openpathsampling · dwhswenson · Nov 2, 2021 · Oct 23, 2021 · Oct 30, 2021 · Oct 30, 2021
diff --git a/paths_cli/commands/compile.py b/paths_cli/commands/compile.py
@@ -56,6 +56,16 @@ def select_loader(filename):
     except KeyError:
         raise RuntimeError(f"Unknown file extension: {ext}")
 
+def register_installed_plugins():
+    plugin_types = (InstanceCompilerPlugin, CategoryPlugin)
+    plugins = get_installed_plugins(
+        default_loader=NamespacePluginLoader('paths_cli.compiling',
+                                             plugin_types),
+        plugin_types=plugin_types
+    )
+    register_plugins(plugins)
+
+
 @click.command(
     'compile',
 )
@@ -66,13 +76,7 @@ def compile_(input_file, output_file):
     with open(input_file, mode='r') as f:
         dct = loader(f)
 
-    plugin_types = (InstanceCompilerPlugin, CategoryPlugin)
-    plugins = get_installed_plugins(
-        default_loader=NamespacePluginLoader('paths_cli.compiling',
-                                             plugin_types),
-        plugin_types=plugin_types
-    )
-    register_plugins(plugins)
+    register_installed_plugins()
 
     objs = do_compile(dct)
     print(f"Saving {len(objs)} user-specified objects to {output_file}....")

diff --git a/paths_cli/compiling/_gendocs/README.md b/paths_cli/compiling/_gendocs/README.md
@@ -0,0 +1,6 @@
+# _gendocs
+
+Tools for generating documentation for the tools import `paths_cli.compiling`.
+Note that this entire directory is considered outside the API, so nothing in
+here should be strongly relied on.
+
diff --git a/paths_cli/compiling/_gendocs/__init__.py b/paths_cli/compiling/_gendocs/__init__.py
@@ -0,0 +1,2 @@
+from .config_handler import load_config, DocCategoryInfo
+from .docs_generator import DocsGenerator
diff --git a/paths_cli/compiling/_gendocs/config_handler.py b/paths_cli/compiling/_gendocs/config_handler.py
@@ -0,0 +1,27 @@
+from collections import namedtuple
+from paths_cli.commands.compile import select_loader
+
+DocCategoryInfo = namedtuple('DocCategoryInfo', ['header', 'description',
+                                                 'type_required'],
+                             defaults=[None, True])
+
+
+def load_config(config_file):
+    """Load a configuration file for gendocs.
+
+    The configuration file should be YAML or JSON, and should map each
+    category name to the headings necessary to fill a DocCategoryInfo
+    instance.
+
+    Parameters
+    ----------
+    config_file : str
+        name of YAML or JSON file
+    """
+    loader = select_loader(config_file)
+    with open(config_file, mode='r', encoding='utf-8') as f:
+        dct = loader(f)
+
+    result = {category: DocCategoryInfo(**details)
+              for category, details in dct.items()}
+    return result
diff --git a/paths_cli/compiling/_gendocs/docs_generator.py b/paths_cli/compiling/_gendocs/docs_generator.py
@@ -0,0 +1,145 @@
+import sys
+from paths_cli.compiling.core import Parameter
+from .json_type_handlers import json_type_to_string
+from .config_handler import DocCategoryInfo
+
+PARAMETER_RST = """* **{p.name}**{type_str} - {p.description}{required}\n"""
+
+
+class DocsGenerator:
+    """This generates the RST to describe options for compile input files.
+
+    Parameters
+    ----------
+    config : Dict[str, DocCategoryInfo]
+        mapping of category name to DocCategoryInfo for that category;
+        usually generated by :method:`.load_config`
+    """
+
+    parameter_template = PARAMETER_RST
+    _ANCHOR_SEP = "--"
+
+    def __init__(self, config):
+        self.config = config
+
+    def format_parameter(self, parameter, type_str=None):
+        """Format a single :class:`.paths_cli.compiling.Parameter` in RST
+        """
+        required = " (required)" if parameter.required else ""
+        return self.parameter_template.format(
+            p=parameter, type_str=type_str, required=required
+        )
+
+    def _get_cat_info(self, category_plugin):
+        cat_info = self.config.get(category_plugin.label, None)
+        if cat_info is None:
+            cat_info = DocCategoryInfo(category_plugin.label)
+        return cat_info
+
+    def generate_category_rst(self, category_plugin):
+        """Generate the RST for a given category plugin.
