Merge pull request #21 from gtfierro/fixing-build

Fixing release process

Author: gtfierro

.github/workflows/artifacts.yml

@@ -4,6 +4,12 @@ on:
   release:
     types:
       - published
+  workflow_dispatch:
+    inputs:
+      run_full_matrix:
+        description: Build all additional architectures (aarch64, universal2, etc.)
+        type: boolean
+        default: true
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -126,13 +132,41 @@ jobs:
           cache-dependency-path: '**/requirements.dev.txt'
       - run: pip install -r python/requirements.dev.txt
       - run: maturin build -m python/Cargo.toml
-      - run: pip install --no-index --find-links=target/wheels/ pyontoenv
+      - run: pip install --no-index --find-links=target/wheels/ ontoenv
       - run: rm -r target/wheels
       - run: maturin sdist -m python/Cargo.toml
       - uses: actions/upload-artifact@v4
         with:
-          name: pyontoenv_dist
+          name: ontoenv_dist
           path: target/wheels/*.tar.gz
+  python_pyontoenv_alias:
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release' || github.event_name == 'workflow_dispatch'
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: true
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - run: |
+          VERSION=$(awk '
+            /^\[workspace.package\]/ { in_section=1; next }
+            /^\[/ { if (in_section) exit; in_section=0 }
+            in_section && $1 ~ /^version/ {
+              gsub(/"/, "", $3);
+              print $3;
+              exit
+            }
+          ' Cargo.toml)
+          echo "ONTOENV_VERSION=$VERSION" >> "$GITHUB_ENV"
+      - run: pip install build
+      - run: python -m build
+        working-directory: ./pyontoenv-shim
+      - uses: actions/upload-artifact@v4
+        with:
+          name: ontoenv_pyontoenv_alias
+          path: pyontoenv-shim/dist/*
 
   wheel_linux:
     runs-on: ubuntu-latest
@@ -147,16 +181,16 @@ jobs:
       - uses: docker/setup-qemu-action@v2
         with:
           platforms: linux/${{ matrix.architecture }}
-        if: github.event_name == 'release' && matrix.architecture != 'x86_64'
+        if: (github.event_name == 'release' || github.event_name == 'workflow_dispatch' && github.event.inputs.run_full_matrix == 'true') && matrix.architecture != 'x86_64'
       - uses: ./.github/actions/setup-rust
         with:
           version: stable
-      - run: sed 's/%arch%/${{ matrix.architecture }}/g' .github/workflows/manylinux_build.sh | sed 's/%for_each_version%/${{ github.event_name == 'release' || '' }}/g' > .github/workflows/manylinux_build_script.sh
-      - run: docker run -v "$(pwd)":/workdir --platform linux/${{ matrix.architecture }} quay.io/pypa/manylinux2014_${{ matrix.architecture }} /bin/bash /workdir/.github/workflows/manylinux_build_script.sh
-        if: github.event_name == 'release' || matrix.architecture == 'x86_64'
+      - run: sed "s/%arch%/${{ matrix.architecture }}/g" .github/workflows/manylinux_build.sh | sed "s/%for_each_version%/${{ (github.event_name == 'release' || (github.event_name == 'workflow_dispatch' && github.event.inputs.run_full_matrix == 'true')) && 'true' || '' }}/g" > .github/workflows/manylinux_build_script.sh
+      - run: docker run -v "$(pwd)":/workdir --platform linux/${{ matrix.architecture }} quay.io/pypa/manylinux_2_28_${{ matrix.architecture }} /bin/bash /workdir/.github/workflows/manylinux_build_script.sh
+        if: github.event_name == 'release' || (github.event_name == 'workflow_dispatch' && github.event.inputs.run_full_matrix == 'true') || matrix.architecture == 'x86_64'
       - uses: actions/upload-artifact@v4
         with:
-          name: pyontoenv_${{ matrix.architecture }}_linux_gnu
+          name: ontoenv_${{ matrix.architecture }}_linux_gnu
           path: target/wheels/*.whl
 
