jupyter trying to modify /gnu/store

> export JUPYTER_PATH="${GUIX_PROFILE:-/gnu/store/ichrcarq2k4lhdmm2izc3f1xjbziz49v-profile}/share/jupyter${JUPYTER_PATH:+:}$JUPYTER_PATH"

> export JUPYTER_CONFIG_DIR="${GUIX_PROFILE:-/gnu/store/ichrcarq2k4lhdmm2izc3f1xjbziz49v-profile}/etc/jupyter${JUPYTER_CONFIG_DIR:+:}$JUPYTER_CONFIG_DIR"

> Dear all,

>

> yesterday I added jupyter to my profile and it worked perfectly

> fine. Overnight I shut down the computer and rebooted today.

> Now jupyter refuses to start with the messages below. It seems that

> jupyter-notebook tries to create directories (or modifiy them) in the location it

> is installed wich is mounted ro. I have no idea why this didn't happen

> yesterday but it seems that there is some misconfiguration somewhere...

>

> Cheers,

> Alex

>

> PS: same effect with jupyterlab from the guix-science channel.

>

> -------------------------------

> ~$ jupyter-notebook

> Traceback (most recent call last):

> File "/gnu/store/1v8dgchnis87a4p3g9i3j1ayv0dfr4ds-python-notebook-6.3.0/bin/.jupyter-notebook-real", line 11, in <module>

> load_entry_point('notebook==6.3.0', 'console_scripts', 'jupyter-notebook')()

> File "/gnu/store/8ncan0ipzb240h23fwfspdhrzkzdw277-python-jupyter-core-4.7.1/lib/python3.8/site-packages/jupyter_core/application.py", line 254, in launch_instance

> return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs)

> File "/gnu/store/i037rnmqzwcc7nrgcswzb8dcckfrngzp-python-traitlets-4.3.3/lib/python3.8/site-packages/traitlets/config/application.py", line 663, in launch_instance

> app.initialize(argv)

> File "/gnu/store/f7y0fd230nc6l2qwq58g7q26rlkwjkf3-python-decorator-5.0.9/lib/python3.8/site-packages/decorator.py", line 232, in fun

> return caller(func, *(extras + args), **kw)

> File "/gnu/store/i037rnmqzwcc7nrgcswzb8dcckfrngzp-python-traitlets-4.3.3/lib/python3.8/site-packages/traitlets/config/application.py", line 87, in catch_config_error

> return method(app, *args, **kwargs)

> File "/gnu/store/1v8dgchnis87a4p3g9i3j1ayv0dfr4ds-python-notebook-6.3.0/lib/python3.8/site-packages/notebook/notebookapp.py", line 2122, in initialize

> super().initialize(argv)

> File "/gnu/store/f7y0fd230nc6l2qwq58g7q26rlkwjkf3-python-decorator-5.0.9/lib/python3.8/site-packages/decorator.py", line 232, in fun

> return caller(func, *(extras + args), **kw)

> File "/gnu/store/i037rnmqzwcc7nrgcswzb8dcckfrngzp-python-traitlets-4.3.3/lib/python3.8/site-packages/traitlets/config/application.py", line 87, in catch_config_error

> return method(app, *args, **kwargs)

> File "/gnu/store/8ncan0ipzb240h23fwfspdhrzkzdw277-python-jupyter-core-4.7.1/lib/python3.8/site-packages/jupyter_core/application.py", line 229, in initialize

> self.migrate_config()

> File "/gnu/store/8ncan0ipzb240h23fwfspdhrzkzdw277-python-jupyter-core-4.7.1/lib/python3.8/site-packages/jupyter_core/application.py", line 155, in migrate_config

> migrate()

> File "/gnu/store/8ncan0ipzb240h23fwfspdhrzkzdw277-python-jupyter-core-4.7.1/lib/python3.8/site-packages/jupyter_core/migrate.py", line 244, in migrate

> ensure_dir_exists(env['jupyter_config'])

> File "/gnu/store/8ncan0ipzb240h23fwfspdhrzkzdw277-python-jupyter-core-4.7.1/lib/python3.8/site-packages/jupyter_core/utils/__init__.py", line 11, in ensure_dir_exists

> os.makedirs(path, mode=mode)

> File "/gnu/store/sd2ic7bpv8fx3imy1j8xcjclx71sv6q0-python-3.8.2/lib/python3.8/os.py", line 213, in makedirs