+
+        Parameters
+        ----------
+        category_plugin : :class:`.CategoryPlugin`
+            the plugin for which we should generate the RST page
+
+        Returns
+        -------
+        str :
+            RST string for this category
+        """
+        cat_info = self._get_cat_info(category_plugin)
+        type_required = cat_info.type_required
+        rst = f".. _compiling--{category_plugin.label}:\n\n"
+        rst += f"{cat_info.header}\n{'=' * len(str(cat_info.header))}\n\n"
+        if cat_info.description:
+            rst += cat_info.description + "\n\n"
+        rst += ".. contents:: :local:\n\n"
+        for obj in category_plugin.type_dispatch.values():
+            rst += self.generate_plugin_rst(
+                obj, category_plugin.label, type_required
+            )
+        return rst
+
+    def generate_plugin_rst(self, plugin, category_name,
+                            type_required=True):
+        """Generate the RST for a given object plugin.
+
+        Parameters
+        ----------
+        plugin : class:`.InstanceCompilerPlugin`
+            the object plugin for to generate the RST for
+        category_name : str
+            the name of the category for this object
+        type_required : bool
+            whether the ``type`` parameter is required in the dict input for
+            compiling this type of object (usually category-dependent)
+
+        Returns
+        -------
+        str :
+            RST string for this object plugin
+        """
+        rst_anchor = f".. _{category_name}{self._ANCHOR_SEP}{plugin.name}:"
+        rst = f"{rst_anchor}\n\n{plugin.name}\n{'-' * len(plugin.name)}\n\n"
+        if plugin.description:
+            rst += plugin.description + "\n\n"
+        if type_required:
+            type_param = Parameter(
+                "type",
+                json_type="",
+                loader=None,
+                description=(f"type identifier; must exactly match the "
+                             f"string ``{plugin.name}``"),
+            )
+            rst += self.format_parameter(
+                type_param, type_str=""
+            )
+
+        name_param = Parameter(
+            "name",
+            json_type="string",
+            loader=None,
+            default="",
+            description="name this object in order to reuse it",
+        )
+        rst += self.format_parameter(name_param, type_str=" (*string*)")
+        for param in plugin.parameters:
+            type_str = f" ({json_type_to_string(param.json_type)})"
+            rst += self.format_parameter(param, type_str)
+
+        rst += "\n\n"
+        return rst
+
+    @staticmethod
+    def _get_filename(cat_info):
+        fname = str(cat_info.header).lower()
+        fname = fname.translate(str.maketrans(' ', '_'))
+        return f"{fname}.rst"
+
+    def generate(self, category_plugins, stdout=False):
+        """Generate RST output for the given plugins.
+
+        This is the main method used to generate the entire set of
+        documentation.
+
+        Parameters
+        ----------
+        category_plugin : List[:class:`.CategoryPlugin`]
+            list of category plugins document
+        stdout : bool
+            if False (default) a separate output file is generated for each
+            category plugin. If True, all text is output to stdout
+            (particularly useful for debugging/dry runs).
+        """
+        for plugin in category_plugins:
+            rst = self.generate_category_rst(plugin)
+            if stdout:
+                sys.stdout.write(rst)
+                sys.stdout.flush()
+            else:
+                cat_info = self._get_cat_info(plugin)
+                filename = self._get_filename(cat_info)
+                with open(filename, 'w') as f:
+                    f.write(rst)
diff --git a/paths_cli/compiling/_gendocs/json_type_handlers.py b/paths_cli/compiling/_gendocs/json_type_handlers.py
@@ -0,0 +1,161 @@
+class JsonTypeHandler:
+    """Abstract class to obtain documentation type from JSON schema type.
+
+    Parameters
+    ----------
+    is_my_type : Callable[Any] -> bool
+        return True if this instance should handle the given input type
+    handler : Callable[Any] -> str
+        convert the input type to a string suitable for the RST docs
+    """
+    def __init__(self, is_my_type, handler):
+        self._is_my_type = is_my_type
+        self.handler = handler
+
+    def is_my_type(self, json_type):
+        """Determine whether this instance should handle this type.
