Fix logic-promotion + Improve test coverage

src/api/writer-generator/python.ts

@@ -165,12 +165,8 @@ export class Python extends Writer<PythonGeneratorOptions> {
 
     private generateRootPackages(groups: TypeSchemaPackageGroups): void {
         this.generateRootInitFile(groups);
-        if (this.forFhirpyClient)
-            this.copyAssets(
-                resolvePyAssets("fhirpy_base_model.py"),
-                Path.resolve(this.opts.outputDir, "fhirpy_base_model.py"),
-            );
-        this.copyAssets(resolvePyAssets("requirements.txt"), Path.resolve(this.opts.outputDir, "requirements.txt"));
+        if (this.forFhirpyClient) this.copyAssets(resolvePyAssets("fhirpy_base_model.py"), "fhirpy_base_model.py");
+        this.copyAssets(resolvePyAssets("requirements.txt"), "requirements.txt");
     }
 
     private generateSDKPackages(groups: TypeSchemaPackageGroups): void {

src/api/writer-generator/writer.ts

@@ -114,6 +114,7 @@ export abstract class FileSystemWriter<T extends FileSystemWriterOptions = FileS
     }
 
     copyAssets(source: string, destination: string) {
+        destination = Path.normalize(`${this.currentDir ?? this.opts.outputDir}/${destination}`);
         const content = fs.readFileSync(source, "utf8");
         this.writtenFilesBuffer[destination] = {
             relPath: destination,

src/typeschema/ir/logic-promotion.ts

@@ -53,7 +53,7 @@ export const promoteLogical = (tsIndex: TypeSchemaIndex, promotes: LogicalPromot
                 return {
                     ...n,
                     base: replace(n.base),
-                    nested: replaceInFields(n.fields),
+                    fields: replaceInFields(n.fields),
                 };
             });
         }

test/api/write-generator/__snapshots__/python.test.ts.snap

@@ -75,4 +75,10 @@ class Patient(DomainResource):
 "
 `;
 
-exports[`Python Writer Generator static files 1`] = `undefined`;
+exports[`Python Writer Generator static files 1`] = `
+"requests>=2.32.0,<3.0.0
+pytest>=8.3.0,<9.0.0
+pydantic>=2.11.0,<3.0.0
+mypy>=1.9.0,<2.0.0
+types-requests>=2.32.0,<3.0.0"
+`;

