From: Efraim Flashner <efraim@flashner.co.il>
To: Zelphir Kaltstahl <zelphirkaltstahl@posteo.de>
Cc: help-guix@gnu.org
Subject: Re: guix import error + New: setting up a jupyterlab environment
Date: Sun, 25 Oct 2020 10:52:31 +0200 [thread overview]
Message-ID: <20201025085231.GB984@E5400> (raw)
In-Reply-To: <98b5e8cc-6dd4-74f3-076a-934af5344c26@posteo.de>
[-- Attachment #1: Type: text/plain, Size: 40501 bytes --]
On Sat, Oct 24, 2020 at 09:42:13PM +0200, Zelphir Kaltstahl wrote:
> Hello Efraim!
>
> On 10/21/20 9:18 AM, Efraim Flashner wrote:
> > On Mon, Oct 19, 2020 at 11:12:35PM +0200, Zelphir Kaltstahl wrote:
> >> Meanwhile I have managed to run the jupyterlab-server tests, as
> >> described in more details here:
> >> https://github.com/jupyterlab/jupyterlab_server/issues/128
> >>
> >> Indeed, in version 1.2.0 the tests fail the same way they fail when I
> >> try to create my environment. This means the next thing to fix would
> >> probably be to use another version of jupyterlab-server. 1.2.0 is a tag
> >> in the jupyterlab-server repository, which _seems_ to be the latest
> >> "stable" version, before a lot of alpha, beta, and release-candidate
> >> versions follow.
> >>
> >> I guess I could switch the commit in my `jupyterlab.scm` file to point
> >> to a different one?
> >>
> >> I can change the version to `2.0.0rc1`, but I do not know how the
> >> checksum is calculated. The checksum is shorter than what I see on
> >> simply PyPI:
> >>
> >> https://files.pythonhosted.org/packages/79/43/5249be5ee741a93f3fa60823caf9a276cadc3103dae16d6e36cc534fefd8/jupyterlab_server-2.0.0rc1.tar.gz#sha256=733b149c5ab8e50ea5f2897c323047257060e7bf2dc0fa88663181427bec605d
> >>
> >> and base32 should only make it longer, not shorter.
> >>
> >> Can you explain how to switch a version manually and calculate the
> >> checksum to match another version?
> > For a tarball like the one at pythonhosted you'd download the file and
> > then run 'guix hash the-file'. If you're using a source code repository
> > then from the top level of the repo you'd run 'guix hash --exclude-vcs
> > --recursive .', or 'guix hash -rx .' for short. The hash layout that
> > Guix uses is the sha256 of the tarball base32 encoded, but with a change
> > in the letters used.
> >
> > For python packages you can specify a version number, so in this case
> > it'd be 'guix import pypi jupyterlab_server/2.0.0rc1'. Some other
> > importers us the '@' symbol to specify version number and I think some
> > don't support using other versions at all.
> >
> > I don't know how compatible different major versions of
> > jupyterlab-server are with each other, so I'd stick with 1.2.0 for now.
>
>
> This means however, that the check phase will fail, because of the
> failing tests in the jupyterlab_server repository on version 1.2.0.
>
> Unless there is a way to disable running those specific tests, I guess
> this means, that only getting the tests to pass in the jupyterlab_server
> repository will solve the problem?
>
I'd suggest starting with my suggestion from the other email, to try
using 'add-installed-pythonpath' to make sure the library is in the
PYTHONPATH. Perhaps that will help the tests pass.
> >> Regards,
> >> Zelphir
> >>
> >> On 10/19/20 8:19 PM, Zelphir Kaltstahl wrote:
> >>> Hello Efraim,
> >>>
> >>> Thanks for your patience! It seems with that I am getting quite far
> >>> (at least it feels like making progress, or even being close to have a
> >>> working environment), up to the "check phase". There some tests
> >>> failing in the "check phase". Here is what I am getting now,
> >>> regardless of whether I stick ("python-ipykernel" ,python-ipykernel)
> >>> in the native inputs or propagated inputs:
> >>>
> >>> ~~~~START~~~~
> >>> running install_egg_info
> >>> Copying jupyterlab_server.egg-info to /gnu/store/2h44ldpcqqd0q7hqpbcqdavcnbjsibfb-python-jupyterlab-server-1.2.0/lib/python3.8/site-packages/jupyterlab_server-1.2.0-py3.8.egg-info
> >>> running install_scripts
> >>> phase `install' succeeded after 0.3 seconds
> >>> starting phase `wrap'
> >>> find-files: /gnu/store/2h44ldpcqqd0q7hqpbcqdavcnbjsibfb-python-jupyterlab-server-1.2.0/bin: No such file or directory
> >>> find-files: /gnu/store/2h44ldpcqqd0q7hqpbcqdavcnbjsibfb-python-jupyterlab-server-1.2.0/sbin: No such file or directory
> >>> phase `wrap' succeeded after 0.0 seconds
> >>> starting phase `check'
> >>> running "python setup.py" with command "test" and parameters ()
> >>> running test
> >>> running egg_info
> >>> writing jupyterlab_server.egg-info/PKG-INFO
> >>> writing dependency_links to jupyterlab_server.egg-info/dependency_links.txt
> >>> writing requirements to jupyterlab_server.egg-info/requires.txt
> >>> writing top-level names to jupyterlab_server.egg-info/top_level.txt
> >>> reading manifest file 'jupyterlab_server.egg-info/SOURCES.txt'
> >>> reading manifest template 'MANIFEST.in'
> >>> warning: no previously-included files matching '*~' found anywhere in distribution
> >>> warning: no previously-included files matching '*.pyc' found anywhere in distribution
> >>> warning: no previously-included files matching '*.pyo' found anywhere in distribution
> >>> warning: no previously-included files matching '.git' found anywhere in distribution
