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TomographicImaging / CIL

A versatile python framework for tomographic imaging
https://tomographicimaging.github.io/CIL/
Apache License 2.0
97 stars 45 forks source link

CIL-Demos environment for v24.1.0 doesn't include ipykernel #1881

Open lauramurgatroyd opened 3 months ago

lauramurgatroyd commented 3 months ago

Description

I created an environment using the instructions in the readme (on a linux machine)

conda create --name cil -c conda-forge -c https://software.repos.intel.com/python/conda -c ccpi cil=24.1.0 astra-toolbox==cuda tigre ccpi-regulariser tomophantom ipywidgets

I tried to run a notebook in CIL-Demos

I got the error:

Running cells with 'cil_24.1 (Python 3.12.4)' requires the ipykernel package.
Run the following command to install 'ipykernel' into the Python environment. 
Command: 'conda install -n cil_24.1 ipykernel --update-deps --force-reinstall'

Please note that the environment I created does contain ipywidgets

Environment

import cil, sys
print(cil.version.version, cil.version.commit_hash, sys.version, sys.platform)

24.1.0 -1 3.12.4 | packaged by conda-forge | (main, Jun 17 2024, 10:23:07) [GCC 12.3.0] linux

paskino commented 3 months ago

what does conda list say after creating the environment?

