backports of #845 & #849

.github/workflows/release.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: Install dependencies
         run: python3 -m pip install flit
       - name: Build package

.github/workflows/test.yaml

@@ -13,12 +13,12 @@ env:
 jobs:
   build-python-package:
     name: Build Python package
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     outputs:
       wheel: ${{ steps.build.outputs.wheel }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: Install build dependencies
         run: python3 -m pip install flit
       - name: Build package
@@ -30,7 +30,7 @@ jobs:
           python3 -m flit build
           echo wheel=`echo dist/*.whl` >> $GITHUB_OUTPUT
       - name: Upload package artifacts
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: python-package
           path: dist/
@@ -42,20 +42,22 @@ jobs:
     strategy:
       matrix:
         include:
-          - {name: "baseline", os: ubuntu-latest, python-version: "3.10", matrix-backend: numpy, nprocs: 1}
-          - {name: "windows", os: windows-latest, python-version: "3.10", matrix-backend: numpy, nprocs: 1}
-          - {name: "macos", os: macos-latest, python-version: "3.10", matrix-backend: numpy, nprocs: 1}
+          - {name: "baseline", os: ubuntu-latest, python-version: "3.12", matrix-backend: numpy, nprocs: 1}
+          - {name: "windows", os: windows-latest, python-version: "3.12", matrix-backend: numpy, nprocs: 1}
+          - {name: "macos", os: macos-latest, python-version: "3.12", matrix-backend: numpy, nprocs: 1}
           - {name: "python 3.7", os: ubuntu-latest, python-version: "3.7", matrix-backend: numpy, nprocs: 1}
           - {name: "python 3.8", os: ubuntu-latest, python-version: "3.8", matrix-backend: numpy, nprocs: 1}
           - {name: "python 3.9", os: ubuntu-latest, python-version: "3.9", matrix-backend: numpy, nprocs: 1}
-          - {name: "scipy matrix", os: ubuntu-latest, python-version: "3.10", matrix-backend: scipy, nprocs: 1}
-          - {name: "mkl linux", os: ubuntu-latest, python-version: "3.10", matrix-backend: mkl, nprocs: 1}
-          - {name: "mkl linux parallel", os: ubuntu-latest, python-version: "3.10", matrix-backend: mkl, nprocs: 2}
-          - {name: "mkl windows", os: windows-latest, python-version: "3.10", matrix-backend: mkl, nprocs: 1}
-          - {name: "mkl macos", os: macos-latest, python-version: "3.10", matrix-backend: mkl, nprocs: 1}
-          - {name: "parallel", os: ubuntu-latest, python-version: "3.10", matrix-backend: numpy, nprocs: 2}
+          - {name: "python 3.10", os: ubuntu-latest, python-version: "3.10", matrix-backend: numpy, nprocs: 1}
+          - {name: "python 3.11", os: ubuntu-latest, python-version: "3.11", matrix-backend: numpy, nprocs: 1}
+          - {name: "scipy matrix", os: ubuntu-latest, python-version: "3.12", matrix-backend: scipy, nprocs: 1}
+          - {name: "mkl linux", os: ubuntu-latest, python-version: "3.12", matrix-backend: mkl, nprocs: 1}
+          - {name: "mkl linux parallel", os: ubuntu-latest, python-version: "3.12", matrix-backend: mkl, nprocs: 2}
+          - {name: "mkl windows", os: windows-latest, python-version: "3.12", matrix-backend: mkl, nprocs: 1}
+          - {name: "mkl macos", os: macos-latest, python-version: "3.12", matrix-backend: mkl, nprocs: 1}
+          - {name: "parallel", os: ubuntu-latest, python-version: "3.12", matrix-backend: numpy, nprocs: 2}
           - {name: "numpy 1.17", os: ubuntu-latest, python-version: "3.7", matrix-backend: numpy, nprocs: 1, numpy-version: ==1.17}
-          - {name: "tensorial", os: ubuntu-latest, python-version: "3.10", matrix-backend: numpy, nprocs: 1, tensorial: test}
+          - {name: "tensorial", os: ubuntu-latest, python-version: "3.12", matrix-backend: numpy, nprocs: 1, tensorial: test}
       fail-fast: false
     env:
       _wheel: ${{ needs.build-python-package.outputs.wheel }}
@@ -70,15 +72,15 @@ jobs:
       NUTILS_TENSORIAL: ${{ matrix.tensorial }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: Move nutils directory
         run: mv nutils _nutils
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Download Python package artifact
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v4
         with:
           name: python-package
           path: dist/
@@ -107,7 +109,7 @@ jobs:
       - name: Post-process coverage
         run: python -um devtools.gha.coverage_report_xml
       - name: Upload coverage
-        uses: codecov/codecov-action@v1
+        uses: codecov/codecov-action@v3
   test-examples:
     needs: build-python-package
     name: 'Test examples ${{ matrix.os }}'
@@ -126,13 +128,15 @@ jobs:
       PYTHONHASHSEED: 0
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: Move nutils directory
         run: mv nutils _nutils
       - name: Set up Python
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
       - name: Download Python package artifact
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v4
         with:
           name: python-package
           path: dist/
@@ -146,10 +150,10 @@ jobs:
         run: python -um unittest discover -b -q -t . -s examples
   test-sphinx:
     name: Test building docs
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: Install dependencies
         run: |
           python3 -um pip install setuptools wheel
@@ -159,16 +163,16 @@ jobs:
   build-and-test-container-image:
     name: Build container image
     needs: build-python-package
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     env:
       # Fixes https://github.com/actions/virtual-environments/issues/3080
       STORAGE_OPTS: overlay.mount_program=/usr/bin/fuse-overlayfs
       _wheel: ${{ needs.build-python-package.outputs.wheel }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: Download Python package artifact
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v4
         with:
           name: python-package
           path: dist/

