merge devel to master to release v0.13.1 #1721
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<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.8.1 → v0.8.2](astral-sh/ruff-pre-commit@v0.8.1...v0.8.2) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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Fix deepmodeling#1688. Though I am not sure whether we should have an upper version. <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **New Features** - Enhanced support for `deepmd` library versions 1.x to 3.x. - Improved handling of model deviation tasks with refined logic for training conditions. - Updated file management for better input/output file linking across tasks. - **Bug Fixes** - Clarified error messages for unsupported library versions. - **Documentation** - Updated documentation strings for argument compatibility and function behavior. - **Refactor** - Adjusted function signatures to accommodate new parameters and improved logic. <!-- end of auto-generated comment: release notes by coderabbit.ai -->
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.8.3 → v0.8.4](astral-sh/ruff-pre-commit@v0.8.3...v0.8.4) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
xref: materialsproject/pymatgen#4243 (comment) <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **Chores** - Updated GitHub Actions workflow configuration with a minor environment variable adjustment to support testing processes. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Reverts deepmodeling#1704 See materialsproject/pymatgen#4243 (comment) <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **Chores** - Updated GitHub Actions workflow configuration for testing. - Simplified test execution process in the CI pipeline. <!-- end of auto-generated comment: release notes by coderabbit.ai -->
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Fix the bug induced by the update of dpdata. Now the reading and writing of ABACUS STRU is by a more general dpdata/abacus interface, and remove some redundant codes. This commit is based on dpdata commit deepmodeling/dpdata#793, and it is valid after that commit is merged. related issue: deepmodeling#1711 <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **Refactor** - Streamlined the workflow for generating atomic structure data by removing redundant parameters and centralizing functionality. - Improved handling of atomic data structures for more efficient processing and organization. - **Tests** - Enhanced the precision of validations by refining comparisons to focus on key attributes, ensuring more robust result accuracy. - Corrected the method name for improved clarity in the test suite. - Added a new key to the test data structure for enhanced functionality in subsequent tests. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Co-authored-by: root <pxlxingliang> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **Chores** - Updated the minimum required version for a key dependency to ensure access to the latest enhancements and fixes. <!-- end of auto-generated comment: release notes by coderabbit.ai --> Co-authored-by: root <pxlxingliang>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.9.2 → v0.9.6](astral-sh/ruff-pre-commit@v0.9.2...v0.9.6) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
📝 WalkthroughWalkthroughThis PR updates dependency versions and enhances code style consistency by adding lint-suppression comments throughout the codebase. The pre-commit configuration is updated to use a newer version of the ruff hook, and the dpdata dependency version in the project configuration is bumped up. In addition, several functions across various modules and tests have been reformatted—for example, assertions and logging statements are condensed or renamed—to improve readability. Importantly, none of these changes alter the functional behavior of the code. Changes
Sequence Diagram(s)sequenceDiagram
participant Generator as DPGen Generator
participant VersionCheck as Version Check Block
Generator->>VersionCheck: Retrieve deepmd_version
VersionCheck-->>Generator: Return deepmd_version
alt Version Supported (>=1.x and <4)
Generator->>Generator: Proceed with file generation
else Version Unsupported
Generator->>Generator: Raise error message for unsupported DeepMD-kit version
end
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Actionable comments posted: 4
🧹 Nitpick comments (24)
dpgen/auto_test/lib/utils.py (1)
23-23: LGTM! Consider modernizing string formatting in future.The linter suppression is consistent with the PR's objectives of improving code style consistency. While the current change is appropriate for this release, consider updating to f-strings in a future PR for better readability:
- bk_dirname = dirname + ".bk%03d" % counter # noqa: UP031 + bk_dirname = f"{dirname}.bk{counter:03d}"dpgen/generator/run.py (23)
205-205: Use f-strings instead of %-formatting.The string formatting uses the older %-style formatting. For better readability and maintainability, use f-strings which are the preferred way in modern Python.
- "graph.%03d%s" % (ii, suffix), # noqa: UP031 + f"graph.{ii:03d}{suffix}",
652-652: Use f-strings instead of %-formatting.The string formatting uses the older %-style formatting. For better readability and maintainability, use f-strings which are the preferred way in modern Python.