+
+        Parameters
+        ----------
+        json_type : Any
+            input type from JSON schema
+
+        Returns
+        -------
+        bool :
+            whether to handle this type with this instance
+        """
+        return self._is_my_type(json_type)
+
+    def __call__(self, json_type):
+        if self.is_my_type(json_type):
+            return self.handler(json_type)
+        return json_type
+
+
+handle_object = JsonTypeHandler(
+    is_my_type=lambda json_type: json_type == "object",
+    handler=lambda json_type: "dict",
+)
+
+
+def _is_listof(json_type):
+    try:
+        return json_type["type"] == "array"
+    except:  # any exception should return false (mostly Key/Type Error)
+        return False
+
+
+handle_listof = JsonTypeHandler(
+    is_my_type=_is_listof,
+    handler=lambda json_type: "list of "
+    + json_type_to_string(json_type["items"]),
+)
+
+
+class RefTypeHandler(JsonTypeHandler):
+    """Handle JSON types of the form {"$ref": "#/definitions/..."}
+
+    Parameters
+    ----------
+    type_name : str
+        the name to use in the RST type
+    def_string : str
+        the string following "#/definitions/" in the JSON type definition
+    link_to : str or None
+        if not None, the RST type will be linked with a ``:ref:`` pointing
+        to the anchor given by ``link_to``
+    """
+    def __init__(self, type_name, def_string, link_to):
+        self.type_name = type_name
+        self.def_string = def_string
+        self.link_to = link_to
+        self.json_check = {"$ref": "#/definitions/" + def_string}
+        super().__init__(is_my_type=self._reftype, handler=self._refhandler)
+
+    def _reftype(self, json_type):
+        return json_type == self.json_check
+
+    def _refhandler(self, json_type):
+        rst = f"{self.type_name}"
+        if self.link_to:
+            rst = f":ref:`{rst} <{self.link_to}>`"
+        return rst
+
+
+class CategoryHandler(RefTypeHandler):
+    """Handle JSON types for OPS category definitions.
+
+    OPS category definitions show up with JSON references pointing to
+    "#/definitions/{CATEGORY}_type". This provides a convenience class over
+    the :class:RefTypeHandler to treat OPS categories.
+
+    Parameters
+    ----------
+    category : str
+        name of the category
+    """
+    def __init__(self, category):
+        self.category = category
+        def_string = f"{category}_type"
+        link_to = f"compiling--{category}"
+        super().__init__(
+            type_name=category, def_string=def_string, link_to=link_to
+        )
+
+
+class EvalHandler(RefTypeHandler):
+    """Handle JSON types for OPS custom evaluation definitions.
+
+    Some parameters for the OPS compiler use the OPS custom evaluation
+    mechanism, which evaluates certain Python-like string input. These are
+    treated as special definition types in the JSON schema, and this object
+    provides a convenience class over :class:`.RefTypeHandler` to treat
+    custom evaluation types.
+
+    Parameters
+    ----------
+    type_name : str
+        name of the custom evaluation type
+    link_to : str or None
+        if not None, the RST type will be linked with a ``:ref:`` pointing
+        to the anchor given by ``link_to``
+    """
+    def __init__(self, type_name, link_to=None):
+        super().__init__(
+            type_name=type_name, def_string=type_name, link_to=link_to
+        )
+
+
+JSON_TYPE_HANDLERS = [
+    handle_object,
+    handle_listof,
+    CategoryHandler("engine"),
+    CategoryHandler("cv"),
+    CategoryHandler("volume"),
+    EvalHandler("EvalInt"),
+    EvalHandler("EvalFloat"),
+]
+
+
+def json_type_to_string(json_type):
+    """Convert JSON schema type to string for RST docs.
+
+    This is the primary public-facing method for dealing with JSON schema
+    types in RST document generation.
+
+    Parameters
+    ----------
+    json_type : Any
+        the type from the JSON schema
+
+    Returns
+    -------
+    str :
+        the type string description to be used in the RST document
+    """
+    for handler in JSON_TYPE_HANDLERS:
+        handled = handler(json_type)
+        if handled != json_type:
+            return handled
+    return json_type
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		from .config_handler import load_config, DocCategoryInfo
		from .docs_generator import DocsGenerator