> makedirs(head, exist_ok=exist_ok)

> File "/gnu/store/sd2ic7bpv8fx3imy1j8xcjclx71sv6q0-python-3.8.2/lib/python3.8/os.py", line 213, in makedirs

> makedirs(head, exist_ok=exist_ok)

> File "/gnu/store/sd2ic7bpv8fx3imy1j8xcjclx71sv6q0-python-3.8.2/lib/python3.8/os.py", line 213, in makedirs

> makedirs(head, exist_ok=exist_ok)

> [Previous line repeated 7 more times]

> File "/gnu/store/sd2ic7bpv8fx3imy1j8xcjclx71sv6q0-python-3.8.2/lib/python3.8/os.py", line 223, in makedirs

> mkdir(name, mode)

> OSError: [Errno 30] Read-only file system: '/home/[user]/.guix-profile/etc/jupyter:'

> ------------------------------

>

> Message: 2

> Date: Sat, 27 Nov 2021 20:08:35 -0500

> From: jgart <jgart@dismail.de>

> To: 52139@debbugs.gnu.org

> Subject: bug#52139: (no subject)

> Message-ID: <20211127200835.GB7916@gac.attlocal.net>

> Content-Type: text/plain; charset=utf-8

>

>

> Hi Alex,

>

> Would you like to submit a patch to remove those environment variables from being set in the jupyter package?

>

>

> I found the cause:

>

> in ~/.guix-profile/etc/profile environment variables are set for jupyter:

>

>> export JUPYTER_PATH="${GUIX_PROFILE:-/gnu/store/ichrcarq2k4lhdmm2izc3f1xjbziz49v-profile}/share/jupyter${JUPYTER_PATH:+:}$JUPYTER_PATH"

>> export JUPYTER_CONFIG_DIR="${GUIX_PROFILE:-/gnu/store/ichrcarq2k4lhdmm2izc3f1xjbziz49v-profile}/etc/jupyter${JUPYTER_CONFIG_DIR:+:}$JUPYTER_CONFIG_DIR"

>

> The jupyter config path causes the problem, since jupyter tries to write

> into it (and it is located in a read only filesystem). Unsetting the

> environment variable solves the issue.

> Hi Alexander,

>

> Alexander Asteroth <alexander.asteroth@h-brs.de> skribis:

>

>> I found the cause:

>>

>> in ~/.guix-profile/etc/profile environment variables are set for jupyter:

>>

>>> export JUPYTER_PATH="${GUIX_PROFILE:-/gnu/store/ichrcarq2k4lhdmm2izc3f1xjbziz49v-profile}/share/jupyter${JUPYTER_PATH:+:}$JUPYTER_PATH"

>>> export JUPYTER_CONFIG_DIR="${GUIX_PROFILE:-/gnu/store/ichrcarq2k4lhdmm2izc3f1xjbziz49v-profile}/etc/jupyter${JUPYTER_CONFIG_DIR:+:}$JUPYTER_CONFIG_DIR"

>>

>> The jupyter config path causes the problem, since jupyter tries to write

>> into it (and it is located in a read only filesystem). Unsetting the

>> environment variable solves the issue.

>

> I can’t reproduce it with:

>

> $ guix describe

> Generacio 196 Dec 06 2021 11:23:08 (nuna)

> guix 9478a25

> repository URL: https://git.savannah.gnu.org/git/guix.git

> branch: master

> commit: 9478a252509a93f3e7f486cbc549631185ba071d

> $ guix shell jupyter -CN --no-cwd -- jupyter notebook

>

> Perhaps that’s because I didn’t trigger actions that would cause Jupyter

> to attempt to write to $JUPYTER_CONFIG_DIR?

>

> The JUPYTER_CONFIG_DIR search path was added to ‘python-jupyter-core’ in

> commit 1683e9d9677d54f695a54fc44ed309287989fc34. Lars, what are you

> thoughts?

>

> Thanks,

> Ludo’.

> I can’t reproduce it with: […]

> The JUPYTER_CONFIG_DIR search path was added to ‘python-jupyter-core’ in

> commit 1683e9d9677d54f695a54fc44ed309287989fc34. Lars, what are you

> thoughts?