- "training_iter0_model should be provided, and the number of models should be equal to %d" # noqa: UP031 - % numb_models + f"training_iter0_model should be provided, and the number of models should be equal to {numb_models}"
1070-1070: Use f-strings instead of %-formatting.The string formatting uses the older %-style formatting. For better readability and maintainability, use f-strings which are the preferred way in modern Python.
- raise RuntimeError("found %d keywords %s" % (len(found), key)) # noqa: UP031 + raise RuntimeError(f"found {len(found)} keywords {key}")
1082-1083: Use f-strings instead of %-formatting.The string formatting uses the older %-style formatting. For better readability and maintainability, use f-strings which are the preferred way in modern Python.
- lmp_lines[idx] = "pair_style deepmd %s %d model_devi.out\n" % ( # noqa: UP031 - graph_list, - trj_freq, + lmp_lines[idx] = f"pair_style deepmd {graph_list} {trj_freq} model_devi.out\n" - "pair_style deepmd %s out_freq %d out_file model_devi.out\n" # noqa: UP031 - % ( - graph_list, - trj_freq, + f"pair_style deepmd {graph_list} out_freq {trj_freq} out_file model_devi.out\n" - "pair_style deepmd %s out_freq %d out_file model_devi.out fparam ${ELE_TEMP}\n" # noqa: UP031 - % ( - graph_list, - trj_freq, + f"pair_style deepmd {graph_list} out_freq {trj_freq} out_file model_devi.out fparam ${{ELE_TEMP}}\n"Also applies to: 1089-1090, 1097-1098
1110-1111: Use f-strings instead of %-formatting.The string formatting uses the older %-style formatting. For better readability and maintainability, use f-strings which are the preferred way in modern Python.
- "dump dpgen_dump all custom %d all.lammpstrj id type x y z\n" # noqa: UP031 - % trj_freq + f"dump dpgen_dump all custom {trj_freq} all.lammpstrj id type x y z\n" - "dump dpgen_dump all custom %d traj/*.lammpstrj id type x y z\n" # noqa: UP031 - % trj_freq + f"dump dpgen_dump all custom {trj_freq} traj/*.lammpstrj id type x y z\n"Also applies to: 1115-1116
1239-1239: Use f-strings instead of %-formatting.The string formatting uses the older %-style formatting. For better readability and maintainability, use f-strings which are the preferred way in modern Python.
- "%s.%03d" % (_calypso_run_opt_path, temp_idx) # noqa: UP031 + f"{_calypso_run_opt_path}.{temp_idx:03d}" - calypso_run_opt_path.append("%s.%03d" % (_calypso_run_opt_path, 0)) # noqa: UP031 + calypso_run_opt_path.append(f"{_calypso_run_opt_path}.{0:03d}") - "%s.%03d" % (_calypso_run_opt_path, temp_idx) # noqa: UP031 + f"{_calypso_run_opt_path}.{temp_idx:03d}"Also applies to: 1242-1242, 1254-1254
1408-1409: Use f-strings instead of %-formatting.The string formatting uses the older %-style formatting. For better readability and maintainability, use f-strings which are the preferred way in modern Python.
- "ase opt traj %s frame %d with f devi %f does not belong to either accurate, candidiate and failed " # noqa: UP031 - % (tt, ii, all_conf[ii][4]) + f"ase opt traj {tt} frame {ii} with f devi {all_conf[ii][4]} does not belong to either accurate, candidiate and failed" - "md traj %s frame %d with f devi %f does not belong to either accurate, candidiate and failed, it should not happen" # noqa: UP031 - % (tt, ii, all_conf[ii][4]) + f"md traj {tt} frame {ii} with f devi {all_conf[ii][4]} does not belong to either accurate, candidiate and failed, it should not happen"Also applies to: 1413-1414
1435-1435: Use f-strings instead of %-formatting.The string formatting uses the older %-style formatting. For better readability and maintainability, use f-strings which are the preferred way in modern Python.
- "nframes (%d) in data sys %s is too small, skip" % (nframes, jj) # noqa: UP031 + f"nframes ({nframes}) in data sys {jj} is too small, skip"
1762-1762: Use f-strings instead of %-formatting.The string formatting uses the older %-style formatting. For better readability and maintainability, use f-strings which are the preferred way in modern Python.
