Bug#1030907: [Help] Possible scikit-learn issue (Was: Bug#1030907: umap-learn: FTBFS (failing tests))
On 2023-02-09 20:37, Andreas Tille wrote: Hi again, Am Thu, Feb 09, 2023 at 05:52:13PM +0100 schrieb Andreas Tille: > That said, the np.matrix discrepancy was only just fixed recently, in > December, by > https://github.com/lmcinnes/umap/pull/946 I've updated the packaging, added the PR, fixed some test issues that were not yet addressed by these patches but there are remaining issues: https://salsa.debian.org/med-team/umap-learn/-/jobs/3925631 Any idea how to fix these? First error looks like it might be https://github.com/lmcinnes/umap/commit/949abd082524fce8c45dfb147bcd8e8ef49eade3 Error 2 *might* be https://github.com/lmcinnes/umap/pull/952 via umap/utils.py:161: in csr_unique
Bug#1030907: [Help] Possible scikit-learn issue (Was: Bug#1030907: umap-learn: FTBFS (failing tests))
Hi again, Am Thu, Feb 09, 2023 at 05:52:13PM +0100 schrieb Andreas Tille: > > That said, the np.matrix discrepancy was only just fixed recently, in > > December, by > > https://github.com/lmcinnes/umap/pull/946 I've updated the packaging, added the PR, fixed some test issues that were not yet addressed by these patches but there are remaining issues: https://salsa.debian.org/med-team/umap-learn/-/jobs/3925631 Any idea how to fix these? Kind regards Andreas. -- http://fam-tille.de
Bug#1030907: [Help] Possible scikit-learn issue (Was: Bug#1030907: umap-learn: FTBFS (failing tests))
Am Thu, Feb 09, 2023 at 04:57:03PM +0100 schrieb Drew Parsons: > tldr; https://github.com/lmcinnes/umap/pull/946 Thanks for the hint. > There's a couple of strange aspects to this problem. The np.matrix seems to > be generated by scipy.sparse. np.matrix is "not recommended" by numpy, but > not actually deprecated (at least not removed) yet. scikit-learn is jumping > the gun by declaring it's not supported. > > On the other hand, scitkit-learn has been "not supporting" it for two years > now. This corner of the debian archive is quite a bit out of date. The > current version of umap (i.e. umap-learn) is 0.5.3, released April last > year. > > That said, the np.matrix discrepancy was only just fixed recently, in > December, by > https://github.com/lmcinnes/umap/pull/946 I did not updated umap-learn since it had a new dependency from tensorflow. However, I can skip those dependency and will upgrade to the latest version. Kind regards Andreas. -- http://fam-tille.de
Bug#1030907: [Help] Possible scikit-learn issue (Was: Bug#1030907: umap-learn: FTBFS (failing tests))
On 2023-02-09 15:02, Andreas Tille wrote: Control: tags -1 help Am Thu, Feb 09, 2023 at 12:50:45AM +0100 schrieb Santiago Vila: Package: src:umap-learn Version: 0.4.5+dfsg-3 Severity: serious Tags: ftbfs Dear maintainer: During a rebuild of all packages in bookworm, your package failed to build: In Salsa CI you can find a more informative log: https://salsa.debian.org/med-team/umap-learn/-/jobs/3923570 Looking at line 1307 and following I'm wondering, whether this issue is rather caused by scikit-learn which is not fully converted to numpy 1.24. Any ideas how to fix this? tldr; https://github.com/lmcinnes/umap/pull/946 There's a couple of strange aspects to this problem. The np.matrix seems to be generated by scipy.sparse. np.matrix is "not recommended" by numpy, but not actually deprecated (at least not removed) yet. scikit-learn is jumping the gun by declaring it's not supported. On the other hand, scitkit-learn has been "not supporting" it for two years now. This corner of the debian archive is quite a bit out of date. The current version of umap (i.e. umap-learn) is 0.5.3, released April last year. That said, the np.matrix discrepancy was only just fixed recently, in December, by https://github.com/lmcinnes/umap/pull/946 Drew
Bug#1030907: [Help] Possible scikit-learn issue (Was: Bug#1030907: umap-learn: FTBFS (failing tests))
Control: tags -1 help Am Thu, Feb 09, 2023 at 12:50:45AM +0100 schrieb Santiago Vila: > Package: src:umap-learn > Version: 0.4.5+dfsg-3 > Severity: serious > Tags: ftbfs > > Dear maintainer: > > During a rebuild of all packages in bookworm, your package failed to build: In Salsa CI you can find a more informative log: https://salsa.debian.org/med-team/umap-learn/-/jobs/3923570 Looking at line 1307 and following I'm wondering, whether this issue is rather caused by scikit-learn which is not fully converted to numpy 1.24. Any ideas how to fix this? Kind regards Andreas. -- http://fam-tille.de
