Merge pull request #338 from jcapriot/pyproject

Pyproject.toml

.azure-pipelines/azure-pipelines-linux.yml

@@ -14,6 +14,8 @@ jobs:
         python.version: '3.9'
       linux-Python310:
         python.version: '3.10'
+      linux-Python311:
+        python.version: '3.11'
   steps:
 
   - bash: |
@@ -33,7 +35,7 @@ jobs:
   - bash: |
       source "${HOME}/conda/etc/profile.d/conda.sh"
       conda activate discretize-test
-      pip install -e .
+      pip install --no-build-isolation --editable .
     displayName: Install requirements and build
     condition: ne(variables['python.version'], '3.10')
 
@@ -48,8 +50,7 @@ jobs:
   - bash: |
       source "${HOME}/conda/etc/profile.d/conda.sh"
       conda activate discretize-test
-      export DISC_COV=1
-      pip install -e .
+      pip install --no-build-isolation --editable . --config-settings=setup-args="-Dcy_line_trace=true"
     displayName: Install requirements and build for Testing
     condition: eq(variables['python.version'], '3.10')
 

.azure-pipelines/azure-pipelines-osx.yml

@@ -11,6 +11,8 @@ jobs:
         python.version: '3.9'
       osx-Python310:
         python.version: '3.10'
+      linux-Python311:
+        python.version: '3.11'
   steps:
 
   - bash: |
@@ -30,7 +32,7 @@ jobs:
   - bash: |
       source "${HOME}/conda/etc/profile.d/conda.sh"
       conda activate discretize-test
-      pip install -e .
+      pip install --no-build-isolation --editable .
     displayName: Install requirements and build
 
   - script: |

.azure-pipelines/azure-pipelines-win.yml

@@ -11,6 +11,8 @@ jobs:
         python.version: '3.9'
       win-Python310:
         python.version: '3.10'
+      linux-Python311:
+        python.version: '3.11'
   steps:
 
   - powershell: Write-Host "##vso[task.prependpath]$env:CONDA\Scripts"
@@ -31,7 +33,7 @@ jobs:
 
   - script: |
       call activate discretize-test
-      pip install -e .
+      pip install --no-build-isolation --editable .
     displayName: Build
 
   - script: |

.gitattributes

@@ -1 +1,16 @@
-.git_archival.txt  export-subst
+.git_archival.txt  export-subst
+# Excluding files from an sdist generated by meson-python
+
+.azure-pipelines/* export-ignore
+.ci/* export-ignore
+docs/* export-ignore
+examples/* export-ignore
+tests/* export-ignore
+tutorials/* export-ignore
+
+.coveragerc export-ignore
+.flake8 export-ignore
+.git* export-ignore
+*.yml export-ignore
+*.yaml export-ignore
+requirements_style.txt export-ignore

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/psf/black
-    rev: 23.1a1
+    rev: 23.9.1
     hooks:
       - id: black
         language_version: python3

azure-pipelines.yml

@@ -25,7 +25,7 @@ stages:
       pool:
         vmImage: ubuntu-latest
       variables:
-        python.version: '3.8'
+        python.version: '3.9'
       steps:
         - script: |
             pip install -r requirements_style.txt
@@ -38,7 +38,7 @@ stages:
       pool:
         vmImage: ubuntu-latest
       variables:
-        python.version: '3.8'
+        python.version: '3.9'
       steps:
         - script: |
             pip install -r requirements_style.txt
@@ -92,13 +92,14 @@ stages:
         - bash: |
             source "${HOME}/conda/etc/profile.d/conda.sh"
             conda activate discretize-test
-            pip install -e .
+            pip install --no-build-isolation --editable .
           displayName: Build package
 
         - bash: |
             source "${HOME}/conda/etc/profile.d/conda.sh"
             conda activate discretize-test
-            python setup.py sdist
+            python -m build --no-isolation --skip-dependency-check --sdist .
+            ls -la dist
             twine upload --skip-existing dist/*
           displayName: Deploy source
           env:
@@ -139,15 +140,17 @@ stages:
             python.version: '3.9'
           win-Python310:
             python.version: '3.10'
+          win-Python311:
+            python.version: '3.11'
       pool:
         vmImage: windows-latest
       steps:
         - task: UsePythonVersion@0
           inputs:
             versionSpec: '$(python.version)'
-        - script: pip install numpy cython twine wheel setuptools_scm
+        - script: pip install build twine
           displayName: Install build dependencies
-        - script: python setup.py bdist_wheel
+        - script: python -m build --wheel .
           displayName: Build Wheel
         - script: twine upload --skip-existing dist/*
           displayName: Upload to PYPI

discretize/Tests/meson.build

@@ -0,0 +1,9 @@
+
+python_sources = [
+  '__init__.py',
+]
+
+py.install_sources(
+  python_sources,
+  subdir: 'discretize/Tests'
+)

discretize/__init__.py

@@ -46,7 +46,6 @@
 try:
     from discretize.tree_mesh import TreeMesh
 except ImportError as err:
-    print(err)
     import os
 
     # Check if being called from non-standard location (i.e. a git repository)
@@ -56,29 +55,30 @@
         # Then we are being run from a repository
         raise ImportError(
             """
-            Unable to import TreeMesh.
+            It would appear that discretize is being imported from its source code
+            directory and is unable to load its compiled extension modules. Try changing
+            your directory and re-launching your python interpreter.
 
