Merge pull request #166 from ocefpaf/numpy_2

Test against numpy 2.0

.github/workflows/test_code_generation.yml

@@ -0,0 +1,48 @@
+name: Test code generation
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  code-generation:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+    - name: checkout
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - name: Setup Micromamba
+      uses: mamba-org/setup-micromamba@v1
+      with:
+        environment-name: TEST
+        init-shell: bash
+        create-args: >-
+          python=3 pip
+          --file requirements-dev.txt
+          --channel conda-forge
+
+    - name: Install nightly version of numpy
+      run: |
+        python -m pip install --pre --index-url https://pypi.anaconda.org/scientific-python-nightly-wheels/simple --extra-index-url https://pypi.org/simple numpy scipy pandas -U
+
+    - name: Test Code Generation
+      run: >
+        git clone https://github.com/TEOS-10/GSW-C.git ../GSW-C
+        && git clone https://github.com/TEOS-10/GSW-Matlab.git ../GSW-Matlab
+        && python tools/copy_from_GSW-C.py
+        && python tools/mat2npz.py
+        && python tools/make_ufuncs.py
+        && python tools/make_wrapped_ufuncs.py
+        && python tools/fix_wrapped_ufunc_typos.py
+
+    - name: Install gsw
+      run: >
+        python -m pip install -v -e  . --no-deps --no-build-isolation --force-reinstall
+        && python -m pytest -s -rxs -v gsw/tests

.github/workflows/tests.yml

@@ -12,13 +12,21 @@ jobs:
       matrix:
         python-version: ["3.9", "3.10", "3.11", "3.12"]
         os: [windows-latest, ubuntu-latest, macos-latest]
+        experimental: [false]
         # Oldest one based on NEP-29 and latest one.
         # See https://numpy.org/neps/nep-0029-deprecation_policy.html
         numpy-version: ["1.23", "1.26"]
         exclude:
           - python-version: "3.12"
             numpy-version: "1.23"
+        include:
+          - python-version: "3.12"
+            os: "ubuntu-latest"
+            experimental: true
       fail-fast: false
+    defaults:
+      run:
+        shell: bash -l {0}
 
     steps:
     - uses: actions/checkout@v4
@@ -31,18 +39,21 @@ jobs:
         create-args: >-
           python=${{ matrix.python-version }} python-build numpy=${{ matrix.numpy-version }} --file requirements-dev.txt --channel conda-forge
 
-    - name: Install gsw
-      shell: bash -l {0}
+    - name: Install unstable dependencies
+      if: matrix.experimental == true
       run: |
-        python -m pip install -e . --no-deps --force-reinstall
+        python -m pip install \
+        --index-url https://pypi.anaconda.org/scientific-python-nightly-wheels/simple/ \
+        --trusted-host pypi.anaconda.org \
+        --no-deps --pre --upgrade \
+        numpy scipy pandas;
+        python -m pip install -v -e  . --no-deps --no-build-isolation --force-reinstall
 
-    - name: Debug
-      shell: bash -l {0}
+    - name: Install gsw
+      if: matrix.experimental != true
       run: |
-        python -c "import numpy; print(f'Running numpy {numpy.__version__}')"
+        python -m pip install -e . --no-deps --force-reinstall
 
     - name: Tests
-      shell: bash -l {0}
       run: |
-        micromamba activate TEST
-        pytest -s -rxs -v gsw/tests
+        python -m pytest -s -rxs -v gsw/tests

gsw/tests/test_check_functions.py

@@ -45,7 +45,7 @@
 mfuncnames = [mf.name for mf in mfuncs]
 
 
-@pytest.fixture(params=[-360, 0, 360])
+@pytest.fixture(params=[-360., 0., 360.])
 def lonshift(request):
     return request.param
 

pyproject.toml

@@ -2,7 +2,8 @@
 build-backend = "setuptools.build_meta"
 requires = [
   "build",
-  "oldest-supported-numpy",
+  'numpy<3,>=2.0.0rc1; python_version >= "3.9"',
+  'oldest-supported-numpy; python_version < "3.9"',
   "pip>9.0.1",
   "setuptools>=42",
   "setuptools_scm[toml]>=3.4",
@@ -60,18 +61,19 @@ write_to_template = "__version__ = '{version}'"
 tag_regex = "^(?P<prefix>v)?(?P<version>[^\\+]+)(?P<suffix>.*)?$"
 
