Merge branch 'devel' into isort

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
deepmodeling · Feb 6, 2023 · acf8c2a · acf8c2a
2 parents fb24871 + 7a1ceb4
commit acf8c2a
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Showing 3 changed files with 46 additions and 37 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -28,5 +28,11 @@ repos:
     hooks:
     - id: isort
     files: \.py$
+# numpydoc
+-   repo: https://github.com/Carreau/velin
+    rev: 0.0.12
+    hooks:
+    - id: velin
+      args: ["--write"]
 ci:
   autoupdate_branch: devel
diff --git a/dpgen/auto_test/Property.py b/dpgen/auto_test/Property.py
@@ -16,8 +16,8 @@ def __init__(self, parameter):
 
         Parameters
         ----------
-        parameters : dict
-                A dict that defines the property.
+        parameter : dict
+            A dict that defines the property.
         """
         pass
 
@@ -31,17 +31,17 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
         Parameters
         ----------
         path_to_work : str
-                The path where the tasks for the property are located
+            The path where the tasks for the property are located
         path_to_equi : str
-                -refine == False: The path to the directory that equilibrated the configuration.
-                -refine == True: The path to the directory that has property confs.
-        refine: str
-                To refine existing property confs or generate property confs from a equilibrated conf
+            -refine == False: The path to the directory that equilibrated the configuration.
+            -refine == True: The path to the directory that has property confs.
+        refine : str
+            To refine existing property confs or generate property confs from a equilibrated conf
 
         Returns
         -------
         task_list: list of str
-                The list of task directories.
+            The list of task directories.
         """
         pass
 
@@ -76,11 +76,11 @@ def compute(self, output_file, print_file, path_to_work):
         Parameters
         ----------
         output_file:
-                The file to output the property in json format
+            The file to output the property in json format
         print_file:
-                The file to output the property in txt format
+            The file to output the property in txt format
         path_to_work:
-                The working directory where the computational tasks locate.
+            The working directory where the computational tasks locate.
         """
         path_to_work = os.path.abspath(path_to_work)
         task_dirs = glob.glob(os.path.join(path_to_work, "task.[0-9]*[0-9]"))
@@ -113,17 +113,16 @@ def _compute_lower(self, output_file, all_tasks, all_res):
         Parameters
         ----------
         output_file:
-                The file to output the property
+            The file to output the property
         all_tasks : list of str
-                The list of directories to the tasks
+            The list of directories to the tasks
         all_res : list of str
-                The list of results
-
+            The list of results
         Returns:
         -------
-        res_data: dist
-                The dict storing the result of the property
-        ptr_data: str
-                The result printed in string format
+        res_data : dist
+            The dict storing the result of the property
+        ptr_data : str
+            The result printed in string format
         """
         pass
diff --git a/dpgen/auto_test/Task.py b/dpgen/auto_test/Task.py
@@ -10,9 +10,9 @@ def __init__(self, inter_parameter, path_to_poscar):
         Parameters
         ----------
         inter_parameter : dict
-                A dict that specifies the interaction.
+            A dict that specifies the interaction.
         path_to_poscar : str
-                The path to POSCAR. Indicating in which system the task will be initialized.
+            The path to POSCAR. Indicating in which system the task will be initialized.
         """
         pass
 
@@ -27,9 +27,12 @@ def make_potential_files(self, output_dir):
         Parameters
         ----------
         output_dir : str
-                The directory storing the potential files.
-        Outputs
-        -------
+            The directory storing the potential files.
+
+        Notes
+        -----
+        The following files are generated:
+
         inter.json: output file
                 The task information is stored in `output_dir/inter.json`
         """
@@ -45,15 +48,15 @@ def make_input_file(self, output_dir, task_type, task_param):
         Parameters
         ----------
         output_dir : str
-                The directory storing the input files.
+            The directory storing the input files.
         task_type : str
-                Can be
-                - "relaxation:": structure relaxation
-                - "static": static computation calculates the energy, force... of a strcture
-        task_parame: dict
-                The parameters of the task.
-                For example the VASP interaction can be provided with
-                { "ediff": 1e-6, "ediffg": 1e-5 }
+            Can be
+            - "relaxation:": structure relaxation
+            - "static": static computation calculates the energy, force... of a strcture
+        task_param : dict
+            The parameters of the task.
+            For example the VASP interaction can be provided with
+            { "ediff": 1e-6, "ediffg": 1e-5 }
         """
         pass
 
@@ -66,16 +69,17 @@ def compute(self, output_dir):
         Parameters
         ----------
         output_dir : str
-                The directory storing the input and output files.
+            The directory storing the input and output files.
 
         Returns
         -------
         result_dict: dict
-                A dict that storing the result. For example:
-                { "energy": xxx, "force": [xxx] }
+            A dict that storing the result. For example:
+            { "energy": xxx, "force": [xxx] }
 
-        Outputs
-        -------
+        Notes
+        -----
+        The following files are generated:
         CONTCAR: output file
                 The output configuration is converted to CONTCAR and stored in the `output_dir`
         """