refact: refactor format backends into dpdata.formats#970
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refact: refactor format backends into dpdata.formats#970njzjz-bot wants to merge 3 commits intodeepmodeling:masterfrom
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Move all format directories (abacus, amber, cp2k, deepmd, dftbplus, fhi_aims, gaussian, gromacs, lammps, lmdb, md, openmx, orca, psi4, pwmat, pymatgen, qe, rdkit, siesta, vasp, xyz) into a new formats/ subdirectory. This addresses issue deepmodeling#934. Changes: - Created dpdata/formats/ directory - Moved all format directories to dpdata/formats/ - Updated all import statements throughout the codebase - Updated relative imports in format modules (from .. to from ...) - Updated dpdata/__init__.py to import from new locations - Updated tests/context.py for new import paths The plugins directory remains at the root level as requested.
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Merging this PR will degrade performance by 14.29%
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| Mode | Benchmark | BASE |
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| ❌ | WallTime | test_cli |
331.5 ms | 371.4 ms | -10.75% |
| ❌ | WallTime | test_import |
9.5 ms | 11.1 ms | -14.29% |
Comparing njzjz-bot:oc-fix-pr-946-ci (ae36482) with master (99ea3bb)
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #970 +/- ##
==========================================
+ Coverage 86.70% 86.71% +0.01%
==========================================
Files 86 89 +3
Lines 8039 8048 +9
==========================================
+ Hits 6970 6979 +9
Misses 1069 1069 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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📝 WalkthroughWalkthroughThis PR centralizes format-related modules under a new dpdata.formats package and updates import paths across the codebase to reference dpdata.formats.*. Package initializers for cp2k, gaussian, and qe were added and many relative imports adjusted for the deeper package nesting. ChangesModule reorganization into dpdata.formats (single cohesive DAG)
Estimated code review effort🎯 3 (Moderate) | ⏱️ ~25 minutes 🚥 Pre-merge checks | ✅ 4 | ❌ 1❌ Failed checks (1 warning)
✅ Passed checks (4 passed)
✏️ Tip: You can configure your own custom pre-merge checks in the settings. ✨ Finishing Touches🧪 Generate unit tests (beta)
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Actionable comments posted: 2
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⚠️ Outside diff range comments (2)
dpdata/bond_order_system.py (1)
81-91:⚠️ Potential issue | 🟠 Major | ⚡ Quick win
data-only initialization still raisesValueErrordue to branch structureWhen
datais provided withoutfile_name/rdkit_mol, Line 81 initializes from data, but control still reaches theelseat Line 91 and raises. This breaks the documenteddatainit path.Proposed fix
- if data: + if data is not None: mol = dpdata.formats.rdkit.utils.system_data_to_mol(data) self.from_rdkit_mol(mol) - if file_name: + elif file_name: self.from_fmt( file_name, fmt, type_map=type_map, begin=begin, step=step, **kwargs ) - elif rdkit_mol: + elif rdkit_mol is not None: self.from_rdkit_mol(rdkit_mol) else: raise ValueError("Please specify a mol/sdf file or a rdkit Mol object")🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the rest with a brief reason, keep changes minimal, and validate. In `@dpdata/bond_order_system.py` around lines 81 - 91, The init path processes `data` but then continues into the file/rdkit branches and hits the final else, causing the erroneous ValueError; update the conditional flow in the BondOrderSystem initializer (or the method handling construction) so that the `data` case stops further branching—either change the `if data:` block to `if data: ... elif file_name: ... elif rdkit_mol: ... else: ...` or keep `if data:` and add an immediate return after calling from_rdkit_mol; ensure you reference the existing calls to dpdata.formats.rdkit.utils.system_data_to_mol, self.from_rdkit_mol, and self.from_fmt when making the change.dpdata/plugins/pymatgen.py (1)
72-72:⚠️ Potential issue | 🟠 Major | ⚡ Quick winAdd missing import
dpdata.systemto fix runtime AttributeError.Line 72 uses
dpdata.system.remove_pbc(data), butdpdata.systemis not imported. Thedpdatapackage does not re-export thesystemmodule in its__init__.py—only individual classes from it are exposed. This will raiseAttributeErrorat runtime whento_systemis called on aPyMatgenMoleculeFormatinstance.Proposed fix — add explicit import
import dpdata.formats.pymatgen.molecule import dpdata.formats.pymatgen.structure +import dpdata.system from dpdata.format import Format🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the rest with a brief reason, keep changes minimal, and validate. In `@dpdata/plugins/pymatgen.py` at line 72, The call data = dpdata.system.remove_pbc(data) fails at runtime because the dpdata.system submodule isn't imported; add an explicit import (e.g., import dpdata.system) at the top of the file and then leave the call in PyMatgenMoleculeFormat.to_system as-is so dpdata.system.remove_pbc(data) resolves correctly.
