xeus-python in JupyterLite
Home Page: https://xeus-python-kernel.readthedocs.io
License: BSD 3-Clause "New" or "Revised" License
⚠️ jupyterlite-xeus-python is DEPRECATED. Please use https://github.com/jupyterlite/xeus. See the migration guide.
![github-actions[bot] avatar](https://avatars.githubusercontent.com/in/15368?v=4 "github-actions[bot]")
There are some issues with the development build instructions. Some are mistakes, and others are places where the instructions might be more helpful.
Here are the current development build instructions, with issues interspersed.
# Clone the repo to your local environment
# Change directory to the jupyterlite_xeus_python directory
Changing into this directory makes the next command not work.
# Install package in development mode
python -m pip install -e .
# Link your development version of the extension with JupyterLab
jupyter labextension develop . --overwrite
This requires jupyter to be installed. What is the best way to do that? Should conda be used, and if so how?
# Rebuild extension Typescript source after making changes
jlpm run build
# Watch the source directory in one terminal, automatically rebuilding when needed
jlpm run watch
# Run JupyterLab in another terminal
jupyter lab
What if we we want to run jupyterlite rather than Jupyter?
Sometimes fails with
Uncaught (in promise) TypeError: Cannot read properties of null (reading 'path')
at e.onmessage (index.js:160:34)
kernels.js:50 Uncaught (in promise) RangeError: Maximum call stack size exceeded
at abort (/euroscipy-2022-jupyterlite-emscripten-forge/extensions/@jupyterlite/xeus-python-kernel/static/xpython_wasm.js:9:20546)
at _abort (/euroscipy-2022-jupyterlite-emscripten-forge/extensions/@jupyterlite/xeus-python-kernel/static/xpython_wasm.js:9:200143)
at /euroscipy-2022-jupyterlite-emscripten-forge/extensions/@jupyterlite/xeus-python-kernel/static/xpython_wasm.wasm
at /euroscipy-2022-jupyterlite-emscripten-forge/extensions/@jupyterlite/xeus-python-kernel/static/xpython_wasm.wasm
at /euroscipy-2022-jupyterlite-emscripten-forge/extensions/@jupyterlite/xeus-python-kernel/static/xpython_wasm.wasm
at /euroscipy-2022-jupyterlite-emscripten-forge/extensions/@jupyterlite/xeus-python-kernel/static/xpython_wasm.wasm
at /euroscipy-2022-jupyterlite-emscripten-forge/extensions/@jupyterlite/xeus-python-kernel/static/xpython_wasm.wasm
at /euroscipy-2022-jupyterlite-emscripten-forge/extensions/@jupyterlite/xeus-python-kernel/static/xpython_wasm.wasm
at /euroscipy-2022-jupyterlite-emscripten-forge/extensions/@jupyterlite/xeus-python-kernel/static/xpython_wasm.wasm
at /euroscipy-2022-jupyterlite-emscripten-forge/extensions/@jupyterlite/xeus-python-kernel/static/xpython_wasm.wasm
Paste the output from your browser Javascript console here.
from jupyterlite_xeus_python import __version__Gives None
The spec registered by the extension uses xeus-python as the kernel name, but in JupyterLab, the kernel name served by /api/kernelspecs is xpython. The mismatch makes Voici can not find the correct kernel for a notebook saved by JupyterLab
xeus-python-kernel/src/index.ts
Lines 30 to 37 in 71e105d
Execusion of cell import pandas hangs. This exception message is shown on the JavaScript Console:
Uncaught (in promise) SyntaxError: Unexpected end of input (at services.js:32:51)
at services.js:32:51
at new Promise ()
at services.js:28:7
jupyter lite build --XeusPythonEnv.packages=openpyxl,pandas,matplotlibimport pandas and run itPandas should be normally imported in several seconds
Uncaught (in promise) SyntaxError: Unexpected end of input (at services.js:32:51)
at services.js:32:51
at new Promise ()
at services.js:28:7
The update to JupyterLite 0.2.0 was done in #155.
There isn't many breaking changes in JupyterLite 0.2.0 that affect jupyterlite-xeus-python.
Except for the removal of ENV_EXTENSIONS from the top-level jupyterlite_core.addons.federated_extensions:
xeus-python-kernel/jupyterlite_xeus_python/env_build_addon.py
Lines 25 to 28 in b00d80d
Maybe it could be useful to enable jupyterlite-xeus-python==0.x to work with JupyterLite 0.2.0, in case #164 or emscripten-forge/recipes#643 would prevent some users from upgrading.
When building from source, the last stage of jlpm run build yields
Failed to parse source map from '/home/sylvain/dev/jupyterlite/xeus-python-kernel/node_modules/@jupyterlite/server/src/app.ts' file: Error: ENOENT: no such file or directory, open '/home/sylvain/dev/jupyterlite/xeus-python-kernel/node_modules/@jupyterlite/server/src/app.ts'
It seems that the source map files are in server/lib instead of server/src.
scipy.misc.face() fails since it can not find the associated data file. There are other similar functions that are missing data files in scipy.misc: scipy.misc.electrocardiogram() and scipy.misc.ascent()
The package from emscripten-forge does contain the .dat files. but somehow they are not visible by the kernel.
jupyter lite build --XeusPythonEnv.packages=scipy
jupyter lite serve
Open JupyterLite and start a new notebook with a xeus-python kernel.
from scipy.misc import face
arr = face()This gives an error:
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
/tmp/xpython_42/1607471528.py in <cell line: 3>()
1 from scipy.misc import face
2
----> 3 arr = face()
/tmp/xeus-python-kernel/envs/xeus-python-kernel/lib/python3.10/site-packages/scipy/misc/_common.py in face(gray)
220 import bz2
221 import os
--> 222 with open(os.path.join(os.path.dirname(__file__), 'face.dat'), 'rb') as f:
223 rawdata = f.read()
224 data = bz2.decompress(rawdata)
FileNotFoundError: [Errno 44] No such file or directory: '/tmp/xeus-python-kernel/envs/xeus-python-kernel/lib/python3.10/site-packages/scipy/misc/face.dat'
From the screenshot below, you can see that there are no .dat file in the scipy.misc folder:
This does work fine in a Pyodide kernel.
No error
The itables package allows for making pandas dataframes more interactive: https://github.com/mwouts/itables
It seems to be working fine with the Pyodide kernel:
However xeus python has issues importing the package with import itables:
FileNotFoundError: [Errno 44] No such file or directory: '/tmp/xeus-python-kernel/envs/jupyterlite-tutorial-demo/lib/python3.10/site-packages/itables/html/itables.css'
While checking the directory content looks fine with:
import os
os.listdir()Create a new environment with itables as a dependency.
itables should work in the xeus python kernel.
At first it looked like it could have been an issue with the service worker not able to find the files.
But digging into this more it seems that the html folder is missing:
This might be similar to #120
Adding plotly to XeusPythonEnv.packages and importing it in a notebook results in the following:
ModuleNotFoundError: No module named 'webbrowser'
For example this deployment: https://scipy-2022-jupyterlite-virtual-poster--7.org.readthedocs.build/en/7/lite/lab/index.html?path=plotly.ipynb
Although the link will probably be invalid soon.
Running import webbrowser on the Pyodide console works fine: https://pyodide.org/en/latest/console.html
plotly depends on the webbrowser module being available.
To reproduce:
pr<TAB> no completions is shownExpected behaviour: completions are shown showing print for example
Observed behaviour: no completion is shown.
I originally observed the behaviour when using jupyterlite build --XeusPython.packages locally
I tried both in Firefox and Chromium, same behaviour.
Pyolite tab-completion seems to work fine e.g. on https://numpy.org/
Output from the browser console:
ERROR: received bad message: NotImplementedError: Python version 3.10 is currently not supported. xpython_wasm.js:9:53168
<empty string> xpython_wasm.js:9:53168
At: xpython_wasm.js:9:53168
/tmp/xeus-python-kernel/envs/xeus-python-kernel/lib/python3.10/site-packages/parso/grammar.py(264): load_grammar xpython_wasm.js:9:53168
/tmp/xeus-python-kernel/envs/xeus-python-kernel/lib/python3.10/site-packages/jedi/api/environment.py(37): get_grammar xpython_wasm.js:9:53168
/tmp/xeus-python-kernel/envs/xeus-python-kernel/lib/python3.10/site-packages/jedi/cache.py(112): wrapper xpython_wasm.js:9:53168
/tmp/xeus-python-kernel/envs/xeus-python-kernel/lib/python3.10/site-packages/jedi/inference/__init__.py(91): __init__ xpython_wasm.js:9:53168
/tmp/xeus-python-kernel/envs/xeus-python-kernel/lib/python3.10/site-packages/jedi/api/__init__.py(119): __init__ xpython_wasm.js:9:53168
/tmp/xeus-python-kernel/envs/xeus-python-kernel/lib/python3.10/site-packages/jedi/api/__init__.py(729): __init__ xpython_wasm.js:9:53168
/tmp/xeus-python-kernel/envs/xeus-python-kernel/lib/python3.10/site-packages/IPython/core/completer.py(1397): _jedi_matches xpython_wasm.js:9:53168
/tmp/xeus-python-kernel/envs/xeus-python-kernel/lib/python3.10/site-packages/IPython/core/completer.py(2054): _complete xpython_wasm.js:9:53168
/tmp/xeus-python-kernel/envs/xeus-python-kernel/lib/python3.10/site-packages/IPython/core/completer.py(1886): _completions xpython_wasm.js:9:53168
<empty string> xpython_wasm.js:9:53168
Message type: complete_request xpython_wasm.js:9:53168
Here is a screenshot in case that helps
First of all, really impressive work to get xeus-python to compile to WebAssembly!
Looks like the kernel does not load in Firefox though. The error logged in the dev tools might be relevant:
TypeError: WebAssembly.Tag is not a constructor
Open https://xeus-python-kernel.readthedocs.io/en/latest/ with Firefox 99.
Should run in Firefox.
The tsconfig currently expects noImplicitAny to be false, to avoid the following typescript error when building: "Type 'typeof globalThis' has no index signature in TS".
This should be fixed by completing the declaration.ts.d file as explained here.