test/api/write-generator/multi-package/__snapshots__/local-package.test.ts.snap

@@ -0,0 +1,317 @@
+// Bun Snapshot v1, https://bun.sh/docs/test/snapshots
+
+exports[`Local Package Folder - Multi-Package Generation TypeScript Generation should generate ExampleNotebook type in custom package folder 1`] = `
+"// WARNING: This file is autogenerated by @atomic-ehr/codegen.
+// GitHub: https://github.com/atomic-ehr/codegen
+// Any manual changes made to this file may be overwritten.
+
+import type { Coding } from "../hl7-fhir-r4-core/Coding";
+import type { DomainResource } from "../hl7-fhir-r4-core/DomainResource";
+import type { Identifier } from "../hl7-fhir-r4-core/Identifier";
+import type { Reference } from "../hl7-fhir-r4-core/Reference";
+
+import type { Element } from "../hl7-fhir-r4-core/Element";
+export type { Coding } from "../hl7-fhir-r4-core/Coding";
+export type { Identifier } from "../hl7-fhir-r4-core/Identifier";
+export type { Reference } from "../hl7-fhir-r4-core/Reference";
+
+// CanonicalURL: http://example.org/fhir/StructureDefinition/ExampleNotebook (pkg: example.folder.structures#0.0.1)
+export interface ExampleNotebook extends DomainResource {
+    author: Reference<"Patient" | "Practitioner">;
+    content: string;
+    _content?: Element;
+    identifier: Identifier;
+    tag?: Coding[];
+    title: string;
+    _title?: Element;
+}
+"
+`;
+
+exports[`Local Package Folder - Multi-Package Generation Python Generation should generate ExampleNotebook type (promoted logical) 1`] = `
+"# WARNING: This file is autogenerated by @atomic-ehr/codegen.
+# GitHub: https://github.com/atomic-ehr/codegen
+# Any manual changes made to this file may be overwritten.
+
+from __future__ import annotations
+from pydantic import BaseModel, ConfigDict, Field, PositiveInt
+from typing import List as PyList, Literal
+
+from fhir_types.hl7_fhir_r4_core.base import Coding, Identifier, Reference
+from fhir_types.hl7_fhir_r4_core.domain_resource import DomainResource
+from fhir_types.hl7_fhir_r4_core.resource_families import DomainResourceFamily
+
+
+class ExampleNotebook(DomainResource):
+    model_config = ConfigDict(validate_by_name=True, serialize_by_alias=True, extra="forbid")
+    resource_type: str = Field(
+        default='ExampleNotebook',
+        alias='resourceType',
+        serialization_alias='resourceType',
+        frozen=True,
+        pattern='ExampleNotebook'
+    )
+    author: Reference = Field(alias="author", serialization_alias="author")
+    content: str = Field(alias="content", serialization_alias="content")
+    identifier: Identifier = Field(alias="identifier", serialization_alias="identifier")
+    tag: PyList[Coding] | None = Field(None, alias="tag", serialization_alias="tag")
+    title: str = Field(alias="title", serialization_alias="title")
+
+    def to_json(self, indent: int | None = None) -> str:
+        return self.model_dump_json(exclude_unset=True, exclude_none=True, indent=indent)
+
+    @classmethod
+    def from_json(cls, json: str) -> ExampleNotebook:
+        return cls.model_validate_json(json)
+
+"
+`;
+
+exports[`Local Package Folder - Multi-Package Generation Python Generation should generate base types for dependencies 1`] = `
+"# WARNING: This file is autogenerated by @atomic-ehr/codegen.
+# GitHub: https://github.com/atomic-ehr/codegen
+# Any manual changes made to this file may be overwritten.
+
+from __future__ import annotations
+from pydantic import BaseModel, ConfigDict, Field, PositiveInt
+from typing import List as PyList, Literal
+
+from fhir_types.hl7_fhir_r4_core.base import Extension, Narrative
+from fhir_types.hl7_fhir_r4_core.resource import Resource
+from fhir_types.hl7_fhir_r4_core.resource_families import ResourceFamily
+
+
+class DomainResource(Resource):
+    model_config = ConfigDict(validate_by_name=True, serialize_by_alias=True, extra="forbid")
+    resource_type: str = Field(
+        default='DomainResource',
+        alias='resourceType',
+        serialization_alias='resourceType',
+        frozen=True,
+        pattern='DomainResource'
+    )
+    contained: PyList[ResourceFamily] | None = Field(None, alias="contained", serialization_alias="contained")
+    extension: PyList[Extension] | None = Field(None, alias="extension", serialization_alias="extension")
+    modifier_extension: PyList[Extension] | None = Field(None, alias="modifierExtension", serialization_alias="modifierExtension")
+    text: Narrative | None = Field(None, alias="text", serialization_alias="text")
+
+    def to_json(self, indent: int | None = None) -> str:
+        return self.model_dump_json(exclude_unset=True, exclude_none=True, indent=indent)
+
+    @classmethod
+    def from_json(cls, json: str) -> DomainResource:
+        return cls.model_validate_json(json)
+
+"
+`;
+