🧹 Nitpick comments (1)
dpdata/plugins/xyz.py (1)
11-14: ⚡ Quick winRuntime imports placed after the
if TYPE_CHECKING:block — invert the order.Lines 13–14 are unconditional runtime imports but appear after the
if TYPE_CHECKING:guard. The conventional (and ruff/isort-expected) layout places theif TYPE_CHECKING:block last among all imports. This ordering may trigger anI001violation depending on the project's ruff configuration.♻️ Proposed fix
+from dpdata.formats.xyz.quip_gap_xyz import QuipGapxyzSystems, format_single_frame +from dpdata.formats.xyz.xyz import coord_to_xyz, xyz_to_coord + if TYPE_CHECKING: from dpdata.utils import FileType -from dpdata.formats.xyz.quip_gap_xyz import QuipGapxyzSystems, format_single_frame -from dpdata.formats.xyz.xyz import coord_to_xyz, xyz_to_coordAs per coding guidelines,
dpdata/**/*.pyfiles must passruff check dpdata/before committing.🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the rest with a brief reason, keep changes minimal, and validate. In `@dpdata/plugins/xyz.py` around lines 11 - 14, The import ordering is wrong: move the TYPE_CHECKING block so it comes after the runtime imports (i.e., place the "if TYPE_CHECKING: from dpdata.utils import FileType" block below the imports of QuipGapxyzSystems, format_single_frame, coord_to_xyz, and xyz_to_coord) to satisfy ruff/isort expectations and avoid I001; ensure the runtime symbols QuipGapxyzSystems, format_single_frame, coord_to_xyz, and xyz_to_coord remain imported unconditionally and only FileType is guarded by TYPE_CHECKING.
🤖 Prompt for all review comments with AI agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
Inline comments:
In `@dpdata/__init__.py`:
- Line 4: Run ruff check and fix the reported lint issues: sort the __all__
lists in dpdata/__init__ and dpdata/formats/deepmd/hdf5.py, replace mutable
default args/attributes in functions/classes (e.g., in ase_calculator.py,
rdf.py, water.py) with None and set defaults inside the function or __init__,
add explicit stacklevel=2 to all warnings.warn calls, rename variables shadowing
builtins (e.g., in driver.py, hdf5.py and pwmat-related files), remove or use
unused loop control variables (abacus, cp2k, fhi_aims, gromacs, lammps, md,
openmx, pwmat modules) or replace with _ if intentionally unused, add strict=...
to zip() calls, and address the remaining RUF/B/BLE/etc. issues (unused
unpacking, unnecessary conversions/concatenations, empty abstract methods,
assert False, missing shebangs, ambiguous names, overly broad exception
handlers) as indicated by ruff to make the codebase clean.
In `@dpdata/plugins/openmx.py`:
- Line 64: The unpacked variable `cs` from the call to
dpdata.formats.openmx.omx.to_system_data(fname, mdname) is unused and causes a
Ruff RUF059 lint error; update the unpack to either capture the unused value as
`_` (e.g., `data, _ = ...`) or assign only `data` (e.g., `data = ...`) inside
openmx.py where the call occurs, and then run ruff check dpdata/ and ruff format
dpdata/ to ensure linting/formatting compliance.