In https://jtp.io/lit/lab/index.html, run "import pandas", the following error happened:
Failed to load resource: the server responded with a status of 404 ()
index.js:540 Error: Shared module @jupyterlab/debugger doesn't exist in shared scope default
at ensureExistence (consumes:19:1)
at consumes:101:1
at consumes:82:1
at webpack/sharing/consume/default/@jupyterlab/debugger (consumes:151:1)
at consumes:265:1
at Array.forEach ()
at webpack_require.f.consumes (consumes:248:1)
at ensure chunk:6:1
at Array.reduce ()
at webpack_require.e (ensure chunk:5:1)
(anonymous) @ index.js:540
/lit/api/translations/default.json:1
Failed to load resource: the server responded with a status of 404 ()
index.es6.js:308 TypeError: object null is not iterable (cannot read property Symbol(Symbol.iterator))
at te.items (model.js:183:21)
at te.items (model.js:563:28)
at te.items (model.js:601:29)
at J._onModelRefreshed (listing.js:1686:40)
at d (index.es6.js:555:18)
at e.emit (index.es6.js:513:17)
at s.emit (index.es6.js:112:17)
at te.onRunningChanged (model.js:513:25)
at d (index.es6.js:555:18)
at e.emit (index.es6.js:513:17)
e.exceptionHandler @ index.es6.js:308
mock-socket.js:763 WebSocket connection to 'wss://jtp.io/lit/api/kernels/c5fe2f87-7770-406f-91eb-64515e61dcce/channels?session_id=e3f1f6d2-6b9a-4f2b-b36d-eb43a66e0ba8' failed
w @ mock-socket.js:763
mock-socket.js:763 WebSocket connection to 'wss://jtp.io/lit/api/kernels/c5fe2f87-7770-406f-91eb-64515e61dcce/channels?session_id=652681c8-bd2f-4c4c-8c73-f0eb9b5a5acd' failed
w @ mock-socket.js:763
index.es6.js:308 TypeError: object null is not iterable (cannot read property Symbol(Symbol.iterator))
at te.items (model.js:183:21)
at te.items (model.js:563:28)
at te.items (model.js:601:29)
at J._onModelRefreshed (listing.js:1686:40)
at d (index.es6.js:555:18)
at e.emit (index.es6.js:513:17)
at s.emit (index.es6.js:112:17)
at te.onRunningChanged (model.js:513:25)
at d (index.es6.js:555:18)
at e.emit (index.es6.js:513:17)
e.exceptionHandler @ index.es6.js:308
mock-socket.js:763 WebSocket connection to 'wss://jtp.io/lit/api/kernels/c5fe2f87-7770-406f-91eb-64515e61dcce/channels?session_id=f4ddb789-279c-4bc3-9cca-1c2c0305eea9' failed
w @ mock-socket.js:763
213.efd3bb893df42f78e3eb.js?v=efd3bb893df42f78e3eb:2 Uncaught (in promise) DOMException: Failed to execute 'importScripts' on 'WorkerGlobalScope': The script at 'https://jtp.io/lit/extensions/@jupyterlite/xeus-python-kernel/static/xpython_wasm.js' failed to load.
at Object.initialize (https://jtp.io/lit/extensions/@jupyterlite/xeus-python-kernel/static/213.efd3bb893df42f78e3eb.js?v=efd3bb893df42f78e3eb:2:10713)
at https://jtp.io/lit/extensions/@jupyterlite/xeus-python-kernel/static/213.efd3bb893df42f78e3eb.js?v=efd3bb893df42f78e3eb:2:10009
at new Promise ()
at new (https://jtp.io/lit/extensions/@jupyterlite/xeus-python-kernel/static/213.efd3bb893df42f78e3eb.js?v=efd3bb893df42f78e3eb:2:9987)
at https://jtp.io/lit/extensions/@jupyterlite/xeus-python-kernel/static/213.efd3bb893df42f78e3eb.js?v=efd3bb893df42f78e3eb:2:9934
at Object. (https://jtp.io/lit/extensions/@jupyterlite/xeus-python-kernel/static/213.efd3bb893df42f78e3eb.js?v=efd3bb893df42f78e3eb:2:11472)
at 213 (https://jtp.io/lit/extensions/@jupyterlite/xeus-python-kernel/static/213.efd3bb893df42f78e3eb.js?v=efd3bb893df42f78e3eb:2:11476)
at r (https://jtp.io/lit/extensions/@jupyterlite/xeus-python-kernel/static/213.efd3bb893df42f78e3eb.js?v=efd3bb893df42f78e3eb:2:11604)
at https://jtp.io/lit/extensions/@jupyterlite/xeus-python-kernel/static/213.efd3bb893df42f78e3eb.js?v=efd3bb893df42f78e3eb:2:11926
at https://jtp.io/lit/extensions/@jupyterlite/xeus-python-kernel/static/213.efd3bb893df42f78e3eb.js?v=efd3bb893df42f78e3eb:2:11934
default.js:493 Uncaught (in promise) Error: Kernel is dead
at C._sendMessage (default.js:493:19)
at C._sendKernelShellControl (default.js:448:14)
at C.sendShellMessage (default.js:424:21)
at C.requestExecute (default.js:778:21)
at e.execute (widget.js:630:31)
at e.execute (widget.js:1182:43)
at actions.js:1889:54
at actions.js:1807:50
at Array.map ()
at e.runSelected (actions.js:1807:37)
I understand that pandas is not pre-installed. I just happened to check. It seems it is only related to the latest version.
Pandas is not pre-installed, so "no module pandas available" should be mentioned.
The execution hangs at [*]: import this
See the zen of Python
Unsatisfied version 5.5.2 from _JUPYTERLAB.CORE_OUTPUT of shared singleton module @jupyterlab/coreutils (required ^5.6.1) remoteEntry.8e4043cf4e118658c12f.js:1:5837
Registering new JupyterLite ServiceWorker https://jupyterlite.github.io/xeus-python-demo/service-worker-b2fb40a.js service-manager.ts:50:16
Default kernel not found, using 'xeus-python' validate.ts:73:12
JupyterLite ServiceWorker was sucessfully registered service-manager.ts:52:16
Kernel filesystem and JupyterLite contents will be synced index.ts:235:16
SingleFile is hooking the IntersectionObserver API to detect and load deferred images. single-file-hooks-frames.js:1:531
Uncaught (in promise) TypeError: s is undefined
d index.js:61
2 index.js:61:12
xeus-python contents will be synced with Jupyter Contents 20.6704bc71563170623fd0.js:1:2688
Starting WebSocket: wss://jupyterlite.github.io/xeus-python-demo/api/kernels/ed718396-d9c7-45c8-bd13-607e9106b8cd default.ts:1251:12
Default kernel not found, using 'xeus-python' validate.ts:73:12
Settings failed to load for (@jupyterlab/csvviewer-extension:csv)
Array [ {…} ]
settingsplugin.ts:42:18
This may happen if {autoStart: false} in (@jupyterlab/csvviewer-extension:csv) or if it is one of the deferredExtensions in page config. settingsplugin.ts:44:20
Settings failed to load for (@jupyterlab/csvviewer-extension:tsv)
Array [ {…} ]
settingsplugin.ts:42:18
This may happen if {autoStart: false} in (@jupyterlab/csvviewer-extension:tsv) or if it is one of the deferredExtensions in page config. settingsplugin.ts:44:20
Settings failed to load for (@jupyterlab/filebrowser-extension:widget)
Array [ {…} ]
settingsplugin.ts:42:18
This may happen if {autoStart: false} in (@jupyterlab/filebrowser-extension:widget) or if it is one of the deferredExtensions in page config. settingsplugin.ts:44:20
Settings failed to load for (@jupyterlab/fileeditor-extension:plugin)
Array [ {…} ]
settingsplugin.ts:42:18
This may happen if {autoStart: false} in (@jupyterlab/fileeditor-extension:plugin) or if it is one of the deferredExtensions in page config. settingsplugin.ts:44:20
Settings failed to load for (@jupyterlab/htmlviewer-extension:plugin)
Array [ {…} ]
settingsplugin.ts:42:18
This may happen if {autoStart: false} in (@jupyterlab/htmlviewer-extension:plugin) or if it is one of the deferredExtensions in page config. settingsplugin.ts:44:20
Error: Dynamic module import is disabled or not supported in this context python_data.js:3:1
Failed to fetch ipywidgets through the "jupyter.widget.control" comm channel, fallback to fetching individual model state. Reason: Control comm did not respond in time 150.b0e841b75317744a7595.js:1:5783
Propriété « -moz-outline-radius » inconnue. Déclaration abandonnée. notebooks:283:23
Propriété « -moz-osx-font-smoothing » inconnue. Déclaration abandonnée. notebooks:638:29
Propriété « -moz-osx-font-smoothing » inconnue. Déclaration abandonnée. notebooks:1387:31
Erreur d’analyse de la valeur pour « -webkit-transition-duration ». Déclaration abandonnée. notebooks:1529:31
Erreur d’analyse de la valeur pour « transition-duration ». Déclaration abandonnée. notebooks:1530:31
Erreur d’analyse de la valeur pour « -webkit-transition-delay ». Déclaration abandonnée. notebooks:1587:30
Erreur d’analyse de la valeur pour « transition-delay ». Déclaration abandonnée. notebooks:1588:30
Erreur d’analyse de la valeur pour « -webkit-transition-delay ». Déclaration abandonnée. notebooks:1605:30
Erreur d’analyse de la valeur pour « transition-delay ». Déclaration abandonnée. notebooks:1606:30
Erreur d’analyse de la valeur pour « -webkit-transition-delay ». Déclaration abandonnée. notebooks:1863:32
Erreur d’analyse de la valeur pour « transition-delay ». Déclaration abandonnée. notebooks:1864:32
Erreur d’analyse de la valeur pour « -webkit-transition-delay ». Déclaration abandonnée. notebooks:1879:32
Erreur d’analyse de la valeur pour « transition-delay ». Déclaration abandonnée. notebooks:1880:32
Erreur d’analyse de la valeur pour « -webkit-transition-delay ». Déclaration abandonnée. notebooks:1900:32
Erreur d’analyse de la valeur pour « transition-delay ». Déclaration abandonnée. notebooks:1901:32
Erreur d’analyse de la valeur pour « -webkit-transition-delay ». Déclaration abandonnée. notebooks:1916:32
Erreur d’analyse de la valeur pour « transition-delay ». Déclaration abandonnée. notebooks:1917:32
Erreur d’analyse de la valeur pour « -webkit-transition-delay ». Déclaration abandonnée. notebooks:1937:32
Erreur d’analyse de la valeur pour « transition-delay ». Déclaration abandonnée. notebooks:1938:32
Erreur d’analyse de la valeur pour « -webkit-transition-delay ». Déclaration abandonnée. notebooks:1953:32
Erreur d’analyse de la valeur pour « transition-delay ». Déclaration abandonnée. notebooks:1954:32
Erreur d’analyse de la valeur pour « -webkit-transition-delay ». Déclaration abandonnée. notebooks:1974:32
Erreur d’analyse de la valeur pour « transition-delay ». Déclaration abandonnée. notebooks:1975:32
Erreur d’analyse de la valeur pour « -webkit-transition-delay ». Déclaration abandonnée. notebooks:1990:32
Erreur d’analyse de la valeur pour « transition-delay ». Déclaration abandonnée. notebooks:1991:32
Erreur d’analyse de la valeur pour « -webkit-transition-delay ». Déclaration abandonnée. notebooks:2016:32
Erreur d’analyse de la valeur pour « transition-delay ». Déclaration abandonnée. notebooks:2017:32
Erreur d’analyse de la valeur pour « -webkit-transition-delay ». Déclaration abandonnée. notebooks:2034:32
Erreur d’analyse de la valeur pour « transition-delay ». Déclaration abandonnée. notebooks:2035:32
Erreur d’analyse de la valeur pour « -webkit-transition-delay ». Déclaration abandonnée. notebooks:2060:32
Erreur d’analyse de la valeur pour « transition-delay ». Déclaration abandonnée. notebooks:2061:32
Erreur d’analyse de la valeur pour « -webkit-transition-delay ». Déclaration abandonnée. notebooks:2078:32
Erreur d’analyse de la valeur pour « transition-delay ». Déclaration abandonnée. notebooks:2079:32
Pseudo-classe ou pseudo-élément « -ms-input-placeholder » inconnu. Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:2291:28
Pseudo-classe ou pseudo-élément « -ms-input-placeholder » inconnu. Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:2294:28
Pseudo-classe ou pseudo-élément « -ms-clear » inconnu. Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:2302:28
Propriété « -moz-outline-radius » inconnue. Déclaration abandonnée. notebooks:2586:25
