From 24eeba6e5a8379ffda4aee0a861459dd14b904db Mon Sep 17 00:00:00 2001
From: Jakub Vonka <jakub.vonka@psi.ch>
Date: Tue, 27 Jan 2026 12:06:08 +0100
Subject: [PATCH] Cleanup - and _

---
 env_backups/jupyter-alpha.yml | 282 ++++++++++++++++++++++++++++++++++
 jupyter_alpha.yml             |  41 -----
 2 files changed, 282 insertions(+), 41 deletions(-)
 create mode 100644 env_backups/jupyter-alpha.yml
 delete mode 100755 jupyter_alpha.yml

diff --git a/env_backups/jupyter-alpha.yml b/env_backups/jupyter-alpha.yml
new file mode 100644
index 0000000..9524fc8
--- /dev/null
+++ b/env_backups/jupyter-alpha.yml
@@ -0,0 +1,282 @@
+name: jupyter_alpha
+channels:
+  - conda-forge
+dependencies:
+  - _libgcc_mutex=0.1=conda_forge
+  - _openmp_mutex=4.5=2_gnu
+  - _python_abi3_support=1.0=hd8ed1ab_2
+  - alsa-lib=1.2.14=hb9d3cd8_0
+  - anyio=4.11.0=pyhcf101f3_0
+  - argon2-cffi=25.1.0=pyhd8ed1ab_0
+  - argon2-cffi-bindings=25.1.0=py313h07c4f96_2
+  - arrow=1.4.0=pyhcf101f3_0
+  - asttokens=3.0.0=pyhd8ed1ab_1
+  - async-lru=2.0.5=pyh29332c3_0
+  - attrs=25.4.0=pyh71513ae_0
+  - babel=2.17.0=pyhd8ed1ab_0
+  - black=25.1.0=pyh866005b_0
+  - bleach=6.2.0=pyh29332c3_4
+  - bleach-with-css=6.2.0=h82add2a_4
+  - brotli=1.2.0=h41a2e66_0
+  - brotli-bin=1.2.0=hf2c8021_0
+  - brotli-python=1.2.0=py313h09d1b84_0
+  - bzip2=1.0.8=hda65f42_8
+  - ca-certificates=2025.10.5=hbd8a1cb_0
+  - cached-property=1.5.2=hd8ed1ab_1
+  - cached_property=1.5.2=pyha770c72_1
+  - cairo=1.18.4=h3394656_0
+  - cffi=2.0.0=py313hf46b229_1
+  - click=8.3.0=pyh707e725_0
+  - colorama=0.4.6=pyhd8ed1ab_1
+  - comm=0.2.3=pyhe01879c_0
+  - contourpy=1.3.3=py313h7037e92_3
+  - cpython=3.13.9=py313hd8ed1ab_101
+  - cycler=0.12.1=pyhd8ed1ab_1
+  - cyrus-sasl=2.1.28=hd9c7081_0
+  - dbus=1.16.2=h3c4dab8_0
+  - debugpy=1.8.17=py313h5d5ffb9_0
+  - decorator=5.2.1=pyhd8ed1ab_0
+  - defusedxml=0.7.1=pyhd8ed1ab_0
+  - double-conversion=3.3.1=h5888daf_0
+  - exceptiongroup=1.3.0=pyhd8ed1ab_0
+  - executing=2.2.1=pyhd8ed1ab_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=hc364b38_1
+  - fonttools=4.60.1=py313h3dea7bd_0
+  - fqdn=1.5.1=pyhd8ed1ab_1
+  - freetype=2.14.1=ha770c72_0
+  - graphite2=1.3.14=hecca717_2
+  - h11=0.16.0=pyhd8ed1ab_0
+  - h2=4.3.0=pyhcf101f3_0
+  - harfbuzz=12.2.0=h15599e2_0
+  - 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=75.1=he02047a_0
+  - idna=3.11=pyhd8ed1ab_0
+  - importlib-metadata=8.7.0=pyhe01879c_1
+  - iniconfig=2.3.0=pyhd8ed1ab_0
