chore: improve type annotations #659

njzjz · 2024-05-17T00:41:30Z

I give up fix type annotations in all files, but it's meaningful to fix the top-module files dpdata/*.py.

Summary by CodeRabbit

New Features
- Added name property to DPDataCalculator class.
- Introduced assertion for rdkit_mol in bond order system.
Improvements
- Enhanced type hinting across various functions and methods.
- Added decorators and type assertion checks for better code validation.
Maintenance
- Introduced a GitHub Actions workflow for running Pyright type checker.
- Updated dependencies and configurations in pyproject.toml.

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>

coderabbitai · 2024-05-17T00:41:49Z

Walkthrough

The update introduces a GitHub Actions workflow for running the Pyright type checker, enhances type hinting across various modules, and makes significant changes to method signatures and class properties. These improvements aim to increase code reliability, maintainability, and type safety. Key updates include modifications to the DPDataCalculator class, bond_order_system, and extensive changes to method signatures in system.py.

Changes

Files	Change Summaries
.github/workflows/pyright.yml	Introduces a GitHub Actions workflow for running Pyright type checker.
dpdata/ase_calculator.py	Updated `DPDataCalculator` class with a `name` property and modifications to `calculate` function.
dpdata/bond_order_system.py	Added assertion for `rdkit_mol` and modified `copy` method.
dpdata/data_type.py	Modified type hints in function signatures.
dpdata/driver.py	Updated type hinting for `get_driver` and `get_minimizer` methods.
dpdata/format.py	Added import and modified assignment in the `decorator` function.
dpdata/stat.py	Added decorators and type assertion checks.
dpdata/system.py	Extensive changes to method signatures and additions.
dpdata/utils.py	Updated `elements_index_map` function with type hints and overloads.
pyproject.toml	Added dependencies and configurations.

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Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>

coderabbitai

Actionable comments posted: 16

Out of diff range and nitpick comments (2)

dpdata/ase_calculator.py (2)
Line range hint 54-75: Add type checks to avoid potential NoneType attribute errors.
-        assert atoms is not None
+        if atoms is None:
+            raise ValueError("`atoms` cannot be None")
Line range hint 1-1: Add the missing import for annotations.
+from __future__ import annotations

dpdata/driver.py

dpdata/bond_order_system.py

dpdata/format.py

dpdata/system.py

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>

codspeed-hq · 2024-05-17T00:47:14Z

CodSpeed Performance Report

Merging #659 will not alter performance

_{Comparing njzjz:improve-typing (24b93d5) with devel (a7bf93d)}

Summary

✅ 2 untouched benchmarks

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>

codecov · 2024-05-17T00:52:19Z

Codecov Report

Attention: Patch coverage is 95.52846% with 11 lines in your changes are missing coverage. Please review.

Project coverage is 84.06%. Comparing base (a7bf93d) to head (24b93d5).

Files	Patch %	Lines
dpdata/bond_order_system.py	60.00%	2 Missing ⚠️
dpdata/system.py	98.09%	2 Missing ⚠️
dpdata/__about__.py	0.00%	1 Missing ⚠️
dpdata/__main__.py	0.00%	1 Missing ⚠️
dpdata/cli.py	0.00%	1 Missing ⚠️
dpdata/driver.py	87.50%	1 Missing ⚠️
dpdata/format.py	50.00%	1 Missing ⚠️
dpdata/md/rdf.py	0.00%	1 Missing ⚠️
dpdata/psi4/input.py	75.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##            devel     #659      +/-   ##
==========================================
+ Coverage   83.86%   84.06%   +0.20%     
==========================================
  Files          81       81              
  Lines        6996     7122     +126     
==========================================
+ Hits         5867     5987     +120     
- Misses       1129     1135       +6

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

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>

njzjz · 2024-05-17T01:07:44Z

@coderabbitai resolve

coderabbitai · 2024-05-17T01:08:44Z

Actions Performed

Comments resolved.

njzjz added 3 commits May 16, 2024 20:36

chore: improve type annotations

cb7b619

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>

add pyright

fbf964a

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>

enable TCH

665c4fe

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>

njzjz added 3 commits May 16, 2024 20:42

run pre-commit

2021a01

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>

fix typo

69d4fa0

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>

fix import issue

04e584b

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>

coderabbitai bot reviewed May 17, 2024

View reviewed changes

run pre-commit

1d1b95f

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>

njzjz added 2 commits May 16, 2024 20:49

Literal

6e7462f

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>

install all dependencies

eed5751

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>

njzjz added 2 commits May 16, 2024 21:06

fix rest errors

77d798c

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>

add py.typed file

8b0700a

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>

njzjz marked this pull request as ready for review May 17, 2024 01:09

njzjz requested a review from wanghan-iapcm May 17, 2024 01:09

remove **kwargs: dict, which is incorrect

24b93d5

wanghan-iapcm approved these changes May 17, 2024

View reviewed changes

wanghan-iapcm merged commit 626e692 into deepmodeling:devel May 17, 2024
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chore: improve type annotations #659

chore: improve type annotations #659

njzjz commented May 17, 2024 •

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chore: improve type annotations #659

chore: improve type annotations #659

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codspeed-hq bot commented May 17, 2024 • edited Loading

CodSpeed Performance Report

Merging #659 will not alter performance

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njzjz commented May 17, 2024 •

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