chore(pre-commit): use mdformat to format Markdown

.pre-commit-config.yaml

@@ -34,8 +34,18 @@ repos:
     hooks:
     - id: velin
       args: ["--write"]
-# Python inside docs
--   repo: https://github.com/asottile/blacken-docs
-    rev: 1.20.0
+# markdown
+-   repo: https://github.com/hukkin/mdformat
+    rev: 1.0.0
     hooks:
-    -   id: blacken-docs
+    -   id: mdformat
+        exclude: "^tests/.*$"
+        additional_dependencies:
+          # - mdformat-myst==0.3.0
+          # See https://github.com/executablebooks/mdformat-myst/issues/13
+          - "git+https://github.com/njzjz-bothub/mdformat-myst@d9c414e#egg=mdformat-myst"
+          - mdformat-ruff==0.1.3
+          - mdformat-web==0.2.0
+          - mdformat-config==0.2.1
+          - mdformat-beautysh==1.0.0
+          - mdformat-gfm-alerts==2.0.0

AGENTS.md

@@ -7,51 +7,60 @@ Always reference these instructions first and fallback to search or bash command
 ## Working Effectively
 
 - **Bootstrap and install the repository:**
+
   - `cd /home/runner/work/dpdata/dpdata` (or wherever the repo is cloned)
   - `uv pip install -e .` -- installs dpdata in development mode with core dependencies (numpy, scipy, h5py, monty, wcmatch)
   - Test installation: `dpdata --version` -- should show version like "dpdata v0.1.dev2+..."
 
 - **Run tests:**
+
   - `cd tests && python -m unittest discover` -- runs all 1826 tests in ~10 seconds. NEVER CANCEL.
   - `cd tests && python -m unittest test_<module>.py` -- run specific test modules (individual modules take ~0.5 seconds)
   - `cd tests && coverage run --source=../dpdata -m unittest discover && coverage report` -- run tests with coverage
 
 - **Linting and formatting:**
+
   - Install ruff: `uv pip install ruff`
   - `ruff check dpdata/` -- lint the main package (takes ~1 second)
   - `ruff format dpdata/` -- format code according to project style
   - `ruff check --fix dpdata/` -- auto-fix linting issues where possible
 
 - **Pre-commit hooks:**
+
   - Install: `uv pip install pre-commit`
   - `pre-commit run --all-files` -- run all hooks on all files
   - Hooks include: ruff linting/formatting, trailing whitespace, end-of-file-fixer, yaml/json/toml checks
 
 ## Validation
 
 - **Always test CLI functionality after making changes:**
+
   - `dpdata --help` -- ensure CLI still works
   - `dpdata --version` -- verify version is correct
   - Test a basic conversion if sample data is available
 
 - **Always run linting before committing:**
+
   - `ruff check dpdata/` -- ensure no new linting errors
   - `ruff format dpdata/` -- ensure code is properly formatted
 
 - **Run relevant tests for your changes:**
+
   - For format-specific changes: `cd tests && python -m unittest test_<format>*.py`
   - For core system changes: `cd tests && python -m unittest test_system*.py test_multisystems.py`
   - For CLI changes: `cd tests && python -m unittest test_cli.py` (if exists)
 
 ## Build and Documentation
 
 - **Documentation:**
+
   - `cd docs && make help` -- see all available build targets
   - `cd docs && make html` -- build HTML documentation (requires additional dependencies)
   - Documentation source is in `docs/` directory using Sphinx
   - **NOTE:** Full docs build requires additional dependencies like `deepmodeling-sphinx` that may not be readily available
 
 - **Package building:**
+
   - Uses setuptools with pyproject.toml configuration
   - `uv pip install build && python -m build` -- create source and wheel distributions
   - Version is managed by setuptools_scm from git tags
@@ -61,6 +70,7 @@ Always reference these instructions first and fallback to search or bash command
 The following are outputs from frequently run commands. Reference them instead of re-running to save time.
 
 ### Repository structure
+
 ```
 /home/runner/work/dpdata/dpdata/
 ├── dpdata/           # Main package code
@@ -82,39 +92,46 @@ The following are outputs from frequently run commands. Reference them instead o
 ```
 
 ### Key dependencies
+
 - Core: numpy>=1.14.3, scipy, h5py, monty, wcmatch
 - Optional: ase (ASE integration), parmed (AMBER), pymatgen (Materials Project), rdkit (molecular analysis)
 - Testing: unittest (built-in), coverage
 - Linting: ruff
 - Docs: sphinx with various extensions
 
 ### Test timing expectations
+
 - Full test suite: ~10 seconds (1826 tests). NEVER CANCEL.
 - Individual test modules: ~0.5 seconds
 - Linting with ruff: ~1 second
 - Documentation build: ~30 seconds
 
