merge devel to master (#535)

Author: wanghan-iapcm

.github/workflows/test.yml

@@ -22,7 +22,7 @@ jobs:
     - name: Install rdkit
       run: python -m pip install rdkit openbabel-wheel
     - name: Install dependencies
-      run: python -m pip install .[amber,ase,pymatgen] coverage
+      run: python -m pip install .[amber,ase,pymatgen] coverage ./tests/plugin
     - name: Test
       run: cd tests && coverage run --source=../dpdata -m unittest && cd .. && coverage combine tests/.coverage && coverage report
     - name: Run codecov

.gitignore

@@ -24,4 +24,7 @@ _version.py
 __pycache__
 docs/_build
 docs/formats.csv
+docs/drivers.csv
+docs/minimizers.csv
 docs/api/
+docs/formats/

.pre-commit-config.yaml

@@ -18,12 +18,12 @@ repos:
     -   id: check-toml
 # Python
 -   repo: https://github.com/psf/black
-    rev: 23.3.0
+    rev: 23.7.0
     hooks:
     -   id: black-jupyter
--   repo: https://github.com/charliermarsh/ruff-pre-commit
+-   repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.0.263
+    rev: v0.0.287
     hooks:
     - id: ruff
       args: ["--fix"]
@@ -35,7 +35,7 @@ repos:
       args: ["--write"]
 # Python inside docs
 -   repo: https://github.com/asottile/blacken-docs
-    rev: 1.13.0
+    rev: 1.16.0
     hooks:
     -   id: blacken-docs
 ci:

.readthedocs.yaml

@@ -0,0 +1,12 @@
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+sphinx:
+   configuration: docs/conf.py
+formats: all
+python:
+   install:
+   - requirements: docs/requirements.txt

README.md

@@ -1,3 +1,9 @@
+# dpdata
+
+[![conda-forge](https://img.shields.io/conda/dn/conda-forge/dpdata?color=red&label=conda-forge&logo=conda-forge)](https://anaconda.org/conda-forge/dpdata)
+[![pip install](https://img.shields.io/pypi/dm/dpdata?label=pip%20install&logo=pypi)](https://pypi.org/project/dpdata)
+[![Documentation Status](https://readthedocs.org/projects/dpdata/badge/)](https://dpdata.readthedocs.io/)
+
 **dpdata** is a python package for manipulating data formats of software in computational science, including DeePMD-kit, VASP, LAMMPS, GROMACS, Gaussian.
 dpdata only works with python 3.7 or above.
 
@@ -82,11 +88,12 @@ The `System` or `LabeledSystem` can be constructed from the following file forma
 | Amber   | multi       | True         | True    | LabeledSystem | 'amber/md'           |
 | Amber/sqm | sqm.out   | False        | False   | System        | 'sqm/out'            |
 | Gromacs | gro         | True         | False   | System        | 'gromacs/gro'        |
-| ABACUS  | STRU        | False        | False   | System        | 'abacus/stru'         |
+| ABACUS  | STRU        | False        | False   | System        | 'abacus/stru'        |
 | ABACUS  | STRU        | False        | True    | LabeledSystem | 'abacus/scf'         |
 | ABACUS  | cif         | True         | True    | LabeledSystem | 'abacus/md'          |
 | ABACUS  | STRU        | True         | True    | LabeledSystem | 'abacus/relax'       |
 | ase     | structure   | True         | True    | MultiSystems  | 'ase/structure'      |
+| DFTB+   | dftbplus    | False        | True    | LabeledSystem | 'dftbplus'           |
 
 
 The 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.

docs/formats.rst

@@ -6,3 +6,10 @@ dpdata supports the following formats:
 .. csv-table:: Supported Formats
    :file: formats.csv
    :header-rows: 1
+
+
+.. toctree::
+   :maxdepth: 1
+   :glob:
+
+   formats/*