> >>> warning: no previously-included files matching '.ipynb_checkpoints' found anywhere in distribution
> >>> writing manifest file 'jupyterlab_server.egg-info/SOURCES.txt'
> >>> running build_ext
> >>> test_get (jupyterlab_server.tests.test_settings_api.SettingsAPITest) ... ERROR
> >>> test_get_bad (jupyterlab_server.tests.test_settings_api.SettingsAPITest) ... ERROR
> >>> test_listing (jupyterlab_server.tests.test_settings_api.SettingsAPITest) ... ERROR
> >>> test_patch (jupyterlab_server.tests.test_settings_api.SettingsAPITest) ... ERROR
> >>> test_patch_bad_data (jupyterlab_server.tests.test_settings_api.SettingsAPITest) ... ERROR
> >>> test_patch_wrong_id (jupyterlab_server.tests.test_settings_api.SettingsAPITest) ... ERROR
> >>> test_bad_put (jupyterlab_server.tests.test_workspaces_api.WorkspacesAPITest) ... ERROR
> >>> test_blank_put (jupyterlab_server.tests.test_workspaces_api.WorkspacesAPITest) ... ERROR
> >>> test_delete (jupyterlab_server.tests.test_workspaces_api.WorkspacesAPITest) ... ERROR
> >>> test_get (jupyterlab_server.tests.test_workspaces_api.WorkspacesAPITest) ... ERROR
> >>> test_listing (jupyterlab_server.tests.test_workspaces_api.WorkspacesAPITest) ... ERROR
> >>> test_put (jupyterlab_server.tests.test_workspaces_api.WorkspacesAPITest) ... ERROR
> >>>
> >>> ======================================================================
> >>> ERROR: test_get (jupyterlab_server.tests.test_settings_api.SettingsAPITest)
> >>> ----------------------------------------------------------------------
> >>> Traceback (most recent call last):
> >>> File "/tmp/guix-build-python-jupyterlab-server-1.2.0.drv-0/jupyterlab_server-1.2.0/jupyterlab_server/tests/test_settings_api.py", line 31, in setUp
> >>> dst = os.path.join(self.lab_config.schemas_dir, '@jupyterlab')
> >>> AttributeError: 'SettingsAPITest' object has no attribute 'lab_config'
> >>>
> >>> ======================================================================
> >>> ERROR: test_get_bad (jupyterlab_server.tests.test_settings_api.SettingsAPITest)
> >>> ----------------------------------------------------------------------
> >>> Traceback (most recent call last):
> >>> File "/tmp/guix-build-python-jupyterlab-server-1.2.0.drv-0/jupyterlab_server-1.2.0/jupyterlab_server/tests/test_settings_api.py", line 31, in setUp
> >>> dst = os.path.join(self.lab_config.schemas_dir, '@jupyterlab')
> >>> AttributeError: 'SettingsAPITest' object has no attribute 'lab_config'
> >>>
> >>> ======================================================================
> >>> ERROR: test_listing (jupyterlab_server.tests.test_settings_api.SettingsAPITest)
> >>> ----------------------------------------------------------------------
> >>> Traceback (most recent call last):
> >>> File "/tmp/guix-build-python-jupyterlab-server-1.2.0.drv-0/jupyterlab_server-1.2.0/jupyterlab_server/tests/test_settings_api.py", line 31, in setUp
> >>> dst = os.path.join(self.lab_config.schemas_dir, '@jupyterlab')
> >>> AttributeError: 'SettingsAPITest' object has no attribute 'lab_config'
> >>>
> >>> ======================================================================
> >>> ERROR: test_patch (jupyterlab_server.tests.test_settings_api.SettingsAPITest)
> >>> ----------------------------------------------------------------------
> >>> Traceback (most recent call last):
> >>> File "/tmp/guix-build-python-jupyterlab-server-1.2.0.drv-0/jupyterlab_server-1.2.0/jupyterlab_server/tests/test_settings_api.py", line 31, in setUp
> >>> dst = os.path.join(self.lab_config.schemas_dir, '@jupyterlab')
> >>> AttributeError: 'SettingsAPITest' object has no attribute 'lab_config'
> >>>
> >>> ======================================================================
> >>> ERROR: test_patch_bad_data (jupyterlab_server.tests.test_settings_api.SettingsAPITest)
> >>> ----------------------------------------------------------------------
> >>> Traceback (most recent call last):
> >>> File "/tmp/guix-build-python-jupyterlab-server-1.2.0.drv-0/jupyterlab_server-1.2.0/jupyterlab_server/tests/test_settings_api.py", line 31, in setUp
> >>> dst = os.path.join(self.lab_config.schemas_dir, '@jupyterlab')
> >>> AttributeError: 'SettingsAPITest' object has no attribute 'lab_config'
> >>>
> >>> ======================================================================
> >>> ERROR: test_patch_wrong_id (jupyterlab_server.tests.test_settings_api.SettingsAPITest)
> >>> ----------------------------------------------------------------------
> >>> Traceback (most recent call last):
> >>> File "/tmp/guix-build-python-jupyterlab-server-1.2.0.drv-0/jupyterlab_server-1.2.0/jupyterlab_server/tests/test_settings_api.py", line 31, in setUp
> >>> dst = os.path.join(self.lab_config.schemas_dir, '@jupyterlab')
> >>> AttributeError: 'SettingsAPITest' object has no attribute 'lab_config'
> >>>
> >>> ======================================================================
> >>> ERROR: test_bad_put (jupyterlab_server.tests.test_workspaces_api.WorkspacesAPITest)
> >>> ----------------------------------------------------------------------
> >>> Traceback (most recent call last):
> >>> File "/tmp/guix-build-python-jupyterlab-server-1.2.0.drv-0/jupyterlab_server-1.2.0/jupyterlab_server/tests/test_workspaces_api.py", line 34, in setUp
> >>> dst = os.path.join(self.lab_config.workspaces_dir, item)