- with open("low_level%d.mdin" % ii, "w") as f: # noqa: UP031 + with open(f"low_level{ii}.mdin", "w") as f: - open(os.path.join(work_path, "init%d.mdin" % ii), "w") as fw, # noqa: UP031 + open(os.path.join(work_path, f"init{ii}.mdin"), "w") as fw, - mdin_str = mdin_str.replace("@GRAPH_FILE%d@" % jj, mm) # noqa: UP031 + mdin_str = mdin_str.replace(f"@GRAPH_FILE{jj}@", mm)Also applies to: 1902-1902, 1922-1922
1978-1979: Use f-strings instead of %-formatting.The string formatting uses the older %-style formatting. For better readability and maintainability, use f-strings which are the preferred way in modern Python.
- "rr should not be iterable! sys: %d rr: %s r: %s" # noqa: UP031 - % (sys_idx[sys_counter], str(rr), str(r)) + f"rr should not be iterable! sys: {sys_idx[sys_counter]} rr: {str(rr)} r: {str(r)}"
2119-2119: Use f-strings instead of %-formatting.The string formatting uses the older %-style formatting. For better readability and maintainability, use f-strings which are the preferred way in modern Python.
- ("TASK=$(basename $(pwd)) && SYS1=${TASK:5:3} && SYS=$((10#$SYS1)) && ") + f"TASK=$(basename $(pwd)) && SYS1=${{TASK:5:3}} && SYS=$((10#$SYS1)) && "
2263-2264: Use f-strings instead of %-formatting.The string formatting uses the older %-style formatting. For better readability and maintainability, use f-strings which are the preferred way in modern Python.
- r"Not all beads generated the same number of lines in the model_devi${ibead}.out file. Check your pimd task carefully." + f"Not all beads generated the same number of lines in the model_devi{ibead}.out file. Check your pimd task carefully." - "Not all beads generated the same number of frames. Check your pimd task carefully." + f"Not all beads generated the same number of frames. Check your pimd task carefully."Also applies to: 2304-2305
2314-2314: Use f-strings instead of %-formatting.The string formatting uses the older %-style formatting. For better readability and maintainability, use f-strings which are the preferred way in modern Python.
- f"{frame_number + ibead * (int(last_step) + 1):d}.lammpstrj", + f"{frame_number + ibead * (int(last_step) + 1)}.lammpstrj",
3083-3083: Use f-strings instead of %-formatting.The string formatting uses the older %-style formatting. For better readability and maintainability, use f-strings which are the preferred way in modern Python.
- fp.write("IN.PSP%d = %s\n" % (idx + 1, ii)) # noqa: UP031 + fp.write(f"IN.PSP{idx + 1} = {ii}\n")
3250-3252: Use f-strings instead of %-formatting.The string formatting uses the older %-style formatting. For better readability and maintainability, use f-strings which are the preferred way in modern Python.
- assert len(fp_pp_files) == len(type_map), ( - "size of fp_pp_files should be the same as the size of type_map" - ) + assert len(fp_pp_files) == len(type_map), f"size of fp_pp_files ({len(fp_pp_files)}) should be the same as the size of type_map ({len(type_map)})"
3309-3311: Use f-strings instead of %-formatting.The string formatting uses the older %-style formatting. For better readability and maintainability, use f-strings which are the preferred way in modern Python.
- assert os.path.isfile(model_file), ( - f"Can not find the deepks model file {model_file}, which is defined in {ii}/INPUT" - ) + assert os.path.isfile(model_file), f"Can not find the deepks model file {model_file}, which is defined in {ii}/INPUT"
3326-3328: Use f-strings instead of %-formatting.The string formatting uses the older %-style formatting. For better readability and maintainability, use f-strings which are the preferred way in modern Python.
- assert "fp_dpks_descriptor" in jdata, ( - "need to define fp_dpks_descriptor in jdata" - ) + assert "fp_dpks_descriptor" in jdata, "need to define fp_dpks_descriptor in jdata"
3338-3340: Use f-strings instead of %-formatting.The string formatting uses the older %-style formatting. For better readability and maintainability, use f-strings which are the preferred way in modern Python.
- assert os.path.isfile(src_file), ( - f"Can not find the pseudopotential file {src_file}" - ) + assert os.path.isfile(src_file), f"Can not find the pseudopotential file {src_file}" - assert os.path.isfile(src_file), ( - f"Can not find the orbital file {src_file}" - ) + assert os.path.isfile(src_file), f"Can not find the orbital file {src_file}" - assert os.path.isfile(src_file), ( - f"Can not find the descriptor file {src_file}" - ) + assert os.path.isfile(src_file), f"Can not find the descriptor file {src_file}"Also applies to: 3344-3346, 3350-3352
3777-3777: Use f-strings instead of %-formatting.The string formatting uses the older %-style formatting. For better readability and maintainability, use f-strings which are the preferred way in modern Python.
