Merge devel to master (#1161)

Author: AnguseZhang

.github/ISSUE_TEMPLATE/request-for-help.md

@@ -13,7 +13,7 @@ Before asking questions, you can
 search the previous issues or discussions
 check [Manual](https://github.com/deepmodeling/dpgen).
 
-Please **do not** post requests for help (e.g. with installing or using dpgen) here. 
+Please **do not** post requests for help (e.g. with installing or using dpgen) here.
 Instead go to [discussions](https://github.com/deepmodeling/dpgen/discussions).
 
 This issue tracker is for tracking dpgen development related issues only.

.github/workflows/test.yml

@@ -10,7 +10,6 @@ jobs:
     strategy:
       matrix:
         python-version: [3.8, 3.9]
-        PYMATGEN_VERSION: [2022.7.19]
 
     steps:
     - uses: actions/checkout@v2
@@ -19,12 +18,16 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
-      run: pip install coverage pymatgen==${{ matrix.PYMATGEN_VERSION }} -e .
+      run: pip install coverage git+https://github.com/materialsproject/pymatgen@b56698019098247ff54f50997a67c562b4375fc3 -e .
     - name: Test
       run: coverage run --source=./dpgen -m unittest -v && coverage report
     - uses: codecov/codecov-action@v3
   pass:
     needs: [build]
     runs-on: ubuntu-latest
+    if: always()
     steps:
-      - run: echo "All jobs passed"
+    - name: Decide whether the needed jobs succeeded or failed
+      uses: re-actors/alls-green@release/v1
+      with:
+        jobs: ${{ toJSON(needs) }}

.gitignore

@@ -42,4 +42,3 @@ dbconfig.json
 _build
 tests/generator/calypso_test_path
 doc/api/
-

.pre-commit-config.yaml

@@ -0,0 +1,38 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+    # there are many log files in tests
+    # TODO: seperate py files and log files
+    -   id: trailing-whitespace
+        exclude: "^tests/.*$"
+    -   id: end-of-file-fixer
+        exclude: "^tests/.*$"
+    -   id: check-yaml
+        exclude: "^conda/.*$"
+    #-   id: check-json
+    -   id: check-added-large-files
+    -   id: check-merge-conflict
+    -   id: check-symlinks
+        exclude: "^tests/tools/run_report_test_output/.*$"
+    -   id: check-toml
+# Python
+-   repo: https://github.com/psf/black
+    rev: 22.12.0
+    hooks:
+    -   id: black-jupyter
+-   repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.0.253
+    hooks:
+    - id: ruff
+      args: ["--fix"]
+# numpydoc
+-   repo: https://github.com/Carreau/velin
+    rev: 0.0.12
+    hooks:
+    - id: velin
+      args: ["--write"]
+ci:
+  autoupdate_branch: devel

README.md

@@ -1,8 +1,12 @@
+![logo](./doc/logo.svg)
+
+--------------------------------------------------------------------------------
+
 # DP-GEN: A concurrent learning platform for the generation of reliable deep learning based potential energy models
 
 [![GitHub release](https://img.shields.io/github/release/deepmodeling/dpgen.svg?maxAge=86400)](https://github.com/deepmodeling/dpgen/releases/)
 [![doi:10.1016/j.cpc.2020.107206](https://img.shields.io/badge/DOI-10.1016%2Fj.cpc.2020.107206-blue)](https://doi.org/10.1016/j.cpc.2020.107206)
-![Citations](https://citations.njzjz.win/10.1016/j.cpc.2020.107206)
+[![Citations](https://citations.njzjz.win/10.1016/j.cpc.2020.107206)](https://badge.dimensions.ai/details/doi/10.1016/j.cpc.2020.107206)
 [![conda install](https://img.shields.io/conda/dn/conda-forge/dpgen?label=conda%20install)](https://anaconda.org/conda-forge/dpgen)
 [![pip install](https://img.shields.io/pypi/dm/dpgen?label=pip%20install)](https://pypi.org/project/dpgen)
 

codecov.yml

@@ -0,0 +1,10 @@
+ignore:
+  - "tests"
+coverage:
+  status:
+    project:
+      default:
+        threshold: 100%
+    patch:
+      default:
+        threshold: 100%

conda/conda_build_config.yaml

@@ -1,5 +1,5 @@
-channel_sources: 
+channel_sources:
   - defaults
   - conda-forge
-channel_targets: 
+channel_targets:
   - deepmodeling

conda/construct.yaml

@@ -11,7 +11,7 @@ channels:
 specs:
   - python 3.8
   - pip
-  - dpgen {{ version }} 
+  - dpgen {{ version }}
 