examples/cahnhilliard.py

@@ -62,7 +62,7 @@ def main(size: Length = parse('10cm'),
     energy:
 
         E(φ) := ∫_Ω ψ(φ) σ / ε + ∫_Ω .5 σ ε ‖∇φ‖² + ∫_Γ (σm + φ σd)
-                \                \                  \ 
+                ╲                ╲                  ╲
                  mixing energy    interface energy   wall energy
 
     Proof: the time derivative of `E` followed by substitution of the strong form

pyproject.toml

@@ -4,15 +4,15 @@ readme = "README.md"
 authors = [
     { name = "Evalf", email = "[email protected]" },
 ]
-requires-python = '~=3.7'
+requires-python = '>=3.7'
 dependencies = [
-    "appdirs~=1.0",
-    "bottombar~=2.0.2",
-    "numpy>=1.17",
-    "nutils-poly~=1.0",
-    "psutil~=5.0",
+    "appdirs >=1,<2",
+    "bottombar >=2,<3",
+    "numpy >=1.17,<2",
+    "nutils-poly >=1,<2",
+    "psutil >=5,<6",
     "stringly",
-    "treelog>=1.0b5",
+    "treelog >=1,<2",
 ]
 dynamic = ["description", "version"]
 classifiers = [
@@ -22,11 +22,11 @@ classifiers = [
 ]
 
 [project.optional-dependencies]
-docs = ["Sphinx>=1.8"]
-export_mpl = ["matplotlib>=1.3", "pillow>2.6"]
-matrix_mkl = ["mkl<2024"]
-matrix_scipy = ["scipy>=0.13"]
-import_gmsh = ["meshio"]
+docs = ["Sphinx >=1.8,<8"]
+export_mpl = ["matplotlib >=3.3,<4"]
+matrix_mkl = ["mkl <2024"]
+matrix_scipy = ["scipy >=0.13,<2"]
+import_gmsh = ["meshio >=4,<6"]
 
 [build-system]
 requires = ["flit_core >=3.2,<4"]

tests/test_expression_v2.py

@@ -560,28 +560,28 @@ def test_define_for_3d(self):
     def test_add_single_field(self):
         ns = expression_v2.Namespace()
         ns.add_field('u', numpy.array([1,2,3]))
-        self.assertEquals(ns.u.argshapes, dict(u=(3,)))
-        self.assertEquals(ns.u.shape, ())
+        self.assertEqual(ns.u.argshapes, dict(u=(3,)))
+        self.assertEqual(ns.u.shape, ())
 
     def test_add_multiple_fields(self):
         ns = expression_v2.Namespace()
         ns.add_field(('u', 'v'), numpy.array([1,2,3]))
-        self.assertEquals(ns.u.argshapes, dict(u=(3,)))
-        self.assertEquals(ns.u.shape, ())
-        self.assertEquals(ns.v.argshapes, dict(v=(3,)))
-        self.assertEquals(ns.v.shape, ())
+        self.assertEqual(ns.u.argshapes, dict(u=(3,)))
+        self.assertEqual(ns.u.shape, ())
+        self.assertEqual(ns.v.argshapes, dict(v=(3,)))
+        self.assertEqual(ns.v.shape, ())
 
     def test_add_single_field_multiple_bases(self):
         ns = expression_v2.Namespace()
         ns.add_field('u', numpy.array([1,2,3]), numpy.array([4,5,6,7]))
-        self.assertEquals(ns.u.argshapes, dict(u=(3,4)))
-        self.assertEquals(ns.u.shape, ())
+        self.assertEqual(ns.u.argshapes, dict(u=(3,4)))
+        self.assertEqual(ns.u.shape, ())
 
