add and run pre-commit to format codes (#1124)

- add pre-commit config, including black and common fixes.
- run pre-commit.
- manually fix a YAML file.
- skip check json and broken symlinks.

Author: njzjz

.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.

.gitignore

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

.pre-commit-config.yaml

@@ -0,0 +1,27 @@
+# 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
+ci:
+  autoupdate_branch: devel

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

@@ -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

doc/autotest/property/Property-get-started-and-input-examples.md

@@ -61,7 +61,7 @@ Key words | data structure | example | description
 **type** | String | "eos" | property type
 skip | Boolean | true | whether to skip current property or not
 start_confs_path | String | "../vasp/confs" | start from the equilibrium configuration in other path only for the current property type
-cal_setting["input_prop"] | String | "lammps_input/lammps_high" |input commands file 
+cal_setting["input_prop"] | String | "lammps_input/lammps_high" |input commands file
 cal_setting["overwrite_interaction"] | Dict | | overwrite the interaction in the `interaction` part only for the current property type
 
 other parameters in `cal_setting` and `cal_type` in `relaxation` also apply in `property`.
@@ -116,4 +116,4 @@ Key words | data structure | example | description
 supercell_size | List of Int | [1,1,10] | the supercell to be constructed, default = [1,1,5]
 min_vacuum_size | Int or Float | 10 | minimum size of vacuum width, default = 20
 add_fix | List of String | ['true','true','false'] | whether to fix atoms in the direction, default = ['true','true','false'] (standard method)
-n_steps | Int | 20 | Number of points for gamma-line calculation, default = 10
+n_steps | Int | 20 | Number of points for gamma-line calculation, default = 10

doc/autotest/property/Property-post.md

@@ -4,4 +4,4 @@ Use command
 ```bash
 dpgen autotest post property.json
 ```
-to post results as `result.json` and `result.out` in each property's path.
+to post results as `result.json` and `result.out` in each property's path.

doc/autotest/property/index.rst

@@ -9,4 +9,4 @@ Property
    Property-make
    Property-run
    Property-post
-   properties/index.rst
+   properties/index.rst