> >>> AttributeError: 'WorkspacesAPITest' object has no attribute 'lab_config'
> >>>
> >>> ======================================================================
> >>> ERROR: test_blank_put (jupyterlab_server.tests.test_workspaces_api.WorkspacesAPITest)
> >>> ----------------------------------------------------------------------
> >>> Traceback (most recent call last):
> >>> File "/tmp/guix-build-python-jupyterlab-server-1.2.0.drv-0/jupyterlab_server-1.2.0/jupyterlab_server/tests/test_workspaces_api.py", line 34, in setUp
> >>> dst = os.path.join(self.lab_config.workspaces_dir, item)
> >>> AttributeError: 'WorkspacesAPITest' object has no attribute 'lab_config'
> >>>
> >>> ======================================================================
> >>> ERROR: test_delete (jupyterlab_server.tests.test_workspaces_api.WorkspacesAPITest)
> >>> ----------------------------------------------------------------------
> >>> Traceback (most recent call last):
> >>> File "/tmp/guix-build-python-jupyterlab-server-1.2.0.drv-0/jupyterlab_server-1.2.0/jupyterlab_server/tests/test_workspaces_api.py", line 34, in setUp
> >>> dst = os.path.join(self.lab_config.workspaces_dir, item)
> >>> AttributeError: 'WorkspacesAPITest' object has no attribute 'lab_config'
> >>>
> >>> ======================================================================
> >>> ERROR: test_get (jupyterlab_server.tests.test_workspaces_api.WorkspacesAPITest)
> >>> ----------------------------------------------------------------------
> >>> Traceback (most recent call last):
> >>> File "/tmp/guix-build-python-jupyterlab-server-1.2.0.drv-0/jupyterlab_server-1.2.0/jupyterlab_server/tests/test_workspaces_api.py", line 34, in setUp
> >>> dst = os.path.join(self.lab_config.workspaces_dir, item)
> >>> AttributeError: 'WorkspacesAPITest' object has no attribute 'lab_config'
> >>>
> >>> ======================================================================
> >>> ERROR: test_listing (jupyterlab_server.tests.test_workspaces_api.WorkspacesAPITest)
> >>> ----------------------------------------------------------------------
> >>> Traceback (most recent call last):
> >>> File "/tmp/guix-build-python-jupyterlab-server-1.2.0.drv-0/jupyterlab_server-1.2.0/jupyterlab_server/tests/test_workspaces_api.py", line 34, in setUp
> >>> dst = os.path.join(self.lab_config.workspaces_dir, item)
> >>> AttributeError: 'WorkspacesAPITest' object has no attribute 'lab_config'
> >>>
> >>> ======================================================================
> >>> ERROR: test_put (jupyterlab_server.tests.test_workspaces_api.WorkspacesAPITest)
> >>> ----------------------------------------------------------------------
> >>> Traceback (most recent call last):
> >>> File "/tmp/guix-build-python-jupyterlab-server-1.2.0.drv-0/jupyterlab_server-1.2.0/jupyterlab_server/tests/test_workspaces_api.py", line 34, in setUp
> >>> dst = os.path.join(self.lab_config.workspaces_dir, item)
> >>> AttributeError: 'WorkspacesAPITest' object has no attribute 'lab_config'
> >>>
> >>> ----------------------------------------------------------------------
> >>> Ran 12 tests in 0.001s
> >>>
> >>> FAILED (errors=12)
> >>> Test failed: <unittest.runner.TextTestResult run=12 errors=12 failures=0>
> >>> error: Test failed: <unittest.runner.TextTestResult run=12 errors=12 failures=0>
> >>> command "python" "-c" "import setuptools, tokenize;__file__='setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\\r\\n', '\\n');f.close();exec(compile(code, __file__, 'exec'))" "test" failed with status 1
> >>> ~~~~~END~~~~~
> >>>
> >>> I have some thoughts about this:
> >>>
> >>> The Python error does not really tell me what is wrong. I don't know
> >>> why the `WorkspacesAPITest` does not have an attribute named `lab_config`.
> >>>
> >>> One can see, that those are all API tests. Since there were problems
> >>> in the previous step with network, perhaps it is a network thing here
> >>> as well? (Is network, even if localhost for testing, available in the
> >>> "check phase"?)
> >>>
> >>> It could also simply be, that some PyPI package has failing tests. I
> >>> don't know how one could then skip such tests.
> >>>
> >>> I guess I will summarize everything in the end and put it in a
> >>> repository as a kind of "guide", so that others can use it or learn
> >>> from the process.
> >>>
> >>> Regards,
> >>> Zelphir
> >>>
> >>> On 10/19/20 6:54 PM, Efraim Flashner wrote:
> >>>> It looks like you need to add python-ipykernel to native-inputs.
> >>>> Unless it's needed to run the program and not just for the test
> >>>> suite, in which case it should go in propagated-inputs. There's no
> >>>> network available in the build environment so it can't retrieve
> >>>> ipykernel while building.
> >>>>
> >>>>
> >>>> On October 19, 2020 2:31:53 PM UTC, Zelphir Kaltstahl
> >>>> <zelphirkaltstahl@posteo.de> wrote:
> >>>>
> >>>> Hello Efraim!
> >>>>
> >>>> Thank you! Your idea of replacing "-" with "_" seems to partially
> >>>> help:
> >>>>
> >>>> The package is downloaded and byte compiled. However, afterwards
> >>>> there is a problem, when it tries to copy the byte-compiled files
> >>>> in the "wrap phase" (comments inserted in some places):
> >>>>
> >>>> ~~~~START~~~~
> >>>> ### ... a lot of output before this ...
