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

3. slic - env for instrument control with slic

4. stand - env for the online run table

5. cdtools_2 - used by Maël for ptychographic reconstructions, needs packages from a private git repo (cdtools) will be renamed as ptychography

6. petra3 - used by Maël for simulation of the optical setup. Will be renamed as optical_simulations

7. 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 ? 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 ? cristallina_diagnostics /sf/cristallina/applications/conda/envs/cristallina_diagnostics # Probably keep ? cuda /sf/cristallina/applications/conda/envs/cuda # ?? ? data_api /sf/cristallina/applications/conda/envs/data_api # ?? ? exp_control /sf/cristallina/applications/conda/envs/exp_control # ?? ? flet /sf/cristallina/applications/conda/envs/flet # ?? Is this needed for the X-ray eye zoom? x frappy /sf/cristallina/applications/conda/envs/frappy
? grum /sf/cristallina/applications/conda/envs/grum # ?? ? 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 o base /sf/cristallina/applications/conda/envs/miniconda ? minimamba /sf/cristallina/applications/conda/envs/minimamba # Do we need it? ? 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 # Mael will decide -> Mael: we can delete it from my side.