lauramurgatroyd commented 3 months ago

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge alsa-lib 1.2.12 h4ab18f5_0 conda-forge aom 3.9.1 hac33072_0 conda-forge astra-toolbox 2.1.0 cudapy312h1af38bc_105 conda-forge asttokens 2.4.1 pyhd8ed1ab_0 conda-forge blosc 1.21.6 hef167b5_0 conda-forge brotli 1.1.0 hd590300_1 conda-forge brotli-bin 1.1.0 hd590300_1 conda-forge brunsli 0.1 h9c3ff4c_0 conda-forge bzip2 1.0.8 h4bc722e_7 conda-forge c-ares 1.32.3 h4bc722e_0 conda-forge c-blosc2 2.15.1 hc57e6cf_0 conda-forge ca-certificates 2024.7.4 hbcca054_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cairo 1.18.0 hebfffa5_3 conda-forge ccpi-regulariser 24.0.1 np126py312_0 ccpi certifi 2024.7.4 pyhd8ed1ab_0 conda-forge cftime 1.6.4 py312h085067d_0 conda-forge charls 2.4.2 h59595ed_0 conda-forge cil 24.1.0 np126py312_0 ccpi cil-data 22.0.0 0 ccpi colorama 0.4.6 pyhd8ed1ab_0 conda-forge comm 0.2.2 pyhd8ed1ab_0 conda-forge contourpy 1.2.1 py312h8572e83_0 conda-forge cudatoolkit 11.8.0 h4ba93d1_13 conda-forge cycler 0.12.1 pyhd8ed1ab_0 conda-forge dav1d 1.2.1 hd590300_0 conda-forge dbus 1.13.6 h5008d03_3 conda-forge decorator 5.1.1 pyhd8ed1ab_0 conda-forge double-conversion 3.3.0 h59595ed_0 conda-forge dxchange 0.1.8 pyhd8ed1ab_0 conda-forge dxfile 0.5 py_1 conda-forge edffile 5.0.0 pyh24bf2e0_1000 conda-forge exceptiongroup 1.2.2 pyhd8ed1ab_0 conda-forge executing 2.0.1 pyhd8ed1ab_0 conda-forge expat 2.6.2 h59595ed_0 conda-forge font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge font-ttf-inconsolata 3.000 h77eed37_0 conda-forge font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge font-ttf-ubuntu 0.83 h77eed37_2 conda-forge fontconfig 2.14.2 h14ed4e7_0 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge fonttools 4.53.1 py312h41a817b_0 conda-forge freetype 2.12.1 h267a509_2 conda-forge giflib 5.2.2 hd590300_0 conda-forge graphite2 1.3.13 h59595ed_1003 conda-forge h5py 3.11.0 nompi_py312hb7ab980_102 conda-forge harfbuzz 9.0.0 hda332d3_1 conda-forge hdf4 4.2.15 h2a13503_7 conda-forge hdf5 1.14.3 nompi_hdf9ad27_105 conda-forge icu 75.1 he02047a_0 conda-forge imagecodecs 2024.6.1 py312h36edd9b_3 conda-forge ipp 2021.12.1 intel_14 https://software.repos.intel.com/python/conda ipython 8.26.0 pyh707e725_0 conda-forge ipywidgets 8.1.3 pyhd8ed1ab_0 conda-forge jedi 0.19.1 pyhd8ed1ab_0 conda-forge jupyterlab_widgets 3.0.11 pyhd8ed1ab_0 conda-forge jxrlib 1.1 hd590300_3 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge kiwisolver 1.4.5 py312h8572e83_1 conda-forge krb5 1.21.3 h659f571_0 conda-forge lcms2 2.16 hb7c19ff_0 conda-forge ld_impl_linux-64 2.40 hf3520f5_7 conda-forge lerc 4.0.0 h27087fc_0 conda-forge libaec 1.1.3 h59595ed_0 conda-forge libastra 2.1.0 cuda11.8hfebff79_111 conda-forge libavif16 1.1.1 h9b56c87_0 conda-forge libblas 3.9.0 23_linux64_openblas conda-forge libbrotlicommon 1.1.0 hd590300_1 conda-forge libbrotlidec 1.1.0 hd590300_1 conda-forge libbrotlienc 1.1.0 hd590300_1 conda-forge libcblas 3.9.0 23_linux64_openblas conda-forge libclang-cpp18.1 18.1.8 default_hf981a13_1 conda-forge libclang13 18.1.8 default_h9def88c_1 conda-forge libcups 2.3.3 h4637d8d_4 conda-forge libcurl 8.9.1 hdb1bdb2_0 conda-forge libdeflate 1.21 h4bc722e_0 conda-forge libdrm 2.4.122 h4ab18f5_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 hd590300_2 conda-forge libexpat 2.6.2 h59595ed_0 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-ng 14.1.0 h77fa898_0 conda-forge libgfortran-ng 14.1.0 h69a702a_0 conda-forge libgfortran5 14.1.0 hc5f4f2c_0 conda-forge libglib 2.80.3 h8a4344b_1 conda-forge libgomp 14.1.0 h77fa898_0 conda-forge libhwy 1.1.0 h00ab1b0_0 conda-forge libiconv 1.17 hd590300_2 conda-forge libjpeg-turbo 3.0.0 hd590300_1 conda-forge libjxl 0.10.3 h66b40c8_0 conda-forge liblapack 3.9.0 23_linux64_openblas conda-forge libllvm14 14.0.6 hcd5def8_4 conda-forge libllvm18 18.1.8 h8b73ec9_1 conda-forge libnetcdf 4.9.2 nompi_h135f659_114 conda-forge libnghttp2 1.58.0 h47da74e_1 conda-forge libnsl 2.0.1 hd590300_0 conda-forge libopenblas 0.3.27 pthreads_hac2b453_1 conda-forge libpciaccess 0.18 hd590300_0 conda-forge libpng 1.6.43 h2797004_0 conda-forge