pref: lazy import modules

njzjz commented 1 month ago

Fix #526.

Summary by CodeRabbit

Refactor
- Removed unnecessary import statements and restructured import handling for improved code organization and readability.
- Reorganized imports within functions to localize dependencies and enhance code modularity.
New Features
- Introduced conditional imports based on TYPE_CHECKING for better resource management and efficiency.
- Added a new method from_dict to the System class for constructing instances from a data dictionary.
Chores
- Updated linting rules in pyproject.toml to include TID253 for banned module-level imports.
- Modified import statements in test files to comply with the new linting rules for better code quality.
Style
- Added # noqa: TID253 comments to specific import statements to adhere to new linting rules and ensure clean code styling.

coderabbitai[bot] commented 1 month ago

Walkthrough

The changes across the dpdata library primarily focus on optimizing import statements to reduce the initial loading time when importing the library. This includes moving imports to within functions where they are used, restructuring conditional imports, and removing unnecessary or redundant imports. Additionally, the linting rules have been updated to enforce these changes, ensuring that module-level imports are minimized.

Changes

Files/Modules	Change Summary
`dpdata/__init__.py`	Removed `fakemodule` class, adjusted `lzma` handling, restructured `USE_RDKIT` logic.
`dpdata/amber/md.py`	Moved `netcdf_file` import from `scipy.io` within the `read_amber_traj` function.
`dpdata/ase_calculator.py`	Added `# noqa: TID253` comment to `ase.calculators.calculator` import for linting.
`dpdata/bond_order_system.py`	Moved `Conformer` import from `rdkit.Chem` within the `to_fmt_obj` method.
`dpdata/deepmd/hdf5.py`	Conditional import of `h5py` based on `TYPE_CHECKING`, local import of `globfilter`.
`dpdata/gaussian/gjf.py`	Reorganized imports, used try-except for `openbabel`, local import of `csr_matrix` and `connected_components`.
`dpdata/periodic_table.py`	Switched from `monty.serialization.loadfn` to `json.load` for loading periodic table data.
`dpdata/plugins/ase.py`	Restructured imports related to ASE modules, added necessary imports within specific functions.
`dpdata/plugins/deepmd.py`	Conditional import of `h5py` based on `TYPE_CHECKING`, local import within `_from_system` function.
`dpdata/plugins/rdkit.py`	Moved `rdkit.Chem` imports to specific methods within classes `MolFormat` and `SdfFormat`.
`dpdata/pymatgen/molecule.py`	Moved `Molecule` import from `pymatgen.core` within the `to_system_data` function.
`dpdata/pymatgen/structure.py`	Removed `Structure` import and associated `try-except` block.
`dpdata/rdkit/sanitize.py`	Removed `openbabel` import, added `rdkit.Chem` and `BondType` imports within specific functions.
`dpdata/rdkit/utils.py`	Moved `Chem` import from `rdkit` to the top of the file.
`dpdata/system.py`	Removed inheritance from `MSONable`, added `from_dict` method and related imports.
`dpdata/unit.py`	Added `# noqa: TID253` comment to `constants` import from `scipy` for linting.
`pyproject.toml`	Introduced new linting rule `TID253` for banned module-level imports.
`tests/test_custom_data_type.py`	Added `# noqa: TID253` comment to `h5py` import for linting.
`tests/test_to_pymatgen_entry.py`	Added `# noqa: TID253` comment to `loadfn` import from `monty.serialization`.

Assessment against linked issues

Objective	Addressed	Explanation
Reduce import time by optimizing module imports (#526)	✅	The changes focus on moving imports to within functions and restructuring conditional imports, which minimizes the initial loading time.

These changes effectively address the primary objective of reducing the import time for the dpdata library, ensuring a more efficient loading process.

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codspeed-hq[bot] commented 1 month ago

CodSpeed Performance Report

Merging #658 will not alter performance

_{Comparing njzjz:move-imports (a236787) with devel (02309f7)}

Summary

✅ 2 untouched benchmarks

codecov[bot] commented 1 month ago

Codecov Report

Attention: Patch coverage is 80.30303% with 13 lines in your changes are missing coverage. Please review.

Project coverage is 83.86%. Comparing base (02309f7) to head (a236787).

Files	Patch %	Lines
dpdata/rdkit/sanitize.py	75.00%	4 Missing :warning:
dpdata/gaussian/gjf.py	66.66%	2 Missing :warning:
dpdata/plugins/ase.py	71.42%	2 Missing :warning:
dpdata/deepmd/hdf5.py	75.00%	1 Missing :warning:
dpdata/plugins/deepmd.py	85.71%	1 Missing :warning:
dpdata/plugins/rdkit.py	80.00%	1 Missing :warning:
dpdata/rdkit/utils.py	50.00%	1 Missing :warning:
dpdata/system.py	87.50%	1 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## devel #658 +/- ## ========================================== + Coverage 83.63% 83.86% +0.22% ========================================== Files 81 81 Lines 7009 6996 -13 ========================================== + Hits 5862 5867 +5 + Misses 1147 1129 -18 ```

:umbrella: View full report in Codecov by Sentry.
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njzjz commented 1 month ago

For the unknown reason, the benchmark doesn't work at all...

deepmodeling / dpdata