Merge pull request #12 from gtfierro/gtf-python-changes

Python changes

Author: gtfierro

.github/workflows/artifacts.yml

@@ -1,10 +1,6 @@
 name: Artifacts
 
 on:
-  push:
-    branches:
-      - main
-      - next
   release:
     types:
       - published

.github/workflows/ci.yml

@@ -0,0 +1,47 @@
+name: Tests
+
+on:
+  push:
+    branches:
+      - '**'  # Triggers on push to all branches
+  pull_request:
+    branches:
+      - '**'  # Triggers on pull request to all branches
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build_and_test:
+    runs-on: ubuntu-latest
+    steps:
+      #- run: cd python && python -m unittest test.py
+      - uses: actions/checkout@v4
+        with:
+          submodules: true
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+      - name: Set up Python
+        run: uv python install
+      - uses: ./.github/actions/setup-rust
+        with:
+          target: aarch64-unknown-linux-gnu
+          version: stable
+      - run: |
+          sudo apt-get update && sudo apt-get install -y g++-aarch64-linux-gnu libssl-dev
+          mkdir .cargo
+          echo -e "[target.aarch64-unknown-linux-gnu]\nlinker = \"aarch64-linux-gnu-gcc\"" >> .cargo/config.toml
+      - name: Build rust stuff
+        run: cargo build --workspace --release
+      - name: Run rust tests
+        run: cargo test --workspace --release
+      - name: Build python package
+        run: uv run maturin build --release --features abi3
+        working-directory: ./python
+      - name: Test python package
+        run: uv run python -m unittest test.py
+        working-directory: ./python
+

lib/src/api.rs

@@ -22,11 +22,10 @@ use petgraph::graph::{Graph as DiGraph, NodeIndex};
 use std::collections::{HashMap, HashSet, VecDeque};
 use std::fs;
 
-/// Searches for the .ontoenv directory in the current directory and then recursively up its parent directories.
+/// Searches for the .ontoenv directory in the given directory and then recursively up its parent directories.
 /// Returns the path to the directory containing the .ontoenv directory if found.
-pub fn find_ontoenv_root() -> Option<PathBuf> {
-    let start_dir = std::env::current_dir().ok()?;
-    let mut current_dir = Some(start_dir.as_path());
+pub fn find_ontoenv_root_from(start_dir: &Path) -> Option<PathBuf> {
+    let mut current_dir = Some(start_dir);
     while let Some(dir) = current_dir {
         if dir.join(".ontoenv").is_dir() {
             return Some(dir.to_path_buf());
@@ -36,6 +35,13 @@ pub fn find_ontoenv_root() -> Option<PathBuf> {
     None
 }
 
+/// Searches for the .ontoenv directory in the current directory and then recursively up its parent directories.
+/// Returns the path to the directory containing the .ontoenv directory if found.
+pub fn find_ontoenv_root() -> Option<PathBuf> {
+    let start_dir = std::env::current_dir().ok()?;
+    find_ontoenv_root_from(&start_dir)
+}
+
 /// These are the different ways to refer to an ontology: either
 /// by a location (file or URL), or the name of the graph (IRI)
 pub enum ResolveTarget {

