Cristallina/cristallina_envs
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Start of a cleanup

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vonka_j
2025-04-09 12:02:45 +02:00
parent d61b9bef93
commit d67371de9d
9 changed files with 162 additions and 25 deletions
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47
README.md Normal file → Executable file
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@@ -4,10 +4,51 @@ Here we collect .yaml files and other instructions necessary to reproduce the co
# Purpose of the environments
1. **analysis** - env for data analysis, kept up to date. Widget and other compatibilities with jupytera not
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. **analyse** - copy of analysis, but with versions of some packages fixed to ensure full compatibility with
jupyter lab from the spawner
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.

19
analysis_edge.yml Normal file → Executable file
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@@ -3,9 +3,7 @@
# Therefore this will follow upstream packages closer but also break from time to time.
name: analysis_edge
channels:
- paulscherrerinstitute
- conda-forge
- defaults
dependencies:
# essentials
- python>=3.11
@@ -19,6 +17,9 @@ dependencies:
- jupyterlab
- ipympl
- joblib
- tqdm # sfdata dependency but here given explicitly
- lmfit
- pytest
# useful development packages
- black
- pytest
@@ -27,6 +28,9 @@ dependencies:
- line_profiler
- loguru
- pylint
- sqlalchemy # X-ray transmission calculations and similar
- xraydb # X-ray transmission calculations and similar
- scikit-image # Image processing
# and extra control parts
- fabric
# Jupyterlab extensions
@@ -36,11 +40,20 @@ dependencies:
# - jupytext # needs to be tested manually
# PSI specific modules
- paulscherrerinstitute::sfdata
# - jungfrau_utils # also dependency
# - paulscherrerinstitute::jungfrau_utils # should be a dependency of sfdata, but not listed there explicitly, so test
# - pip:
# - ipytest
## Dependencies
# - bitshuffle # dependency of sfdata
# - colorama # dependency of sfdata
## Probably can be removed
# - astropy # Used for conversion of magnet coordinates, probably not needed any more
# - loguru # Not sure if it's needed in the analysis env
# - pyqt # Not sure if it's needed in the analysis env
# still necessary manually afterwards:

11
cristallina_diagnostics.yml Normal file → Executable file
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@@ -2,10 +2,7 @@
# Therefore this will follow upstream packages closer but also break from time to time.
name: cristallina_diagnostics
channels:
- paulscherrerinstitute
- conda-forge
- defaults
dependencies:
# mflow / pyzmq still has issues with 3.11
- python>=3.10,<3.11
@@ -18,7 +15,7 @@ dependencies:
- voila
- nb_conda_kernels # for discovery of other kernels
# PSI specific modules
- pyepics
- pyepics # Does this need to be from paulscherrerinstitute?
# for slic
- paulscherrerinstitute::bsread
@@ -33,9 +30,9 @@ dependencies:
- colorama
- tqdm
- rich
- conda-forge::fuzzywuzzy
- conda-forge::logzero
- conda-forge::yaspin
- fuzzywuzzy
- logzero
- yaspin
# slic
- pip:

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jupyter_alpha.yml Executable file
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@@ -0,0 +1,39 @@
# Bare Jupyter Lab installation _without_ analysis tools.
# This is to have the most up-to-date jupyter server packages.
#
# Caveat: it requires the same/similar ipympl packages
#
name: jupyter_alpha
channels:
- conda-forge
dependencies:
- python
- pip
- numpy
- pandas
- numba
- matplotlib
- ipython
- jupyterlab
- ipympl
- black
- pytest
- loguru
# Jupyterlab extensions
- nb_conda_kernels # for discovery of other kernels
- jupyterlab_code_formatter
- jupyter-collaboration
# disabled until stable with collaboration: - jupytext
# PSI specific modules
#- paulscherrerinstitute::jungfrau_utils
#- bitshuffle
#- paulscherrerinstitute::sfdata
# - pip:
#- ipytest
# still necessary manually afterwards:
# pip install jupyterlab_hdf
# jupyter labextension install @jupyterlab/hdf5

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optical_simulations.yml Normal file
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@@ -0,0 +1,23 @@
# Environment used by Maël for simulating optical setup, based on the PyOptica library.
# Previous environment name: "petra3" (don't ask me why)
# Should be ready to be tested.
name: optical_simulations
channels:
- conda-forge
dependencies:
- python=3.7.12
- ipython
- numpy
- pandas
- scipy
- scikit-image
- matplotlib
- ipympl
- tqdm
# for execution and kernel discovery within jupyter
- ipykernel
- pip:
# optical simulation
- pyoptica

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ptychography.yml Normal file
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@@ -0,0 +1,20 @@
# Environment used by Maël for ptychographic reconstructions. Requires a package from a private git repo (cdtools)
# Previous environment name: *cdtools*
# Work in progress
name: ptychography
channels:
- conda-forge
dependencies:
- python
- ipython
- numpy
- scipy
- matplotlib
- ipympl
# for execution and kernel discovery within jupyter
- ipykernel
# DAQ
- paulscherrerinstitute::bsread
# maybe useful for some special application:

24
slic.yml Normal file → Executable file
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@@ -10,24 +10,28 @@
# NOTE: $NEW_ENV_NAME is optional and defaults to slic
name: slic
channels:
- conda-forge
dependencies:
# was pinned to 3.8 but works with 3.9 now as well
# - python==3.8
- python
# defaults
- ipython
- numpy
- scipy
- matplotlib
- ipympl
# for execution and kernel discovery within jupyter
- ipykernel
# DAQ
- paulscherrerinstitute::bsread
- paulscherrerinstitute::cam_server_client
# maybe useful for some special application:
# - paulscherrerinstitute::cam_server_client
- paulscherrerinstitute::data_api
# - paulscherrerinstitute::detector_integration_api # unused here
- paulscherrerinstitute::elog
- paulscherrerinstitute::pyepics >=3.4.2
- pyepics # Used to be from paulscherrerinstitute, but changed here
# Own DAQ
- pyvisa-py
- pyserial
- pyusb
# data
- paulscherrerinstitute::jungfrau_utils >=3
- paulscherrerinstitute::sfdata
@@ -38,8 +42,8 @@ dependencies:
# terminal
- colorama
- tqdm
- conda-forge::fuzzywuzzy
- conda-forge::logzero
- conda-forge::yaspin
- fuzzywuzzy
- logzero
- yaspin
- loguru

4
stand.yml Normal file → Executable file
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@@ -1,7 +1,7 @@
# For stand
name: stand
channels:
- defaults
- conda-forge
dependencies:
- python
- pip
@@ -9,7 +9,7 @@ dependencies:
- cherrypy
- openpyxl
- pytables
- conda-forge::streamlit=1.9.2
- conda-forge::streamlit=1.9.2 # Does this still need to be a fixed version?
- conda-forge::python-dotenv
- pyyaml
- simplejson

0
test Normal file
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