---
Outside diff comments:
In `@dpdata/bond_order_system.py`:
- Around line 81-91: The init path processes `data` but then continues into the
file/rdkit branches and hits the final else, causing the erroneous ValueError;
update the conditional flow in the BondOrderSystem initializer (or the method
handling construction) so that the `data` case stops further branching—either
change the `if data:` block to `if data: ... elif file_name: ... elif rdkit_mol:
... else: ...` or keep `if data:` and add an immediate return after calling
from_rdkit_mol; ensure you reference the existing calls to
dpdata.formats.rdkit.utils.system_data_to_mol, self.from_rdkit_mol, and
self.from_fmt when making the change.
In `@dpdata/plugins/pymatgen.py`:
- Line 72: The call data = dpdata.system.remove_pbc(data) fails at runtime
because the dpdata.system submodule isn't imported; add an explicit import
(e.g., import dpdata.system) at the top of the file and then leave the call in
PyMatgenMoleculeFormat.to_system as-is so dpdata.system.remove_pbc(data)
resolves correctly.
---
Nitpick comments:
In `@dpdata/plugins/xyz.py`:
- Around line 11-14: The import ordering is wrong: move the TYPE_CHECKING block
so it comes after the runtime imports (i.e., place the "if TYPE_CHECKING: from
dpdata.utils import FileType" block below the imports of QuipGapxyzSystems,
format_single_frame, coord_to_xyz, and xyz_to_coord) to satisfy ruff/isort
expectations and avoid I001; ensure the runtime symbols QuipGapxyzSystems,
format_single_frame, coord_to_xyz, and xyz_to_coord remain imported
unconditionally and only FileType is guarded by TYPE_CHECKING.
🪄 Autofix (Beta)
Fix all unresolved CodeRabbit comments on this PR:
- Push a commit to this branch (recommended)
- Create a new PR with the fixes
ℹ️ Review info
⚙️ Run configuration
Configuration used: Organization UI
Review profile: CHILL
Plan: Pro
Run ID: 9d56fd68-bd9e-45f8-b025-b4160b3f00b9
📒 Files selected for processing (99)
dpdata/__init__.pydpdata/bond_order_system.pydpdata/formats/__init__.pydpdata/formats/abacus/__init__.pydpdata/formats/abacus/md.pydpdata/formats/abacus/relax.pydpdata/formats/abacus/scf.pydpdata/formats/abacus/stru.pydpdata/formats/amber/__init__.pydpdata/formats/amber/mask.pydpdata/formats/amber/md.pydpdata/formats/amber/sqm.pydpdata/formats/cp2k/__init__.pydpdata/formats/cp2k/cell.pydpdata/formats/cp2k/output.pydpdata/formats/deepmd/__init__.pydpdata/formats/deepmd/comp.pydpdata/formats/deepmd/hdf5.pydpdata/formats/deepmd/mixed.pydpdata/formats/deepmd/raw.pydpdata/formats/dftbplus/__init__.pydpdata/formats/dftbplus/output.pydpdata/formats/fhi_aims/__init__.pydpdata/formats/fhi_aims/output.pydpdata/formats/gaussian/__init__.pydpdata/formats/gaussian/fchk.pydpdata/formats/gaussian/gjf.pydpdata