Interactive Window for new conda env creates kernel using different conda os.sys.path #7186
Comments
psobolewskiPhD
added
the
bug
|
@psobolewskiPhD can you go to the command line and do a 'jupyter kernelspec list --json' and then upload the results here? The kernelspec we created on disk is likely incorrect. In particular there should be one referencing the napari-openCV python path. |
rchiodo
added
info-needed
|
Here's the output of that command run with the openCV conda env.
{
"kernelspecs": {
"python396jvsc74a57bd0816b70f018d099e6c56d1daea057a52b352940530c59e3e12a7d6ca05df28a9a": {
"resource_dir": "/Users/piotrsobolewski/Library/Jupyter/kernels/python396jvsc74a57bd0816b70f018d099e6c56d1daea057a52b352940530c59e3e12a7d6ca05df28a9a",
"spec": {
"argv": [
"/Users/piotrsobolewski/Dev/miniforge3/envs/TF-StarDist-napari/bin/python",
"-m",
"ipykernel_launcher",
"-f",
"{connection_file}"
],
"env": {
"SHELL": "/opt/homebrew/bin/fish",
"TMPDIR": "/var/folders/sy/y3_x27j14cxg3_vhycs6cr_h0000gn/T/",
"CONDA_SHLVL": "2",
"PYTHONUNBUFFERED": "1",
"CONDA_PROMPT_MODIFIER": "(TF-StarDist-napari) ",
"_tide_right_prompt_display_var": "_tide_right_prompt_display_62598",
"ORIGINAL_XDG_CURRENT_DESKTOP": "undefined",
"PYTHONIOENCODING": "utf-8",
"USER": "piotrsobolewski",
"VSCODE_VERBOSE_LOGGING": "true",
"COMMAND_MODE": "unix2003",
"CONDA_EXE": "/Users/piotrsobolewski/Dev/miniforge3/bin/conda",
"SSH_AUTH_SOCK": "/private/tmp/com.apple.launchd.3Ynle5JFbz/Listeners",
"VSCODE_PIPE_LOGGING": "true",
"__CF_USER_TEXT_ENCODING": "0x1F5:0x0:0x0",
"VSCODE_LOG_STACK": "true",
"FZF_DEFAULT_OPTS": "--cycle --layout=reverse --border --height=90% --preview-window=wrap --marker=\"*\"",
"VSCODE_AMD_ENTRYPOINT": "vs/workbench/services/extensions/node/extensionHostProcess",
"ELECTRON_RUN_AS_NODE": "1",
"_CE_CONDA": "",
"CONDA_PREFIX_1": "/Users/piotrsobolewski/Dev/miniforge3",
"PATH": "/Users/piotrsobolewski/Dev/miniforge3/envs/TF-StarDist-napari/bin:/Users/piotrsobolewski/Dev/miniforge3/condabin:/Applications/CMake.app/Contents/bin:/usr/local/texlive/2020/bin/custom:/Users/piotrsobolewski/Library/Python/3.8/bin:/Users/piotrsobolewski/.cargo/bin:/opt/homebrew/bin:/opt/homebrew/opt/fzf/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Library/TeX/texbin",
"CONDA_PREFIX": "/Users/piotrsobolewski/Dev/miniforge3/envs/TF-StarDist-napari",
"__CFBundleIdentifier": "com.microsoft.VSCodeInsiders",
"PWD": "/",
"VSCODE_HANDLES_UNCAUGHT_ERRORS": "true",
"EDITOR": "nano",
"R_LIBS_SITE": "/opt/homebrew/lib/R/4.0/site-library",
"XPC_FLAGS": "0x0",
"VSCODE_LOG_NATIVE": "false",
"_CE_M": "",
"XPC_SERVICE_NAME": "0",
"SHLVL": "2",
"R_LD_LIBRARY_PATH": "/opt/homebrew/lib/R/lib",
"HOME": "/Users/piotrsobolewski",
"APPLICATION_INSIGHTS_NO_DIAGNOSTIC_CHANNEL": "true",
"VSCODE_IPC_HOOK_EXTHOST": "/var/folders/sy/y3_x27j14cxg3_vhycs6cr_h0000gn/T/vscode-ipc-12326662-fbab-48a2-84b3-e2c9ed26f256.sock",
"VSCODE_NLS_CONFIG": "{\"locale\":\"en-us\",\"availableLanguages\":{},\"_languagePackSupport\":true}",
"CONDA_PYTHON_EXE": "/Users/piotrsobolewski/Dev/miniforge3/bin/python",
"LOGNAME": "piotrsobolewski",
"LC_CTYPE": "en_US.UTF-8",
