Comparison with EBI fork

.github/workflows/run-precommit.yaml

@@ -17,10 +17,7 @@ jobs:
         with:
           distribution: 'zulu' # See 'Supported distributions' for available options
           java-version: '21'
-      - run: |
-          mkdir --parents $HOME/.local/bin
-          wget https://github.com/phillord/tawny-bubo/releases/download/0.3.2/bubo -O $HOME/.local/bin/bubo
-          chmod +x $HOME/.local/bin/bubo
+      - run: make fetch_bubo
         shell: bash
       - run: python -m pip install pre-commit
         shell: bash

.gitignore

@@ -9,9 +9,12 @@ Cargo.lock
 
 # IDEs
 .vscode/
+.claude/
 
 # Mac OS X
 .DS_Store
+/dev/bubo-0.4.0
 /flamegraph.svg
 /perf.data
 /perf.data.old
+.cargo-ok

.pre-commit-config.yaml

@@ -8,6 +8,7 @@ repos:
         args: ["--check", "--"]
         pass_filenames: false
     -   id: clippy
+        args: ["--workspace", "--all-targets"]
         pass_filenames: false
 -   repo: local
     hooks:

Cargo.toml

@@ -25,20 +25,29 @@ indexmap={workspace=true}
 oxiri={workspace=true}
 pest = "2.7.8"
 pest_derive = "2.7.8"
-pretty_rdf={workspace=true}
+horned-pretty-rdf={workspace=true}
+horned-catalog={workspace=true}
+rustc-hash = "2"
 oxrdf={workspace=true}
 oxrdfio={workspace=true}
-ureq={version="2.1.1", optional=true}
+ureq={version="3.3.0", optional=true}
 
 [workspace]
-members=["horned-bin"]
-default-members=[".", "horned-bin"]
+members=["horned-bin", "horned-pretty-rdf", "horned-catalog", "horned-macro"]
+default-members=[".", "horned-bin", "horned-pretty-rdf", "horned-catalog", "horned-macro"]
 
 [workspace.dependencies]
-indexmap="1.0.2"
+# `features = ["std"]` is required for tier-3 wasm targets (e.g. wasm64-unknown-
+# unknown): indexmap 1.x has no default features and only exposes the RandomState
+# default + `IndexMap::new()` when its build script sees `CARGO_FEATURE_STD`;
+# otherwise it falls back to an autocfg sysroot probe that fails where there is no
+# prebuilt std, compiling no-std. Harmless elsewhere (std is on there anyway).
+indexmap = { version = "1.0.2", features = ["std"] }
+mktemp="0.5.1"
 oxiri="0.2.11"
-##pretty_rdf={path="./pretty_rdf"}
-pretty_rdf="0.11.0"
+horned-pretty-rdf={path="./horned-pretty-rdf", version="2.0.0"}
+horned-catalog={path="./horned-catalog", version="0.1.0"}
+horned-macro={path="./horned-macro", version="0.1.0"}
 oxrdf="0.3.0"
 oxrdfio="0.2.0"
 
@@ -48,13 +57,15 @@ remote = ["ureq"]
 encoding = ["quick-xml/encoding"]
 
 [dev-dependencies]
+proptest = "1"
 horned-owl = {path=".", features = ["remote"]}
 criterion = "0.7.0"
-mktemp = "0.5.1"
+mktemp = {workspace = true}
 pretty_assertions = "1.0.0"
 slurp = "1.0.1"
-test-generator =  { version = "^0.3" }
+rstest = "0.23"
 horned-bin = {path="horned-bin"}
+horned-macro = {workspace = true}
 
 [profile.release]
 debug = true
@@ -63,3 +74,8 @@ debug = true
 name = "horned"
 harness = false
 
+
+# web-time: a drop-in `std::time::Instant` that works on wasm (where the std
+# clock traps). Used via the `crate::time` shim (src/lib.rs).
+[target.'cfg(target_arch = "wasm32")'.dependencies]
+web-time = "1"

Makefile

@@ -26,10 +26,17 @@ bench-prepare:
 
 
 ## Build the Unit test Ontology code
+##
+## `test_resources` (the test-generator proc-macro driving src/ont/*
+## fixture discovery) globs those directories at compile time with
+## nothing telling Cargo to invalidate the build when files there
+## change, so a stale test binary can silently miss new/changed/removed
+## fixtures. `cargo clean` unconditionally after bubo runs so the next
+## `cargo test` always sees current fixtures.
 just-bubo:
 	$(MAKE) -C src/ont/bubo
 
-bubo: just-bubo clean test
+bubo: just-bubo test
 
 clean:
 	cargo clean
@@ -112,9 +119,13 @@ triples-round-all:
 	done
 
 clippy:
-	cargo clippy
+	cargo clippy --workspace --all-targets
 
 install:
 	cargo install --path horned-bin
 
+fetch_bubo:
+	wget https://github.com/phillord/tawny-bubo/releases/download/0.4.0/bubo-0.4.0 -O dev/bubo-0.4.0
+	chmod +x dev/bubo-0.4.0
+
 -include makefile-local

README.md

@@ -15,7 +15,7 @@ with millions of terms.
   + [x] RDF/XML
   + [x] OWL/XML
   + [x] Functional Syntax
-  + [ ] Manchester Syntax
+  + [x] Manchester Syntax
 + A [visitor](https://en.wikipedia.org/wiki/Visitor_pattern) trait to navigate and manipulate ontologies
 + Traits and implementations for several types of ontologies
 
