drop 39 (#74)

* drop 39

* changelog

* Package updates

* Tweaks for wheel builds

* Another changelog

.github/workflows/ci.yml

@@ -22,21 +22,19 @@ jobs:
   core:
     uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@main
     with:
-      default_python: "3.11"
       submodules: false
       coverage: codecov
       toxdeps: tox-pypi-filter
       libraries: |
         apt:
           - libfftw3-dev
       envs: |
-        - linux: py311
+        - linux: py312
 
   tests:
     needs: [core]
     uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@main
     with:
-      default_python: "3.11"
       submodules: false
       coverage: codecov
       toxdeps: tox-pypi-filter
@@ -46,7 +44,12 @@ jobs:
         brew:
           - fftw
       envs: |
-        - macos: py39
+        # Mac Arm
+        #- macos: py311
+        #  runs-on: macos-latest
+        # Mac Intel
+        - macos: py311
+          runs-on: macos-12
         - linux: py310
 
   conda-linux:
@@ -61,7 +64,7 @@ jobs:
         with:
           activate-environment: pyflct-test
           environment-file: pyflct-env.yml
-          python-version: 3.11
+          python-version: 3.12
       - name: Install pyflct
         shell: bash -el {0}
         run: |
@@ -81,7 +84,7 @@ jobs:
     needs: [core]
     uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@main
     with:
-      default_python: "3.11"
+      default_python: "3.12"
       submodules: false
       pytest: false
       toxdeps: tox-pypi-filter
@@ -107,16 +110,19 @@ jobs:
     needs: [tests]
     uses: OpenAstronomy/github-actions-workflows/.github/workflows/publish.yml@main
     with:
-      test_extras: "dev"
+      test_extras: "test"
       test_command: 'pytest -p no:warnings --doctest-rst -m "not mpl_image_compare" --pyargs pyflct'
       submodules: false
       libraries: libfftw3-dev
       targets: |
-        - cp39-manylinux*_x86_64
-        - cp39-macosx_x86_64
-        - cp310-manylinux*_x86_64
+        #- cp310-macosx_arm64
         - cp310-macosx_x86_64
-        - cp311-manylinux*_x86_64
+        - cp310-manylinux_x86_64
+        #- cp311-macosx_arm64
         - cp311-macosx_x86_64
+        - cp311-manylinux_x86_64
+        #- cp312-macosx_arm64
+        - cp312-macosx_x86_64
+        - cp312-manylinux_x86_64
     secrets:
       pypi_token: ${{ secrets.pypi_token }}

.readthedocs.yaml

@@ -5,6 +5,8 @@ build:
   tools:
     python: "mambaforge-4.10"
   jobs:
+    post_checkout:
+      - git fetch --unshallow || true
     pre_install:
       - git update-index --assume-unchanged .rtd-environment.yml docs/conf.py
 

.rtd-environment.yml

@@ -1,10 +1,10 @@
-name: pyflct
+name: pyflct_rtd
 channels:
   - conda-forge
 dependencies:
   - graphviz!=2.42.*
   - pip
-  - python=3.9
+  - python=3.12
   - fftw
   - gcc_linux-64
   - pip:

changelog/74.breaking.2.rst

@@ -0,0 +1,4 @@
+Update to wheels:
+
+Linux base goes from manylinux2014 to manylinux_2_28
+macOS base goes from 10.9 to 12.0

changelog/74.breaking.rst

@@ -0,0 +1 @@
+Dropped Python 3.9 support.

changelog/74.feature.1.rst

@@ -0,0 +1 @@
+Build with numpy 2.0.0 as the base.

changelog/74.feature.rst

@@ -0,0 +1 @@
+Added Python 3.12 wheels.

docs/conf.py

@@ -1,34 +1,12 @@
 """
 Configuration file for the Sphinx documentation builder.
-
-isort:skip_file
 """
 
-# flake8: NOQA: E402
-
 # -- stdlib imports ------------------------------------------------------------
 import os
-import sys
 import datetime
-from pkg_resources import get_distribution
 from packaging.version import Version
 
-# -- Check for dependencies ----------------------------------------------------
-
-doc_requires = get_distribution("pyflct").requires(extras=("docs",))
-missing_requirements = []
-for requirement in doc_requires:
-    try:
-        get_distribution(requirement)
-    except Exception as e:
-        missing_requirements.append(requirement.name)
-if missing_requirements:
-    print(
-        f"The {' '.join(missing_requirements)} package(s) could not be found and "
-        "is needed to build the documentation, please install the 'docs' requirements."
-    )
-    sys.exit(1)
-
 # -- Read the Docs Specific Configuration --------------------------------------
 
 # This needs to be done before sunpy is imported
@@ -41,7 +19,7 @@
     os.environ["HIDE_PARFIVE_PROGESS"] = "True"
 
 # -- Non stdlib imports --------------------------------------------------------
-from pyflct import __version__  # NOQA
+from pyflct import __version__
 