python/README.md

@@ -7,29 +7,46 @@
 ## Usage
 
 ```python
-from ontoenv import Config, OntoEnv
+from ontoenv import OntoEnv
 from rdflib import Graph
 
-cfg = Config(["../brick"], strict=False, offline=True)
-
-# make environment
-env = OntoEnv(cfg)
-
+# creates a new environment in the current directory, or loads
+# an existing one. To use a different directory, pass the 'path'
+# argument: OntoEnv(path="/path/to/env")
+# OntoEnv() will discover ontologies in the current directory and
+# its subdirectories
+env = OntoEnv()
+
+# add an ontology from a file path.
+# env.add returns the name of the ontology, which is its URI
+# e.g. "https://brickschema.org/schema/1.4-rc1/Brick"
+brick_name = env.add("../brick/Brick.ttl")
+print(f"Added ontology {brick_name}")
+
+# get the graph of the ontology we just added
+# env.get returns an rdflib.Graph
+brick_graph = env.get(brick_name)
+print(f"Brick graph has {len(brick_graph)} triples")
+
+# get the full closure of the ontology, including all of its imports
+# also returns an rdflib.Graph
+brick_closure_graph = env.get_closure(brick_name)
+print(f"Brick closure has {len(brick_closure_graph)} triples")
+
+# you can also add ontologies from a URL
+rec_name = env.add("https://w3id.org/rec/rec.ttl")
+rec_graph = env.get(rec_name)
+print(f"REC graph has {len(rec_graph)} triples")
+
+# if you have an rdflib.Graph with an owl:Ontology declaration,
+# you can transitively import its dependencies into the graph
 g = Graph()
-# put the transitive owl:imports closure into 'g'
-env.get_closure("https://brickschema.org/schema/1.4-rc1/Brick", g)
-
-# or, get the graph directly
-g = env.get_closure("https://brickschema.org/schema/1.4-rc1/Brick")
-
-brick = Graph()
-brick.parse("Brick.ttl", format="turtle")
-# transitively import dependencies into the 'brick' graph, using the owl:imports declarations
-env.import_dependencies(brick)
-
-# pull Brick graph out of environment
-brick = env.get_graph("https://brickschema.org/schema/1.4-rc1/Brick")
-
-# import graphs by name
-env.import_graph(brick, "https://w3id.org/rec")
+# this graph just has one triple: the ontology declaration for Brick
+g.parse(data="""
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+<https://brickschema.org/schema/1.4-rc1/Brick> a owl:Ontology .
+""")
+# this will load all of the owl:imports of the Brick ontology into 'g'
+env.import_dependencies(g)
+print(f"Graph with imported dependencies has {len(g)} triples")
 ```

python/example.py

@@ -0,0 +1,46 @@
+from ontoenv import Config, OntoEnv, version
+from rdflib import Graph
+print(version)
+
+
+cfg = Config(["../brick"], strict=False, offline=False)
+
+print("Make env")
+env = OntoEnv(cfg)
+print(env)
+print("get brick")
+g = Graph()
+env.get_closure("https://brickschema.org/schema/1.4-rc1/Brick", g)
+print(len(g))
+
+print("get brick 2")
+brick = Graph()
+brick.parse("../brick/Brick.ttl", format="turtle")
+env.import_dependencies(brick)
+print(len(brick))
+brick_name = env.add("https://brickschema.org/schema/1.4/Brick.ttl")
+print(f"Added {brick_name}")
+del env
+
+print("new env")
+env2 = OntoEnv()
+print(env2.store_path())
+
+print("get brick again from URL")
+brick = env2.get("https://brickschema.org/schema/1.4/Brick")
+print(len(brick))
+print(brick)
+print(type(brick))
+
+print("brick closure", env2.list_closure("https://brickschema.org/schema/1.4/Brick"))
+
+env2.import_graph(brick, "https://w3id.org/rec")
+brick.serialize("test.ttl", format="turtle")
+
+print("qudtqk deps", env2.get_dependents('http://qudt.org/2.1/vocab/quantitykind'))
+
+# get an rdflib.Dataset (https://rdflib.readthedocs.io/en/stable/apidocs/rdflib.html#rdflib.Dataset)
+ds = env2.to_rdflib_dataset()
+for graphname in ds.graphs():
+    graph = ds.graph(graphname)
+    print(f"Graph {graphname} has {len(graph)} triples")

python/pyproject.toml

@@ -22,5 +22,10 @@ build-backend = "maturin"
 
 [dependency-groups]
 dev = [
+    "maturin>=1.9.0",
     "pytest>=8.3.5",
 ]
+
+[tool.uv]
+# Rebuild package when any rust files change
+cache-keys = [{file = "pyproject.toml"}, {file = "Cargo.toml"}, {file = "**/*.rs"}]