From 26d899cc0f754c057467f2578c2d090e3ef6d47d Mon Sep 17 00:00:00 2001 From: Jakub Vonka Date: Mon, 26 Jan 2026 16:15:42 +0100 Subject: [PATCH] Cleanup --- analysis-addams.yml | 44 +++++ analysis-esr.yml | 0 analysis-stable.yml | 62 ++++++ analysis.yml | 64 ++++++ analysis_edge.yml | 56 ++++++ diagnostics-crq.yml | 38 ++++ env_backups/slic-crq.yml | 278 ++++++++++++++++++++++++++ env_backups/slic.yml | 413 +++++++++++++++++++++++++++++++++++++++ env_backups/slic2.yml | 268 +++++++++++++++++++++++++ jupyter-alpha.yml | 39 ++++ jupyter_alpha.yml | 4 +- jupyter_beta.yml | 41 ++++ optical_simulations.yml | 0 ptychography.yml | 0 slic.yml | 60 ++++++ smarpod.yml | 60 ++++++ 16 files changed, 1426 insertions(+), 1 deletion(-) create mode 100755 analysis-addams.yml mode change 100644 => 100755 analysis-esr.yml create mode 100755 analysis-stable.yml create mode 100755 analysis.yml create mode 100755 analysis_edge.yml create mode 100755 diagnostics-crq.yml create mode 100644 env_backups/slic-crq.yml create mode 100644 env_backups/slic.yml create mode 100644 env_backups/slic2.yml create mode 100755 jupyter-alpha.yml create mode 100755 jupyter_beta.yml mode change 100644 => 100755 optical_simulations.yml mode change 100644 => 100755 ptychography.yml create mode 100755 slic.yml create mode 100755 smarpod.yml diff --git a/analysis-addams.yml b/analysis-addams.yml new file mode 100755 index 0000000..430f709 --- /dev/null +++ b/analysis-addams.yml @@ -0,0 +1,44 @@ +# Copy of the analysis-edge.yml with the addition of a SPEC2NEXUS package to read spec files (produced for example at the ADDAMS beamline). +name: analysis_edge +channels: + - conda-forge +dependencies: +# essentials + - python>=3.13 # Frozen to this version, because pyspec is not compatible with newer versions for the moment + - pip + - numpy + - scipy + - pandas + - numba + - matplotlib + - ipython + - jupyterlab + - ipympl + - joblib + - tqdm # sfdata dependency but here given explicitly + - lmfit + - pytest +# useful development packages + - black + - pytest + - h5py # sfdata dependency but here given explicitly + - pint + - line_profiler + - loguru + - pylint + - ipytest # used to be taken from pip, but here we test the conda-forge version + - 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 + - nb_conda_kernels # for discovery of other kernels +# - jupyterlab-drawio + - jupyterlab_code_formatter + # - jupytext # needs to be tested manually +# PSI specific modules + - paulscherrerinstitute::sfdata +# - paulscherrerinstitute::jungfrau_utils # should be a dependency of sfdata, but not listed there explicitly, so t + - pip: + - spec2nexus diff --git a/analysis-esr.yml b/analysis-esr.yml old mode 100644 new mode 100755 diff --git a/analysis-stable.yml b/analysis-stable.yml new file mode 100755 index 0000000..eed05ed --- /dev/null +++ b/analysis-stable.yml @@ -0,0 +1,62 @@ +# Analysis environment meant to be more stable and a bit behind the 'analysis' environment + +name: analysis-stable +channels: + - conda-forge +dependencies: +# essentials + - python=3.12 # keep at 3.12 beause of bitshuffle + - pip + - numpy + - scipy + - pandas + - numba + - matplotlib + - ipython + - jupyterlab + - ipympl + - joblib + - tqdm # sfdata dependency but here given explicitly + - lmfit + - pytest + - bitshuffle=0.5.2=py312h5fdea32_5 # this specific build of bitshuffle works with python 3.12 + # for higher versions new build must be found +# useful development packages + - black + - pytest # for testing the cristallina package + - h5py # sfdata dependency but here given explicitly + - pint + - line_profiler + - loguru + - pylint + - ipytest # used to be taken from pip, but here we test the conda-forge version + - sqlalchemy # X-ray transmission calculations and similar + - xraydb # X-ray transmission calculations and similar + - scikit-image # Image processing + - partialjson # For processing unfinished runs +# and extra control parts + - fabric +# Jupyterlab extensions + - nb_conda_kernels # for discovery of other kernels +# - jupyterlab-drawio + - jupyterlab_code_formatter + # - jupytext # needs to be tested manually +# PSI specific modules + - paulscherrerinstitute::sfdata + - paulscherrerinstitute::jungfrau_utils # should be a dependency of sfdata, but not listed there explicitly + - paulscherrerinstitute::data_api + - pip: + - -e /sf/cristallina/applications/cristallina # Creates a "local package" of cristallina .This shows a deprication warning and + # should be changed to using .toml in the future. + + # If wanted, jupyterlab_hdf can be added for nicer tables + # pip install jupyterlab_hdf + # jupyter labextension install @jupyterlab/hdf5 + +## Dependencies +# - colorama # dependency of sfdata + +## Probably can be removed +# - astropy # Used for conversion of magnet coordinates, probably not needed any more +# - pyqt # Not sure if it's needed in the analysis env + diff --git a/analysis.yml b/analysis.yml new file mode 100755 index 0000000..6858345 --- /dev/null +++ b/analysis.yml @@ -0,0 +1,64 @@ +# Analysis environment derived from the same set of packages but using +# the most up-to-date packages from conda-forge. +# Therefore this will follow upstream packages closer but also break from time to time. +# For more conservative use, use 'analysis-stable' + +name: analysis +channels: + - conda-forge +dependencies: +# essentials + - python=3.12 # keep at 3.12 beause of bitshuffle + - pip + - numpy + - scipy + - pandas + - numba + - matplotlib + - ipython + - jupyterlab + - ipympl + - joblib + - tqdm # sfdata dependency but here given explicitly + - lmfit + - pytest + - bitshuffle=0.5.2=py312h5fdea32_5 # this specific build of bitshuffle works with python 3.12 + # for higher versions new build must