/formats/gaussian/log.pydpdata/formats/gromacs/__init__.pydpdata/formats/gromacs/gro.pydpdata/formats/lammps/__init__.pydpdata/formats/lammps/dump.pydpdata/formats/lammps/lmp.pydpdata/formats/lmdb/__init__.pydpdata/formats/lmdb/format.pydpdata/formats/md/__init__.pydpdata/formats/md/msd.pydpdata/formats/md/pbc.pydpdata/formats/md/rdf.pydpdata/formats/md/water.pydpdata/formats/openmx/__init__.pydpdata/formats/openmx/omx.pydpdata/formats/orca/__init__.pydpdata/formats/orca/output.pydpdata/formats/psi4/__init__.pydpdata/formats/psi4/input.pydpdata/formats/psi4/output.pydpdata/formats/pwmat/__init__.pydpdata/formats/pwmat/atomconfig.pydpdata/formats/pwmat/movement.pydpdata/formats/pymatgen/__init__.pydpdata/formats/pymatgen/molecule.pydpdata/formats/pymatgen/structure.pydpdata/formats/qe/__init__.pydpdata/formats/qe/scf.pydpdata/formats/qe/traj.pydpdata/formats/rdkit/__init__.pydpdata/formats/rdkit/sanitize.pydpdata/formats/rdkit/utils.pydpdata/formats/siesta/__init__.pydpdata/formats/siesta/aiMD_output.pydpdata/formats/siesta/output.pydpdata/formats/vasp/__init__.pydpdata/formats/vasp/outcar.pydpdata/formats/vasp/poscar.pydpdata/formats/vasp/xml.pydpdata/formats/xyz/__init__.pydpdata/formats/xyz/quip_gap_xyz.pydpdata/formats/xyz/xyz.pydpdata/plugins/3dmol.pydpdata/plugins/abacus.pydpdata/plugins/amber.pydpdata/plugins/cp2k.pydpdata/plugins/deepmd.pydpdata/plugins/dftbplus.pydpdata/plugins/fhi_aims.pydpdata/plugins/gaussian.pydpdata/plugins/gromacs.pydpdata/plugins/lammps.pydpdata/plugins/lmdb.pydpdata/plugins/openmx.pydpdata/plugins/orca.pydpdata/plugins/psi4.pydpdata/plugins/pwmat.pydpdata/plugins/pymatgen.pydpdata/plugins/qe.pydpdata/plugins/rdkit.pydpdata/plugins/siesta.pydpdata/plugins/vasp.pydpdata/plugins/xyz.pydpdata/siesta/__init__.pydpdata/system.pydpdata/vasp/__init__.pydpdata/xyz/__init__.pytests/context.pytests/test_abacus_stru_dump.pytests/test_lammps_lmp_dump.pytests/test_lammps_spin.pytests/test_lmdb.py
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Pull request overview
This PR rebases the prior directory reorganization (moving format implementations under dpdata.formats) and updates internal imports/tests accordingly, with the stated goal of restoring backward-compatible access to historically public helper modules/namespaces after the move.
Changes:
- Relocates/introduces many format implementation modules under
dpdata/formats/**(e.g., VASP/LAMMPS/QE/Gaussian/CP2K/LMDB, etc.). - Updates plugin modules and some core code to import from
dpdata.formats.*instead of historical locations. - Adds a lazy attribute-based loader in
dpdata/__init__.pyfor some format modules (cp2k,gaussian,qe).
Reviewed changes
Copilot reviewed 44 out of 99 changed files in this pull request and generated 4 comments.
