diff --git a/README.md b/README.md index ef054e1..86e08a3 100755 --- a/README.md +++ b/README.md @@ -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 + diff --git a/cristallina_diagnostics.yml b/cristallina_diagnostics.yml deleted file mode 100755 index 4ea61e9..0000000 --- a/cristallina_diagnostics.yml +++ /dev/null @@ -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 diff --git a/optical_simulations.yml b/optical_simulations.yml index 4a9f89e..0c47c60 100644 --- a/optical_simulations.yml +++ b/optical_simulations.yml @@ -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 diff --git a/ptychography.yml b/ptychography.yml index ae8eb22..313577d 100644 --- a/ptychography.yml +++ b/ptychography.yml @@ -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: - \ No newline at end of file +# 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 + diff --git a/stand.yml b/stand.yml index 0b44eac..f1366df 100755 --- a/stand.yml +++ b/stand.yml @@ -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 + + diff --git a/test b/test deleted file mode 100644 index e69de29..0000000