+exports[`Local Package Folder - Multi-Package Generation Python Generation should generate Patient resource 1`] = `
+"# WARNING: This file is autogenerated by @atomic-ehr/codegen.
+# GitHub: https://github.com/atomic-ehr/codegen
+# Any manual changes made to this file may be overwritten.
+
+from __future__ import annotations
+from pydantic import BaseModel, ConfigDict, Field, PositiveInt
+from typing import List as PyList, Literal
+
+from fhir_types.hl7_fhir_r4_core.base import (\\
+    Address, Attachment, BackboneElement, CodeableConcept, ContactPoint, HumanName, Identifier, Period, Reference
+)
+from fhir_types.hl7_fhir_r4_core.domain_resource import DomainResource
+from fhir_types.hl7_fhir_r4_core.resource_families import DomainResourceFamily
+
+
+class PatientCommunication(BackboneElement):
+    model_config = ConfigDict(validate_by_name=True, serialize_by_alias=True, extra="forbid")
+    language: CodeableConcept = Field(alias="language", serialization_alias="language")
+    preferred: bool | None = Field(None, alias="preferred", serialization_alias="preferred")
+
+class PatientContact(BackboneElement):
+    model_config = ConfigDict(validate_by_name=True, serialize_by_alias=True, extra="forbid")
+    address: Address | None = Field(None, alias="address", serialization_alias="address")
+    gender: Literal["male", "female", "other", "unknown"] | None = Field(None, alias="gender", serialization_alias="gender")
+    name: HumanName | None = Field(None, alias="name", serialization_alias="name")
+    organization: Reference | None = Field(None, alias="organization", serialization_alias="organization")
+    period: Period | None = Field(None, alias="period", serialization_alias="period")
+    relationship: PyList[CodeableConcept] | None = Field(None, alias="relationship", serialization_alias="relationship")
+    telecom: PyList[ContactPoint] | None = Field(None, alias="telecom", serialization_alias="telecom")
+
+class PatientLink(BackboneElement):
+    model_config = ConfigDict(validate_by_name=True, serialize_by_alias=True, extra="forbid")
+    other: Reference = Field(alias="other", serialization_alias="other")
+    type: Literal["replaced-by", "replaces", "refer", "seealso"] = Field(alias="type", serialization_alias="type")
+
+
+class Patient(DomainResource):
+    model_config = ConfigDict(validate_by_name=True, serialize_by_alias=True, extra="forbid")
+    resource_type: str = Field(
+        default='Patient',
+        alias='resourceType',
+        serialization_alias='resourceType',
+        frozen=True,
+        pattern='Patient'
+    )
+    active: bool | None = Field(None, alias="active", serialization_alias="active")
+    address: PyList[Address] | None = Field(None, alias="address", serialization_alias="address")
+    birth_date: str | None = Field(None, alias="birthDate", serialization_alias="birthDate")
+    communication: PyList[PatientCommunication] | None = Field(None, alias="communication", serialization_alias="communication")
+    contact: PyList[PatientContact] | None = Field(None, alias="contact", serialization_alias="contact")
+    deceased_boolean: bool | None = Field(None, alias="deceasedBoolean", serialization_alias="deceasedBoolean")
+    deceased_date_time: str | None = Field(None, alias="deceasedDateTime", serialization_alias="deceasedDateTime")
+    gender: Literal["male", "female", "other", "unknown"] | None = Field(None, alias="gender", serialization_alias="gender")
+    general_practitioner: PyList[Reference] | None = Field(None, alias="generalPractitioner", serialization_alias="generalPractitioner")
+    identifier: PyList[Identifier] | None = Field(None, alias="identifier", serialization_alias="identifier")
+    link: PyList[PatientLink] | None = Field(None, alias="link", serialization_alias="link")
+    managing_organization: Reference | None = Field(None, alias="managingOrganization", serialization_alias="managingOrganization")
+    marital_status: CodeableConcept | None = Field(None, alias="maritalStatus", serialization_alias="maritalStatus")
+    multiple_birth_boolean: bool | None = Field(None, alias="multipleBirthBoolean", serialization_alias="multipleBirthBoolean")
+    multiple_birth_integer: int | None = Field(None, alias="multipleBirthInteger", serialization_alias="multipleBirthInteger")
+    name: PyList[HumanName] | None = Field(None, alias="name", serialization_alias="name")
+    photo: PyList[Attachment] | None = Field(None, alias="photo", serialization_alias="photo")
+    telecom: PyList[ContactPoint] | None = Field(None, alias="telecom", serialization_alias="telecom")
+
+    def to_json(self, indent: int | None = None) -> str:
+        return self.model_dump_json(exclude_unset=True, exclude_none=True, indent=indent)
+
+    @classmethod
+    def from_json(cls, json: str) -> Patient:
+        return cls.model_validate_json(json)
+
+"
+`;
+
+exports[`Local Package Folder - Multi-Package Generation C# Generation should generate ExampleNotebook type (promoted logical) 1`] = `
+"// WARNING: This file is autogenerated by @atomic-ehr/codegen.
+// GitHub: https://github.com/atomic-ehr/codegen
+// Any manual changes made to this file may be overwritten.
+
+
+namespace Fhir.Types.ExampleFolderStructures;
+
+public class ExampleNotebook : DomainResource {
+    public required ResourceReference Author { get; set; }
+    public required string Content { get; set; }
+    public required Identifier Identifier { get; set; }
+    public Coding[]? Tag { get; set; }
+    public required string Title { get; set; }
+
+    public override string ToString() => 
+        JsonSerializer.Serialize(this, Helper.JsonSerializerOptions);
+
+}
+
+"
+`;
+
+exports[`Local Package Folder - Multi-Package Generation C# Generation should generate DomainResource base class 1`] = `
+"// WARNING: This file is autogenerated by @atomic-ehr/codegen.
+// GitHub: https://github.com/atomic-ehr/codegen
+// Any manual changes made to this file may be overwritten.
+
+
+namespace Fhir.Types.Hl7FhirR4Core;
+
+public class DomainResource : Resource {
+    public Resource[]? Contained { get; set; }
+    public Extension[]? Extension { get; set; }
+    public Extension[]? ModifierExtension { get; set; }
+    public Narrative? Text { get; set; }
+
+    public override string ToString() => 
+        JsonSerializer.Serialize(this, Helper.JsonSerializerOptions);
+
+}
+
+"
+`;
+
+exports[`Local Package Folder - Multi-Package Generation C# Generation should generate Resource base class 1`] = `
+"// WARNING: This file is autogenerated by @atomic-ehr/codegen.
+// GitHub: https://github.com/atomic-ehr/codegen
+// Any manual changes made to this file may be overwritten.
+
+
+namespace Fhir.Types.Hl7FhirR4Core;
+
+public class Resource {
+    public string? Id { get; set; }
+    public string? ImplicitRules { get; set; }
+    public string? Language { get; set; }
+    public Meta? Meta { get; set; }
+
+    public override string ToString() => 
+        JsonSerializer.Serialize(this, Helper.JsonSerializerOptions);
+
+}
+
+"
+`;
+
+exports[`Local Package Folder - Multi-Package Generation C# Generation should generate Patient resource 1`] = `
+"// WARNING: This file is autogenerated by @atomic-ehr/codegen.
+// GitHub: https://github.com/atomic-ehr/codegen
+// Any manual changes made to this file may be overwritten.
+
+
+namespace Fhir.Types.Hl7FhirR4Core;
+
+public class Patient : DomainResource {
+    public bool? Active { get; set; }
+    public Address[]? Address { get; set; }
+    public string? BirthDate { get; set; }
+    public PatientCommunication[]? Communication { get; set; }
+    public PatientContact[]? Contact { get; set; }
+    public bool? DeceasedBoolean { get; set; }
+    public string? DeceasedDateTime { get; set; }
+    public AdministrativeGenderEnum? Gender { get; set; }
+    public ResourceReference[]? GeneralPractitioner { get; set; }
+    public Identifier[]? Identifier { get; set; }
+    public PatientLink[]? Link { get; set; }
+    public ResourceReference? ManagingOrganization { get; set; }
+    public CodeableConcept? MaritalStatus { get; set; }
+    public bool? MultipleBirthBoolean { get; set; }
+    public int? MultipleBirthInteger { get; set; }
+    public HumanName[]? Name { get; set; }
+    public Attachment[]? Photo { get; set; }
+    public ContactPoint[]? Telecom { get; set; }
+
+    public class PatientCommunication : BackboneElement {
+        public required CodeableConcept Language { get; set; }
+        public bool? Preferred { get; set; }
+
+        public override string ToString() => 
+            JsonSerializer.Serialize(this, Helper.JsonSerializerOptions);
+
+    }
+
+    public class PatientContact : BackboneElement {
+        public Address? Address { get; set; }
+        public AdministrativeGenderEnum? Gender { get; set; }
+        public HumanName? Name { get; set; }
+        public ResourceReference? Organization { get; set; }
+        public Period? Period { get; set; }
+        public CodeableConcept[]? Relationship { get; set; }
+        public ContactPoint[]? Telecom { get; set; }
+
+        public override string ToString() => 
+            JsonSerializer.Serialize(this, Helper.JsonSerializerOptions);
+
+    }
+
+    public class PatientLink : BackboneElement {
+        public required ResourceReference Other { get; set; }
+        public required LinkTypeEnum Type { get; set; }
+
+        public override string ToString() => 
+            JsonSerializer.Serialize(this, Helper.JsonSerializerOptions);
+
+    }
+
+
+    public override string ToString() => 
+        JsonSerializer.Serialize(this, Helper.JsonSerializerOptions);
+
+}
+
+"
+`;