Conda environment specifications

Here we collect .yaml files and other instructions necessary to reproduce the conda environments for Cristallina.

Purpose of the environments

1. analysis-edge - env for data analysis, kept up to date. Widget and other compatibilities with jupytera not guaranteed. Works well when running up-to-date jupyterlab not from the spawner but started individually in the node with jupyter notebook

2. analysis-stable - copy of analysis-edge, but staying behind a bit to eliminate new issues

3. analysis-opencv - another version of analysis with the rather large OpenCV package for more complex image analysis

4. slic - env for instrument control with slic

5. stand - env for the online run table

6. ptychography - used by Maël for ptychographic reconstructions, needs packages from a private git repo (cdtools).

7. optical_simulations - used by Maël for simulation of the optical setup.

8. jupyter_alpha - testing env for the newest versions of jupyter collaboration

Full list of environments

x - will be deleted o - will be kept ? - Unclear yet

x analyse /sf/cristallina/applications/conda/envs/analyse
x analysis /sf/cristallina/applications/conda/envs/analysis
o analysis_edge /sf/cristallina/applications/conda/envs/analysis_edge # Should become analysis, more conservative copy of analysis-edge o analysis_forge /sf/cristallina/applications/conda/envs/analysis_forge # Keep B? cam_server /sf/cristallina/applications/conda/envs/cam_server # ?? m cdtools_2 /sf/cristallina/applications/conda/envs/cdtools_2 # Mael will decide -> Mael: keep it and rename it "ptychography" x cdtools_deprecated /sf/cristallina/applications/conda/envs/cdtools_deprecated # Mael: Can be deleted -check if more than slic cristallina_diagnostics /sf/cristallina/applications/conda/envs/cristallina_diagnostics # Probably keep x cuda /sf/cristallina/applications/conda/envs/cuda # ?? x data_api /sf/cristallina/applications/conda/envs/data_api # ?? x exp_control /sf/cristallina/applications/conda/envs/exp_control # ?? x flet /sf/cristallina/applications/conda/envs/flet # ?? Is this needed for the X-ray eye zoom? x frappy /sf/cristallina/applications/conda/envs/frappy
x grum /sf/cristallina/applications/conda/envs/grum # ?? x image /sf/cristallina/applications/conda/envs/image # ?? ? jupyter /sf/cristallina/applications/conda/envs/jupyter # ?? o jupyter_alpha /sf/cristallina/applications/conda/envs/jupyter_alpha # Testing env for the newest versions of jupyter collaboration x base /sf/cristallina/applications/conda/envs/miniconda x minimamba /sf/cristallina/applications/conda/envs/minimamba # Do we need it? x pandas /sf/cristallina/applications/conda/envs/pandas # ??
m petra3 /sf/cristallina/applications/conda/envs/petra3 # Mael: used for simulations of optical setup. Will be renamed "optical_simulations" (nothing to do with petra) x petra3_analysis /sf/cristallina/applications/conda/envs/petra3_analysis
? shimadzu /sf/cristallina/applications/conda/envs/shimadzu # ?? o slic /sf/cristallina/applications/conda/envs/slic # Keep, but perhaps use Sven's latest slic env as base? x slic2 /sf/cristallina/applications/conda/envs/slic2 x speckles /sf/cristallina/applications/conda/envs/speckles ? stand /sf/cristallina/applications/conda/envs/stand # Is it still needed? m zhinst /sf/cristallina/applications/conda/envs/zhinst #TODO store in subfolder