Propriété « -moz-outline-radius » inconnue. Déclaration abandonnée. notebooks:2652:25
Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:2807:72
Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:2824:84
Pseudo-classe ou pseudo-élément « -ms-input-placeholder » inconnu. Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:2880:26
Pseudo-classe ou pseudo-élément « -ms-input-placeholder » inconnu. Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:2883:26
Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:2929:35
Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:2934:35
Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:2939:35
Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:2947:37
Pseudo-classe ou pseudo-élément « -ms-input-placeholder » inconnu. Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:2982:38
Pseudo-classe ou pseudo-élément « -ms-input-placeholder » inconnu. Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:2984:38
Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:3006:47
Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:3008:47
Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:3012:47
Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:3017:47
Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:3023:49
Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:3025:46
Propriété « -moz-osx-font-smoothing » inconnue. Déclaration abandonnée. notebooks:3157:31
Pseudo-classe ou pseudo-élément « -ms-input-placeholder » inconnu. Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:3334:14
Pseudo-classe ou pseudo-élément « -ms-input-placeholder » inconnu. Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:3337:14
Pseudo-classe ou pseudo-élément « -ms-input-placeholder » inconnu. Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:3389:26
Pseudo-classe ou pseudo-élément « -ms-input-placeholder » inconnu. Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:3391:26
Pseudo-classe ou pseudo-élément « -ms-clear » inconnu. Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:3502:14
Pseudo-classe ou pseudo-élément « -ms-input-placeholder » inconnu. Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:3521:34
Pseudo-classe ou pseudo-élément « -ms-input-placeholder » inconnu. Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:3523:34
Pseudo-classe ou pseudo-élément « -ms-expand » inconnu. Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:4027:27
Propriété « -moz-osx-font-smoothing » inconnue. Déclaration abandonnée. notebooks:4070:27
Propriété « -moz-osx-font-smoothing » inconnue. Déclaration abandonnée. notebooks:4281:27
Propriété « -moz-osx-font-smoothing » inconnue. Déclaration abandonnée. notebooks:4291:27
Propriété « -moz-osx-font-smoothing » inconnue. Déclaration abandonnée. notebooks:4302:29
Propriété « -moz-osx-font-smoothing » inconnue. Déclaration abandonnée. notebooks:5929:29
Propriété « -moz-osx-font-smoothing » inconnue. Déclaration abandonnée. notebooks:5963:31
Erreur d’analyse de la valeur pour « -webkit-transition-delay ». Déclaration abandonnée. notebooks:6258:30
Erreur d’analyse de la valeur pour « transition-delay ». Déclaration abandonnée. notebooks:6259:30
Erreur d’analyse de la valeur pour « -webkit-transition-delay ». Déclaration abandonnée. notebooks:6270:30
Erreur d’analyse de la valeur pour « transition-delay ». Déclaration abandonnée. notebooks:6271:30
Erreur d’analyse de la valeur pour « -webkit-transition-delay ». Déclaration abandonnée. notebooks:6354:28
Erreur d’analyse de la valeur pour « transition-delay ». Déclaration abandonnée. notebooks:6355:28
Erreur d’analyse de la valeur pour « -webkit-transition-delay ». Déclaration abandonnée. notebooks:6374:28
Erreur d’analyse de la valeur pour « transition-delay ». Déclaration abandonnée. notebooks:6375:28
Erreur d’analyse de la valeur pour « -webkit-transition-delay ». Déclaration abandonnée. notebooks:6394:28
Erreur d’analyse de la valeur pour « transition-delay ». Déclaration abandonnée. notebooks:6395:28
Erreur d’analyse de la valeur pour « -webkit-transition-delay ». Déclaration abandonnée. notebooks:6414:28
Erreur d’analyse de la valeur pour « transition-delay ». Déclaration abandonnée. notebooks:6415:28
Erreur d’analyse de la valeur pour « -webkit-transition-delay ». Déclaration abandonnée. notebooks:6496:28
Erreur d’analyse de la valeur pour « transition-delay ». Déclaration abandonnée. notebooks:6497:28
Erreur d’analyse de la valeur pour « -webkit-transition-delay ». Déclaration abandonnée. notebooks:6516:28
Erreur d’analyse de la valeur pour « transition-delay ». Déclaration abandonnée. notebooks:6517:28
Erreur d’analyse de la valeur pour « -webkit-transition-delay ». Déclaration abandonnée. notebooks:6536:28
Erreur d’analyse de la valeur pour « transition-delay ». Déclaration abandonnée. notebooks:6537:28
Erreur d’analyse de la valeur pour « -webkit-transition-delay ». Déclaration abandonnée. notebooks:6556:28
Erreur d’analyse de la valeur pour « transition-delay ». Déclaration abandonnée. notebooks:6557:28
Erreur d’analyse de la valeur pour « -webkit-transition-delay ». Déclaration abandonnée. notebooks:6674:30
Erreur d’analyse de la valeur pour « transition-delay ». Déclaration abandonnée. notebooks:6675:30
Erreur d’analyse de la valeur pour « -webkit-transition-delay ». Déclaration abandonnée. notebooks:6690:30
Erreur d’analyse de la valeur pour « transition-delay ». Déclaration abandonnée. notebooks:6691:30
Erreur d’analyse de la valeur pour « -webkit-transition-delay ». Déclaration abandonnée. notebooks:6721:34
Erreur d’analyse de la valeur pour « transition-delay ». Déclaration abandonnée. notebooks:6722:34
Erreur d’analyse de la valeur pour « -webkit-transition-delay ». Déclaration abandonnée. notebooks:6737:34
Erreur d’analyse de la valeur pour « transition-delay ». Déclaration abandonnée. notebooks:6738:34
Erreur d’analyse de la valeur pour « -webkit-transition-delay ». Déclaration abandonnée. notebooks:6795:30
Erreur d’analyse de la valeur pour « transition-delay ». Déclaration abandonnée. notebooks:6796:30
Erreur d’analyse de la valeur pour « -webkit-transition-delay ». Déclaration abandonnée. notebooks:6807:30
Erreur d’analyse de la valeur pour « transition-delay ». Déclaration abandonnée. notebooks:6808:30
Propriété « -moz-outline-radius » inconnue. Déclaration abandonnée. notebooks:7284:25
Erreur d’analyse de la valeur pour « -webkit-transform ». Déclaration abandonnée. notebooks:7299:34
Erreur d’analyse de la valeur pour « transform ». Déclaration abandonnée. notebooks:7300:34
Propriété « -moz-outline-radius » inconnue. Déclaration abandonnée. notebooks:7388:25
Propriété « -moz-osx-font-smoothing » inconnue. Déclaration abandonnée. notebooks:7596:29
Propriété « -moz-outline-radius » inconnue. Déclaration abandonnée. notebooks:7687:27
Pseudo-classe ou pseudo-élément « -ms-input-placeholder » inconnu. Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:7751:47
Pseudo-classe ou pseudo-élément « -ms-input-placeholder » inconnu. Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:7753:47
Pseudo-classe ou pseudo-élément « -ms-input-placeholder » inconnu. Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:7786:20
Pseudo-classe ou pseudo-élément « -ms-input-placeholder » inconnu. Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:7789:20
Erreur d’analyse de la valeur pour « -webkit-transition-delay ». Déclaration abandonnée. notebooks:7819:30
Erreur d’analyse de la valeur pour « transition-delay ». Déclaration abandonnée. notebooks:7820:30
Erreur d’analyse de la valeur pour « -webkit-transition-delay ». Déclaration abandonnée. notebooks:7835:30
Erreur d’analyse de la valeur pour « transition-delay ». Déclaration abandonnée. notebooks:7836:30
Erreur d’analyse de la valeur pour « -webkit-transition-delay ». Déclaration abandonnée. notebooks:7853:30
Erreur d’analyse de la valeur pour « transition-delay ». Déclaration abandonnée. notebooks:7854:30
Erreur d’analyse de la valeur pour « -webkit-transition-delay ». Déclaration abandonnée. notebooks:8087:30
Erreur d’analyse de la valeur pour « transition-delay ». Déclaration abandonnée. notebooks:8088:30
Erreur d’analyse de la valeur pour « -webkit-transition-delay ». Déclaration abandonnée. notebooks:8103:30
Erreur d’analyse de la valeur pour « transition-delay ». Déclaration abandonnée. notebooks:8104:30
Erreur d’analyse de la valeur pour « -webkit-transition-delay ». Déclaration abandonnée. notebooks:21:30
Erreur d’analyse de la valeur pour « transition-delay ». Déclaration abandonnée. notebooks:22:30
Erreur d’analyse de la valeur pour « -webkit-transition-delay ». Déclaration abandonnée. notebooks:39:30
Erreur d’analyse de la valeur pour « transition-delay ». Déclaration abandonnée. notebooks:40:30
Propriété « -moz-outline-radius » inconnue. Déclaration abandonnée. notebooks:51:23
Propriété « -moz-osx-font-smoothing » inconnue. Déclaration abandonnée. notebooks:5:54
Erreur d’analyse de la valeur pour « overflow ». Déclaration abandonnée. notebooks:78:13
Pseudo-classe ou pseudo-élément « -ms-input-placeholder » inconnu. Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:121:26
Propriété « -moz-outline-radius » inconnue. Déclaration abandonnée. notebooks:56:23
Propriété « -moz-outline-radius » inconnue. Déclaration abandonnée. notebooks:67:23
Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:48:61
Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:55:61
Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:84:51
Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:90:51
Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:108:45
Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:113:45
Propriété « -moz-border-radius » inconnue. Déclaration abandonnée. notebooks:244:22
Erreur d’analyse de la valeur pour « content ». Déclaration abandonnée. notebooks:1:174
Jeu de règles ignoré suite à un mauvais sélecteur. notebooks:1:1318
Erreur d’analyse de la valeur pour « display ». Déclaration abandonnée. notebooks:1:2750
Propriété « -moz-osx-font-smoothing » inconnue. Déclaration abandonnée. notebooks:11:27
Propriété « -moz-box-shadow » inconnue. Déclaration abandonnée. notebooks:504:19
Default kernel not found, using 'xeus-python' 13 validate.ts:73:12
Build fails with:
FileNotFoundError: [Errno 2] No such file or directory: '\tmp\xeus-python-kernel\envs\xeus-python-kernel\Scripts/pip-script.py'
Error:
Executing transaction: done
[LiteBuildApp] ERROR | [lite] [post_build] [jupyterlite-xeus-python] [ERR] [Errno 2] No such file or directory: '\tmp\xeus-python-kernel\envs\xeus-python-kernel\Scripts/pip-script.py'
Traceback (most recent call last):
File "C:\Users\DavidNilsson\anaconda3\envs\xeus-python-kernel\Lib\site-packages\doit\doit_cmd.py", line 294, in run
return command.parse_execute(args)
...
