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deepmodeling / deepmd-kit

A deep learning package for many-body potential energy representation and molecular dynamics
https://docs.deepmodeling.com/projects/deepmd/
GNU Lesser General Public License v3.0
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fix: add mendeleev to dependencies; remove dpdata; remove catching ImportError #3878

Closed njzjz closed 2 weeks ago

njzjz commented 2 weeks ago

Fix #3743.

Summary by CodeRabbit

coderabbitai[bot] commented 2 weeks ago
Walkthrough ## Walkthrough The changes aim to simplify the dependency management and import handling for `dpdata` and `mendeleev` within the project by removing redundant `try-except` blocks, consolidating the imports, and adjusting the package dependencies in `pyproject.toml`. This addresses a specific test failure and improves the overall test and documentation setup. ## Changes | File | Change Summary | |---------------------------------------|------------------------------------------------------------------------------------------------------| | `deepmd/utils/econf_embd.py` | Removed redundant `try-except` block; consolidated imports. | | `pyproject.toml` | Moved `mendeleev` to `dependencies` section; adjusted `test` and `docs` sections dependencies. | | `source/tests/common/test_econf_embd.py` | Removed import and existence checks for `mendeleev`; simplified test setup. | ## Sequence Diagram(s) *No sequence diagrams are necessary as the changes are mainly around import handling and dependency management.* ## Assessment against linked issues | Objective | Addressed | Explanation | |----------------------------------------------------------------------------------------------------------|-----------|--------------------------------------------------------------------------------------------------| | Simplify import handling for `mendeleev` and ensure it's in the main dependencies section (#3743). | ✅ | | | Fix the `tests.common.test_econf_embd.TestEConfEmbd.test_fe` by ensuring `mendeleev` is correctly imported (#3743). | ✅ | |
Recent review details **Configuration used: CodeRabbit UI** **Review profile: CHILL**
Commits Files that changed from the base of the PR and between 7ec57555d0e4f761b590d16c8d83af3b9f0d71c5 and a41dcb6210ca9ae4e58eaadba4d82936b0424f59.
Files selected for processing (3) * deepmd/utils/econf_embd.py (2 hunks) * pyproject.toml (2 hunks) * source/tests/common/test_econf_embd.py (1 hunks)
Files skipped from review due to trivial changes (1) * source/tests/common/test_econf_embd.py
Files skipped from review as they are similar to previous changes (1) * deepmd/utils/econf_embd.py
Additional comments not posted (3)
pyproject.toml (3)
`50-50`: Moving `mendeleev` from `dev-dependencies` to `dependencies` ensures it is always available, preventing runtime errors. --- `50-50`: Removal of `mendeleev` from `dev-dependencies` is consistent with its addition to `dependencies`. --- `50-50`: Update to `sphinx>=3.1.1` in the docs section is approved. Please verify compatibility with existing documentation setups.
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codecov[bot] commented 2 weeks ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 82.70%. Comparing base (c644314) to head (a41dcb6).

Additional details and impacted files ```diff @@ Coverage Diff @@ ## devel #3878 +/- ## ======================================= Coverage 82.70% 82.70% ======================================= Files 517 517 Lines 50141 50137 -4 Branches 2984 2985 +1 ======================================= - Hits 41469 41467 -2 + Misses 7762 7760 -2 Partials 910 910 ```

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

njzjz commented 2 weeks ago

shall we add dpdata and mendeleev to dependencies?

I don't find the meaning of using dpdata - the element table has already been hard-coded in econf_embd.py

https://github.com/deepmodeling/deepmd-kit/blob/7ec57555d0e4f761b590d16c8d83af3b9f0d71c5/deepmd/utils/econf_embd.py#L133

wanghan-iapcm commented 2 weeks ago

yes, please remove the import of dpdata.