   wheel_linux_musl:
@@ -172,17 +206,17 @@ jobs:
       - uses: docker/setup-qemu-action@v2
         with:
           platforms: linux/${{ matrix.architecture }}
-        if: github.event_name == 'release' && matrix.architecture != 'x86_64'
+        if: (github.event_name == 'release' || github.event_name == 'workflow_dispatch' && github.event.inputs.run_full_matrix == 'true') && matrix.architecture != 'x86_64'
       - uses: ./.github/actions/setup-rust
         with:
           version: stable
-      - run: sed 's/%arch%/${{ matrix.architecture }}/g' .github/workflows/musllinux_build.sh | sed 's/%for_each_version%/${{ github.event_name == 'release' || '' }}/g' > .github/workflows/musllinux_build_script.sh
+      - run: sed "s/%arch%/${{ matrix.architecture }}/g" .github/workflows/musllinux_build.sh | sed "s/%for_each_version%/${{ (github.event_name == 'release' || (github.event_name == 'workflow_dispatch' && github.event.inputs.run_full_matrix == 'true')) && 'true' || '' }}/g" > .github/workflows/musllinux_build_script.sh
       - run: docker run -v "$(pwd)":/workdir --platform linux/${{ matrix.architecture }} quay.io/pypa/musllinux_1_2_${{ matrix.architecture }} /bin/bash /workdir/.github/workflows/musllinux_build_script.sh
-        if: github.event_name == 'release' || matrix.architecture == 'x86_64'
+        if: github.event_name == 'release' || (github.event_name == 'workflow_dispatch' && github.event.inputs.run_full_matrix == 'true') || matrix.architecture == 'x86_64'
       - run: find .
       - uses: actions/upload-artifact@v4
         with:
-          name: pyontoenv_${{ matrix.architecture }}_linux_musl
+          name: ontoenv_${{ matrix.architecture }}_linux_musl
           path: target/wheels/*.whl
 
   wheel_mac:
@@ -211,19 +245,19 @@ jobs:
       - run: pip install -r python/requirements.dev.txt
       - run: maturin build --release --features abi3
         working-directory: ./python
-      - run: pip install --no-index --find-links=target/wheels/ pyontoenv
+      - 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
         working-directory: ./python
       - run: maturin build --release --target x86_64-apple-darwin --features abi3
         working-directory: ./python
-        if: github.event_name == 'release'
+        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
         working-directory: ./python
-        if: github.event_name == 'release'
+        if: github.event_name == 'release' || (github.event_name == 'workflow_dispatch' && github.event.inputs.run_full_matrix == 'true')
       - uses: actions/upload-artifact@v4
         with:
-          name: pyontoenv_macos
+          name: ontoenv_macos
           path: target/wheels/*.whl
 
   wheel_windows:
@@ -244,32 +278,33 @@ jobs:
       - run: pip install -r python/requirements.dev.txt
       - run: maturin build --release --features abi3
         working-directory: ./python
-      - run: pip install --no-index --find-links=target/wheels/ pyontoenv
+      - 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
       - uses: actions/upload-artifact@v4
         with:
-          name: pyontoenv_windows
+          name: ontoenv_windows
           path: target/wheels/*.whl
 