- os.symlink(pp, "qmmm%d.parm7" % ii) # noqa: UP031 + os.symlink(pp, f"qmmm{ii}.parm7") - os.symlink(os.path.join(rst7_prefix, ss[0]), "init%d.rst7" % ii) # noqa: UP031 + os.symlink(os.path.join(rst7_prefix, ss[0]), f"init{ii}.rst7")Also applies to: 3781-3781
3831-3831: Use f-strings instead of %-formatting.The string formatting uses the older %-style formatting. For better readability and maintainability, use f-strings which are the preferred way in modern Python.
- raise RuntimeError("unknown task %d, something wrong" % jj) # noqa: UP031 + raise RuntimeError(f"unknown task {jj}, something wrong")
4206-4206: Use f-strings instead of %-formatting.The string formatting uses the older %-style formatting. For better readability and maintainability, use f-strings which are the preferred way in modern Python.
- dlog.info("failed tasks: %6d in %6d %6.2f %% " % (nfail, ntask, rfail * 100.0)) # noqa: UP031 + dlog.info(f"failed tasks: {nfail:6d} in {ntask:6d} {rfail * 100.0:6.2f} % ") - dlog.info("failed frame: %6d in %6d " % (icount, tcount)) # noqa: UP031 + dlog.info(f"failed frame: {icount:6d} in {tcount:6d} ") - "failed frame: %6d in %6d %6.2f %% " % (icount, tcount, rfail * 100.0) # noqa: UP031 + f"failed frame: {icount:6d} in {tcount:6d} {rfail * 100.0:6.2f} % "Also applies to: 4298-4298, 4302-4302
4537-4537: Use f-strings instead of %-formatting.The string formatting uses the older %-style formatting. For better readability and maintainability, use f-strings which are the preferred way in modern Python.
- dlog.info("failed frame: %6d in %6d " % (tcount - icount, tcount)) # noqa: UP031 + dlog.info(f"failed frame: {tcount - icount:6d} in {tcount:6d} ") - "failed frame: %6d in %6d %6.2f %% " # noqa: UP031 - % (tcount - icount, tcount, rfail * 100.0) + f"failed frame: {tcount - icount:6d} in {tcount:6d} {rfail * 100.0:6.2f} % "Also applies to: 4541-4542
4785-4785: Use f-strings instead of %-formatting.The string formatting uses the older %-style formatting. For better readability and maintainability, use f-strings which are the preferred way in modern Python.
- dlog.info("continue from iter %03d task %02d" % (iter_rec[0], iter_rec[1])) # noqa: UP031 + dlog.info(f"continue from iter {iter_rec[0]:03d} task {iter_rec[1]:02d}") - task_name = "task %02d" % jj # noqa: UP031 + task_name = f"task {jj:02d}"Also applies to: 4798-4798
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📒 Files selected for processing (62)
.pre-commit-config.yaml(1 hunks)doc/conf.py(1 hunks)dpgen/__init__.py(1 hunks)dpgen/auto_test/EOS.py(1 hunks)dpgen/auto_test/Elastic.py(1 hunks)dpgen/auto_test/Gamma.py(3 hunks)dpgen/auto_test/Interstitial.py(9 hunks)dpgen/auto_test/Surface.py(3 hunks)dpgen/auto_test/VASP.py(2 hunks)dpgen/auto_test/Vacancy.py(1 hunks)dpgen/auto_test/common_prop.py(2 hunks)dpgen/auto_test/lib/abacus.py(3 hunks)dpgen/auto_test/lib/lammps.py(8 hunks)dpgen/auto_test/lib/lmp.py(3 hunks)dpgen/auto_test/lib/mfp_eosfit.py(14 hunks)dpgen/auto_test/lib/pwscf.py(3 hunks)dpgen/auto_test/lib/siesta.py(4 hunks)dpgen/auto_test/lib/utils.py(1 hunks)dpgen/auto_test/lib/vasp.py(5 hunks)dpgen/auto_test/refine.py(2 hunks)dpgen/auto_test/reproduce.py(3 hunks)dpgen/collect/collect.py(2 hunks)dpgen/data/gen.py(18 