"VSCODE_IPC_HOOK": "/Users/piotrsobolewski/Library/Application Support/Code - Insiders/1.60.0-insider-main.sock",
"VSCODE_CODE_CACHE_PATH": "/Users/piotrsobolewski/Library/Application Support/Code - Insiders/CachedData/9dd4f31a21d63deea5e1fc322cfc802413b31d95",
"CONDA_DEFAULT_ENV": "TF-StarDist-napari",
"VSCODE_PID": "62587",
"VSCODE_CWD": "/",
"_": "/Users/piotrsobolewski/Dev/miniforge3/envs/TF-StarDist-napari/bin/python"
},
"display_name": "Python 3.9.6 64-bit ('TF-StarDist-napari': conda)",
"language": "python",
"interrupt_mode": "signal",
"metadata": {
"interpreter": {
"sysPrefix": "/Users/piotrsobolewski/Dev/miniforge3/envs/TF-StarDist-napari",
"envType": "Conda",
"envName": "TF-StarDist-napari",
"envPath": "/Users/piotrsobolewski/Dev/miniforge3/envs/TF-StarDist-napari",
"path": "/Users/piotrsobolewski/Dev/miniforge3/envs/TF-StarDist-napari/bin/python",
"architecture": 3,
"sysVersion": "3.9.6 | packaged by conda-forge | (default, Jul 6 2021, 08:51:19) \n[Clang 11.1.0 ]",
"version": {
"raw": "3.9.6",
"major": 3,
"minor": 9,
"patch": 6,
"build": [],
"prerelease": [
"final",
"0"
]
},
"companyDisplayName": "Anaconda, Inc.",
"displayName": "Python 3.9.6 64-bit ('TF-StarDist-napari': conda)"
}
}
}
},
"python396jvsc74a57bd0e28c8163570c4952bc1689be032c95942704d7787747e3f647782f91cc6f83df": {
"resource_dir": "/Users/piotrsobolewski/Library/Jupyter/kernels/python396jvsc74a57bd0e28c8163570c4952bc1689be032c95942704d7787747e3f647782f91cc6f83df",
"spec": {
"argv": [
"/Users/piotrsobolewski/Dev/miniforge3/envs/TF-decon/bin/python",
"-m",
"ipykernel_launcher",
"-f",
"{connection_file}"
],
"env": {
"SHELL": "/opt/homebrew/bin/fish",
"TMPDIR": "/var/folders/sy/y3_x27j14cxg3_vhycs6cr_h0000gn/T/",
"CONDA_SHLVL": "2",
"PYTHONUNBUFFERED": "1",
"CONDA_PROMPT_MODIFIER": "(TF-decon) ",
"_tide_right_prompt_display_var": "_tide_right_prompt_display_34214",
"ORIGINAL_XDG_CURRENT_DESKTOP": "undefined",
"PYTHONIOENCODING": "utf-8",
"USER": "piotrsobolewski",
"VSCODE_VERBOSE_LOGGING": "true",
"COMMAND_MODE": "unix2003",
"CONDA_EXE": "/Users/piotrsobolewski/Dev/miniforge3/bin/conda",
"SSH_AUTH_SOCK": "/private/tmp/com.apple.launchd.3Ynle5JFbz/Listeners",
"VSCODE_PIPE_LOGGING": "true",
"__CF_USER_TEXT_ENCODING": "0x1F5:0x0:0x0",
"VSCODE_LOG_STACK": "true",
"FZF_DEFAULT_OPTS": "--cycle --layout=reverse --border --height=90% --preview-window=wrap --marker=\"*\"",
"VSCODE_AMD_ENTRYPOINT": "vs/workbench/services/extensions/node/extensionHostProcess",
"ELECTRON_RUN_AS_NODE": "1",
"_CE_CONDA": "",
"CONDA_PREFIX_1": "/Users/piotrsobolewski/Dev/miniforge3",
"PATH": "/Users/piotrsobolewski/Dev/miniforge3/envs/TF-decon/bin:/Users/piotrsobolewski/Dev/miniforge3/condabin:/Applications/CMake.app/Contents/bin:/usr/local/texlive/2020/bin/custom:/Users/piotrsobolewski/Library/Python/3.8/bin:/Users/piotrsobolewski/.cargo/bin:/opt/homebrew/bin:/opt/homebrew/opt/fzf/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin",
"CONDA_PREFIX": "/Users/piotrsobolewski/Dev/miniforge3/envs/TF-decon",
"VSCODE_BROWSER_CODE_LOADING": "bypassHeatCheck",
"__CFBundleIdentifier": "com.microsoft.VSCodeInsiders",
"PWD": "/",
"VSCODE_HANDLES_UNCAUGHT_ERRORS": "true",
"EDITOR": "nano",
"R_LIBS_SITE": "/opt/homebrew/lib/R/4.0/site-library",
