Merge pull request #69 from NSLS-II/server-only

Manage kernel env separately

README.md

@@ -1,11 +1,9 @@
 # Scientific Python Binder for NSLS-II
 
-Run this on Binder (free public cloud resources) using this link:
+This defines the container image run on https://jupyter.nsls2.bnl.gov.
 
-[![Binder](http://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/NSLS-II/scipy-binder/main)
-
-Or run it on the NSLS-II JupyterHub at SDCC by visiting
-
-https://jupyter.sdcc.bnl.gov/jupyterhub/nsls/
-
-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/`.

binder/environment.yml

@@ -1,95 +1,14 @@
 channels:
   - conda-forge
 dependencies:
-  - amostra
-  - area-detector-handlers
-  - arvpyf
-  - atsas-pipelines
-  - blosc
-  - bokeh
-  - boto3
-  - botorch
-  - bottleneck
-  - chxtools
-  - csxtools>=0.1.14
-  - dask
-  - dask-image
-  - dask-jobqueue
+  - python=3.9
   - dask-labextension
-  - dask-ml
-  - dask-xgboost
-  - databroker>=2.0.0b23
-  - edrixs>=0.0.8
-  - eiger-io
-  - fabio
-  - gpytorch
-  - graphviz
-  - h5py>=3.6
-  - hvplot
-  - hxntools
-  - ipympl
+  - jupyter-server-proxy
   - jupyterhub-singleuser=1.3.0  # match JupyterHub deployment version
-  - jupyterlab=3.2.*
   - jupyterlab-h5web
-  - line_profiler
-  - lixtools>=2023.1.23.0
-  - lmfit>=0.9.9
-  - matplotlib>=3.5
-  - memory_profiler
-  - mendeleev
-  - modestimage  # change to force rebuild to get new build
-  - nbclassic>=0.2.8
   - nbgitpuller
-  - nbserverproxy
-  # - netcdf4  # jams up the solver, and unclear whether it is actually used
   - nbconvert-webpdf
   - nodejs
   - notebook
-  - nslsii
-  - numba
-  - numexpr
-  - numpy>=1.22
-  - openmpi>=4.1.4
-  - pandas
-  - papermill
-  - periodictable
-  - photutils
   - pip  # mamba warns us to explicitly list this dependency
-  - py-xgboost
-  - py4xs>=2023.1.23.0
-  - pyarrow
-  - pycentroids
-  - pychx >=4.1.2
-  - pyfai
-  - pymongo
-  - pypdf2
-  - pystackreg
-  - pytables
-  - python-blosc
-  - python-graphviz
-  - python=3.9
-  - pytorch
-  - pyxrf>=0.0.9
-  - reportlab
-  - requests
-  - sasview
-  - scikit-learn
-  - scipy>=1.9
-  - seaborn
-  - shadow3
-  - sip
-  - sixtools>=0.0.2
-  - smi-analysis>=0.2.0
-  - srwpy
-  - tiled>=0.1.0a92
-  - tornado
-  - tzlocal <3  # tzlocal 3 broke API on Python 3.7 and the fix turned into a rabbithole
   - voila
-  - xarray
-  - xray-vision >=0.0.10
-  - xraylarch>=0.9.45
-  - zarr
-  - pip:
-    - mimesis
-    - pyzbar
-    - pyhyperscattering[all]

binder/kernel.json

@@ -0,0 +1,14 @@
+{
+ "argv": [
+  "/nsls2/conda/envs/2023-3.1-py310-tiled/bin/python",
+  "-m",
+  "ipykernel_launcher",
+  "-f",
+  "{connection_file}"
+ ],
+ "display_name": "Python 3 (ipykernel)",
+ "language": "python",
+ "metadata": {
+  "debugger": true
+ }
+}

binder/postBuild

@@ -1,4 +1,7 @@
 #!/bin/bash
 
-MPLBACKEND=Agg python -c "import matplotlib.pyplot"  # Build font cache.
-
+# Replace the default Python 3 kernel, which would use the Jupyter server
+# environment, with one that points into /nsls2/conda/ which is expected
+# to be mounted in when the container is run.
+mv /srv/conda/envs/notebook/share/jupyter/kernels/python3 /srv/conda/envs/notebook/share/jupyter/kernels/external_python3
+mv ./binder/kernel.json /srv/conda/envs/notebook/share/jupyter/kernels/external_python3/kernel.json