hunks)dpgen/data/reaction.py(1 hunks)dpgen/data/surf.py(7 hunks)dpgen/data/tools/bcc.py(1 hunks)dpgen/data/tools/cessp2force_lin.py(2 hunks)dpgen/data/tools/create_random_disturb.py(4 hunks)dpgen/data/tools/diamond.py(1 hunks)dpgen/data/tools/fcc.py(1 hunks)dpgen/data/tools/hcp.py(1 hunks)dpgen/data/tools/io_lammps.py(3 hunks)dpgen/data/tools/sc.py(1 hunks)dpgen/generator/arginfo.py(2 hunks)dpgen/generator/lib/abacus_scf.py(9 hunks)dpgen/generator/lib/calypso_check_outcar.py(1 hunks)dpgen/generator/lib/calypso_run_model_devi.py(2 hunks)dpgen/generator/lib/calypso_run_opt.py(2 hunks)dpgen/generator/lib/gaussian.py(2 hunks)dpgen/generator/lib/lammps.py(5 hunks)dpgen/generator/lib/make_calypso.py(6 hunks)dpgen/generator/lib/pwmat.py(1 hunks)dpgen/generator/lib/pwscf.py(3 hunks)dpgen/generator/lib/run_calypso.py(8 hunks)dpgen/generator/lib/siesta.py(4 hunks)dpgen/generator/lib/utils.py(3 hunks)dpgen/generator/run.py(43 hunks)dpgen/simplify/simplify.py(4 hunks)dpgen/tools/collect_data.py(2 hunks)dpgen/tools/relabel.py(4 hunks)dpgen/tools/stat_sys.py(2 hunks)pyproject.toml(1 hunks)tests/auto_test/data.vasp.kp.gf/make_kp_test.py(1 hunks)tests/auto_test/test_abacus.py(2 hunks)tests/data/test_coll_abacus.py(1 hunks)tests/data/test_gen_bulk_abacus.py(1 hunks)tests/generator/comp_sys.py(7 hunks)tests/generator/gromacs/model_devi_case/model_devi.py(1 hunks)tests/generator/test_make_fp.py(26 hunks)tests/generator/test_make_md.py(11 hunks)tests/generator/test_make_train.py(10 hunks)tests/generator/test_post_fp.py(8 hunks)
✅ Files skipped from review due to trivial changes (49)
- dpgen/data/tools/bcc.py
- dpgen/data/tools/fcc.py
- dpgen/data/tools/hcp.py
- dpgen/data/tools/diamond.py
- doc/conf.py
- tests/generator/gromacs/model_devi_case/model_devi.py
- dpgen/init.py
- dpgen/collect/collect.py
- dpgen/auto_test/Vacancy.py
- dpgen/generator/lib/utils.py
- dpgen/auto_test/EOS.py
- dpgen/data/reaction.py
- tests/auto_test/data.vasp.kp.gf/make_kp_test.py
- dpgen/tools/collect_data.py
- dpgen/data/tools/cessp2force_lin.py
- dpgen/auto_test/refine.py
- dpgen/auto_test/Elastic.py
- dpgen/data/tools/sc.py
- dpgen/auto_test/lib/siesta.py
- dpgen/data/tools/io_lammps.py
- dpgen/auto_test/common_prop.py
- dpgen/auto_test/lib/lmp.py
- dpgen/generator/lib/siesta.py
- dpgen/generator/lib/gaussian.py
- dpgen/auto_test/lib/pwscf.py
- dpgen/generator/lib/calypso_run_opt.py
- dpgen/generator/lib/pwmat.py
- tests/generator/comp_sys.py
- dpgen/generator/lib/lammps.py
- dpgen/auto_test/VASP.py
- dpgen/generator/lib/calypso_run_model_devi.py
- dpgen/tools/relabel.py
- dpgen/auto_test/Surface.py
- dpgen/generator/lib/pwscf.py
- dpgen/generator/lib/make_calypso.py
- dpgen/auto_test/lib/lammps.py
- dpgen/auto_test/lib/vasp.py
- dpgen/auto_test/reproduce.py
- tests/generator/test_make_md.py
- dpgen/auto_test/Gamma.py
- dpgen/data/surf.py
- dpgen/auto_test/lib/mfp_eosfit.py
- tests/generator/test_make_train.py
- dpgen/generator/lib/run_calypso.py
- tests/generator/test_post_fp.py
- tests/generator/test_make_fp.py
- dpgen/simplify/simplify.py
- dpgen/auto_test/Interstitial.py
- dpgen/data/gen.py
⏰ Context from checks skipped due to timeout of 90000ms (1)
- GitHub Check: build (3.12)
🔇 Additional comments (17)
dpgen/tools/stat_sys.py (2)
