Cristallina/cristallina_envs
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Updating ymls and readme

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vonka_j
2025-09-03 16:22:55 +02:00
parent 17440bf98c
commit 7af6366958
6 changed files with 63 additions and 76 deletions
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29
README.md
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@@ -13,9 +13,9 @@ guaranteed. Works well when running up-to-date jupyterlab not from the spawner b
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**
5. **ptychography** - used by Maël for ptychographic reconstructions, needs packages from a private git repo (cdtools).
6. **petra3** - used by Maël for simulation of the optical setup. Will be renamed as **optical_simulations**
6. **optical_simulations** - used by Maël for simulation of the optical setup.
7. **jupyter_alpha** - testing env for the newest versions of jupyter collaboration
@@ -28,22 +28,22 @@ 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 # ??
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
? 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?
-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
? grum /sf/cristallina/applications/conda/envs/grum # ??
? image /sf/cristallina/applications/conda/envs/image # ??
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
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 # ??
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 # ??
@@ -51,4 +51,5 @@ o slic /sf/cristallina/applications/conda/envs/slic
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.
m zhinst /sf/cristallina/applications/conda/envs/zhinst #TODO store in subfolder

39
cristallina_diagnostics.yml
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@@ -1,39 +0,0 @@
# the most up-to-date packages from conda-forge.
# Therefore this will follow upstream packages closer but also break from time to time.
name: cristallina_diagnostics
channels:
- conda-forge
dependencies:
# mflow / pyzmq still has issues with 3.11
- python>=3.10,<3.11
- pip
- numpy
- pandas
- ipython
- ipykernel
# for notebooks into web applications
- voila
- nb_conda_kernels # for discovery of other kernels
# PSI specific modules
- pyepics # Does this need to be from paulscherrerinstitute?
# for slic
- paulscherrerinstitute::bsread
- paulscherrerinstitute::cam_server_client
# - paulscherrerinstitute::cta_lib
- paulscherrerinstitute::data_api
- paulscherrerinstitute::elog
- paulscherrerinstitute::jungfrau_utils >=3
- paulscherrerinstitute::sfdata
# terminal
- colorama
- tqdm
- rich
- fuzzywuzzy
- logzero
- yaspin
# slic
- pip:
- -e /sf/cristallina/applications/slic/slic-package

5
optical_simulations.yml
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@@ -10,14 +10,17 @@ dependencies:
- ipython
- numpy
- pandas
- joblib
- lmfit
- scipy
- scikit-image
- matplotlib
- ipympl
- tqdm
- pip
# for execution and kernel discovery within jupyter
- ipykernel
- pip:
- pip:
# optical simulation
- pyoptica

40
ptychography.yml
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@@ -1,6 +1,13 @@
# Environment used by Maël for ptychographic reconstructions. Requires a package from a private git repo (cdtools)
# Previous environment name: *cdtools*
# Work in progress
######## IMPORTANT #############
# The main package is not included in this yaml because the repository is private (early 2025)
# https://cdtools-developers.github.io/cdtools/installation.html
# Once the environment is setup using the present yaml file, clone the private repo and run
# pip install . --no-deps
# from top level directory (the directory including the setup.py file)
name: ptychography
channels:
@@ -8,13 +15,28 @@ channels:
dependencies:
- python
- ipython
- numpy
- scipy
- matplotlib
- ipympl
# for execution and kernel discovery within jupyter
- tqdm
- joblib
- lmfit
- pip
#for execution and kernel discovery within jupyter
- ipykernel
# DAQ
- paulscherrerinstitute::bsread
# maybe useful for some special application:
# Dependencies for cdtools
- numpy >= 1.0
- scipy >= 1.0
- matplotlib >= 2.0
- pytorch >= 1.9.0
- python-dateutil
- h5py >= 2.1
- pytest
- pooch
- sphinx >= 4.3.0
- sphinx-argparse
- sphinx_rtd_theme >= 0.5.1
- pip:
# PyTorch is also a dependencies for cdtools - but they dropped anaconda support.
- torch
- torchvision
- torchaudio

26
stand.yml
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@@ -3,16 +3,16 @@ name: stand
channels:
- conda-forge
dependencies:
- python
- pip
- ipython
- cherrypy
- openpyxl
- pytables
- conda-forge::streamlit=1.9.2 # Does this still need to be a fixed version?
- conda-forge::python-dotenv
- pyyaml
- simplejson
# Jupyterlab extensions
- pip:
- streamlit-aggrid
- python=3.12
- pip
- ipython
- cherrypy
- openpyxl
- pytables
- python-dotenv
- pyyaml
- simplejson
- streamlit-aggrid # Previously gotten from pip, but now fine from conda-forge
- streamlit # Previously fixed to =1.9.2

0
test
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