 ### Common workflows
+
 1. **Adding a new format:**
+
    - Create module in `dpdata/<format>/`
    - Implement format classes inheriting from appropriate base classes
    - Add tests in `tests/test_<format>*.py`
    - Register format in the plugin system
 
-2. **Fixing bugs:**
+1. **Fixing bugs:**
+
    - Write test that reproduces the bug first
    - Make minimal fix to pass the test
    - Run full test suite to ensure no regressions
    - Run linting to ensure code style compliance
 
-3. **CLI changes:**
+1. **CLI changes:**
+
    - Modify `dpdata/cli.py`
    - Test with `dpdata --help` and specific commands
    - Add/update tests if needed
 
 ## Troubleshooting
 
 - **Installation timeouts:** Network timeouts during `uv pip install` are common. If this occurs, try:
+
   - Individual package installation: `uv pip install numpy scipy h5py monty wcmatch`
   - Use `--timeout` option: `uv pip install --timeout 300 -e .`
   - Verify existing installation works: `dpdata --version` should work even if reinstall fails

docs/systems/bond_order_system.md

@@ -1,6 +1,7 @@
-
 ## BondOrderSystem
+
 A new class {class}`BondOrderSystem <dpdata.BondOrderSystem>` which inherits from class {class}`System <dpdata.System>` is introduced in dpdata. This new class contains information of chemical bonds and formal charges (stored in `BondOrderSystem.data['bonds']`, `BondOrderSystem.data['formal_charges']`). Now BondOrderSystem can only read from .mol/.sdf formats, because of its dependency on rdkit (which means rdkit must be installed if you want to use this function). Other formats, such as pdb, must be converted to .mol/.sdf format (maybe with software like open babel).
+
 ```python
 import dpdata
 
@@ -11,8 +12,10 @@ system_2 = dpdata.BondOrderSystem(
     "tests/bond_order/methane.sdf", fmt="sdf"
 )  # read from .sdf file
 ```
+
 In sdf file, all molecules must be of the same topology (i.e. conformers of the same molecular configuration).
 `BondOrderSystem <dpdata.BondOrderSystem>` also supports initialize from a {class}`rdkit.Chem.rdchem.Mol` object directly.
+
 ```python
 from rdkit import Chem
 from rdkit.Chem import AllChem
@@ -25,21 +28,26 @@ system = dpdata.BondOrderSystem(rdkit_mol=mol)
 ```
 
 ### Bond Order Assignment
+
 The {class}`BondOrderSystem <dpdata.BondOrderSystem>` implements a more robust sanitize procedure for rdkit Mol, as defined in {class}`dpdata.rdkit.santizie.Sanitizer`. This class defines 3 level of sanitization process by: low, medium and high. (default is medium).
-+ low: use `rdkit.Chem.SanitizeMol()` function to sanitize molecule.
-+ medium: before using rdkit, the programm will first assign formal charge of each atom to avoid inappropriate valence exceptions. However, this mode requires the rightness of the bond order information in the given molecule.
-+ high: the program will try to fix inappropriate bond orders in aromatic hetreocycles, phosphate, sulfate, carboxyl, nitro, nitrine, guanidine groups. If this procedure fails to sanitize the given molecule, the program will then try to call `obabel` to pre-process the mol and repeat the sanitization procedure. **That is to say, if you wan't to use this level of sanitization, please ensure `obabel` is installed in the environment.**
-According to our test, our sanitization procedure can successfully read 4852 small molecules in the PDBBind-refined-set. It is necessary to point out that the in the molecule file (mol/sdf), the number of explicit hydrogens has to be correct. Thus, we recommend to use
- `obabel xxx -O xxx -h` to pre-process the file. The reason why we do not implement this hydrogen-adding procedure in dpdata is that we can not ensure its correctness.
+
+- low: use `rdkit.Chem.SanitizeMol()` function to sanitize molecule.
+- medium: before using rdkit, the programm will first assign formal charge of each atom to avoid inappropriate valence exceptions. However, this mode requires the rightness of the bond order information in the given molecule.
+- high: the program will try to fix inappropriate bond orders in aromatic hetreocycles, phosphate, sulfate, carboxyl, nitro, nitrine, guanidine groups. If this procedure fails to sanitize the given molecule, the program will then try to call `obabel` to pre-process the mol and repeat the sanitization procedure. **That is to say, if you wan't to use this level of sanitization, please ensure `obabel` is installed in the environment.**
+  According to our test, our sanitization procedure can successfully read 4852 small molecules in the PDBBind-refined-set. It is necessary to point out that the in the molecule file (mol/sdf), the number of explicit hydrogens has to be correct. Thus, we recommend to use
+  `obabel xxx -O xxx -h` to pre-process the file. The reason why we do not implement this hydrogen-adding procedure in dpdata is that we can not ensure its correctness.
 
 ```python
 import dpdata
 
 for sdf_file in glob.glob("bond_order/refined-set-ligands/obabel/*sdf"):
     syst = dpdata.BondOrderSystem(sdf_file, sanitize_level="high", verbose=False)
 ```
+
 ### Formal Charge Assignment
+
 BondOrderSystem implement a method to assign formal charge for each atom based on the 8-electron rule (see below). Note that it only supports common elements in bio-system: B,C,N,O,P,S,As
+
 ```python
 import dpdata
 

docs/systems/mixed.md

@@ -10,13 +10,15 @@ This also helps to mixture the type information together for model training with
 Here are examples using `deepmd/npy/mixed` format:
 
 - Dump a MultiSystems into a mixed type numpy directory:
+
 ```python
 import dpdata
 
