style: require explicit device and dtype by njzjz · Pull Request #4001 · deepmodeling/deepmd-kit

njzjz · 2024-07-22T07:21:14Z

Add a linter to require explicit device and dtype for {np,tf,pt}.{tensor,zeros,ones,arange,range,empty,full,rand,eye,linspace}.

EDP01: Require explicit device when initializing a PyTorch tensor.
EDP02: Require explicit dtype when initializing a NumPy array, a TensorFlow tensor, or a PyTorch tensor.

Missing device or dtype often causes a problem.

Note: I am not going to fix the existing codes in this PR, as too many (200+) lines violate the rules. Fixing them takes a long time which I don't have. I disable rules on those lines.

Summary by CodeRabbit

New Features
- Added enhanced linting capabilities through a new deepmd_checker plugin in the pyproject.toml configuration.
Bug Fixes
- Improved code clarity and compliance by suppressing pylint warnings related to explicit data types across multiple files.
Documentation
- Numerous comments added to clarify the suppression of linting messages, enhancing code maintainability and readability.

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

coderabbitai · 2024-07-22T07:21:46Z

Walkthrough

This update introduces enhancements to the linting configuration and improves code quality across various files in the deepmd project. Key changes include the addition of Pylint integration with specific configurations to suppress warnings related to explicit data types in numpy and tensor operations. This promotes better code readability while maintaining functional integrity.

Changes

Files	Change Summary
`.pre-commit-config.yaml`	Added Pylint hook with custom setup to improve linting process.
`deepmd/...` (multiple files)	Added comments to suppress Pylint warnings about explicit data types during numpy array and tensor initializations, enhancing clarity without changing logic.
`pyproject.toml`	Introduced configuration for Pylint to load the `deepmd_checker` plugin and control messages reported by the linter.

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        # YWolfeee: support polar normalization, initialize to a more appropriate point
        if self.shift_diag:
-            mean_polar = np.zeros([len(self.sel_type), 9])
+            mean_polar = np.zeros([len(self.sel_type), 9])  # pylint: disable=no-explicit-dtype


        self.nei_type = tf.constant(nei_type, dtype=tf.int32)

-        avg_zero = np.zeros([self.ntypes, self.ndescrpt]).astype(
+        avg_zero = np.zeros([self.ntypes, self.ndescrpt]).astype(  # pylint: disable=no-explicit-dtype


            GLOBAL_NP_FLOAT_PRECISION
        )
-        std_ones = np.ones([self.ntypes, self.ndescrpt]).astype(
+        std_ones = np.ones([self.ntypes, self.ndescrpt]).astype(  # pylint: disable=no-explicit-dtype


        with tf.variable_scope("descrpt_attr" + suffix, reuse=reuse):
            if davg is None:
-                davg = np.zeros([self.ntypes, self.ndescrpt])
+                davg = np.zeros([self.ntypes, self.ndescrpt])  # pylint: disable=no-explicit-dtype


+                davg = np.zeros([self.ntypes, self.ndescrpt])  # pylint: disable=no-explicit-dtype
            if dstd is None:
-                dstd = np.ones([self.ntypes, self.ndescrpt])
+                dstd = np.ones([self.ntypes, self.ndescrpt])  # pylint: disable=no-explicit-dtype


                -1, self.ndescrpt
            )  # shape is [nframes*nall, self.ndescrpt]
-            xyz_scatter = torch.empty(
+            xyz_scatter = torch.empty(  # pylint: disable=no-explicit-dtype


coderabbitai

Actionable comments posted: 7

codecov · 2024-07-22T07:36:46Z

Codecov Report

Attention: Patch coverage is 75.58140% with 42 lines in your changes missing coverage. Please review.

Project coverage is 82.83%. Comparing base (6199b03) to head (2ebb158).
Report is 108 commits behind head on devel.

Files with missing lines	Patch %	Lines
deepmd/pt/utils/preprocess.py	0.00%	15 Missing ⚠️
deepmd/tf/infer/deep_eval.py	72.22%	5 Missing ⚠️
deepmd/pt/model/descriptor/se_r.py	50.00%	2 Missing ⚠️
deepmd/pt/model/descriptor/se_t.py	0.00%	2 Missing ⚠️
deepmd/tf/descriptor/loc_frame.py	50.00%	2 Missing ⚠️
deepmd/tf/infer/deep_tensor.py	0.00%	2 Missing ⚠️
deepmd/tf/nvnmd/descriptor/se_atten.py	0.00%	2 Missing ⚠️
deepmd/dpmodel/atomic_model/linear_atomic_model.py	0.00%	1 Missing ⚠️
deepmd/dpmodel/infer/deep_eval.py	50.00%	1 Missing ⚠️
deepmd/pt/model/descriptor/gaussian_lcc.py	0.00%	1 Missing ⚠️
... and 9 more

Additional details and impacted files

@@           Coverage Diff           @@
##            devel    #4001   +/-   ##
=======================================
  Coverage   82.83%   82.83%           
=======================================
  Files         522      522           
  Lines       50889    50901   +12     
  Branches     3015     3011    -4     
=======================================
+ Hits        42154    42165   +11     
- Misses       7798     7799    +1     
  Partials      937      937

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

njzjz · 2024-07-22T20:29:14Z

CodeQL alerts are not related to this PR (but it's expected to fix them in a separated PR)

Add a linter to require explicit `device` and `dtype` for `{np,tf,pt}.{tensor,zeros,ones,arange,range,empty,full,rand,eye,linspace}`. - EDP01: Require explicit device when initializing a PyTorch tensor. - EDP02: Require explicit dtype when initializing a NumPy array, a TensorFlow tensor, or a PyTorch tensor. Missing `device` or `dtype` often causes a problem. Note: I am not going to fix the existing codes in this PR, as too many (200+) lines violate the rules. Fixing them takes a long time which I don't have. I disable rules on those lines.  ## Summary by CodeRabbit - **New Features** - Added enhanced linting capabilities through a new `deepmd_checker` plugin in the `pyproject.toml` configuration. - **Bug Fixes** - Improved code clarity and compliance by suppressing pylint warnings related to explicit data types across multiple files. - **Documentation** - Numerous comments added to clarify the suppression of linting messages, enhancing code maintainability and readability.  --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>

njzjz added 3 commits July 22, 2024 02:12

add checker

1d2f028

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

disable

1656d94

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

grammar fix

2ebb158

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

njzjz requested review from iProzd and wanghan-iapcm July 22, 2024 07:21

github-actions Bot added the Python label Jul 22, 2024

github-advanced-security AI found potential problems Jul 22, 2024

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coderabbitai Bot reviewed Jul 22, 2024

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wanghan-iapcm approved these changes Jul 23, 2024

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iProzd approved these changes Jul 23, 2024

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wanghan-iapcm added this pull request to the merge queue Jul 23, 2024

github-merge-queue Bot removed this pull request from the merge queue due to failed status checks Jul 23, 2024

wanghan-iapcm added this pull request to the merge queue Jul 23, 2024

github-merge-queue Bot removed this pull request from the merge queue due to failed status checks Jul 23, 2024

njzjz added this pull request to the merge queue Jul 24, 2024

Merged via the queue into deepmodeling:devel with commit 73ea96d Jul 24, 2024

njzjz deleted the checker branch July 24, 2024 04:01

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