   publish_pypi:
     if: github.event_name == 'release'
     runs-on: ubuntu-latest
     environment:
       name: publish
-      url: https://pypi.org/p/pyontoenv
+      url: https://pypi.org/p/ontoenv
     permissions:
       id-token: write
     needs:
       - python_sdist
+      - python_pyontoenv_alias
       - wheel_windows
       - wheel_mac
       - wheel_linux
       - wheel_linux_musl
     steps:
       - uses: actions/download-artifact@v4
         with:
-          pattern: pyontoenv_*
+          pattern: ontoenv_*
           path: dist
           merge-multiple: true
       - uses: pypa/gh-action-pypi-publish@release/v1
@@ -301,15 +336,6 @@ jobs:
           registry-token: ${{ secrets.CARGO_REGISTRY_TOKEN }}
         env:
           CARGO_REGISTRY_TOKEN: ${{ secrets.CARGO_REGISTRY_TOKEN }}
-      - name: Wait for crate index propagation
-        run: sleep 45
-      - name: Publish pyontoenv crate
-        uses: katyo/publish-crates@v2
-        with:
-          path: './python'
-          registry-token: ${{ secrets.CARGO_REGISTRY_TOKEN }}
-        env:
-          CARGO_REGISTRY_TOKEN: ${{ secrets.CARGO_REGISTRY_TOKEN }}
   full_archive:
     if: github.event_name == 'release'
     runs-on: ubuntu-latest

.github/workflows/manylinux_build.sh

@@ -1,24 +1,32 @@
 # from https://github.com/oxigraph/oxigraph/blob/main/.github/workflows/manylinux_build.sh
+set -euxo pipefail
 cd /workdir
-yum -y install centos-release-scl-rh
-yum -y install llvm-toolset-7.0
-source scl_source enable llvm-toolset-7.0
+if command -v dnf >/dev/null 2>&1; then
+  dnf -y update
+  dnf -y install clang cmake make gcc-c++
+elif command -v yum >/dev/null 2>&1; then
+  yum -y update
+  yum -y install clang cmake make gcc-c++
+else
+  echo "No supported package manager found (dnf/yum)" >&2
+  exit 1
+fi
 curl https://static.rust-lang.org/rustup/dist/%arch%-unknown-linux-gnu/rustup-init --output rustup-init
 chmod +x rustup-init
 ./rustup-init -y --profile minimal --default-toolchain stable
 source "$HOME/.cargo/env"
-export PATH="${PATH}:/opt/python/cp37-cp37m/bin:/opt/python/cp38-cp38/bin:/opt/python/cp39-cp39/bin:/opt/python/cp310-cp310/bin:/opt/python/cp311-cp311/bin"
+export PATH="${PATH}:/opt/python/cp37-cp37m/bin:/opt/python/cp38-cp38/bin:/opt/python/cp39-cp39/bin:/opt/python/cp310-cp310/bin:/opt/python/cp311-cp311/bin:/opt/python/cp312-cp312/bin"
 cd python
 python3.12 -m venv venv
 source venv/bin/activate
 pip install -r requirements.dev.txt
 maturin develop --release
-maturin build --release --features abi3 --compatibility manylinux2014
+maturin build --release --features abi3 --compatibility manylinux_2_28
 if [ %for_each_version% ]; then
   for VERSION in 8 9 10 11 12; do
-    maturin build --release --interpreter "python3.$VERSION" --compatibility manylinux2014
+    maturin build --release --interpreter "python3.$VERSION" --compatibility manylinux_2_28
   done
   for VERSION in 9 10; do
-    maturin build --release --interpreter "pypy3.$VERSION" --compatibility manylinux2014
+    maturin build --release --interpreter "pypy3.$VERSION" --compatibility manylinux_2_28
   done
 fi

Cargo.lock

@@ -9,7 +9,7 @@
 Project components:
 - CLI: `ontoenv` (installable via `cargo install ontoenv-cli`)
 - Rust library: [`ontoenv`](https://docs.rs/ontoenv/latest/ontoenv/)
-- Python bindings: [`pyontoenv`](https://pypi.org/project/pyontoenv/)
+- Python bindings: [`ontoenv`](https://pypi.org/project/ontoenv/)
 
 ## Overview
 
@@ -47,7 +47,7 @@ Ontologies fetched from a URL often declare a different, usually versioned, onto
 
