dependency bump: metatensor 0.9, metatomic 0.1.14, featomic 0.7.4 by sofiia-chorna · Pull Request #1144 · metatensor/metatrain

sofiia-chorna · 2026-05-15T15:35:24Z

reopen from #1128

dump to:

metatensor-learn >=0.5.0,<0.6
metatensor-operations >=0.5.0,<0.6
metatensor-torch >=0.9.0,<0.10
metatomic-torch >=0.1.14,<0.2
metatomic-ase >=0.1.1,<0.2
featomic-torch >=0.7.4,<0.8

Please go the the Preview tab and select the appropriate PR template:

📚 Documentation preview 📚: https://metatrain--1144.org.readthedocs.build/en/1144/

Luthaf · 2026-05-18T08:53:56Z

Featomic releases are now live on PyPI!

pfebrer · 2026-05-18T09:49:49Z

The errors are super strange, they come from importing torch 😅

pfebrer · 2026-05-18T09:54:04Z

And in soap-bpnn we have problems, can they be because of torch-spex?

pfebrer · 2026-05-18T14:30:58Z

Well, we have advanced to the next bug 😄

Luthaf · 2026-05-18T14:38:56Z

For the doc error I'm not sure where it comes from, but I'd fix the deprecation warnings and then check again.

For the windows test build, it looks like the wheel for sphericart-torch fails to build on Windows, and this part of the code has been touched recently. I'd try to run with sphericart 1.0.8 to see if this helps, and otherwise we'll need to enable more verbose logs on CI. Also ping @frostedoyster in case you have an idea about what's going on here!

Removed version constraint for 'featomic' package.

pfebrer · 2026-05-19T06:55:56Z

@sofiia-chorna could you try to build the documentation locally and see if you understand what's happening?

sofiia-chorna · 2026-05-19T07:34:06Z

Traceback
=========

    Traceback (most recent call last):
      File "/Users/sofiia/cosmo/metatrain-fork/.tox/docs/lib/python3.11/site-packages/sphinx/cmd/build.py", line 414, in build_main
        app = Sphinx(
              ^^^^^^^
      File "/Users/sofiia/cosmo/metatrain-fork/.tox/docs/lib/python3.11/site-packages/sphinx/application.py", line 305, in __init__
        self.config.setup(self)
      File "/Users/sofiia/cosmo/metatrain-fork/docs/src/conf.py", line 92, in setup
        setup_architectures_docs()
      File "/Users/sofiia/cosmo/metatrain-fork/docs/src/architectures/generate.py", line 157, in setup_architectures_docs
        preload_documentation_module(architecture_name)
      File "/Users/sofiia/cosmo/metatrain-fork/.tox/docs/lib/python3.11/site-packages/metatrain/utils/architectures.py", line 233, in preload_documentation_module
        spec.loader.exec_module(documentation)
      File "<frozen importlib._bootstrap_external>", line 940, in exec_module
      File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
      File "/Users/sofiia/cosmo/metatrain-fork/.tox/docs/lib/python3.11/site-packages/metatrain/pet/documentation.py", line 73, in <module>
        from metatrain.pet.modules.finetuning import FinetuneHypers, NoFinetuneHypers
      File "/Users/sofiia/cosmo/metatrain-fork/.tox/docs/lib/python3.11/site-packages/metatrain/pet/__init__.py", line 1, in <module>
        from .model import PET
      File "/Users/sofiia/cosmo/metatrain-fork/.tox/docs/lib/python3.11/site-packages/metatrain/pet/model.py", line 43, in <module>
        class PET(ModelInterface[ModelHypers]):
      File "/Users/sofiia/cosmo/metatrain-fork/.tox/docs/lib/python3.11/site-packages/metatrain/pet/model.py", line 58, in PET
        __default_metadata__ = ModelMetadata(
                               ^^^^^^^^^^^^^^
      File "/Users/sofiia/cosmo/metatrain-fork/.tox/docs/lib/python3.11/site-packages/metatomic/torch/documentation.py", line 491, in __init__
        raise THIS_CODE_SHOULD_NOT_RUN
    RuntimeError: This is the documentation-only version of this class, it should not be used at runtime. If you see this error while running examples, check above for the actual error message.

