IR progress

src/styx/backend/python/core.py

@@ -1,6 +1,7 @@
 import dataclasses
 from typing import Any, Generator, Iterable
 
+from styx.backend.python.documentation import docs_to_docstring
 from styx.backend.python.interface import compile_interface
 from styx.backend.python.pycodegen.core import PyModule
 from styx.backend.python.pycodegen.scope import Scope
@@ -34,7 +35,9 @@ def to_python(interfaces: Iterable[Interface]) -> Generator[tuple[str, list[str]
                 package=interface.package,
                 package_symbol=global_scope.add_or_dodge(python_snakify(interface.package.name)),
                 scope=Scope(parent=global_scope),
-                module=PyModule(),
+                module=PyModule(
+                    docstr=docs_to_docstring(interface.package.docs),
+                ),
             )
         package_data = packages[interface.package.name]
 
@@ -44,7 +47,7 @@ def to_python(interfaces: Iterable[Interface]) -> Generator[tuple[str, list[str]
         interface_module = PyModule()
         compile_interface(interface=interface, package_scope=package_data.scope, interface_module=interface_module)
         package_data.module.imports.append(f"from .{interface_module_symbol} import *")
-        yield interface_module.text(), [interface.package.name, interface_module_symbol]
+        yield interface_module.text(), [package_data.package_symbol, interface_module_symbol]
 
     for package_data in packages.values():
-        yield package_data.module.text(), [package_data.package_symbol]
+        yield package_data.module.text(), [package_data.package_symbol, "__init__"]

src/styx/backend/python/documentation.py

@@ -38,14 +38,16 @@ def docs_to_docstring(docs: Documentation) -> str | None:
         if len(docs.literature) == 1:
             re += f"Literature: {docs.literature[0]}"
         else:
-            re += f"Literature:\n{'\n'.join(docs.literature)}"
+            entries = '\n'.join(docs.literature)
+            re += f"Literature:\n{entries}"
 
-    if docs.authors:
+    if docs.urls:
         re = _ensure_double_linebreak_if_not_empty(re)
         if len(docs.urls) == 1:
             re += f"URL: {docs.urls[0]}"
         else:
-            re += f"URLs:\n{'\n'.join(docs.urls)}"
+            entries = '\n'.join(docs.urls)
+            re += f"URLs:\n{entries}"
 
     if re:
         return re

src/styx/backend/python/interface.py

@@ -48,7 +48,6 @@ def _compile_struct(
             docstring_body=docs_to_docstring(param.param.docs),
         )
         pyargs = func_cargs_building.args
-        interface_module.funcs.append(func_cargs_building)
     else:
         func_cargs_building = PyFunc(
             name="run",
@@ -78,7 +77,6 @@ def _compile_struct(
             )
             struct_class.methods.append(func_outputs)
         pyargs = struct_class.fields
-        interface_module.funcs.append(struct_class)
 
     # Collect param python symbols
     for elem in param.struct.iter_params():
@@ -131,20 +129,22 @@ def _compile_struct(
             "execution.run(cargs)",
             "return ret",
         ])
+        interface_module.funcs_and_classes.append(func_cargs_building)
     else:
         if has_outputs:
             _compile_outputs_building(
                 param=param,
                 func=func_outputs,
                 lookup=lookup,
-                access_via_self=False,
+                access_via_self=True,
             )
             func_outputs.body.extend([
                 "return ret",
             ])
         func_cargs_building.body.extend([
             "return cargs",
         ])
+        interface_module.funcs_and_classes.append(struct_class)
 
 
 def _compile_cargs_building(

src/styx/backend/python/lookup.py

@@ -19,7 +19,7 @@ def _collect_output_field_symbols(
         ) -> None:
             scope = Scope(parent=package_scope)
             for output in param.param.outputs:
-                output_field_symbol = scope.add_or_dodge(output.name)
+                output_field_symbol = scope.add_or_dodge(python_snakify(output.name))
                 assert output.id_ not in lookup_output_field_symbol
                 lookup_output_field_symbol[output.id_] = output_field_symbol
 