File "C:\Users\DavidNilsson\anaconda3\Lib\shutil.py", line 256, in copyfile
with open(src, 'rb') as fsrc:
^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '\tmp\xeus-python-kernel\envs\xeus-python-kernel\Scripts/pip-script.py'
Two issues,
Building with the jupyterlite with pyodide-kernel works fine, but not with Xeus.
Tried multiple conda env setups, same issue.
Logs attached. Please advise.
XeusBuildIssueFileNotFound.txt
cc. @nthiery
As discussed here #96 (comment)
We would need to remove the check here and find the proper way to pass them dependencies to micromamba/mamba/conda, or simply invoke pip with the right install prefix.
Sometimes the kernel doesn't get ready.
The kernel should get ready when opening a notebook or after restarting it.
Currently jupyterlite-xeus-python supports reading dependencies from an environment.yml file which is great 👍
However some folks new to Python and likely to use JupyterLite might not be familiar with the whole conda world of packages. This might not be an issue if they are just using an existing JupyterLite site. However it could become one if they want to build their own site.
Maybe the kernel addon could also support reading dependencies from a requirements.txt if available. And "translate" it to an environment.yml transparently before triggering the build.
This might need #102 first, as not all packages on PyPI are available on conda-forge.
This came up in discussions after the presentation about JupyterLite at a Python meetup: https://www.meetup.com/fr-FR/groupe-dutilisateurs-python-grenoble/events/291818929/
A few projects in the emscripten forge organization have now been updated to use the new empack >=3.0.0:
Update the xeus python kernel to empack>=3.0.0.
This will likely require the next version of jupyterlite-xeus-python to be 0.9.0.
JupyterLite recently integrated the File-system access, we should implement support for this here. jupyterlite/jupyterlite#655
Upgrading to xeus-python-kernel>0.9.0 breaks the build process of our site, throwing this error:
- package 'bw2io-0.9.dev21-py_0' is excluded by strict repo priority
[LiteBuildApp] No archive (yet): brightway-hub-jupyterlite.tgz
[LiteBuildApp] jupyter-lite.(json|ipynb): 1 files
/home/runner/micromamba-root/envs/build-env/lib/python3.10/site-packages/jupyterlite_core/optional.py:22: UserWarning: install libarchive-c for better perfomance when working with archives: No module named 'libarchive'
warnings.warn(hint.format(error=error))
/home/runner/micromamba-root/envs/build-env/lib/python3.10/site-packages/jupyterlite_core/optional.py:22: UserWarning: [lite] [translation] install `jupyterlab_server` to load translations: No module named 'jupyterlab_server'
warnings.warn(hint.format(error=error))
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/ / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
/ /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
/ .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
/_/
error libmamba Error opening for writing "/tmp/xeus-python-kernel/envs/xeus-python-kernel/.mambarc": No such file or directory
error libmamba Selected channel specific (or force-reinstall) job, but package is not available from channel. Solve job will fail.
error libmamba Selected channel specific (or force-reinstall) job, but package is not available from channel. Solve job will fail.
Encountered problems while solving:
- package 'bw2io-0.9.dev21-py_0' is excluded by strict repo priority
The environment can't be solved, aborting the operation
error libmamba Could not solve for environment specs
critical libmamba UnsatisfiableError
[LiteBuildApp] ERROR | [lite] [post_build] [jupyterlite-xeus-python] [ERR] Command '['/home/runner/micromamba-bin/micromamba', 'create', '--yes', '--root-prefix', '/tmp/xeus-python-kernel', '--name', 'xeus-python-kernel', '--platform=emscripten-32', '-c', 'https://repo.mamba.pm/emscripten-forge', '-c', 'https://repo.mamba.pm/conda-forge', '-c', 'https://conda.anaconda.org/conda-forge', '-c', 'nodefaults', 'python=3.10', 'xeus-lite', 'xeus-python=0.15.9', 'pandas', 'numpy', 'matplotlib', 'https://repo.mamba.pm/emscripten-forge::peewee', 'https://repo.mamba.pm/emscripten-forge::lxml', 'https://conda.anaconda.org/cmutel::bw2io=0.9.dev21', 'https://conda.anaconda.org/cmutel::bw2data=4.0.0.dev21', 'https://conda.anaconda.org/cmutel::bw2calc=1.0.dev13']' returned non-zero exit status 1.
Traceback (most recent call last):
File "/home/runner/micromamba-root/envs/build-env/lib/python3.10/site-packages/doit/doit_cmd.py", line 294, in run
return command.parse_execute(args)
File "/home/runner/micromamba-root/envs/build-env/lib/python3.10/site-packages/doit/cmd_base.py", line 150, in parse_execute
return self.execute(params, args)
File "/home/runner/micromamba-root/envs/build-env/lib/python3.10/site-packages/doit/cmd_base.py", line 570, in execute
return self._execute(**exec_params)
File "/home/runner/micromamba-root/envs/build-env/lib/python3.10/site-packages/doit/cmd_run.py", line 265, in _execute
return runner.run_all(self.control.task_dispatcher())
File "/home/runner/micromamba-root/envs/build-env/lib/python3.10/site-packages/doit/runner.py", line 254, in run_all
self.run_tasks(task_dispatcher)
File "/home/runner/micromamba-root/envs/build-env/lib/python3.10/site-packages/doit/runner.py", line 213, in run_tasks
node = task_dispatcher.generator.send(node)
File "/home/runner/micromamba-root/envs/build-env/lib/python3.10/site-packages/doit/control.py", line 629, in _dispatcher_generator
next_step = node.step()
File "/home/runner/micromamba-root/envs/build-env/lib/python3.10/site-packages/doit/control.py", line 336, in step
return next(self.generator)
File "/home/runner/micromamba-root/envs/build-env/lib/python3.10/site-packages/doit/control.py", line 345, in _func
for value in decorated(*args, **kwargs):
File "/home/runner/micromamba-root/envs/build-env/lib/python3.10/site-packages/doit/control.py", line 473, in _add_task
new_tasks = generate_tasks(to_load, task_gen, ref.__doc__)
File "/home/runner/micromamba-root/envs/build-env/lib/python3.10/site-packages/doit/loader.py", line 390, in generate_tasks
for task_dict, x_doc in flat_generator(gen_result, gen_doc):
File "/home/runner/micromamba-root/envs/build-env/lib/python3.10/site-packages/doit/loader.py", line 27, in flat_generator
for item in gen:
File "/home/runner/micromamba-root/envs/build-env/lib/python3.10/site-packages/jupyterlite_core/manager.py", line 145, in _delayed_gather
for task in _gather():
File "/home/runner/micromamba-root/envs/build-env/lib/python3.10/site-packages/jupyterlite_core/manager.py", line 138, in _gather
raise error
File "/home/runner/micromamba-root/envs/build-env/lib/python3.10/site-packages/jupyterlite_core/manager.py", line 128, in _gather
for task in getattr(addon, attr)(self):
File "/home/runner/micromamba-root/envs/build-env/lib/python3.10/site-packages/jupyterlite_xeus_python/env_build_addon.py", line 79, in post_build
env_prefix = build_and_pack_emscripten_env(
File "/home/runner/micromamba-root/envs/build-env/lib/python3.10/site-packages/jupyterlite_xeus_python/build.py", line 249, in build_and_pack_emscripten_env
raise e
File "/home/runner/micromamba-root/envs/build-env/lib/python3.10/site-packages/jupyterlite_xeus_python/build.py", line 193, in build_and_pack_emscripten_env
create_env(env_name, root_prefix, specs, channels)
File "/home/runner/micromamba-root/envs/build-env/lib/python3.10/site-packages/jupyterlite_xeus_python/build.py", line 69, in create_env
run(
File "/home/runner/micromamba-root/envs/build-env/lib/python3.10/subprocess.py", line 526, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['/home/runner/micromamba-bin/micromamba', 'create', '--yes', '--root-prefix', '/tmp/xeus-python-kernel', '--name', 'xeus-python-kernel', '--platform=emscripten-32', '-c', 'https://repo.mamba.pm/emscripten-forge', '-c', 'https://repo.mamba.pm/conda-forge', '-c', 'https://conda.anaconda.org/conda-forge', '-c', 'nodefaults', 'python=3.10', 'xeus-lite', 'xeus-python=0.15.9', 'pandas', 'numpy', 'matplotlib', 'https://repo.mamba.pm/emscripten-forge::peewee', 'https://repo.mamba.pm/emscripten-forge::lxml', 'https://conda.anaconda.org/cmutel::bw2io=0.9.dev21', 'https://conda.anaconda.org/cmutel::bw2data=4.0.0.dev21', 'https://conda.anaconda.org/cmutel::bw2calc=1.0.dev13']' returned non-zero exit status 1.