Show a summary per file
| File | Description |
|---|---|
dpdata/__init__.py |
Switches top-level exports to dpdata.formats.* and adds lazy __getattr__ for some format modules. |
dpdata/system.py |
Updates internal imports to dpdata.formats.md.pbc and dpdata.formats.amber.mask. |
dpdata/bond_order_system.py |
Updates RDKit helpers import path to dpdata.formats.rdkit.*. |
dpdata/plugins/3dmol.py |
Updates XYZ helper import path to dpdata.formats.xyz.xyz. |
dpdata/plugins/abacus.py |
Points ABACUS plugin imports to dpdata.formats.abacus.*. |
dpdata/plugins/amber.py |
Points Amber plugin imports to dpdata.formats.amber.*. |
dpdata/plugins/cp2k.py |
Points CP2K plugin imports to dpdata.formats.cp2k.output. |
dpdata/plugins/deepmd.py |
Points DeePMD plugin imports to dpdata.formats.deepmd.*. |
dpdata/plugins/dftbplus.py |
Points DFTB+ plugin imports to dpdata.formats.dftbplus.output. |
dpdata/plugins/fhi_aims.py |
Points FHI-aims plugin imports to dpdata.formats.fhi_aims.output. |
dpdata/plugins/gaussian.py |
Points Gaussian plugin imports to dpdata.formats.gaussian.* and updates doc references. |
dpdata/plugins/gromacs.py |
Points Gromacs plugin imports to dpdata.formats.gromacs.gro. |
dpdata/plugins/lammps.py |
Points LAMMPS plugin imports to dpdata.formats.lammps.*. |
dpdata/plugins/lmdb.py |
Registers LMDB format via dpdata.formats.lmdb.format.LMDBFormat. |
dpdata/plugins/openmx.py |
Points OpenMX plugin imports to dpdata.formats.openmx.* and dpdata.formats.md.pbc. |
dpdata/plugins/orca.py |
Points ORCA plugin imports to dpdata.formats.orca.output. |
dpdata/plugins/psi4.py |
Points Psi4 plugin imports to dpdata.formats.psi4.*. |
dpdata/plugins/pwmat.py |
Points PWMAT plugin imports to dpdata.formats.pwmat.*. |
dpdata/plugins/pymatgen.py |
Points pymatgen plugin imports to dpdata.formats.pymatgen.*. |
dpdata/plugins/qe.py |
Points QE plugin imports to dpdata.formats.qe.* and dpdata.formats.md.pbc. |
dpdata/plugins/rdkit.py |
Points RDKit plugin imports to dpdata.formats.rdkit.utils. |
dpdata/plugins/siesta.py |
Points SIESTA plugin imports to dpdata.formats.siesta.*. |
dpdata/plugins/vasp.py |
Points VASP plugin imports to dpdata.formats.vasp.*. |
dpdata/plugins/xyz.py |
Points XYZ plugin imports to dpdata.formats.xyz.*. |
dpdata/formats/__init__.py |
Introduces the dpdata.formats package marker. |
dpdata/formats/abacus/md.py |
Adds/relocates ABACUS MD reader under formats. |
dpdata/formats/abacus/relax.py |
Adds/relocates ABACUS relax reader under formats. |
dpdata/formats/abacus/scf.py |
Adjusts imports for ABACUS SCF under formats. |
dpdata/formats/abacus/stru.py |
Adjusts imports for ABACUS STRU under formats. |
dpdata/formats/amber/mask.py |
Adds/relocates Amber mask utilities under formats. |
dpdata/formats/amber/md.py |
Adjusts imports for Amber MD under formats. |
dpdata/formats/amber/sqm.py |
Adds/relocates SQM parsing/input generation under formats. |
dpdata/formats/cp2k/cell.py |
Adds/relocates CP2K cell helper under formats. |
dpdata/formats/cp2k/output.py |
Adjusts imports for CP2K output reader under formats. |
dpdata/formats/deepmd/comp.py |
Adds/relocates deepmd/npy (“comp”) support under formats. |
dpdata/formats/deepmd/hdf5.py |
Adds/relocates deepmd/hdf5 support under formats. |
dpdata/formats/deepmd/mixed.py |
Adds/relocates deepmd mixed-type utilities under formats. |
dpdata/formats/deepmd/raw.py |
Adds/relocates deepmd/raw support under formats. |
dpdata/formats/dftbplus/output.py |
Adds/relocates DFTB+ output reader under formats. |
dpdata/formats/fhi_aims/output.py |
Adds/relocates FHI-aims output reader under formats. |
dpdata/formats/gaussian/fchk.py |
Adjusts relative imports for Gaussian fchk under formats. |
dpdata/formats/gaussian/gjf.py |