 ignore_duplicate_files: True
 

doc/autotest/Auto-test.md

@@ -15,7 +15,7 @@ If, for some reasons, the main program terminated at stage `run`, one can easily
 `relax.json` is the parameter file. An example for `deepmd` relaxation is given as:
 ```json
 {
-        "structures":   "confs/mp-*",
+        "structures":   ["confs/mp-*"],
         "interaction": {
                 "type":         "deepmd",
                 "model":        "frozen_model.pb",
@@ -30,8 +30,8 @@ where the key `structures` provides the structures to relax. `interaction` is pr
 ### Task type
 There are now six task types implemented in the package: `vasp`, `abacus`, `deepmd`, `meam`, `eam_fs`, and `eam_alloy`. An `inter.json` file in json format containing the interaction parameters will be written in the directory of each task after `make`. We give input examples of the `interaction` part for each type below:
 
-**VASP**: 
-    
+**VASP**:
+
 The default of `potcar_prefix` is "".
 ```json
 	"interaction": {
@@ -41,8 +41,8 @@ The default of `potcar_prefix` is "".
 		"potcars":	{"Al": "POTCAR.al", "Mg": "POTCAR.mg"}
 	}
 ```
-**ABACUS**: 
-    
+**ABACUS**:
+
 The default of `potcar_prefix` is "". The path of potcars/orb_files/deepks_desc is `potcar_prefix` + `potcars`/`orb_files`/`deepks_desc`.
 ```json
 	"interaction": {
@@ -62,7 +62,7 @@ The default of `potcar_prefix` is "". The path of potcars/orb_files/deepks_desc
 ```json
 	"interaction": {
 		"type":		 "deepmd",
-		"model":	 "frozen_model.pb", 
+		"model":	 "frozen_model.pb",
 		"type_map":      {"Al": 0, "Mg": 1}
 	}
 ```
@@ -81,8 +81,8 @@ Please make sure the [USER-MEAMC package](https://lammps.sandia.gov/doc/Packages
 Please make sure the [MANYBODY package](https://lammps.sandia.gov/doc/Packages_details.html#pkg-manybody) has already been installed in LAMMPS
 ```json
 	"interaction": {
-		"type":		 "eam_fs (eam_alloy)", 
-		"model":	 "AlMg.eam.fs (AlMg.eam.alloy)", 
+		"type":		 "eam_fs (eam_alloy)",
+		"model":	 "AlMg.eam.fs (AlMg.eam.alloy)",
 		"type_map":      {"Al": 1, "Mg": 2}
 	}
 ```
@@ -96,9 +96,9 @@ Now the supported property types are `eos`, `elastic`, `vacancy`, `interstitial`
 There are three operations in auto test package, namely `make`, `run`, and `post`. Here we take `eos` property as an example for property type.
 
 ### Make
-The `INCAR`, `POSCAR`, `POTCAR` input files for VASP or `in.lammps`, `conf.lmp`, and the interatomic potential files for LAMMPS will be generated in the directory `confs/mp-*/relaxation/relax_task` for relaxation or `confs/mp-*/eos_00/task.[0-9]*[0-9]` for EOS. The `machine.json` file is not needed for `make`. Example: 
+The `INCAR`, `POSCAR`, `POTCAR` input files for VASP or `in.lammps`, `conf.lmp`, and the interatomic potential files for LAMMPS will be generated in the directory `confs/mp-*/relaxation/relax_task` for relaxation or `confs/mp-*/eos_00/task.[0-9]*[0-9]` for EOS. The `machine.json` file is not needed for `make`. Example:
 ```bash
-dpgen autotest make relaxation.json 
+dpgen autotest make relaxation.json
 ```
 
 ### Run
@@ -110,5 +110,5 @@ dpgen autotest run relaxation.json machine.json
 ### Post
 The post process of calculation results would be performed. `result.json` in json format will be generated in `confs/mp-*/relaxation/relax_task` for relaxation and `result.json` in json format and `result.out` in txt format in `confs/mp-*/eos_00` for EOS. The `machine.json` file is also not needed for `post`. Example:
 ```bash
-dpgen autotest post relaxation.json 
+dpgen autotest post relaxation.json
 ```

doc/autotest/index.rst

@@ -9,13 +9,13 @@ Auto test
    :caption: Guidelines
 
    Auto-test
-  
+
 .. _Main-components::
 
 .. toctree::
    :maxdepth: 2
    :caption: Main components
-   
+
    Task-type
    Property-type
    Make-run-and-post
@@ -25,7 +25,7 @@ Auto test
 .. toctree::
    :maxdepth: 2
    :caption: Structure relaxation
-   
+
    relaxation/index.rst
 
 .. _Property::
@@ -41,13 +41,13 @@ Auto test
 .. toctree::
    :maxdepth: 2
    :caption: Refine
-   
+
    refine/index.rst
 
 .. _Reproduce::
 
 .. toctree::
    :maxdepth: 2
    :caption: Reproduce
-   
+
    reproduce/index.rst