"XPC_FLAGS": "0x0",
"VSCODE_LOG_NATIVE": "false",
"_CE_M": "",
"XPC_SERVICE_NAME": "0",
"SHLVL": "2",
"R_LD_LIBRARY_PATH": "/opt/homebrew/lib/R/lib",
"HOME": "/Users/piotrsobolewski",
"APPLICATION_INSIGHTS_NO_DIAGNOSTIC_CHANNEL": "true",
"VSCODE_IPC_HOOK_EXTHOST": "/var/folders/sy/y3_x27j14cxg3_vhycs6cr_h0000gn/T/vscode-ipc-5635c4c6-45e0-4720-b139-23af62473609.sock",
"VSCODE_NLS_CONFIG": "{\"locale\":\"en-us\",\"availableLanguages\":{},\"_languagePackSupport\":true}",
"CONDA_PYTHON_EXE": "/Users/piotrsobolewski/Dev/miniforge3/bin/python",
"LOGNAME": "piotrsobolewski",
"LC_CTYPE": "en_US.UTF-8",
"VSCODE_IPC_HOOK": "/Users/piotrsobolewski/Library/Application Support/Code - Insiders/1.59.0-insider-main.sock",
"VSCODE_CODE_CACHE_PATH": "/Users/piotrsobolewski/Library/Application Support/Code - Insiders/CachedData/104bc571e956e4af623905ef10dfcc8f0fdac625",
"CONDA_DEFAULT_ENV": "TF-decon",
"VSCODE_PID": "34207",
"VSCODE_CWD": "/",
"_": "/Users/piotrsobolewski/Dev/miniforge3/envs/TF-decon/bin/python"
},
"display_name": "Python 3.9.6 64-bit ('TF-decon': conda)",
"language": "python",
"interrupt_mode": "signal",
"metadata": {
"interpreter": {
"sysPrefix": "/Users/piotrsobolewski/Dev/miniforge3/envs/TF-decon",
"envType": "Conda",
"envName": "TF-decon",
"envPath": "/Users/piotrsobolewski/Dev/miniforge3/envs/TF-decon",
"path": "/Users/piotrsobolewski/Dev/miniforge3/envs/TF-decon/bin/python",
"architecture": 3,
"sysVersion": "3.9.6 | packaged by conda-forge | (default, Jul 6 2021, 08:51:19) \n[Clang 11.1.0 ]",
"version": {
"raw": "3.9.6",
"major": 3,
"minor": 9,
"patch": 6,
"build": [],
"prerelease": [
"final",
"0"
]
},
"companyDisplayName": "Anaconda, Inc.",
"displayName": "Python 3.9.6 64-bit ('TF-decon': conda)"
}
}
}
},
"python396jvsc74a57bd04db1ab0c13f4e93b5723ac1462919ee4fa4e13f3520c53d1bcc8b45e4369161a": {
"resource_dir": "/Users/piotrsobolewski/Library/Jupyter/kernels/python396jvsc74a57bd04db1ab0c13f4e93b5723ac1462919ee4fa4e13f3520c53d1bcc8b45e4369161a",
"spec": {
"argv": [
"/Users/piotrsobolewski/Dev/miniforge3/envs/napari-pyCL/bin/python",
"-m",
"ipykernel_launcher",
"-f",
"{connection_file}"
],
"env": {
"SHELL": "/opt/homebrew/bin/fish",
"TMPDIR": "/var/folders/sy/y3_x27j14cxg3_vhycs6cr_h0000gn/T/",
"CONDA_SHLVL": "2",
"PYTHONUNBUFFERED": "1",
"CONDA_PROMPT_MODIFIER": "(napari-pyCL) ",
"_tide_right_prompt_display_var": "_tide_right_prompt_display_34214",
"ORIGINAL_XDG_CURRENT_DESKTOP": "undefined",
"PYTHONIOENCODING": "utf-8",
"USER": "piotrsobolewski",
"VSCODE_VERBOSE_LOGGING": "true",
"COMMAND_MODE": "unix2003",
"CONDA_EXE": "/Users/piotrsobolewski/Dev/miniforge3/bin/conda",
"SSH_AUTH_SOCK": "/private/tmp/com.apple.launchd.3Ynle5JFbz/Listeners",
"VSCODE_PIPE_LOGGING": "true",
"__CF_USER_TEXT_ENCODING": "0x1F5:0x0:0x0",
"VSCODE_LOG_STACK": "true",
"FZF_DEFAULT_OPTS": "--cycle --layout=reverse --border --height=90% --preview-window=wrap --marker=\"*\"",
"VSCODE_AMD_ENTRYPOINT": "vs/workbench/services/extensions/node/extensionHostProcess",
"ELECTRON_RUN_AS_NODE": "1",
"_CE_CONDA": "",
"CONDA_PREFIX_1": "/Users/piotrsobolewski/Dev/miniforge3",
