Merge branch 'add-fit-flag'

Author: JR-1991

.github/workflows/test.yml

@@ -0,0 +1,25 @@
+name: Go Tests
+
+on:
+  push:
+    branches:
+      - '**'
+  pull_request:
+
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Setup Go
+        uses: actions/setup-go@v5
+        with:
+          go-version-file: go.mod
+          cache: true
+
+      - name: Run tests
+        run: go test ./...

README.md

@@ -4,7 +4,7 @@
 
 **A comprehensive Go implementation of the EnzymeML data exchange format for enzymatic data**
 
-[![Go Version](https://img.shields.io/badge/Go-1.19+-00ADD8?style=flat-square&logo=go)](https://golang.org/)
+[![Go Version](https://img.shields.io/badge/Go-1.25+-00ADD8?style=flat-square&logo=go)](https://golang.org/)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg?style=flat-square)](https://opensource.org/licenses/MIT)
 
 ---
@@ -22,6 +22,7 @@
     - [Requirements](#requirements)
   - [📖 Usage](#-usage)
     - [Quick Start](#quick-start)
+    - [🌐 Start v2 REST API](#-start-v2-rest-api)
     - [🗄️ Database Example](#️-database-example)
   - [🤝 Contributing](#-contributing)
   - [📄 License](#-license)
@@ -50,12 +51,12 @@ EnzymeML Go implements the complete **EnzymeML v2 specification**, providing you
 Get started with EnzymeML Go in seconds:
 
 ```bash
-go get github.com/enzymeml-go
+go get github.com/EnzymeML/enzymeml-go
 ```
 
 ### Requirements
 
-- **Go 1.19+** - Ensure you have a recent version of Go installed
+- **Go 1.25+** - Ensure you have a recent version of Go installed
 - **Modern Go modules** - This package uses Go modules for dependency management
 
 ## 📖 Usage
@@ -67,28 +68,112 @@ package main
 
 import (
     "fmt"
-    "github.com/enzymeml-go"
+    enzymeml_v2 "github.com/EnzymeML/enzymeml-go/src"
 )
 
 func main() {
-    // Your EnzymeML Go code here
-    fmt.Println("Welcome to EnzymeML Go!")
+    doc := enzymeml_v2.EnzymeMLDocument{Name: "Example"}
+    fmt.Println(doc.Name)
 }
 ```
 
+### 🌐 Start v2 REST API
+
+Create a `main.go`:
+
+```go
+package main
+
+import (
+ "log"
+ "net/http"
+
+ apiv2 "github.com/EnzymeML/enzymeml-go/src/api/v2"
+ enzymeml_v2 "github.com/EnzymeML/enzymeml-go/src"
+ database "github.com/EnzymeML/enzymeml-go/src/database/v2"
+)
+
+func main() {
+ models := []interface{}{
+  &enzymeml_v2.EnzymeMLDocument{},
+  &enzymeml_v2.Creator{},
+  &enzymeml_v2.Vessel{},
+  &enzymeml_v2.Protein{},
+  &enzymeml_v2.Complex{},
+  &enzymeml_v2.SmallMolecule{},
+  &enzymeml_v2.Reaction{},
+  &enzymeml_v2.ReactionElement{},
+  &enzymeml_v2.ModifierElement{},
+  &enzymeml_v2.Equation{},
+  &enzymeml_v2.Variable{},
+  &enzymeml_v2.Parameter{},
+  &enzymeml_v2.Measurement{},
+  &enzymeml_v2.MeasurementData{},
+  &enzymeml_v2.UnitDefinition{},
+  &enzymeml_v2.BaseUnit{},
+ }
+
+ dbManager, err := database.NewDBManager("enzymeml.db", models)
+ if err != nil {
+  log.Fatalf("failed to init DB: %v", err)
+ }
+ defer dbManager.Close()
+
+ handler, err := apiv2.NewHandler(dbManager)
+ if err != nil {
+  log.Fatalf("failed to build API handler: %v", err)
+ }
+
+ log.Println("v2 API listening on :8080")
+ log.Fatal(http.ListenAndServe(":8080", handler))
+}
+```
+
+Run:
+
+```bash
+go run .
+```
+
+Example CRUD for documents:
+
+```bash
+curl -X POST http://localhost:8080/v2/documents \
+  -H "Content-Type: application/json" \
+  -d '{"name":"my-doc","version":"2.0.0"}'
+
+curl http://localhost:8080/v2/documents
+curl http://localhost:8080/v2/documents/1
+
+curl -X PUT http://localhost:8080/v2/documents/1 \
+  -H "Content-Type: application/json" \
+  -d '{"name":"my-doc-updated","version":"2.0.1"}'
+
+curl -X DELETE http://localhost:8080/v2/documents/1
+```
+
+The API exposes CRUD for all v2 resources under `/v2`:
+`documents`, `creators`, `vessels`, `proteins`, `complexes`, `small-molecules`, `reactions`, `reaction-elements`, `modifier-elements`, `equations`, `variables`, `parameters`, `measurements`, `measurement-data`, `unit-definitions`, `base-units`.
+
+With Huma, docs/spec are available automatically:
+
+- `http://localhost:8080/v2/docs`
+- `http://localhost:8080/v2/openapi.json`
+- `http://localhost:8080/v2/openapi.yaml`
+
 ### 🗄️ Database Example
 
 For a comprehensive example of how to use EnzymeML Go to create an enzymatic data database and power web applications, check out our detailed example:
 
 **👉 [Database Example](./examples/database_example/)**
 
 This example demonstrates:
+
 - Setting up an EnzymeML-compliant database
 - Storing and retrieving enzymatic data
 - Web application integration
 - Best practices for data management
 
-
 ## 🤝 Contributing
 
 We welcome contributions from the community! Please feel free to submit a pull request.
@@ -101,4 +186,4 @@ This project is licensed under the **MIT License** - see the [LICENSE](LICENSE)
 
 <div align="center">
 <strong>Made with ❤️ by the EnzymeML Team</strong>
-</div>
+</div>

examples/database_example/Readme.md

@@ -1,24 +1,30 @@
-# Database Example
+# v2 API Example
 
-This example demonstrates how to:
+This example starts the EnzymeML v2 REST API using SQLite.
 
-1. Set up a SQLite database for EnzymeML documents
-2. Create and store a sample EnzymeML document with:
-    - Creator information
-    - Reaction vessel specifications
-    - Proteins (enzymes)
-    - Small molecules (substrates and products)
-    - Reaction definitions
-    - Measurement conditions
+## Run
 
-## Prerequisites
+```bash
+go run main.go
+```
+
+The server starts at `http://localhost:8080`.
 
-- Go 1.20 or later
-- SQLite 3.41 or later
-- EnzymeML Go package
+Interactive docs and OpenAPI:
 
-## Run the example
+- `http://localhost:8080/v2/docs`
+- `http://localhost:8080/v2/openapi.json`
+- `http://localhost:8080/v2/openapi.yaml`
+
+## Quick check
 
 ```bash
-go run main.go
+curl -X POST http://localhost:8080/v2/documents \
+  -H "Content-Type: application/json" \
+  -d '{"name":"my-doc","version":"2.0.0"}'
+
+curl http://localhost:8080/v2/documents
+curl http://localhost:8080/v2/openapi.json
 ```
+
+The API includes CRUD endpoints for all v2 resources under `/v2`.