+  - ipython_pygments_lexers=1.1.1=pyhd8ed1ab_0
+  - ipywidgets=8.1.8=pyhd8ed1ab_0
+  - isoduration=20.11.0=pyhd8ed1ab_1
+  - jedi=0.19.2=pyhd8ed1ab_1
+  - jinja2=3.1.6=pyhd8ed1ab_0
+  - json5=0.12.1=pyhd8ed1ab_0
+  - jsonpointer=3.0.0=py313h78bf25f_2
+  - jsonschema=4.25.1=pyhe01879c_0
+  - jsonschema-specifications=2025.9.1=pyhcf101f3_0
+  - jsonschema-with-format-nongpl=4.25.1=he01879c_0
+  - jupyter-collaboration=4.1.1=pyhcf101f3_0
+  - jupyter-collaboration-ui=2.1.1=pyhcf101f3_0
+  - jupyter-docprovider=2.1.1=pyhcf101f3_0
+  - jupyter-lsp=2.3.0=pyhcf101f3_0
+  - jupyter_client=8.6.3=pyhd8ed1ab_1
+  - jupyter_core=5.9.1=pyhc90fa1f_0
+  - jupyter_events=0.12.0=pyh29332c3_0
+  - jupyter_server=2.17.0=pyhcf101f3_0
+  - jupyter_server_fileid=0.9.2=pyhd8ed1ab_1
+  - jupyter_server_terminals=0.5.3=pyhd8ed1ab_1
+  - jupyter_server_ydoc=2.1.1=pyhcf101f3_0
+  - jupyter_ydoc=3.1.0=pyhe01879c_0
+  - jupyterlab_code_formatter=3.0.2=pyhd8ed1ab_1
+  - jupyterlab_pygments=0.3.0=pyhd8ed1ab_2
+  - jupyterlab_server=2.28.0=pyhcf101f3_0
+  - jupyterlab_widgets=3.0.16=pyhcf101f3_1
+  - keyutils=1.6.3=hb9d3cd8_0
+  - kiwisolver=1.4.9=py313hc8edb43_2
+  - krb5=1.21.3=h659f571_0
+  - lcms2=2.17=h717163a_0
+  - ld_impl_linux-64=2.44=h1aa0949_4
+  - lerc=4.0.0=h0aef613_1
+  - libblas=3.9.0=38_h4a7cf45_openblas
+  - libbrotlicommon=1.2.0=h09219d5_0
+  - libbrotlidec=1.2.0=hd53d788_0
+  - libbrotlienc=1.2.0=h02bd7ab_0
+  - libcblas=3.9.0=38_h0358290_openblas
+  - libclang-cpp21.1=21.1.5=default_h99862b1_1
+  - libclang13=21.1.5=default_h746c552_1
+  - libcups=2.3.3=hb8b1518_5
+  - libdeflate=1.25=h17f619e_0
+  - libdrm=2.4.125=hb03c661_1
+  - libedit=3.1.20250104=pl5321h7949ede_0
+  - libegl=1.7.0=ha4b6fd6_2
+  - libexpat=2.7.1=hecca717_0
+  - libffi=3.5.2=h9ec8514_0
+  - libfreetype=2.14.1=ha770c72_0
+  - libfreetype6=2.14.1=h73754d4_0
+  - libgcc=15.2.0=h767d61c_7
+  - libgcc-ng=15.2.0=h69a702a_7
+  - libgfortran=15.2.0=h69a702a_7
+  - libgfortran5=15.2.0=hcd61629_7
+  - libgl=1.7.0=ha4b6fd6_2
+  - libglib=2.86.1=h32235b2_1
+  - libglvnd=1.7.0=ha4b6fd6_2
+  - libglx=1.7.0=ha4b6fd6_2
+  - libgomp=15.2.0=h767d61c_7
+  - libiconv=1.18=h3b78370_2
+  - libjpeg-turbo=3.1.2=hb03c661_0
+  - liblapack=3.9.0=38_h47877c9_openblas
+  - libllvm21=21.1.5=hf7376ad_0
+  - liblzma=5.8.1=hb9d3cd8_2
+  - libmpdec=4.0.0=h4bc722e_0
+  - libntlm=1.8=hb9d3cd8_0
+  - libopenblas=0.3.30=pthreads_h94d23a6_3
+  - libopengl=1.7.0=ha4b6fd6_2
+  - libpciaccess=0.18=hd590300_0
