fix(pt): name installable packages when no neighbor-list backend is importable - #6037
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The DPA-4 / SeZM descriptor needs a neighbor-list backend at runtime, and
nothing declared one. `vesin` appears nowhere in the project metadata, and the
`nvalchemi` extra pulls `nvalchemi-toolkit` for `deepmd.pt.nvalchemi`, which is
a different distribution from the `nvalchemi-toolkit-ops` that provides the
`nvalchemiops` import the neighbor list uses. A plain install therefore builds
a model and then stops at
RuntimeError: SeZM neighbor-list construction requires either
'nvalchemiops' or 'vesin', but neither is importable.
`pip check` stays clean throughout, because the requirement is never declared.
The message also names import names, which are not what a user installs.
Add a `dpa4` extra covering what the descriptor needs at runtime -- `e3nn` for
the S2 grid projections and `vesin[torch]` for the neighbor list -- and give
the error the pip commands that resolve it.
`nvalchemi-toolkit-ops` is deliberately not in the extra: it is an alternative
neighbor-list backend rather than an addition, and requiring it would tie the
extra to CUDA and to `python<3.15`. It is offered in the error message instead.
The existing `nvalchemi` extra is untouched.
for more information, see https://pre-commit.ci
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Included review availability: Your plan provides up to 8 included reviews per hour; 7 remain after this review. 📝 WalkthroughWalkthroughThe missing-neighbor-backend error now recommends the ChangesDPA-4 backend support
Priority: ⬇️ Low Estimated code review effort: 2 (Simple) | ~10 minutes Change: Bug fix Suggested reviewers: Merge Risk: ⚪ Minimal · up to The SeZM error now provides pip-installable backend guidance, and the updated test avoids the Python 3.10 collection issue. No merge-blocking risk remains. 🚥 Pre-merge checks | ✅ 5✅ Passed checks (5 passed)
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Inline comments:
In `@source/tests/pt/test_neighbor_backend_missing.py`:
- Line 13: Update the test dependency configuration so the test extra includes
tomli only for Python versions below 3.11, then modify the tomllib import in
test_neighbor_backend_missing.py to fall back to tomli when tomllib is
unavailable. Keep tomllib as the preferred import on supported Python versions.
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deepmd/pt/model/model/sezm_model.pypyproject.tomlsource/tests/pt/test_neighbor_backend_missing.py
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Blocking issue remains in the current head and is already captured by the existing exact-line review thread, so I am not duplicating the inline comment. This repository supports Python 3.10, but the new test imports the stdlib tomllib, which is only available from Python 3.11. The exact-head Test Python workflow is currently failing on Python 3.10 jobs. Please add a Python<3.11 tomli test dependency and use a tomllib/tomli fallback (or otherwise avoid the 3.11-only import) so the test can collect on the supported minimum version.
The dependency extra and the revised missing-backend error itself look consistent with the stated runtime contract; this request is specifically for the supported-version test breakage.
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The premise of the previous commit was wrong. It claimed nothing in the project metadata declared a neighbor-list backend, having checked only pyproject.toml. deepmd assembles extras through a custom build backend, and backend/find_pytorch.py already declares e3nn>=0.5.9, vesin[torch] and nvalchemi-toolkit-ops>=0.3.1 under the `torch` extra -- visible in the built metadata as `vesin[torch]; extra == "torch"`. Upstream 99c1ece put them there deliberately. The dpa4 extra was therefore a duplicate of an extra that already exists, so it is removed. What remains is the half that does not depend on that premise. The documented PyTorch CPU install in doc/install/easy-install.md is pip install torch --index-url https://download.pytorch.org/whl/cpu pip install deepmd-kit with no extra, so that path has no neighbor-list backend. It reaches a model build and stops on a message naming the imports 'nvalchemiops' and 'vesin', neither of which is what a user installs. The message now gives the distributions and points at the extra that ships them, `torch`. Also drops the test that parsed pyproject.toml: it imported tomllib, which is stdlib only on 3.11+, while the project supports 3.10, and it broke collection on every 3.10 CI shard.
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Re-reviewed the complete current diff because the head changed from ecf307da92ac8a8e2700b52f96d2ec9979452910 to this head. The previous Python 3.10 blocker is fixed: the tomllib-based metadata test and duplicated dpa4 extra were removed, leaving only the runtime error-message improvement plus focused tests that monkeypatch both neighbor backends unavailable. The old inline thread is now outdated, and I did not find a new high-confidence correctness, compatibility, packaging, or test blocker in the current two-file diff.
Disposition: COMMENT / NEEDS HUMAN REVIEW for now because exact-head CI is still incomplete. Test CUDA, Build C++, Build C library, CodeQL, and package/PyPI are green; Test Python and Test C++ are still running. Once those finish green, this head is suitable for approval absent new changes/discussion.
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## master #6037 +/- ##
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- Coverage 77.74% 77.50% -0.25%
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Files 1155 1155
Lines 139640 139640
Branches 5056 5062 +6
==========================================
- Hits 108569 108226 -343
- Misses 29188 29529 +341
- Partials 1883 1885 +2 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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Exact-head CI has now completed successfully: Test Python, Test C++, Test CUDA, Build C++, Build C library, CodeQL, and package/PyPI are all green. The complete current two-file diff was substantively reviewed on this same head in the previous monitoring pass; the prior Python 3.10 tomllib blocker is fixed/outdated, and no new high-confidence correctness, compatibility, packaging, or test blocker has appeared. Approving this head.
— Agent: ChatGPT; Model: GPT-5.6 Sol; GitHub account: njzjz-bot; reviewed head: f08995c; trigger: scheduled all-PR monitoring
The DPA-4 / SeZM descriptor needs
vesinornvalchemiopsat runtime, and both ship with thetorchextra. An environment that has the rest of the PyTorch stack but no neighbor-list backendbuilds a model and then stops at:
nvalchemiopsandvesinare import names. Neither is what a user types into pip: the first comesfrom the distribution
nvalchemi-toolkit-ops, and the second needs itstorchextra, because thetorch bindings ship separately from
vesinitself. So the message names two things that cannot beinstalled as written.
That gap is not hypothetical.
backend/find_pytorch.pyrecords the case in its own comment — conda-forgeships
vesinbut notvesin-torch— which is exactly an environment whereimport vesinsucceeds,is_vesin_torch_available()is false, and this message is all the user gets.Change
The
RuntimeErrornow gives commands that resolve it, and points at the extra that ships a backend:Text only. No dependency, default, or behaviour changes; the selection logic is untouched.
nvalchemi-toolkit-opsis offered as an alternative rather than recommended: it is a CUDA packagerestricted to Linux and
python>=3.11, whereasvesin[torch]is portable.Tests
source/tests/pt/test_neighbor_backend_missing.pymakes both backends report unavailable and checksthat the message names the installable distributions and the extra. Both tests fail against the old
message and pass against the new one.
Note on the no-extra install
pip install deepmd-kitwith no extra — the PyTorch CPU path indoc/install/easy-install.md— doesnot reach this message today.
e3nnsits in the sametorchextra, anddeepmd/pt/model/descriptor/sezm_nn/projection.pyimports it at module scope, so that install failsearlier with
ModuleNotFoundError: e3nn. #6036 makes that import lazy; with it applied, the CPU pathreaches this message too.