 # -- Project information -------------------------------------------------------
 project = "pyflct"
@@ -168,8 +146,9 @@
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
+html_theme = "sunpy"
 
-from sunpy_sphinx_theme.conf import *  # NOQA
+from sunpy_sphinx_theme import PNG_ICON
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
@@ -189,16 +168,13 @@
 ]
 
 # -- Sphinx Gallery ------------------------------------------------------------
-from sphinx_gallery.sorting import ExampleTitleSortKey
-
 sphinx_gallery_conf = {
     "backreferences_dir": os.path.join("generated", "modules"),
     "filename_pattern": "^((?!skip_).)*$",
     "examples_dirs": os.path.join("..", "examples"),
-    "within_subsection_order": ExampleTitleSortKey,
+    "within_subsection_order": "ExampleTitleSortKey",
     "gallery_dirs": os.path.join("generated", "gallery"),
-    # Comes from the theme.
-    "default_thumb_file": png_icon,
+    "default_thumb_file": PNG_ICON,
     "abort_on_example_error": False,
     "plot_gallery": "True",
     "remove_config_comments": True,

pyflct/__init__.py

@@ -1,2 +1,4 @@
-from .flct import *  # NOQA
-from .version import version as __version__
+from pyflct.flct import flct
+from pyflct.version import version as __version__
+
+__all__ = ["flct", "__version__"]

pyflct/_dev/__init__.py

@@ -0,0 +1,7 @@
+"""
+This package contains utilities that are only used when developing drms in a
+copy of the source repository.
+
+These files are not installed, and should not be assumed to exist at
+runtime.
+"""

pyflct/flct.py

@@ -1,6 +1,6 @@
 import numpy as np
 
-from .utils import column_row_of_two
+from pyflct.utils import column_row_of_two
 
 try:
     from pyflct import _flct as _pyflct

pyflct/flct.pyx

@@ -32,76 +32,56 @@ cdef extern from "numpy/arrayobject.h":
     void PyArray_ENABLEFLAGS(np.ndarray arr, int flags)
 
 def read_two_images(file_name, transpose=0):
-
     cdef int nx
     cdef int ny
     cdef double *arr
     cdef double *barr
     file_name = file_name.encode('utf-8')
-
     ier = read2images(file_name, &nx, &ny, &arr, &barr, transpose)
-
     cdef view.array cy_arr = <double[:nx, :ny]> arr
     cdef view.array cy_barr = <double[:nx, :ny]> barr
-
     a = np.array(cy_arr)
     b = np.array(cy_barr)
-
     return (ier, a, b)
 
 def read_three_images(file_name, transpose=0):
-
     cdef int nx
     cdef int ny
     cdef double *arr
     cdef double *barr
     cdef double *carr
     file_name = file_name.encode('utf-8')
-
     ier = read3images(file_name, &nx, &ny, &arr, &barr, &carr,transpose)
-
     cdef view.array cy_arr = <double[:nx, :ny]> arr
     cdef view.array cy_barr = <double[:nx, :ny]> barr
     cdef view.array cy_carr = <double[:nx, :ny]> carr
-
     a = np.array(cy_arr)
     b = np.array(cy_barr)
     c = np.array(cy_carr)
-
     return (ier, a, b, c)
 
 
 def write_two_images(file_name, arr, barr, transpose=0):
-
     nx, ny = arr.shape
-
     arr = arr.reshape((-1))
     barr = barr.reshape((-1))
-
     cdef np.ndarray[np.double_t, ndim=1, mode="c"] arr_c = np.ascontiguousarray(arr, dtype = np.double)
     cdef np.ndarray[np.double_t, ndim=1, mode="c"] barr_c = np.ascontiguousarray(barr, dtype = np.double)
-
     file_name = file_name.encode('utf-8')
     ier = write2images(file_name, <double *> arr_c.data, <double *> barr_c.data, nx, ny, transpose)
-
     return ier
 
 
 def write_three_images(file_name, arr, barr, carr, transpose=0):
-
     nx, ny = arr.shape
-
     arr = arr.reshape((-1))
     barr = barr.reshape((-1))
     carr = carr.reshape((-1))
-
     cdef np.ndarray[np.double_t, ndim=1, mode="c"] arr_c = np.ascontiguousarray(arr, dtype = np.double)
     cdef np.ndarray[np.double_t, ndim=1, mode="c"] barr_c = np.ascontiguousarray(barr, dtype = np.double)
     cdef np.ndarray[np.double_t, ndim=1, mode="c"] carr_c = np.ascontiguousarray(carr, dtype = np.double)
-
     file_name = file_name.encode('utf-8')
     ier = write3images(file_name, <double *> arr_c.data, <double *> barr_c.data, <double *> carr_c.data, nx, ny, transpose)
-
     return ier
 
