Merge pull request #7 from ycexiao/entry-point

feat: add `diffpy.app runmacro <`.dp-in` file>` entry point

Author: sbillinge

news/entry-point.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* Add ``diffpy.app runmacro <file>`` command.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

pyproject.toml

@@ -51,7 +51,7 @@ exclude = []  # exclude packages matching these glob patterns (empty by default)
 namespaces = false  # to disable scanning PEP 420 namespaces (true by default)
 
 [project.scripts]
-diffpy-apps = "diffpy.apps.app:main"
+"diffpy.app" = "diffpy.apps.apps:main"
 
 [tool.setuptools.dynamic]
 dependencies = {file = ["requirements/pip.txt"]}

src/diffpy/apps/app_runmacro.py

@@ -0,0 +1,282 @@
+import inspect
+from collections import OrderedDict
+from pathlib import Path
+
+import yaml
+from textx import metamodel_from_str
+
+from diffpy.apps.pdfadapter import PDFAdapter
+
+grammar = r"""
+Program:
+    commands*=Command
+    variable=VariableBlock
+;
+
+Command:
+    LoadCommand | SetCommand | CreateCommand | SaveCommand
+;
+
+LoadCommand:
+    'load' component=ID name=ID 'from' source=STRING
+;
+
+SetCommand:
+    'set' name=ID attribute=ID 'as' value+=Value[eolterm]
+    | 'set' name=ID 'as' value+=Value[eolterm]
+;
+
+CreateCommand:
+    'create' 'equation' 'variables' value+=Value[eolterm]
+;
+
+SaveCommand:
+    'save' 'to' source=STRING
+;
+
+VariableBlock:
+    'variables:' '---' content=/[\s\S]*?(?=---)/ '---'
+;
+
+Value:
+    STRICTFLOAT | INT | STRING | RawValue
+;
+
+RawValue:
+    /[^\s]+/
+;
+"""
+
+
+class MacroParser:
+    def __init__(self):
+        self.pdfadapter = PDFAdapter()
+        self.meta_model = metamodel_from_str(grammar)
+        self.meta_model.register_obj_processors(
+            {
+                "SetCommand": self.set_command_processor,
+                "LoadCommand": self.load_command_processor,
+                "VariableBlock": self.parameter_block_processor,
+                "CreateCommand": self.create_command_processor,
+                "SaveCommand": self.save_command_processor,
+            }
+        )
+        # key: method_name.argument_name
+        # value: argument_value
+        self.inputs = {}
+        # key: structure name or profile name set in the macro
+        # value: 'structure' or 'profile'
+        self.variables = OrderedDict()
+
+    def parse(self, code):
+        self.meta_model.model_from_str(code)
+
+    def input_as_list(self, key, value):
+        if key in self.inputs:
+            if not isinstance(self.inputs[key], list):
+                self.inputs[key] = [self.inputs[key]]
+            else:
+                self.inputs[key].append(value)
+        else:
+            if isinstance(value, list):
+                self.inputs[key] = value
+            else:
+                self.inputs[key] = [value]
+
+    def load_command_processor(self, command):
+        if command.component == "structure":
+            # TODO: support multiple structures input in the future
+            key = "initialize_structures.structure_paths"
+            variable = "structure"
+        elif command.component == "profile":
+            key = "initialize_profile.profile_path"
+            variable = "profile"
+        else:
+            raise ValueError(
+                f"Unknown component type: {command.component} "
+                "Please use 'structure' or 'profile'."
+            )
+        source_path = Path(command.source)
+        if not source_path.exists():
+            raise FileNotFoundError(
+                f"{command.component} {source_path} not found. "
+                "Please ensure the path is correct and the file exists."
+            )
+        self.inputs[key] = str(source_path)
+        self.variables[command.name] = variable
+        if variable == "structure":
+            self.input_as_list("initialize_structures.names", command.name)
+
+    def set_command_processor(self, command):
+        if command.name == "equation":
+            key = "initialize_contribution.equation"
+        elif command.name in self.variables:
+            if self.variables[command.name] == "structure":
+                if command.attribute == "spacegroup":
+                    key = "initialize_structures.spacegroups"
+                else:
+                    key = "initialize_structures." + command.attribute
+            elif self.variables[command.name] == "profile":
+                key = "initialize_profile." + command.attribute
+            else:
+                raise ValueError(
+                    f"Unknown variable type for name: {command.name}. "
+                    "This is an internal error. Please report this issue to "
+                    "the developers."
+                )
+        else:
+            raise ValueError(
+                f"Unknown name in set command: {command.name}. "
+                "Please ensure that it is typed correctly as 'equation' or "
+                "it matches a previously loaded structure or "
+                "profile. "
+            )
+        self.input_as_list(key, command.value)
+
+    def parameter_block_processor(self, variable_block):
+        self.inputs["set_initial_variable_values.variable_name_to_value"] = {}
+        self.inputs["refine_variables.variable_names"] = []
+        parameters = yaml.safe_load(variable_block.content)
+        if not isinstance(parameters, list):
+            raise ValueError(
+                "Parameter block should contain a list of parameters. "
+                "Please use the following format:\n"
+                "- param1  # use default initial value\n"
+                "- param2: initial_value\n"
+            )
+        for item in parameters:
+            if isinstance(item, str):
+                self.inputs["refine_variables.variable_names"].append(
+                    item.replace(".", "_")
+                )
+            elif isinstance(item, dict):
+                pname, pvalue = list(item.items())[0]
+                self.inputs[
+                    "set_initial_variable_values.variable_name_to_value"
+                ][pname.replace(".", "_")] = pvalue
+                self.inputs["refine_variables.variable_names"].append(
+                    pname.replace(".", "_")
+                )
+            else:
+                raise ValueError(
+                    "Variables block items are not correctly formatted. "
+                    "Please use the following format:\n"
+                    "- param1  # use default initial value\n"
+                    "- param2: initial_value\n"
+                )
+
+    def create_command_processor(self, command):
+        self.inputs["add_contribution_variables.variable_names"] = (
+            command.value
+        )
+
+    def save_command_processor(self, command):
+        self.inputs["save_results.result_path"] = command.source
+
+    def required_args(self, func):
+        sig = inspect.signature(func)
+        return [
+            name
+            for name, p in sig.parameters.items()
+            if p.default is inspect.Parameter.empty
+            and p.kind
+            in (
+                inspect.Parameter.POSITIONAL_ONLY,
+                inspect.Parameter.POSITIONAL_OR_KEYWORD,
+                inspect.Parameter.KEYWORD_ONLY,
+            )
+        ]
+
+    def call_pdfadapter_method(self, method_name, function_requirement):
+        func = getattr(self.pdfadapter, method_name)
+        required_arguments = self.required_args(func)
+        arguments = {
+            key.split(".")[1]: value
+            for key, value in self.inputs.items()
+            if key.startswith(method_name)
+        }
+        if not all(arg in arguments for arg in required_arguments):
+            missing_args = [
+                arg for arg in required_arguments if arg not in arguments
+            ]
+            if function_requirement == "required":
+                raise ValueError(
+                    "Missing required arguments for function "
+                    f"'{method_name}' {', '.join(missing_args)}. "
+                    "Please provide these arguments in the macro file."
+                )
+            elif function_requirement == "optional":
+                print(
+                    "Missing required arguments for function "
+                    f"'{method_name}' {', '.join(missing_args)}. "
+                    "This function will be skipped. "
+                    "Please provide these arguments in the macro file "
+                    "to activate this function."
+                )
+                return
+        func(**arguments)
+
+    def preprocess(self):
+        methods_to_call = [
+            ("initialize_profile", "required"),
+            ("initialize_structures", "required"),
+            ("initialize_contribution", "required"),
+            ("initialize_recipe", "required"),
+            ("add_contribution_variables", "optional"),
+            ("set_initial_variable_values", "optional"),
+        ]
+        for method in methods_to_call:
+            self.call_pdfadapter_method(*method)
+
+    def run(self):
+        methods_to_call = [
+            ("refine_variables", "required"),
+            ("save_results", "optional"),
+        ]
+        for method in methods_to_call:
+            self.call_pdfadapter_method(*method)
+        return self.pdfadapter.get_results()
+
+
+def runmacro(args):
+    dpin_path = Path(args.file)
+    if not dpin_path.exists():
+        raise FileNotFoundError(
+            f"{str(dpin_path)} not found. Please check if this file "
+            "exists and provide the correct path to it."
+        )
+    dsl_code = dpin_path.read_text()
+    parser = MacroParser()
+    parser.parse(dsl_code)
+    parser.preprocess()
+    return parser.run()
+
+
+if __name__ == "__main__":
+    parser = MacroParser()
+    code = f"""
+load structure G1 from "{str(Path(__file__).parents[3] / "tests/data/Ni.cif")}"
+load profile exp_ni from "{str(Path(__file__).parents[3] / "tests/data/Ni.gr")}"
+
+set G1 spacegroup as auto
+set exp_ni q_range as 0.1 25
+set exp_ni calculation_range as 1.5 50 0.01
+create equation variables s0
+set equation as "s0*G1"
+save to "results.json"
+
+variables:
+---
+- G1.a: 3.52
+- s0: 0.4
+- G1.Uiso_0: 0.005
+- G1.delta2: 2
+- qdamp: 0.04
+- qbroad: 0.02
+---
+"""  # noqa: E501
+    parser.parse(code)
+    parser.preprocess()
+    recipe = parser.pdfadapter.recipe
+    for pname, param in recipe._parameters.items():
+        print(f"{pname}: {param.value}")

