Merge branch 'master' into ruff_auto

.github/workflows/test.yml → .github/workflows/sage_test.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        version: [9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 10.1, 10.2, latest]
+        version: [9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 10.1, 10.2, 10.3, latest]
 
     container:
       image: sagemath/sagemath:${{ matrix.version }}
@@ -20,7 +20,7 @@ jobs:
         run: sage --version
 
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install PLink
         run:
@@ -47,3 +47,15 @@ jobs:
 
       - name: Do the tests
         run: sage -python -m snappy.test
+
+      - name: Build docs
+        # Doesn't just do "make html" as neither "make" nor "zip" is
+        # installed in this image.
+        run: |
+          cd /__w/SnapPy/SnapPy/doc_src
+          sage -python -m sphinx -b html -E -d _build/doctrees . _build/doc
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: doc-${{ matrix.version }}
+          path: /__w/SnapPy/SnapPy/doc_src/_build/doc/*

.github/workflows/linux.yml → .github/workflows/wheels.yml

@@ -1,4 +1,4 @@
-name: Linux Wheels
+name: Wheels
 
 on: [push, pull_request]
 
@@ -7,34 +7,37 @@ jobs:
     name: Build wheels on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
-        os: [ubuntu-20.04]
+        os: [ubuntu-22.04, macos-12, macos-14, windows-2019]
 
     steps:
       - uses: actions/checkout@v3
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.15.0
+        uses: pypa/cibuildwheel@v2.19.2
         env:
-          # Skip Python 3.12, 32 bit Linux, and PyPy
+          # Skip Python 32 bit Linux, and PyPy
+          CIBW_ENVIRONMENT: SNAPPY_ALWAYS_BUILD_CYOPENGL=True
+          CIBW_ENVIRONMENT_MACOS: >
+            SNAPPY_ALWAYS_BUILD_CYOPENGL=True
+            MACOSX_DEPLOYMENT_TARGET=10.12
+          CIBW_BUILD: "cp38-* cp39-* cp310-* cp311-* cp312-*"
           CIBW_SKIP: "*-manylinux_i686 *musllinux* pp*"
           CIBW_BEFORE_ALL_LINUX: yum install -y tk mesa-libGLU-devel
           CIBW_BEFORE_BUILD: >
-            pip install cython FXrays low_index sphinx sphinx_rtd_theme &&
-            pip install --pre --extra-index-url https://test.pypi.org/simple cypari &&
-            pip install git+https://github.com/3-manifolds/PLink &&
-            pip install git+https://github.com/3-manifolds/snappy_manifolds &&
-            pip install git+https://github.com/3-manifolds/Spherogram
+            pip install cython
           CIBW_BEFORE_TEST: >
-            pip install cython low_index &&
+            pip install low_index &&
             pip install --pre --extra-index-url https://test.pypi.org/simple cypari &&
             pip install git+https://github.com/3-manifolds/PLink &&
             pip install git+https://github.com/3-manifolds/snappy_manifolds &&
             pip install git+https://github.com/3-manifolds/Spherogram
           CIBW_REPAIR_WHEEL_COMMAND_LINUX: auditwheel repair --strip -w {dest_dir} {wheel}
-          CIBW_TEST_COMMAND: python -m snappy.test --skip-modern-opengl
+          CIBW_TEST_COMMAND: python -m snappy.test --skip-gui
+
 
       - uses: actions/upload-artifact@v3
         with:
-          name: snappy_linux_wheels
+          name: snappy_all_wheels
           path: ./wheelhouse/*.whl

CI_README

@@ -0,0 +1,9 @@
+The locations of the files controlling continuous integration are:
+
+.cirrus.yml
+
+For Mac OS ARM only. Machine seems to be headless - so skipping GUI tests.
+
+.github/workflows
+
+For everything else.

cython/SnapPy.pyx

@@ -1,4 +1,5 @@
 # cython: language_level=3str
+# cython: embedsignature = False
 
 ctypedef double Real
 

cython/SnapPyHP.pyx

@@ -1,6 +1,7 @@
 # distutils: language = c++
 # distutils: sources = SnapPyHP.cpp
 # cython: language_level=3str
+# cython: embedsignature = False
 
 ctypedef qd_real Real
 

cython/core/abelian_group.pyx

@@ -231,7 +231,7 @@ cdef class PresentationMatrix():
         Continue until no units remain.  When a generator is removed,
         remember its column index.
         """
-        cdef int temp, m, i = 0, j = 0, k, l
+        cdef int i = 0, j = 0, k, l
         while len(self._units) > 0:
             for i, j in self._units:
                 break

cython/core/basic.pyx

@@ -41,7 +41,7 @@ try:
 except ImportError:
     pass
 
-from .matrix import matrix, vector, SimpleMatrix
+from .matrix import matrix
 from . import number
 
