add cli (#265)

* add cli

* fix tests

* fix the typo in doc

* fix tests

Author: njzjz

dpdata/cli.py

@@ -0,0 +1,75 @@
+"""Command line interface for dpdata."""
+import argparse
+
+from . import __version__
+from .system import System, LabeledSystem, MultiSystems
+
+
+def dpdata_cli():
+    """dpdata cli.
+
+    Examples
+    --------
+    .. code-block:: bash
+
+        $ dpdata -iposcar POSCAR -odeepmd/npy -O data -n
+    """
+    parser = argparse.ArgumentParser(
+        description="dpdata: Manipulating multiple atomic simulation data formats",
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+    )
+
+    parser.add_argument("from_file", type=str, help="read data from a file")
+    parser.add_argument("--to_file", "-O", type=str, help="dump data to a file")
+    parser.add_argument("--from_format", "-i", type=str, default="auto", help="the format of from_file")
+    parser.add_argument("--to_format", "-o", type=str, help="the format of to_file")
+    parser.add_argument("--no-labeled", "-n", action="store_true", help="labels aren't provided")
+    parser.add_argument("--multi", "-m", action="store_true", help="the system contains multiple directories")
+    parser.add_argument("--type-map", "-t", type=str, nargs="+", help="type map")
+
+    parser.add_argument('--version', action='version', version='dpdata v%s' % __version__)
+
+    parsed_args = parser.parse_args()
+    convert(**vars(parsed_args))
+
+
+def convert(*,
+            from_file: str,
+            from_format: str = "auto",
+            to_file: str = None,
+            to_format: str = None,
+            no_labeled: bool = False,
+            multi: bool = False,
+            type_map: list = None,
+            **kwargs):
+    """Convert files from one format to another one.
+    
+    Parameters
+    ----------
+    from_file : str
+        read data from a file
+    from_format : str
+        the format of from_file
+    to_file : str
+        dump data to a file
+    to_format : str
+        the format of to_file
+    no_labeled : bool
+        labels aren't provided
+    multi : bool
+        the system contains multiple directories
+    type_map : list
+        type map
+    """
+    if multi:
+        s = MultiSystems.from_file(from_file, fmt=from_format, type_map=type_map, labeled=not no_labeled)
+    elif not no_labeled:
+        s = LabeledSystem(from_file, fmt=from_format, type_map=type_map)
+    else:
+        s = System(from_file, fmt=from_format, type_map=type_map)
+    if to_format is not None:
+        out = s.to(to_format, to_file)
+        if isinstance(out, str):
+            print(out)
+    else:
+        print(s)

dpdata/system.py

@@ -1082,6 +1082,21 @@ def to_fmt_obj(self, fmtobj, directory, *args, **kwargs):
         for fn, ss in zip(fmtobj.to_multi_systems(self.systems.keys(), directory, **kwargs), self.systems.values()):
             ss.to_fmt_obj(fmtobj, fn, *args, **kwargs)
         return self
+    
+    def to(self, fmt: str, *args, **kwargs) -> "MultiSystems":
+        """Dump systems to the specific format.
+        
+        Parameters
+        ----------
+        fmt : str
+            format
+        
+        Returns
+        -------
+        MultiSystems
+            self
+        """
+        return self.to_fmt_obj(load_format(fmt), *args, **kwargs)
 
     def __getitem__(self, key):
         """Returns proerty stored in System by key or by idx"""

setup.py

@@ -55,6 +55,7 @@
         'amber': ['parmed'],
         'pymatgen': ['pymatgen'],
         'docs': ['sphinx', 'recommonmark', 'sphinx_rtd_theme>=1.0.0rc1', 'numpydoc', 'm2r2', 'deepmodeling-sphinx'],
-    }
+    },
+    entry_points={"console_scripts": ["dpdata = dpdata.cli:dpdata_cli"]},
 )
 

tests/test_cli.py

@@ -0,0 +1,17 @@
+import unittest
+from context import dpdata
+from poscars.poscar_ref_oh import TestPOSCARoh
+import subprocess as sp
+
+
+class TestCli(unittest.TestCase, TestPOSCARoh):
+    
+    @classmethod
+    def setUpClass(cls) -> None:
+        sp.check_output(["dpdata", "poscars/conf.lmp", "--type-map", "O", "H", "-olammps/lmp", "-O", "tmp.lmp", "--no-labeled"])
+        cls.system = dpdata.System('tmp.lmp', fmt='lammps/lmp',
+                             type_map = ['O', 'H'])
+
+    @classmethod
+    def tearDownClass(cls) -> None:
+        cls.system = None