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haesleinhuepf / bia-bob

BIA Bob is a Jupyter+LLM-based assistant for interacting with image data and for working on Bio-image Analysis tasks.
BSD 3-Clause "New" or "Revised" License
83 stars 6 forks source link

Installation/ Setup Problem #147

Closed marabuuu closed 1 month ago

marabuuu commented 1 month ago

Hi @haesleinhuepf,

Probably a me-problem, but still I wanted to document that I am struggling with the bia-bob setup. It would be super cool if you could help me. In my Jupyter notebook, I receive the following error message: Screenshot 2024-07-08 at 10 27 55 Comment: I provided platynereis dumerilii.tif in the same folder as the notebook.

LogicError                                Traceback (most recent call last)
Cell In[4], line 1
----> 1 get_ipython().run_line_magic('bob', 'Load platynereis_dumerilii.tif and show it')

File [~/miniforge3/envs/bob_env/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2456](http://localhost:8888/~/miniforge3/envs/bob_env/lib/python3.9/site-packages/IPython/core/interactiveshell.py#line=2455), in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth)
   2454     kwargs['local_ns'] = self.get_local_scope(stack_depth)
   2455 with self.builtin_trap:
-> 2456     result = fn(*args, **kwargs)
   2458 # The code below prevents the output from being displayed
   2459 # when using magics with decorator @output_can_be_silenced
   2460 # when the last Python token in the expression is a ';'.
   2461 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False):

File [~/miniforge3/envs/bob_env/lib/python3.9/site-packages/bia_bob/_machinery.py:118](http://localhost:8888/~/miniforge3/envs/bob_env/lib/python3.9/site-packages/bia_bob/_machinery.py#line=117), in bob(line, cell)
    116     text = f"The modified notebook has been saved as [{filename}]({filename})."
    117 else:
--> 118     code, text = generate_response_to_user(Context.model, user_input, image)
    120     if image is not None:
    121         # we need to add this information to the history.
    122         generate_response_to_user(Context.model,
    123                                   user_prompt=f"Assume there is an image stored in variable `{image_name}`. The image can be described like this: {response}. Just confirm this with 'ok'.",
    124                                   system_prompt="")

File [~/miniforge3/envs/bob_env/lib/python3.9/site-packages/bia_bob/_utilities.py:14](http://localhost:8888/~/miniforge3/envs/bob_env/lib/python3.9/site-packages/bia_bob/_utilities.py#line=13), in generate_response_to_user(model, user_prompt, image, additional_system_prompt, max_number_attempts, system_prompt)
     12 for attempt in range(1, max_number_attempts + 1):
     13     if system_prompt is None:
---> 14         system_prompt = create_system_prompt()
     15     if additional_system_prompt is not None:
     16         system_prompt += "\n" + additional_system_prompt

File [~/miniforge3/envs/bob_env/lib/python3.9/site-packages/bia_bob/_utilities.py:196](http://localhost:8888/~/miniforge3/envs/bob_env/lib/python3.9/site-packages/bia_bob/_utilities.py#line=195), in create_system_prompt(reusable_variables_block)
    194 # Iterate over discovered entry points and load them
    195 for ep in bia_bob_plugins:
--> 196     func = ep.load()
    198     # load instructions from a plugin
    199     instructions = func()

File [~/miniforge3/envs/bob_env/lib/python3.9/site-packages/importlib_metadata/__init__.py:183](http://localhost:8888/~/miniforge3/envs/bob_env/lib/python3.9/site-packages/importlib_metadata/__init__.py#line=182), in EntryPoint.load(self)
    178 """Load the entry point from its definition. If only a module
    179 is indicated by the value, return that module. Otherwise,
    180 return the named object.
    181 """
    182 match = cast(Match, self.pattern.match(self.value))
--> 183 module = import_module(match.group('module'))
    184 attrs = filter(None, (match.group('attr') or '').split('.'))
    185 return functools.reduce(getattr, attrs, module)

File [~/miniforge3/envs/bob_env/lib/python3.9/importlib/__init__.py:127](http://localhost:8888/~/miniforge3/envs/bob_env/lib/python3.9/importlib/__init__.py#line=126), in import_module(name, package)
    125             break
    126         level += 1
--> 127 return _bootstrap._gcd_import(name[level:], package, level)

File <frozen importlib._bootstrap>:1030, in _gcd_import(name, package, level)

