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Bug 2220422 - F39FailsToInstall: python3-pybids+plotting, python3-pybids+test, python3-pybids+tests, python3-pybids
Summary: F39FailsToInstall: python3-pybids+plotting, python3-pybids+test, python3-pybi...
Keywords:
Status: CLOSED ERRATA
Alias: None
Product: Fedora
Classification: Fedora
Component: python-pybids
Version: 39
Hardware: Unspecified
OS: Unspecified
unspecified
unspecified
Target Milestone: ---
Assignee: Ankur Sinha (FranciscoD)
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard: AcceptedFreezeException
: 2237541 (view as bug list)
Depends On: 2220239 2220279 2220356
Blocks: F39FailsToInstall PYTHON3.12 F39BetaFreezeException
TreeView+ depends on / blocked
 
Reported: 2023-07-05 19:18 UTC by Fedora Fails To Install
Modified: 2023-09-06 23:38 UTC (History)
5 users (show)

Fixed In Version: python-pybids-0.16.3-3.fc40 python-pybids-0.16.3-3.fc39
Doc Type: If docs needed, set a value
Doc Text:
Clone Of:
Environment:
Last Closed: 2023-09-06 23:38:54 UTC
Type: ---
Embargoed:


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System ID Private Priority Status Summary Last Updated
Github bids-standard pybids issues 1012 0 None open Python3.12: Test fails with ValueError 2023-07-26 13:23:23 UTC

Description Fedora Fails To Install 2023-07-05 19:18:23 UTC
Hello,

Please note that this comment was generated automatically by https://pagure.io/releng/blob/main/f/scripts/ftbfs-fti/follow-policy.py
If you feel that this output has mistakes, please open an issue at https://pagure.io/releng/

Your package (python-pybids) Fails To Install in Fedora 39:

can't install python3-pybids+plotting:
  - nothing provides python3.11dist(graphviz) needed by python3-pybids+plotting-0.16.1-2.fc39.noarch
  - nothing provides python(abi) = 3.11 needed by python3-pybids+plotting-0.16.1-2.fc39.noarch
  
can't install python3-pybids+test:
  - nothing provides python3.11dist(bsmschema) needed by python3-pybids+test-0.16.1-2.fc39.noarch
  - nothing provides python(abi) = 3.11 needed by python3-pybids+test-0.16.1-2.fc39.noarch
  - nothing provides python3.11dist(pytest) >= 3.3 needed by python3-pybids+test-0.16.1-2.fc39.noarch
  
can't install python3-pybids+tests:
  - nothing provides python(abi) = 3.11 needed by python3-pybids+tests-0.16.1-2.fc39.noarch
  
can't install python3-pybids:
  - nothing provides python(abi) = 3.11 needed by python3-pybids-0.16.1-2.fc39.noarch
  - nothing provides python3.11dist(numpy) >= 1.19 needed by python3-pybids-0.16.1-2.fc39.noarch
  - nothing provides python3.11dist(click) >= 8 needed by python3-pybids-0.16.1-2.fc39.noarch
  - nothing provides python3.11dist(scipy) >= 1.5 needed by python3-pybids-0.16.1-2.fc39.noarch
  - nothing provides python3.11dist(bids-validator) >= 1.11 needed by python3-pybids-0.16.1-2.fc39.noarch
  - nothing provides python3.11dist(num2words) >= 0.5.5 needed by python3-pybids-0.16.1-2.fc39.noarch
  - nothing provides python3.11dist(pandas) >= 0.25.2 needed by python3-pybids-0.16.1-2.fc39.noarch
  - nothing provides python3.11dist(sqlalchemy) >= 1.3.16 needed by python3-pybids-0.16.1-2.fc39.noarch
  
If you know about this problem and are planning on fixing it, please acknowledge so by setting the bug status to ASSIGNED. If you don't have time to maintain this package, consider orphaning it, so maintainers of dependent packages realize the problem.


If you don't react accordingly to the policy for FTBFS/FTI bugs (https://docs.fedoraproject.org/en-US/fesco/Fails_to_build_from_source_Fails_to_install/), your package may be orphaned in 8+ weeks.


P.S. The data was generated solely from koji buildroot, so it might be newer than the latest compose or the content on mirrors. To reproduce, use the koji/local repo only, e.g. in mock:

    $ mock -r fedora-39-x86_64 --config-opts mirrored=False install python3-pybids+plotting python3-pybids+test python3-pybids+tests python3-pybids


P.P.S. If this bug has been reported in the middle of upgrading multiple dependent packages, please consider using side tags: https://docs.fedoraproject.org/en-US/fesco/Updates_Policy/#updating-inter-dependent-packages

Thanks!

Comment 1 Fedora Fails To Install 2023-07-13 11:57:01 UTC
Hello,

Please note that this comment was generated automatically by https://pagure.io/releng/blob/main/f/scripts/ftbfs-fti/follow-policy.py
If you feel that this output has mistakes, please open an issue at https://pagure.io/releng/

This package fails to install and maintainers are advised to take one of the following actions:

 - Fix this bug and close this bugzilla once the update makes it to the repository.
   (The same script that posted this comment will eventually close this bugzilla
   when the fixed package reaches the repository, so you don't have to worry about it.)

or

 - Move this bug to ASSIGNED if you plan on fixing this, but simply haven't done so yet.

or

 - Orphan the package if you no longer plan to maintain it.