"PATH": "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-pyCL/bin:/Users/piotrsobolewski/Dev/miniforge3/condabin:/Applications/CMake.app/Contents/bin:/usr/local/texlive/2020/bin/custom:/Users/piotrsobolewski/Library/Python/3.8/bin:/Users/piotrsobolewski/.cargo/bin:/opt/homebrew/bin:/opt/homebrew/opt/fzf/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin",
"CONDA_PREFIX": "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-pyCL",
"VSCODE_BROWSER_CODE_LOADING": "bypassHeatCheck",
"__CFBundleIdentifier": "com.microsoft.VSCodeInsiders",
"PWD": "/",
"VSCODE_HANDLES_UNCAUGHT_ERRORS": "true",
"EDITOR": "nano",
"R_LIBS_SITE": "/opt/homebrew/lib/R/4.0/site-library",
"XPC_FLAGS": "0x0",
"VSCODE_LOG_NATIVE": "false",
"_CE_M": "",
"XPC_SERVICE_NAME": "0",
"SHLVL": "2",
"R_LD_LIBRARY_PATH": "/opt/homebrew/lib/R/lib",
"HOME": "/Users/piotrsobolewski",
"APPLICATION_INSIGHTS_NO_DIAGNOSTIC_CHANNEL": "true",
"VSCODE_IPC_HOOK_EXTHOST": "/var/folders/sy/y3_x27j14cxg3_vhycs6cr_h0000gn/T/vscode-ipc-5635c4c6-45e0-4720-b139-23af62473609.sock",
"VSCODE_NLS_CONFIG": "{\"locale\":\"en-us\",\"availableLanguages\":{},\"_languagePackSupport\":true}",
"CONDA_PYTHON_EXE": "/Users/piotrsobolewski/Dev/miniforge3/bin/python",
"LOGNAME": "piotrsobolewski",
"LC_CTYPE": "en_US.UTF-8",
"VSCODE_IPC_HOOK": "/Users/piotrsobolewski/Library/Application Support/Code - Insiders/1.59.0-insider-main.sock",
"VSCODE_CODE_CACHE_PATH": "/Users/piotrsobolewski/Library/Application Support/Code - Insiders/CachedData/104bc571e956e4af623905ef10dfcc8f0fdac625",
"CONDA_DEFAULT_ENV": "napari-pyCL",
"VSCODE_PID": "34207",
"VSCODE_CWD": "/",
"_": "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-pyCL/bin/python"
},
"display_name": "Python 3.9.6 64-bit ('napari-pyCL': conda)",
"language": "python",
"interrupt_mode": "signal",
"metadata": {
"debugger": true,
"originalSpecFile": "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-pyCL/share/jupyter/kernels/python3/kernel.json",
"interpreter": {
"sysPrefix": "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-pyCL",
"envType": "Conda",
"envName": "napari-pyCL",
"envPath": "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-pyCL",
"path": "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-pyCL/bin/python",
"architecture": 3,
"sysVersion": "3.9.6 | packaged by conda-forge | (default, Jul 6 2021, 08:51:19) \n[Clang 11.1.0 ]",
"version": {
"raw": "3.9.6",
"major": 3,
"minor": 9,
"patch": 6,
"build": [],
"prerelease": [
"final",
"0"
]
},
"companyDisplayName": "Anaconda, Inc.",
"displayName": "Python 3.9.6 64-bit ('napari-pyCL': conda)"
}
}
}
},
"python396jvsc74a57bd0e774fd5465d7f0f97c28cc36044fc3a68588bc24bb9947703fa3e2268745eab9": {
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"spec": {
"argv": [
"/Users/piotrsobolewski/Dev/miniforge3/envs/napari-pyCL-D/bin/python",
"-m",
"ipykernel_launcher",
"-f",
"{connection_file}"
],
"env": {
"SHELL": "/opt/homebrew/bin/fish",
"TMPDIR": "/var/folders/sy/y3_x27j14cxg3_vhycs6cr_h0000gn/T/",
"CONDA_SHLVL": "2",
"PYTHONUNBUFFERED": "1",
"CONDA_PROMPT_MODIFIER": "(napari-pyCL-D) ",
"_tide_right_prompt_display_var": "_tide_right_prompt_display_88956",
"ORIGINAL_XDG_CURRENT_DESKTOP": "undefined",
"PYTHONIOENCODING": "utf-8",