 # SnapPy components
@@ -52,6 +52,7 @@ from . import twister
 from . import snap
 from . import verify
 from .verify import complex_volume as verify_complex_volume
+from .cusps import compute_cusp_shapes as cusps_compute_cusp_shapes
 from . import decorated_isosig
 from .ptolemy import manifoldMethods as ptolemyManifoldMethods
 from .export_stl import stl
@@ -370,24 +371,6 @@ class MatrixWithExplanations():
         self.explain_rows = explain_rows
         self.explain_columns = explain_columns
 
-    def __add__(self, other):
-
-        assert self.explain_columns == other.explain_columns, (
-            "matrices with different columns")
-
-        if isinstance(self.matrix, SimpleMatrix):
-            newMatrix = SimpleMatrix(self.matrix.data + other.matrix.data)
-        elif _within_sage:
-            newMatrix = self.matrix.stack(other.matrix)
-        else:
-            raise ValueError('Matrix type in MatrixWithExplanations '
-                             'not supported')
-
-        return MatrixWithExplanations(
-            newMatrix,
-            self.explain_rows+other.explain_rows,
-            self.explain_columns)
-
     def __repr__(self, _type_str = "MatrixWithExplanations"):
 
         def format_explain_list(l):
@@ -419,12 +402,6 @@ class NeumannZagierTypeEquations(MatrixWithExplanations):
         return MatrixWithExplanations.__repr__(self,
                                                "NeumannZagierTypeEquations")
 
-    def __add__(self, other):
-        mat = MatrixWithExplanations.__add__(self, other)
-
-        return NeumannZagierTypeEquations(
-            mat.matrix, mat.explain_rows, mat.explain_columns)
-
 # C type for a function of Real returning an object
 ctypedef object (*func_real_to_obj)(Real)
 
@@ -601,7 +578,7 @@ class LengthSpectrumInfo(Info):
                 lenStr += " + "
             else:
                 lenStr += " - "
-            lenStr += "%17.14f*I" % absImag
+            lenStr += "%16.14f*I" % absImag
 
         if 'word' in self:
             return LengthSpectrumFormatStringWithWord % (

cython/core/dirichlet.pyx

@@ -707,7 +707,8 @@ class DirichletDomain(CDirichletDomain):
     is a local maximum of injectivity radius.  It will have ideal
     vertices if the manifold is not closed.
 
-    Instantiate as M.dirichlet_domain() where M is a Manifold to
+    Instantiate as M.dirichlet_domain()
+    where M is a Manifold to
     obtain a Dirichlet Domain centered at a point which maximizes
     injectivity radius.
 
@@ -721,7 +722,7 @@ class DirichletDomain(CDirichletDomain):
     You can also create a Dirichlet Domain from a file listing matrix
     generators for the group, in SnapPea's "% Generator" format, via
 
-       D = DirichletDomain(generator_file='test.gens')
+    >>> D = DirichletDomain(generator_file='test.gens') # doctest: +SKIP
 
     Or from matrices:
 
@@ -733,7 +734,7 @@ class DirichletDomain(CDirichletDomain):
 
     The group elements for the face-pairings of the Dirichlet domain
     can be given as words in the original generators by setting
-    include_words = True.
+    ``include_words = True``.
 
     """
 

cython/core/fundamental_group.pyx

@@ -95,6 +95,10 @@ def word_as_list(word, int num_generators):
 
     return word_list
 
+def list_as_word(int_list, int num_generators, verbose_form):
+    return _letter_seperator(verbose_form).join(
+        int_to_gen_string(g, num_generators, verbose_form)
+        for g in int_list)
 
 cdef class CFundamentalGroup():
     cdef c_GroupPresentation *c_group_presentation
@@ -223,10 +227,7 @@ cdef class CFundamentalGroup():
             return words[1:]
         else:
             n = self.num_original_generators()
-            return [_letter_seperator(verbose_form).join(
-                            int_to_gen_string(g, n, verbose_form)
-                            for g in word)
-                    for word in words[1:]]
+            return [ list_as_word(word, n, verbose_form) for word in words[1:]]
 
     def _word_moves(self):
         cdef int *c_moves