File <frozen importlib._bootstrap>:1007, in _find_and_load(name, import_)

File <frozen importlib._bootstrap>:972, in _find_and_load_unlocked(name, import_)

File <frozen importlib._bootstrap>:228, in _call_with_frames_removed(f, *args, **kwds)

File <frozen importlib._bootstrap>:1030, in _gcd_import(name, package, level)

File <frozen importlib._bootstrap>:1007, in _find_and_load(name, import_)

File <frozen importlib._bootstrap>:986, in _find_and_load_unlocked(name, import_)

File <frozen importlib._bootstrap>:680, in _load_unlocked(spec)

File <frozen importlib._bootstrap_external>:850, in exec_module(self, module)

File <frozen importlib._bootstrap>:228, in _call_with_frames_removed(f, *args, **kwds)

File [~/miniforge3/envs/bob_env/lib/python3.9/site-packages/pyclesperanto_prototype/__init__.py:1](http://localhost:8888/~/miniforge3/envs/bob_env/lib/python3.9/site-packages/pyclesperanto_prototype/__init__.py#line=0)
----> 1 from ._tier0 import *
      2 from ._tier1 import *
      3 from ._tier2 import *

File [~/miniforge3/envs/bob_env/lib/python3.9/site-packages/pyclesperanto_prototype/_tier0/__init__.py:55](http://localhost:8888/~/miniforge3/envs/bob_env/lib/python3.9/site-packages/pyclesperanto_prototype/_tier0/__init__.py#line=54)
     53 from sys import platform
     54 if platform == "darwin":
---> 55     device_name = str(get_device())
     56     if "Intel" in device_name:
     57         select_device("CPU")

File [~/miniforge3/envs/bob_env/lib/python3.9/site-packages/pyclesperanto_prototype/_tier0/_device.py:45](http://localhost:8888/~/miniforge3/envs/bob_env/lib/python3.9/site-packages/pyclesperanto_prototype/_tier0/_device.py#line=44), in get_device()
     43 def get_device() -> Device:
     44     """Get the current device GPU class."""
---> 45     return _current_device._instance or select_device()

File [~/miniforge3/envs/bob_env/lib/python3.9/site-packages/pyclesperanto_prototype/_tier0/_device.py:75](http://localhost:8888/~/miniforge3/envs/bob_env/lib/python3.9/site-packages/pyclesperanto_prototype/_tier0/_device.py#line=74), in select_device(name, dev_type, score_key, device_index)
     71 except:
     72     pass
---> 75 device = filter_devices(name, dev_type, score_key)[device_index]
     76 if name is not None and name not in device.name:
     77     warnings.warn(f"No OpenCL device found with {name} in their name. Using {device.name} instead.")

File [~/miniforge3/envs/bob_env/lib/python3.9/site-packages/pyclesperanto_prototype/_tier0/_device.py:107](http://localhost:8888/~/miniforge3/envs/bob_env/lib/python3.9/site-packages/pyclesperanto_prototype/_tier0/_device.py#line=106), in filter_devices(name, dev_type, score_key)
     95 """Filter devices based on various options
     96 
     97 :param name: First device that contains ``name`` will be returned, defaults to None
   (...)
    104 :rtype: List[cl.Device]
    105 """
    106 devices = []
--> 107 for platform in cl.get_platforms():
    108     for device in platform.get_devices():
    109         if name and name.lower() in device.name.lower():

LogicError: clGetPlatformIDs failed: PLATFORM_NOT_FOUND_KHR

My steps:

#because of Issue with M1 and M2 Chips
mamba clean --all 
mamba update mamba -c conda-forge

#following the documentation
mamba env create -f https://github.com/haesleinhuepf/bia-bob/raw/main/environment.yml
mamba activate bob_env
pip install bia-bob 

#following linked page in documentation to set key as environment variable
echo "export OPENAI_API_KEY='yourkey'" >> ~/.zshrc
source ~/.zshrc
echo $OPENAI_API_KEY

Libraries in bob_env:

# Name                    Version                   Build  Channel
aicsimageio               4.10.0             pyhd8ed1ab_0    conda-forge
annotated-types           0.7.0              pyhd8ed1ab_0    conda-forge
anyio                     4.4.0              pyhd8ed1ab_0    conda-forge
aom                       3.9.1                h7bae524_0    conda-forge
appdirs                   1.4.4              pyh9f0ad1d_0    conda-forge
appnope                   0.1.4              pyhd8ed1ab_0    conda-forge
argon2-cffi               23.1.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0           py39h0f82c59_4    conda-forge
arrow                     1.3.0              pyhd8ed1ab_0    conda-forge
asciitree                 0.3.3                      py_2    conda-forge
asttokens                 2.4.1              pyhd8ed1ab_0    conda-forge
async-lru                 2.0.4              pyhd8ed1ab_0    conda-forge
attrs                     23.2.0             pyh71513ae_0    conda-forge
aws-c-auth                0.7.22               h3776fb2_6    conda-forge
aws-c-cal                 0.6.15               h94d0942_1    conda-forge
aws-c-common              0.9.23               h99b78c6_0    conda-forge
aws-c-compression         0.2.18               h94d0942_7    conda-forge
aws-c-event-stream        0.4.2               he43e89f_14    conda-forge
aws-c-http                0.8.2                h4f006d9_3    conda-forge
aws-c-io                  0.14.9               ha70251c_3    conda-forge
aws-c-mqtt                0.10.4               h80c1ce3_7    conda-forge
aws-c-s3                  0.5.10               h6cb31ac_4    conda-forge
aws-c-sdkutils            0.1.16               h94d0942_3    conda-forge
aws-checksums             0.1.18               h94d0942_7    conda-forge
aws-crt-cpp               0.26.12              h431af13_1    conda-forge
aws-sdk-cpp               1.11.329             h617e15d_6    conda-forge
azure-core-cpp            1.12.0               hd01fc5c_0    conda-forge
azure-identity-cpp        1.8.0                h0a11218_1    conda-forge
azure-storage-blobs-cpp   12.11.0              h77cc766_1    conda-forge
azure-storage-common-cpp  12.6.0               h7024f69_1    conda-forge
azure-storage-files-datalake-cpp 12.10.0              h64d02d0_1    conda-forge
babel                     2.14.0             pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.12.3             pyha770c72_0    conda-forge
bia-bob                   0.18.0                   pypi_0    pypi
bioformats_jar            2020.5.27          pyhd8ed1ab_0    conda-forge
bleach                    6.1.0              pyhd8ed1ab_0    conda-forge
blosc                     1.21.6               h5499902_0    conda-forge
bokeh                     3.4.2              pyhd8ed1ab_0    conda-forge
brotli                    1.1.0                hb547adb_1    conda-forge
brotli-bin                1.1.0                hb547adb_1    conda-forge
brotli-python             1.1.0            py39hb198ff7_1    conda-forge
brunsli                   0.1                  h9f76cd9_0    conda-forge
bzip2                     1.0.8                h93a5062_5    conda-forge
c-ares                    1.28.1               h93a5062_0    conda-forge
c-blosc2                  2.15.0               h5063078_1    conda-forge
ca-certificates           2024.6.2             hf0a4a13_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               hc6c324b_2    conda-forge
certifi                   2024.6.2           pyhd8ed1ab_0    conda-forge
cffi                      1.16.0           py39he153c15_0    conda-forge
charls                    2.4.2                h13dd4ca_0    conda-forge
charset-normalizer        3.3.2              pyhd8ed1ab_0    conda-forge
click                     8.1.7           unix_pyh707e725_0    conda-forge
click-default-group       1.2.4              pyhd8ed1ab_0    conda-forge
cloudpickle               3.0.0              pyhd8ed1ab_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
comm                      0.2.2              pyhd8ed1ab_0    conda-forge
contourpy                 1.2.1            py39h48c5dd5_0    conda-forge
cycler                    0.12.1             pyhd8ed1ab_0    conda-forge
cytoolz                   0.12.3           py39h17cfd9d_0    conda-forge
dask                      2024.6.2           pyhd8ed1ab_0    conda-forge
dask-core                 2024.6.2           pyhd8ed1ab_0    conda-forge
dask-expr                 1.1.6              pyhd8ed1ab_0    conda-forge
dav1d                     1.2.1                hb547adb_0    conda-forge