+  - libpng=1.6.50=h421ea60_1
+  - libpq=18.0=h3675c94_0
+  - libsodium=1.0.20=h4ab18f5_0
+  - libsqlite=3.51.0=hee844dc_0
+  - libstdcxx=15.2.0=h8f9b012_7
+  - libstdcxx-ng=15.2.0=h4852527_7
+  - libtiff=4.7.1=h9d88235_1
+  - libuuid=2.41.2=he9a06e4_0
+  - libvulkan-loader=1.4.328.1=h5279c79_0
+  - libwebp-base=1.6.0=hd42ef1d_0
+  - libxcb=1.17.0=h8a09558_0
+  - libxcrypt=4.4.36=hd590300_1
+  - libxkbcommon=1.13.0=hca5e8e5_0
+  - libxml2=2.15.1=h26afc86_0
+  - libxml2-16=2.15.1=ha9997c6_0
+  - libxslt=1.1.43=h711ed8c_1
+  - libzlib=1.3.1=hb9d3cd8_2
+  - llvmlite=0.45.1=py313hdd307be_0
+  - loguru=0.7.3=pyh707e725_0
+  - markupsafe=3.0.3=py313h3dea7bd_0
+  - matplotlib=3.10.7=py313h78bf25f_0
+  - matplotlib-base=3.10.7=py313h683a580_0
+  - matplotlib-inline=0.2.1=pyhd8ed1ab_0
+  - mistune=3.1.4=pyhcf101f3_0
+  - munkres=1.1.4=pyhd8ed1ab_1
+  - mypy_extensions=1.1.0=pyha770c72_0
+  - nb_conda_kernels=2.5.1=pyh707e725_2
+  - nbclient=0.10.2=pyhd8ed1ab_0
+  - nbconvert-core=7.16.6=pyhcf101f3_1
+  - nbformat=5.10.4=pyhd8ed1ab_1
+  - ncurses=6.5=h2d0b736_3
+  - nest-asyncio=1.6.0=pyhd8ed1ab_1
+  - notebook-shim=0.2.4=pyhd8ed1ab_1
+  - numba=0.62.1=py313hd8e3f9f_0
+  - numpy=2.3.4=py313hf6604e3_0
+  - openjpeg=2.5.4=h55fea9a_0
+  - openldap=2.6.10=he970967_0
+  - openssl=3.5.4=h26f9b46_0
+  - overrides=7.7.0=pyhd8ed1ab_1
+  - packaging=25.0=pyh29332c3_1
+  - pandas=2.3.3=py313h08cd8bf_1
+  - pandocfilters=1.5.0=pyhd8ed1ab_0
+  - parso=0.8.5=pyhcf101f3_0
+  - pathspec=0.12.1=pyhd8ed1ab_1
+  - pcre2=10.46=h1321c63_0
+  - pexpect=4.9.0=pyhd8ed1ab_1
+  - pillow=12.0.0=py313h50355cd_0
+  - pip=25.2=pyh145f28c_0
+  - pixman=0.46.4=h54a6638_1
+  - pluggy=1.6.0=pyhd8ed1ab_0
+  - prometheus_client=0.23.1=pyhd8ed1ab_0
+  - prompt-toolkit=3.0.52=pyha770c72_0
+  - psutil=7.1.3=py313h54dd161_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
+  - pycrdt=0.12.43=py313h5c7d99a_0
+  - pycrdt-store=0.1.2=pyhd8ed1ab_0
+  - pycrdt-websocket=0.16.0=pyhd8ed1ab_0
+  - pygments=2.19.2=pyhd8ed1ab_0
+  - pyparsing=3.2.5=pyhcf101f3_0
+  - pyside6=6.9.3=py313h85046ba_1
+  - pysocks=1.7.1=pyha55dd90_7
+  - pytest=8.4.2=pyhcf101f3_1
+  - python=3.13.9=hc97d973_101_cp313
+  - python-dateutil=2.9.0.post0=pyhe01879c_2
+  - python-fastjsonschema=2.21.2=pyhe01879c_0
+  - python-gil=3.13.9=h4df99d1_101
+  - python-json-logger=2.0.7=pyhd8ed1ab_0
+  - python-tzdata=2025.2=pyhd8ed1ab_0
+  - python_abi=3.13=8_cp313
+  - pytz=2025.2=pyhd8ed1ab_0