42-42: LGTM!The addition of the
# noqa: UP031comment is consistent with the codebase-wide effort to suppress linting warnings for string formatting.
75-75: LGTM!The addition of the
# noqa: UP031comment is consistent with the codebase-wide effort to suppress linting warnings for string formatting.tests/data/test_coll_abacus.py (1)
25-27: LGTM!The assertion statement has been reformatted for better readability while maintaining the same functionality.
dpgen/data/tools/create_random_disturb.py (2)
77-77: LGTM!The
# noqa: UP031comments have been added to suppress linting warnings for string formatting, which is acceptable as the code functionality remains unchanged.Also applies to: 139-139, 211-211
195-195: LGTM!The code correctly assigns atom masses to the
masseskey to maintain compatibility with dpdata's expected structure.dpgen/auto_test/lib/abacus.py (3)
164-166: LGTM!The assertion statements have been reformatted for better readability while maintaining the same functionality.
Also applies to: 172-174, 180-182
336-336: LGTM!The
# noqa: UP031comment has been added to suppress a linting warning for string formatting, which is acceptable as the code functionality remains unchanged.
7-7:✅ Verification successful
Verify the updated import path.
The import path for
make_unlabeled_struhas been updated fromdpdata.abacus.scftodpdata.abacus.stru. Please ensure this change is compatible with the latest version of dpdata.
🌐 Web query:
What is the latest version of dpdata and where is make_unlabeled_stru located in it?💡 Result:
The latest version of dpdata available via conda-forge is v0.2.23[10].
The
make_unlabeled_strufunction is located in the dpdata.abacus.stru module[3][5]. This module handles parsing and generating structural data for ABACUS (Atomic-orbital Based Ab-initio Computation at UStc), a software package for electronic structure calculations.For example:
from dpdata.abacus.stru import make_unlabeled_struThis function assists in creating unlabeled structural data for compatibility with workflows requiring atomic configurations without energy/force labels[3][5].
Citations:
- 1: https://www.jisasoftech.com/dpdp-act-2023-key-updates-and-whats-new-in-2025-for-data-protection/
- 2: https://github.com/LiuGroupHNU/dpdata-1/blob/master/README.md
- 3: https://docs.deepmodeling.com/projects/dpdata/en/stable/api/dpdata.html
- 4: https://docs.deepmodeling.com/_/downloads/dpdata/en/latest/pdf/
- 5: https://docs.deepmodeling.com/projects/dpdata/en/master/api/dpdata.html
- 6: https://deepmd-kit.readthedocs.io/en/latest/data/dpdata.html
- 7: https://github.com/deepmodeling/dpdata
- 8: https://github.com/deepmodeling/dpdata/blob/master/README.md
- 9: https://docs.deepmodeling.com/projects/dpdata/en/master/index.html
- 10: https://anaconda.org/conda-forge/dpdata
Import Path Verified: The updated import statement is correct.
After reviewing the latest dpdata documentation, we can confirm that
make_unlabeled_struis now located in thedpdata.abacus.strumodule as of dpdata v0.2.23. The change fromdpdata.abacus.scftodpdata.abacus.struis valid and compatible with the latest version.
- File: dpgen/auto_test/lib/abacus.py, Line 7
- Change Verified:
from dpdata.abacus.stru import make_unlabeled_struis correct.tests/auto_test/test_abacus.py (1)
219-264: LGTM! Improved test precision with selective key comparison.The changes enhance the test by:
- Fixing the typo in the function name.
- Adding selective comparison of essential structure attributes.
dpgen/generator/lib/abacus_scf.py (4)
6-6: LGTM! Improved code readability and organization.The changes enhance the code by:
- Using the correct module for imports.
- Reformatting assertions for better readability.
- Adding consistent lint suppressions.
Also applies to: 48-53, 80-83, 95-97, 102-105, 108-111, 121-130, 133-143, 147-149, 154-157, 161-164, 180-183, 187-190
214-240: LGTM! Enhanced data validation and format consistency.The changes improve robustness by:
- Adding shape validation for cells and coords.