debugpy                   1.8.2            py39hbf7db11_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
distributed               2024.6.2           pyhd8ed1ab_0    conda-forge
distro                    1.9.0                    pypi_0    pypi
docformatter              1.7.5              pyhd8ed1ab_0    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
et_xmlfile                1.1.0              pyhd8ed1ab_0    conda-forge
exceptiongroup            1.2.0              pyhd8ed1ab_2    conda-forge
executing                 2.0.1              pyhd8ed1ab_0    conda-forge
expat                     2.6.2                hebf3989_0    conda-forge
fasteners                 0.17.3             pyhd8ed1ab_0    conda-forge
ffmpeg                    7.0.1           gpl_h5b99759_104    conda-forge
flexcache                 0.3                pyhd8ed1ab_0    conda-forge
flexparser                0.3.1              pyhd8ed1ab_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               h82840c6_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.53.0           py39hfea33bf_0    conda-forge
fqdn                      1.5.1              pyhd8ed1ab_0    conda-forge
freetype                  2.12.1               hadb7bae_2    conda-forge
fribidi                   1.0.10               h27ca646_0    conda-forge
fsspec                    2024.6.1           pyhff2d567_0    conda-forge
gettext                   0.22.5               h8fbad5d_2    conda-forge
gettext-tools             0.22.5               h8fbad5d_2    conda-forge
gflags                    2.2.2             hc88da5d_1004    conda-forge
giflib                    5.2.2                h93a5062_0    conda-forge
glog                      0.7.1                heb240a5_0    conda-forge
gmp                       6.3.0                h7bae524_2    conda-forge
gnutls                    3.7.9                hd26332c_0    conda-forge
graphite2                 1.3.13            hebf3989_1003    conda-forge
h11                       0.14.0             pyhd8ed1ab_0    conda-forge
h2                        4.1.0              pyhd8ed1ab_0    conda-forge
harfbuzz                  9.0.0                h1836168_0    conda-forge
hpack                     4.0.0              pyh9f0ad1d_0    conda-forge
httpcore                  1.0.5              pyhd8ed1ab_0    conda-forge
httpx                     0.27.0             pyhd8ed1ab_0    conda-forge
hyperframe                6.0.1              pyhd8ed1ab_0    conda-forge
icu                       73.2                 hc8870d7_0    conda-forge
idna                      3.7                pyhd8ed1ab_0    conda-forge
imagecodecs               2024.6.1         py39habf2b62_2    conda-forge
imageio                   2.34.2             pyh12aca89_0    conda-forge
imageio-ffmpeg            0.5.1              pyhd8ed1ab_0    conda-forge
importlib-metadata        8.0.0              pyha770c72_0    conda-forge
importlib-resources       6.4.0              pyhd8ed1ab_0    conda-forge
importlib_metadata        8.0.0                hd8ed1ab_0    conda-forge
importlib_resources       6.4.0              pyhd8ed1ab_0    conda-forge
ipycanvas                 0.13.2             pyhd8ed1ab_0    conda-forge
ipyevents                 2.0.2              pyhd8ed1ab_0    conda-forge
ipykernel                 6.29.5             pyh57ce528_0    conda-forge
ipython                   8.18.1             pyh707e725_3    conda-forge
ipywidgets                8.1.3              pyhd8ed1ab_0    conda-forge
isoduration               20.11.0            pyhd8ed1ab_0    conda-forge
jedi                      0.19.1             pyhd8ed1ab_0    conda-forge
jgo                       1.0.5              pyhd8ed1ab_0    conda-forge
jinja2                    3.1.4              pyhd8ed1ab_0    conda-forge
joblib                    1.4.2              pyhd8ed1ab_0    conda-forge
jpype1                    1.5.0            py39h48c5dd5_1    conda-forge
json5                     0.9.25             pyhd8ed1ab_0    conda-forge
jsonpointer               3.0.0            py39h2804cbe_0    conda-forge
jsonschema                4.22.0             pyhd8ed1ab_0    conda-forge
jsonschema-specifications 2023.12.1          pyhd8ed1ab_0    conda-forge
jsonschema-with-format-nongpl 4.22.0             pyhd8ed1ab_0    conda-forge
jupyter-lsp               2.2.5              pyhd8ed1ab_0    conda-forge
jupyter_client            8.6.2              pyhd8ed1ab_0    conda-forge
jupyter_core              5.7.2            py39h2804cbe_0    conda-forge
jupyter_events            0.10.0             pyhd8ed1ab_0    conda-forge
