fix: add mendeleev to dependencies; remove dpdata; remove catching ImportError

[njzjz]

Fix #3743.

Summary by CodeRabbit

• Chores
  • Consolidated imports and removed redundant exception handling for dpdata and mendeleev.
  • Updated dependencies in pyproject.toml to include mendeleev in the main section and update packages for testing and documentation.

[coderabbitai]

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).	✅

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Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 7ec5755 and a41dcb6.

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.

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50-50: Removal of mendeleev from dev-dependencies is consistent with its addition to dependencies.

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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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[wanghan-iapcm]

shall we add dpdata and mendeleev to dependencies?

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 82.70%. Comparing base (c644314) to head (a41dcb6).
Report is 116 commits behind head on devel.

Additional details and impacted files

@@           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           

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[njzjz]

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

deepmd-kit/deepmd/utils/econf_embd.py

Line 133 in 7ec5755

"Og" : [2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2],

[wanghan-iapcm]

yes, please remove the import of dpdata.