Luthaf · 2026-05-19T07:35:37Z

Is there anything else above?

sofiia-chorna · 2026-05-19T07:42:02Z

examples seem to be generated cleanly but it crashes in setup_architectures_docs(). let me attach logs:
tox-docs.log

sofiia-chorna · 2026-05-19T13:05:46Z

did not manage to setup it on CI (torch cpu index) so far! on CI only tox -e tests fails due to setup, locally it passes:
tox-tests-override-rerun.log

…chorna/metatrain-js into bump-deps-metatensor-0.9

sofiia-chorna · 2026-05-20T11:25:17Z

i think it remains to have the release of metatomic v0.1.14 publised metatensor/metatomic#231 and updated here and we are good?

readthedocs fails due to the same issue as CI (fixed with temporal use of torch cpu index)


    Traceback (most recent call last):
      File "/home/docs/checkouts/readthedocs.org/user_builds/metatrain/envs/1144/lib/python3.13/site-packages/sphinx/cmd/build.py", line 414, in build_main
        app = Sphinx(
            srcdir=args.sourcedir,
        ...<14 lines>...
            exception_on_warning=args.exception_on_warning,
        )
      File "/home/docs/checkouts/readthedocs.org/user_builds/metatrain/envs/1144/lib/python3.13/site-packages/sphinx/application.py", line 305, in __init__
        self.config.setup(self)
        ~~~~~~~~~~~~~~~~~^^^^^^
      File "/home/docs/checkouts/readthedocs.org/user_builds/metatrain/checkouts/1144/docs/src/conf.py", line 92, in setup
        setup_architectures_docs()
        ~~~~~~~~~~~~~~~~~~~~~~~~^^
      File "/home/docs/checkouts/readthedocs.org/user_builds/metatrain/checkouts/1144/docs/src/architectures/generate.py", line 157, in setup_architectures_docs
        preload_documentation_module(architecture_name)
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^
      File "/home/docs/checkouts/readthedocs.org/user_builds/metatrain/envs/1144/lib/python3.13/site-packages/metatrain/utils/architectures.py", line 233, in preload_documentation_module
        spec.loader.exec_module(documentation)
        ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^
      File "<frozen importlib._bootstrap_external>", line 1027, in exec_module
      File "<frozen importlib._bootstrap>", line 488, in _call_with_frames_removed
      File "/home/docs/checkouts/readthedocs.org/user_builds/metatrain/envs/1144/lib/python3.13/site-packages/metatrain/pet/documentation.py", line 73, in <module>
        from metatrain.pet.modules.finetuning import FinetuneHypers, NoFinetuneHypers
      File "/home/docs/checkouts/readthedocs.org/user_builds/metatrain/envs/1144/lib/python3.13/site-packages/metatrain/pet/__init__.py", line 1, in <module>
        from .model import PET
      File "/home/docs/checkouts/readthedocs.org/user_builds/metatrain/envs/1144/lib/python3.13/site-packages/metatrain/pet/model.py", line 43, in <module>
        class PET(ModelInterface[ModelHypers]):
        ...<1414 lines>...
                return checkpoint
      File "/home/docs/checkouts/readthedocs.org/user_builds/metatrain/envs/1144/lib/python3.13/site-packages/metatrain/pet/model.py", line 58, in PET
        __default_metadata__ = ModelMetadata(
            references={"architecture": ["https://arxiv.org/abs/2305.19302v3"]}
        )
      File "/home/docs/checkouts/readthedocs.org/user_builds/metatrain/envs/1144/lib/python3.13/site-packages/metatomic/torch/documentation.py", line 491, in __init__
        raise THIS_CODE_SHOULD_NOT_RUN
    RuntimeError: This is the documentation-only version of this class, it should not be used at runtime. If you see this error while running examples, check above for the actual error message.

Luthaf · 2026-05-20T15:09:08Z

cscs-ci run

pfebrer

Ok, a couple things and we are good 👍

pfebrer · 2026-05-20T15:16:56Z

+    "ignore:`compute_requested_neighbors_from_options` is deprecated and will be removed in a future version:UserWarning",
+    # metatomic 0.1.12 deprecations
+    "ignore:the 'features' output name is deprecated:UserWarning",
+    "ignore:the 'features' quantity is deprecated:UserWarning",
+    "ignore:the 'features' quantity is deprecated:DeprecationWarning",
+    "ignore:the 'non_conservative_forces' output name is deprecated:UserWarning",
+    "ignore:the 'momenta' quantity is deprecated:DeprecationWarning",
+    "ignore:the 'positions' quantity is deprecated:DeprecationWarning",
+    "ignore:the 'masses' quantity is deprecated:DeprecationWarning",
+    "ignore:the 'velocities' quantity is deprecated:DeprecationWarning",
+    "ignore:the 'charges' quantity is deprecated:DeprecationWarning",
+    "ignore:`per_atom` is deprecated:DeprecationWarning",
+    "ignore:ModelOutput.quantity is deprecated:DeprecationWarning"