static:jupyter-lite.json
. pre_status:static:jupyter-lite.json
tarball: jupyterlite-app-0.1.1.tgz 7MB
output: /home/runner/work/brightway-hub/brightway-hub/dist
lite dir: /home/runner/work/brightway-hub/brightway-hub
apps:
sourcemaps: True
unused packages: True
archive:archive
contents:contents
lite:jupyter-lite.json
mathjax:status
mimetypes:jupyter-lite.json
serve:contents
settings:overrides
translation:translation
. status:archive:archive
. status:contents:contents
contents: 3 files
. status:lite:jupyter-lite.json
. status:mathjax:status
jupyter-server-mathjax: None
configured MathJax dir: /home/runner/work/brightway-hub/brightway-hub/traitlets.Undefined
effective MathJax dir: None
. status:mimetypes:jupyter-lite.json
filetypes: 26
. status:serve:contents
url: http://127.0.0.1:8000/
server: tornado
headers:
. status:settings:overrides
overrides.json: 0
. status:translation:translation
translation files: 0 files
static:output_dir
. pre_init:static:output_dir
static:unpack
. init:static:unpack
federated_extensions:copy:ext:jupyterlab_pygments
federated_extensions:copy:ext:@jupyterlite/xeus-python-kernel
. pre_build:federated_extensions:copy:ext:jupyterlab_pygments
. pre_build:federated_extensions:copy:ext:@jupyterlite/xeus-python-kernel
contents:copy:README.md
contents:copy:demo.ipynb
contents:copy:peewee_test.ipynb
lite:patch:jupyter-lite.json
translation:copy
. build:contents:copy:README.md
. build:contents:copy:demo.ipynb
. build:contents:copy:peewee_test.ipynb
. build:lite:patch:jupyter-lite.json
MERGED /home/runner/work/brightway-hub/brightway-hub/dist/jupyter-lite.json from [PosixPath('/home/runner/work/brightway-hub/brightway-hub/dist/jupyter-lite.json'), PosixPath('/home/runner/work/brightway-hub/brightway-hub/jupyter-lite.json')]
. build:translation:copy
contents:contents:.
federated_extensions:patch
jupyterlite-xeus-python:xeus:copy:ext:@jupyterlite/xeus-python-kernel
Error: Process completed with exit code 3.
For a working version, compare branch main of our repo.
For the broken version, compare branch environment_upgrade branch of our repo.
build-environment.yml (this breaks the site build):
name: build-env
channels:
- conda-forge
dependencies:
- python=3.10
- jupyter_server=2.7.1 # https://anaconda.org/conda-forge/jupyter_server/files
- jupyterlite-core==0.1.1 # https://anaconda.org/conda-forge/jupyterlite-core/files
- jupyterlite-xeus-python==0.9.0 # https://anaconda.org/conda-forge/jupyterlite-xeus-python/files
build-environment.yml (this works fine):
name: build-env
channels:
- conda-forge
dependencies:
- python=3.10
- jupyter_server=2.7.1 # https://anaconda.org/conda-forge/jupyter_server/files
- jupyterlite-core==0.1.1 # https://anaconda.org/conda-forge/jupyterlite-core/files
- pip
- pip:
- jupyterlite-xeus-python==0.8.1 # https://github.com/jupyterlite/xeus-python-kernel/releases
environment.yml:
name: xeus-python-kernel
channels:
- https://repo.mamba.pm/emscripten-forge # check packages at https://beta.mamba.pm/channels
- https://conda.anaconda.org/conda-forge
- nodefaults
dependencies:
# DATA SCIENCE
- pandas
- numpy
# PLOTTING
- matplotlib
# BRIGHTWAY DEPENDENCIES (NOT PURE PYTHON)
- https://repo.mamba.pm/emscripten-forge::peewee # required by Brightway
- https://repo.mamba.pm/emscripten-forge::lxml # required by Brightway
# BRIGHTWAY CORE
- https://conda.anaconda.org/cmutel::bw2io=0.9.dev21 # https://anaconda.org/cmutel/bw2io/files
- https://conda.anaconda.org/cmutel::bw2data=4.0.0.dev21 # https://anaconda.org/cmutel/bw2data/files
- https://conda.anaconda.org/cmutel::bw2calc=1.0.dev13 # https://anaconda.org/cmutel/bw2calc/files
Site build completes successfully.
0.1.1Version 16.6 (18615.3.12.11.2)Paste the output from your browser Javascript console here.
pathlib.Path('.').is_dir() incorrectly returns False when run in XPython kernel.
Since Pandas use is_dir() in file path checking, some Pandas I/O methods like DataFrame.to_csv() fails in XPython with the error Cannot save file into a non-existent directory: '.'
from pathlib import Path
Path('.').is_dir()FalseThe result of above cell should be True as it is in the Pyodide kernel.
I'm trying to use this jupyterlite addon in a custom jupyterlite deployment built via jupyterlite-sphinx. However, I'm struggling to get it working and I'm wondering if it's not related to the way this addon behaves with the ignore-sys-prefix JupyterLite setting. None of the values set below for this setting yields the expected results (I guess?).
My custom jupyter lite build is very similar to the example given in this documentation and the one used for the ipycanvas documentation. I use the following packages:
"XeusPythonEnv": {
"packages": ["numpy", "matplotlib", "ipytone", "jupyterlab_widgets", "traitlets", "traittypes", "ipywidgets"]
},
ignore-sys-prefix: trueNo xeus-python kernel visible in the list of kernels and no federated extension copied into the JupyterLite build
Content of build/html/lite/jupyter-lite.json:
{
"jupyter-config-data": {
"appName": "JupyterLite",
"appUrl": "./lab",
"appVersion": "0.1.0-beta.7",
"baseUrl": "./",
"faviconUrl": "./lab/favicon.ico",
"federated_extensions": [],
"fullLabextensionsUrl": "./extensions",
"fullMathjaxUrl": "https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js",
"fullStaticUrl": "./build",
"licensesUrl": "./lab/api/licenses",
"mathjaxConfig": "TeX-AMS_CHTML-full,Safe",
"preferredPath": "/"
},
"jupyter-lite-schema-version": 0
}%build/html/lite/extensions directory:@jupyterlite/xeus-python-kernel
ignore-sys-prefix: []xeus-python kernel visible in the list of kernels and all federated extensions installed in my environment copied into the JupyterLite build (which is not what I expect and which may have different versions than the versions installed in the xeus environment)
Content of build/html/lite/jupyter-lite.json:
{
"jupyter-config-data": {
"appName": "JupyterLite",
"appUrl": "./lab",
"appVersion": "0.1.0-beta.7",
"baseUrl": "./",
"faviconUrl": "./lab/favicon.ico",
"federated_extensions": [
{
"extension": "./extension",
"liteExtension": true,
"load": "static/remoteEntry.7363ca86b6eb68446da2.js",
"name": "@jupyterlite/xeus-python-kernel",
"style": "./style"
},
... all extensions from my jupyterlab env ...
],
"fullLabextensionsUrl": "./extensions",
"fullMathjaxUrl": "./static/jupyter_server_mathjax/MathJax.js",
"fullStaticUrl": "./build",
"licensesUrl": "./lab/api/licenses",
"mathjaxConfig": "TeX-AMS-MML_HTMLorMML-full,Safe",
"preferredPath": "/"
},
"jupyter-lite-schema-version": 0
}%build/html/lite/extensions directory:@jupyterlite/xeus-python-kernel
+ all extensions from my jupyterlab env
ignore-sys-prefix: ["jupyterlite-xeus-python"]Same results than with 2.
ignore-sys-prefix: ["federated_extensions"]No xeus-python kernel visible in the list of kernels and but the expected federated extensions are copied into the JupyterLite build
Content of build/html/lite/jupyter-lite.json:
{
"jupyter-config-data": {
"appName": "JupyterLite",
"appUrl": "./lab",
"appVersion": "0.1.0-beta.7",
"baseUrl": "./",
"faviconUrl": "./lab/favicon.ico",
"federated_extensions": [
{
"extension": "./extension",
"liteExtension": false,
"load": "static/remoteEntry.3421943a0ce73f10909d.js",
"name": "@jupyter-widgets/jupyterlab-manager"
},
{
"extension": "./extension",
"liteExtension": false,
"load": "static/remoteEntry.31dd2990580e09632145.js",
"name": "ipytone"
}
],
"fullLabextensionsUrl": "./extensions",
"fullMathjaxUrl": "./static/jupyter_server_mathjax/MathJax.js",
"fullStaticUrl": "./build",
"licensesUrl": "./lab/api/licenses",
"mathjaxConfig": "TeX-AMS-MML_HTMLorMML-full,Safe",
"preferredPath": "/"
},
"jupyter-lite-schema-version": 0
}%build/html/lite/extensions directory:@jupyterlite/xeus-python-kernel # although not all files are present (remoteEntry, etc.)
@jupyter-widgets
ipytone
xeus-python kernel visible in the list of kernels.XeusPythonEnv packages copied into the JupyterLite buildCurrently importing pandas gives the following warning:
/tmp/xeus-python-kernel/envs/xeus-python-kernel/lib/python3.10/site-packages/dateutil/zoneinfo/__init__.py:26: UserWarning: I/O error(44): No such file or directory
warnings.warn("I/O error({0}): {1}".format(e.errno, e.strerror))
This does not seem to be the case with Pyodide:
In this example the version is not exactly the same which might explain the difference (although unlikely?).
To make sure the new packages can be used correctly in the xeus python kernel, we should add a UI test that imports popular packages like scipy to make sure they work properly.
