Merge pull request #69 from jcapriot/pyproject

Pyproject.toml

.git_archival.txt

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

.gitattributes

@@ -0,0 +1,13 @@
+.git_archival.txt  export-subst
+# Excluding files from an sdist generated by meson-python
+
+.github/* export-ignore
+docs/* export-ignore
+examples/* export-ignore
+tests/* export-ignore
+
+.coveragerc export-ignore
+.flake8 export-ignore
+.git* export-ignore
+*.yml export-ignore
+*.yaml export-ignore

.github/workflows/test_with_conda.yml

@@ -20,7 +20,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest"]
-        python-version: [3.8, 3.9, "3.10", "3.11"]
+        python-version: [3.8, 3.9, "3.10", "3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v2
@@ -35,11 +35,14 @@ jobs:
           libdlf
           cython
           setuptools_scm
+          meson-python>=0.14.0
+          meson
+          ninja
+          build
           discretize
           matplotlib
           jupyter
           utm
-          numba
           pytest
           pytest-cov
           sphinx
@@ -49,16 +52,20 @@ jobs:
           graphviz
           pillow
         cache-environment: true
+    - name: Install numba
+      if: matrix.python-version != '3.12'
+      # Numba doesn't work on python 3.12 just yet, so conditionally install it into the environment:
+      run: |
+        micromamba install numba
     - name: Install Our Package
       run: |
-        export BUILD_GEOANA_EXT=1
-        pip install -e .
+        pip install --no-build-isolation --editable . --config-settings=setup-args="-Dwith_extensions=true"
         conda list
     - name: Run Tests
       run: |
         pytest --cov-config=.coveragerc --cov=geoana --cov-report=xml -s -v -W ignore::DeprecationWarning
     - name: "Upload coverage to Codecov"
-      if: ${{ matrix.python-version }} == '3.10'
+      if: matrix.python-version == '3.11'
       uses: codecov/codecov-action@v3
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
@@ -84,6 +91,10 @@ jobs:
           libdlf
           cython
           setuptools_scm
+          meson-python>=0.14.0
+          meson
+          ninja
+          build
           discretize
           matplotlib
           jupyter
@@ -100,8 +111,7 @@ jobs:
         cache-environment: true
     - name: Prepare source distribution
       run: |
-        export BUILD_GEOANA_EXT=1
-        python setup.py sdist
+        python -m build --no-isolation --skip-dependency-check --sdist . --config-settings=setup-args="-Dwith_extensions=true"
     - name: Publish package
       uses: pypa/gh-action-pypi-publish@release/v1
       with:
@@ -110,8 +120,7 @@ jobs:
         skip_existing: true
     - name: Install package
       run: |
-        export BUILD_GEOANA_EXT=1
-        pip install -e .
+        pip install --no-build-isolation --editable . --config-settings=setup-args="-Dwith_extensions=true"
     - name: Build documentation
       run: |
         cd docs

geoana/__init__.py

@@ -4,17 +4,19 @@
 
 __author__ = 'SimPEG developers'
 __license__ = 'MIT'
-__copyright__ = 'Copyright 2017 SimPEG developers'
+__copyright__ = 'Copyright 2023 SimPEG developers'
+
+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 geoana.version import version as __version__
-except ImportError:
+    __version__ = version("geoana")
+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
+    # warning here, but this case *should* be rare. geoana should be
     # installed properly!
     from datetime import datetime
 

geoana/earthquake/meson.build

@@ -0,0 +1,10 @@
+
+python_sources = [
+  '__init__.py',
+  'oksar.py',
+]
+
+py.install_sources(
+  python_sources,
+  subdir: 'geoana/earthquake'
+)

geoana/em/fdem/meson.build

@@ -0,0 +1,14 @@
+
+python_sources = [
+  '__init__.py',
+  'base.py',
+  'halfspace.py',
+  'layered.py',
+  'simple_functions.py',
+  'wholespace.py',
+]
+
+py.install_sources(
+  python_sources,
+  subdir: 'geoana/em/fdem'
+)

geoana/em/meson.build

@@ -0,0 +1,14 @@
+
+python_sources = [
+  '__init__.py',
+  'base.py',
+]
+
+py.install_sources(
+  python_sources,
+  subdir: 'geoana/em'
+)
+
+subdir('fdem')
+subdir('static')
+subdir('tdem')

geoana/em/static/meson.build

@@ -0,0 +1,13 @@
+
+python_sources = [
+  '__init__.py',
+  'freespace.py',
+  'halfspace.py',
+  'sphere.py',
+  'wholespace.py',
+]
+
+py.install_sources(
+  python_sources,
+  subdir: 'geoana/em/static'
+)

geoana/em/tdem/meson.build

@@ -0,0 +1,13 @@
+
+python_sources = [
+  '__init__.py',
+  'base.py',
+  'halfspace.py',
+  'simple_functions.py',
+  'wholespace.py',
+]
+
+py.install_sources(
+  python_sources,
+  subdir: 'geoana/em/tdem'
+)

geoana/kernels/_extensions/meson.build

@@ -0,0 +1,84 @@
+# 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]
+
+cython_cpp_args = cython_c_args
+
+module_path = 'geoana/kernels/_extensions'
+
+py.extension_module(
+    'potential_field_prism',
+    'potential_field_prism.pyx',
+    include_directories: incdir_numpy,
+    c_args: cython_c_args,
+    install: true,
+    subdir: module_path,
+    dependencies : [py_dep, np_dep],
+)
+
+py.extension_module(
+    'rTE',
+    ['rTE.pyx', '_rTE.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'],
+)
+
+python_sources = [
+  '__init__.py',
+]
+
+py.install_sources(
+  python_sources,
+  subdir: module_path
+)

geoana/kernels/meson.build

@@ -0,0 +1,16 @@
+
+python_sources = [
+  '__init__.py',
+  'potential_field_prism.py',
+  'tranverse_electric_reflections.py',
+]
+
+py.install_sources(
+  python_sources,
+  subdir: 'geoana/kernels'
+)
+
+with_extensions = get_option('with_extensions')
+if with_extensions
+    subdir('_extensions')
+endif

geoana/meson.build

@@ -0,0 +1,18 @@
+
+python_sources = [
+  '__init__.py',
+  'gravity.py',
+  'plotting_utils.py',
+  'shapes.py',
+  'spatial.py',
+  'utils.py',
+]
+
+py.install_sources(
+  python_sources,
+  subdir: 'geoana'
+)
+
+subdir('earthquake')
+subdir('em')
+subdir('kernels')