"USER": "piotrsobolewski",
"VSCODE_VERBOSE_LOGGING": "true",
"COMMAND_MODE": "unix2003",
"CONDA_EXE": "/Users/piotrsobolewski/Dev/miniforge3/bin/conda",
"SSH_AUTH_SOCK": "/private/tmp/com.apple.launchd.3Ynle5JFbz/Listeners",
"VSCODE_PIPE_LOGGING": "true",
"__CF_USER_TEXT_ENCODING": "0x1F5:0x0:0x0",
"VSCODE_LOG_STACK": "true",
"FZF_DEFAULT_OPTS": "--cycle --layout=reverse --border --height=90% --preview-window=wrap --marker=\"*\"",
"VSCODE_AMD_ENTRYPOINT": "vs/workbench/services/extensions/node/extensionHostProcess",
"ELECTRON_RUN_AS_NODE": "1",
"_CE_CONDA": "",
"CONDA_PREFIX_1": "/Users/piotrsobolewski/Dev/miniforge3",
"PATH": "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-pyCL-D/bin:/Users/piotrsobolewski/Dev/miniforge3/condabin:/Applications/CMake.app/Contents/bin:/usr/local/texlive/2020/bin/custom:/Users/piotrsobolewski/Library/Python/3.8/bin:/Users/piotrsobolewski/.cargo/bin:/opt/homebrew/bin:/opt/homebrew/opt/fzf/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Library/TeX/texbin",
"CONDA_PREFIX": "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-pyCL-D",
"__CFBundleIdentifier": "com.microsoft.VSCodeInsiders",
"PWD": "/",
"VSCODE_HANDLES_UNCAUGHT_ERRORS": "true",
"EDITOR": "nano",
"R_LIBS_SITE": "/opt/homebrew/lib/R/4.0/site-library",
"XPC_FLAGS": "0x0",
"VSCODE_LOG_NATIVE": "false",
"_CE_M": "",
"XPC_SERVICE_NAME": "0",
"SHLVL": "2",
"R_LD_LIBRARY_PATH": "/opt/homebrew/lib/R/lib",
"HOME": "/Users/piotrsobolewski",
"APPLICATION_INSIGHTS_NO_DIAGNOSTIC_CHANNEL": "true",
"VSCODE_IPC_HOOK_EXTHOST": "/var/folders/sy/y3_x27j14cxg3_vhycs6cr_h0000gn/T/vscode-ipc-8494599d-afca-4649-9c28-4f40acf9e32a.sock",
"VSCODE_NLS_CONFIG": "{\"locale\":\"en-us\",\"availableLanguages\":{},\"_languagePackSupport\":true}",
"CONDA_PYTHON_EXE": "/Users/piotrsobolewski/Dev/miniforge3/bin/python",
"LOGNAME": "piotrsobolewski",
"LC_CTYPE": "en_US.UTF-8",
"VSCODE_IPC_HOOK": "/Users/piotrsobolewski/Library/Application Support/Code - Insiders/1.60.0-insider-main.sock",
"VSCODE_CODE_CACHE_PATH": "/Users/piotrsobolewski/Library/Application Support/Code - Insiders/CachedData/9dd4f31a21d63deea5e1fc322cfc802413b31d95",
"CONDA_DEFAULT_ENV": "napari-pyCL-D",
"VSCODE_PID": "88944",
"VSCODE_CWD": "/",
"_": "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-pyCL-D/bin/python"
},
"display_name": "Python 3.9.6 64-bit ('napari-pyCL-D': conda)",
"language": "python",
"interrupt_mode": "signal",
"metadata": {
"interpreter": {
"sysPrefix": "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-pyCL-D",
"envType": "Conda",
"envName": "napari-pyCL-D",
"envPath": "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-pyCL-D",
"path": "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-pyCL-D/bin/python",
"architecture": 3,
"sysVersion": "3.9.6 | packaged by conda-forge | (default, Jul 6 2021, 08:51:19) \n[Clang 11.1.0 ]",
"version": {
"raw": "3.9.6",
"major": 3,
"minor": 9,
"patch": 6,
"build": [],
"prerelease": [
"final",
"0"
]
},
"companyDisplayName": "Anaconda, Inc.",
"displayName": "Python 3.9.6 64-bit ('napari-pyCL-D': conda)"
}
}
}
},
"python396jvsc74a57bd0afe641fd5ac8524bd158abb495a60bea9cf594c409ae1159e03c1788ff37ce8b": {