src/styx/backend/python/pycodegen/core.py

@@ -201,9 +201,10 @@ class PyModule(PyGen):
 
     imports: LineBuffer = field(default_factory=list)
     header: LineBuffer = field(default_factory=list)
-    funcs: list[PyFunc | PyDataClass] = field(default_factory=list)
+    funcs_and_classes: list[PyFunc | PyDataClass] = field(default_factory=list)
     footer: LineBuffer = field(default_factory=list)
     exports: list[str] = field(default_factory=list)
+    docstr: str | None = None
 
     def generate(self) -> LineBuffer:
         exports = (
@@ -217,13 +218,16 @@ def generate(self) -> LineBuffer:
         )
 
         return blank_after([
+            *(
+                ['"""', *linebreak_paragraph(self.docstr), '"""'] if self.docstr else []
+             ),
             *comment([
                 "This file was auto generated by Styx.",
                 "Do not edit this file directly.",
             ]),
             *blank_before(self.imports),
             *blank_before(self.header),
-            *[line for func in self.funcs for line in blank_before(func.generate(), 2)],
+            *[line for func in self.funcs_and_classes for line in blank_before(func.generate(), 2)],
             *blank_before(self.footer),
             *blank_before(exports, 2),
         ])

src/styx/frontend/boutiques/core.py

@@ -331,6 +331,9 @@ def _get_urls(bt: dict) -> list[str]:
 
     parent_input: dict | None = None
     if "type" not in bt:  # Root boutiques descriptor
+        if (bt_id := bt.get("id", bt.get("name"))) is None:
+            raise Exception(f"Descriptor is missing id/name: {bt_id}")
+
         groups, ir_id_lookup = _collect_inputs(bt, id_counter)
         outputs = _collect_outputs(bt, ir_id_lookup, id_counter)
 
@@ -342,11 +345,11 @@ def _get_urls(bt: dict) -> list[str]:
 
         return ir.DParam(
             id_=id_counter.next(),
-            name=bt.get("id", bt["name"]),
+            name=bt_id,
             outputs=outputs,
             docs=docs,
         ), ir.DStruct(
-            name=bt.get("id", bt["name"]),
+            name=bt_id,
             groups=groups,
             docs=docs,
         )
@@ -444,7 +447,11 @@ def _collect_inputs(bt, id_counter):
     return groups, ir_id_lookup
 
 
-def from_boutiques(tool: dict, package_name: str) -> ir.Interface:
+def from_boutiques(
+    tool: dict,
+    package_name: str,
+    package_docs: ir.Documentation | None = None,
+) -> ir.Interface:
     """Convert a Boutiques tool to a Styx descriptor."""
     hash_ = _hash_from_boutiques(tool)
 
@@ -462,6 +469,7 @@ def from_boutiques(tool: dict, package_name: str) -> ir.Interface:
             name=package_name,
             version=tool.get("tool-version"),
             docker=docker,
+            docs=package_docs if package_docs else ir.Documentation(),
         ),
         command=ir.PStruct(
             param=dparam,
@@ -476,7 +484,7 @@ def from_boutiques(tool: dict, package_name: str) -> ir.Interface:
     print(json_path)
     with open(json_path, "r", encoding="utf-8") as json_file:
         json_data = json.load(json_file)
-    ir_data = from_boutiques(json_data, package_name="AFNI")
+    ir_data = from_boutiques(json_data, package_name="afni", package_docs=ir.Documentation(urls=["Helo hehe"]))
     from styx.ir.pretty_print import pretty_print
 
     pretty_print(ir_data)
@@ -485,8 +493,8 @@ def from_boutiques(tool: dict, package_name: str) -> ir.Interface:
     print(stats(ir_data))
     from styx.backend.python.core import to_python
 
-    for module, module_path in to_python([ir_data]):
+    for py, module_path in to_python([ir_data]):
         print("=" * 80)
         print("File: " + ".".join(module_path))
         print("-" * 80)
-        print(module.text())
+        print(py)