 dpdata.MultiSystems(*systems).to_deepmd_npy_mixed("mixed_dir")
 ```
 
 - Load a mixed type data into a MultiSystems:
+
 ```python
 import dpdata
 

docs/systems/multi.md

@@ -1,15 +1,16 @@
 # `MultiSystems`
 
-The Class {class}`dpdata.MultiSystems`  can read data  from a dir which may contains many files of different systems, or from single xyz file which contains different systems.
+The Class {class}`dpdata.MultiSystems` can read data from a dir which may contains many files of different systems, or from single xyz file which contains different systems.
 
-Use {meth}`dpdata.MultiSystems.from_dir` to read from a  directory, {class}`dpdata.MultiSystems` will walk in the directory
-Recursively  and  find all file with specific file_name. Supports all the file formats that {class}`dpdata.LabeledSystem` supports.
+Use {meth}`dpdata.MultiSystems.from_dir` to read from a directory, {class}`dpdata.MultiSystems` will walk in the directory
+Recursively and find all file with specific file_name. Supports all the file formats that {class}`dpdata.LabeledSystem` supports.
 
 Use {meth}`dpdata.MultiSystems.from_file` to read from single file. Single-file support is available for the `quip/gap/xyz` and `ase/structure` formats.
 
 For example, for `quip/gap xyz` files, single .xyz file may contain many different configurations with different atom numbers and atom type.
 
 The following commands relating to {class}`dpdata.MultiSystems` may be useful.
+
 ```python
 # load data
 
@@ -40,6 +41,7 @@ xyz_multi_systems.to_deepmd_raw("./my_deepmd_data/")
 ```
 