jupyter_server            2.14.1             pyhd8ed1ab_0    conda-forge
jupyter_server_terminals  0.5.3              pyhd8ed1ab_0    conda-forge
jupyterlab                4.2.3              pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.3.0              pyhd8ed1ab_1    conda-forge
jupyterlab_server         2.27.2             pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        3.0.11             pyhd8ed1ab_0    conda-forge
jxrlib                    1.1                  h93a5062_3    conda-forge
khronos-opencl-icd-loader 2023.04.17           hf50ae52_1    conda-forge
kiwisolver                1.4.5            py39hbd775c9_1    conda-forge
krb5                      1.21.3               h237132a_0    conda-forge
lame                      3.100             h1a8c8d9_1003    conda-forge
lcms2                     2.16                 ha0e7c42_0    conda-forge
lerc                      4.0.0                h9a09cb3_0    conda-forge
libabseil                 20240116.2      cxx17_hebf3989_0    conda-forge
libaec                    1.1.3                hebf3989_0    conda-forge
libarrow                  16.1.0          hcc492dc_10_cpu    conda-forge
libarrow-acero            16.1.0          h00cdb27_10_cpu    conda-forge
libarrow-dataset          16.1.0          h00cdb27_10_cpu    conda-forge
libarrow-substrait        16.1.0          hc68f6b8_10_cpu    conda-forge
libasprintf               0.22.5               h8fbad5d_2    conda-forge
libasprintf-devel         0.22.5               h8fbad5d_2    conda-forge
libass                    0.17.1               hf20b609_2    conda-forge
libavif16                 1.0.4                h9a910c9_5    conda-forge
libblas                   3.9.0           22_osxarm64_openblas    conda-forge
libbrotlicommon           1.1.0                hb547adb_1    conda-forge
libbrotlidec              1.1.0                hb547adb_1    conda-forge
libbrotlienc              1.1.0                hb547adb_1    conda-forge
libcblas                  3.9.0           22_osxarm64_openblas    conda-forge
libcrc32c                 1.1.2                hbdafb3b_0    conda-forge
libcurl                   8.8.0                h7b6f9a7_1    conda-forge
libcxx                    17.0.6               he7857fb_2    conda-forge
libdeflate                1.20                 h93a5062_0    conda-forge
libedit                   3.1.20191231         hc8eb9b7_2    conda-forge
libev                     4.33                 h93a5062_2    conda-forge
libevent                  2.1.12               h2757513_1    conda-forge
libexpat                  2.6.2                hebf3989_0    conda-forge
libffi                    3.4.2                h3422bc3_5    conda-forge
libgettextpo              0.22.5               h8fbad5d_2    conda-forge
libgettextpo-devel        0.22.5               h8fbad5d_2    conda-forge
libgfortran               5.0.0           13_2_0_hd922786_3    conda-forge
libgfortran5              13.2.0               hf226fd6_3    conda-forge
libglib                   2.80.2               h59d46d9_1    conda-forge
libgoogle-cloud           2.25.0               hfe08963_0    conda-forge
libgoogle-cloud-storage   2.25.0               h3fa5b87_0    conda-forge
libgrpc                   1.62.2               h9c18a4f_0    conda-forge
libhwloc                  2.10.0          default_h7685b71_1001    conda-forge
libhwy                    1.1.0                h2ffa867_0    conda-forge
libiconv                  1.17                 h0d3ecfb_2    conda-forge
libidn2                   2.3.7                h93a5062_0    conda-forge
libintl                   0.22.5               h8fbad5d_2    conda-forge
libintl-devel             0.22.5               h8fbad5d_2    conda-forge
libjpeg-turbo             3.0.0                hb547adb_1    conda-forge
libjxl                    0.10.2               h07599a0_0    conda-forge
liblapack                 3.9.0           22_osxarm64_openblas    conda-forge
libllvm14                 14.0.6               hd1a9a77_4    conda-forge
libnghttp2                1.58.0               ha4dd798_1    conda-forge
libopenblas               0.3.27          openmp_h6c19121_0    conda-forge
libopenvino               2024.2.0             h5c9529b_1    conda-forge
libopenvino-arm-cpu-plugin 2024.2.0             h5c9529b_1    conda-forge
libopenvino-auto-batch-plugin 2024.2.0             hcd65546_1    conda-forge
libopenvino-auto-plugin   2024.2.0             hcd65546_1    conda-forge
libopenvino-hetero-plugin 2024.2.0             h88cb26a_1    conda-forge