- Ensuring consistent 3D format.
- Improving file path construction.
256-287: LGTM! Enhanced function documentation and error handling.The changes improve the function by:
- Adding comprehensive docstring.
- Simplifying the function signature.
- Adding robust error handling and sensible defaults.
300-314: LGTM! Improved array handling and attribute support.The changes enhance the code by:
- Using numpy arrays for atom types.
- Adding support for move and spins attributes.
dpgen/generator/lib/calypso_check_outcar.py (1)
53-53: LGTM! The linter suppression is justified.The use of %-formatting here is intentional as it needs to match VASP's OUTCAR format requirements. The
noqa: UP031comment appropriately suppresses the warning while maintaining compatibility with VASP parsers..pre-commit-config.yaml (1)
31-31:❓ Verification inconclusive
Verify compatibility with the updated ruff version.
Please ensure that v0.9.6 is the intended version and check for any breaking changes or new rules that might affect the codebase.
🌐 Web query:
What are the breaking changes in ruff v0.9.6 compared to v0.7.4?💡 Result:
The key breaking changes between Ruff v0.7.4 and v0.9.6 include updates across formatter styles, configuration defaults, and diagnostic behaviors based on provided sources[1][2][3]. Here are the significant updates:
Formatter Style Changes
- Ruff2025 style guide adoption: Starting with v***.*_*****_*****._______._______.__.__.__.__.__.__._***_., code formatting aligns with stricter rules under "Ruff2025", potentially altering existing code layouts[1][2].
Configuration & Behavior Updates
Target Python Version
- Default Python target version: Changed from Python _.8 (prior) ****to ******._9 (post-v*******_). Projects without explicit
target_versionconfigurations may see new linting errors[1][2].Diagnostic Locations
- pydoclint diagnostics: Now point ****to ****the first line ****of ****the docstring instead ****of arbitrary positions[1][2].
Installer Paths
- Standalone installer directory: Changed ****from
~/.cargo/bin****to XDG-compliant paths (~/.local/bin)[1][2].Line Width Calculations
- Unicode character handling: Line widths ****now use an updated Unicode library (unicode-width) affecting
E501checks[1][2].Rule Updates
Renamed/Moved Rules
TRY302(useless-try-except) renamed ****toTRY203for consistency with external linters[1][2].Removed Settings
lintallow-unused-imports: Deprecated ****in favor ****oflint.pyflakesallow-unused-imports[1][2].
These updates require reviewing configurations (
target_version, exclude paths), adjusting suppression comments (noqaplacement), and rechecking formatted code against new style rules[1][2].Citations:
- 1: https://ruff.io/docs/release-notes.html
- 2: https://docs.powertools.aws.dev/lambda/python/stage/changelog/
- 3: https://github.com/astral-sh/ruff/blob/main/BREAKING_CHANGES.md
- 4: https://astral.sh/blog/ruff-v0.7.0
- 5: https://astral.sh/blog/ruff-v0.8.0
- 6: https://airflow.apache.org/docs/apache-airflow/stable/release_notes.html
- 7: https://pypi.org/project/ruff/
- 8: https://xon.sh/changelog.html
- 9: https://astral.sh/blog/ruff-v0.6.0
- 10: https://transportation.ky.gov/Highway-Design/Drainage%20Manual/HEC-14(2006-7).pdf
Ruff v0.9.6 Compatibility Verification
Please ensure that using
rev: v0.9.6is intentional. Note that compared to v0.7.4, Ruff v0.9.6 introduces several breaking changes that may impact your codebase:
- Formatter Style Update: Adoption of the Ruff2025 style guide could alter existing code formatting.
- Target Python Version Change: The default target Python version may have shifted (e.g., from Python 3.8 to 3.9), which might result in new linting errors if not explicitly set.
- Diagnostic Adjustments: Diagnostics from tools like pydoclint now point to the docstring’s first line, potentially affecting error locations.
- Installer Path Modification: The standalone installer now uses XDG-compliant paths, differing from previous defaults.
- Rule Updates: Some rule names have changed (e.g.,
TRY302renamed toTRY203), and certain settings (likelintallow-unused-imports) have been deprecated.Review your configuration and any suppression comments to ensure they align with these updates.
dpgen/generator/arginfo.py (1)
300-301: LGTM! Documentation update improves version requirement clarity.The documentation changes accurately clarify that the virial trust bounds can be used with any DeePMD-kit version 2 or above, rather than limiting it to specific v2.x versions.
