Merge pull request #54 from ocefpaf/GHA

add GitHub Actions testing

.github/dependabot.yml

@@ -0,0 +1,11 @@
+# See https://docs.github.com/en/code-security/supply-chain-security/keeping-your-dependencies-updated-automatically/keeping-your-actions-up-to-date-with-dependabot
+
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "daily"
+    labels:
+      - "Bot"

.github/workflows/tests.yml

@@ -0,0 +1,43 @@
+
+name: Tests
+
+on:
+  pull_request:
+  push:
+
+jobs:
+  run:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        os: [ubuntu-latest, macos-latest]
+      fail-fast: false
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Setup Micromamba
+      uses: mamba-org/provision-with-micromamba@v14
+      with:
+        environment-file: false
+
+    - name: Install GFortran macOS
+      if: contains(matrix.os, 'macos')
+      # available gfotran are: 8, 9, and 10 (latest)
+      run: |
+        ln -s /usr/local/bin/gfortran-10 /usr/local/bin/gfortran
+        which gfortran
+
+    - name: Python ${{ matrix.python-version }}
+      shell: bash -l {0}
+      run: >
+        micromamba create --name TEST python=${{ matrix.python-version }} --file requirements.txt --file requirements-dev.txt --channel conda-forge
+        && micromamba activate TEST
+        && pip install -e . --no-deps --force-reinstall
+
+    - name: Tests
+      shell: bash -l {0}
+      run: |
+        micromamba activate TEST
+        pytest -s -rxs -v src

pyproject.toml

@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools>=42,<60", "setuptools_scm[toml]>=3.4", "oldest-supported-numpy"]
+build-backend = "setuptools.build_meta"

requirements-dev.txt

@@ -0,0 +1,2 @@
+mpmath
+pytest

requirements.txt

@@ -1,8 +1,6 @@
-# Add your requirements here like:
 six
-numpy>=1.4
+numpy>=1.19
 numdifftools>=0.2
-scipy>=1.1
+scipy>=1.7
 matplotlib
-mpmath
 numba

setup.cfg

@@ -4,21 +4,21 @@
 [metadata]
 summary = Wave Analysis for Fatigue and Oceanography
 author = WAFO-group
-author-email = none
+author_email = none
 license = GPLv3
 license_file = LICENSE.txt
-home-page = http://www.maths.lth.se/matstat/wafo/
+home_page = http://www.maths.lth.se/matstat/wafo/
 long_description = file: README.rst, CHANGELOG.rst, LICENSE.txt
 long_description_content_type = text/x-rst
 # Add here all kinds of additional classifiers as defined under
 # https://pypi.python.org/pypi?%3Aaction=list_classifiers
 classifiers =
     Development Status :: 4 - Beta
     Programming Language :: Python
-    Programming Language :: Python :: 3.5
-    Programming Language :: Python :: 3.6
-    Programming Language :: Python :: 3.7
     Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
     Environment :: Console
     Intended Audience :: Education
     Intended Audience :: Science/Research

setup.py

@@ -64,7 +64,6 @@
 from numpy.distutils.misc_util import Configuration
 from distutils.command.sdist import sdist
 
-pkg_resources.require('setuptools>=39.2') # setuptools >=38.3.0     # version with most `setup.cfg` bugfixes
 ROOT = os.path.abspath(os.path.dirname(__file__))
 PACKAGE_NAME = 'wafo'
 

src/wafo/covariance/core.py

@@ -29,7 +29,7 @@
 from ..containers import PlotData
 from ..misc import sub_dict_select, nextpow2  # , JITImport
 from .. import spectrum as _wafospec
-from scipy.sparse.linalg.dsolve.linsolve import spsolve
+from scipy.sparse.linalg import spsolve
 from scipy.sparse.base import issparse
 from scipy.signal.windows import parzen
 # _wafospec = JITImport('wafo.spectrum')

src/wafo/misc.py

@@ -2,7 +2,11 @@
 Misc
 '''
 
-import collections
+try:
+    from collections.abc import Callable
+except ImportError:
+    from collections import Callable
+
 import fractions
 import numbers
 import sys
@@ -244,7 +248,7 @@ def check_shapes(condlist, funclist):
     out = np.full(shape, fillvalue, dtype)
     for cond, func in zip(condlist, funclist):
         if cond.any():
-            if isinstance(func, collections.Callable):
+            if isinstance(func, Callable):
                 temp = tuple(np.extract(cond, arr) for arr in arrays) + args
                 np.place(out, cond, func(*temp, **kw))
             else:  # func is a scalar value or a array

src/wafo/stats/distributions.py

@@ -7,9 +7,9 @@
 #
 from copy import copy
 from functools import partial
-from ._distn_infrastructure import entropy, rv_discrete, rv_continuous, rv_frozen
+from ._distn_infrastructure import rv_discrete, rv_continuous, rv_frozen
 
-from scipy.stats import _continuous_distns
+from scipy.stats import _continuous_distns, entropy
 from scipy.stats import _discrete_distns
 from scipy.stats._constants import _EULER
 # from scipy.stats._continuous_distns import *

src/wafo/stats/estimation.py

@@ -11,7 +11,7 @@
 import scipy.stats as ss
 from scipy.stats._distn_infrastructure import rv_frozen as _rv_frozen
 from scipy import special
-from scipy.linalg import pinv2
+from scipy.linalg import pinv
 from scipy import optimize
 from scipy.special import expm1  # pylint: disable=no-name-in-module
 import numpy as np
@@ -1290,11 +1290,11 @@ def _invert_hessian(self, hessian):
         if somefixed:
             allfixed = np.all(np.isfinite(self.par_fix))
             if not allfixed:
-                pcov = -pinv2(hessian[self.i_notfixed, :][..., self.i_notfixed])
+                pcov = -pinv(hessian[self.i_notfixed, :][..., self.i_notfixed])
                 for row, i in enumerate(list(self.i_notfixed)):
                     par_cov[i, self.i_notfixed] = pcov[row, :]
         else:
-            par_cov = -pinv2(hessian)
+            par_cov = -pinv(hessian)
         return par_cov
 
     def _compute_cov(self, par):