libopenvino-ir-frontend   2024.2.0             h88cb26a_1    conda-forge
libopenvino-onnx-frontend 2024.2.0             h32b5460_1    conda-forge
libopenvino-paddle-frontend 2024.2.0             h32b5460_1    conda-forge
libopenvino-pytorch-frontend 2024.2.0             h00cdb27_1    conda-forge
libopenvino-tensorflow-frontend 2024.2.0             h2741c3b_1    conda-forge
libopenvino-tensorflow-lite-frontend 2024.2.0             h00cdb27_1    conda-forge
libopus                   1.3.1                h27ca646_1    conda-forge
libparquet                16.1.0          hcf52c46_10_cpu    conda-forge
libpng                    1.6.43               h091b4b1_0    conda-forge
libprotobuf               4.25.3               hbfab5d5_0    conda-forge
libre2-11                 2023.09.01           h7b2c953_2    conda-forge
libsodium                 1.0.18               h27ca646_1    conda-forge
libsqlite                 3.46.0               hfb93653_0    conda-forge
libssh2                   1.11.0               h7a5bd25_0    conda-forge
libtasn1                  4.19.0               h1a8c8d9_0    conda-forge
libthrift                 0.19.0               h026a170_1    conda-forge
libtiff                   4.6.0                h07db509_3    conda-forge
libunistring              0.9.10               h3422bc3_0    conda-forge
libutf8proc               2.8.0                h1a8c8d9_0    conda-forge
libvpx                    1.14.1               h7bae524_0    conda-forge
libwebp-base              1.4.0                h93a5062_0    conda-forge
libxcb                    1.16                 hf2054a2_0    conda-forge
libxml2                   2.12.7               ha661575_1    conda-forge
libxslt                   1.1.39               h223e5b9_0    conda-forge
libzlib                   1.3.1                hfb2fe0b_1    conda-forge
libzopfli                 1.0.3                h9f76cd9_0    conda-forge
llvm-openmp               18.1.8               hde57baf_0    conda-forge
llvmlite                  0.43.0           py39hf770e8f_0    conda-forge
locket                    1.0.0              pyhd8ed1ab_0    conda-forge
lxml                      5.2.2            py39hdd42ab6_0    conda-forge
lz4                       4.3.3            py39hf99b9d6_0    conda-forge
lz4-c                     1.9.4                hb7217d7_0    conda-forge
mako                      1.3.5              pyhd8ed1ab_0    conda-forge
markupsafe                2.1.5            py39h17cfd9d_0    conda-forge
matplotlib                3.9.0            py39hdf13c20_0    conda-forge
matplotlib-base           3.9.0            py39h1398496_0    conda-forge
matplotlib-inline         0.1.7              pyhd8ed1ab_0    conda-forge
maven                     3.9.8                hce30654_0    conda-forge
metakernel                0.30.2                   pypi_0    pypi
mistune                   3.0.2              pyhd8ed1ab_0    conda-forge
msgpack-python            1.0.8            py39ha1e04a5_0    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
nbclient                  0.10.0             pyhd8ed1ab_0    conda-forge
nbconvert-core            7.16.4             pyhd8ed1ab_1    conda-forge
nbformat                  5.10.4             pyhd8ed1ab_0    conda-forge
ncurses                   6.5                  hb89a1cb_0    conda-forge
nest-asyncio              1.6.0              pyhd8ed1ab_0    conda-forge
nettle                    3.9.1                h40ed0f5_0    conda-forge
networkx                  3.2.1              pyhd8ed1ab_0    conda-forge
notebook-shim             0.2.4              pyhd8ed1ab_0    conda-forge
numba                     0.60.0           py39h2d4ef1e_0    conda-forge
numcodecs                 0.12.1           py39hbf7db11_1    conda-forge
numpy                     1.26.4           py39h7aa2656_0    conda-forge
ome-types                 0.5.1.post1        pyhd8ed1ab_0    conda-forge
openai                    1.35.9                   pypi_0    pypi
openh264                  2.4.1                hebf3989_0    conda-forge
openjdk                   17.0.11              h3fcba2d_0    conda-forge
openjpeg                  2.5.2                h9f1df11_0    conda-forge
openpyxl                  3.1.4            py39hfb846b4_0    conda-forge
openssl                   3.3.1                hfb2fe0b_1    conda-forge
orc                       2.0.1                h47ade37_1    conda-forge
overrides                 7.7.0              pyhd8ed1ab_0    conda-forge
p11-kit                   0.24.1               h29577a5_0    conda-forge
packaging                 24.1               pyhd8ed1ab_0    conda-forge