 def pyflct_plate_carree(transpose, f1, f2, nxorig, nyorig, deltat, deltas, sigma,
@@ -113,7 +93,6 @@ def pyflct_plate_carree(transpose, f1, f2, nxorig, nyorig, deltat, deltas, sigma
     cdef np.ndarray[np.double_t, ndim=1, mode="c"] vx_c = np.ascontiguousarray(vx, dtype = np.double)
     cdef np.ndarray[np.double_t, ndim=1, mode="c"] vy_c = np.ascontiguousarray(vy, dtype = np.double)
     cdef np.ndarray[np.double_t, ndim=1, mode="c"] vm_c = np.ascontiguousarray(vm, dtype = np.double)
-
     ierflct = flct_pc(transpose, <double *> f1_c.data, <double *> f2_c.data, nxorig, nyorig, deltat,
                       deltas, sigma, <double *> vx_c.data, <double *> vy_c.data, <double *> vm_c.data,
                       thresh, absflag, filter, kr, skip, poffset, qoffset, interpolate, latmin, latmax,
@@ -131,34 +110,24 @@ def pyflct(transpose, f1, f2, nxorig, nyorig, deltat, deltas, sigma,
     cdef np.ndarray[np.double_t, ndim=1, mode="c"] vx_c = np.ascontiguousarray(vx, dtype = np.double)
     cdef np.ndarray[np.double_t, ndim=1, mode="c"] vy_c = np.ascontiguousarray(vy, dtype = np.double)
     cdef np.ndarray[np.double_t, ndim=1, mode="c"] vm_c = np.ascontiguousarray(vm, dtype = np.double)
-
     ierflct = flct(transpose, <double *> f1_c.data, <double *> f2_c.data, nxorig, nyorig, deltat,
                    deltas, sigma, <double *> vx_c.data, <double *> vy_c.data, <double *> vm_c.data,
                    thresh, absflag, filter, kr, skip, poffset, qoffset, interpolate, biascor, verbose)
-
     return ierflct, vx_c, vy_c, vm_c
 
 # This is created to deal with the arrays which were first read by IDL
 def swap_order_two(arr, barr):
-
     ier = write_two_images("temp.dat", arr, barr, 0)
-
     ier, cy_arr, cy_barr = read_two_images("temp.dat", transpose=1)
     os.remove("temp.dat")
-
     a = np.array(cy_arr)
     b = np.array(cy_barr)
-
     return a, b
 
 
 def swap_order_three(arr, barr, carr):
-
     temp = np.zeros_like(arr)
-
     arr, barr = swap_order_two(arr,barr)
     carr, temp = swap_order_two(carr, temp)
-
     del temp
-
     return arr, barr, carr

pyflct/setup_package.py

@@ -1,5 +1,7 @@
 import os
 import sys
+import platform
+import subprocess
 from glob import glob
 from collections import defaultdict
 from distutils.core import Extension
@@ -18,15 +20,21 @@ def get_extensions():
     cfg["sources"].extend(sorted(glob(os.path.join("cextern", "*.c"))))
     cfg["sources"].extend(sorted(glob(os.path.join(ROOT, "*.c"))))
     cfg["sources"].extend(sorted(glob(os.path.join(ROOT, "flct.pyx"))))
-    cfg["libraries"].append("fftw3")
 
-    if get_compiler() == "msvc":
+    if get_compiler().lower() == "msvc":
         # Anaconda paths
         cfg["include_dirs"].append(os.path.join(sys.prefix, "Library", "include"))
         cfg["library_dirs"].append(os.path.join(sys.prefix, "Library", "lib"))
     else:
         cfg["libraries"].append("m")
-        cfg["include_dirs"].append("/usr/include/")
-        cfg["extra_compile_args"].extend(["-O3", "-Wall", "-fomit-frame-pointer", "-fPIC"])
-
+        # We assume we have brew installed on Mac OS to provide FFTW3
+        if platform.system().lower() == "darwin":
+            brew_path = (
+                subprocess.run(["brew", "--prefix"], stdout=subprocess.PIPE).stdout.decode("utf-8").replace("\n", "")
+            )
+            cfg["include_dirs"].append(f"{brew_path}/include")
+        cfg["libraries"].append("fftw3")
+        cfg["include_dirs"].append("/usr/include")
+        cfg["include_dirs"].append("/usr/local/include")
+        cfg["extra_compile_args"].extend(["-O3", "-w", "-fomit-frame-pointer", "-fPIC"])
     return [Extension("pyflct._flct", **cfg)]

pyflct/version.py

@@ -11,7 +11,6 @@
 
     warnings.warn(f'could not determine {__name__.split(".")[0]} package version; this indicates a broken installation')
     del warnings
-
     version = "0.0.0"
 
 from packaging.version import parse as _parse