FourCIPP 1.3.0__py3-none-any.whl → 1.5.0__py3-none-any.whl

fourcipp/fourc_input.py

@@ -496,6 +496,7 @@ class FourCInput:
         validate_sections_only: bool = False,
         convert_to_native_types: bool = True,
         sort_function: Callable[[dict], dict] | None = _sort_by_section_names,
+        use_fourcipp_yaml_style: bool = True,
     ) -> None:
         """Dump object to yaml.
 
@@ -506,6 +507,7 @@ class FourCInput:
                 Requiredness of the sections themselves is ignored.
             convert_to_native_types: Convert all sections to native Python types
             sort_function: Function to sort the sections.
+            use_fourcipp_yaml_style: If FourCIPP yaml style is to be used
         """
 
         if validate or validate_sections_only:
@@ -520,7 +522,7 @@ class FourCInput:
         if convert_to_native_types:
             self.convert_to_native_types()
 
-        dump_yaml(self.inlined, input_file_path, sort_function)
+        dump_yaml(self.inlined, input_file_path, sort_function, use_fourcipp_yaml_style)
 
     def validate(
         self,

fourcipp/utils/cli.py

@@ -34,9 +34,12 @@ from fourcipp.utils.configuration import (
     show_config,
 )
 from fourcipp.utils.typing import Path
+from fourcipp.utils.yaml_io import dump_yaml, load_yaml
 
 
-def modify_input_with_defaults(input_path: Path, overwrite: bool) -> None:
+def modify_input_with_defaults(
+    input_path: Path, overwrite: bool
+) -> None:  # pragma: no cover
     """Apply user defaults to an input file located at input_path.
 
     Args:
@@ -62,6 +65,24 @@ def modify_input_with_defaults(input_path: Path, overwrite: bool) -> None:
     logger.info(f"Input file incl. user defaults is now '{output_filename}'.")
 
 
+def format_file(
+    input_file: str, sort_sections: bool = False
+) -> None:  # pragma: no cover
+    """Formatting file.
+
+    Args:
+        input_file: File to format
+        sort_sections: Sort sections
+    """
+    if sort_sections:
+        # Requires reading the config
+        fourc_input = FourCInput.from_4C_yaml(input_file)
+        fourc_input.dump(input_file, use_fourcipp_yaml_style=True)
+    else:
+        # No config required, is purely a style question
+        dump_yaml(load_yaml(input_file), input_file, use_fourcipp_yaml_style=True)
+
+
 def main() -> None:
     """Main CLI interface."""
     # Set up the logger
@@ -110,6 +131,23 @@ def main() -> None:
         type=str,
     )
 
+    # Format parser
+    format_parser = subparsers.add_parser(
+        "format",
+        help="Format the file in fourcipp style. This sorts the sections and uses the flow styles from FourCIPP",
+    )
+
+    format_parser.add_argument(
+        "input-file",
+        help=f"4C input file.",
+        type=str,
+    )
+
+    format_parser.add_argument(
+        "--sort-sections",
+        action="store_true",
+        help=f"Overwrite existing input file.",
+    )
     # Replace "-" with "_" for variable names
     kwargs: dict = {}
     for key, value in vars(main_parser.parse_args(sys.argv[1:])).items():
@@ -126,3 +164,5 @@ def main() -> None:
             input_path = pathlib.Path(kwargs.pop("input_file"))
             overwrite = kwargs.pop("overwrite")
             modify_input_with_defaults(input_path, overwrite)
+        case "format":
+            format_file(**kwargs)

fourcipp/utils/yaml_io.py

@@ -63,13 +63,17 @@ def load_yaml(path_to_yaml_file: Path) -> dict:
 
 
 def dict_to_yaml_string(
-    data: dict, sort_function: Callable[[dict], dict] | None = None
+    data: dict,
+    sort_function: Callable[[dict], dict] | None = None,
+    use_fourcipp_yaml_style: bool = True,
 ) -> str:
     """Dump dict as yaml.
 
+    The FourCIPP yaml style sets flow
     Args:
         data: Data to dump.
         sort_function: Function to sort the data.
+        use_fourcipp_yaml_style: If FourCIPP yaml style is to be used
 
     Returns:
         YAML string representation of the data
@@ -81,11 +85,60 @@ def dict_to_yaml_string(
     # Convert dictionary into a ryml tree
     tree = ryml.parse_in_arena(bytearray(json.dumps(data).encode("utf8")))
 