+  - pyyaml=6.0.3=py313h3dea7bd_0
+  - pyzmq=27.1.0=py312hfb55c3c_0
+  - qhull=2020.2=h434a139_5
+  - qt6-main=6.9.3=h5c1c036_1
+  - readline=8.2=h8c095d6_2
+  - referencing=0.37.0=pyhcf101f3_0
+  - requests=2.32.5=pyhd8ed1ab_0
+  - rfc3339-validator=0.1.4=pyhd8ed1ab_1
+  - rfc3986-validator=0.1.1=pyh9f0ad1d_0
+  - rfc3987-syntax=1.1.0=pyhe01879c_1
+  - rpds-py=0.28.0=py313h843e2db_1
+  - send2trash=1.8.3=pyh0d859eb_1
+  - setuptools=80.9.0=pyhff2d567_0
+  - six=1.17.0=pyhe01879c_1
+  - sniffio=1.3.1=pyhd8ed1ab_1
+  - soupsieve=2.8=pyhd8ed1ab_0
+  - sqlite-anyio=0.2.3=pyhaa4b35c_1
+  - stack_data=0.6.3=pyhd8ed1ab_1
+  - terminado=0.18.1=pyh0d859eb_0
+  - tinycss2=1.4.0=pyhd8ed1ab_0
+  - tk=8.6.13=noxft_hd72426e_102
+  - tornado=6.5.2=py313h07c4f96_2
+  - traitlets=5.14.3=pyhd8ed1ab_1
+  - typing-extensions=4.15.0=h396c80c_0
+  - typing_extensions=4.15.0=pyhcf101f3_0
+  - typing_utils=0.1.0=pyhd8ed1ab_1
+  - tzdata=2025b=h78e105d_0
+  - uri-template=1.3.0=pyhd8ed1ab_1
+  - urllib3=2.5.0=pyhd8ed1ab_0
+  - wayland=1.24.0=hd6090a7_1
+  - wcwidth=0.2.14=pyhd8ed1ab_0
+  - webcolors=25.10.0=pyhd8ed1ab_0
+  - webencodings=0.5.1=pyhd8ed1ab_3
+  - websocket-client=1.9.0=pyhd8ed1ab_0
+  - widgetsnbextension=4.0.15=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=2.46=hb03c661_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=6.0.2=hb03c661_0
+  - xorg-libxi=1.8.2=hb9d3cd8_0
+  - xorg-libxrandr=1.5.4=hb9d3cd8_0
+  - xorg-libxrender=0.9.12=hb9d3cd8_0
+  - xorg-libxtst=1.2.5=hb9d3cd8_3
+  - xorg-libxxf86vm=1.1.6=hb9d3cd8_0
+  - yaml=0.2.5=h280c20c_3
+  - zeromq=4.3.5=h387f397_9
+  - zipp=3.23.0=pyhd8ed1ab_0
+  - zlib-ng=2.2.5=hde8ca8f_0
+  - zstandard=0.25.0=py313h54dd161_1
+  - zstd=1.5.7=hb8e6e7a_2
+  - pip:
+      - beautifulsoup4==4.13.5
+      - certifi==2025.8.3
+      - charset-normalizer==3.4.3
+      - cristallina==0.2.post1.dev23+g0f23e46
+      - ipykernel==6.30.1
+      - ipympl==0.9.7
+      - ipython==9.5.0
+      - jupyterlab==4.4.8
+      - lark==1.3.0
+      - notebook==7.4.5
+      - platformdirs==4.4.0
+      - tomli==2.2.1
+      - types-python-dateutil==2.9.0.20250822
+prefix: /sf/cristallina/applications/conda/envs/jupyter_alpha
diff --git a/jupyter_alpha.yml b/jupyter_alpha.yml
deleted file mode 100755
index 0a2b2db..0000000
--- a/jupyter_alpha.yml
+++ /dev/null
@@ -1,41 +0,0 @@
-# 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
-  
-   # 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