"resource_dir": "/Users/piotrsobolewski/Library/Jupyter/kernels/python396jvsc74a57bd0afe641fd5ac8524bd158abb495a60bea9cf594c409ae1159e03c1788ff37ce8b",
"spec": {
"argv": [
"/Users/piotrsobolewski/Dev/miniforge3/envs/TF-SD2/bin/python",
"-m",
"ipykernel_launcher",
"-f",
"{connection_file}"
],
"env": {
"SHELL": "/opt/homebrew/bin/fish",
"TMPDIR": "/var/folders/sy/y3_x27j14cxg3_vhycs6cr_h0000gn/T/",
"CONDA_SHLVL": "2",
"PYTHONUNBUFFERED": "1",
"CONDA_PROMPT_MODIFIER": "(TF-SD2) ",
"_tide_right_prompt_display_var": "_tide_right_prompt_display_34214",
"ORIGINAL_XDG_CURRENT_DESKTOP": "undefined",
"PYTHONIOENCODING": "utf-8",
"USER": "piotrsobolewski",
"VSCODE_VERBOSE_LOGGING": "true",
"COMMAND_MODE": "unix2003",
"CONDA_EXE": "/Users/piotrsobolewski/Dev/miniforge3/bin/conda",
"SSH_AUTH_SOCK": "/private/tmp/com.apple.launchd.3Ynle5JFbz/Listeners",
"VSCODE_PIPE_LOGGING": "true",
"__CF_USER_TEXT_ENCODING": "0x1F5:0x0:0x0",
"VSCODE_LOG_STACK": "true",
"FZF_DEFAULT_OPTS": "--cycle --layout=reverse --border --height=90% --preview-window=wrap --marker=\"*\"",
"VSCODE_AMD_ENTRYPOINT": "vs/workbench/services/extensions/node/extensionHostProcess",
"ELECTRON_RUN_AS_NODE": "1",
"_CE_CONDA": "",
"CONDA_PREFIX_1": "/Users/piotrsobolewski/Dev/miniforge3",
"PATH": "/Users/piotrsobolewski/Dev/miniforge3/envs/TF-SD2/bin:/Users/piotrsobolewski/Dev/miniforge3/condabin:/Applications/CMake.app/Contents/bin:/usr/local/texlive/2020/bin/custom:/Users/piotrsobolewski/Library/Python/3.8/bin:/Users/piotrsobolewski/.cargo/bin:/opt/homebrew/bin:/opt/homebrew/opt/fzf/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin",
"CONDA_PREFIX": "/Users/piotrsobolewski/Dev/miniforge3/envs/TF-SD2",
"VSCODE_BROWSER_CODE_LOADING": "bypassHeatCheck",
"__CFBundleIdentifier": "com.microsoft.VSCodeInsiders",
"PWD": "/",
"VSCODE_HANDLES_UNCAUGHT_ERRORS": "true",
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"_CE_M": "",
"XPC_SERVICE_NAME": "0",
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"R_LD_LIBRARY_PATH": "/opt/homebrew/lib/R/lib",
"HOME": "/Users/piotrsobolewski",
"APPLICATION_INSIGHTS_NO_DIAGNOSTIC_CHANNEL": "true",
"VSCODE_IPC_HOOK_EXTHOST": "/var/folders/sy/y3_x27j14cxg3_vhycs6cr_h0000gn/T/vscode-ipc-5635c4c6-45e0-4720-b139-23af62473609.sock",
"VSCODE_NLS_CONFIG": "{\"locale\":\"en-us\",\"availableLanguages\":{},\"_languagePackSupport\":true}",
"CONDA_PYTHON_EXE": "/Users/piotrsobolewski/Dev/miniforge3/bin/python",
"LOGNAME": "piotrsobolewski",
"LC_CTYPE": "en_US.UTF-8",
"VSCODE_IPC_HOOK": "/Users/piotrsobolewski/Library/Application Support/Code - Insiders/1.59.0-insider-main.sock",
"VSCODE_CODE_CACHE_PATH": "/Users/piotrsobolewski/Library/Application Support/Code - Insiders/CachedData/104bc571e956e4af623905ef10dfcc8f0fdac625",
"CONDA_DEFAULT_ENV": "TF-SD2",
"VSCODE_PID": "34207",
"VSCODE_CWD": "/",
"_": "/Users/piotrsobolewski/Dev/miniforge3/envs/TF-SD2/bin/python"
},
"display_name": "Python 3.9.6 64-bit ('TF-SD2': conda)",
"language": "python",
"interrupt_mode": "signal",
"metadata": {
"interpreter": {
"sysPrefix": "/Users/piotrsobolewski/Dev/miniforge3/envs/TF-SD2",
"envType": "Conda",
"envName": "TF-SD2",
"envPath": "/Users/piotrsobolewski/Dev/miniforge3/envs/TF-SD2",