-            It would appear that discretize is being imported from its repository.
-            If this is intentional, you need to run:
-
-            python setup.py build_ext --inplace
-
-            to compile the cython code.
+            If this was intentional, you need to install discretize in an editable mode.
             """
         )
+    else:
+        raise err
 from discretize import tests
 
 __author__ = "SimPEG Team"
 __license__ = "MIT"
 __copyright__ = "2013 - 2023, SimPEG Developers, https://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
-    from discretize.version import version as __version__
-except ImportError:
+    __version__ = version("discretize")
+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!

discretize/_extensions/meson.build

@@ -0,0 +1,100 @@
+# NumPy include directory
+# The try-except is needed because when things are
+# split across drives on Windows, there is no relative path and an exception
+# gets raised. There may be other such cases, so add a catch-all and switch to
+# an absolute path. Relative paths are needed when for example a virtualenv is
+# placed inside the source tree; Meson rejects absolute paths to places inside
+# the source tree.
+# For cross-compilation it is often not possible to run the Python interpreter
+# in order to retrieve numpy's include directory. It can be specified in the
+# cross file instead:
+#   [properties]
+#   numpy-include-dir = /abspath/to/host-pythons/site-packages/numpy/core/include
+#
+# This uses the path as is, and avoids running the interpreter.
+incdir_numpy = meson.get_external_property('numpy-include-dir', 'not-given')
+if incdir_numpy == 'not-given'
+  incdir_numpy = run_command(py,
+    [
+      '-c',
+      '''import os
+import numpy as np
+try:
+  incdir = os.path.relpath(np.get_include())
+except Exception:
+  incdir = np.get_include()
+print(incdir)
+  '''
+    ],
+    check: true
+  ).stdout().strip()
+else
+  _incdir_numpy_abs = incdir_numpy
+endif
+inc_np = include_directories(incdir_numpy)
+np_dep = declare_dependency(include_directories: inc_np)
+
+# Deal with M_PI & friends; add `use_math_defines` to c_args or cpp_args
+# Cython doesn't always get this right itself (see, e.g., gh-16800), so
+# explicitly add the define as a compiler flag for Cython-generated code.
+is_windows = host_machine.system() == 'windows'
+if is_windows
+  use_math_defines = ['-D_USE_MATH_DEFINES']
+else
+  use_math_defines = []
+endif
+
+numpy_nodepr_api = '-DNPY_NO_DEPRECATED_API=NPY_1_9_API_VERSION'
+c_undefined_ok = ['-Wno-maybe-uninitialized']
+
+cython_c_args = [numpy_nodepr_api, use_math_defines]
+
+cy_line_trace = get_option('cy_line_trace')
+if cy_line_trace
+  cython_c_args += ['-DCYTHON_TRACE_NOGIL=1']
+endif
+
+cython_cpp_args = cython_c_args
+
+module_path = 'discretize/_extensions'
+
+py.extension_module(
+    'interputils_cython',
+    'interputils_cython.pyx',
+    include_directories: incdir_numpy,
+    c_args: cython_c_args,
+    install: true,
+    subdir: module_path,
+    dependencies : [py_dep, np_dep],
+)
+
+py.extension_module(
+    'tree_ext',
+    ['tree_ext.pyx' , 'tree.cpp'],
+    include_directories: incdir_numpy,
+    cpp_args: cython_cpp_args,
+    install: true,
+    subdir: module_path,
+    dependencies : [py_dep, np_dep],
+    override_options : ['cython_language=cpp'],
+)
+
+py.extension_module(
+    'simplex_helpers',
+    'simplex_helpers.pyx',
+    include_directories: incdir_numpy,
+    cpp_args: cython_cpp_args,
+    install: true,
+    subdir: module_path,
+    dependencies : [py_dep, np_dep],
+    override_options : ['cython_language=cpp'],
+)
+
+python_sources = [
+  '__init__.py',
+]
+
+py.install_sources(
+  python_sources,
+  subdir: module_path
+)

discretize/base/meson.build

@@ -0,0 +1,12 @@
+
+python_sources = [
+  '__init__.py',
+  'base_mesh.py',
+  'base_regular_mesh.py',
+  'base_tensor_mesh.py',
+]
+
+py.install_sources(
+  python_sources,
+  subdir: 'discretize/base'
+)

discretize/meson.build

@@ -0,0 +1,24 @@
+
+python_sources = [
+  '__init__.py',
+  'curvilinear_mesh.py',
+  'cylindrical_mesh.py',
+  'tensor_cell.py',
+  'tensor_mesh.py',
+  'tests.py',
+  'tree_mesh.py',
+  'unstructured_mesh.py',
+  'View.py',
+]
+
+py.install_sources(
+  python_sources,
+  subdir: 'discretize'
+)
+
+subdir('base')
+subdir('_extensions')
+subdir('mixins')
+subdir('operators')
+subdir('utils')
+subdir('Tests')

discretize/mixins/meson.build

@@ -0,0 +1,13 @@
+
+python_sources = [
+  '__init__.py',
+  'mesh_io.py',
+  'mpl_mod.py',
+  'omf_mod.py',
+  'vtk_mod.py',
+]
+
+py.install_sources(
+  python_sources,
+  subdir: 'discretize/mixins'
+)

discretize/operators/inner_products.py

@@ -37,7 +37,7 @@ def get_face_inner_product(  # NOQA D102
         invert_model=False,
         invert_matrix=False,
         do_fast=True,
-        **kwargs
+        **kwargs,
     ):
         # Inherited documentation from discretize.base.BaseMesh
         if "invProp" in kwargs:
@@ -71,7 +71,7 @@ def get_edge_inner_product(  # NOQA D102
         invert_model=False,
         invert_matrix=False,
         do_fast=True,
-        **kwargs
+        **kwargs,
     ):
         # Inherited documentation from discretize.base.BaseMesh
         if "invProp" in kwargs:
@@ -150,7 +150,7 @@ def _getInnerProduct(
         invert_model=False,
         invert_matrix=False,
         do_fast=True,
-        **kwargs
+        **kwargs,
     ):
         """Get the inner product matrix.