Also applies to: 354-355
pyproject.toml (1)
22-22: Dependency Version Update: dpdata>=0.2.23The dpdata dependency has been updated from a previous constraint (>=0.2.17) to require version 0.2.23 or higher. This aligns with the PR’s objective of updating dependencies and ensures that any newer features or fixes in dpdata are available to the project. Please verify that this change is compatible with all modules that depend on dpdata (for example, any version-related checks or feature usage in
dpgen/generator/run.py).
| @@ -76,6 +76,7 @@ def test(self): | |||
| def testSTRU(self): | |||
| jdata = self.jdata | |||
| jdata["from_poscar_path"] = "./Cu.STRU" | |||
| jdata["potcars"] = ["abacus.in/Cu_ONCV_PBE-1.0.upf"] | |||
There was a problem hiding this comment.
💡 Verification agent
🧩 Analysis chain
Verify the UPF file path.
Please ensure that the UPF file exists at the specified path.
Run the following script to verify the file exists:
🏁 Script executed:
#!/bin/bash
# Description: Verify the UPF file exists.
# Test: Check if the file exists.
if [ -f "abacus.in/Cu_ONCV_PBE-1.0.upf" ]; then
echo "UPF file exists."
else
echo "UPF file not found."
fiLength of output: 91
Action Required: UPF File Missing
The file referenced in the "potcars" array in tests/data/test_gen_bulk_abacus.py (line 79) is not found on disk. Please ensure that either:
- The file
abacus.in/Cu_ONCV_PBE-1.0.upfis added to the repository in the correct location, or - The UPF file path is updated in the code to reference a valid, existing file.
Please address this to avoid issues during runtime.
| ) < Version("4"): | ||
| # 2.x |
There was a problem hiding this comment.
Update version check to support DeePMD-kit 4.x.
The version check limits DeePMD-kit version to 3.x, but according to the AI summary, the upper limit should be updated to 4.x.
- ) < Version("4"):
+ ) < Version("5"):Also applies to: 525-525
| @@ -818,7 +818,7 @@ def run_train_dp(iter_index, jdata, mdata): | |||
| commands.append(f"{train_command} compress") | |||
| else: | |||
| raise RuntimeError( | |||
| "DP-GEN currently only supports for DeePMD-kit 1.x or 2.x version!" | |||
| "DP-GEN currently only supports for DeePMD-kit 1.x to 3.x version!" | |||
There was a problem hiding this comment.
Update version check to support DeePMD-kit 4.x.
The version check limits DeePMD-kit version to 3.x, but according to the AI summary, the upper limit should be updated to 4.x.
- "DP-GEN currently only supports for DeePMD-kit 1.x to 3.x version!"
+ "DP-GEN currently only supports for DeePMD-kit 1.x to 4.x version!"📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| "DP-GEN currently only supports for DeePMD-kit 1.x to 3.x version!" | |
| "DP-GEN currently only supports for DeePMD-kit 1.x to 4.x version!" |
| @@ -1695,7 +1695,7 @@ def _make_model_devi_native_gromacs(iter_index, jdata, mdata, conf_systems): | |||
| # only support for deepmd v2.0 | |||
| if Version(mdata["deepmd_version"]) < Version("2.0"): | |||
| raise RuntimeError( | |||
| "Only support deepmd-kit 2.x for model_devi_engine='gromacs'" | |||
| "Only support deepmd-kit v2 or above for model_devi_engine='gromacs'" | |||
There was a problem hiding this comment.
Update version check to support DeePMD-kit 4.x.
The version check limits DeePMD-kit version to 3.x, but according to the AI summary, the upper limit should be updated to 4.x.
- "Only support deepmd-kit v2 or above for model_devi_engine='gromacs'"
+ "Only support deepmd-kit v2 or above for model_devi_engine='gromacs'. Currently supports up to v4.x"📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| "Only support deepmd-kit v2 or above for model_devi_engine='gromacs'" | |
| "Only support deepmd-kit v2 or above for model_devi_engine='gromacs'. Currently supports up to v4.x" |
Summary by CodeRabbit
Chores / Style Enhancements
Dependency Update
Compatibility Improvements
Test & Documentation Refinements