 [tool.ruff]
-select = [
+lint.select = [
     "A", # flake8-builtins
     "B", # flake8-bugbear
     "C4", # flake8-comprehensions
     "F", # flakes
     "I", # import sorting
     "UP", # upgrade
+    "NPY201",  # numpy 2.0
 ]
 target-version = "py38"
 line-length = 105
 
-ignore = [
+lint.ignore = [
     "F401",  # module imported but unused
     "E501",  # line too long
     "E713",  # test for membership should be 'not in'
@@ -81,7 +83,7 @@ exclude = [
   "tools",
 ]
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 "docs/conf.py" = [
   "A001",  # variable is shadowing a python builtin
 ]

requirements-dev.txt

@@ -1,9 +1,11 @@
 check-manifest
+dask
 numpydoc
+pandas>=2
 pytest
+scipy
 setuptools_scm
 sphinx
 sphinx_rtd_theme
 twine
-pandas>=2
-dask
+xarray

setup.py

@@ -7,7 +7,7 @@
 import shutil
 import sys
 
-import pkg_resources
+import numpy
 from setuptools import Extension, setup
 from setuptools.command.build_ext import build_ext as _build_ext
 
@@ -21,7 +21,7 @@ def read(*parts):
 class build_ext(_build_ext):
     # Extension builder from pandas without the cython stuff
     def build_extensions(self):
-        numpy_incl = pkg_resources.resource_filename("numpy", "core/include")
+        numpy_incl = numpy.get_include()
 
         for ext in self.extensions:
             if hasattr(ext, "include_dirs") and not numpy_incl in ext.include_dirs:

tools/c_header_parser.py

@@ -8,7 +8,7 @@
 import numpy as np
 
 
-basedir = Path('..').resolve()
+basedir = Path(__file__).parent.parent
 
 def get_signatures(strip_extern=True, srcdir='src'):
     """

tools/copy_from_GSW-C.py

@@ -3,26 +3,31 @@
 Copy all relevant .c and .h files from Python-C, if they are newer.
 
 This is a simple utility, to be run from this directory.  It assumes that
-an up-to-date GSW-C github repo and the present GSW-Python repo are
+an up-to-date GSW-C GitHub repo and the present GSW-Python repo are
 siblings in the directory tree.
 """
 
+import sys
 import shutil
 from pathlib import Path
 
+current = Path(__file__).parent
+srcdir = Path(current.parent.parent, "GSW-C")
 
-fnames = ['gsw_oceanographic_toolbox.c',
-          'gsw_saar.c',
-          'gsw_saar_data.h',
-          'gsw_internal_const.h',
-          'gswteos-10.h']
+destdir = Path(current.parent, "src", "c_gsw")
+
+fnames = [
+    "gsw_oceanographic_toolbox.c",
+    "gsw_saar.c",
+    "gsw_saar_data.h",
+    "gsw_internal_const.h",
+    "gswteos-10.h",
+    ]
 
-srcdir = Path('..', '..', 'GSW-C')
-destdir = Path('..', 'src', 'c_gsw')
 
 if not srcdir.exists():
     raise IOError(
-        f"Could not find the GSW-C source code in {srcdir}."
+        f"Could not find the GSW-C source code in {srcdir}. "
         "Please read the development notes to find how to setup your GSW-Python development environment."
         )
 
@@ -31,4 +36,4 @@
     dest = destdir.joinpath(fname)
     if src.stat().st_mtime > dest.stat().st_mtime:
         shutil.copyfile(str(src), str(dest))
-        print('copied %s to %s' % (src, dest))
+        print(f"copied {src} to {dest}")

tools/fix_wrapped_ufunc_typos.py

@@ -9,7 +9,7 @@
 from pathlib import Path
 import shutil
 
-basedir = Path('..').resolve()
+basedir = Path(__file__).parent.parent
 wrapmod = basedir.joinpath('gsw', '_wrapped_ufuncs.py')
 
 orig = wrapmod.with_suffix('.orig')

tools/make_ufuncs.py

@@ -14,7 +14,7 @@
 
 blacklist = ['add_barrier']
 