libpq 16.3 ha72fbe1_0 conda-forge libsqlite 3.46.0 hde9e2c9_0 conda-forge libssh2 1.11.0 h0841786_0 conda-forge libstdcxx-ng 14.1.0 hc0a3c3a_0 conda-forge libtiff 4.6.0 h46a8edc_4 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libwebp-base 1.4.0 hd590300_0 conda-forge libxcb 1.16 hd590300_0 conda-forge libxcrypt 4.4.36 hd590300_1 conda-forge libxkbcommon 1.7.0 h2c5496b_1 conda-forge libxml2 2.12.7 he7c6b58_4 conda-forge libxslt 1.1.39 h76b75d6_0 conda-forge libzip 1.10.1 h2629f0a_3 conda-forge libzlib 1.3.1 h4ab18f5_1 conda-forge libzopfli 1.0.3 h9c3ff4c_0 conda-forge llvmlite 0.43.0 py312h9c5d478_0 conda-forge lz4-c 1.9.4 hcb278e6_0 conda-forge matplotlib 3.9.1 py312h7900ff3_2 conda-forge matplotlib-base 3.9.1 py312h854627b_2 conda-forge matplotlib-inline 0.1.7 pyhd8ed1ab_0 conda-forge munkres 1.1.4 pyh9f0ad1d_0 conda-forge mysql-common 8.3.0 h70512c7_5 conda-forge mysql-libs 8.3.0 ha479ceb_5 conda-forge ncurses 6.5 h59595ed_0 conda-forge netcdf4 1.7.1 nompi_py312h1ef7fb6_101 conda-forge numba 0.60.0 py312h83e6fd3_0 conda-forge numpy 1.26.4 py312heda63a1_0 conda-forge olefile 0.47 pyhd8ed1ab_0 conda-forge openjpeg 2.5.2 h488ebb8_0 conda-forge openssl 3.3.1 h4bc722e_2 conda-forge packaging 24.1 pyhd8ed1ab_0 conda-forge pandas 2.2.2 py312h1d6d2e6_1 conda-forge parso 0.8.4 pyhd8ed1ab_0 conda-forge pcre2 10.44 h0f59acf_0 conda-forge pexpect 4.9.0 pyhd8ed1ab_0 conda-forge pickleshare 0.7.5 py_1003 conda-forge pillow 10.4.0 py312h287a98d_0 conda-forge pip 24.2 pyhd8ed1ab_0 conda-forge pixman 0.43.2 h59595ed_0 conda-forge prompt-toolkit 3.0.47 pyha770c72_0 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge pure_eval 0.2.3 pyhd8ed1ab_0 conda-forge pygments 2.18.0 pyhd8ed1ab_0 conda-forge pyparsing 3.1.2 pyhd8ed1ab_0 conda-forge pyside6 6.7.2 py312hb5137db_2 conda-forge python 3.12.4 h194c7f8_0_cpython conda-forge python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge python_abi 3.12 4_cp312 conda-forge pytz 2024.1 pyhd8ed1ab_0 conda-forge pywavelets 1.6.0 py312h085067d_0 conda-forge qhull 2020.2 h434a139_5 conda-forge qt6-main 6.7.2 hb12f9c5_4 conda-forge rav1e 0.6.6 he8a937b_2 conda-forge readline 8.2 h8228510_1 conda-forge scipy 1.14.0 py312hc2bc53b_1 conda-forge setuptools 72.1.0 pyhd8ed1ab_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge snappy 1.2.1 ha2e4443_0 conda-forge spefile 1.6.1 pyhd3deb0d_0 conda-forge stack_data 0.6.2 pyhd8ed1ab_0 conda-forge svt-av1 2.1.2 hac33072_0 conda-forge tifffile 2024.7.24 pyhd8ed1ab_0 conda-forge tigre 2.6 np126py312_0 ccpi tk 8.6.13 noxft_h4845f30_101 conda-forge tomophantom 2.0.0 np126py312_0 ccpi tornado 6.4.1 py312h9a8786e_0 conda-forge tqdm 4.66.5 pyhd8ed1ab_0 conda-forge traitlets 5.14.3 pyhd8ed1ab_0 conda-forge typing_extensions 4.12.2 pyha770c72_0 conda-forge tzdata 2024a h0c530f3_0 conda-forge wayland 1.23.0 h5291e77_0 conda-forge wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge wheel 0.44.0 pyhd8ed1ab_0 conda-forge widgetsnbextension 4.0.11 pyhd8ed1ab_0 conda-forge xcb-util 0.4.1 hb711507_2 conda-forge xcb-util-cursor 0.1.4 h4ab18f5_2 conda-forge xcb-util-image 0.4.0 hb711507_2 conda-forge xcb-util-keysyms 0.4.1 hb711507_0 conda-forge xcb-util-renderutil 0.3.10 hb711507_0 conda-forge xcb-util-wm 0.4.2 hb711507_0 conda-forge xkeyboard-config 2.42 h4ab18f5_0 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.1.1 hd590300_0 conda-forge xorg-libsm 1.2.4 h7391055_0 conda-forge xorg-libx11 1.8.9 hb711507_1 conda-forge xorg-libxau 1.0.11 hd590300_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h0b41bf4_2 conda-forge xorg-libxrender 0.9.11 hd590300_0 conda-forge xorg-renderproto 0.11.1 h7f98852_1002 conda-forge xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xz 5.2.6 h166bdaf_0 conda-forge zfp 1.0.1 hac33072_1 conda-forge zlib 1.3.1 h4ab18f5_1 conda-forge zlib-ng 2.2.1 he02047a_0 conda-forge zstd 1.5.6 ha6fb4c9_0 conda-forge

paskino commented 3 months ago

How do you run the cell?

Clearly you don't have jupyter lab or notebook installed, which isn't in the install instructions. You can't run without ipykermel even with vscode, but that'll tell you directly and install it