ||
- gpytorch # same | ||
- graphviz # same | ||
- h5py>=3.6 # pinned less strictly | ||
- hvplot # missing | ||
- hxntools # pinned up | ||
- ipympl # pinned up | ||
- jupyterhub-singleuser=1.3.0 # SERVER match JupyterHub deployment version | ||
- jupyterlab=3.2.* # unpinned | ||
- jupyterlab-h5web # SERVER | ||
- line_profiler # missing | ||
- lixtools>=2023.1.23.0 # unpinned | ||
- lmfit>=0.9.9 # unpinned | ||
- matplotlib>=3.5 # pinned higher | ||
- memory_profiler # same | ||
- mendeleev # same | ||
- modestimage # same | ||
- nbclassic>=0.2.8 # SERVER | ||
- nbgitpuller # SERVER | ||
- nbserverproxy # SERVER | ||
# - netcdf4 # jams up the solver, and unclear whether it is actually used | ||
- nbconvert-webpdf # SERVER | ||
- nodejs # same | ||
- notebook # SERVER | ||
- nslsii # pinned up | ||
- numba # secondary | ||
- numexpr # same | ||
- numpy>=1.22 # pinned higher | ||
- openmpi>=4.1.4 # missing | ||
- pandas # same | ||
- papermill # same | ||
- periodictable # same | ||
- photutils # same | ||
- dask-labextension | ||
- jupyterhub-singleuser=1.3.0 # match JupyterHub deployment version | ||
- jupyterlab-h5web | ||
- nbgitpuller | ||
- nbserverproxy | ||
- nbconvert-webpdf | ||
- nodejs | ||
- notebook | ||
- pip # mamba warns us to explicitly list this dependency | ||
- py-xgboost # missing | ||
- py4xs>=2023.1.23.0 # same | ||
- pyarrow # same | ||
- pycentroids # same | ||
- pychx >=4.1.2 # same | ||
- pyfai # same | ||
- pymongo # pinned up | ||
- pypdf2 # same | ||
- pystackreg # same | ||
- pytables # same | ||
- python-blosc # missing | ||
- python-graphviz # same | ||
- python=3.9 # pinned higher (3.10) | ||
- pytorch # same | ||
- pyxrf>=0.0.9 3 pinned higher | ||
- reportlab # same | ||
- requests # same | ||
- sasview # removed, unsupported on pyqt>=5.15 | ||
- scikit-learn # same | ||
- scipy>=1.9 # same | ||
- seaborn # missing | ||
- shadow3 # missing | ||
- sip # missing | ||
- sixtools>=0.0.2 # unpinned | ||
- smi-analysis>=0.2.0 # unpinned | ||
- srwpy # missing | ||
- tiled>=0.1.0a92 # pinned higher | ||
- tornado # same | ||
- tzlocal <3 # banned 3.0 only; tzlocal 3 broke API on Python 3.7 and the fix turned into a rabbithole | ||
- voila # SERVER | ||
- xarray # secondary | ||
- xray-vision >=0.0.10 # pinned higher | ||
- xraylarch>=0.9.45 # pinned higher | ||
- zarr # secondary | ||
- pip: | ||
- mimesis | ||
- pyzbar | ||
- pyhyperscattering[all] | ||
- voila |
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#!/bin/bash | ||
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MPLBACKEND=Agg python -c "import matplotlib.pyplot" # Build font cache. | ||
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python -m ipykernel install --name python3-custom --display-name "Python 3 (custom)" |