python3Packages.pydicom: 2.1.1 -> 2.1.2 #107550

tfmoraes · 2020-12-24T22:48:30Z

Motivation for this change

Update Pydicom to 2.1.2 and fix #106262

Things done

tfmoraes · 2020-12-24T23:18:27Z

The only problem is with nitime but it's not because of Pydicom.

❯ nix-shell -p nixpkgs-review --run "nixpkgs-review pr 107550"                                                                                                
$ git -c fetch.prune=false fetch --force https://github.com/NixOS/nixpkgs master:refs/nixpkgs-review/0 pull/107550/head:refs/nixpkgs-review/1
remote: Enumerating objects: 26, done.
remote: Counting objects: 100% (26/26), done.
remote: Compressing objects: 100% (10/10), done.
remote: Total 31 (delta 17), reused 18 (delta 16), pack-reused 5
Unpacking objects: 100% (31/31), 52.75 KiB | 412.00 KiB/s, done.
From https://github.com/NixOS/nixpkgs
   a4d86d5425b..ae46445e624  master                -> refs/nixpkgs-review/0
   e78a2d39f0e..d27486656c3  refs/pull/107550/head -> refs/nixpkgs-review/1
$ git worktree add /home/thiago/.cache/nixpkgs-review/pr-107550/nixpkgs ae46445e62484b06e8e61acea54fda3e43a08252
Preparing worktree (detached HEAD ae46445e624)
HEAD is now at ae46445e624 Merge pull request #107540 from flokli/websocketpp-fix-cross
$ nix-env -f /home/thiago/.cache/nixpkgs-review/pr-107550/nixpkgs -qaP --xml --out-path --show-trace
$ git merge --no-commit d27486656c3ac589a68492d78d933e2b51fc86e8
Automatic merge went well; stopped before committing as requested
$ nix-env -f /home/thiago/.cache/nixpkgs-review/pr-107550/nixpkgs -qaP --xml --out-path --show-trace --meta
24 packages updated:
python3.7-dcmstack python3.7-dicom2nifti python3.7-dipy python3.7-heudiconv python3.7-nibabel python3.7-nilearn python3.7-nipy python3.7-nipype python3.7-nitime python3.7-pybids python37Packages.pydicom (2.1.1 → 2.1.2) python3.8-dicom2nifti python3.8-dipy python3.8-nibabel python3.8-nilearn python3.8-nipy python3.8-nipype python3.8-pybids python38Packages.pydicom (2.1.1 → 2.1.2) python3.9-dicom2nifti python3.9-dipy python3.9-nibabel python3.9-nipy python39Packages.pydicom (2.1.1 → 2.1.2)

$ nix --experimental-features nix-command build --no-link --keep-going --option build-use-sandbox relaxed -f /home/thiago/.cache/nixpkgs-review/pr-107550/build.nix
error: --- Error --- nix-daemon
builder for '/nix/store/s1fly98c55djaa0ynifdmsxm19xkzm5m-python3.7-nitime-0.8.1.drv' failed with exit code 1; last 10 log lines:
      format='%.2f')
  
  nitime/tests/test_viz.py::test_drawmatrix_channels
    /build/nitime-0.8.1/nitime/viz.py:351: MatplotlibDeprecationWarning: The 'norm' parameter to Colorbar has no effect because it is overridden by the mappable; it is deprecated since 3.3 and will be removed two minor releases later.
      format='%.2f')
  
  -- Docs: https://docs.pytest.org/en/stable/warnings.html
  =========================== short test summary info ============================
  FAILED nitime/tests/test_utils.py::test_detect_lines - AssertionError: Harmon...
  ================== 1 failed, 67 passed, 7 warnings in 24.54s ===================
error: --- Error ----------------------------------------------------------------------------------------------------------------------------------------- nix
1 dependencies of derivation '/nix/store/q6y6ka8imn6lqvxsa26xsxsym7mc3vwn-env.drv' failed to build

