Make ontoenv-python CLI optional and fix release workflow

- gate the Rust CLI import behind an optional `cli` feature and provide a stub when
it’s disabled  - build all wheels with `abi3` + `cli` while letting
`cargo publish` verify without the CLI dependency  - add
`.github/scripts/wait_for_crates.sh` and call it from `publish_crates`
- rename upload artifacts so binaries use `ontoenv_*` and Python wheels
  use `pyontoenv_*`

Author: gtfierro

.github/workflows/artifacts.yml

@@ -131,7 +131,7 @@ jobs:
           cache: pip
           cache-dependency-path: '**/requirements.dev.txt'
       - run: pip install -r python/requirements.dev.txt
-      - run: maturin build -m python/Cargo.toml
+      - run: maturin build -m python/Cargo.toml --features "cli"
       - run: pip install --no-index --find-links=target/wheels/ ontoenv
       - run: rm -r target/wheels
       - run: maturin sdist -m python/Cargo.toml
@@ -243,16 +243,16 @@ jobs:
           cache: pip
           cache-dependency-path: '**/requirements.dev.txt'
       - run: pip install -r python/requirements.dev.txt
-      - run: maturin build --release --features abi3
+      - run: maturin build --release --features "abi3 cli"
         working-directory: ./python
       - run: pip install --no-index --find-links=target/wheels/ ontoenv
       - run: rm -r target/wheels
-      - run: maturin build --release --target universal2-apple-darwin --features abi3
+      - run: maturin build --release --target universal2-apple-darwin --features "abi3 cli"
         working-directory: ./python
-      - run: maturin build --release --target x86_64-apple-darwin --features abi3
+      - run: maturin build --release --target x86_64-apple-darwin --features "abi3 cli"
         working-directory: ./python
         if: github.event_name == 'release' || (github.event_name == 'workflow_dispatch' && github.event.inputs.run_full_matrix == 'true')
-      - run: maturin build --release --target aarch64-apple-darwin --features abi3
+      - run: maturin build --release --target aarch64-apple-darwin --features "abi3 cli"
         working-directory: ./python
         if: github.event_name == 'release' || (github.event_name == 'workflow_dispatch' && github.event.inputs.run_full_matrix == 'true')
       - uses: actions/upload-artifact@v4
@@ -276,11 +276,11 @@ jobs:
           cache-dependency-path: '**/requirements.dev.txt'
       - run: Remove-Item -LiteralPath "C:\msys64\" -Force -Recurse
       - run: pip install -r python/requirements.dev.txt
-      - run: maturin build --release --features abi3
+      - run: maturin build --release --features "abi3 cli"
         working-directory: ./python
       - run: pip install --no-index --find-links=target/wheels/ ontoenv
       - run: rm -r target/wheels
-      - run: maturin build --release -m python/Cargo.toml --features abi3
+      - run: maturin build --release -m python/Cargo.toml --features "abi3 cli"
       - uses: actions/upload-artifact@v4
         with:
           name: pyontoenv_windows_${{ github.run_attempt }}

.github/workflows/manylinux_build.sh

@@ -20,13 +20,13 @@ cd python
 python3.12 -m venv venv
 source venv/bin/activate
 pip install -r requirements.dev.txt
-maturin develop --release
-maturin build --release --features abi3 --compatibility manylinux_2_28
+maturin develop --release --features "abi3 cli"
+maturin build --release --features "abi3 cli" --compatibility manylinux_2_28
 if [ %for_each_version% ]; then
   for VERSION in 8 9 10 11 12; do
-    maturin build --release --interpreter "python3.$VERSION" --compatibility manylinux_2_28
+    maturin build --release --features "abi3 cli" --interpreter "python3.$VERSION" --compatibility manylinux_2_28
   done
   for VERSION in 9 10; do
-    maturin build --release --interpreter "pypy3.$VERSION" --compatibility manylinux_2_28
+    maturin build --release --features "abi3 cli" --interpreter "pypy3.$VERSION" --compatibility manylinux_2_28
   done
 fi

