docs: add docs for Format (#451)

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: njzjz

dpdata/format.py

@@ -6,36 +6,158 @@
 
 
 class Format(ABC):
+    """The abstract base class for all formats.
+
+    To add a new format, one should create a new class inherited from this class, and then
+
+    - implement several methods, such as :meth:`from_system`;
+    - register the format with a key;
+    - add documentation in the class docstring;
+
+    The new format can be either insider or outside the package.
+    """
+
     __FormatPlugin = Plugin()
     __FromPlugin = Plugin()
     __ToPlugin = Plugin()
 
     @staticmethod
     def register(key):
+        """Register a format plugin.
+
+        By default, after a format plugin is registered, the following methods
+        will be registered as well for :meth:`System`, :meth:`LabeledSystem`, :meth:`MultiSystems`, and
+        :meth:`BondOrderSystem`:
+
+        - from_{key.replace('/', '_')}
+        - to_{key.replace('/', '_')}
+        - from({key}, ...)
+        - to({key}, ...)
+
+        The decorator should be explicitly executed before :mod:`dpdata.system`
+        is imported. A module will be imported automatically if it
+
+        - is a submodule of :mod:`dpdata.plugins`;
+        - is registered at the `dpdata.plugins` entry point
+
+        Parameters
+        ----------
+        key : str
+            The key to register the plugin.
+
+        Returns
+        -------
+        function
+            The decorator function.
+
+        Examples
+        --------
+        Register a format plugin:
+
+        >>> @Format.register('test')
+        ... @Format.register('test2')
+        ... class TestFormat(Format):
+        ...     pass
+        """
         return Format.__FormatPlugin.register(key)
 
     @staticmethod
     def register_from(key):
+        """Register a from method if the target method name is not default.
+
+        Parameters
+        ----------
+        key : str
+            The key to register the plugin.
+
+        Returns
+        -------
+        function
+            The decorator function.
+
+        Examples
+        --------
+        Register a from method:
+
+        >>> @Format.register_from('from_test_haha')
+        ... @Format.register('test)
+        ... class TestFormat(Format):
+        ...     pass
+
+        This will register a from method named from_test_haha, although the
+        format name is test.
+        """
         return Format.__FromPlugin.register(key)
 
     @staticmethod
     def register_to(key):
+        """Register a to method if the target method name is not default.
+
+        Parameters
+        ----------
+        key : str
+            The key to register the plugin.
+
+        Returns
+        -------
+        function
+            The decorator function.
+
+        Examples
+        --------
+        Register a to method:
+
+        >>> @Format.register_to('to_test_haha')
+        ... @Format.register('test')
+        ... class TestFormat(Format):
+        ...     pass
+
+        This will register a to method named to_test_haha, although the
+        format name is test.
+        """
         return Format.__ToPlugin.register(key)
 
     @staticmethod
     def get_formats():
+        """Get all registered formats."""
         return Format.__FormatPlugin.plugins
 
     @staticmethod
     def get_from_methods():
+        """Get all registered from methods."""
         return Format.__FromPlugin.plugins
 
     @staticmethod
     def get_to_methods():
+        """Get all registered to methods."""
         return Format.__ToPlugin.plugins
 
     @staticmethod
     def post(func_name):
+        """Register a post function for from method.
+
+        Such function will be called after the "from" method is called.
+
+        Parameters
+        ----------
+        func_name : str or list of str
+            The name of the post function.
+
+        Returns
+        -------
+        function
+            The decorator function.
+
+        Examples
+        --------
+        Register a post function:
+
+        >>> @Format.post('remove_pbc')
+        ... @Format.register('test')
+        ... class TestFormat(Format):
+        ...     pass
+        """
+
         def decorator(object):
             if not isinstance(func_name, (list, tuple, set)):
                 object.post_func = (func_name,)
@@ -46,60 +168,119 @@ def decorator(object):
         return decorator
 
     def from_system(self, file_name, **kwargs):
-        """System.from.
+        """Implement System.from that converts from this format to System.
 
         Parameters
         ----------
         file_name : str
-            file name
+            file name, i.e. the first argument
         **kwargs : dict
-            other parameters
+            keyword arguments that will be passed from the method
 
         Returns
         -------
-        data: dict
-            system data
+        data : dict
+            system data, whose keys are defined in System.DTYPES
         """
         raise NotImplementedError(
             "%s doesn't support System.from" % (self.__class__.__name__)
         )
 
     def to_system(self, data, *args, **kwargs):
-        """System.to.
+        """Implement System.to that converts from System to this format.
 