> >>>>
> >>>> byte-compiling /gnu/store/yr7q21bws1xgx3p2dy9cfdiknjpsajm6-python-jupyterlab-server-1.2.0/lib/python3.8/site-packages/jupyterlab_server/__init__.py to __init__.cpython-38.pyc
> >>>> byte-compiling /gnu/store/yr7q21bws1xgx3p2dy9cfdiknjpsajm6-python-jupyterlab-server-1.2.0/lib/python3.8/site-packages/jupyterlab_server/_version.py to _version.cpython-38.pyc
> >>>> byte-compiling /gnu/store/yr7q21bws1xgx3p2dy9cfdiknjpsajm6-python-jupyterlab-server-1.2.0/lib/python3.8/site-packages/jupyterlab_server/app.py to app.cpython-38.pyc
> >>>> byte-compiling /gnu/store/yr7q21bws1xgx3p2dy9cfdiknjpsajm6-python-jupyterlab-server-1.2.0/lib/python3.8/site-packages/jupyterlab_server/handlers.py to handlers.cpython-38.pyc
> >>>> byte-compiling /gnu/store/yr7q21bws1xgx3p2dy9cfdiknjpsajm6-python-jupyterlab-server-1.2.0/lib/python3.8/site-packages/jupyterlab_server/listings_handler.py to listings_handler.cpython-38.pyc
> >>>> byte-compiling /gnu/store/yr7q21bws1xgx3p2dy9cfdiknjpsajm6-python-jupyterlab-server-1.2.0/lib/python3.8/site-packages/jupyterlab_server/process.py to process.cpython-38.pyc
> >>>> byte-compiling /gnu/store/yr7q21bws1xgx3p2dy9cfdiknjpsajm6-python-jupyterlab-server-1.2.0/lib/python3.8/site-packages/jupyterlab_server/process_app.py to process_app.cpython-38.pyc
> >>>> byte-compiling /gnu/store/yr7q21bws1xgx3p2dy9cfdiknjpsajm6-python-jupyterlab-server-1.2.0/lib/python3.8/site-packages/jupyterlab_server/server.py to server.cpython-38.pyc
> >>>> byte-compiling /gnu/store/yr7q21bws1xgx3p2dy9cfdiknjpsajm6-python-jupyterlab-server-1.2.0/lib/python3.8/site-packages/jupyterlab_server/servertest.py to servertest.cpython-38.pyc
> >>>> byte-compiling /gnu/store/yr7q21bws1xgx3p2dy9cfdiknjpsajm6-python-jupyterlab-server-1.2.0/lib/python3.8/site-packages/jupyterlab_server/settings_handler.py to settings_handler.cpython-38.pyc
> >>>> byte-compiling /gnu/store/yr7q21bws1xgx3p2dy9cfdiknjpsajm6-python-jupyterlab-server-1.2.0/lib/python3.8/site-packages/jupyterlab_server/themes_handler.py to themes_handler.cpython-38.pyc
> >>>> byte-compiling /gnu/store/yr7q21bws1xgx3p2dy9cfdiknjpsajm6-python-jupyterlab-server-1.2.0/lib/python3.8/site-packages/jupyterlab_server/workspaces_handler.py to workspaces_handler.cpython-38.pyc
> >>>> byte-compiling /gnu/store/yr7q21bws1xgx3p2dy9cfdiknjpsajm6-python-jupyterlab-server-1.2.0/lib/python3.8/site-packages/jupyterlab_server/tests/__init__.py to __init__.cpython-38.pyc
> >>>> byte-compiling /gnu/store/yr7q21bws1xgx3p2dy9cfdiknjpsajm6-python-jupyterlab-server-1.2.0/lib/python3.8/site-packages/jupyterlab_server/tests/test_settings_api.py to test_settings_api.cpython-38.pyc
> >>>> byte-compiling /gnu/store/yr7q21bws1xgx3p2dy9cfdiknjpsajm6-python-jupyterlab-server-1.2.0/lib/python3.8/site-packages/jupyterlab_server/tests/test_workspaces_api.py to test_workspaces_api.cpython-38.pyc
> >>>> byte-compiling /gnu/store/yr7q21bws1xgx3p2dy9cfdiknjpsajm6-python-jupyterlab-server-1.2.0/lib/python3.8/site-packages/jupyterlab_server/tests/utils.py to utils.cpython-38.pyc
> >>>>
> >>>> ### ... seems byte-compiling went without problems, but not comes the problem ...
> >>>>
> >>>> running install_egg_info
> >>>> Copying jupyterlab_server.egg-info to /gnu/store/yr7q21bws1xgx3p2dy9cfdiknjpsajm6-python-jupyterlab-server-1.2.0/lib/python3.8/site-packages/jupyterlab_server-1.2.0-py3.8.egg-info
> >>>> running install_scripts
> >>>> phase `install' succeeded after 0.3 seconds
> >>>> starting phase `wrap'
> >>>> find-files: /gnu/store/yr7q21bws1xgx3p2dy9cfdiknjpsajm6-python-jupyterlab-server-1.2.0/bin: No such file or directory
> >>>> find-files: /gnu/store/yr7q21bws1xgx3p2dy9cfdiknjpsajm6-python-jupyterlab-server-1.2.0/sbin: No such file or directory
> >>>> phase `wrap' succeeded after 0.0 seconds
> >>>> starting phase `check'
> >>>> running "python setup.py" with command "test" and parameters ()
> >>>> running test
> >>>> Searching for ipykernel
> >>>> Reading https://pypi.org/simple/ipykernel/
> >>>> Download error on https://pypi.org/simple/ipykernel/: [Errno -2] Name or service not known -- Some packages may not be found!
> >>>> Couldn't find index page for 'ipykernel' (maybe misspelled?)
> >>>> Scanning index of all packages (this may take a while)
> >>>> Reading https://pypi.org/simple/
> >>>> Download error on https://pypi.org/simple/: [Errno -2] Name or service not known -- Some packages may not be found!
> >>>> No local packages or working download links found for ipykernel
> >>>> error: Could not find suitable distribution for Requirement.parse('ipykernel')
> >>>> command "python" "-c" "import setuptools, tokenize;__file__='setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\\r\\n', '\\n');f.close();exec(compile(code, __file__, 'exec'))" "test" failed with status 1
> >>>> ~~~~~END~~~~~
> >>>>
> >>>> So it seems, that while the download URL is corrected, there is
> >>>> another place, where Guix has an error now, resulting in a final
> >>>> error shown in command line:
> >>>>
> >>>> ~~~~START~~~~
> >>>> $ guix time-machine --channels=channels.scm -- environment --manifest=manifest.scm --load=jupyterlab.scm
> >>>> Updating channel 'guix' from Git repository at 'https://git.savannah.gnu.org/git/guix.git'...
> >>>> substitute: updating substitutes from 'https://ci.guix.gnu.org'... 100.0%
> >>>> The following derivations will be built:
> >>>> /gnu/store/wzmfn9m45bmsbrx094rv3lf3w0rpmw49-python-pytest-check-links-0.3.0.drv
> >>>> /gnu/store/96xf5mrg134mcsp01b0m1qs1lxkb401a-python-jupyterlab-server-1.2.0.drv
> >>>> /gnu/store/32a28hd7aainwn0hfsnf3blh8prmfz61-jupyterlab_server-1.2.0.tar.gz.drv
> >>>>
> >>>> 3,9 MB will be downloaded
> >>>> downloading from https://ci.guix.gnu.org/nar/lzip/54kpl9psx16jwic4gpnjwh44kim04wlk-python-notebook-5.7.4 ...
> >>>> python-notebook-5.7.4 3.7MiB 5.1MiB/s 00:01 [##################] 100.0%
> >>>>
> >>>> building /gnu/store/32a28hd7aainwn0hfsnf3blh8prmfz61-jupyterlab_server-1.2.0.tar.gz.drv...
> >>>> downloading from https://files.pythonhosted.org/packages/source/j/jupyterlab_server/jupyterlab_server-1.2.0.tar.gz ...
> >>>> building /gnu/store/wzmfn9m45bmsbrx094rv3lf3w0rpmw49-python-pytest-check-links-0.3.0.drv...
> >>>> building /gnu/store/96xf5mrg134mcsp01b0m1qs1lxkb401a-python-jupyterlab-server-1.2.0.drv...
> >>>> \ 'check' phasebuilder for `/gnu/store/96xf5mrg134mcsp01b0m1qs1lxkb401a-python-jupyterlab-server-1.2.0.drv' failed with exit code 1
> >>>> build of /gnu/store/96xf5mrg134mcsp01b0m1qs1lxkb401a-python-jupyterlab-server-1.2.0.drv failed
> >>>> View build log at '/var/log/guix/drvs/96/xf5mrg134mcsp01b0m1qs1lxkb401a-python-jupyterlab-server-1.2.0.drv.bz2'.
> >>>> guix environment: error: build of `/gnu/store/96xf5mrg134mcsp01b0m1qs1lxkb401a-python-jupyterlab-server-1.2.0.drv' failed
> >>>> ~~~~~END~~~~~
> >>>>
> >>>> Apparently ipykernel is not found, but when I visit
> >>>> https://pypi.org/simple/ipykernel/, I see packages there.
> >>>>
> >>>> From the logs:
> >>>>
> >>>> ~~~~START~~~~
> >>>> Download error on https://pypi.org/simple/ipykernel/: [Errno -2] Name or service not known -- Some packages may not be found!
> >>>> Couldn't find index page for 'ipykernel' (maybe misspelled?)
> >>>> ~~~~~END~~~~~
> >>>>
> >>>> Do I need to add another input in my `jupyterlab.scm`? (How?) Or
> >>>> perhaps I need to create a separate `ipykernel.scm` which
> >>>> contains the output of `guix import pypi --recursive ipykernel`?
> >>>>
> >>>> However, it somehow seems to fail for PyPI simple in general
> >>>> (from the logs again):
> >>>>
> >>>> ~~~~START~~~~
> >>>> Reading https://pypi.org/simple/
> >>>> Download error on https://pypi.org/simple/: [Errno -2] Name or service not known -- Some packages may not be found!
> >>>> No local packages or working download links found for ipykernel
> >>>> error: Could not find suitable distribution for Requirement.parse('ipykernel')
> >>>> command "python" "-c" "import setuptools, tokenize;__file__='setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\\r\\n', '\\n');f.close();exec(compile(code, __file__, 'exec'))" "test" failed with status 1
> >>>> ~~~~~END~~~~~
> >>>>
> >>>> Thanks,
> >>>> Zelphir
> >>>>
> >>>>
> >>>> On 10/18/20 6:35 PM, Efraim Flashner wrote:
> >>>>> On Sun, Oct 18, 2020 at 01:55:49PM +0200, Zelphir Kaltstahl wrote:
> >>>>>> Hello Guix Users, hello Zimoun and Tobias!
> >>>>>>
> >>>>>> Thanks for your information regarding the importer syntax thing.
> >>>>>>
> >>>>>> I continued trying to get a jupyterlab environment today.
> >>>>>>
> >>>>>> Here is what I did so far:
> >>>>>>
> >>>>>> (1) Create my manifest file:
> >>>>>>
> >>>>>> ~~~~START~~~~
> >>>>>> (specifications->manifest
> >>>>>> '("python"))
> >>>>>> ~~~~~END~~~~~
> >>>>>>
> >>>>>> (2) Create my channels file:
> >>>>>>
> >>>>>> ~~~~START~~~~
> >>>>>> $ guix describe --format=channels > channels.scm
> >>>>>> $ cat channels.scm
> >>>>>> (list (channel
> >>>>>> (name 'guix)
> >>>>>> (url "https://git.savannah.gnu.org/git/guix.git")
> >>>>>> (commit
> >>>>>> "6ca673b30dac281ba27a8dac242c0ac83e5e354b")
> >>>>>> (introduction
> >>>>>> (make-channel-introduction
> >>>>>> "9edb3f66fd807b096b48283debdcddccfea34bad"
> >>>>>> (openpgp-fingerprint
> >>>>>> "BBB0 2DDF 2CEA F6A8 0D1D E643 A2A0 6DF2 A33A 54FA")))))
> >>>>>> ~~~~~END~~~~~
> >>>>>>
> >>>>>> (3) Create my jupyterlab PyPI import file, this time around using the
> >>>>>> "/" instead of "@" for specifying the version:
> >>>>>>
> >>>>>> ~~~~START~~~~
> >>>>>> $ guix import pypi --recursive jupyterlab/2.1.5 > jupyterlab.scm
> >>>>>> ~~~~~END~~~~~
> >>>>>>
> >>>>>> (4) Add missing import expressions and add output expression at the end:
> >>>>>>
> >>>>>> ~~~~START~~~~
> >>>>>> ;; add module imports
> >>>>>> (use-modules
> >>>>>> (guix packages)
> >>>>>> (guix download)
> >>>>>> (guix build-system python)
> >>>>>> ((guix licenses) #:prefix license:)
> >>>>>> ;; use `guix environment --ad-hoc python-jinja2 -- guix package -A python-jinja2` to find the location of python-jinja2, which is gnu/packages/python-xyz.scm
> >>>>> This can be just 'guix package -A python-jinja2', no need for the
> >>>>> environment.
> >>>>>
> >>>>>> (gnu packages python-xyz)
> >>>>>> ;; for python-tornado
> >>>>>> (gnu packages python-web)
> >>>>>> ;; for python-pytest
> >>>>>> (gnu packages check))
> >>>>>>
> >>>>>> ;; QUESTION: Why are those required packages not imported by guix automatically?
> >>>>>> ;; QUESTION: Why are the manually imported packages not actually in files with their own name, but instead jinja2 -> python-xyz, tornado -> python-web, and pytest -> check?
> >>>>>> ;; QUESTION: Is my process of finding the files in which the packages are correct or just working by chance?
> >>>>>>
> >>>>>> (define-public python-jupyterlab-server
> >>>>>> (package
> >>>>>> (name "python-jupyterlab-server")
> >>>>>> (version "1.2.0")
> >>>>>> (source
> >>>>>> (origin
> >>>>>> (method url-fetch)
> >>>>>> (uri (pypi-uri "jupyterlab-server" version))
> >>>>>> (sha256
> >>>>>> (base32
> >>>>>> "132xby7531rbrjg9bqvsx86birr1blynjxy8gi5kcnb6x7fxjcal"))))
> >>>>>> (build-system python-build-system)
> >>>>>> (propagated-inputs
> >>>>>> `(("python-jinja2" ,python-jinja2)
> >>>>>> ("python-json5" ,python-json5)
> >>>>>> ("python-jsonschema" ,python-jsonschema)
> >>>>>> ("python-notebook" ,python-notebook)
> >>>>>> ("python-requests" ,python-requests)))
> >>>>>> (native-inputs
> >>>>>> `(("python-pytest" ,python-pytest)
> >>>>>> ("python-requests" ,python-requests)))
> >>>>>> (home-page "https://jupyter.org")
> >>>>>> (synopsis "JupyterLab Server")
> >>>>>> (description "JupyterLab Server")
> >>>>>> (license license:bsd-3)))
> >>>>>>
> >>>>>> (define-public python-jupyterlab
> >>>>>> (package
> >>>>>> (name "python-jupyterlab")
> >>>>>> (version "2.1.5")
> >>>>>> (source
> >>>>>> (origin
> >>>>>> (method url-fetch)
> >>>>>> (uri (pypi-uri "jupyterlab" version))
> >>>>>> (sha256
> >>>>>> (base32
> >>>>>> "162jn51cg36fsn4l2zhnb5n4nbkhm9wlv974ggcnmdij3i4r4yya"))))
> >>>>>> (build-system python-build-system)
> >>>>>> (propagated-inputs
> >>>>>> `(("python-jinja2" ,python-jinja2)
> >>>>>> ("python-jupyterlab-server"
> >>>>>> ,python-jupyterlab-server)
> >>>>>> ("python-notebook" ,python-notebook)
> >>>>>> ("python-tornado" ,python-tornado)))
> >>>>>> (native-inputs
> >>>>>> `(("python-pytest" ,python-pytest)
> >>>>>> ("python-pytest-check-links"
> >>>>>> ,python-pytest-check-links)
> >>>>>> ("python-requests" ,python-requests)
> >>>>>> ("python-virtualenv" ,python-virtualenv)
> >>>>>> ("python-wheel" ,python-wheel)))
> >>>>>> (home-page "http://jupyter.org")
> >>>>>> (synopsis
> >>>>>> "The JupyterLab notebook server extension.")
> >>>>>> (description
> >>>>>> "The JupyterLab notebook server extension.")
> >>>>>> (license license:bsd-3)))
> >>>>>>
> >>>>>> python-jupyterlab
> >>>>>> ~~~~~END~~~~~
> >>>>>>
> >>>>>> And as noted in the comments, I have 3 questions at this point:
> >>>>>>
> >>>>>> (Q1) Why are those required packages not imported by guix automatically?
> >>>>>> (My guess: This functionality simply has not yet been implemented.)
> >>>>>>
> >>>>>> (Q2) Why are the manually imported packages not actually in files with
> >>>>>> their own name, but instead jinja2 -> python-xyt, tornado -> python-web,
> >>>>>> and pytest -> check? Why not (gnu packages python pytest) for example?
> >>>>>>
> >>>>>> (Q3) Is my process of finding the files in which the packages are
> >>>>>> correct or just working by chance? Basically I am creating temporary
> >>>>>> environments, in which I then lookup "where would the package be
> >>>>>> installed" and then exit the temporary environment to use that
> >>>>>> information in my imported package file's import expressions /
> >>>>>> use-modules expression. This seems to be a bit of a convoluted process,
> >>>>>> though worth it, if it always works in the end.
> >>>>>>
> >>>>>> (4) Now I run my time-machine command:
> >>>>>>
> >>>>>> ~~~~START~~~~
> >>>>>> $ guix time-machine --channels=channels.scm -- environment --manifest=manifest.scm --load=jupyterlab.scm
> >>>>>> ~~~~~END~~~~~
> >>>>>>
> >>>>>> This take a moment and then I get an error (the full output is longer,
> >>>>>> but when running it multiple times, already successful steps are not all
> >>>>>> done repeatedly, so the output is then reduced to what fails):
> >>>>>>
> >>>>>> ~~~~START~~~~
> >>>>>> $ guix time-machine --channels=channels.scm -- environment --manifest=manifest.scm --load=jupyterlab.scm
> >>>>>> Updating channel 'guix' from Git repository at 'https://git.savannah.gnu.org/git/guix.git'...
> >>>>>> The following derivations will be built:
> >>>>>> /gnu/store/wzmfn9m45bmsbrx094rv3lf3w0rpmw49-python-pytest-check-links-0.3.0.drv
> >>>>>> /gnu/store/n9i421lrbwrr8d0947w5vma7rhy3iyba-python-jupyterlab-server-1.2.0.drv
> >>>>>> /gnu/store/s7jc2dbb0bnrahxklmszmpfv8klgw3sd-jupyterlab-server-1.2.0.tar.gz.drv
> >>>>>>
> >>>>>> 4,2 MB will be downloaded
> >>>>>> downloading from https://ci.guix.gnu.org/nar/lzip/2nahbs5v8q073gjmy224gk0h5lsh1kkw-python-nbconvert-5.0.0b1 ...
> >>>>>> python-nbconvert-5.0.0b1 301KiB 2.0MiB/s 00:00 [##################] 100.0%
> >>>>>>
> >>>>>> building /gnu/store/s7jc2dbb0bnrahxklmszmpfv8klgw3sd-jupyterlab-server-1.2.0.tar.gz.drv...
> >>>>>> |builder for `/gnu/store/s7jc2dbb0bnrahxklmszmpfv8klgw3sd-jupyterlab-server-1.2.0.tar.gz.drv' failed to produce output path `/gnu/store/92md7gh966n4fzj6al267lqq4xjx0ncf-jupyterlab-server-1.2.0.tar.gz'
> >>>>>> build of /gnu/store/s7jc2dbb0bnrahxklmszmpfv8klgw3sd-jupyterlab-server-1.2.0.tar.gz.drv failed
> >>>>>> View build log at '/var/log/guix/drvs/s7/jc2dbb0bnrahxklmszmpfv8klgw3sd-jupyterlab-server-1.2.0.tar.gz.drv.bz2'.
> >>>>>> cannot build derivation `/gnu/store/n9i421lrbwrr8d0947w5vma7rhy3iyba-python-jupyterlab-server-1.2.0.drv': 1 dependencies couldn't be built
> >>>>>> killing process 7384
> >>>>>> guix environment: error: build of `/gnu/store/n9i421lrbwrr8d0947w5vma7rhy3iyba-python-jupyterlab-server-1.2.0.drv' failed
> >>>>>> ~~~~~END~~~~~
> >>>>>>
> >>>>>> OK, an error, perhaps I can understand it. Lets look at that log file:
> >>>>>>
> >>>>>> ~~~~START~~~~
> >>>>>> $ cp /var/log/guix/drvs/s7/jc2dbb0bnrahxklmszmpfv8klgw3sd-jupyterlab-server-1.2.0.tar.gz.drv.bz2 .
> >>>>>> $ bzip2 --decompress jc2dbb0bnrahxklmszmpfv8klgw3sd-jupyterlab-server-1.2.0.tar.gz.drv.bz2
> >>>>>> $ cat jc2dbb0bnrahxklmszmpfv8klgw3sd-jupyterlab-server-1.2.0.tar.gz.drv
> >>>>>>
> >>>>>> Starting download of /gnu/store/92md7gh966n4fzj6al267lqq4xjx0ncf-jupyterlab-server-1.2.0.tar.gz
> >>>>>> From https://files.pythonhosted.org/packages/source/j/jupyterlab-server/jupyterlab-server-1.2.0.tar.gz...
> >>>>>> download failed "https://files.pythonhosted.org/packages/source/j/jupyterlab-server/jupyterlab-server-1.2.0.tar.gz" 404 "Not Found"
> >>>>>>
> >>>>>> Starting download of /gnu/store/92md7gh966n4fzj6al267lqq4xjx0ncf-jupyterlab-server-1.2.0.tar.gz
> >>>>>> From https://ci.guix.gnu.org/file/jupyterlab-server-1.2.0.tar.gz/sha256/132xby7531rbrjg9bqvsx86birr1blynjxy8gi5kcnb6x7fxjcal...
> >>>>>> download failed "https://ci.guix.gnu.org/file/jupyterlab-server-1.2.0.tar.gz/sha256/132xby7531rbrjg9bqvsx86birr1blynjxy8gi5kcnb6x7fxjcal" 404 "Not Found"
> >>>>>>
> >>>>>> Starting download of /gnu/store/92md7gh966n4fzj6al267lqq4xjx0ncf-jupyterlab-server-1.2.0.tar.gz
> >>>>>> From https://tarballs.nixos.org/sha256/132xby7531rbrjg9bqvsx86birr1blynjxy8gi5kcnb6x7fxjcal...
> >>>>>> download failed "https://tarballs.nixos.org/sha256/132xby7531rbrjg9bqvsx86birr1blynjxy8gi5kcnb6x7fxjcal" 404 "Not Found"
> >>>>>>
> >>>>>> Starting download of /gnu/store/92md7gh966n4fzj6al267lqq4xjx0ncf-jupyterlab-server-1.2.0.tar.gz
> >>>>>> From https://archive.softwareheritage.org/api/1/content/sha256:5431d9dde96659364b7cc877693d5d21e7b80cea7ae3959ecc2b87518e5f5d8c/raw/...
> >>>>>> download failed "https://archive.softwareheritage.org/api/1/content/sha256:5431d9dde96659364b7cc877693d5d21e7b80cea7ae3959ecc2b87518e5f5d8c/raw/" 404 "Not Found"
> >>>>>> failed to download "/gnu/store/92md7gh966n4fzj6al267lqq4xjx0ncf-jupyterlab-server-1.2.0.tar.gz" from "https://files.pythonhosted.org/packages/source/j/jupyterlab-server/jupyterlab-server-1.2.0.tar.gz"
> >>>>>> ~~~~~END~~~~~
> >>>>>>
> >>>>>> So it seems, that the jupyterlab-server file is simply not downloadable
> >>>>>> any longer!