-    # remove all style bits to enable a YAML style output
+    def check_is_vector(tree: ryml.Tree, node_id: int) -> bool:
+        """Check if sequence is of ints, floats or sequence there of.
+
+        In 4C metadata terms, list of strings, bools, etc. could also be vectors.
+        For the sake of simplicity these are omitted.
+
+        Args:
+            tree (ryml.Tree): Tree to check
+            node_id (int): Node id
+
+        Returns:
+            returns if entry is a vector
+        """
+
+        for sub_node, _ in ryml.walk(tree, node_id):
+            # Ignore the root node
+            if sub_node == node_id:
+                continue
+
+            # If sequence contains a dict
+            if tree.is_map(sub_node):
+                return False
+
+            # If sequence contains a sequence
+            elif tree.is_seq(sub_node):
+                if not check_is_vector(tree, sub_node):
+                    return False
+
+            # Else it's a value
+            else:
+                val = tree.val(sub_node).tobytes().decode("ascii")
+                is_not_numeric = (
+                    tree.is_val_quoted(sub_node)  # string
+                    or tree.val_is_null(sub_node)  # null
+                    or val == "true"  # bool
+                    or val == "false"  # bool
+                )
+                if is_not_numeric:
+                    return False
+
+        return True
+
+    # Change style bits to avoid JSON output and format vectors correctly
     # see https://github.com/biojppm/rapidyaml/issues/520
-    for node_id, _ in ryml.walk(tree):
-        if tree.is_map(node_id) or tree.is_seq(node_id):
+    for node_id, depth in ryml.walk(tree):
+        if tree.is_map(node_id):
             tree.set_container_style(node_id, ryml.NOTYPE)
+        elif tree.is_seq(node_id):
+            if (
+                not use_fourcipp_yaml_style  # do not do special formatting
+                or depth == 1  # is a section
+                or not check_is_vector(tree, node_id)  # is not a vector
+            ):
+                tree.set_container_style(node_id, ryml.NOTYPE)
 
         if tree.has_key(node_id):
             tree.set_key_style(node_id, ryml.NOTYPE)
@@ -97,15 +150,17 @@ def dump_yaml(
     data: dict,
     path_to_yaml_file: Path,
     sort_function: Callable[[dict], dict] | None = None,
+    use_fourcipp_yaml_style: bool = True,
 ) -> None:
     """Dump yaml to file.
 
     Args:
         data: Data to dump.
         path_to_yaml_file: Yaml file path
-        sort_function: Function to sort the data.
+        sort_function: Function to sort the data
+        use_fourcipp_yaml_style: If FourCIPP yaml style is to be used
     """
     pathlib.Path(path_to_yaml_file).write_text(
-        dict_to_yaml_string(data, sort_function),
+        dict_to_yaml_string(data, sort_function, use_fourcipp_yaml_style),
         encoding="utf-8",
     )

fourcipp/version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '1.3.0'
-__version_tuple__ = version_tuple = (1, 3, 0)
+__version__ = version = '1.5.0'
+__version_tuple__ = version_tuple = (1, 5, 0)
 
 __commit_id__ = commit_id = None

{fourcipp-1.3.0.dist-info → fourcipp-1.5.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: FourCIPP
-Version: 1.3.0
+Version: 1.5.0
 Summary: A streamlined Python Parser for 4C input files
 Author: FourCIPP Authors
 License: The MIT License (MIT)