pandas                    2.2.2            py39h998126f_1    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
parso                     0.8.4              pyhd8ed1ab_0    conda-forge
partd                     1.4.2              pyhd8ed1ab_0    conda-forge
patsy                     0.5.6              pyhd8ed1ab_0    conda-forge
pcre2                     10.44                h297a79d_0    conda-forge
pexpect                   4.9.0              pyhd8ed1ab_0    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    10.4.0           py39h3baf582_0    conda-forge
pint                      0.24.1             pyhd8ed1ab_1    conda-forge
pip                       24.0               pyhd8ed1ab_0    conda-forge
pixman                    0.43.4               hebf3989_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_1    conda-forge
platformdirs              4.2.2              pyhd8ed1ab_0    conda-forge
prometheus_client         0.20.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.47             pyha770c72_0    conda-forge
psutil                    6.0.0            py39hfea33bf_0    conda-forge
pthread-stubs             0.4               h27ca646_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pugixml                   1.14                 h13dd4ca_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pyarrow                   16.1.0           py39h2beb185_4    conda-forge
pyarrow-core              16.1.0          py39h883cd64_4_cpu    conda-forge
pyarrow-hotfix            0.6                pyhd8ed1ab_0    conda-forge
pyclesperanto-prototype   0.24.4             pyhd8ed1ab_0    conda-forge
pycparser                 2.22               pyhd8ed1ab_0    conda-forge
pydantic                  2.8.0              pyhd8ed1ab_0    conda-forge
pydantic-compat           0.1.2              pyhd8ed1ab_0    conda-forge
pydantic-core             2.20.0           py39h0019b8a_0    conda-forge
pygments                  2.18.0             pyhd8ed1ab_0    conda-forge
pyobjc-core               10.3.1           py39h336d860_0    conda-forge
pyobjc-framework-cocoa    10.3.1           py39h336d860_0    conda-forge
pyopencl                  2024.2.7         py39hb3a5b6b_0    conda-forge
pyparsing                 3.1.2              pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.9.19          hd7ebdb9_0_cpython    conda-forge
python-dateutil           2.9.0              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.20.0             pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge
python-tzdata             2024.1             pyhd8ed1ab_0    conda-forge
python_abi                3.9                      4_cp39    conda-forge
pytools                   2024.1.6           pyhd8ed1ab_0    conda-forge
pytz                      2024.1             pyhd8ed1ab_0    conda-forge
pywavelets                1.6.0            py39h161d348_0    conda-forge
pyyaml                    6.0.1            py39h0f82c59_1    conda-forge
pyzmq                     26.0.3           py39he7f0319_0    conda-forge
qhull                     2020.2               hc021e02_2    conda-forge
rav1e                     0.6.6                h69fbcac_2    conda-forge
re2                       2023.09.01           h4cba328_2    conda-forge
readline                  8.2                  h92ec313_1    conda-forge
referencing               0.35.1             pyhd8ed1ab_0    conda-forge
requests                  2.32.3             pyhd8ed1ab_0    conda-forge
resource_backed_dask_array 0.1.0              pyhd8ed1ab_1    conda-forge
rfc3339-validator         0.1.4              pyhd8ed1ab_0    conda-forge
rfc3986-validator         0.1.1              pyh9f0ad1d_0    conda-forge
rpds-py                   0.18.1           py39h0019b8a_0    conda-forge
ruff                      0.5.0            py39hb586919_0    conda-forge
scikit-image              0.19.3           py39hde7b980_2    conda-forge
scikit-learn              1.5.1            py39h3c33c8b_0    conda-forge
scipy                     1.13.1           py39h3d5391c_0    conda-forge
scyjava                   1.10.0             pyhd8ed1ab_1    conda-forge
seaborn                   0.13.2               hd8ed1ab_2    conda-forge
seaborn-base              0.13.2             pyhd8ed1ab_2    conda-forge
send2trash                1.8.3              pyh31c8845_0    conda-forge
setuptools                70.1.1             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
skan                      0.11.1             pyhd8ed1ab_0    conda-forge
snappy                    1.2.1                hd02b534_0    conda-forge