If you do not take one of these actions, the process at https://docs.fedoraproject.org/en-US/fesco/Fails_to_build_from_source_Fails_to_install/#_package_removal_for_long_standing_ftbfs_and_fti_bugs will continue.
This package may be orphaned in 7+ weeks.
This is the first reminder (step 3) from the policy.

Don't hesitate to ask for help on devel.org if you are unsure how to fix this bug.

Comment 2 Sandro 2023-07-26 13:23:24 UTC
Test failure:

=================================== FAILURES ===================================
_________ test_run_variable_collection_bad_length_to_df_all_dense_vars _________
run_coll_bad_length = <BIDSRunVariableCollection['PTval', 'RT', 'gain', 'loss', 'parametric gain', 'respcat', 'respnum', 'trial_type']>
    def test_run_variable_collection_bad_length_to_df_all_dense_vars(run_coll_bad_length):
    
        timing_cols = {'onset', 'duration'}
        entity_cols = {'subject', 'run', 'task',  'suffix', 'datatype'}
        cond_names = {'PTval', 'RT', 'gain', 'loss', 'parametric gain', 'respcat',
                      'respnum', 'trial_type'}
        md_names = {'TaskName', 'RepetitionTime', 'extension', 'SliceTiming'}
        condition = {'condition'}
        ampl = {'amplitude'}
    
        unif_coll = run_coll_bad_length.to_dense(sampling_rate=10)
    
>       df = unif_coll.to_df()
bids/variables/tests/test_collections.py:238: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
bids/variables/collections.py:625: in to_df
    return super().to_df(
bids/variables/collections.py:152: in to_df
    dfs = [v.to_df(True, True, timing=True) for v in variables]
bids/variables/variables.py:618: in to_df
    df['onset'] = self.timestamps.values.astype(float) / 1e+9
/usr/lib64/python3.12/site-packages/pandas/core/frame.py:3980: in __setitem__
    self._set_item(key, value)
/usr/lib64/python3.12/site-packages/pandas/core/frame.py:4174: in _set_item
    value = self._sanitize_column(value)
/usr/lib64/python3.12/site-packages/pandas/core/frame.py:4915: in _sanitize_column
    com.require_length_match(value, self.index)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
data = array([0.0000e+00, 1.0000e-01, 2.0000e-01, ..., 4.3206e+03, 4.3207e+03,
       4.3208e+03])
index = RangeIndex(start=0, stop=43210, step=1)
    def require_length_match(data, index: Index) -> None:
        """
        Check the length of data matches the length of the index.
        """
        if len(data) != len(index):
>           raise ValueError(
                "Length of values "
                f"({len(data)}) "
                "does not match length of index "
                f"({len(index)})"
            )
E           ValueError: Length of values (43209) does not match length of index (43210)
/usr/lib64/python3.12/site-packages/pandas/core/common.py:571: ValueError

I reported it upstream.

Comment 3 Fedora Release Engineering 2023-08-16 07:17:35 UTC
This bug appears to have been reported against 'rawhide' during the Fedora Linux 39 development cycle.
Changing version to 39.

Comment 4 Fedora Update System 2023-09-05 12:00:08 UTC
FEDORA-2023-7af62fc24a has been submitted as an update to Fedora 40. https://bodhi.fedoraproject.org/updates/FEDORA-2023-7af62fc24a

Comment 5 Fedora Update System 2023-09-05 12:01:37 UTC
FEDORA-2023-7af62fc24a has been pushed to the Fedora 40 stable repository.
If problem still persists, please make note of it in this bug report.

Comment 6 Fedora Update System 2023-09-05 12:02:29 UTC
FEDORA-2023-cae9a8b6f8 has been submitted as an update to Fedora 39. https://bodhi.fedoraproject.org/updates/FEDORA-2023-cae9a8b6f8

Comment 7 Miro Hrončok 2023-09-05 21:55:39 UTC
*** Bug 2237541 has been marked as a duplicate of this bug. ***

Comment 8 Fedora Update System 2023-09-06 01:32:42 UTC
FEDORA-2023-cae9a8b6f8 has been pushed to the Fedora 39 testing repository.
Soon you'll be able to install the update with the following command:
`sudo dnf upgrade --enablerepo=updates-testing --refresh --advisory=FEDORA-2023-cae9a8b6f8`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2023-cae9a8b6f8

See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.

Comment 9 František Zatloukal 2023-09-06 09:03:19 UTC
Discussed in ticket: https://pagure.io/fedora-qa/blocker-review/issue/1279

The decision to classify this bug as an AcceptedFreezeException was made:

"We usually pull in FTI fixes."

Comment 10 Fedora Update System 2023-09-06 23:38:54 UTC
FEDORA-2023-cae9a8b6f8 has been pushed to the Fedora 39 stable repository.
If problem still persists, please make note of it in this bug report.


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