be found +# useful development packages + - black + - pytest # for testing the cristallina package + - h5py # sfdata dependency but here given explicitly + - pint + - line_profiler + - loguru + - pylint + - ipytest # used to be taken from pip, but here we test the conda-forge version + - sqlalchemy # X-ray transmission calculations and similar + - xraydb # X-ray transmission calculations and similar + - scikit-image # Image processing + - partialjson # For processing unfinished runs +# and extra control parts + - fabric +# Jupyterlab extensions + - nb_conda_kernels # for discovery of other kernels +# - jupyterlab-drawio + - jupyterlab_code_formatter + # - jupytext # needs to be tested manually +# PSI specific modules + - paulscherrerinstitute::sfdata + - paulscherrerinstitute::jungfrau_utils # should be a dependency of sfdata, but not listed there explicitly + - paulscherrerinstitute::data_api + - pip: + - -e /sf/cristallina/applications/cristallina # Creates a "local package" of cristallina + # If wanted, jupyterlab_hdf can be added for nicer tables + # pip install jupyterlab_hdf + # jupyter labextension install @jupyterlab/hdf5 + +## Dependencies +# - colorama # dependency of sfdata + +## Probably can be removed +# - astropy # Used for conversion of magnet coordinates, probably not needed any more +# - pyqt # Not sure if it's needed in the analysis env + + diff --git a/analysis_edge.yml b/analysis_edge.yml new file mode 100755 index 0000000..cf25fef --- /dev/null +++ b/analysis_edge.yml @@ -0,0 +1,56 @@ +# The old Analysis-edge environment derived from the same set of packages but using +# the most up-to-date packages from conda-forge. This env will be replaced by 'analysis' +# Therefore this will follow upstream packages closer but also break from time to time. +name: analysis_edge +channels: + - conda-forge +dependencies: +# essentials + - python>=3.11 + - pip + - numpy + - scipy + - pandas + - numba + - matplotlib + - ipython + - jupyterlab + - ipympl + - joblib + - tqdm # sfdata dependency but here given explicitly + - lmfit + - pytest +# useful development packages + - black + - pytest + - h5py # sfdata dependency but here given explicitly + - pint + - line_profiler + - loguru + - pylint + - ipytest # used to be taken from pip, but here we test the conda-forge version + - 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 + - nb_conda_kernels # for discovery of other kernels +# - jupyterlab-drawio + - jupyterlab_code_formatter + # - jupytext # needs to be tested manually +# PSI specific modules + - paulscherrerinstitute::sfdata +# - 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: +# pip install jupyterlab_hdf +# jupyter labextension install @jupyterlab/hdf5 diff --git a/diagnostics-crq.yml b/diagnostics-crq.yml new file mode 100755 index 0000000..7252916 --- /dev/null +++ b/diagnostics-crq.yml @@ -0,0 +1,38 @@ +# the most up-to-date packages from conda-forge. +# Therefore this will follow upstream packages closer but also break from time to time. +name: diagnostics-crq +channels: + - conda-forge +dependencies: + - python=3.12 #mflow / pyzmq still has issues with 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 + +# 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 - local package + - pip: + - -e /sf/cristallina/applications/slic/slic-package diff --git a/env_backups/slic-crq.yml b/env_backups/slic-crq.yml new file mode 100644 index 0000000..627909e --- /dev/null +++ b/env_backups/slic-crq.yml @@ -0,0 +1,278 @@ +name: slic-crq +channels: + - paulscherrerinstitute + - conda-forge +dependencies: + - _libgcc_mutex=0.1=conda_forge + - _openmp_mutex=4.5=2_gnu + - adwaita-icon-theme=48.0=unix_0 + - alsa-lib=1.2.14=hb9d3cd8_0 + - argon2-cffi=23.1.0=pyhd8ed1ab_1 + - argon2-cffi-bindings=21.2.0=py311h9ecbd09_5 + - asttokens=3.0.0=pyhd8ed1ab_1 + - at-spi2-atk=2.38.0=h0630a04_3 + - at-spi2-core=2.40.3=h0630a04_0 + - atk-1.0=2.38.0=h04ea711_2 + - attr=2.5.1=h166bdaf_1 + - bcrypt=4.3.0=py311h9e33e62_0 + - bitshuffle=0.5.2=py311h49a552a_5 + - brotli=1.1.0=hb9d3cd8_2 + - brotli-bin=1.1.0=hb9d3cd8_2 + - brotli-python=1.1.0=py311hfdbb021_2 + - bsread=1.5.7=py_0 + - bzip2=1.0.8=h4bc722e_7 + - c-ares=1.34.5=hb9d3cd8_0 + - ca-certificates=2025.4.26=hbd8a1cb_0 + - cachannel=3.2.0=py311h41425db_0 + - cached-property=1.5.2=hd8ed1ab_1 + - cached_property=1.5.2=pyha770c72_1 + - cairo=1.18.4=h3394656_0 + - cam_server_client=5.6.5=py_0 + - certifi=2025.1.31=pyhd8ed1ab_0 + - cffi=1.17.1=py311hf29c0ef_0 + - charset-normalizer=3.4.1=pyhd8ed1ab_0 + - click=8.1.8=pyh707e725_0 + - colorama=0.4.6=pyhd8ed1ab_1 + - comm=0.2.2=pyhd8ed1ab_1 + - contourpy=1.3.2=py311hd18a35c_0 + - cryptography=44.0.2=py311hafd3f86_0 + - cta_lib=1.0.1=py_0 + - cycler=0.12.1=pyhd8ed1ab_1 + - cyrus-sasl=2.1.27=h54b06d7_7 + - data_api=0.8.8=py_0 + - dbus=1.13.6=h5008d03_3 + - dbus-python=1.3.2=py311hf24dd5a_5 + - debugpy=1.8.14=py311hfdbb021_0 + - decorator=5.2.1=pyhd8ed1ab_0 + - double-conversion=3.3.1=h5888daf_0 + - elog=1.3.16=py_0 + - epics-base=7.0.7.0=h2dfad98_0 + - epoxy=1.5.10=h166bdaf_1 + - exceptiongroup=1.2.2=pyhd8ed1ab_1 + - executing=2.2.0=pyhd8ed1ab_0 + - expat=2.7.0=h5888daf_0 + - font-ttf-dejavu-sans-mono=2.37=hab24e00_0 + - font-ttf-inconsolata=3.000=h77eed37_0 + - font-ttf-source-code-pro=2.038=h77eed37_0 + - font-ttf-ubuntu=0.83=h77eed37_3 + - fontconfig=2.15.0=h7e30c49_1 + - fonts-conda-ecosystem=1=0 + - fonts-conda-forge=1=0 + - fonttools=4.57.0=py311h2dc5d0c_0 + - freetype=2.13.3=ha770c72_1 + - fribidi=1.0.10=h36c2ea0_0 + - fuzzywuzzy=0.18.0=pyhd8ed1ab_1 + - gdk-pixbuf=2.42.12=hb9ae30d_0 + - glib=2.84.1=h07242d1_0 + - glib-tools=2.84.1=h4833e2c_0 + - graphite2=1.3.13=h59595ed_1003 + - gst-plugins-base=1.24.11=h651a532_0 + - gstreamer=1.24.11=hc37bda9_0 + - gtk3=3.24.43=h0c6a113_5 + - h2=4.2.0=pyhd8ed1ab_0 + - h5py=3.12.1=nompi_py311h5ed33ec_103 + - harfbuzz=11.1.0=h3beb420_0 + - hdf5=1.14.4=nompi_h2d575fe_105 + - hicolor-icon-theme=0.17=ha770c72_2 + - hpack=4.1.0=pyhd8ed1ab_0 + - hyperframe=6.1.0=pyhd8ed1ab_0 + - icu=75.1=he02047a_0 + - idna=3.10=pyhd8ed1ab_1 + - importlib-metadata=8.6.1=pyha770c72_0 + - importlib_resources=6.5.2=pyhd8ed1ab_0 + - ipykernel=6.29.5=pyh3099207_0 + - ipympl=0.9.7=pyhd8ed1ab_1 + - ipython=9.2.0=pyhfb0248b_0 + - ipython_pygments_lexers=1.1.1=pyhd8ed1ab_0 + - ipywidgets=8.1.6=pyhd8ed1ab_0 + - jedi=0.19.2=pyhd8ed1ab_1 + - jungfrau_utils=3.16.0=py_0 + - jupyter_client=8.6.3=pyhd8ed1ab_1 + - jupyter_core=5.7.2=pyh31011fe_1 + - jupyterlab_widgets=3.0.14=pyhd8ed1ab_0 + - keyutils=1.6.1=h166bdaf_0 + - kiwisolver=1.4.7=py311hd18a35c_0 + - krb5=1.21.3=h659f571_0 + - lcms2=2.17=h717163a_0 + - ld_impl_linux-64=2.43=h712a8e2_4 + - lerc=4.0.0=h0aef613_1 + - levenshtein=0.27.1=py311hfdbb021_0 + - libaec=1.1.3=h59595ed_0 + - libblas=3.9.0=31_h59b9bed_openblas + - libbrotlicommon=1.1.0=hb9d3cd8_2 + - libbrotlidec=1.1.0=hb9d3cd8_2 + - libbrotlienc=1.1.0=hb9d3cd8_2 + - libcap=2.75=h39aace5_0 + - libcblas=3.9.0=31_he106b2a_openblas + - libclang-cpp20.1=20.1.3=default_h1df26ce_0 + - libclang13=20.1.3=default_he06ed0a_0 + - libcups=2.3.3=h4637d8d_4 + - libcurl=8.13.0=h332b0f4_0 + - libdeflate=1.23=h86f0d12_0 + - libdrm=2.4.124=hb9d3cd8_0 + - libedit=3.1.20250104=pl5321h7949ede_0 + - libegl=1.7.0=ha4b6fd6_2 + - libev=4.33=hd590300_2 + - libexpat=2.7.0=h5888daf_0 + - libffi=3.4.6=h2dba641_1 + - libfreetype=2.13.3=ha770c72_1 + - libfreetype6=2.13.3=h48d6fc4_1 + - libgcc=14.2.0=h767d61c_2 + - libgcc-ng=14.2.0=h69a702a_2 + - libgfortran=14.2.0=h69a702a_2 + - libgfortran5=14.2.0=hf1ad2bd_2 + - libgl=1.7.0=ha4b6fd6_2 + - libglib=2.84.1=h2ff4ddf_0 + - libglvnd=1.7.0=ha4b6fd6_2 + - libglx=1.7.0=ha4b6fd6_2 + - libgomp=14.2.0=h767d61c_2 + - libiconv=1.18=h4ce23a2_1 + - libjpeg-turbo=3.1.0=hb9d3cd8_0 + - liblapack=3.9.0=31_h7ac8fdf_openblas + - libllvm20=20.1.3=he9d0ab4_0 + - liblzma=5.8.1=hb9d3cd8_0 + - libnghttp2=1.64.0=h161d5f1_0 + - libnsl=2.0.1=hd590300_0 + - libntlm=1.8=hb9d3cd8_0 + - libogg=1.3.5=hd0c01bc_1 + - libopenblas=0.3.29=pthreads_h94d23a6_0 + - libopengl=1.7.0=ha4b6fd6_2 + - libopus=1.5.2=hd0c01bc_0 + - libpciaccess=0.18=hd590300_0 + - libpng=1.6.47=h943b412_0 + - libpq=17.4=h27ae623_1 + - librsvg=2.58.4=he92a37e_3 + - libsodium=1.0.20=h4ab18f5_0 + - libsqlite=3.49.1=hee588c1_2 + - libssh2=1.11.1=hcf80075_0 + - libstdcxx=14.2.0=h8f9b012_2 + - libstdcxx-ng=14.2.0=h4852527_2 + - libtiff=4.7.0=hd9ff511_4 + - libudev1=257.4=hbe16f8c_1 + - libusb=1.0.28=hb9d3cd8_0 + - libuuid=2.38.1=h0b41bf4_0 + - libvorbis=1.3.7=h9c3ff4c_0 + - libwebp-base=1.5.0=h851e524_0 + - libxcb=1.17.0=h8a09558_0 + - libxcrypt=4.4.36=hd590300_1 + - libxkbcommon=1.9.0=h65c71a3_0 + - libxml2=2.13.7=h4bc477f_1 + - libxslt=1.1.39=h76b75d6_0 + - libzlib=1.3.1=hb9d3cd8_2 + - llvmlite=0.44.0=py311h9c9ff8c_1 + - loguru=0.7.2=py311h38be061_2 + - logzero=1.7.0=py311h38be061_6 + - lxml=5.4.0=py311hbd2c71b_0 + - markdown-it-py=3.0.0=pyhd8ed1ab_1 + - matplotlib=3.10.1=py311h38be061_0 + - matplotlib-base=3.10.1=py311h2b939e6_0 + - matplotlib-inline=0.1.7=pyhd8ed1ab_1 + - mdurl=0.1.2=pyhd8ed1ab_1 + - mesalib=25.0.4=hfd93750_1 + - mflow=0.2.0=pyh39e3cac_2 + - munkres=1.1.4=pyh9f0ad1d_0 + - mysql-common=9.2.0=h266115a_0 + - mysql-libs=9.2.0=he0572af_0 + - ncurses=6.5=h2d0b736_3 + - nest-asyncio=1.6.0=pyhd8ed1ab_1 + - numba=0.61.2=py311h4e1c48f_0 + - numpy=2.2.5=py311h5d046bc_0 + - openjpeg=2.5.3=h5fbd93e_0 + - openldap=2.6.9=he970967_0 + - openssl=3.5.0=h7b32b05_0 + - packaging=25.0=pyh29332c3_1 + - pandas=2.2.3=py311h7db5c69_3 + - pango=1.56.3=h9ac818e_1 + - parso=0.8.4=pyhd8ed1ab_1 + - partialjson=0.0.8=pyhd8ed1ab_1 + - passlib=1.7.4=pyhd8ed1ab_2 + - pcre2=10.44=hba22ea6_2 + - perl=5.32.1=7_hd590300_perl5 + - pexpect=4.9.0=pyhd8ed1ab_1 + - pickleshare=0.7.5=pyhd8ed1ab_1004 + - pillow=11.1.0=py311h1322bbf_0 + - pip=25.1=pyh8b19718_0 + - pixman=0.44.2=h29eaf8c_0 + - platformdirs=4.3.7=pyh29332c3_0 + - playsound=1.3.0=pyhd8ed1ab_1 + - prompt-toolkit=3.0.51=pyha770c72_0 + - psutil=7.0.0=py311h9ecbd09_0 + - pthread-stubs=0.4=hb9d3cd8_1002 + - ptyprocess=0.7.0=pyhd8ed1ab_1 + - pure_eval=0.2.3=pyhd8ed1ab_1 + - pycparser=2.22=pyh29332c3_1 + - pyepics=3.5.7=py311h38be061_1 + - pygments=2.19.1=pyhd8ed1ab_0 + - pyparsing=3.2.3=pyhd8ed1ab_1 + - pyserial=3.5=pyhd8ed1ab_1 + - pyside6=6.9.0=py311h9053184_0 + - pysocks=1.7.1=pyha55dd90_7 + - python=3.11.12=h9e4cc4f_0_cpython + - python-dateutil=2.9.0.post0=pyhff2d567_1 + - python-levenshtein=0.27.1=pyhff2d567_0 + - python-tzdata=2025.2=pyhd8ed1ab_0 + - python_abi=3.11=7_cp311 + - pytz=2025.2=pyhd8ed1ab_0 + - pyusb=1.3.1=pyhd8ed1ab_0 + - pyvisa=1.14.1=pyhd8ed1ab_1 + - pyvisa-py=0.7.2=pyhd8ed1ab_1 + - pyzmq=26.4.0=py311h7deb3e3_0 + - qhull=2020.2=h434a139_5 + - qt6-main=6.9.0=h6441bc3_1 + - rapidfuzz=3.13.0=py311hfdbb021_0 + - readline=8.2=h8c095d6_2 + - requests=2.32.3=pyhd8ed1ab_1 + - rich=14.0.0=pyh29332c3_0 + - scipy=1.15.2=py311h8f841c2_0 + - setuptools=79.0.1=pyhff2d567_0 + - sfdata=0.4.1=py_0 + - six=1.17.0=pyhd8ed1ab_0 + - spirv-tools=2025.1=h84d6215_0 + - stack_data=0.6.3=pyhd8ed1ab_1 + - termcolor=2.3.0=pyhd8ed1ab_0 + - tk=8.6.13=noxft_h4845f30_101 + - tornado=6.4.2=py311h9ecbd09_0 + - tqdm=4.67.1=pyhd8ed1ab_1 + - traitlets=5.14.3=pyhd8ed1ab_1 + - typing-extensions=4.13.2=h0e9735f_0 + - typing_extensions=4.13.2=pyh29332c3_0 + - tzdata=2025b=h78e105d_0 + - unicodedata2=16.0.0=py311h9ecbd09_0 + - urllib3=2.4.0=pyhd8ed1ab_0 + - wayland=1.23.1=h3e06ad9_1 + - wcwidth=0.2.13=pyhd8ed1ab_1 + - wheel=0.45.1=pyhd8ed1ab_1 + - widgetsnbextension=4.0.14=pyhd8ed1ab_0 + - wxpython=4.2.3=py311h552b8c3_0 + - wxwidgets=3.2.7=hba9cfa6_0 + - xarray=2025.3.1=pyhd8ed1ab_0 + - xcb-util=0.4.1=hb711507_2 + - xcb-util-cursor=0.1.5=hb9d3cd8_0 + - xcb-util-image=0.4.0=hb711507_2 + - xcb-util-keysyms=0.4.1=hb711507_0 + - xcb-util-renderutil=0.3.10=hb711507_0 + - xcb-util-wm=0.4.2=hb711507_0 + - xkeyboard-config=2.44=hb9d3cd8_0 + - xorg-libice=1.1.2=hb9d3cd8_0 + - xorg-libsm=1.2.6=he73a12e_0 + - xorg-libx11=1.8.12=h4f16b4b_0 + - xorg-libxau=1.0.12=hb9d3cd8_0 + - xorg-libxcomposite=0.4.6=hb9d3cd8_2 + - xorg-libxcursor=1.2.3=hb9d3cd8_0 + - xorg-libxdamage=1.1.6=hb9d3cd8_0 + - xorg-libxdmcp=1.1.5=hb9d3cd8_0 + - xorg-libxext=1.3.6=hb9d3cd8_0 + - xorg-libxfixes=6.0.1=hb9d3cd8_0 + - xorg-libxi=1.8.2=hb9d3cd8_0 + - xorg-libxinerama=1.1.5=h5888daf_1 + - xorg-libxrandr=1.5.4=hb9d3cd8_0 + - xorg-libxrender=0.9.12=hb9d3cd8_0 + - xorg-libxshmfence=1.3.3=hb9d3cd8_0 + - xorg-libxtst=1.2.5=hb9d3cd8_3 + - xorg-libxxf86vm=1.1.6=hb9d3cd8_0 + - yaspin=3.1.0=pyhd8ed1ab_0 + - zeromq=4.3.5=h3b0a872_7 + - zipp=3.21.0=pyhd8ed1ab_1 + - zstandard=0.23.0=py311h9ecbd09_2 + - zstd=1.5.7=hb8e6e7a_2 +prefix: /sf/cristallina/applications/it/envs/slic-crq diff --git a/env_backups/slic.yml b/env_backups/slic.yml new file mode 100644 index 0000000..a5496c4 --- /dev/null +++ b/env_backups/slic.yml @@ -0,0 +1,413 @@ +name: slic +channels: + - file:///gfa/.mounts/sf_cristallina/applications/conda/envs/cta/conda-bld + - paulscherrerinstitute + - defaults + - conda-forge +dependencies: + - _libgcc_mutex=0.1=conda_forge + - _openmp_mutex=4.5=6_kmp_llvm + - aiofiles=24.1.0=pyhd8ed1ab_1 + - aiosqlite=0.21.0=pyhaa4b35c_0 + - alsa-lib=1.2.3.2=h166bdaf_0 + - anyio=4.10.0=pyhe01879c_0 + - aom=3.5.0=h27087fc_0 + - argon2-cffi-bindings=25.1.0=py39hd399759_0 + - arrow=1.3.0=pyhd8ed1ab_1 + - async-lru=2.0.5=pyh29332c3_0 + - atk-1.0=2.38.0=h04ea711_2 + - attr=2.5.2=h39aace5_0 + - attrs=25.3.0=pyh71513ae_0 + - babel=2.17.0=pyhd8ed1ab_0 + - backcall=0.2.0=pyhd3eb1b0_0 + - bcrypt=4.3.0=py39h20260ba_1 + - beautifulsoup4=4.13.4=pyha770c72_0 + - black=25.1.0=pyha5154f8_0 + - blas=1.0=mkl + - bleach-with-css=6.2.0=h82add2a_4 + - blosc=1.21.5=h0f2a231_0 + - bottleneck=1.5.0=py39hf3d9206_0 + - brotli=1.0.9=h166bdaf_9 + - brotli-bin=1.0.9=h166bdaf_9 + - brotli-python=1.0.9=py39h5a03fae_9 + - brotlipy=0.7.0=py39h8cd3c5a_1007 + - brunsli=0.1=h2531618_0 + - bzip2=1.0.8=hda65f42_8 + - c-ares=1.34.5=hb9d3cd8_0 + - c-blosc2=2.12.0=hb4ffafa_0 + - ca-certificates=2025.11.12=hbd8a1cb_0 + - cachannel=3.2.0=py39hb93dfd8_0 + - cached-property=1.5.2=hd8ed1ab_1 + - cached_property=1.5.2=pyha770c72_1 + - cairo=1.16.0=ha12eb4b_1010 + - cam_server=5.3.1=py39_0 + - cam_server_client=5.6.5=py_0 + - certifi=2025.8.3=pyhd8ed1ab_0 + - cffi=1.17.1=py39h1fdaa30_0 + - cfitsio=4.2.0=hd9d235c_0 + - charls=2.4.2=h59595ed_0 + - cheroot=10.0.1=pyhd8ed1ab_1 + - click=8.1.8=pyh707e725_0 + - cloudpickle=3.1.1=pyhd8ed1ab_0 + - colorama=0.4.6=pyhd8ed1ab_1 + - comm=0.2.3=pyhe01879c_0 + - commonmark=0.9.1=pyhd3eb1b0_0 + - contourpy=1.3.0=py39h74842e3_2 + - cryptography=45.0.6=py39hb2f7f84_0 + - cta_lib=1.0.5=py39_0 + - cytoolz=1.0.1=py39h8cd3c5a_0 + - dask-core=2024.8.0=pyhd8ed1ab_0 + - data_api=0.8.8=py_0 + - dataclasses=0.8=pyh6d0b6a4_7 + - dav1d=1.2.1=h5eee18b_0 + - dbus=1.13.18=hb2f20db_0 + - dbus-python=1.3.2=py39h1c6aa96_4 + - debugpy=1.8.16=py39haef64b4_0 + - defusedxml=0.7.1=pyhd3eb1b0_0 + - elog=1.3.16=py_0 + - entrypoints=0.4=pyhd8ed1ab_1 + - epics-base=7.0.9.0=pl5321h2669dad_9 + - exceptiongroup=1.3.0=pyhd8ed1ab_0 + - expat=2.7.3=hecca717_0 + - flit-core=3.12.0=pyhd8ed1ab_0 + - font-ttf-dejavu-sans-mono=2.37=hd3eb1b0_0 + - font-ttf-inconsolata=3.000=h77eed37_0 + - font-ttf-source-code-pro=2.038=h77eed37_0 + - font-ttf-ubuntu=0.83=h77eed37_3 + - fontconfig=2.14.2=h14ed4e7_0 + - fonts-anaconda=1=h8fa9717_0 + - fonts-conda-ecosystem=1=hd3eb1b0_0 + - fonttools=4.59.1=py39heb7d2ae_0 + - fqdn=1.5.1=pyhd8ed1ab_1 + - freetype=2.12.1=h267a509_2 + - fribidi=1.0.16=hb03c661_0 + - fsspec=2025.7.0=pyhd8ed1ab_0 + - future=1.0.0=pyhd8ed1ab_2 + - fuzzywuzzy=0.18.0=pyhd8ed1ab_1 + - gdk-pixbuf=2.42.10=h5eee18b_1 + - gettext=0.25.1=h3f43e3d_1 + - gettext-tools=0.25.1=h3f43e3d_1 + - giflib=5.2.2=h5eee18b_0 + - glib=2.80.2=hf974151_0 + - glib-tools=2.80.2=hb6ce0ca_0 + - gmp=6.3.0=hac33072_2 + - gobject-introspection=1.78.1=py39h42194e9_1 + - graphite2=1.3.14=hecca717_2 + - gst-plugins-base=1.20.2=hcf0ee16_0 + - gstreamer=1.20.3=hd4edc92_2 + - gtk2=2.24.33=h73c1081_2 + - h11=0.16.0=pyhd8ed1ab_0 + - h2=4.2.0=pyhd8ed1ab_0 + - h5py=3.13.0=nompi_py39h30a5a8d_100 + - harfbuzz=4.2.0=h40b6f09_0 + - hdf5=1.14.3=nompi_hdf9ad27_105 + - hpack=4.1.0=pyhd8ed1ab_0 + - httpcore=1.0.9=pyh29332c3_0 + - httpx=0.28.1=pyhd8ed1ab_0 + - hyperframe=6.1.0=pyhd8ed1ab_0 + - icu=69.1=h9c3ff4c_0 + - idna=3.10=pyhd8ed1ab_1 + - imagecodecs=2023.1.23=py39hd061359_0 + - imageio=2.37.0=pyhfb79c49_0 + - importlib-metadata=8.7.0=pyhe01879c_1 + - importlib-resources=6.5.2=pyhd8ed1ab_0 + - importlib_metadata=8.7.0=h40b2b14_1 + - importlib_resources=6.5.2=pyhd8ed1ab_0 + - intel-openmp=2023.1.0=hdb19cb5_46306 + - ipykernel=6.30.1=pyh82676e8_0 + - ipython=8.18.1=pyh707e725_3 + - ipython_genutils=0.2.0=pyhd8ed1ab_2 + - ipython_pygments_lexers=1.1.1=pyhd8ed1ab_0 + - ipywidgets=8.1.7=pyhd8ed1ab_0 + - isoduration=20.11.0=pyhd8ed1ab_1 + - jaraco.functools=4.3.0=pyhd8ed1ab_0 + - jbig=2.1=h7f98852_2003 + - jedi=0.19.2=pyhd8ed1ab_1 + - jinja2=3.1.6=pyhd8ed1ab_0 + - jpeg=9e=h5eee18b_3 + - jsonpointer=3.0.0=py39hf3d152e_1 + - jupyter_client=8.6.3=pyhd8ed1ab_1 + - jupyter_core=5.8.1=pyh31011fe_0 + - jupyter_ydoc=3.1.0=pyhe01879c_0 + - jupyterlab_pygments=0.3.0=pyhd8ed1ab_2 + - jupyterlab_widgets=3.0.15=pyhd8ed1ab_0 + - jxrlib=1.1=hd590300_3 + - keyutils=1.6.3=hb9d3cd8_0 + - kiwisolver=1.4.7=py39h74842e3_0 + - krb5=1.21.3=h143b758_0 + - lark=1.2.2=pyhd8ed1ab_1 + - lazy-loader=0.4=pyhd8ed1ab_2 + - lazy_loader=0.4=pyhd8ed1ab_2 + - lcms2=2.15=hfd0df8a_0 + - ld_impl_linux-64=2.45=bootstrap_ha15bf96_4 + - lerc=4.0.0=h0aef613_1 + - levenshtein=0.27.1=py39hf88036b_0 + - libaec=1.1.4=h3f801dc_0 + - libasprintf=0.25.1=h3f43e3d_1 + - libasprintf-devel=0.25.1=h3f43e3d_1 + - libavif=0.11.1=h8182462_2 + - libblas=3.9.0=20_linux64_mkl + - libbrotlicommon=1.0.9=h166bdaf_9 + - libbrotlidec=1.0.9=h166bdaf_9 + - libbrotlienc=1.0.9=h166bdaf_9 + - libcap=2.77=h3ff7636_0 + - libcblas=3.9.0=20_linux64_mkl + - libclang=13.0.1=default_hb5137d0_10 + - libcurl=8.8.0=hca28451_1 + - libdeflate=1.17=h5eee18b_1 + - libedit=3.1.20250104=pl5321h7949ede_0 + - libev=4.33=hd590300_2 + - libevent=2.1.10=h28343ad_4 + - libexpat=2.7.3=hecca717_0 + - libffi=3.4.6=h2dba641_1 + - libgcc=15.2.0=he0feb66_12 + - libgcc-ng=15.2.0=h69a702a_12 + - libgettextpo=0.25.1=h3f43e3d_1 + - libgettextpo-devel=0.25.1=h3f43e3d_1 + - libgfortran-ng=7.5.0=h14aa051_20 + - libgfortran4=7.5.0=h14aa051_20 + - libgfortran5=15.2.0=h68bc16d_12 + - libgirepository=1.78.1=h003a4f0_1 + - libglib=2.80.2=hf974151_0 + - libglu=9.0.3=h5888daf_1 + - libglvnd=1.7.0=ha4b6fd6_2 + - libgomp=15.2.0=he0feb66_12 + - libiconv=1.18=h3b78370_2 + - liblapack=3.9.0=20_linux64_mkl + - libllvm11=11.1.0=h9e868ea_6 + - libllvm13=13.0.1=hf817b99_2 + - libllvm14=14.0.6=hecde1de_4 + - liblzma=5.8.1=hb9d3cd8_2 + - liblzma-devel=5.8.1=hb9d3cd8_2 + - libnghttp2=1.58.0=h47da74e_1 + - libnsl=2.0.1=hb9d3cd8_1 + - libogg=1.3.5=h27cfd23_1 + - libopenblas=0.3.28=pthreads_h94d23a6_0 + - libopengl=1.7.0=ha4b6fd6_2 + - libopus=1.5.2=hd0c01bc_0 + - libpng=1.6.43=h2797004_0 + - libpq=14.5=hfc447b1_7 + - libsodium=1.0.20=h4ab18f5_0 + - libsqlite=3.46.0=hde9e2c9_0 + - libssh2=1.11.0=h0841786_0 + - libstdcxx=15.2.0=h934c35e_12 + - libstdcxx-ng=15.2.0=hdf11a46_12 + - libtiff=4.5.0=h6adf6a1_2 + - libudev1=257.10=hd0affe5_2 + - libusb=1.0.29=h73b1eb8_0 + - libuuid=2.41.2=he9a06e4_0 + - libvorbis=1.3.7=h54a6638_2 + - libwebp=1.3.2=h11a3e52_0 + - libwebp-base=1.3.2=h5eee18b_1 + - libxcb=1.13=h7f98852_1004 + - libxcrypt=4.4.36=hd590300_1 + - libxkbcommon=1.0.3=he3ba5ed_0 + - libxml2=2.9.14=haae042b_4 + - libxslt=1.1.33=h0ef7038_3 + - libzlib=1.2.13=h4ab18f5_6 + - libzopfli=1.0.3=he6710b0_0 + - llvm-openmp=20.1.8=h4922eb0_0 + - llvmlite=0.43.0=py39h6a678d5_0 + - locket=1.0.0=py39h06a4308_0 + - loguru=0.7.3=pyh707e725_0 + - logzero=1.7.0=py39hf3d152e_6 + - lxml=4.8.0=py39hb9d737c_3 + - lz4-c=1.9.4=h6a678d5_1 + - markdown-it-py=3.0.0=pyhd8ed1ab_1 + - markupsafe=3.0.2=py39h9399b63_1 + - matplotlib=3.9.2=py39h06a4308_0 + - matplotlib-base=3.9.2=py39h16632d1_2 + - matplotlib-inline=0.1.7=pyhd8ed1ab_1 + - mdurl=0.1.2=pyhd8ed1ab_1 + - mflow=0.2.0=pyh39e3cac_2 + - mistune=3.1.3=pyh29332c3_0 + - mkl=2023.2.0=ha770c72_50498 + - mkl-service=2.4.1=py39h5af75a1_1 + - mkl_fft=1.3.10=py39h191f12f_1 + - mkl_random=1.2.8=py39hafd1009_0 + - more-itertools=10.7.0=pyhd8ed1ab_0 + - mypy_extensions=1.1.0=pyha770c72_0 + - mysql-common=8.0.33=hf1915f5_6 + - mysql-libs=8.0.33=hca2cd23_6 + - ncurses=6.5=h2d0b736_3 + - nest-asyncio=1.6.0=pyhd8ed1ab_1 + - networkx=3.2.1=py39h06a4308_0 + - ninja=1.13.2=h171cf75_0 + - ninja-base=1.10.2=hd09550d_5 + - nspr=4.38=h29cc59b_0 + - nss=3.100=hca3bf56_0 + - numba=0.60.0=py39h0320e7d_0 + - numexpr=2.10.1=mkl_py39h4145518_2 + - numpy=1.26.4=py39h5f9d8c6_0 + - numpy-base=1.26.4=py39hb5e798b_0 + - openjpeg=2.5.2=he7f1fd0_0 + - openssl=3.6.0=h26f9b46_0 + - overrides=7.7.0=pyhd8ed1ab_1 + - packaging=25.0=pyh29332c3_1 + - pandas=2.2.3=py39h3b40f6f_1 + - pandoc=3.8.2.1=ha770c72_0 + - pandocfilters=1.5.0=pyhd3eb1b0_0 + - pango=1.50.7=hbd2fdc8_0 + - partd=1.4.2=pyhd8ed1ab_0 + - paste=3.10.1=pyhd8ed1ab_1 + - pathlib2=2.3.7.post1=py39hf3d152e_4 + - pathspec=0.12.1=pyhd8ed1ab_1 + - pcre=8.45=h295c915_0 + - pcre2=10.43=hcad00b1_0 + - perl=5.32.1=7_hd590300_perl5 + - pickleshare=0.7.5=pyhd8ed1ab_1004 + - pillow=10.4.0=py39h5eee18b_0 + - pip=25.2=pyh8b19718_0 + - pixman=0.46.4=h54a6638_1 + - platformdirs=4.3.8=pyhe01879c_0 + - prometheus_client=0.22.1=pyhd8ed1ab_0 + - prompt-toolkit=3.0.51=pyha770c72_0 + - prompt_toolkit=3.0.51=hd8ed1ab_0 + - psutil=7.0.0=py39h8cd3c5a_0 + - pthread-stubs=0.4=hb9d3cd8_1002 + - ptyprocess=0.7.0=pyhd3eb1b0_2 + - pure_eval=0.2.3=pyhd8ed1ab_1 + - pybind11-abi=11=hc364b38_1 + - pycairo=1.25.0=py39hc92de75_1 + - pycrdt=0.12.27=py39h2bddf42_0 + - pycrdt-websocket=0.15.5=pyhd8ed1ab_0 + - pyepics=3.5.8=py39hf3d152e_0 + - pygments=2.19.2=pyhd8ed1ab_0 + - pygobject=3.46.0=py39hb25b1be_1 + - pyopenssl=25.1.0=pyhd8ed1ab_0 + - pyparsing=3.2.3=pyhe01879c_2 + - pypubsub=4.0.3=pyhd8ed1ab_1 + - pyqt=5.12.3=py39hf3d152e_8 + - pyqt-impl=5.12.3=py39hde8b62d_8 + - pyqt5-sip=4.19.18=py39he80948d_8 + - pyqtchart=5.12=py39h0fcd23e_8 + - pyqtwebengine=5.12.1=py39h0fcd23e_8 + - pyro5=5.15=pyhd8ed1ab_1 + - pyrsistent=0.20.0=py39h8cd3c5a_1 + - pyserial=3.5=pyhd8ed1ab_1 + - pysocks=1.7.1=pyha55dd90_7 + - python=3.9.19=h0755675_0_cpython + - python-dateutil=2.9.0post0=py39h06a4308_2 + - python-fastjsonschema=2.21.2=pyhe01879c_0 + - python-json-logger=2.0.7=py39h06a4308_0 + - python-levenshtein=0.27.1=pyhff2d567_0 + - python-tzdata=2025.2=pyhd8ed1ab_0 + - python_abi=3.9=8_cp39 + - pytz=2024.1=py39h06a4308_0 + - pyvisa=1.14.1=pyhd8ed1ab_1 + - pyvisa-py=0.7.2=pyhd8ed1ab_1 + - pywavelets=1.6.0=py39hd92a3bb_0 + - pyyaml=6.0.2=py39h9399b63_2 + - pyzmq=27.0.2=py39haa5fa38_0 + - qhull=2020.2=h434a139_5 + - qt=5.12.9=h1304e3e_6 + - qtpy=2.4.3=pyhd8ed1ab_1 + - rapidfuzz=3.13.0=py39hf88036b_0 + - readline=8.2=h8c095d6_2 + - referencing=0.36.2=pyh29332c3_0 + - regex=2025.7.34=py39hd399759_0 + - requests=2.32.5=pyhd8ed1ab_0 + - rfc3339-validator=0.1.4=pyhd8ed1ab_1 + - rfc3986-validator=0.1.1=py39h06a4308_0 + - rfc3987-syntax=1.1.0=pyhe01879c_1 + - rich=14.1.0=pyhe01879c_0 + - rpds-py=0.27.0=py39h17f49b6_0 + - scipy=1.13.1=py39haf93ffa_0 + - send2trash=1.8.3=pyh0d859eb_1 + - serpent=1.41=pyhd8ed1ab_1 + - setuptools=80.9.0=pyhff2d567_0 + - snappy=1.1.10=hdb0a2a9_1 + - sniffio=1.3.1=pyhd8ed1ab_1 + - sortedcontainers=2.4.0=pyhd8ed1ab_1 + - soupsieve=2.7=pyhd8ed1ab_0 + - sqlite=3.46.0=h6d4b2fc_0 + - sqlite-anyio=0.2.3=pyhaa4b35c_1 + - stack_data=0.6.3=pyhd8ed1ab_1 + - tbb=2021.8.0=hdb19cb5_0 + - termcolor=3.1.0=pyhd8ed1ab_0 + - terminado=0.18.1=pyh0d859eb_0 + - tifffile=2023.8.12=pyhd8ed1ab_0 + - tinycss2=1.4.0=pyhd8ed1ab_0 + - tk=8.6.14=h39e8969_0 + - toml=0.10.2=pyhd8ed1ab_1 + - tomli=2.2.1=pyhe01879c_2 + - toolz=1.0.0=pyhd8ed1ab_1 + - tornado=6.5.2=py39hd399759_0 + - tqdm=4.67.1=pyhd8ed1ab_1 + - traitlets=5.14.3=pyhd8ed1ab_1 + - trio=0.30.0=py39hf3d152e_0 + - typed-ast=1.5.5=py39hd1e30aa_1 + - types-python-dateutil=2.9.0.20250809=pyhd8ed1ab_0 + - typing-extensions=4.14.1=h4440ef1_0 + - typing_extensions=4.14.1=pyhe01879c_0 + - typing_utils=0.1.0=pyhd8ed1ab_1 + - tzdata=2025b=h78e105d_0 + - unicodedata2=16.0.0=py39h8cd3c5a_0 + - uri-template=1.3.0=pyhd8ed1ab_1 + - urllib3=2.5.0=pyhd8ed1ab_0 + - webcolors=24.11.1=pyhd8ed1ab_0 + - webencodings=0.5.1=pyhd8ed1ab_3 + - websocket-client=1.8.0=pyhd8ed1ab_1 + - wheel=0.45.1=pyhd8ed1ab_1 + - widgetsnbextension=4.0.14=pyhd8ed1ab_0 + - wxpython=4.1.1=py39hea8757a_7 + - xorg-kbproto=1.0.7=hb9d3cd8_1003 + - xorg-libice=1.1.2=hb9d3cd8_0 + - xorg-libsm=1.2.6=he73a12e_0 + - xorg-libx11=1.8.4=h0b41bf4_0 + - xorg-libxau=1.0.12=hb03c661_1 + - xorg-libxdmcp=1.1.5=hb03c661_1 + - xorg-libxext=1.3.4=h0b41bf4_2 + - xorg-libxrender=0.9.10=h7f98852_1003 + - xorg-renderproto=0.11.1=hb9d3cd8_1003 + - xorg-xextproto=7.3.0=hb9d3cd8_1004 + - xorg-xproto=7.0.31=hb9d3cd8_1008 + - xz=5.8.1=hbcc6ac9_2 + - xz-gpl-tools=5.8.1=hbcc6ac9_2 + - xz-tools=5.8.1=hb9d3cd8_2 + - y-py=0.6.2=py39he612d8f_1 + - yaml=0.2.5=h280c20c_3 + - ypy-websocket=0.12.4=pyhd8ed1ab_1 + - zeromq=4.3.5=h387f397_9 + - zfp=1.0.1=h909a3a2_3 + - zipp=3.23.0=pyhd8ed1ab_0 + - zlib=1.2.13=h4ab18f5_6 + - zlib-ng=2.0.7=h0b41bf4_0 + - zstandard=0.23.0=py39hd399759_3 + - zstd=1.5.6=ha6fb4c9_0 + - pip: + - appdirs==1.4.4 + - argon2-cffi==21.3.0 + - asttokens==2.0.5 + - bitshuffle==0.5.2 + - bleach==4.1.0 + - bottle==0.12.19 + - bsread==1.5.7 + - charset-normalizer==3.3.2 + - cycler==0.11.0 + - cython==3.2.1 + - decorator==5.1.1 + - executing==0.8.3 + - ipympl==0.9.3 + - jaraco-functools==3.3.0 + - json5==0.9.6 + - jungfrau-utils==3.15.6 + - jupyterlab-pygments==0.1.2 + - mlzlog==0.3.5 + - munkres==1.1.4 + - nbconvert==7.16.4 + - outcome==1.1.0 + - parso==0.8.3 + - passlib==1.7.4 + - pexpect==4.8.0 + - playaudio==1.0.5 + - playsound==1.3.0 + - pure-eval==0.2.2 + - pycparser==2.21 + - pyusb==1.2.1 + - six==1.16.0 + - stack-data==0.2.0 + - stand==0.1 + - wcwidth==0.2.5 + - yaspin==2.2.0 +prefix: /sf/cristallina/applications/conda/envs/slic diff --git a/env_backups/slic2.yml b/env_backups/slic2.yml new file mode 100644 index 0000000..f033d99 --- /dev/null +++ b/env_backups/slic2.yml @@ -0,0 +1,268 @@ +name: slic2 +channels: + - paulscherrerinstitute + - conda-forge +dependencies: + - _libgcc_mutex=0.1=conda_forge + - _openmp_mutex=4.5=2_gnu + - adwaita-icon-theme=48.0=unix_0 + - alsa-lib=1.2.13=hb9d3cd8_0 + - argon2-cffi=23.1.0=pyhd8ed1ab_1 + - argon2-cffi-bindings=21.2.0=py311h9ecbd09_5 + - asttokens=3.0.0=pyhd8ed1ab_1 + - at-spi2-atk=2.38.0=h0630a04_3 + - at-spi2-core=2.40.3=h0630a04_0 + - atk-1.0=2.38.0=h04ea711_2 + - attr=2.5.1=h166bdaf_1 + - bcrypt=4.3.0=py311h9e33e62_0 + - bitshuffle=0.5.2=py311he0e6697_5 + - brotli=1.1.0=hb9d3cd8_2 + - brotli-bin=1.1.0=hb9d3cd8_2 + - brotli-python=1.1.0=py311hfdbb021_2 + - bsread=1.5.7=py_0 + - bzip2=1.0.8=h4bc722e_7 + - c-ares=1.34.4=hb9d3cd8_0 + - ca-certificates=2025.1.31=hbcca054_0 + - cachannel=3.2.0=py311h41425db_0 + - cached-property=1.5.2=hd8ed1ab_1 + - cached_property=1.5.2=pyha770c72_1 + - cairo=1.18.4=h3394656_0 + - certifi=2025.1.31=pyhd8ed1ab_0 + - cffi=1.17.1=py311hf29c0ef_0 + - charset-normalizer=3.4.1=pyhd8ed1ab_0 + - click=8.1.8=pyh707e725_0 + - colorama=0.4.6=pyhd8ed1ab_1 + - comm=0.2.2=pyhd8ed1ab_1 + - contourpy=1.3.1=py311hd18a35c_0 + - cryptography=44.0.2=py311hafd3f86_0 + - cycler=0.12.1=pyhd8ed1ab_1 + - cyrus-sasl=2.1.27=h54b06d7_7 + - data_api=0.8.8=py_0 + - dbus=1.13.6=h5008d03_3 + - debugpy=1.8.13=py311hfdbb021_0 + - decorator=5.2.1=pyhd8ed1ab_0 + - double-conversion=3.3.1=h5888daf_0 + - elog=1.3.16=py_0 + - epics-base=7.0.7.0=h2dfad98_0 + - epoxy=1.5.10=h166bdaf_1 + - exceptiongroup=1.2.2=pyhd8ed1ab_1 + - executing=2.1.0=pyhd8ed1ab_1 + - expat=2.6.4=h5888daf_0 + - font-ttf-dejavu-sans-mono=2.37=hab24e00_0 + - font-ttf-inconsolata=3.000=h77eed37_0 + - font-ttf-source-code-pro=2.038=h77eed37_0 + - font-ttf-ubuntu=0.83=h77eed37_3 + - fontconfig=2.15.0=h7e30c49_1 + - fonts-conda-ecosystem=1=0 + - fonts-conda-forge=1=0 + - fonttools=4.56.0=py311h2dc5d0c_0 + - freetype=2.13.3=h48d6fc4_0 + - fribidi=1.0.10=h36c2ea0_0 + - fuzzywuzzy=0.18.0=pyhd8ed1ab_1 + - gdk-pixbuf=2.42.12=hb9ae30d_0 + - glib=2.82.2=h07242d1_1 + - glib-tools=2.82.2=h4833e2c_1 + - graphite2=1.3.13=h59595ed_1003 + - gst-plugins-base=1.24.7=h0a52356_0 + - gstreamer=1.24.7=hf3bb09a_0 + - gtk3=3.24.43=h021d004_4 + - h2=4.2.0=pyhd8ed1ab_0 + - h5py=3.13.0=nompi_py311hb639ac4_100 + - harfbuzz=10.4.0=h76408a6_0 + - hdf5=1.14.3=nompi_h2d575fe_109 + - hicolor-icon-theme=0.17=ha770c72_2 + - hpack=4.1.0=pyhd8ed1ab_0 + - hyperframe=6.1.0=pyhd8ed1ab_0 + - icu=75.1=he02047a_0 + - idna=3.10=pyhd8ed1ab_1 + - importlib-metadata=8.6.1=pyha770c72_0 + - ipykernel=6.29.5=pyh3099207_0 + - ipympl=0.9.7=pyhd8ed1ab_1 + - ipython=9.0.2=pyhfb0248b_0 + - ipython_pygments_lexers=1.1.1=pyhd8ed1ab_0 + - ipywidgets=8.1.5=pyhd8ed1ab_1 + - jedi=0.19.2=pyhd8ed1ab_1 + - jungfrau_utils=3.16.0=py_0 + - jupyter_client=8.6.3=pyhd8ed1ab_1 + - jupyter_core=5.7.2=pyh31011fe_1 + - jupyterlab_widgets=3.0.13=pyhd8ed1ab_1 + - keyutils=1.6.1=h166bdaf_0 + - kiwisolver=1.4.7=py311hd18a35c_0 + - krb5=1.21.3=h659f571_0 + - lcms2=2.17=h717163a_0 + - ld_impl_linux-64=2.43=h712a8e2_4 + - lerc=4.0.0=h27087fc_0 + - levenshtein=0.27.1=py311hfdbb021_0 + - libaec=1.1.3=h59595ed_0 + - libblas=3.9.0=31_h59b9bed_openblas + - libbrotlicommon=1.1.0=hb9d3cd8_2 + - libbrotlidec=1.1.0=hb9d3cd8_2 + - libbrotlienc=1.1.0=hb9d3cd8_2 + - libcap=2.75=h39aace5_0 + - libcblas=3.9.0=31_he106b2a_openblas + - libclang-cpp19.1=19.1.7=default_hb5137d0_2 + - libclang13=20.1.1=default_h9c6a7e4_0 + - libcups=2.3.3=h4637d8d_4 + - libcurl=8.12.1=h332b0f4_0 + - libdeflate=1.23=h4ddbbb0_0 + - libdrm=2.4.124=hb9d3cd8_0 + - libedit=3.1.20250104=pl5321h7949ede_0 + - libegl=1.7.0=ha4b6fd6_2 + - libev=4.33=hd590300_2 + - libexpat=2.6.4=h5888daf_0 + - libffi=3.4.6=h2dba641_0 + - libgcc=14.2.0=h767d61c_2 + - libgcc-ng=14.2.0=h69a702a_2 + - libgfortran=14.2.0=h69a702a_2 + - libgfortran5=14.2.0=hf1ad2bd_2 + - libgl=1.7.0=ha4b6fd6_2 + - libglib=2.82.2=h2ff4ddf_1 + - libglvnd=1.7.0=ha4b6fd6_2 + - libglx=1.7.0=ha4b6fd6_2 + - libgomp=14.2.0=h767d61c_2 + - libiconv=1.18=h4ce23a2_1 + - libjpeg-turbo=3.0.0=hd590300_1 + - liblapack=3.9.0=31_h7ac8fdf_openblas + - libllvm19=19.1.7=ha7bfdaf_1 + - libllvm20=20.1.1=ha7bfdaf_0 + - liblzma=5.6.4=hb9d3cd8_0 + - libnghttp2=1.64.0=h161d5f1_0 + - libnsl=2.0.1=hd590300_0 + - libntlm=1.8=hb9d3cd8_0 + - libogg=1.3.5=h4ab18f5_0 + - libopenblas=0.3.29=pthreads_h94d23a6_0 + - libopengl=1.7.0=ha4b6fd6_2 + - libopus=1.3.1=h7f98852_1 + - libpciaccess=0.18=hd590300_0 + - libpng=1.6.47=h943b412_0 + - libpq=17.4=h27ae623_0 + - librsvg=2.58.4=h49af25d_2 + - libsodium=1.0.20=h4ab18f5_0 + - libsqlite=3.49.1=hee588c1_2 + - libssh2=1.11.1=hf672d98_0 + - libstdcxx=14.2.0=h8f9b012_2 + - libstdcxx-ng=14.2.0=h4852527_2 + - libtiff=4.7.0=hd9ff511_3 + - libudev1=257.4=hbe16f8c_1 + - libusb=1.0.28=hb9d3cd8_0 + - libuuid=2.38.1=h0b41bf4_0 + - libvorbis=1.3.7=h9c3ff4c_0 + - libwebp-base=1.5.0=h851e524_0 + - libxcb=1.17.0=h8a09558_0 + - libxcrypt=4.4.36=hd590300_1 + - libxkbcommon=1.8.1=hc4a0caf_0 + - libxml2=2.13.6=h8d12d68_0 + - libxslt=1.1.39=h76b75d6_0 + - libzlib=1.3.1=hb9d3cd8_2 + - llvmlite=0.44.0=py311h9c9ff8c_1 + - loguru=0.7.2=py311h38be061_2 + - logzero=1.7.0=py311h38be061_6 + - lxml=5.3.1=py311hcfaa980_0 + - matplotlib=3.10.1=py311h38be061_0 + - matplotlib-base=3.10.1=py311h2b939e6_0 + - matplotlib-inline=0.1.7=pyhd8ed1ab_1 + - mesalib=25.0.2=he8ffa69_1 + - mflow=0.2.0=pyh39e3cac_2 + - munkres=1.1.4=pyh9f0ad1d_0 + - mysql-common=9.0.1=h266115a_5 + - mysql-libs=9.0.1=he0572af_5 + - ncurses=6.5=h2d0b736_3 + - nest-asyncio=1.6.0=pyhd8ed1ab_1 + - numba=0.61.0=py311h4e1c48f_1 + - numpy=2.1.3=py311h71ddf71_0 + - openjpeg=2.5.3=h5fbd93e_0 + - openldap=2.6.9=he970967_0 + - openssl=3.4.1=h7b32b05_0 + - packaging=24.2=pyhd8ed1ab_2 + - pandas=2.2.3=py311h7db5c69_1 + - pango=1.56.3=h861ebed_0 + - parso=0.8.4=pyhd8ed1ab_1 + - passlib=1.7.4=pyhd8ed1ab_2 + - pcre2=10.44=hba22ea6_2 + - perl=5.32.1=7_hd590300_perl5 + - pexpect=4.9.0=pyhd8ed1ab_1 + - pickleshare=0.7.5=pyhd8ed1ab_1004 + - pillow=11.1.0=py311h1322bbf_0 + - pip=25.0.1=pyh8b19718_0 + - pixman=0.44.2=h29eaf8c_0 + - platformdirs=4.3.7=pyh29332c3_0 + - prompt-toolkit=3.0.50=pyha770c72_0 + - psutil=7.0.0=py311h9ecbd09_0 + - pthread-stubs=0.4=hb9d3cd8_1002 + - ptyprocess=0.7.0=pyhd8ed1ab_1 + - pure_eval=0.2.3=pyhd8ed1ab_1 + - pycparser=2.22=pyh29332c3_1 + - pyepics=3.4.3=py_0 + - pygments=2.19.1=pyhd8ed1ab_0 + - pyparsing=3.2.2=pyhd8ed1ab_0 + - pyserial=3.5=pyhd8ed1ab_1 + - pyside6=6.8.2=py311h9053184_1 + - pysocks=1.7.1=pyha55dd90_7 + - python=3.11.11=h9e4cc4f_2_cpython + - python-dateutil=2.9.0.post0=pyhff2d567_1 + - python-levenshtein=0.27.1=pyhff2d567_0 + - python-tzdata=2025.2=pyhd8ed1ab_0 + - python_abi=3.11=5_cp311 + - pytz=2024.1=pyhd8ed1ab_0 + - pyusb=1.3.1=pyhd8ed1ab_0 + - pyvisa=1.14.1=pyhd8ed1ab_1 + - pyvisa-py=0.7.2=pyhd8ed1ab_1 + - pyzmq=26.3.0=py311h7deb3e3_0 + - qhull=2020.2=h434a139_5 + - qt6-main=6.8.2=h588cce1_0 + - rapidfuzz=3.12.2=py311hfdbb021_0 + - readline=8.2=h8c095d6_2 + - requests=2.32.3=pyhd8ed1ab_1 + - scipy=1.15.2=py311h8f841c2_0 + - setuptools=75.8.2=pyhff2d567_0 + - sfdata=0.4.1=py_0 + - six=1.17.0=pyhd8ed1ab_0 + - spirv-tools=2024.3=h84d6215_0 + - stack_data=0.6.3=pyhd8ed1ab_1 + - termcolor=2.3.0=pyhd8ed1ab_0 + - tk=8.6.13=noxft_h4845f30_101 + - tornado=6.4.2=py311h9ecbd09_0 + - tqdm=4.67.1=pyhd8ed1ab_1 + - traitlets=5.14.3=pyhd8ed1ab_1 + - typing-extensions=4.12.2=hd8ed1ab_1 + - typing_extensions=4.12.2=pyha770c72_1 + - tzdata=2025b=h78e105d_0 + - unicodedata2=16.0.0=py311h9ecbd09_0 + - urllib3=2.3.0=pyhd8ed1ab_0 + - wayland=1.23.1=h3e06ad9_0 + - wcwidth=0.2.13=pyhd8ed1ab_1 + - wheel=0.45.1=pyhd8ed1ab_1 + - widgetsnbextension=4.0.13=pyhd8ed1ab_1 + - wxpython=4.2.2=py311h356f471_6 + - wxwidgets=3.2.6=hf87bdbc_3 + - xarray=2025.3.0=pyhd8ed1ab_0 + - xcb-util=0.4.1=hb711507_2 + - xcb-util-cursor=0.1.5=hb9d3cd8_0 + - xcb-util-image=0.4.0=hb711507_2 + - xcb-util-keysyms=0.4.1=hb711507_0 + - xcb-util-renderutil=0.3.10=hb711507_0 + - xcb-util-wm=0.4.2=hb711507_0 + - xkeyboard-config=2.43=hb9d3cd8_0 + - xorg-libice=1.1.2=hb9d3cd8_0 + - xorg-libsm=1.2.6=he73a12e_0 + - xorg-libx11=1.8.12=h4f16b4b_0 + - xorg-libxau=1.0.12=hb9d3cd8_0 + - xorg-libxcomposite=0.4.6=hb9d3cd8_2 + - xorg-libxcursor=1.2.3=hb9d3cd8_0 + - xorg-libxdamage=1.1.6=hb9d3cd8_0 + - xorg-libxdmcp=1.1.5=hb9d3cd8_0 + - xorg-libxext=1.3.6=hb9d3cd8_0 + - xorg-libxfixes=6.0.1=hb9d3cd8_0 + - xorg-libxi=1.8.2=hb9d3cd8_0 + - xorg-libxinerama=1.1.5=h5888daf_1 + - xorg-libxrandr=1.5.4=hb9d3cd8_0 + - xorg-libxrender=0.9.12=hb9d3cd8_0 + - xorg-libxshmfence=1.3.3=hb9d3cd8_0 + - xorg-libxtst=1.2.5=hb9d3cd8_3 + - xorg-libxxf86vm=1.1.6=hb9d3cd8_0 + - yaspin=3.1.0=pyhd8ed1ab_0 + - zeromq=4.3.5=h3b0a872_7 + - zipp=3.21.0=pyhd8ed1ab_1 + - zstandard=0.23.0=py311h9ecbd09_1 + - zstd=1.5.7=hb8e6e7a_2 +prefix: /sf/cristallina/applications/conda/envs/slic2 diff --git a/jupyter-alpha.yml b/jupyter-alpha.yml new file mode 100755 index 0000000..7bd778f --- /dev/null +++ b/jupyter-alpha.yml @@ -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 diff --git a/jupyter_alpha.yml b/jupyter_alpha.yml index 5a40176..0a2b2db 100755 --- a/jupyter_alpha.yml +++ b/jupyter_alpha.yml @@ -26,7 +26,9 @@ dependencies: - jupyterlab_code_formatter - jupyter-collaboration # disabled until stable with collaboration: - jupytext - + + # cristallina + # # PSI specific modules #- paulscherrerinstitute::jungfrau_utils #- bitshuffle diff --git a/jupyter_beta.yml b/jupyter_beta.yml new file mode 100755 index 0000000..20dcdc5 --- /dev/null +++ b/jupyter_beta.yml @@ -0,0 +1,41 @@ +# 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_beta +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 + + # cristallina + # + # PSI specific modules + #- paulscherrerinstitute::jungfrau_utils + #- bitshuffle + #- paulscherrerinstitute::sfdata + # - pip: + #- ipytest + +# still necessary manually afterwards: +# pip install jupyterlab_hdf +# jupyter labextension install @jupyterlab/hdf5 diff --git a/optical_simulations.yml b/optical_simulations.yml old mode 100644 new mode 100755 diff --git a/ptychography.yml b/ptychography.yml old mode 100644 new mode 100755 diff --git a/slic.yml b/slic.yml new file mode 100755 index 0000000..ef182d4 --- /dev/null +++ b/slic.yml @@ -0,0 +1,60 @@ +# SLIC environment description +# This is the default SLIC environment +# We are trying to be fairly up-to-date here, at the moment this is compatible with python 3.9. + + +# use via: +# conda env create --name $NEW_ENV_NAME --file $THIS_FILE_NAME +# e.g. +# conda env create --name slic --file conda-env.yml +# NOTE: $NEW_ENV_NAME is optional and defaults to slic + +name: slic +channels: + - conda-forge +dependencies: + - python=3.12 # keep at 3.11 beause of cachannel + - ipython + - numpy + - scipy + - matplotlib + - ipympl + - playsound + - bitshuffle>=0.5.2 # should work accoding to Sven's yaml +# for execution and kernel discovery within jupyter + - ipykernel + - partialjson # For parsing unfinished json files +# DAQ + - paulscherrerinstitute::bsread + # maybe useful for some special application: + - paulscherrerinstitute::cam_server_client # Needed for the KB focusing script + - paulscherrerinstitute::data_api + - paulscherrerinstitute::elog + - pyepics>=3.4.2 # Used to be from paulscherrerinstitute, but changed here +# Own DAQ + - pyvisa-py + - pyserial + - pyusb + - dbus-python +# data + - paulscherrerinstitute::jungfrau_utils>=3.16.0 + - paulscherrerinstitute::sfdata +# GUI + - wxpython +# CTA + - paulscherrerinstitute::cta_lib +# Channel access + - paulscherrerinstitute::cachannel # The package is still quite archaic and may not work with 3.12. Trying here +# terminal + - colorama + - tqdm + - fuzzywuzzy + - logzero + - yaspin + - loguru + - rich + + + - pip: + - -e /sf/cristallina/applications/slic/slic-package # Creates a "local package" of slic. This shows a deprication warning and + # should be changed to using .toml in the future. diff --git a/smarpod.yml b/smarpod.yml new file mode 100755 index 0000000..5f81af6 --- /dev/null +++ b/smarpod.yml @@ -0,0 +1,60 @@ +# Copy of the slic-crq env. Added packages to control the smaract hexapod. (Added later with pip install from a folder). The env is temporary and will be deleted once the hexapod is in epics. + +# use via: +# conda env create --name $NEW_ENV_NAME --file $THIS_FILE_NAME +# e.g. +# conda env create --name slic --file conda-env.yml +# NOTE: $NEW_ENV_NAME is optional and defaults to slic + +name: smarpod +channels: + - conda-forge +dependencies: + - python=3.11 # keep at 3.11 beause of cachannel + - ipython + - numpy + - scipy + - matplotlib + - ipympl + - playsound + - bitshuffle=0.5.2=py311h49a552a_5 # this specific build of bitshuffle works with python 3.11, for higher versions new build must be found +# for execution and kernel discovery within jupyter + - ipykernel + - partialjson # For parsing unfinished json files +# DAQ + - paulscherrerinstitute::bsread + # maybe useful for some special application: + - paulscherrerinstitute::cam_server_client # Needed for the KB focusing script + - paulscherrerinstitute::data_api + - paulscherrerinstitute::elog + - pyepics>=3.4.2 # Used to be from paulscherrerinstitute, but changed here +# Own DAQ + - pyvisa-py + - pyserial + - pyusb + - dbus-python +# data + - paulscherrerinstitute::jungfrau_utils>=3.16.0 + - paulscherrerinstitute::sfdata +# GUI + - wxpython +# CTA + - paulscherrerinstitute::cta_lib +# Channel access + - paulscherrerinstitute::cachannel # The package is still quite archaic and does not work with 3.12. + # The code is aparently already ready, but the package has not been built +# terminal + - colorama + - tqdm + - fuzzywuzzy + - logzero + - yaspin + - loguru + - rich + + - setuptools==58.2.0 # newer versions of setuptools can't build the smarct hexapod package + + - pip: + - -e /sf/cristallina/applications/slic/slic-package # Creates a "local package" of slic. This shows a deprication warning and + # should be changed to using .toml in the future. + - /sf/cristallina/applications/devices/SmarPod/SDK/Python/packages/smaract.smarpod-1.9.20.zip # Smaract hexapod