"path": "/Users/piotrsobolewski/Dev/miniforge3/envs/TF-SD2/bin/python",
"architecture": 3,
"sysVersion": "3.9.6 | packaged by conda-forge | (default, Jul 6 2021, 08:51:19) \n[Clang 11.1.0 ]",
"version": {
"raw": "3.9.6",
"major": 3,
"minor": 9,
"patch": 6,
"build": [],
"prerelease": [
"final",
"0"
]
},
"companyDisplayName": "Anaconda, Inc.",
"displayName": "Python 3.9.6 64-bit ('TF-SD2': conda)"
}
}
}
},
"python396jvsc74a57bd04583e14f17286c267a654b2994ed34fd426d7fb36ca9bac8a3c391cad9fcb58e": {
"resource_dir": "/Users/piotrsobolewski/Library/Jupyter/kernels/python396jvsc74a57bd04583e14f17286c267a654b2994ed34fd426d7fb36ca9bac8a3c391cad9fcb58e",
"spec": {
"argv": [
"python",
"-m",
"ipykernel_launcher",
"-f",
"{connection_file}"
],
"env": {},
"display_name": "Python 3.9.6 64-bit ('napari-openCV': conda)",
"language": "python",
"interrupt_mode": "signal",
"metadata": {
"interpreter": {
"sysPrefix": "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-openCV",
"envType": "Conda",
"envName": "napari-openCV",
"envPath": "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-openCV",
"path": "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-openCV/bin/python",
"architecture": 3,
"sysVersion": "3.9.6 | packaged by conda-forge | (default, Jul 6 2021, 08:51:19) \n[Clang 11.1.0 ]",
"version": {
"raw": "3.9.6",
"major": 3,
"minor": 9,
"patch": 6,
"build": [],
"prerelease": [
"final",
"0"
]
},
"companyDisplayName": "Anaconda, Inc.",
"displayName": "Python 3.9.6 64-bit ('napari-openCV': conda)"
}
}
}
},
"python3": {
"resource_dir": "/Users/piotrsobolewski/Dev/miniforge3/envs/napari-openCV/share/jupyter/kernels/python3",
"spec": {
"argv": [
"/Users/piotrsobolewski/Dev/miniforge3/envs/napari-openCV/bin/python",
"-m",
"ipykernel_launcher",
"-f",
"{connection_file}"
],
"env": {},
"display_name": "Python 3 (ipykernel)",
"language": "python",
"interrupt_mode": "signal",
"metadata": {
"debugger": true
}
}
}
}
}
The last one `python396jvsc74a57bd04583e14f17286c267a654b2994ed34fd426d7fb36ca9bac8a3c391cad9fcb58e/` is the new one, the issue, it's also the first new env I've done in 10+ days: did something change in vscode/jupyter? I'm in the Insider branch.
|
|
I think the problem is here: That shouldn't be happening. We should be setting that here: But something must have gone wrong. Can you:
If you don't have time for that, you could possibly fix the kernelspec yourself. Make the In the meantime, we'll try reproing this issue locally. |
rchiodo
added
notebook-execution
|
I deleted the dir. I got the same effect in VS Code: So it looks the same dir name was rebuilt properly. Below is the entire Output tab.
User belongs to experiment group 'jupyterTestcf'
User belongs to experiment group 'jupyterEnhancedDataViewer'
Error 2021-08-20 20:41:34: Exception while attempting zmq : [Error: No native build was found for platform=darwin arch=arm64 runtime=electron abi=89 uv=1 armv=8 libc=glibc node=14.16.0 electron=13.1.8
loaded from: /Users/piotrsobolewski/.vscode-insiders/extensions/ms-toolsai.jupyter-2021.8.2028630014/out/client/node_modules/zeromq
Info 2021-08-20 20:41:34: Attempting to start a server because of preload conditions ...