> >>>>>>
> >>>>>> Trying using wget:
> >>>>>>
> >>>>>> ~~~~START~~~~
> >>>>>> $ wget https://files.pythonhosted.org/packages/source/j/jupyterlab-server/jupyterlab-server-1.2.0.tar.gz
> >>>>>> --2020-10-18 13:49:52-- https://files.pythonhosted.org/packages/source/j/jupyterlab-server/jupyterlab-server-1.2.0.tar.gz
> >>>>>> Resolving files.pythonhosted.org (files.pythonhosted.org)... 2a04:4e42:9::319, 151.101.37.63
> >>>>>> Connecting to files.pythonhosted.org (files.pythonhosted.org)|2a04:4e42:9::319|:443... failed: Connection refused.
> >>>>>> Connecting to files.pythonhosted.org (files.pythonhosted.org)|151.101.37.63|:443... connected.
> >>>>>> HTTP request sent, awaiting response... 404 Not Found
> >>>>>> 2020-10-18 13:49:53 ERROR 404: Not Found.
> >>>>>> ~~~~~END~~~~~
> >>>>>>
> >>>>>> So now I am out of ideas. It seems the file is not available any longer
> >>>>>> and the definition of jupyterlab needs to be updated somewhere, so that
> >>>>>> it does not try to download an old or non-existent version of
> >>>>>> jupyter-labserver. But how is this usually done? Can I specify it
> >>>>>> somewhere in one of the 3 files I have, or am I dependent on someone
> >>>>>> fixing the jupyterlab-server dependency / input for juypterlab?
> >>>>>>
> >>>>>> Thanks for your help so far! Tell me, if I need to provide any more
> >>>>>> information to solve the problem.
> >>>>> Try chaning the URL line to (uri (pypi-uri "jupyterlab_server" version)),
> >>>>> with an underscore (_). I don't have any special suggestions for knowing
> >>>>> that it should be an underscore instead of a dash. The best I have is
> >>>>> the output from 'guix import pypi jupyterlab-server:
> >>>>>
> >>>>> (ins)efraim@E5400 ~$ guix import pypi jupyterlab-server
> >>>>>
> >>>>> Starting download of /tmp/guix-file.ayJ41F
> >>>>> From https://files.pythonhosted.org/packages/92/54/5f321ca4cebfb644ac59eb21601b46a2ff9831ffe1b4e5a588f2a7e98d48/jupyterlab_server-1.2.0.tar.gz...
> >>>>> …er-1.2.0.tar.gz 22KiB 57KiB/s 00:00 [##################] 100.0%
> >>>>>
> >>>>>
> >>>>>
> >>>>>> Best regards,
> >>>>>> Zelphir
> >>>>>>
> >>>>>>
> >>>>>> On 10/16/20 2:25 PM, Tobias Geerinckx-Rice wrote:
> >>>>>>> Zelphir,
> >>>>>>>
> >>>>>>> Zelphir Kaltstahl 写道：
> >>>>>>>> $ guix import pypi 'jupyterlab@2.1.5' --recursive
> >>>>>>> It will work if you substitute ‘/’ for ‘@’. Yes, this is a happy
> >>>>>>> accident specific to the PyPI importer, and I'm sure you can guess why
> >>>>>>> it happens to work.
> >>>>>>>
> >>>>>>>>> guix import hackage mtl@2.1.3.1
> >>>>>>>> But that is in the "hackage" import section. Is the same not available
> >>>>>>>> for PyPI?
> >>>>>>> [...]
> >>>>>>>
> >>>>>>>> Do the various importers work differently?
> >>>>>>> Unfortunately so. It would be great(TM) if PACKAGE[@VERSION] were
> >>>>>>> standard. Each importer could handle it properly (e.g., by turning it
> >>>>>>> into "/") or return a friendlier ‘the foo importer does not yet
> >>>>>>> support versions’ error.
> >>>>>>>
> >>>>>>> I don't have the time, but this sounds like a good intermediate-level
> >>>>>>> hack for someone who does :-)
> >>>>>>>
> >>>>>>> Kind regards,
> >>>>>>>
> >>>>>>> T G-R
> >>>>>> --
> >>>>>> repositories: https://notabug.org/ZelphirKaltstahl
> >>>> --
> >>>> repositories: https://notabug.org/ZelphirKaltstahl
> >>>> --
> >>>> Sent from my Android device with K-9 Mail. Please excuse my brevity.
> >>> --
> >>> repositories: https://notabug.org/ZelphirKaltstahl
> >> --
> >> repositories: https://notabug.org/ZelphirKaltstahl
> Regards,
> Zelphir
>
> --
> repositories: https://notabug.org/ZelphirKaltstahl
>
>
--
Efraim Flashner <efraim@flashner.co.il> אפרים פלשנר
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next prev parent reply other threads:[~2020-10-25 8:53 UTC|newest]
Thread overview: 15+ messages / expand[flat|nested] mbox.gz Atom feed top
2020-10-16 11:50 guix import error Zelphir Kaltstahl
2020-10-16 12:19 ` zimoun
2020-10-16 12:25 ` Tobias Geerinckx-Rice
2020-10-16 13:51 ` zimoun
2020-10-18 11:55 ` guix import error + New: setting up a jupyterlab environment Zelphir Kaltstahl
2020-10-18 16:35 ` Efraim Flashner
2020-10-19 14:31 ` Zelphir Kaltstahl
2020-10-19 16:54 ` Efraim Flashner
2020-10-19 18:19 ` Zelphir Kaltstahl
2020-10-19 21:12 ` Zelphir Kaltstahl
2020-10-21 7:18 ` Efraim Flashner
2020-10-24 19:42 ` Zelphir Kaltstahl
2020-10-25 8:52 ` Efraim Flashner [this message]
2020-10-25 11:49 ` Zelphir Kaltstahl
2020-10-21 7:09 ` Efraim Flashner
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