src/diffpy/apps/apps.py

@@ -0,0 +1,57 @@
+import argparse
+
+from diffpy.apps.app_runmacro import runmacro
+from diffpy.apps.version import __version__  # noqa
+
+
+class DiffpyHelpFormatter(argparse.RawDescriptionHelpFormatter):
+    """Format subcommands without showing an extra placeholder entry."""
+
+    def _format_action(self, action):
+        if isinstance(action, argparse._SubParsersAction):
+            return "".join(
+                self._format_action(subaction)
+                for subaction in self._iter_indented_subactions(action)
+            )
+        return super()._format_action(action)
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        prog="diffpy.apps",
+        description=(
+            "User applications to help with tasks using diffpy packages\n\n"
+            "For more information, visit: "
+            "https://github.com/diffpy/diffpy.apps/"
+        ),
+        formatter_class=DiffpyHelpFormatter,
+    )
+
+    parser.add_argument(
+        "--version",
+        action="store_true",
+        help="Show the program's version number and exit",
+    )
+    apps_parsers = parser.add_subparsers(
+        title="Available applications",
+        dest="application",
+    )
+    runmacro_parser = apps_parsers.add_parser(
+        "runmacro",
+        help="Run a macro `<.dp-in>` file",
+    )
+    runmacro_parser.add_argument(
+        "file",
+        type=str,
+        help="Path to the  `<.dp-in>` macro file to be run",
+    )
+    runmacro_parser.set_defaults(func=runmacro)
+    args = parser.parse_args()
+    if args.application is None:
+        parser.print_help()
+    else:
+        args.func(args)
+
+
+if __name__ == "__main__":
+    main()