         Parameters
         ----------
         data : dict
-            system data
+            system data, whose keys are defined in System.DTYPES
         *args : list
-            other parameters
+            arguments that will be passed from the method
         **kwargs : dict
-            other parameters
+            keyword arguments that will be passed from the method
         """
         raise NotImplementedError(
             "%s doesn't support System.to" % (self.__class__.__name__)
         )
 
     def from_labeled_system(self, file_name, **kwargs):
+        """Implement LabeledSystem.from that converts from this format to LabeledSystem.
+
+        Parameters
+        ----------
+        file_name : str
+            file name, i.e. the first argument
+        **kwargs : dict
+            keyword arguments that will be passed from the method
+
+        Returns
+        -------
+        data : dict
+            system data, whose keys are defined in LabeledSystem.DTYPES
+        """
         raise NotImplementedError(
             "%s doesn't support LabeledSystem.from" % (self.__class__.__name__)
         )
 
     def to_labeled_system(self, data, *args, **kwargs):
+        """Implement LabeledSystem.to that converts from LabeledSystem to this format.
+
+        By default, LabeledSystem.to will fallback to System.to.
+
+        Parameters
+        ----------
+        data : dict
+            system data, whose keys are defined in LabeledSystem.DTYPES
+        *args : list
+            arguments that will be passed from the method
+        **kwargs : dict
+            keyword arguments that will be passed from the method
+        """
         return self.to_system(data, *args, **kwargs)
 
     def from_bond_order_system(self, file_name, **kwargs):
+        """Implement BondOrderSystem.from that converts from this format to BondOrderSystem.
+
+        Parameters
+        ----------
+        file_name : str
+            file name, i.e. the first argument
+        **kwargs : dict
+            keyword arguments that will be passed from the method
+
+        Returns
+        -------
+        data : dict
+            system data
+        """
         raise NotImplementedError(
             "%s doesn't support BondOrderSystem.from" % (self.__class__.__name__)
         )
 
     def to_bond_order_system(self, data, rdkit_mol, *args, **kwargs):
+        """Implement BondOrderSystem.to that converts from BondOrderSystem to this format.
+
+        By default, BondOrderSystem.to will fallback to LabeledSystem.to.
+
+        Parameters
+        ----------
+        data : dict
+            system data
+        rdkit_mol : rdkit.Chem.rdchem.Mol
+            rdkit mol object
+        *args : list
+            arguments that will be passed from the method
+        **kwargs : dict
+            keyword arguments that will be passed from the method
+        """
         return self.to_system(data, *args, **kwargs)
 
     class MultiModes:
-        """File mode for MultiSystems
-        0 (default): not implemented
-        1: every directory under the top-level directory is a system.
+        """File mode for MultiSystems.
+
+        The current implemented modes are:
+
+            - 0 (default): not implemented
+            - 1: every directory under the top-level directory is a system.
         """
 
         NotImplemented = 0
@@ -108,14 +289,16 @@ class MultiModes:
     MultiMode = MultiModes.NotImplemented
 
     def from_multi_systems(self, directory, **kwargs):
-        """MultiSystems.from.
+        """Implement MultiSystems.from that converts from this format to MultiSystems.
+
+        By default, this method follows MultiMode to implement the conversion.
 
         Parameters
         ----------
         directory : str
             directory of system
         **kwargs : dict
-            other parameters
+            keyword arguments that will be passed from the method
 
         Returns
         -------
@@ -133,6 +316,19 @@ def from_multi_systems(self, directory, **kwargs):
         )
 
     def to_multi_systems(self, formulas, directory, **kwargs):
+        """Implement MultiSystems.to that converts from MultiSystems to this format.
+
+        By default, this method follows MultiMode to implement the conversion.
+
+        Parameters
+        ----------
+        formulas : list[str]
+            list of formulas
+        directory : str
+            directory of system
+        **kwargs : dict
+            keyword arguments that will be passed from the method
+        """
         if self.MultiMode == self.MultiModes.Directory:
             return [os.path.join(directory, ff) for ff in formulas]
         raise NotImplementedError(
@@ -149,7 +345,7 @@ def mix_system(self, *system, type_map, **kwargs):
         type_map : list of str
             Maps atom type to name
         **kwargs : dict
-            other parameters
+            keyword arguments that will be passed from the method
 
         Returns
         -------