We have to get rid of all these warnings ASAP after this PR 😅

ok i will do it in the follow-up PR

sofiia-chorna · 2026-05-20T16:29:12Z

cscs-ci run

Luthaf · 2026-05-21T08:03:50Z

cscs-ci run

pfebrer · 2026-05-21T11:45:40Z

Thank youuuu

…lse) merge The reference fixture's storage changed slightly when the scaler switched from the manual TensorBlock rebuild to block.copy(deep=False) (from PR metatensor#1144). Regenerated via test_checkpoint_did_not_change.

The merge with PR metatensor#1144 replaced our regex catch-alls for torch.jit deprecations and the plural-name family ('features', 'positions', 'momenta', etc.) with PR metatensor#1144's narrower per-warning entries. macOS CI was failing 61 tests on a metatomic 0.1.14 UserWarning about Model.requested_inputs(use_new_names=False) that no remaining filter caught. Restore the regex catch-alls, add an explicit ignore for the new requested_inputs deprecation, and fix the one offending call site (cli/eval.py) to pass use_new_names=True so we no longer emit the warning from our own code.

sofiia-chorna added 10 commits May 11, 2026 21:20

Use targetinfo quantity as modeloutput quantity was deprecated

2da11ce

is_auxiliary_output - also match singular "feature"

903841e

gap: recreate tensorblocks

a66b3f5

copy blocks

f0d92ea

update tests for stricter validation

3098dfd

scaler: copy block before second tensormap

ecb59c2

revert regex for backward compat with current metatomic

74c798f

update regex for metatensor 0.9 validation message

bd7d3e5

bump metatensor to 0.9, metatomic to 0.1.12

bca162f

add featomic rc

88c4c1b

Update gap extras

0941346

pfebrer mentioned this pull request May 18, 2026

Bump uv to make CI run with the new metatensor releases #1146

Merged

Merge branch 'main' into bump-deps-metatensor-0.9

3f1f460

pfebrer added 2 commits May 18, 2026 18:35

Remove the extra dependency for gap

ed438ad

Removed version constraint for 'featomic' package.

Pin sphericart on windows

132446c

Luthaf mentioned this pull request May 19, 2026

Allow creating the documentation-only classes metatensor/metatomic#230

Merged

4 tasks

sofiia-chorna added 4 commits May 19, 2026 14:11

temporary override metatomic with pr branch

4056239

temporary filter warning for overriding metatomic-torch

6668d00

temporary: attempt to add cpu torch index

18d0b6b

temporary: another attempr to use cpu torch index

2359204

another try on cpu torch from GF

449c925

Luthaf force-pushed the bump-deps-metatensor-0.9 branch from 449c925 to bc5f33d Compare May 20, 2026 08:02

Another try for CPU torch

8394fd3

Luthaf force-pushed the bump-deps-metatensor-0.9 branch from bc5f33d to 8394fd3 Compare May 20, 2026 08:14

Merge branch 'bump-deps-metatensor-0.9' of https://github.com/sofiia-…

2c6da58

…chorna/metatrain-js into bump-deps-metatensor-0.9

sofiia-chorna added 4 commits May 20, 2026 13:37

temporar: try to fix readthedocs job

0b8dfc3

point to release candidate or metatomic-torch

1be8c8f

use metatomic-torch 0.1.14

56c397a

drop cpu torch workarounds

b7cd29e

sofiia-chorna changed the title ~~dependency bump: metatensor 0.9 + metatomic 0.1.12~~ dependency bump: metatensor 0.9, metatomic 0.1.14, featomic 0.7.4 May 20, 2026

sofiia-chorna marked this pull request as ready for review May 20, 2026 15:07

sofiia-chorna requested review from DavideTisi, frostedoyster, johannes-spies, jwa7 and pfebrer as code owners May 20, 2026 15:07

pfebrer reviewed May 20, 2026

View reviewed changes

use block.copy(deep=False)

86ed229

sofiia-chorna force-pushed the bump-deps-metatensor-0.9 branch from b16bfae to 86ed229 Compare May 20, 2026 16:08

Move sphericart pin

a77ec42

pfebrer approved these changes May 21, 2026

View reviewed changes

pfebrer merged commit 331f676 into metatensor:main May 21, 2026
21 checks passed

sofiia-chorna mentioned this pull request May 21, 2026

finish migrating off metatomic 0.1.12 deprecated apis #1150

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