-basedir = Path('..').resolve()
+basedir = Path(__file__).parent.parent
 
 modfile_head_top = """
 /*
@@ -358,19 +358,19 @@ def write_modfile(modfile_name, srcdir):
         f.write(''.join(chunks))
 
     funcnamelist1.sort()
-    with open(srcdir + '_ufuncs1.list', 'w') as f:
+    with open(srcdir.joinpath('_ufuncs1.list'), 'w') as f:
         f.write('\n'.join(funcnamelist1))
 
     funcnamelist2.sort()
-    with open(srcdir + '_ufuncs2.list', 'w') as f:
+    with open(srcdir.joinpath('_ufuncs2.list'), 'w') as f:
         f.write('\n'.join(funcnamelist2))
 
     funcnamelist = funcnamelist1 + funcnamelist2 + funcnamelist3
     funcnamelist.sort()
-    with open(srcdir + '_ufuncs.list', 'w') as f:
+    with open(srcdir.joinpath('_ufuncs.list'), 'w') as f:
         f.write('\n'.join(funcnamelist))
 
 if __name__ == '__main__':
-    srcdir = 'src'
+    srcdir = basedir.joinpath('src')
     modfile_name = basedir.joinpath(srcdir, '_ufuncs.c')
     write_modfile(modfile_name, srcdir=srcdir)

tools/make_wrapped_ufuncs.py

@@ -16,7 +16,7 @@
                              fix_outputs_doc,
                              docstring_from_sections)
 
-basedir = Path('..').resolve()
+basedir = Path(__file__).parent.parent
 
 
 # Functions that are Matlab subroutines, or exclusive to
@@ -205,8 +205,8 @@ def uf_wrapper(ufname):
     return wrapper_template % subs
 
 if __name__ == '__main__':
-    srcdir = 'src'
-    with open(srcdir + '_ufuncs.list') as f:
+    srcdir = basedir.joinpath('src')
+    with open(srcdir.joinpath('_ufuncs.list')) as f:
         ufunclist = [name.strip() for name in f.readlines()]
         ufunclist = [name for name in ufunclist if name not in blacklist]
 
@@ -232,5 +232,5 @@ def uf_wrapper(ufname):
                 f.write(wrapped)
                 wrapped_ufnames.append(ufname)
     wrapped_ufnames.sort()
-    with open(srcdir + '_wrapped_ufuncs.list', 'w') as f:
+    with open(srcdir.joinpath('_wrapped_ufuncs.list'), 'w') as f:
         f.write('\n'.join(wrapped_ufnames) + '\n')

tools/mat2npz.py

@@ -45,8 +45,14 @@ def loadmatdict(fname):
 
 # The following relative path will depend on the directory layout for
 # whoever is running this utility.
-gsw_data_file = Path('..', '..', '..', 'gsw_matlab_%s' % mat_zip_ver,
-                     'library', 'gsw_data_%s.mat' % data_ver)
+basedir = Path(__file__).parent.parent
+gsw_data_file = Path(
+    basedir.parent,
+    "GSW-Matlab",
+    "Toolbox",
+    "library",
+    f"gsw_data_{data_ver}.mat",
+    )
 print(gsw_data_file)
 
 gsw_data = loadmatdict(gsw_data_file)
@@ -55,5 +61,5 @@ def loadmatdict(fname):
 cv_vars = gsw_data['gsw_cv']
 cv_vars['gsw_data_file'] = str(gsw_data_file)
 cv_vars['mat_zip_ver'] = mat_zip_ver
-fname = Path('..', 'gsw', 'tests', 'gsw_cv_%s' % data_ver)
+fname = Path(basedir, "gsw", "tests", f"gsw_cv_{data_ver}")
 np.savez(str(fname), **cv_vars)

tools/matlab_parser.py

@@ -5,8 +5,7 @@
 import re
 from pathlib import Path
 
-
-basedir = Path('..').resolve()
+basedir = Path(__file__).parent.parent
 
 gsw_matlab_dir = basedir.joinpath('..', 'GSW-Matlab', 'Toolbox').resolve()
 if not gsw_matlab_dir.exists():