Use meson build in place of numpy distutils (#12)

* first attempt at meson building

* include mkl-devel in build requirements

* change version

* relax version a bit

* use examples from numpy

* update github workflow, reenable thread locks

* update meson build file for mkl linkage parameters

* remove print outs

* remove setup.py file

* install setuptools

* add option to force sdl usage

* do not fail fast on tests

* move thread lock allocation

* update some meta information

* ignore pycharm files

* be a bit more accurate about the argument types

* Be a little safer about free the lock

* split __dealloc__ into a dealloc and a __del__ method for safety

* determine initialization status dynamically

* make _initialized a function

* just use if self.handle[i]

* use mamba

* cache the environment

* fix indices and indptr

* stop overwriting dtype

* undo some types

* more type resetting

* unsetting some more

* make call type a little more accurate

* switch back to conda (with defaults)

* reset some build scripts

* switch back to mamba, but don't use mkl 2024

* ensure cleared cache

* retry this

* dynamic initialized (again)

* be explicit about initializing handle and iparm

* don't cache

* generate c sources in tree for cython coverage

* enable coverage build option

* have meson conditionally generate c file in source directory when doing coverage.

* add coverage configuration to pyproject.toml

* remove all pytest-cov related options to pytest

* fix coverage determination, split long lines

* generate coverage.xml

* fix command

* add comments to meson build file

* update distribution script

* update gitignore

* add a test for mkl=2024

* update test name

* fix matrix variable name

* add test for windows and mac on mkl 2024

* mkl-2024 is not on macos

Author: jcapriot

.bumpversion.cfg

@@ -0,0 +1,4 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
+ref-names: $Format:%D$

.coveragerc

@@ -0,0 +1,11 @@
+.git_archival.txt  export-subst
+# Excluding files from an sdist generated by meson-python
+
+.azure-pipelines/* export-ignore
+.ci/* export-ignore
+tests/* export-ignore
+
+.flake8 export-ignore
+.git* export-ignore
+*.yml export-ignore
+*.yaml export-ignore

.git_archival.txt

@@ -14,61 +14,71 @@ on:
 
 jobs:
   build-and-test:
-    name: Testing (${{ matrix.python-version }}, ${{ matrix.os }})
+    name: Testing (Python ${{ matrix.python-version }}, on ${{ matrix.os }}, with MKL ${{ matrix.mkl-version }})
     runs-on: ${{ matrix.os }}
     defaults:
       run:
         shell: bash -l {0}
     strategy:
-      fail-fast: True
+      fail-fast: False
       matrix:
-        os: [ubuntu-latest, macOS-latest, windows-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        mkl-version: ['2023']  # currently 2024 fails building for some reason...
+        include:
+          - os: ubuntu-latest
+            python-version: "3.12"
+            coverage: ${{ true }}
+          - os: ubuntu-latest
+            python-version: "3.12"
+            mkl-version: '2024'
+          - os: windows-latest
+            python-version: "3.12"
+            mkl-version: '2024'
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Setup Conda
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
-        auto-update-conda: true
-        activate-environment: dev
         python-version: ${{ matrix.python-version }}
-    - name: Install Env
+        mamba-version: '*'
+        channels: conda-forge, defaults
+        channel-priority: true
+        activate-environment: dev
+
+    - name: Conda information
       run: |
         conda info
         conda list
         conda config --show
-        conda install --quiet --yes pip numpy scipy cython mkl pytest pytest-cov mkl-devel
 
-    - name: Install Our Package
-      if: ${{ matrix.os != 'windows-latest' }}
+    - name: Create environment
       run: |
-        echo $CONDA_PREFIX
-        export TEST_COV=1
-        pip install -v -e .
-        conda list
+        mamba install --quiet --yes pip numpy scipy cython mkl=${{ matrix.mkl-version }} pytest \
+          mkl-devel pkg-config meson-python meson ninja setuptools_scm \
+          ${{ matrix.coverage && 'coverage' || ''}}
 
-    - name: Install Our Package on Windows
-      if: ${{ matrix.os == 'windows-latest' }}
+    - name: Install Our Package
       run: |
-        echo $CONDA_PREFIX
-        export MKLROOT="$CONDA_PREFIX\Library"
-        echo $MKLROOT
-        pip install -v -e .
+        python -m pip install --no-build-isolation --verbose --editable . \
+          --config-setting=compile-args=-v \
+          ${{ matrix.coverage && '--config-settings=setup-args="-Dcy_coverage=true"' || ''}}
         conda list
 
     - name: Run Tests
       run: |
-        pytest --cov-config=.coveragerc --cov-report=xml --cov=pydiso -s -v
+        ${{ matrix.coverage && 'coverage run -m' || '' }} pytest -s -v
+        ${{ matrix.coverage && 'coverage xml' || '' }} 
 
     - name: Upload coverage
-      if: ${{ matrix.os == 'ubuntu-latest' }} and {{ matrix.python-version == '3.8' }}
-      uses: codecov/codecov-action@v2
+      if: ${{ matrix.coverage }}
+      uses: codecov/codecov-action@v4
       with:
         verbose: true # optional (default = false)
 
   distribute:
-    name: Distributing from 3.8
+    name: Distributing from 3.11
     needs: build-and-test
     if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
     runs-on: ubuntu-latest
@@ -77,29 +87,31 @@ jobs:
         shell: bash -l {0}
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Setup Conda
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
-        auto-update-conda: true
+        python-version: 3.11
+        mamba-version: '*'
+        channels: conda-forge, defaults
+        channel-priority: true
         activate-environment: dev
-        python-version: 3.8
 
     - name: Install Env
       run: |
         conda info
         conda list
         conda config --show
-        conda install --quiet --yes pip numpy scipy cython mkl mkl-devel
 
-    - name: Install Our Package
+    - name: Create environment
       run: |
-        echo $CONDA_PREFIX
-        pip install -v -e .
+        mamba install --quiet --yes pip numpy scipy cython mkl=2023 \
+          mkl-devel pkg-config meson-python meson ninja setuptools_scm \
+          python-build
 
     - name: Generate Source Distribution
       run: |
-        python setup.py sdist
+        python -m build --no-isolation --skip-dependency-check --sdist .
 
     - name: pypi-publish
       uses: pypa/[email protected]

.gitattributes

@@ -1,7 +1,12 @@
 build
+dist
+coverage_html_report
 *.so
 pydiso.egg-info
 __pycache__
 mkl_solver.c
+mkl_solver.c.dep
 .coverage
 coverage.xml
+
+.idea/

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

@@ -1,36 +1,29 @@
 # pydiso
 
 Pydiso is a python wrapper for the pardiso solver. It is currently implemented for the
-Intel MKL's version of pardiso. It's goal is to expose the full functionality of pardiso
+Intel MKL's version of pardiso. Its goal is to expose the full functionality of pardiso
 to python, allowing the user to customize it as necessary for their use cases.
 
 # Installation
 
 
-### Installing from source
+## Installing from source
 
 The wrapper is written in cython and links to the mkl libraries dynamically. Therefore,
 it needs to find the necessary header files associated with the MKL installation to compile.
-For conda users, these headers can be installed with `mkl-devel` package that is available
-on the default channel, conda-forge channel, the intel channel, or others, e.g.
+The meson build backend uses pkg-config to identify the locations of the mkl header files
+and library dynamic libraries. Most development installations of MKL should provide the
+necessary pkg-config files for this. For example, conda users can be install the necessary
+configuration information with `mkl-devel` package that is available on the default channel,
+conda-forge channel, the intel channel, or others, e.g.
 
 `conda install mkl-devel`
 
-Most of the time, your respective numpy installations will then be intelligent enough to
-identify the location of the installed MKL. However if you run into issues automatically
-finding the library headers, you will need to set the `MKLROOT` environment variable to
-point to the correct location. On Linux and MacOS the `mkl-rt` library and `mkl.h` are
-usually in the same folder, and thus the root should point to that directory. On Windows
-the `mkl-rt.h` and `mkl-rt.lib` are not in the same folder but seperated a level into
-`Library` and `Include` directories, and in this case `MKLROOT` would point to the folder
-containing them.
+If you have installed the configuration files to a non-standard location, you will need to set
+`PKG_CONFIG_PATH` to point to that location.
 
-After the necessary MKL files are accessible, you should be able to do the standard install
-script common to python packages by running either
 
-`python setup.py install`
-
-or, equivalently
+After the necessary MKL files are accessible, you should be able to install by running
 
 `pip install .`
 

.gitignore

@@ -0,0 +1,50 @@
+project(
+  'pydiso',
+  'c', 'cython',
+  # Note that the git commit hash cannot be added dynamically here
+  # (it is dynamically generated though setuptools_scm)
+  version: run_command('python',
+    [
+      '-c',
+      '''
+from setuptools_scm import get_version
+print(get_version())'''
+    ],
+    check: true
+).stdout().strip(),
+
+  license: 'MIT',
+  meson_version: '>= 1.1.0',
+  default_options: [
+    'buildtype=debugoptimized',
+    'b_ndebug=if-release',
+  ],
+)
+
+# https://mesonbuild.com/Python-module.html
+py_mod = import('python')
+py = py_mod.find_installation(pure: false)
+py_dep = py.dependency()
+
+cc = meson.get_compiler('c')
+cy = meson.get_compiler('cython')
+# generator() doesn't accept compilers, only found programs - cast it.
+cython = find_program(cy.cmd_array()[0])
+
+_global_c_args = cc.get_supported_arguments(
+  '-Wno-unused-but-set-variable',
+  '-Wno-unused-function',
+  '-Wno-conversion',
+  '-Wno-misleading-indentation',
+)
+add_project_arguments(_global_c_args, language : 'c')
+
+# We need -lm for all C code (assuming it uses math functions, which is safe to
+# assume for SciPy). For C++ it isn't needed, because libstdc++/libc++ is
+# guaranteed to depend on it.
+m_dep = cc.find_library('m', required : false)
+if m_dep.found()
+  add_project_link_arguments('-lm', language : 'c')
+endif
+
+subdir('pydiso')

MANIFEST.in

@@ -0,0 +1,10 @@
+option('cy_coverage', type : 'boolean', value : false)
+
+option('use-sdl', type: 'boolean', value: true,
+       description: 'Use the single dynamic library.')
+
+option('use-ilp64', type: 'boolean', value: false,
+       description: 'Use ILP64 (64-bit integer) BLAS and LAPACK interfaces')
+
+option('mkl-threading', type: 'string', value: 'auto',
+        description: 'MKL threading method, one of: `seq`, `iomp`, `gomp`, `tbb`')

README.md

@@ -1,4 +1,19 @@
-__version__ = "0.0.3"
 __author__ = "SimPEG Team"
 __license__ = "MIT"
 __copyright__ = "2021, SimPEG Developers, http://simpeg.xyz"
+
+from importlib.metadata import version, PackageNotFoundError
+
+# Version
+try:
+    # - Released versions just tags:       0.8.0
+    # - GitHub commits add .dev#+hash:     0.8.1.dev4+g2785721
+    # - Uncommitted changes add timestamp: 0.8.1.dev4+g2785721.d20191022
+    __version__ = version("pydiso")
+except PackageNotFoundError:
+    # If it was not installed, then we don't know the version. We could throw a
+    # warning here, but this case *should* be rare. discretize should be
+    # installed properly!
+    from datetime import datetime
+
+    __version__ = "unknown-" + datetime.today().strftime("%Y%m%d")