/Users/piotrsobolewski/Dev/miniforge3/envs/TF-StarDist-napari/lib/python3.9/site-packages/traitlets/traitlets.py:2196: FutureWarning: Supporting extra quotes around Unicode is deprecated in traitlets 5.0. Use '/Users/piotrsobolewski/Dev/PyCL' instead of '"/Users/piotrsobolewski/Dev/PyCL"' – or use CUnicode. Info 2021-08-20 20:43:22: Python Daemon (pid: 16928): write to stderr: [I 20:43:22.319 NotebookApp] [Jupytext Server Extension] Deriving a JupytextContentsManager from LargeFileManager [I 20:43:22.319 NotebookApp] [Jupytext Server Extension] Deriving a JupytextContentsManager from LargeFileManager Info 2021-08-20 20:43:22: Python Daemon (pid: 16928): write to stderr: [I 20:43:22.323 NotebookApp] Serving notebooks from local directory: /Users/piotrsobolewski/Dev/PyCL [I 20:43:22.323 NotebookApp] Serving notebooks from local directory: /Users/piotrsobolewski/Dev/PyCL Info 2021-08-20 20:43:22: Python Daemon (pid: 16928): write to stderr: [I 20:43:22.323 NotebookApp] Jupyter Notebook 6.4.0 is running at: [I 20:43:22.323 NotebookApp] Jupyter Notebook 6.4.0 is running at: Info 2021-08-20 20:43:22: Python Daemon (pid: 16928): write to stderr: [I 20:43:22.323 NotebookApp] http://localhost:8888/?token=4a6a731ba5bd790106cd41d2dcccc3dda255fc51f75d5e50 [I 20:43:22.323 NotebookApp] http://localhost:8888/?token=4a6a731ba5bd790106cd41d2dcccc3dda255fc51f75d5e50 Info 2021-08-20 20:43:22: Process Execution: > ~/Dev/miniforge3/envs/TF-StarDist-napari/bin/python (daemon) ~/.vscode-insiders/extensions/ms-toolsai.jupyter-2021.8.2028630014/pythonFiles/vscode_datascience_helpers/getServerInfo.py
[I 20:43:22.323 NotebookApp] or http://127.0.0.1:8888/?token=4a6a731ba5bd790106cd41d2dcccc3dda255fc51f75d5e50 Info 2021-08-20 20:43:22: Process Execution: > ~/Dev/miniforge3/envs/TF-StarDist-napari/bin/python (daemon) ~/.vscode-insiders/extensions/ms-toolsai.jupyter-2021.8.2028630014/pythonFiles/vscode_datascience_helpers/getServerInfo.py
Info 2021-08-20 20:43:22: Python Daemon (pid: 16926): Execute rpc method exec_file in DS Daemon Info 2021-08-20 20:43:22: Python Daemon (pid: 16926): Execute rpc method exec_file from /Users/piotrsobolewski/Dev/miniforge3/envs/TF-StarDist-napari/bin/python Info 2021-08-20 20:43:22: Python Daemon (pid: 16926): Exec file /Users/piotrsobolewski/.vscode-insiders/extensions/ms-toolsai.jupyter-2021.8.2028630014/pythonFiles/vscode_datascience_helpers/getServerInfo.py with args [] Info 2021-08-20 20:43:22: /Users/piotrsobolewski/Dev/miniforge3/envs/TF-StarDist-napari/lib/python3.9/site-packages/traitlets/traitlets.py:2196: FutureWarning: Supporting extra quotes around Unicode is deprecated in traitlets 5.0. Use '/Users/piotrsobolewski/Dev/PyCL' instead of '"/Users/piotrsobolewski/Dev/PyCL"' – or use CUnicode. Info 2021-08-20 20:43:22: Python Daemon (pid: 16926): execute file /Users/piotrsobolewski/.vscode-insiders/extensions/ms-toolsai.jupyter-2021.8.2028630014/pythonFiles/vscode_datascience_helpers/getServerInfo.py [I 20:43:22.463 NotebookApp] Creating new notebook in / [I 20:43:22.464 NotebookApp] Saving Untitled.ipynb
[I 20:43:22.691 NotebookApp] Kernel started: 4be7d37d-2f18-456b-9e14-26a7e0cfa67a, name: python396jvsc74a57bd04583e14f17286c267a654b2994ed34fd426d7fb36ca9bac8a3c391cad9fcb58e [W 20:43:22.697 NotebookApp] delete /default-aaf74eff-7801-4113-8b98-45f8dd17bac1.ipynb
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The env var isn't being picked up by VS code. You likely need to start VS code from the fish shell. However it looks like it at least attempted to set the environment in the kernelspec, but even if the TF_BUILD env, there isn't enough tracing to see what might have gone wrong. We need to repro locally. I've managed to do so, so we should be able to debug what's going wrong. |
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Thanks for looking into it. |
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Yeah me too now. Here's the one it generated for me: |
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This should be fixed in our next jupyter extension build (which I believe will be tonight?) |
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Works perfectly now! Thanks!! |
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Marked as verified based on comment above. |
Environment data
Expected behaviour
In a new conda environment (
napari-openCV) after setting it as the Python interpreter in VS Code and first time running cells in an Interactive Window eg.:VS Code asks to install
ipykernelwhich works fine from conda. The interactive window launches and shows the name of the conda env in the top right (also bottom left blue bar). The actual kernel should use this conda env (and has in the past, last on Aug 7, 2021). So the should return:(This is returned by running this cell in ipython with the conda env active.)
Thus, all installed packages in this conda env are available.
Actual behaviour
The Interactive Window shows the correct conda env in the kernel:
But the return from
os.sys.pathis a different, old conda env:Packages unique to the
napari-openCVare not available.Steps to reproduce:
Logs
Output for
Jupyterin theOutputpanel (View→Output, change the drop-down the upper-right of theOutputpanel toJupyter)The text was updated successfully, but these errors were encountered: