Added analyse env yml and updated readme

README.md

@@ -2,3 +2,12 @@
 
 Here we collect .yaml files and other instructions necessary to reproduce the conda environments for Cristallina.
 
+# Purpose of the environments
+
+1. analysis - 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
+
+3. slic - env for instrument control with slic

analyse_explicit_versions.yml

@@ -0,0 +1,319 @@
+name: analyse
+channels:
+  - conda-forge
+  - paulscherrerinstitute
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1=conda_forge
+  - _openmp_mutex=4.5=2_gnu
+  - alsa-lib=1.2.6.1=h7f98852_0
+  - anyio=3.5.0=py310h06a4308_0
+  - appdirs=1.4.4=pyhd3eb1b0_0
+  - argon2-cffi=21.3.0=pyhd3eb1b0_0
+  - argon2-cffi-bindings=21.2.0=py310h7f8727e_0
+  - asteval=0.9.27=pyhd8ed1ab_0
+  - asttokens=2.0.5=pyhd3eb1b0_0
+  - attr=2.5.1=h166bdaf_1
+  - attrs=21.4.0=pyhd3eb1b0_0
+  - babel=2.9.1=pyhd3eb1b0_0
+  - backcall=0.2.0=pyhd3eb1b0_0
+  - bcrypt=3.2.2=py310h5764c6d_0
+  - beautifulsoup4=4.11.1=py310h06a4308_0
+  - bitshuffle=0.4.2=py310hc952fd0_0
+  - black=22.6.0=py310h06a4308_0
+  - blas=1.0=mkl
+  - bleach=4.1.0=pyhd3eb1b0_0
+  - bottleneck=1.3.5=py310ha9d4c09_0
+  - brotli=1.0.9=h5eee18b_7
+  - brotli-bin=1.0.9=h5eee18b_7
+  - brotlipy=0.7.0=py310h7f8727e_1002
+  - bzip2=1.0.8=h7b6447c_0
+  - c-ares=1.18.1=h7f8727e_0
+  - ca-certificates=2022.9.24=ha878542_0
+  - cached-property=1.5.2=py_0
+  - certifi=2022.9.24=pyhd8ed1ab_0
+  - cffi=1.15.1=py310h74dc2b5_0
+  - charset-normalizer=2.0.4=pyhd3eb1b0_0
+  - click=8.0.4=py310h06a4308_0
+  - colorama=0.4.5=py310h06a4308_0
+  - conda-package-handling=1.8.1=py310h7f8727e_0
+  - configupdater=3.1=pyhd8ed1ab_0
+  - coverage=6.3.2=py310h7f8727e_0
+  - cryptography=37.0.1=py310h9ce1e76_0
+  - curl=7.84.0=h5eee18b_0
+  - cycler=0.11.0=pyhd3eb1b0_0
+  - cython=0.29.30=py310h6a678d5_0
+  - cytoolz=0.11.0=py310h7f8727e_0
+  - dbus=1.13.18=hb2f20db_0
+  - debugpy=1.5.1=py310h295c915_0
+  - decorator=5.1.1=pyhd3eb1b0_0
+  - defusedxml=0.7.1=pyhd3eb1b0_0
+  - entrypoints=0.4=py310h06a4308_0
+  - executing=0.8.3=pyhd3eb1b0_0
+  - expat=2.4.8=h27087fc_0
+  - fftw=3.3.9=h27cfd23_1
+  - font-ttf-dejavu-sans-mono=2.37=hd3eb1b0_0
+  - font-ttf-inconsolata=2.001=hcb22688_0
+  - font-ttf-source-code-pro=2.030=hd3eb1b0_0
+  - font-ttf-ubuntu=0.83=h8b1ccd4_0
+  - fontconfig=2.14.0=h8e229c2_0
+  - fonts-anaconda=1=h8fa9717_0
+  - fonts-conda-ecosystem=1=hd3eb1b0_0
+  - fonttools=4.25.0=pyhd3eb1b0_0
+  - freetype=2.11.0=h70c0345_0
+  - future=0.18.2=py310h06a4308_1
+  - gettext=0.21.0=hf68c758_0
+  - giflib=5.2.1=h7b6447c_0
+  - git=2.34.1=pl5262hc120c5b_0
+  - glib=2.72.1=h6239696_0
+  - glib-tools=2.72.1=h6239696_0
+  - greenlet=1.1.1=py310h295c915_0
+  - gst-plugins-base=1.20.3=hf6a322e_0
+  - gstreamer=1.20.3=hd4edc92_0
+  - h5py=3.6.0=nompi_py310he751f51_100
+  - hdf5=1.12.1=h69dfa17_1
+  - icu=70.1=h27087fc_0
+  - idna=3.3=pyhd3eb1b0_0
+  - importlib-metadata=4.11.3=py310h06a4308_0
+  - iniconfig=1.1.1=pyhd3eb1b0_0
+  - intel-openmp=2021.4.0=h06a4308_3561
+  - ipykernel=6.15.2=py310h06a4308_0
+  - ipympl=0.8.7=pyhd3eb1b0_0
+  - ipython=8.4.0=py310h06a4308_0
+  - ipython_genutils=0.2.0=pyhd3eb1b0_1
+  - ipywidgets=7.6.5=pyhd3eb1b0_1
+  - jack=1.9.18=h8c3723f_1002
+  - jedi=0.18.1=py310h06a4308_1
+  - jinja2=3.0.3=pyhd3eb1b0_0
+  - joblib=1.1.0=pyhd3eb1b0_0
+  - jpeg=9e=h7f8727e_0
+  - json-c=0.16=h5eee18b_0
+  - json5=0.9.6=pyhd3eb1b0_0
+  - jsonschema=4.4.0=py310h06a4308_0
+  - jupyter_client=7.3.5=py310h06a4308_0
+  - jupyter_core=4.10.0=py310h06a4308_0
+  - jupyter_server=1.18.1=py310h06a4308_0
+  - jupyterlab=3.2.8=pyhd8ed1ab_0
+  - jupyterlab-drawio=0.9.0=pyhd8ed1ab_0
+  - jupyterlab_code_formatter=1.4.10=pyhd8ed1ab_1
+  - jupyterlab_pygments=0.1.2=py_0
+  - jupyterlab_server=2.12.0=py310h06a4308_0
+  - jupyterlab_widgets=1.0.0=pyhd3eb1b0_1
+  - jupytext=1.13.7=pyhd0ecf6b_0
+  - keyutils=1.6.1=h166bdaf_0
+  - kiwisolver=1.4.2=py310h295c915_0
+  - krb5=1.19.3=h3790be6_0
+  - lcms2=2.12=h3be6417_0
+  - ld_impl_linux-64=2.38=h1181459_1
+  - lerc=3.0=h295c915_0
+  - libarchive=3.5.2=hb890918_3
+  - libbrotlicommon=1.0.9=h5eee18b_7
+  - libbrotlidec=1.0.9=h5eee18b_7
+  - libbrotlienc=1.0.9=h5eee18b_7
+  - libcap=2.64=ha37c62d_0
+  - libclang=14.0.6=default_hc1a23ef_0
+  - libclang13=14.0.6=default_h31cde19_0
+  - libcups=2.3.3=h3e49a29_2
+  - libcurl=7.84.0=h91b91d3_0
+  - libdb=6.2.32=h6a678d5_1
+  - libdeflate=1.8=h7f8727e_5
+  - libedit=3.1.20210910=h7f8727e_0
+  - libev=4.33=h7f8727e_1
+  - libevent=2.1.10=h9b69904_4
+  - libffi=3.4.2=h7f98852_5
+  - libflac=1.3.4=h27087fc_0
+  - libgcc-ng=12.1.0=h8d9b700_16
+  - libgfortran-ng=7.5.0=ha8ba4b0_17
+  - libgfortran4=7.5.0=ha8ba4b0_17
+  - libglib=2.72.1=h2d90d5f_0
+  - libgomp=12.1.0=h8d9b700_16
+  - libiconv=1.16=h7f8727e_2
+  - libllvm11=11.1.0=h9e868ea_5
+  - libllvm14=14.0.6=he0ac6c6_0
+  - libmamba=0.25.0=hd8a31e3_2
+  - libmambapy=0.25.0=py310hab0e683_2
+  - libnghttp2=1.47.0=h727a467_0
+  - libnsl=2.0.0=h7f98852_0
+  - libogg=1.3.5=h27cfd23_1
+  - libopenblas=0.3.18=hf726d26_0
+  - libopus=1.3.1=h7b6447c_0
+  - libpng=1.6.37=hbc83047_0
+  - libpq=14.5=hd77ab85_0
+  - libsndfile=1.0.31=h9c3ff4c_1
+  - libsodium=1.0.18=h7b6447c_0
+  - libsolv=0.7.22=h6239696_0
+  - libsqlite=3.39.2=h753d276_1
+  - libssh2=1.10.0=h8f2d780_0
+  - libstdcxx-ng=12.1.0=ha89aaad_16
+  - libtiff=4.4.0=hecacb30_0
+  - libtool=2.4.6=h295c915_1008
+  - libuuid=2.32.1=h7f98852_1000
+  - libuv=1.44.2=h166bdaf_0
+  - libvorbis=1.3.7=h7b6447c_0
+  - libwebp=1.2.2=h55f646e_0
+  - libwebp-base=1.2.2=h7f8727e_0
+  - libxcb=1.13=h7f98852_1004
+  - libxkbcommon=1.0.3=he3ba5ed_0
+  - libxml2=2.9.14=h22db469_4
+  - libzlib=1.2.12=h166bdaf_1
+  - line_profiler=3.3.1=py310hd09550d_0
+  - llvmlite=0.38.0=py310h4ff587b_0
+  - lmfit=1.0.3=pyhd8ed1ab_0
+  - lz4-c=1.9.3=h295c915_1
+  - lzo=2.10=h516909a_1000
+  - markdown-it-py=1.1.0=pyhd8ed1ab_0
+  - markupsafe=2.1.1=py310h7f8727e_0
+  - matplotlib=3.5.2=py310h06a4308_0
+  - matplotlib-base=3.5.2=py310hf590b9c_0
+  - matplotlib-inline=0.1.6=py310h06a4308_0
+  - mdit-py-plugins=0.3.0=py310h06a4308_0
+  - mistune=0.8.4=py310h7f8727e_1000
+  - mkl=2021.4.0=h06a4308_640
+  - mkl-service=2.4.0=py310h7f8727e_0
+  - mkl_fft=1.3.1=py310h2b4bcf5_1
+  - mkl_random=1.2.2=py310h00e6091_0
+  - munkres=1.1.4=py_0
+  - mypy_extensions=0.4.3=py310h06a4308_0
+  - mysql-common=8.0.30=haf5c9bc_0
+  - mysql-libs=8.0.30=h28c427c_0
+  - nb_conda_kernels=2.3.1=py310h06a4308_0
+  - nbclassic=0.3.5=pyhd3eb1b0_0
+  - nbclient=0.5.13=py310h06a4308_0
+  - nbconvert=6.4.4=py310h06a4308_0
+  - nbformat=5.3.0=py310h06a4308_0
+  - ncurses=6.3=h5eee18b_3
+  - nest-asyncio=1.5.5=py310h06a4308_0
+  - nodejs=18.7.0=h96d913c_0
+  - notebook=6.4.12=py310h06a4308_0
+  - nspr=4.33=h295c915_0
+  - nss=3.78=h2350873_0
+  - numba=0.55.1=py310ha5257ce_1
+  - numexpr=2.8.3=py310hcea2de6_0
+  - numpy=1.21.5=py310h1794996_3
+  - numpy-base=1.21.5=py310hcba007f_3
+  - openssl=1.1.1q=h166bdaf_0
+  - packaging=21.3=pyhd3eb1b0_0
+  - pandas=1.4.3=py310h6a678d5_0
+  - pandocfilters=1.5.0=pyhd3eb1b0_0
+  - paramiko=2.8.1=pyhd3eb1b0_0
+  - parso=0.8.3=pyhd3eb1b0_0
+  - pathspec=0.9.0=py310h06a4308_0
+  - pcre=8.45=h295c915_0
+  - pcre2=10.37=he7ceb23_1
+  - perl=5.26.2=h14c3975_0
+  - pexpect=4.8.0=pyhd3eb1b0_3
+  - pickleshare=0.7.5=pyhd3eb1b0_1003
+  - pillow=9.2.0=py310hace64e9_1
+  - pip=22.1.2=py310h06a4308_0
+  - platformdirs=2.5.2=py310h06a4308_0
+  - pluggy=1.0.0=py310h06a4308_1
+  - ply=3.11=py310h06a4308_0
+  - portaudio=19.6.0=h7b6447c_4
+  - prometheus_client=0.14.1=py310h06a4308_0
+  - prompt-toolkit=3.0.20=pyhd3eb1b0_0
+  - psutil=5.9.0=py310h5eee18b_0
+  - pthread-stubs=0.3=h0ce48e5_1
+  - ptyprocess=0.7.0=pyhd3eb1b0_2
+  - pulseaudio=14.0=h583eb01_5
+  - pure_eval=0.2.2=pyhd3eb1b0_0
+  - py=1.11.0=pyhd3eb1b0_0
+  - pybind11-abi=4=hd8ed1ab_3
+  - pycosat=0.6.3=py310h7f8727e_0
+  - pycparser=2.21=pyhd3eb1b0_0
+  - pygments=2.11.2=pyhd3eb1b0_0
+  - pynacl=1.5.0=py310h5eee18b_0
+  - pyopenssl=22.0.0=pyhd3eb1b0_0
+  - pyparsing=3.0.9=py310h06a4308_0
+  - pyqt=5.15.7=py310h29803b5_0
+  - pyqt5-sip=12.11.0=py310hd8f1fbe_0
+  - pyrsistent=0.18.0=py310h7f8727e_0
+  - pyscaffold=4.2.1=pyhd8ed1ab_0
+  - pysocks=1.7.1=py310h06a4308_0
+  - pytest=7.1.2=py310h06a4308_0
+  - pytest-cov=3.0.0=pyhd3eb1b0_0
+  - python=3.10.5=h582c2e5_0_cpython
+  - python-dateutil=2.8.2=pyhd3eb1b0_0
+  - python-fastjsonschema=2.16.2=py310h06a4308_0
+  - python_abi=3.10=2_cp310
+  - pytz=2022.1=py310h06a4308_0
+  - pyzmq=23.2.0=py310h6a678d5_0
+  - qt=5.15.4=hf11cfaa_0
+  - qt-main=5.15.4=ha5833f6_2
+  - qt-webengine=5.15.4=hcbadb6c_3
+  - readline=8.1.2=h7f8727e_1
+  - regex=2022.7.9=py310h5eee18b_0
+  - reproc=14.2.3=h7f98852_0
+  - reproc-cpp=14.2.3=h9c3ff4c_0
+  - requests=2.28.1=py310h06a4308_0
+  - ruamel_yaml=0.15.100=py310h7f8727e_0
+  - scipy=1.7.3=py310hfa59a62_0
+  - scp=0.14.1=pyhd3eb1b0_0
+  - send2trash=1.8.0=pyhd3eb1b0_1
+  - setuptools=63.4.1=py310h06a4308_0
+  - setuptools-scm=7.0.4=py310h06a4308_0
+  - sfdata=0.2.8=py_0
+  - sip=6.6.2=py310h6a678d5_0
+  - six=1.16.0=pyhd3eb1b0_1
+  - sniffio=1.2.0=py310h06a4308_1
+  - soupsieve=2.3.1=pyhd3eb1b0_0
+  - sqlalchemy=1.4.39=py310h5eee18b_0
+  - sqlite=3.39.2=h4ff8645_1
+  - stack_data=0.2.0=pyhd3eb1b0_0
+  - tbb=2021.5.0=hd09550d_0
+  - terminado=0.13.1=py310h06a4308_0
+  - testpath=0.6.0=py310h06a4308_0
+  - tk=8.6.12=h1ccaba5_0
+  - toml=0.10.2=pyhd3eb1b0_0
+  - tomli=2.0.1=py310h06a4308_0
+  - tomlkit=0.11.1=py310h06a4308_0
+  - toolz=0.11.2=pyhd3eb1b0_0
+  - tornado=6.2=py310h5eee18b_0
+  - tqdm=4.64.0=py310h06a4308_0
+  - traitlets=5.1.1=pyhd3eb1b0_0
+  - typed-ast=1.4.3=py310h7f8727e_1
+  - typing=3.10.0.0=py310h06a4308_0
+  - typing-extensions=4.3.0=py310h06a4308_0
+  - typing_extensions=4.3.0=py310h06a4308_0
+  - tzdata=2022c=h04d1e81_0
+  - uncertainties=3.1.7=pyhd8ed1ab_0
+  - urllib3=1.26.11=py310h06a4308_0
+  - wcwidth=0.2.5=pyhd3eb1b0_0
+  - webencodings=0.5.1=py310h06a4308_1
+  - websocket-client=0.58.0=py310h06a4308_4
+  - wheel=0.37.1=pyhd3eb1b0_0
+  - widgetsnbextension=3.5.2=py310h06a4308_0
+  - xarray=0.20.1=pyhd3eb1b0_1
+  - xcb-util=0.4.0=h166bdaf_0
+  - xcb-util-image=0.4.0=h166bdaf_0
+  - xcb-util-keysyms=0.4.0=h166bdaf_0
+  - xcb-util-renderutil=0.3.9=h166bdaf_0
+  - xcb-util-wm=0.4.1=h166bdaf_0
+  - xorg-libxau=1.0.9=h7f98852_0
+  - xorg-libxdmcp=1.1.3=h7f98852_0
+  - xraydb=4.4.7=pyhd8ed1ab_0
+  - xrayutilities=1.7.3=py310h96516ba_0
+  - xz=5.2.5=h7f8727e_1
+  - yaml=0.2.5=h7b6447c_0
+  - yaml-cpp=0.7.0=h27087fc_1
+  - zeromq=4.3.4=h2531618_0
+  - zipp=3.8.0=py310h06a4308_0
+  - zlib=1.2.12=h166bdaf_1
+  - zstd=1.5.2=ha4553b6_0
+  - pip:
+    - automat==20.2.0
+    - constantly==15.1.0
+    - hkdf==0.0.3
+    - humanize==4.3.0
+    - hyperlink==21.0.0
+    - incremental==21.3.0
+    - ipytest==0.12.0
+    - jungfrau-utils==3.7.2
+    - pyasn1==0.4.8
+    - pyasn1-modules==0.2.8
+    - pyyaml==6.0
+    - service-identity==21.1.0
+    - spake2==0.8
+    - twisted==22.8.0
+    - txaio==22.2.1
+    - txtorcon==22.0.0
+prefix: /sf/cristallina/applications/conda/envs/analyse