Link to currently reviewing PR:
https://github.com/NixOS/nixpkgs/pull/107550

1 package failed to build:
python37Packages.nitime

23 packages built:
python37Packages.dcmstack python37Packages.dicom2nifti python37Packages.dipy python37Packages.heudiconv python37Packages.nibabel python37Packages.nilearn python37Packages.nipy python37Packages.nipype python37Packages.pybids python37Packages.pydicom python38Packages.dicom2nifti python38Packages.dipy python38Packages.nibabel python38Packages.nilearn python38Packages.nipy python38Packages.nipype python38Packages.pybids python38Packages.pydicom python39Packages.dicom2nifti python39Packages.dipy python39Packages.nibabel python39Packages.nipy python39Packages.pydicom

pkgs/development/python-modules/pydicom/default.nix

SuperSandro2000 · 2020-12-25T00:44:26Z

Result of nixpkgs-review pr 107550 run on x86_64-linux 1

24 packages built:

python37Packages.dcmstack
python37Packages.dicom2nifti
python37Packages.dipy
python37Packages.heudiconv
python37Packages.nibabel
python37Packages.nilearn
python37Packages.nipy
python37Packages.nipype
python37Packages.nitime
python37Packages.pybids
python37Packages.pydicom
python38Packages.dicom2nifti
python38Packages.dipy
python38Packages.nibabel
python38Packages.nilearn
python38Packages.nipy
python38Packages.nipype
python38Packages.pybids
python38Packages.pydicom
python39Packages.dicom2nifti
python39Packages.dipy
python39Packages.nibabel
python39Packages.nipy
python39Packages.pydicom

SuperSandro2000 · 2020-12-25T01:52:25Z

Result of nixpkgs-review pr 107550 run on x86_64-darwin 1

3 packages failed to build:

python37Packages.nitime
python38Packages.nipype
python39Packages.nipype

22 packages built:

python37Packages.dcmstack
python37Packages.dicom2nifti
python37Packages.dipy
python37Packages.heudiconv
python37Packages.nibabel
python37Packages.nilearn
python37Packages.nipy
python37Packages.nipype
python37Packages.pybids
python37Packages.pydicom
python38Packages.dicom2nifti
python38Packages.dipy
python38Packages.nibabel
python38Packages.nilearn
python38Packages.nipy
python38Packages.pybids
python38Packages.pydicom
python39Packages.dicom2nifti
python39Packages.dipy
python39Packages.nibabel
python39Packages.nipy
python39Packages.pydicom

tfmoraes · 2020-12-26T20:12:29Z

@SuperSandro2000 thanks! Please, can you try to build nitime and nipype in Mac with the previous version of Pydicom? I think it'll not work because Pydicom wasn't building before.

SuperSandro2000 · 2020-12-27T01:19:44Z

@SuperSandro2000 thanks! Please, can you try to build nitime and nipype in Mac with the previous version of Pydicom? I think it'll not work because Pydicom wasn't building before.

They are also broken on master.

pkgs/development/python-modules/pydicom/default.nix

rmcgibbo · 2020-12-31T06:38:32Z

It looks like I made a near-exact dupe of this: #107864

tfmoraes · 2020-12-31T18:10:57Z

Before pydicom-data in my derivation was pointing to master. After seeing @rmcgibbo now the my derivation is pointing to explicitaly to a commit revision like in the @rmcgibbo derivation.

pkgs/development/python-modules/pydicom/default.nix

SuperSandro2000 · 2020-12-31T23:17:09Z

This is a semi-automatic executed nixpkgs-review. If you find some bugs or got suggestions for further things to search or run please reach out to SuperSandro2000 on IRC.