Adds/relocates Gaussian input generator/parser under formats. |
dpdata/formats/gaussian/log.py |
Adjusts relative imports for Gaussian log under formats. |
dpdata/formats/gromacs/gro.py |
Adjusts relative imports for Gromacs gro under formats. |
dpdata/formats/lammps/dump.py |
Adds/relocates LAMMPS dump parsing/writing under formats. |
dpdata/formats/lammps/lmp.py |
Adds/relocates LAMMPS data-file parsing/writing under formats. |
dpdata/formats/lmdb/format.py |
Adds/relocates LMDB format implementation under formats. |
dpdata/formats/md/msd.py |
Adds/relocates MSD implementation under formats. |
dpdata/formats/md/pbc.py |
Adds/relocates PBC utilities under formats. |
dpdata/formats/md/rdf.py |
Adds/relocates RDF implementation under formats. |
dpdata/formats/md/water.py |
Adds/relocates water analysis utilities under formats. |
dpdata/formats/openmx/omx.py |
Adjusts relative imports for OpenMX under formats. |
dpdata/formats/orca/output.py |
Adds/relocates ORCA output reader under formats. |
dpdata/formats/psi4/input.py |
Adds/relocates Psi4 input writer under formats. |
dpdata/formats/psi4/output.py |
Adds/relocates Psi4 output reader under formats. |
dpdata/formats/pwmat/atomconfig.py |
Adjusts relative imports for PWMAT atomconfig under formats. |
dpdata/formats/pwmat/movement.py |
Adjusts relative imports for PWMAT movement under formats. |
dpdata/formats/pymatgen/molecule.py |
Adds/relocates pymatgen Molecule conversion under formats. |
dpdata/formats/pymatgen/structure.py |
Adds/relocates pymatgen Structure conversion under formats. |
dpdata/formats/qe/scf.py |
Adds/relocates QE SCF parsing under formats. |
dpdata/formats/qe/traj.py |
Fixes relative imports within QE traj under formats. |
dpdata/formats/rdkit/utils.py |
Adds/relocates RDKit helper utilities under formats. |
dpdata/formats/siesta/aiMD_output.py |
Adds/relocates SIESTA aiMD output reader under formats. |
dpdata/formats/siesta/output.py |
Adds/relocates SIESTA output reader under formats. |
dpdata/formats/vasp/outcar.py |
Adds/relocates VASP OUTCAR parsing under formats. |
dpdata/formats/vasp/poscar.py |
Adds/relocates VASP POSCAR parsing/writing under formats. |
dpdata/formats/vasp/xml.py |
Adds/relocates VASP XML parsing under formats. |
dpdata/formats/xyz/quip_gap_xyz.py |
Adds/relocates QUIP/GAP XYZ support under formats. |
dpdata/formats/xyz/xyz.py |
Adds/relocates basic XYZ conversions under formats. |
tests/context.py |
Updates import smoke-loading to dpdata.formats.*. |
tests/test_abacus_stru_dump.py |
Updates ABACUS test imports to dpdata.formats.abacus.*. |
tests/test_lammps_lmp_dump.py |
Updates LAMMPS test imports to dpdata.formats.lammps.*. |
tests/test_lammps_spin.py |
Updates LAMMPS test imports to dpdata.formats.lammps.*. |
tests/test_lmdb.py |
Updates LMDB test imports to dpdata.formats.lmdb.*. |
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This PR fixes the CI failures from #946 after moving implementation modules.
Changes:
dpdata.formats.dpdata.mdinstead ofdpdata.formats.md.dpdata.lammps/dpdata.vaspas top-level exports.dpdata.formats.dpdata.formats.cp2k.cell.cell_to_low_triangledpdata.formats.gaussian.gjf.detect_multiplicitydpdata.formats.qe.traj.convert_celldmdpdata.md.msd.msddpdata.md.water.*Local checks:
cd tests && uv run pytest test_msd.py test_water_ions.py -q→ 3 passeduv run pytest tests/test_cell_to_low_triangle.py tests/test_gaussian_driver.py::TestMakeGaussian::test_detect_multiplicity tests/test_qe_cp_traj.py::TestConverCellDim -q→ 8 passeduv run pyright→ 0 errors / 0 warningsgit grep -n "formats\.md\|from dpdata\.formats\.md\|dpdata\.formats\.md" -- . ':(exclude)tests/data'→ no matchesAuthored by OpenClaw (model: custom-chat-jinzhezeng-group/gpt-5.5)