BLD Replace setup.py with meson-python build

Author: luispedro

.github/workflows/test-python-package-with-conda.yml

@@ -171,6 +171,7 @@ jobs:
       run: |
         micromamba install --file tests-requirements.txt --name mahotas_test_env
         micromamba install --name mahotas_test_env freeimage imread
+        python -m pip install "meson-python>=0.17.1,<0.18" "meson>=1.2.3" ninja
     - name: Build
       shell: bash -l {0}
       run: |

.gitignore

@@ -1,6 +1,7 @@
 wheelhouse
 dist/
 build/
+/.mesonpy-*
 mahotas.egg-info/
 *.pyc
 *.so

MANIFEST.in

@@ -1,28 +1,29 @@
+PIP_EDITABLE = python -m pip install --editable . --no-deps --no-build-isolation
+
 debug: mahotas/*.cpp mahotas/*.h mahotas/*.hpp
-	DEBUG=2 python setup.py build --build-lib=.
+	$(PIP_EDITABLE) --config-settings=build-dir=build/debug --config-settings=setup-args=-Dbuildtype=debug --config-settings=setup-args=-Dglibcpp_debug=true
 
 debug3: mahotas/*.cpp mahotas/*.h mahotas/*.hpp
-	DEBUG=2 python3 setup.py build --build-lib=.
+	python3 -m pip install --editable . --no-deps --no-build-isolation --config-settings=build-dir=build/debug --config-settings=setup-args=-Dbuildtype=debug --config-settings=setup-args=-Dglibcpp_debug=true
 
 fast: mahotas/*.cpp mahotas/*.h mahotas/*.hpp
-	python setup.py build --build-lib=.
+	$(PIP_EDITABLE) --config-settings=build-dir=build/fast --config-settings=setup-args=-Dbuildtype=release
 
 install:
-	python setup.py install
+	python -m pip install .
 
 fast3: mahotas/*.cpp mahotas/*.h mahotas/*.hpp
-	python3 setup.py build --build-lib=.
+	python3 -m pip install --editable . --no-deps --no-build-isolation --config-settings=build-dir=build/fast --config-settings=setup-args=-Dbuildtype=release
 
 clean:
-	rm -rf build mahotas/*.so mahotas/features/*.so
+	rm -rf build dist .mesonpy-* mahotas/*.so mahotas/features/*.so
 
 tests: debug
 	pytest -v
 
 docs:
 	rm -rf build/docs
 	cd docs && make html && cp -r build/html ../build/docs
-	@echo python setup.py upload_docs
+	@echo python -m build
 
 .PHONY: clean docs tests fast debug install fast3 debug3
-

Makefile

@@ -152,6 +152,14 @@ If you want an editable install for development, use:
 pip install -e .[tests]
 ```
 
+The build is Meson-based. To rebuild the editable install in release or debug
+mode after the initial development install, use:
+
+```bash
+make fast
+make debug
+```
+
 If you run into issues, the manual has more [extensive documentation on
 mahotas
 installation](https://mahotas.readthedocs.io/en/latest/install.html),
@@ -184,30 +192,28 @@ You can access this information using the `mahotas.citation()` function.
 Development happens on github
 ([https://github.com/luispedro/mahotas](https://github.com/luispedro/mahotas)).
 
-You can set the `DEBUG` environment variable before compilation to get a
-debug version:
+The `Makefile` that is shipped with the source of mahotas can be useful
+too. `make debug` rebuilds the editable install with a Meson debug build and
+enables `_GLIBCXX_DEBUG`. `make fast` rebuilds it in release mode. `make tests`
+runs the test suite after a debug rebuild.
 
 ```bash
-export DEBUG=1
 make debug
 pytest -v
 ```
 
-You can set it to the value `2` to get extra checks:
+If you want the equivalent of the old `DEBUG=1` build without
+`_GLIBCXX_DEBUG`, invoke pip directly:
 
 ```bash
-export DEBUG=2
-make debug
-pytest -v
+python -m pip install -e . --no-deps --no-build-isolation \
+  --config-settings=build-dir=build/debug \
+  --config-settings=setup-args=-Dbuildtype=debug
 ```
 
-Be careful not to use this in production unless you are chasing a bug.
-Debug level 2 is very slow as it adds many runtime checks.
-
-The `Makefile` that is shipped with the source of mahotas can be useful
-too. `make debug` will create a debug build. `make fast` will create a
-non-debug build (you need to `make clean` in between). `make tests` will
-run the test suite.
+Be careful not to use the debug build in production unless you are chasing a
+bug. The `_GLIBCXX_DEBUG` configuration used by `make debug` is very slow as it
+adds many runtime checks.
 
 ## Links & Contacts
 

README.md

@@ -0,0 +1,37 @@
+#!/usr/bin/env python3
+
+from __future__ import annotations
+
+import argparse
+from pathlib import Path
+import re
+
+
+ROOT = Path(__file__).resolve().parents[1]
+VERSION_FILE = ROOT / "mahotas" / "mahotas_version.py"
+
+
+def read_version() -> str:
+    version_source = VERSION_FILE.read_text(encoding="utf-8")
+    match = re.search(r"__version__\s*=\s*['\"]([^'\"]+)['\"]", version_source)
+    if match is None:
+        raise SystemExit(f"Could not parse version from {VERSION_FILE}")
+    return match.group(1)
+
+
+def main() -> None:
+    parser = argparse.ArgumentParser()
+    parser.add_argument("action", choices=["numpy-include", "version"])
+    args = parser.parse_args()
+
+    if args.action == "version":
+        print(read_version())
+        return
+
+    import numpy
+
+    print(numpy.get_include())
+
+
+if __name__ == "__main__":
+    main()

build-aux/meson-helper.py

@@ -19,37 +19,35 @@ Debug Mode
 ----------
 
 If you compile mahotas in debug mode, then it will run slower but perform a lot
-of runtime checks. This is controlled by the ``DEBUG`` environment variable.
+of runtime checks.
 
 There are two levels:
 
-1.  ``DEBUG=1`` This turns on assertions. The code will run slower, but
+1.  A Meson ``debug`` build turns on assertions. The code will run slower, but
     probably not noticeably slower, except for very large images.
-2.  ``DEBUG=2`` This turns on the assertions and additionally uses the debug
-    version of the C++ library (this only works if you are using GCC). Some of
-    the internal code also picks up on the ``DEBUG=2`` and adds even more
-    sanity checking. The result will be code that runs **much slower** as all
-    operations done through iterators into standard containers are now checked
-    (including many inner loop operations). However, it catches many errors.
+2.  ``make debug`` uses a Meson ``debug`` build and additionally defines
+    ``_GLIBCXX_DEBUG``. This only has an effect with libstdc++, but when
+    available it enables checked iterators in the C++ standard library. The
+    result will be code that runs **much slower** as many iterator operations
+    are now checked. However, it catches many errors.
 
 The Makefile that comes with the source helps you::
 
     make clean
     make debug
-    make test
+    make tests
 
 will rebuild in debug mode and run all tests. When you are done testing, use
 the ``fast`` Make target to get the non-debug build::
 
     make clean
     make fast
 
-Using make will not change your environment. The ``DEBUG`` variable is set
-internally only.
+Using make will rebuild the editable install in your current Python
+environment with the requested configuration.
 
 If you don't know about it, check out `ccache <https://ccache.samba.org/>`__
 which is a great tool if you are developing in compiled languages (this is not
 specific to mahotas or even Python). It will allow you to quickly perform
 ``make clean; make debug`` and ``make clean; make fast`` so you never get your
 builds mixed up.
-

docs/source/contributing.rst

@@ -31,15 +31,25 @@ For development, install from a checkout with::
 
     pip install -e .[tests]
 
-You will need to have ``numpy`` and a ``C++`` compiler.
+This installs the test dependencies and the Meson build tools needed by the
+``Makefile`` rebuild targets. You will also need a ``C++`` compiler.
+
+To rebuild the editable install after changes, use::
+
+    make fast
+    make debug
 
 Visual Studio
 ~~~~~~~~~~~~~
 
-For compiling from source in Visual Studio, use::
+On Windows, Meson will use Visual Studio automatically when you build from
+source. For a normal install, use::
+
+    python -m pip install .
+
+For a debug-style editable install, use::
 
-    python setup.py build_ext -c msvc
-    pip install .
+    python -m pip install -e . --no-deps --no-build-isolation --config-settings=build-dir=build/debug --config-settings=setup-args=-Dbuildtype=debug
 
 
 Bleeding Edge (Development)

docs/source/install.rst

@@ -1,2 +1,2 @@
 all:
-	cd .. && DEBUG=2 python setup.py build_ext --build-lib=. -U NDEBUG
+	$(MAKE) -C .. debug