Result of nixpkgs-review pr 107550 run on x86_64-linux 1

1 packages failed to build and are new build failures:

python37Packages.heudiconv
python37Packages.nilearn
python37Packages.nipype
python37Packages.pybids
python38Packages.nilearn
python38Packages.nipype
python38Packages.pybids

17 packages built:

python37Packages.dcmstack
python37Packages.dicom2nifti
python37Packages.dipy
python37Packages.nibabel
python37Packages.nipy
python37Packages.nitime
python37Packages.pydicom
python38Packages.dicom2nifti
python38Packages.dipy
python38Packages.nibabel
python38Packages.nipy
python38Packages.pydicom
python39Packages.dicom2nifti
python39Packages.dipy
python39Packages.nibabel
python39Packages.nipy
python39Packages.pydicom

cfn-lint

/build/source/test/unit/rules/functions/test_sub_needed.py:30: DeprecationWarning: invalid escape sequence \$

tfmoraes · 2020-12-31T23:20:02Z

@SuperSandro2000 cfn-lint is not building because of a bug. This bug was already post and is being fixed by @rmcgibbo in #108079

tfmoraes · 2021-01-01T21:57:17Z

I rebased to the master after the merge of the PR that fixes cfn-lint, now everything is building correctly:

❯ nix-shell -p nixpkgs-review --run "nixpkgs-review pr 107550"                                                                                                             
$ git -c fetch.prune=false fetch --force https://github.com/NixOS/nixpkgs master:refs/nixpkgs-review/0 pull/107550/head:refs/nixpkgs-review/1
From https://github.com/NixOS/nixpkgs
   5a214b6b687..f0e774407c3  master                -> refs/nixpkgs-review/0
 + bf3a52ae0a7...4553efaedd2 refs/pull/107550/head -> refs/nixpkgs-review/1  (forced update)
$ git worktree add /home/thiago/.cache/nixpkgs-review/pr-107550-3/nixpkgs f0e774407c3ce6ac41d79a5a564a9265b6efc600
Preparing worktree (detached HEAD f0e774407c3)
HEAD is now at f0e774407c3 Merge pull request #108141 from AndersonTorres/update-wio
$ nix-env -f /home/thiago/.cache/nixpkgs-review/pr-107550-3/nixpkgs -qaP --xml --out-path --show-trace
$ git merge --no-commit 4553efaedd2e0f209daa75eca77559eca8b2099d
Updating f0e774407c3..4553efaedd2
Fast-forward
 pkgs/development/python-modules/pydicom/default.nix | 48 +++++++++++++++++++++++++++++++++++++-----------
 1 file changed, 37 insertions(+), 11 deletions(-)
$ nix-env -f /home/thiago/.cache/nixpkgs-review/pr-107550-3/nixpkgs -qaP --xml --out-path --show-trace --meta
24 packages updated:
python3.7-dcmstack python3.7-dicom2nifti python3.7-dipy python3.7-heudiconv python3.7-nibabel python3.7-nilearn python3.7-nipy python3.7-nipype python3.7-nitime python3.7-pybids python37Packages.pydicom (2.1.1 → 2.1.2) python3.8-dicom2nifti python3.8-dipy python3.8-nibabel python3.8-nilearn python3.8-nipy python3.8-nipype python3.8-pybids python38Packages.pydicom (2.1.1 → 2.1.2) python3.9-dicom2nifti python3.9-dipy python3.9-nibabel python3.9-nipy python39Packages.pydicom (2.1.1 → 2.1.2)

$ nix --experimental-features nix-command build --no-link --keep-going --option build-use-sandbox relaxed -f /home/thiago/.cache/nixpkgs-review/pr-107550-3/build.nix

Link to currently reviewing PR:
https://github.com/NixOS/nixpkgs/pull/107550

24 packages built:
python37Packages.dcmstack python37Packages.dicom2nifti python37Packages.dipy python37Packages.heudiconv python37Packages.nibabel python37Packages.nilearn python37Packages.nipy python37Packages.nipype python37Packages.nitime python37Packages.pybids python37Packages.pydicom python38Packages.dicom2nifti python38Packages.dipy python38Packages.nibabel python38Packages.nilearn python38Packages.nipy python38Packages.nipype python38Packages.pybids python38Packages.pydicom python39Packages.dicom2nifti python39Packages.dipy python39Packages.nibabel python39Packages.nipy python39Packages.pydicom