 - Install from crates.io with `cargo install --locked ontoenv-cli`
 - From a local checkout, run `cargo install --path cli --locked` to build the current workspace
-- Install via PyPI with `pip install pyontoenv` to get the CLI together with the Python bindings
+- Install via PyPI with `pip install ontoenv` to get the CLI together with the Python bindings
 - Download a binary from the [Releases](https://github.com/gtfierro/ontoenv-rs/releases) tab
 
 ### Usage
@@ -151,11 +151,11 @@ Notes:
 - `ontoenv list missing` — missing imports (i.e. not found in environment); add `--json` for JSON array
 - `ontoenv why <IRI> [<IRI> ...]` — show who imports the given ontology as paths; add `--json` to emit a single JSON document mapping each IRI to path arrays
 
-## Python API (`pyontoenv`)
+## Python API (`ontoenv`)
 
 ##### Installation
 
-`pip install pyontoenv` (requires Python 3.9+; prebuilt wheels ship for common platforms. Building from source needs a Rust toolchain.)
+`pip install ontoenv` (requires Python 3.9+; prebuilt wheels ship for common platforms. Building from source needs a Rust toolchain.)
 
 ### Basic usage
 

README.md

@@ -0,0 +1,5 @@
+# pyontoenv compatibility package
+
+This is a lightweight wrapper that depends on the main `ontoenv` wheel and re-exports its public API so that existing `pip install pyontoenv` workflows continue to function.
+
+It contains no additional functionality beyond importing `ontoenv`.

pyontoenv-shim/README.md

@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools>=68"]
+build-backend = "setuptools.build_meta"

pyontoenv-shim/pyproject.toml

@@ -0,0 +1,46 @@
+from __future__ import annotations
+
+import os
+from pathlib import Path
+
+from setuptools import find_packages, setup
+
+ROOT = Path(__file__).parent.resolve()
+
+version = os.environ.get("ONTOENV_VERSION")
+if not version:
+    raise RuntimeError("ONTOENV_VERSION must be set when building pyontoenv shim")
+
+readme = (
+    (ROOT / "README.md").read_text(encoding="utf-8")
+    if (ROOT / "README.md").exists()
+    else "Compatibility wrapper that installs the ontoenv package."
+)
+
+setup(
+    name="pyontoenv",
+    version=version,
+    description="Compatibility wrapper that depends on the ontoenv package.",
+    long_description=readme,
+    long_description_content_type="text/markdown",
+    author="Gabe Fierro",
+    author_email="[email protected]",
+    url="https://github.com/gtfierro/ontoenv-rs",
+    license="BSD-3-Clause",
+    python_requires=">=3.9",
+    install_requires=[f"ontoenv=={version}"],
+    packages=find_packages(where="src"),
+    package_dir={"": "src"},
+    include_package_data=True,
+    classifiers=[
+        "License :: OSI Approved :: BSD License",
+        "Programming Language :: Python",
+        "Programming Language :: Python :: 3",
+        "Programming Language :: Python :: 3 :: Only",
+        "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.12",
+        "Programming Language :: Python :: 3.13",
+    ],
+)

pyontoenv-shim/setup.py

@@ -0,0 +1,13 @@
+"""Compatibility wrapper that proxies to the real ``ontoenv`` package."""
+
+from importlib import import_module
+
+_ontoenv = import_module("ontoenv")
+
+# Re-export the public surface.
+from ontoenv import *  # type: ignore  # noqa: F401,F403
+
+version = getattr(_ontoenv, "version", None)
+__version__ = version if isinstance(version, str) else getattr(_ontoenv, "__version__", "0.0.0")
+
+__all__ = getattr(_ontoenv, "__all__", [])

pyontoenv-shim/src/pyontoenv/__init__.py

@@ -1,5 +1,5 @@
 [package]
-name = "pyontoenv"
+name = "ontoenv-python"
 version.workspace = true
 edition.workspace = true
 license.workspace = true
@@ -11,7 +11,7 @@ build = "build.rs"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 [lib]
-name = "pyontoenv"
+name = "ontoenv_python"
 crate-type = ["cdylib"]
 doc = false