     def test_add_single_field_with_shape(self):
         ns = expression_v2.Namespace()
         ns.add_field('u', numpy.array([1,2,3]), shape=(2,))
-        self.assertEquals(ns.u.argshapes, dict(u=(3,2)))
-        self.assertEquals(ns.u.shape, (2,))
+        self.assertEqual(ns.u.argshapes, dict(u=(3,2)))
+        self.assertEqual(ns.u.shape, (2,))
 
     def test_copy(self):
         ns1 = expression_v2.Namespace()

tests/test_function.py

@@ -24,7 +24,7 @@ def test_cast_invalid_argument(self):
             function.Array.cast('132')
 
     def test_cast_different_shapes(self):
-        with self.assertRaisesRegex(ValueError, 'cannot convert \[\[1, 2, 3\], \[4, 5\]\] to Array: all input arrays must have the same shape'):
+        with self.assertRaisesRegex(ValueError, 'cannot convert \\[\\[1, 2, 3\\], \\[4, 5\\]\\] to Array: all input arrays must have the same shape'):
             function.Array.cast([[1,2,3],[4,5]])
 
     def test_ndim(self):
@@ -53,11 +53,11 @@ def test_iter_known(self):
         self.assertEqual(b.as_evaluable_array.eval(), 2)
 
     def test_binop_notimplemented(self):
-        with self.assertRaisesRegex(TypeError, '^operand type\(s\) all returned NotImplemented from __array_ufunc__'):
+        with self.assertRaisesRegex(TypeError, '^operand type\\(s\\) all returned NotImplemented from __array_ufunc__'):
             function.Argument('a', ()) + '1'
 
     def test_rbinop_notimplemented(self):
-        with self.assertRaisesRegex(TypeError, '^operand type\(s\) all returned NotImplemented from __array_ufunc__'):
+        with self.assertRaisesRegex(TypeError, '^operand type\\(s\\) all returned NotImplemented from __array_ufunc__'):
             '1' + function.Argument('a', ())
 
     def test_deprecated_simplified(self):
@@ -76,7 +76,7 @@ def test_index(self):
         self.assertEqual(function.Array.cast(2).__index__(), 2)
         with self.assertRaisesRegex(ValueError, "cannot convert non-constant array to index: arguments=foo"):
             function.Argument('foo', shape=(), dtype=int).__index__()
-        with self.assertRaisesRegex(ValueError, "cannot convert non-scalar array to index: shape=\(2,\)"):
+        with self.assertRaisesRegex(ValueError, "cannot convert non-scalar array to index: shape=\\(2,\\)"):
             function.Array.cast([2, 3]).__index__()
         with self.assertRaisesRegex(ValueError, "cannot convert non-integer array to index: dtype=float"):
             function.Array.cast(2.5).__index__()

tests/test_solver.py

@@ -34,9 +34,9 @@ def _test_recursion_cache(testcase, solver_iter):
                     with testcase.assertLogs('nutils', 'DEBUG') as cm:
                         v = read(length)
                     testcase.assertEqual(v, reference[:length])
-                    testcase.assertRegex('\n'.join(cm.output), '\[cache\.Recursion [0-9a-f]{40}\] start iterating')
-                    testcase.assertRegex('\n'.join(cm.output), '\[cache\.Recursion [0-9a-f]{40}\.0000\] load' if i and max(lengths[:i]) > 0
-                                                          else '\[cache\.Recursion [0-9a-f]{40}\.0000\] cache exhausted')
+                    testcase.assertRegex('\n'.join(cm.output), '\\[cache\\.Recursion [0-9a-f]{40}\\] start iterating')
+                    testcase.assertRegex('\n'.join(cm.output), '\\[cache\\.Recursion [0-9a-f]{40}\\.0000\\] load' if i and max(lengths[:i]) > 0
+                                                          else '\\[cache\\.Recursion [0-9a-f]{40}\\.0000\\] cache exhausted')
 
 
 def _test_solve_cache(testcase, solver_gen):
@@ -46,10 +46,10 @@ def _test_solve_cache(testcase, solver_gen):
         with testcase.assertLogs('nutils', 'DEBUG') as cm:
             v2, info = _edit(solver_gen().solve_withinfo(1e-5))
         testcase.assertEqual(v1, v2)
-        testcase.assertRegex('\n'.join(cm.output), '\[cache\.function [0-9a-f]{40}\] load')
+        testcase.assertRegex('\n'.join(cm.output), '\\[cache\\.function [0-9a-f]{40}\\] load')
         with testcase.assertLogs('nutils', 'DEBUG') as cm:
             solver_gen().solve(1e-6)
-        testcase.assertRegex('\n'.join(cm.output), '\[cache\.function [0-9a-f]{40}\] failed to load')
+        testcase.assertRegex('\n'.join(cm.output), '\\[cache\\.function [0-9a-f]{40}\\] failed to load')
 
 
 class laplace(TestCase):