$ nix-shell /home/thiago/.cache/nixpkgs-review/pr-107550-3/shell.nix

SuperSandro2000 · 2021-01-02T16:37:56Z

This is a semi-automatic executed nixpkgs-review which does not build all packages (e.g. lumo, tensorflow or torch)
If you find some bugs or got suggestions for further things to search or run please reach out to SuperSandro2000 on IRC.

Result of nixpkgs-review pr 107550 run on x86_64-linux 1

24 packages built:

python37Packages.dcmstack
python37Packages.dicom2nifti
python37Packages.dipy
python37Packages.heudiconv
python37Packages.nibabel
python37Packages.nilearn
python37Packages.nipy
python37Packages.nipype
python37Packages.nitime
python37Packages.pybids
python37Packages.pydicom
python38Packages.dicom2nifti
python38Packages.dipy
python38Packages.nibabel
python38Packages.nilearn
python38Packages.nipy
python38Packages.nipype
python38Packages.pybids
python38Packages.pydicom
python39Packages.dicom2nifti
python39Packages.dipy
python39Packages.nibabel
python39Packages.nipy
python39Packages.pydicom

SuperSandro2000 · 2021-01-04T11:20:36Z

This is a semi-automatic executed nixpkgs-review which does not build all packages (e.g. lumo, tensorflow or pytorch)
If you find some bugs or got suggestions for further things to search or run please reach out to SuperSandro2000 on IRC.

Result of nixpkgs-review pr 107550 run on x86_64-darwin 1

1 package failed to build and are new build failure:

python37Packages.nitime

24 packages built:

python37Packages.dcmstack
python37Packages.dicom2nifti
python37Packages.dipy
python37Packages.heudiconv
python37Packages.nibabel
python37Packages.nilearn
python37Packages.nipy
python37Packages.nipype
python37Packages.pybids
python37Packages.pydicom
python38Packages.dicom2nifti
python38Packages.dipy
python38Packages.nibabel
python38Packages.nilearn
python38Packages.nipy
python38Packages.nipype
python38Packages.pybids
python38Packages.pydicom
python39Packages.dicom2nifti
python39Packages.dipy
python39Packages.nibabel
python39Packages.nipy
python39Packages.nipype
python39Packages.pydicom

rmcgibbo · 2021-01-05T05:57:51Z

It looks like perhaps this did not build on x86_64-darwin on hydra, despite building for Sandro: https://hydra.nixos.org/build/134332798

rmcgibbo · 2021-01-05T05:59:31Z

The only failing test looks like it might be something about the filesystem and mtimes?

=================================== FAILURES ===================================
_______________________ TestDeferredRead.test_time_check _______________________

self = <pydicom.tests.test_filereader.TestDeferredRead object at 0x1222b7c10>

    def test_time_check(self):
        """Deferred read warns if file has been modified"""
        ds = dcmread(self.testfile_name, defer_size="2 kB")
        from time import sleep
    
        sleep(0.1)
        with open(self.testfile_name, "r+") as f:
            f.write("\0")  # "touch" the file
    
        msg = r"Deferred read warning -- file modification time has changed"
        with pytest.warns(UserWarning, match=msg):
>           ds.PixelData
E           Failed: DID NOT WARN. No warnings of type (<class 'UserWarning'>,) was emitted. The list of emitted warnings is: [].