During the build, using this command in Miniforge, jupyter lite build --XeusPythonEnv.packages=ipyvuetify,ipywidgets,ipyflex, numpy, plotly, pandas I get the following error message (see below). I believe this is because of the settings on my company laptop that prohibits me from visiting the Anaconda website. Is there a way I could get around this issue?
emscripten-forge/emscrip Using cache
emscripten-forge/noarch Using cache
conda-forge/emscripten-3 [====================] (00m:00s) 404 Failed
pkgs/main/noarch [> ] (00m:08s) Failure when receiving data from the peer
pkgs/r/emscripten-32 [> ] (00m:08s) Failure when receiving data from the peer
pkgs/main/emscripten-32 [> ] (00m:08s) Failure when receiving data from the peer
pkgs/r/noarch [> ] (00m:07s) Failure when receiving data from the peer
pkgs/msys2/emscripten-32 [> ] (00m:07s) Failure when receiving data from the peer
pkgs/msys2/noarch [> ] (00m:07s) Failure when receiving data from the peer
conda-forge/noarch [ ] (00m:04s) 2 MB / ?? (236.52 KB/s)
ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "C:\Users\reddeda\AppData\Local\Continuum\miniconda3\lib\site-packages\conda\exceptions.py", line 1080, in __call__
return func(*args, **kwargs)
File "C:\Users\reddeda\AppData\Local\Continuum\miniconda3\lib\site-packages\mamba\mamba.py", line 898, in exception_converter
raise e
File "C:\Users\reddeda\AppData\Local\Continuum\miniconda3\lib\site-packages\mamba\mamba.py", line 892, in exception_converter
exit_code = _wrapped_main(*args, **kwargs)
File "C:\Users\reddeda\AppData\Local\Continuum\miniconda3\lib\site-packages\mamba\mamba.py", line 851, in _wrapped_main
result = do_call(args, p)
File "C:\Users\reddeda\AppData\Local\Continuum\miniconda3\lib\site-packages\mamba\mamba.py", line 732, in do_call
exit_code = install(args, parser, "install")
File "C:\Users\reddeda\AppData\Local\Continuum\miniconda3\lib\site-packages\mamba\mamba.py", line 515, in install
index = load_channels(pool, channels, repos)
File "C:\Users\reddeda\AppData\Local\Continuum\miniconda3\lib\site-packages\mamba\utils.py", line 106, in load_channels
use_cache=use_cache,
File "C:\Users\reddeda\AppData\Local\Continuum\miniconda3\lib\site-packages\mamba\utils.py", line 81, in get_index is_downloaded = dlist.download(True)
RuntimeError: Download error (56) Failure when receiving data from the peer [**https://repo.anaconda.com/pkgs/main/noarch/repodata.json**]
Received HTTP code 403 from proxy after CONNECT
When I tried to execute a simple Python code, "from IPython.display import display" on the xeus kernel, the code never succeeds forever.
The simple code should be succeeded.
Building a fresh JupyterLite site with nbformat as a dependency gives the following issue:
environment.yml with the following content:name: test
channels:
- https://repo.mamba.pm/emscripten-forge
- https://repo.mamba.pm/conda-forge
dependencies:
- nbformatpython -m pip install jupyterlite-xeus-pythonjupyter lite buildjupyter lite serveIt should be possible to import nbformat.
This came up when checking if plotly works with the xeus python kernel in JupyterLite:
import plotly.graph_objects as go
fig = go.Figure()
fig.add_trace(go.Scatter(y=[2, 1, 4, 3]))
fig.add_trace(go.Bar(y=[1, 4, 3, 2]))
fig.update_layout(title="Hello Figure")
fig.show()
cc. @psychemedia
Specifying an environment containing pip may result in unwanted errors:
name: xeus-python-kernel
channels:
- https://repo.mamba.pm/emscripten-forge
- https://repo.mamba.pm/conda-forge
dependencies:
- pip
We should take care of this case and drop pip from the list automatically.
We need to add some tests for the kernel:
It's seems that packing the environment with empack does not work on windows. We should add some CI on Windows and check this.
git clone https://github.com/yuvipanda/requirements
cd requirements
jupyter lite build . --output-dir _output --contents . --config jupyterlite_config.json
cd _output
python3 -m http.server 9000
Go to localhost:9000, see jupyterlite. Try to start the xpython kernel, it never starts. If you type print("hello world") it never runs.
The relevant part of the repo is jupyterlite_config.json, which is:
{
"XeusPythonEnv": {
"packages": ["numpy", "matplotlib", "ipyleaflet", "flask"]
}
}I can run python code, as well as install additional packages.
Output of pip list:
Package Version Editable project location
----------------------- ------------------ --------------------------------------
alembic 1.8.0
anyio 3.6.1
appnope 0.1.3
argon2-cffi 21.3.0
argon2-cffi-bindings 21.2.0
asttokens 2.0.5
async-generator 1.10
attrs 21.4.0
Babel 2.10.3
backcall 0.2.0
beautifulsoup4 4.11.1
binderhub 0.2.0+979.g2d15492
black 22.6.0
bleach 5.0.1
cachetools 5.2.0
certifi 2022.6.15
certipy 0.1.3
cffi 1.15.1
chardet 5.0.0
charset-normalizer 2.1.0
click 8.1.3
cloudpickle 2.1.0
commonmark 0.9.1
cryptography 37.0.2
debugpy 1.6.0
decorator 5.1.1
defusedxml 0.7.1
docker 5.0.3
docutils 0.18.1
doit 0.36.0
empack 0.7.1
entrypoints 0.4
escapism 1.0.1
executing 0.8.3
fastapi 0.78.0
fastjsonschema 2.15.3
flake8 4.0.1
google-auth 2.9.0
greenlet 1.1.2
h11 0.13.0
httptools 0.4.0
idna 3.3
importlib-metadata 4.12.0
ipykernel 6.15.0
ipython 8.4.0
ipython-genutils 0.2.0
iso8601 1.0.2
jedi 0.18.1
Jinja2 3.1.2
json5 0.9.8
jsonschema 4.6.1
jupyter-client 7.3.4
jupyter-core 4.10.0
jupyter-repo2docker 2022.2.0
jupyter-server 1.18.0
jupyter-telemetry 0.1.0
jupyterhub 2.3.1
jupyterlab 3.4.3
jupyterlab-pygments 0.2.2
jupyterlab-server 2.14.0
jupyterlite 0.1.0b10
jupyterlite-xeus-python 0.5.1
keyring 23.6.0
kubernetes 24.2.0
Mako 1.2.1
MarkupSafe 2.1.1
matplotlib-inline 0.1.3
mccabe 0.6.1
mistune 0.8.4
mypy-extensions 0.4.3
nbclassic 0.3.7
nbclient 0.6.6
nbconvert 6.5.0
nbformat 5.4.0
nest-asyncio 1.5.5
notebook 6.4.12
notebook-shim 0.1.0
oauthlib 3.2.0
packaging 21.3
pamela 1.0.0
pandocfilters 1.5.0
parso 0.8.3
pathspec 0.9.0
pexpect 4.8.0
pickleshare 0.7.5
pip 22.0.4
pkginfo 1.8.3
platformdirs 2.5.2
prometheus-client 0.14.1
prompt-toolkit 3.0.30
psutil 5.9.1
ptyprocess 0.7.0
pure-eval 0.2.2
pyasn1 0.4.8
pyasn1-modules 0.2.8
pycodestyle 2.8.0
pycparser 2.21
pydantic 1.9.1
pyflakes 2.4.0
Pygments 2.12.0
PyJWT 2.4.0
pyOpenSSL 22.0.0
pyparsing 3.0.9
pyrsistent 0.18.1
python-dateutil 2.8.2
python-dotenv 0.20.0
python-json-logger 2.0.2
pytz 2022.1
PyYAML 6.0
pyzmq 23.2.0
readme-renderer 35.0
repo2jupyterlite 0.1 /Users/yuvipanda/code/repo2jupyterlite
requests 2.28.1
requests-oauthlib 1.3.1
requests-toolbelt 0.9.1
rfc3986 2.0.0
rich 12.4.4
rsa 4.8
ruamel.yaml 0.17.21
ruamel.yaml.clib 0.2.6
semver 2.13.0
Send2Trash 1.8.0
setuptools 60.10.0
six 1.16.0
sniffio 1.2.0
soupsieve 2.3.2.post1
SQLAlchemy 1.4.39
stack-data 0.3.0
starlette 0.19.1
terminado 0.15.0
tinycss2 1.1.1
toml 0.10.2
tomli 2.0.1
tornado 6.1
traitlets 5.3.0
twine 4.0.1
typer 0.4.1
typing_extensions 4.3.0
urllib3 1.26.9
uvicorn 0.18.2
uvloop 0.16.0
versioneer 0.22
watchfiles 0.15.0
wcwidth 0.2.5
webencodings 0.5.1
websocket-client 1.3.3
websockets 10.3
wheel 0.37.1
zipp 3.8.0
Am not using conda or anything.
Paste the output from your browser Javascript console here.warning: Browser does not support creating object URLs. Built-in browser image decoding will not be available. [xpython_wasm.js:9:206004](http://localhost:9000/_output/extensions/@jupyterlite/xeus-python-kernel/static/xpython_wasm.js) make_xkernel 1 [xpython_wasm.js:9:52899](http://localhost:9000/_output/extensions/@jupyterlite/xeus-python-kernel/static/xpython_wasm.js) make_xkernel 2
As noticed in #181 (comment), there seems to be an issue with hatch not picking up the files listed in .gitignore.
As a result, they are not included in the wheel shared-data and cause issues like #177 since some files are missing.
#181 updated the .gitignore to narrow the scope of the ignored files, so they can be included in the wheel correctly.
However this feels a bit error-prone and it would be easy to get back to the same issue by adding new entries to the .gitignore.
Some next steps would be:
jupyterlite-xeus-python to make sure the kernel can at least without errorsOn the demo website the xeus-python files are a bit over 10MB in size:
This size can grow quite significantly as more packages are added by default. For example:
Not sure how feasible it is, but maybe there is a way to trim that down a little bit.
Also raised by @jasongrout in jupyter-widgets/ipywidgets#3491 (comment).
Package conflicts when trying a build by "jupyter lite build" command
Should be no error
jupyterlite-pyodide-kernel-piplite:patch jupyterlite-xeus-python:xeus:copy:ext:@jupyterlite/xeus-python-kernel Collecting package metadata (current_repodata.json): done Solving environment: donePackage Plan
environment location: /tmp/xeus-python-kernel/envs/xeus-python-kernel
Preparing transaction: done
Verifying transaction: done
Executing transaction: doneTo activate this environment, use
$ conda activate /tmp/xeus-python-kernel/envs/xeus-python-kernel
To deactivate an active environment, use
$ conda deactivate
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: |
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failedUnsatisfiableError: The following specifications were found to be incompatible with each other:
Output in format: Requested package -> Available versions
Package python conflicts for:
xeus-python -> ipython -> python[version='>=3.6|>=3.8|>=3.9']
pip -> python[version='>=3|>=3.6|>=3.7']
xeus-python -> python
jupyterlab -> async-lru[version='>=1.0.0'] -> python[version='>=2.7|>=3.4|>=3.9']
pip -> setuptools -> python[version='!=3.0,!=3.1,!=3.2,!=3.3,!=3.4|>=3.8|2.7.*|>=3.6']
jupyterlab -> python[version='>=3.5|>=3.6|>=3.7|>=3.8']Package packaging conflicts for:
jupyterlab -> packaging
jupyterlab -> jupyterlab_server[version='>=2.19.0,<3'] -> packaging[version='>=21.3']Package traitlets conflicts for:
jupyterlab -> ipykernel -> traitlets[version='>=4.2.1|>=5.1|>=5.3.0|>=5|>=5.1.0|>=5.4.0|>=5.6.0']
jupyterlab -> traitletsPackage stack_data conflicts for:
xeus-python -> ipython -> stack_data
jupyterlab -> ipython -> stack_dataPackage emscripten-abi conflicts for:
xeus-lite -> emscripten-abi=3.1.27
python=3.10 -> emscripten-abi=3.1.27
pip -> python[version='>=3.7'] -> emscripten-abi=3.1.27
xeus-python -> emscripten-abi=3.1.27
jupyterlab -> python[version='>=3.8'] -> emscripten-abi=3.1.27Package pyparsing conflicts for:
pip -> setuptools -> pyparsing
jupyterlab -> packaging -> pyparsing[version='<3,>=2.0.2|>=2.0.2,!=3.0.5|>=2.0.2,<3|>=2.0.2']Package wheel conflicts for:
pip -> wheel
jupyterlab -> jupyter-packaging[version='>=0.7,<1'] -> wheel
python=3.10 -> pip -> wheelPackage ipython conflicts for:
jupyterlab -> ipykernel -> ipython[version='>=7.23.1']
jupyterlab -> ipythonThe following specifications were found to be incompatible with your system:
Your installed version is: not available
[LiteBuildApp] ERROR | [lite] [post_build] [jupyterlite-xeus-python] [ERR] Command '['/Users/xxx/miniconda/condabin/conda', 'install', '--yes', '--prefix', PosixPath('/tmp/xeus-python-kernel/envs/xeus-python-kernel'), '-c', 'https://repo.mamba.pm/emscripten-forge', '-c', 'https://repo.mamba.pm/conda-forge', '-c', 'conda-forge', 'python=3.10', 'xeus-lite', 'xeus-python', 'python', 'pip', 'jupyterlab']' returned non-zero exit status 1.