sniffio                   1.3.1              pyhd8ed1ab_0    conda-forge
sortedcontainers          2.4.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.5                pyhd8ed1ab_1    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
stackview                 0.7.10             pyhd8ed1ab_0    conda-forge
statsmodels               0.14.2           py39h161d348_0    conda-forge
svt-av1                   2.1.2                h7bae524_0    conda-forge
tbb                       2021.12.0            h420ef59_1    conda-forge
tblib                     3.0.0              pyhd8ed1ab_0    conda-forge
terminado                 0.18.1             pyh31c8845_0    conda-forge
threadpoolctl             3.5.0              pyhc1e730c_0    conda-forge
tifffile                  2024.6.18          pyhd8ed1ab_0    conda-forge
tinycss2                  1.3.0              pyhd8ed1ab_0    conda-forge
tk                        8.6.13               h5083fa2_1    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
toolz                     0.12.1             pyhd8ed1ab_0    conda-forge
toposort                  1.10               pyhd8ed1ab_0    conda-forge
tornado                   6.4.1            py39hfea33bf_0    conda-forge
tqdm                      4.66.4             pyhd8ed1ab_0    conda-forge
traitlets                 5.14.3             pyhd8ed1ab_0    conda-forge
transforms3d              0.4.2              pyhd8ed1ab_0    conda-forge
types-python-dateutil     2.9.0.20240316     pyhd8ed1ab_0    conda-forge
typing-extensions         4.12.2               hd8ed1ab_0    conda-forge
typing_extensions         4.12.2             pyha770c72_0    conda-forge
typing_utils              0.1.0              pyhd8ed1ab_0    conda-forge
tzdata                    2024a                h0c530f3_0    conda-forge
unicodedata2              15.1.0           py39h0f82c59_0    conda-forge
untokenize                0.1.1                      py_0    conda-forge
uri-template              1.3.0              pyhd8ed1ab_0    conda-forge
urllib3                   2.2.2              pyhd8ed1ab_1    conda-forge
wcwidth                   0.2.13             pyhd8ed1ab_0    conda-forge
webcolors                 24.6.0             pyhd8ed1ab_0    conda-forge
webencodings              0.5.1              pyhd8ed1ab_2    conda-forge
websocket-client          1.8.0              pyhd8ed1ab_0    conda-forge
wheel                     0.43.0             pyhd8ed1ab_1    conda-forge
widgetsnbextension        4.0.11             pyhd8ed1ab_0    conda-forge
wrapt                     1.16.0           py39h17cfd9d_0    conda-forge
x264                      1!164.3095           h57fd34a_2    conda-forge
x265                      3.5                  hbc6ce65_3    conda-forge
xarray                    2024.6.0           pyhd8ed1ab_1    conda-forge
xorg-libxau               1.0.11               hb547adb_0    conda-forge
xorg-libxdmcp             1.1.3                h27ca646_0    conda-forge
xsdata                    24.3.1             pyhd8ed1ab_0    conda-forge
xyzservices               2024.6.0           pyhd8ed1ab_0    conda-forge
xz                        5.2.6                h57fd34a_0    conda-forge
yaml                      0.2.5                h3422bc3_2    conda-forge
zarr                      2.18.2             pyhd8ed1ab_0    conda-forge
zeromq                    4.3.5                hcc0f68c_4    conda-forge
zfp                       1.0.1                ha84d530_1    conda-forge
zict                      3.0.0              pyhd8ed1ab_0    conda-forge
zipp                      3.19.2             pyhd8ed1ab_0    conda-forge
zlib                      1.3.1                hfb2fe0b_1    conda-forge
zlib-ng                   2.2.1                h00cdb27_0    conda-forge
zstandard                 0.22.0           py39h0b77d07_1    conda-forge
zstd                      1.5.6                hb46c0d2_0    conda-forge

Best, Mara

haesleinhuepf commented 1 month ago

Hi @marabuuu ,

this error:

LogicError: clGetPlatformIDs failed: PLATFORM_NOT_FOUND_KHR

Is an error related to Pyclesperanto. Can you just uninstall it using 

pip uninstall pyclesperanto_prototype

?

I will also try to implement something that failures of this kind don't harm bob.

marabuuu commented 1 month ago

Hi @haesleinhuepf,

Can you just uninstall it using pip uninstall pyclesperanto_prototype

Thank you for the hint, this worked for me.

I will also try to implement something that failures of this kind don't harm bob.

This would be super cool, thanks!

Best, Mara