> stat: cannot statx '/gnu/store/djb0y6kn86ijbvkx93q48q484krp1kbb-profile/etc/jupyter:/home/aster/.config/jupyter/migrated': No such file or directory

> Hi,

>

>> I can’t reproduce it with: […]

> I cannot reproduce it either and this migration should not happen™,

> because the phase 'disable-migration should disable it. (See

> /gnu/store/8ncan0ipzb240h23fwfspdhrzkzdw277-python-jupyter-core-4.7.1/lib/python3.8/site-packages/jupyter_core/application.py:145).

>

> Alexander: Does this file exists for you too?

>

> guix shell python-notebook -- sh -c "stat \$JUPYTER_CONFIG_DIR/migrated"

>

>> The JUPYTER_CONFIG_DIR search path was added to ‘python-jupyter-core’ in

>> commit 1683e9d9677d54f695a54fc44ed309287989fc34. Lars, what are you

>> thoughts?

> Please *do not* remove this environment variable. It is required, because

> packages like jupyterlab drop a config file into this directory. Without

> it the jupyterlab extension will not be loaded by default and a simple

> `guix shell python-jupyterlab -- jupyter lab` will not work.

>

> Cheers,

> Lars

>> The JUPYTER_CONFIG_DIR search path was added to ‘python-jupyter-core’ in

>> commit 1683e9d9677d54f695a54fc44ed309287989fc34. Lars, what are you

>> thoughts?

> Please *do not* remove this environment variable. It is required, because

> packages like jupyterlab drop a config file into this directory.

> But precisely: as Alexander wrote, when JUPYTER_CONFIG_DIR points to the

> store, jupyterlab cannot drop a config file there. Or am I missing

> something?

> BTW, if JUPYTER_CONFIG_DIR is meant to contain a directory name, as

> opposed to a colon-separated search path, we should make this change:

>> But precisely: as Alexander wrote, when JUPYTER_CONFIG_DIR points to the

>> store, jupyterlab cannot drop a config file there. Or am I missing

>> something?

> sorry, my message was unclear here. The config file is written at

> build time.

>> BTW, if JUPYTER_CONFIG_DIR is meant to contain a directory name, as

>> opposed to a colon-separated search path, we should make this change:

> Looking at the documentation[1] again this is correct, but I feel we

> should use JUPYTER_CONFIG_PATH instead, because it supports

> colon-delimited entries, see attached patch. However that does not get

> rid of error messages like these, when trying to use Settings→JupyterLab

> Theme for example:

>

> [W 08:10:14.476 LabApp] 500 PUT /lab/api/workspaces/lab?1639383014500 (127.0.0.1): [Errno 30] Read-only file system: '/gnu/store/8q7wdpdddfqh46plbbsa3rwci5092n5y-profile/etc/jupyter/lab'

>

> So it seems that JUPYTER_CONFIG_PATH overrides the default

> JUPYTER_CONFIG_DIR, when the latter is not set. Or maybe guix-science’s

> jupyterlab is simply too old – not sure right now.

> +++ b/gnu/packages/python-xyz.scm

> @@ -8478,7 +8478,7 @@ (define-public python-jupyter-core

> ;; search paths.

> (native-search-paths

> (list (search-path-specification

> - (variable "JUPYTER_CONFIG_DIR")

> + (variable "JUPYTER_CONFIG_PATH")

> (files '("etc/jupyter")))

> (search-path-specification

> (variable "JUPYTER_PATH")

> @@ -12145,8 +12145,6 @@ (define-public python-nbconvert

> (when tests?

> ;; Some tests invoke the installed nbconvert binary.

> (add-installed-pythonpath inputs outputs)

> - ;; Tries to write to this path.

> - (unsetenv "JUPYTER_CONFIG_DIR")

> ;; Tests depend on templates installed to output.

> (setenv "JUPYTER_PATH"

> (string-append

> @@ -12254,6 +12252,8 @@ (define-public python-notebook

> ;; Some tests do not expect all files to be installed in the

> ;; same directory, but JUPYTER_PATH contains multiple entries.

> (unsetenv "JUPYTER_PATH")

> + ;; Interferes with tests that check paths.

> + (unsetenv "JUPYTER_CONFIG_PATH")

> ;; Some tests need HOME

> (setenv "HOME" "/tmp")

> (with-directory-excursion "/tmp"

> If that works for you, go for it.

> [W 13:52:18.502 LabApp] 500 PUT /lab/api/workspaces/lab?1639227138494 (127.0.0.1): [Errno 30] Read-only file system: '[user]/.guix-profile/etc/jupyter/lab'