@@ -34,7 +34,7 @@ To use the latest version of the library in your Rust project, add the following
 ```toml
 [dependencies]
 ...
-horned-owl = "1.0.0"
+horned-owl = "2.1.0"
 ```
 
 

benches/horned.rs

@@ -1,9 +1,13 @@
 use criterion::criterion_main;
 
-mod io;
+mod io_read;
+mod io_write;
+mod iteration;
 mod model;
 
-use crate::io::io;
+use crate::io_read::io_read;
+use crate::io_write::io_write;
+use crate::iteration::iteration;
 use crate::model::model;
 
-criterion_main!(model, io);
+criterion_main!(model, io_read, io_write, iteration);

benches/io.rs → benches/io_read.rs

@@ -7,7 +7,7 @@ use std::fs::{File, create_dir_all};
 use std::io::BufReader;
 use std::time::Duration;
 
-fn io_read(c: &mut Criterion) {
+fn bench_io_read(c: &mut Criterion) {
     let mut group = c.benchmark_group("io_read");
     group.plot_config(PlotConfiguration::default().summary_scale(AxisScale::Logarithmic));
 
@@ -58,7 +58,6 @@ fn io_read(c: &mut Criterion) {
                     ParserConfiguration {
                         rdf: RDFParserConfiguration {
                             format: Some(oxrdfio::RdfFormat::Turtle),
-                            ..Default::default()
                         },
                         ..Default::default()
                     },
@@ -70,9 +69,9 @@ fn io_read(c: &mut Criterion) {
 }
 
 criterion_group! {
-    name = io;
+    name = io_read;
     config = Criterion::default()
     .sample_size(50)
     .measurement_time(Duration::from_secs(20));
-    targets = io_read
+    targets = bench_io_read
 }

benches/io_write.rs

@@ -0,0 +1,81 @@
+use criterion::{AxisScale, BenchmarkId, Criterion, PlotConfiguration, criterion_group};
+use horned_owl::model::{Build, MutableOntology, RcStr};
+use horned_owl::ontology::component_mapped::RcComponentMappedOntology;
+use horned_owl::ontology::set::SetOntology;
+use horned_pretty_rdf::ox::WriterQuadSerializerAdaptor;
+use oxrdfio::RdfSerializer;
+use std::io::sink;
+use std::time::Duration;
+
+fn build_ontology(n: isize) -> RcComponentMappedOntology {
+    let b = Build::new_rc();
+    let mut o: SetOntology<RcStr> = SetOntology::new_rc();
+    for i in 1..=n {
+        o.declare(b.class(format!("https://www.example.com/o{}", i)));
+    }
+    o.into()
+}
+
+fn bench_io_write(c: &mut Criterion) {
+    let mut group = c.benchmark_group("io_write");
+    group.plot_config(PlotConfiguration::default().summary_scale(AxisScale::Logarithmic));
+
+    for n in [10, 100, 1_000, 2500, 5000, 10_000].iter() {
+        let ont = build_ontology(*n);
+
+        // RDF/XML: pretty formatter (horned-pretty-rdf)
+        group.bench_function(BenchmarkId::new("rdf_xml_pretty_io_write", n), |b| {
+            b.iter(|| {
+                horned_owl::io::rdf::writer::write(sink(), &ont).ok();
+            })
+        });
+
+        // RDF/XML: plain oxrdfio serializer
+        group.bench_function(BenchmarkId::new("rdf_xml_plain_io_write", n), |b| {
+            b.iter(|| {
+                let f = WriterQuadSerializerAdaptor::new(
+                    RdfSerializer::from_format(oxrdfio::RdfFormat::RdfXml).for_writer(sink()),
+                );
+                horned_owl::io::rdf::writer::write_to_rdf_formatter(&ont, f).ok();
+            })
+        });
+
+        group.bench_function(BenchmarkId::new("ttl_io_write", n), |b| {
+            b.iter(|| {
+                horned_owl::io::rdf::writer::write_to_rdf_format(sink(), &ont, "ttl").ok();
+            })
+        });
+
+        group.bench_function(BenchmarkId::new("nt_io_write", n), |b| {
+            b.iter(|| {
+                horned_owl::io::rdf::writer::write_to_rdf_format(sink(), &ont, "nt").ok();
+            })
+        });
+
+        group.bench_function(BenchmarkId::new("owx_io_write", n), |b| {
+            b.iter(|| {
+                horned_owl::io::owx::writer::write(sink(), &ont, None).ok();
+            })
+        });
+
+        group.bench_function(BenchmarkId::new("ofn_io_write", n), |b| {
+            b.iter(|| {
+                horned_owl::io::ofn::writer::write(sink(), &ont, None).ok();
+            })
+        });
+
+        group.bench_function(BenchmarkId::new("omn_io_write", n), |b| {
+            b.iter(|| {
+                horned_owl::io::omn::writer::write(sink(), &ont, None).ok();
+            })
+        });
+    }
+}
+
+criterion_group! {
+    name = io_write;
+    config = Criterion::default()
+    .sample_size(50)
+    .measurement_time(Duration::from_secs(20));
+    targets = bench_io_write
+}