Not sure this is the right place to report it, but the very recent deployments of jupyterlite + xeus-python-kernel (last version: 0.15.9) on RTD did not work for me. Jupyterlite is built and deployed without error but the xeus python kernel fails to start when visiting the web page (see browser output below).
Links to a deployment that is not working (using xeus-python 0.15.9):
Links to a deployment that is working (pinning xeus-python <=0.15.7):
No error when the xeus kernel is initialized.
The relevant console logs:
The error is raised here:
It seems that Safari is not working with the JupyterLite version based on the XEUS-Python kernel (even in a Private Window).
1+1
1+1
1+1 can be calculated on JL in Safari.
- python=3.10
- xeus-lite
- xeus-python=0.15.9
- ipycanvas
Paste the output from your browser Javascript console here.
agg, JypyterLite/XPython has trouble to show graphics inline
The workaround is to add %matplotlib inline, but this should not be necessary. BTW, this command just sets the Matplotlib backend.
There is a trick (explained below) how Pyodide kernel does it.
As explained in the description
Expected behavior is like JupyterLab/IPython behaves (in the above description)
Pyodide kernel paches the matplotlib.pyplot.show function in runtime to enable similar behavior
XPython kernel already behave properly when the Matplnotlib backend is inline since %matplotlib inline sets this backend. We only need to make the inline backend setted initialy.
Matplotlib uses the MPLBACKEND environment variable in the backend resolution
So, it should be enouth to add
os.environ["MPLBACKEND"] = 'module://matplotlib_inline.backend_inline'
somewhere early enough in the XPython kernel. I have tried to figure out where it could be, but I am not familiar how XPython kernel works. I have tested inside a notebook:
plt.show() should work without `
It would be really useful if there was a minimum viable example of adding the xeus-python-kernel to the JupyterLite demo site, along with an example of pre-installing two custom packages into the kernel.
cc. @benbovy
As discussed in geigr/ipytone#78 (comment) it would be nice to be able to install a dev install of a Python package inside of the xeus-python env.
cannot run xeus-python-kernel when installed via pip.
mamba create -n myenv python
mamba activate myenv
python -m pip install jupyterlite
python -m pip install jupyterlite-xeus-python
jupyter lite build
jupyter lite serve
xeus being available
Failed to load resource: the server responded with a status of 404 (File not found)
remoteEntry.9bcbbbb4e48c29cec308.js:1 Failed to load resource: the server responded with a status of 404 (File not found)
bootstrap.js:85 EventisTrusted: truebubbles: falsecancelBubble: falsecancelable: falsecomposed: falsecurrentTarget: nulldefaultPrevented: falseeventPhase: 0path: (5) [script, head, html, document, Window]returnValue: truesrcElement: scripttarget: scripttimeStamp: 128type: "error"[[Prototype]]: Event
(anonymous) @ bootstrap.js:85
8131.931d811.js:1 Failed to create module: package: @jupyterlite/xeus-python-kernel; module: ./extension
c @ 8131.931d811.js:1
8131.931d811.js:1 Uncaught (in promise) TypeError: Cannot read properties of undefined (reading 'get')
at c (8131.931d811.js:1)
at 8131.931d811.js:1
at Array.forEach ()
at f (8131.931d811.js:1)
8131.931d811.js:1 TypeError: Cannot read properties of undefined (reading 'get')
at c (8131.931d811.js:1)
at 8131.931d811.js:1
at Array.forEach ()
at f (8131.931d811.js:1)
(anonymous) @ 8131.931d811.js:1
:8000/api/contents/all.json:1 Failed to load resource: the server responded with a status of 404 (File not found)
It is said "Pyodide comes with a robust Javascript ⟺ Python foreign function interface so that you can freely mix these two languages in your code with minimal friction. " at https://pyodide.org/en/stable/ .
I am just wondering whether xeus-python has similar feature or plan to do so.
Please clarify.
Thank you in advance,
At the moment it can be confusing that packages must be specified explicitly in a XeusPythonEnv.packages list.
Folks familiar with Binder might expect dependencies installed in a build environment to also be available in the kernel.
The fact that there could be a mismatch between the frontend extension and the package in the kernel is the issue (for example with widgets).
This is already mentioned in the documentation in the case of the Pyodide kernel: https://jupyterlite.readthedocs.io/en/latest/howto/configure/simple_extensions.html#the-case-of-jupyter-widgets-and-custom-renderers
But also applies for the jupyterlite-xeus-python kernel.
For a site deployer, having a single environment.yml would make things more convenient.
It's not clear yet how this should be handle and whether the empack step in the xeus-python addon should accept a environment.yml as is.
The main issue will probably be packages required for the build (for example jupyterlab or jupyter-server to index content) don't need to be installed in the kernel.
cc @nthiery since we discussed this use case over a video call
Added the disabledExtensions option into the jupyter-lite.json to opt out two kernels(Pyodide and Web Worker) in the UI but it doesn't work.
I installed JupyterLite locally by https://jupyterlite.readthedocs.io/en/latest/quickstart/standalone.html.
I tried a hosting on the localhost URL with 8000 port by the command, "jupyter lite serve".
I found there are 3 kernels (Pyodide, Web Worker, XPython) in the main Launcher UI.
I added the disabledExtensions option into the jupyter-lite.json in the _output folder https://jupyterlite.readthedocs.io/en/latest/howto/configure/advanced/extensions.html#disabling-extensions-at-runtime.
"disabledExtensions": [
"@jupyterlite/javascript-kernel-extension",
"@jupyterlite/pyodide-kernel-extension"
]
Again I tried a hosting on the localhost URL with 8000 port by the command, "jupyter lite serve".
Two kernels(pyodide and javascript) should be disappeared in the UI. Only the xeus kernel should be there.
jupyter lite build gives me an odd error
conda create -y -n jlite-tuto python=3.11
conda activate jlite-tuto
pip install jupyterlite
pip install jupyterlab_server
pip install jupyterlite-xeus-python
mkdir foo
cd foo
jupyter lite init
jupyter lite buildand I'm getting this error (full log below)
ValueError: '/private/tmp/xeus-python-kernel/envs/xeus-python-kernel/lib/python3.10/site-packages' is not in the subpath of '/tmp/xeus-python-kernel/envs/xeus-python-kernel' OR one path is relative and the other is absolute.jupyter lite build
static:jupyter-lite.json
. pre_status:static:jupyter-lite.json
tarball: jupyterlite-app-0.1.0.tgz 7MB
output: /Users/myusername/git/jlite-tuto/foo/_output
lite dir: /Users/myusername/git/jlite-tuto/foo
apps:
sourcemaps: True
unused packages: True
archive:archive
contents:contents
jupyterlite-pyodide-kernel-pyodide:pyodide
lite:jupyter-lite.json
mathjax:status
mimetypes:jupyter-lite.json
serve:contents
settings:overrides
translation:translation
. status:archive:archive
[LiteBuildApp] No archive (yet): foo-jupyterlite.tgz
. status:contents:contents
contents: 0 files
. status:jupyterlite-pyodide-kernel-pyodide:pyodide
URL: None
archive: []
cache: 0 files
local: 0 files
. status:lite:jupyter-lite.json
[LiteBuildApp] jupyter-lite.(json|ipynb): 0 files
. status:mathjax:status
jupyter-server-mathjax: None
configured MathJax dir: /Users/myusername/git/jlite-tuto/foo/traitlets.Undefined
effective MathJax dir: None
. status:mimetypes:jupyter-lite.json
filetypes: 26
. status:serve:contents
url: http://127.0.0.1:8000/
server: tornado
headers:
. status:settings:overrides
overrides.json: 0
. status:translation:translation
translation files: 0 files
static:output_dir
-- pre_init:static:output_dir
static:unpack
-- init:static:unpack
federated_extensions:copy:ext:jupyterlab_pygments
federated_extensions:copy:ext:@jupyterlite/pyodide-kernel-extension
federated_extensions:copy:ext:@jupyterlite/xeus-python-kernel
federated_extensions:copy:ext:@jupyterlite/javascript-kernel-extension
. pre_build:federated_extensions:copy:ext:jupyterlab_pygments
. pre_build:federated_extensions:copy:ext:@jupyterlite/pyodide-kernel-extension
. pre_build:federated_extensions:copy:ext:@jupyterlite/xeus-python-kernel
. pre_build:federated_extensions:copy:ext:@jupyterlite/javascript-kernel-extension
translation:copy
. build:translation:copy
federated_extensions:patch
jupyterlite-pyodide-kernel-piplite:patch
jupyterlite-xeus-python:xeus:copy:ext:@jupyterlite/xeus-python-kernel
Collecting package metadata (current_repodata.json): done
Solving environment: done
Package Plan
environment location: /tmp/xeus-python-kernel/envs/xeus-python-kernel
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
To activate this environment, use
$ conda activate /tmp/xeus-python-kernel/envs/xeus-python-kernel
To deactivate an active environment, use
$ conda deactivate
Collecting package metadata (current_repodata.json): done
Solving environment: |
Warning: >10 possible package resolutions (only showing differing packages):
environment location: /tmp/xeus-python-kernel/envs/xeus-python-kernel
added / updated specs:
- python=3.10
- xeus-lite
- xeus-python=0.15.9
The following NEW packages will be INSTALLED:
asttokens conda-forge/noarch::asttokens-2.2.1-pyhd8ed1ab_0
backcall conda-forge/noarch::backcall-0.2.0-pyh9f0ad1d_0
backports conda-forge/noarch::backports-1.0-pyhd8ed1ab_3
backports.functoo~ conda-forge/noarch::backports.functools_lru_cache-1.6.5-pyhd8ed1ab_0
decorator conda-forge/noarch::decorator-5.1.1-pyhd8ed1ab_0
emscripten-abi emscripten-forge/noarch::emscripten-abi-3.1.27-hb0f4dca_6
executing conda-forge/noarch::executing-1.2.0-pyhd8ed1ab_0
ipython emscripten-forge/emscripten-32::ipython-8.14.0-py310h8bed8af_1
jedi conda-forge/noarch::jedi-0.18.2-pyhd8ed1ab_0
matplotlib-inline conda-forge/noarch::matplotlib-inline-0.1.6-pyhd8ed1ab_0
numpy emscripten-forge/emscripten-32::numpy-1.25.1-py310h6d2fff6_0
parso conda-forge/noarch::parso-0.8.3-pyhd8ed1ab_0
pexpect conda-forge/noarch::pexpect-4.8.0-pyh1a96a4e_2
pickleshare conda-forge/noarch::pickleshare-0.7.5-py_1003
pip conda-forge/noarch::pip-23.2.1-pyhd8ed1ab_0
prompt-toolkit conda-forge/noarch::prompt-toolkit-3.0.39-pyha770c72_0
ptyprocess conda-forge/noarch::ptyprocess-0.7.0-pyhd3deb0d_0
pure_eval conda-forge/noarch::pure_eval-0.2.2-pyhd8ed1ab_0
pygments conda-forge/noarch::pygments-2.15.1-pyhd8ed1ab_0
pyparsing conda-forge/noarch::pyparsing-3.1.0-pyhd8ed1ab_0
python emscripten-forge/emscripten-32::python-3.10.2-h_hash_26_cpython
requests-wasm-pol~ emscripten-forge/emscripten-32::requests-wasm-polyfill-0.3.0-h8bed8af_0
setuptools emscripten-forge/emscripten-32::setuptools-64.0.0-py310h8bed8af_0
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
stack_data conda-forge/noarch::stack_data-0.6.2-pyhd8ed1ab_0
traitlets conda-forge/noarch::traitlets-5.9.0-pyhd8ed1ab_0
wcwidth conda-forge/noarch::wcwidth-0.2.6-pyhd8ed1ab_0
wheel conda-forge/noarch::wheel-0.41.0-pyhd8ed1ab_0
xeus-lite emscripten-forge/emscripten-32::xeus-lite-1.0.1-hf0acc6b_0
xeus-python emscripten-forge/emscripten-32::xeus-python-0.15.9-h4d17c68_1
xeus-python-shell conda-forge/noarch::xeus-python-shell-0.6.0-pyhd8ed1ab_0
xeus-python-shell~ conda-forge/noarch::xeus-python-shell-raw-0.6.0-pyhd8ed1ab_0
Downloading and Extracting Packages
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
[LiteBuildApp] ERROR | [lite] [post_build] [jupyterlite-xeus-python] [ERR] '/private/tmp/xeus-python-kernel/envs/xeus-python-kernel/lib/python3.10/site-packages' is not in the subpath of '/tmp/xeus-python-kernel/envs/xeus-python-kernel' OR one path is relative and the other is absolute.
Traceback (most recent call last):
File "/Users/myusername/miniconda3/envs/jlite-tuto/lib/python3.11/site-packages/doit/doit_cmd.py", line 294, in run
return command.parse_execute(args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/myusername/miniconda3/envs/jlite-tuto/lib/python3.11/site-packages/doit/cmd_base.py", line 150, in parse_execute
return self.execute(params, args)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/myusername/miniconda3/envs/jlite-tuto/lib/python3.11/site-packages/doit/cmd_base.py", line 570, in execute
return self._execute(**exec_params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/myusername/miniconda3/envs/jlite-tuto/lib/python3.11/site-packages/doit/cmd_run.py", line 265, in _execute
return runner.run_all(self.control.task_dispatcher())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/myusername/miniconda3/envs/jlite-tuto/lib/python3.11/site-packages/doit/runner.py", line 254, in run_all
self.run_tasks(task_dispatcher)
File "/Users/myusername/miniconda3/envs/jlite-tuto/lib/python3.11/site-packages/doit/runner.py", line 213, in run_tasks
node = task_dispatcher.generator.send(node)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/myusername/miniconda3/envs/jlite-tuto/lib/python3.11/site-packages/doit/control.py", line 629, in _dispatcher_generator
next_step = node.step()
^^^^^^^^^^^
File "/Users/myusername/miniconda3/envs/jlite-tuto/lib/python3.11/site-packages/doit/control.py", line 336, in step
return next(self.generator)
^^^^^^^^^^^^^^^^^^^^
File "/Users/myusername/miniconda3/envs/jlite-tuto/lib/python3.11/site-packages/doit/control.py", line 345, in _func
for value in decorated(*args, **kwargs):
File "/Users/myusername/miniconda3/envs/jlite-tuto/lib/python3.11/site-packages/doit/control.py", line 473, in _add_task
new_tasks = generate_tasks(to_load, task_gen, ref.doc)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/myusername/miniconda3/envs/jlite-tuto/lib/python3.11/site-packages/doit/loader.py", line 390, in generate_tasks
for task_dict, x_doc in flat_generator(gen_result, gen_doc):
File "/Users/myusername/miniconda3/envs/jlite-tuto/lib/python3.11/site-packages/doit/loader.py", line 27, in flat_generator
for item in gen:
File "/Users/myusername/miniconda3/envs/jlite-tuto/lib/python3.11/site-packages/jupyterlite_core/manager.py", line 145, in _delayed_gather
for task in _gather():
File "/Users/myusername/miniconda3/envs/jlite-tuto/lib/python3.11/site-packages/jupyterlite_core/manager.py", line 138, in _gather
raise error
File "/Users/myusername/miniconda3/envs/jlite-tuto/lib/python3.11/site-packages/jupyterlite_core/manager.py", line 128, in _gather
for task in getattr(addon, attr)(self):
File "/Users/myusername/miniconda3/envs/jlite-tuto/lib/python3.11/site-packages/jupyterlite_xeus_python/env_build_addon.py", line 82, in post_build
env_prefix = build_and_pack_emscripten_env(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/myusername/miniconda3/envs/jlite-tuto/lib/python3.11/site-packages/jupyterlite_xeus_python/build.py", line 343, in build_and_pack_emscripten_env
raise e
File "/Users/myusername/miniconda3/envs/jlite-tuto/lib/python3.11/site-packages/jupyterlite_xeus_python/build.py", line 304, in build_and_pack_emscripten_env
pack_env(
File "/Users/myusername/miniconda3/envs/jlite-tuto/lib/python3.11/site-packages/empack/pack.py", line 143, in pack_env
included_files = filter_env(
^^^^^^^^^^^
File "/Users/myusername/miniconda3/envs/jlite-tuto/lib/python3.11/site-packages/empack/filter_env.py", line 113, in filter_env
for pkg_meta in iterate_env_pkg_meta(env_prefix):
File "/Users/myusername/miniconda3/envs/jlite-tuto/lib/python3.11/site-packages/empack/filter_env.py", line 69, in iterate_env_pkg_meta
for pkg_meta in iterate_pip_pkg_record(env_prefix):
File "/Users/myusername/miniconda3/envs/jlite-tuto/lib/python3.11/site-packages/empack/filter_env.py", line 20, in iterate_pip_pkg_record
relative_site_packages = site_packages.relative_to(env_prefix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/myusername/miniconda3/envs/jlite-tuto/lib/python3.11/pathlib.py", line 730, in relative_to
raise ValueError("{!r} is not in the subpath of {!r}"
ValueError: '/private/tmp/xeus-python-kernel/envs/xeus-python-kernel/lib/python3.10/site-packages' is not in the subpath of '/tmp/xeus-python-kernel/envs/xeus-python-kernel' OR one path is relative and the other is absolute.
I am using macos monterey 12.6.7, Intel processor
uname -a
Darwin zoi 21.6.0 Darwin Kernel Version 21.6.0: Thu Jun 8 23:57:12 PDT 2023; root:xnu-8020.240.18.701.6~1/RELEASE_X86_64 x86_64For some reason, this fails with an error in xeus-python but works in pyodide/pyolite:
import os
import pathlib
os.path.exists("/drive/idontexist")
pathlib.Path("/drive/idontexist").exists()
In xeus-python it prints:
---------------------------------------------------------------------------
OSError Traceback (most recent call last)
/tmp/xpython_42/3913635030.py in <cell line: 4>()
2 import pathlib
3 os.path.exists("/drive/idontexist")
----> 4 pathlib.Path("/drive/idontexist").exists()
/tmp/xeus-python-kernel/envs/xeus-python-kernel/lib/python3.10/pathlib.py in exists(self)
1286 """
1287 try:
-> 1288 self.stat()
1289 except OSError as e:
1290 if not _ignore_error(e):
/tmp/xeus-python-kernel/envs/xeus-python-kernel/lib/python3.10/pathlib.py in stat(self, follow_symlinks)
1093 os.stat() does.
1094 """
-> 1095 return self._accessor.stat(self, follow_symlinks=follow_symlinks)
1096
1097 def owner(self):
OSError: [Errno 28] Invalid argument: '/drive/idontexist'
I've just started migrating to the xeus-python-kernel and I'm experiencing some unusual behaviour with opening local files using pandas.
I was opening files distributed with the JupyterLite as expected, but then updated the kernel on Github Pages, reloaded the JupyterLite environment, restarted kernels etc and tried to load the same files in from the same notebooks, but now the pandas file reads report as FileNotFoundError [Errno 44] No such file or directory.
The data files are visible in the file browser.
If I open and save the data files as is, they are still not found when I try to load them in.
I could clear the cache / local storage of all files and try a clean start, but the files saved to storage include many changes and would rather not have to export all the files and update the original repo with the changes, or import the files back in. (In part, I'm trying to shakedown the environment for student use and find issues and workarounds before things go live.)
Are there any tricks I could try / debug steps I could take to help identify any glitches?
#167 added UI tests and this following TODO:
xeus-python-kernel/.eslintignore
Lines 9 to 10 in 886b9a4
We should consider removing it and making sure ESLint can run in the ui-tests folder too.
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