Maybe that test could just be disabled.

tfmoraes · 2021-01-05T13:44:13Z

@rmcgibbo I have PR to update nitime to its last version. Please, can you try if this error happens yet? #108407

rmcgibbo · 2021-01-05T17:14:37Z

@tfmoraes: I don't think I understand. It looks like the error I posted above is not related to nitime.

tfmoraes · 2021-01-05T17:19:19Z

sorry @rmcgibbo, I confused the word mtime with nitime :)

tfmoraes requested review from FRidh and jonringer as code owners December 24, 2020 22:48

ofborg bot added the 6.topic: python label Dec 24, 2020

ofborg bot requested a review from bcdarwin December 24, 2020 22:57

ofborg bot added 10.rebuild-darwin: 11-100 10.rebuild-linux: 11-100 labels Dec 24, 2020

SuperSandro2000 reviewed Dec 24, 2020

View reviewed changes

tfmoraes force-pushed the pydicom-2.1.2 branch from d274866 to cde6318 Compare December 24, 2020 23:28

SuperSandro2000 approved these changes Dec 27, 2020

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tfmoraes force-pushed the pydicom-2.1.2 branch from 354090b to a1f47a1 Compare December 27, 2020 15:46

SuperSandro2000 approved these changes Dec 27, 2020

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rmcgibbo mentioned this pull request Dec 31, 2020

python3Packages.pydicom: unbreak #107864

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rmcgibbo approved these changes Dec 31, 2020

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tfmoraes force-pushed the pydicom-2.1.2 branch from a1f47a1 to bf3a52a Compare December 31, 2020 18:05

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tfmoraes force-pushed the pydicom-2.1.2 branch from bf3a52a to 2b7ac57 Compare December 31, 2020 23:13

python3Packages.pydicom: 2.1.1 -> 2.1.2

4553efa

tfmoraes force-pushed the pydicom-2.1.2 branch from 2b7ac57 to 4553efa Compare January 1, 2021 21:27

tfmoraes requested a review from SuperSandro2000 January 1, 2021 22:49

SuperSandro2000 merged commit f14e007 into NixOS:master Jan 4, 2021

tfmoraes deleted the pydicom-2.1.2 branch January 4, 2021 16:48

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python3Packages.pydicom: 2.1.1 -> 2.1.2 #107550

python3Packages.pydicom: 2.1.1 -> 2.1.2 #107550

tfmoraes commented Dec 24, 2020 •

edited

tfmoraes commented Dec 24, 2020

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tfmoraes commented Dec 26, 2020

SuperSandro2000 commented Dec 27, 2020

rmcgibbo commented Dec 31, 2020 •

edited

tfmoraes commented Dec 31, 2020

SuperSandro2000 commented Dec 31, 2020

tfmoraes commented Dec 31, 2020

tfmoraes commented Jan 1, 2021

SuperSandro2000 commented Jan 2, 2021

SuperSandro2000 commented Jan 4, 2021

rmcgibbo commented Jan 5, 2021

rmcgibbo commented Jan 5, 2021

tfmoraes commented Jan 5, 2021

rmcgibbo commented Jan 5, 2021

tfmoraes commented Jan 5, 2021

python3Packages.pydicom: 2.1.1 -> 2.1.2 #107550

python3Packages.pydicom: 2.1.1 -> 2.1.2 #107550

Conversation

tfmoraes commented Dec 24, 2020 • edited

Motivation for this change

Things done

tfmoraes commented Dec 24, 2020

SuperSandro2000 commented Dec 25, 2020

SuperSandro2000 commented Dec 25, 2020

tfmoraes commented Dec 26, 2020

SuperSandro2000 commented Dec 27, 2020

rmcgibbo commented Dec 31, 2020 • edited

tfmoraes commented Dec 31, 2020

SuperSandro2000 commented Dec 31, 2020

tfmoraes commented Dec 31, 2020

tfmoraes commented Jan 1, 2021

SuperSandro2000 commented Jan 2, 2021

SuperSandro2000 commented Jan 4, 2021

rmcgibbo commented Jan 5, 2021

rmcgibbo commented Jan 5, 2021

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tfmoraes commented Jan 5, 2021

tfmoraes commented Dec 24, 2020 •

edited

rmcgibbo commented Dec 31, 2020 •

edited