 You may also use the following code to parse muti-system:
+
 ```python
 from dpdata import LabeledSystem, MultiSystems
 from glob import glob

docs/systems/system.md

@@ -1,84 +1,103 @@
 # `System` and `LabeledSystem`
 
 This section gives some examples on how dpdata works. Firstly one needs to import the module in a python 3.x compatible code.
+
 ```python
 import dpdata
 ```
+
 The typicall workflow of `dpdata` is
 
 1. Load data from vasp or lammps or deepmd-kit data files.
-2. Manipulate data
-3. Dump data to in a desired format
-
+1. Manipulate data
+1. Dump data to in a desired format
 
 ### Load data
+
 ```python
 d_poscar = dpdata.System("POSCAR", fmt="vasp/poscar")
 ```
+
 or let dpdata infer the format (`vasp/poscar`) of the file from the file name extension
+
 ```python
 d_poscar = dpdata.System("my.POSCAR")
 ```
+
 The number of atoms, atom types, coordinates are loaded from the `POSCAR` and stored to a data {class}`System <dpdata.System>` called `d_poscar`.
 A data {class}`System <dpdata.System>` (a concept used by [deepmd-kit](https://github.com/deepmodeling/deepmd-kit)) contains frames that has the same number of atoms of the same type. The order of the atoms should be consistent among the frames in one {class}`System <dpdata.System>`.
 It is noted that `POSCAR` only contains one frame.
 If the multiple frames stored in, for example, a `OUTCAR` is wanted,
+
 ```python
 d_outcar = dpdata.LabeledSystem("OUTCAR")
 ```
+
 The labels provided in the `OUTCAR`, i.e. energies, forces and virials (if any), are loaded by {class}`LabeledSystem <dpdata.LabeledSystem>`. It is noted that the forces of atoms are always assumed to exist. {class}`LabeledSystem <dpdata.LabeledSystem>` is a derived class of {class}`System <dpdata.System>`.
 
 The {class}`System <dpdata.System>` or {class}`LabeledSystem <dpdata.LabeledSystem>` can be constructed from the [supported file formats](../formats.rst) with the `format key` in the table passed to argument `fmt`.
 
-
-
 ### Access data
+
 These properties stored in {class}`System <dpdata.System>` and {class}`LabeledSystem <dpdata.LabeledSystem>` can be accessed by operator `[]` with the key of the property supplied, for example
+
 ```python
 coords = d_outcar["coords"]
 ```
-Available properties are (nframe: number of frames in the system, natoms: total number of atoms in the system)
 
-| key		|  type		| dimension		| are labels	| description
-| ---		| ---		| ---			| ---		| ---
-| 'atom_names'	| list of str	| ntypes		| False		| The name of each atom type
-| 'atom_numbs'	| list of int	| ntypes		| False		| The number of atoms of each atom type
-| 'atom_types'	| np.ndarray	| natoms		| False		| Array assigning type to each atom
-| 'cells'	| np.ndarray	| nframes x 3 x 3	| False		| The cell tensor of each frame
-| 'coords'	| np.ndarray	| nframes x natoms x 3	| False		| The atom coordinates
-| 'energies'	| np.ndarray	| nframes		| True		| The frame energies
-| 'forces'	| np.ndarray	| nframes x natoms x 3	| True		| The atom forces
-| 'virials'	| np.ndarray	| nframes x 3 x 3	| True		| The virial tensor of each frame
+Available properties are (nframe: number of frames in the system, natoms: total number of atoms in the system)
 
+| key          | type        | dimension            | are labels | description                           |
+| ------------ | ----------- | -------------------- | ---------- | ------------------------------------- |
+| 'atom_names' | list of str | ntypes               | False      | The name of each atom type            |
+| 'atom_numbs' | list of int | ntypes               | False      | The number of atoms of each atom type |
+| 'atom_types' | np.ndarray  | natoms               | False      | Array assigning type to each atom     |
+| 'cells'      | np.ndarray  | nframes x 3 x 3      | False      | The cell tensor of each frame         |
+| 'coords'     | np.ndarray  | nframes x natoms x 3 | False      | The atom coordinates                  |
+| 'energies'   | np.ndarray  | nframes              | True       | The frame energies                    |
+| 'forces'     | np.ndarray  | nframes x natoms x 3 | True       | The atom forces                       |
+| 'virials'    | np.ndarray  | nframes x 3 x 3      | True       | The virial tensor of each frame       |
 
 ### Dump data
+
 The data stored in {class}`System <dpdata.System>` or {class}`LabeledSystem <dpdata.LabeledSystem>` can be dumped in 'lammps/lmp' or 'vasp/poscar' format, for example:
+
 ```python
 d_outcar.to("lammps/lmp", "conf.lmp", frame_idx=0)
 ```
+
 The first frames of `d_outcar` will be dumped to 'conf.lmp'
+
 ```python
 d_outcar.to("vasp/poscar", "POSCAR", frame_idx=-1)
 ```
+
 The last frames of `d_outcar` will be dumped to 'POSCAR'.
 
 The data stored in `LabeledSystem` can be dumped to deepmd-kit raw format, for example
+
 ```python
 d_outcar.to("deepmd/raw", "dpmd_raw")
 ```
+
 Or a simpler command:
+
 ```python
 dpdata.LabeledSystem("OUTCAR").to("deepmd/raw", "dpmd_raw")
 ```
+
 Frame selection can be implemented by
+
 ```python
 dpdata.LabeledSystem("OUTCAR").sub_system([0, -1]).to("deepmd/raw", "dpmd_raw")
 ```
-by which only the first and last frames are dumped to `dpmd_raw`.
 
+by which only the first and last frames are dumped to `dpmd_raw`.
 
 ### replicate
+
 dpdata will create a super cell of the current atom configuration.
+
 ```python
 dpdata.System("./POSCAR").replicate(
     (
@@ -88,11 +107,13 @@ dpdata.System("./POSCAR").replicate(
     )
 )
 ```
-tuple(1,2,3) means don't copy atom configuration in x direction, make 2 copys in y direction, make 3 copys in z direction.
 
+tuple(1,2,3) means don't copy atom configuration in x direction, make 2 copys in y direction, make 3 copys in z direction.
 
 ### perturb
+
 By the following example, each frame of the original system (`dpdata.System('./POSCAR')`) is perturbed to generate three new frames. For each frame, the cell is perturbed by 5% and the atom positions are perturbed by 0.6 Angstrom. `atom_pert_style` indicates that the perturbation to the atom positions is subject to normal distribution. Other available options to `atom_pert_style` are`uniform` (uniform in a ball), and `const` (uniform on a sphere).
+
 ```python
 perturbed_system = dpdata.System("./POSCAR").perturb(
     pert_num=3,
@@ -104,7 +125,9 @@ print(perturbed_system.data)
 ```
 
 ### replace
+
 By the following example, Random 8 Hf atoms in the system will be replaced by Zr atoms with the atom postion unchanged.
+
 ```python
 s = dpdata.System("tests/poscars/POSCAR.P42nmc", fmt="vasp/poscar")
 s.replace("Hf", "Zr", 8)