.github/workflows/musllinux_build.sh

@@ -9,11 +9,10 @@ cd python
 python3.12 -m venv venv
 source venv/bin/activate
 pip install -r requirements.dev.txt
-maturin develop --release
-maturin build --release --features abi3 --compatibility musllinux_1_2
+maturin develop --release --features "abi3 cli"
+maturin build --release --features "abi3 cli" --compatibility musllinux_1_2
 if [ %for_each_version% ]; then
   for VERSION in 8 9 10 11 12; do
-    maturin build --release --interpreter "python3.$VERSION" --compatibility musllinux_1_2
+    maturin build --release --features "abi3 cli" --interpreter "python3.$VERSION" --compatibility musllinux_1_2
   done
 fi
-

python/Cargo.toml

@@ -18,7 +18,7 @@ doc = false
 [dependencies]
 pyo3 = { version = "0.25", features = ["extension-module"] }
 ontoenv.workspace = true
-ontoenv-cli.workspace = true
+ontoenv-cli = { workspace = true, optional = true }
 anyhow.workspace = true
 oxigraph.workspace = true
 env_logger.workspace = true
@@ -28,4 +28,6 @@ log.workspace = true
 pyo3-build-config = "0.25"
 
 [features]
+default = []
 abi3 = ["pyo3/abi3-py39"]
+cli = ["ontoenv-cli"]

python/pyproject.toml

@@ -17,7 +17,7 @@ license = "bsd-3-clause"
 ontoenv = "ontoenv._cli:main"
 
 [tool.maturin]
-features = ["pyo3/extension-module"]
+features = ["pyo3/extension-module", "cli"]
 # This tells maturin to put the compiled native module
 # INSIDE the 'ontoenv' package directory.
 module-name = "ontoenv._native"

python/src/lib.rs

@@ -6,13 +6,16 @@ use ::ontoenv::options::{CacheMode, Overwrite, RefreshStrategy};
 use ::ontoenv::transform;
 use ::ontoenv::ToUriString;
 use anyhow::Error;
+#[cfg(feature = "cli")]
 use ontoenv_cli;
 use oxigraph::model::{BlankNode, Literal, NamedNode, NamedOrBlankNodeRef, Term};
 use pyo3::{
     prelude::*,
     types::{IntoPyDict, PyString, PyTuple},
     exceptions::PyValueError,
 };
+#[cfg(not(feature = "cli"))]
+use pyo3::exceptions::PyRuntimeError;
 use std::borrow::Borrow;
 use std::collections::{HashMap, HashSet};
 use std::path::PathBuf;
@@ -122,6 +125,7 @@ fn term_to_python<'a>(
 
 /// Run the Rust CLI implementation and return its process-style exit code.
 #[pyfunction]
+#[cfg(feature = "cli")]
 fn run_cli(py: Python<'_>, args: Option<Vec<String>>) -> PyResult<i32> {
     let argv = args.unwrap_or_else(|| std::env::args().collect());
     let code = py.allow_threads(move || match ontoenv_cli::run_from_args(argv) {
@@ -134,6 +138,16 @@ fn run_cli(py: Python<'_>, args: Option<Vec<String>>) -> PyResult<i32> {
     Ok(code)
 }
 
+/// Fallback stub when the CLI feature is disabled at compile time.
+#[pyfunction]
+#[cfg(not(feature = "cli"))]
+#[allow(unused_variables)]
+fn run_cli(_py: Python<'_>, _args: Option<Vec<String>>) -> PyResult<i32> {
+    Err(PyErr::new::<PyRuntimeError, _>(
+        "ontoenv was built without CLI support; rebuild with the 'cli' feature",
+    ))
+}
+
 #[pyclass(name = "Ontology")]
 #[derive(Clone)]
 struct PyOntology {