{fourcipp-1.3.0.dist-info → fourcipp-1.5.0.dist-info}/RECORD

@@ -1,8 +1,8 @@
 fourcipp/__init__.py,sha256=4pz7DVXErSbUcLqPTaHnQfdJzKkpfZDivBqbHbTgpRE,1388
-fourcipp/fourc_input.py,sha256=w37dzvfuzGXv0EdzfGABKjmAwxx-4Ba7dTyzjyk_ApI,23803
-fourcipp/version.py,sha256=0Oc4EBzGTJOvXX0Vym4evglW1NQPpe8RLn8TdxsKzfs,704
-fourcipp/config/4C_metadata.yaml,sha256=3n3Uj24iblvsfqUI-8H2LYMHOROjeHl68Nok0F22Unc,11868927
-fourcipp/config/4C_schema.json,sha256=67giZGZSKXkjO_NCbZzx-blVdGB6BFXRbHrXkmqB_T4,16412275
+fourcipp/fourc_input.py,sha256=TXVP-N_FTadt4L8MPH3VZXeT7i5uy7Btz3H-N0pxMr0,23948
+fourcipp/version.py,sha256=sfeo6QRBwy3wEFaKhAEbFPpF98FLjoe4Car1c6NnghQ,704
+fourcipp/config/4C_metadata.yaml,sha256=A2cJVUA_PMZ3Y_mGP-M3VhpQhLbSn1a1oh3gfGpJ9GQ,11868923
+fourcipp/config/4C_schema.json,sha256=wDRSORrXQpg8cIhIOxeD2GTqfewUE4ygbPSeluSH7b0,16412271
 fourcipp/config/config.yaml,sha256=n2c2a6E4HKfAdNWOQz1kLUuf5p4NLxIddaAi2t5eM38,460
 fourcipp/legacy_io/__init__.py,sha256=y6aTjgUe61OQSl1NMiZ-fQAGTab_xNT1eJTnaTnsIkc,5744
 fourcipp/legacy_io/element.py,sha256=b8--f3IR9nB68R25mk4DHHOBdDLqASewtAdPZAkA2t4,3971
@@ -11,7 +11,7 @@ fourcipp/legacy_io/node.py,sha256=e7m0W7dai_b1XgaqD37k3QS44ySCas3HetmyTLS9_78,35
 fourcipp/legacy_io/node_topology.py,sha256=hqGGzhyNhFX-BMW8SzztfzM8zoZLLltVScMv-p4hDH0,5394
 fourcipp/legacy_io/particle.py,sha256=0rxwdiMnHI1QUGZPqWgsxqyslrxB7aq7qxgNMb_y_rk,2166
 fourcipp/utils/__init__.py,sha256=ccdlf4taJ0mKLg_ru8ilXEa72PoO9N2UIxHNHDEtQmY,1151
-fourcipp/utils/cli.py,sha256=43Nmy9tnoQzwWMZwpktWVv3T3a3y4qDzfuDB1bHogbA,4658
+fourcipp/utils/cli.py,sha256=I0N6mcJQGX7seLtXpfrPJA5EWrmhgOph_gHrrxEs6JE,5801
 fourcipp/utils/configuration.py,sha256=HDrvHrH4K5mdienzVsAt_sh9j2Pv81bxWBqqbeNb1KE,6461
 fourcipp/utils/converter.py,sha256=D40YQ96WqPEEpB7fwAB5XC2v-jRki4v1sIJ-ngO08nU,5194
 fourcipp/utils/dict_utils.py,sha256=uC0uaBNP3Wh2v3kFy9JHnAYARMukAN4cl40pmiBT13Y,12891
@@ -19,10 +19,10 @@ fourcipp/utils/metadata.py,sha256=98jz9Gm8qdvZ-b1jwYObNJTaiMQWwbknvS70Nv6Gwhk,12
 fourcipp/utils/not_set.py,sha256=04C_3axe2cupBYgfpgDAcGs1zHVzG3I58UGO58TH05A,2017
 fourcipp/utils/typing.py,sha256=8iX9PuKe8B1WJ3vEjiM5ZfefvgYnaZDiSdB7Nx9SrVw,1625
 fourcipp/utils/validation.py,sha256=FejHOj1MddaU7gEpMN-f8Mz3rYjflakd1qcsKnctHqA,5292
-fourcipp/utils/yaml_io.py,sha256=yShbQ7d_zv_tGK_3ym3NilrfL7HpsEt_8JvDqZYnuFY,3606
-fourcipp-1.3.0.dist-info/licenses/LICENSE,sha256=lkSOHdH9IZ8c3Vnz0fFjqls1cRlmLADBP8QEIwUlH3o,1082
-fourcipp-1.3.0.dist-info/METADATA,sha256=4G6YxfZlgnnDMV19Yz3UblMfxHpnMCAqWonlpsgmdcY,7947
-fourcipp-1.3.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-fourcipp-1.3.0.dist-info/entry_points.txt,sha256=44XBG4bwhuq1EwOZ0U055HYP8_qN6_d30ecVsa5Igng,53
-fourcipp-1.3.0.dist-info/top_level.txt,sha256=oZ6jgFFmvi157VwGUEFuKT3D8oS5mOkpOVx8zZURZrQ,9
-fourcipp-1.3.0.dist-info/RECORD,,
+fourcipp/utils/yaml_io.py,sha256=bs78Mc3fIz0kK5wgwwu89OhaDpLzECTRBQtIpnifTqk,5559
+fourcipp-1.5.0.dist-info/licenses/LICENSE,sha256=lkSOHdH9IZ8c3Vnz0fFjqls1cRlmLADBP8QEIwUlH3o,1082
+fourcipp-1.5.0.dist-info/METADATA,sha256=drGpZmzC-ufasdYWbwoXz_DoU-gOw7bLoP11yxlTwLo,7947
+fourcipp-1.5.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+fourcipp-1.5.0.dist-info/entry_points.txt,sha256=44XBG4bwhuq1EwOZ0U055HYP8_qN6_d30ecVsa5Igng,53
+fourcipp-1.5.0.dist-info/top_level.txt,sha256=oZ6jgFFmvi157VwGUEFuKT3D8oS5mOkpOVx8zZURZrQ,9
+fourcipp-1.5.0.dist-info/RECORD,,