Merge branch 'master' into test_on_sage_9.8

3-manifolds · Jul 22, 2023 · ef4122f · ef4122f
2 parents 7dc6c84 + 2137d3d
commit ef4122f
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diff --git a/.cirrus.yml b/.cirrus.yml
@@ -0,0 +1,29 @@
+cirrus_wheels_macos_arm64_task:
+  name: Build macOS arm64 wheels.
+  macos_instance:
+    image: ghcr.io/cirruslabs/macos-ventura-xcode:latest
+  env:
+    CIBW_ARCHS_MACOS: arm64
+    CIBW_SKIP: pp* cp38*
+    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
+    CIBW_BEFORE_TEST: >
+      pip install cython 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_TEST_COMMAND: python -m snappy.test --skip-modern-opengl
+  install_pre_requirements_script:
+    - brew install python3
+    - python3 --version
+  install_cibuildwheel_script:
+    - python3 -m pip install cibuildwheel
+  run_cibuildwheel_script:
+    - python3 -m cibuildwheel --output-dir wheelhouse
+  wheels_artifacts:
+    path: "wheelhouse/*"
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
@@ -0,0 +1,27 @@
+name: Lint
+on:
+  push: { branches: [ "master" ] }
+  pull_request: { branches: [ "master" ] }
+
+jobs:
+  codespell:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Install dependencies
+        shell: bash -l {0}
+        run: |
+          sudo apt-get install -y codespell
+          sudo apt-get install -y pycodestyle
+      - name: Run codespell
+        shell: bash -l {0}
+        run: codespell -L ans,arithmetics,inout,trough,compresser,rime,ba python
+      - name: Run pycodestyle
+        shell: bash -l {0}
+        # We currently only check for some warnings. We should enable & fix more of them.
+        run: |
+          pycodestyle --select=E111,E21,E221,E222,E225,E227,E228,E241,E251,E262,E265,E271,E272,E30,E401,E701,E702,E703,E704,E711,E713,E714,E721,W2,W3,W6 python/
+          pycodestyle --filename=*.pyx --select=W2 cython/
+
+env:
+  MAKEFLAGS: -j2
diff --git a/.github/workflows/linux.yml b/.github/workflows/linux.yml
@@ -11,12 +11,12 @@ jobs:
         os: [ubuntu-20.04]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v3
         name: Install Python
         with:
-          python-version: '3.8'
+          python-version: '3.9'
 
       - name: Install cibuildwheel
         run: |
@@ -30,21 +30,21 @@ jobs:
           CIBW_SKIP: cp27-* cp35-* *-manylinux_i686 *musllinux* pp*
           CIBW_BEFORE_ALL_LINUX: yum install -y tk mesa-libGLU-devel
           CIBW_BEFORE_BUILD: >
-            pip install cython sphinx FXrays &&
-            pip install --index-url https://test.pypi.org/simple cypari &&
+            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 git+https://github.com/3-manifolds/low_index
+            pip install git+https://github.com/3-manifolds/Spherogram
           CIBW_BEFORE_TEST: >
-            pip install cython &&
+            pip install cython 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 &&
-            pip install git+https://github.com/3-manifolds/low_index
+            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
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
         with:
+          name: snappy_linux_wheels
           path: ./wheelhouse/*.whl
diff --git a/.github/workflows/macos.yml b/.github/workflows/macos.yml
@@ -11,12 +11,12 @@ jobs:
         os: [macos-11]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v3
         name: Install Python
         with:
-          python-version: '3.8'
+          python-version: '3.9'
 
       - name: Install cibuildwheel
         run: |
@@ -27,23 +27,23 @@ jobs:
           python -m cibuildwheel --output-dir wheelhouse
         env:
           # Skip Python 2.7, 3.5, 3.11, 32 bit Linux, and PyPy
-          CIBW_SKIP: cp27-* cp35-* pp*
-          CIBW_ARCHS_MACOS: "x86_64"
-          CIBW_BEFORE_BUILD: >            
-            pip install cython sphinx FXrays &&
-            pip install --index-url https://test.pypi.org/simple cypari &&
+          CIBW_SKIP: cp27-* cp35-* cp36-* cp37-* pp*
+          CIBW_ARCHS_MACOS: x86_64 universal2
+          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 git+https://github.com/3-manifolds/low_index 
+            pip install git+https://github.com/3-manifolds/Spherogram
           CIBW_BEFORE_TEST: >
-            pip install cython &&
+            pip install cython 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 &&
-            pip install git+https://github.com/3-manifolds/low_index 
+            pip install git+https://github.com/3-manifolds/Spherogram
           CIBW_TEST_COMMAND: python -m snappy.test --skip-modern-opengl
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
         with:
+          name: snappy_macos_wheels
           path: ./wheelhouse/*.whl
diff --git a/.github/workflows/macos_older_pythons.yml b/.github/workflows/macos_older_pythons.yml
@@ -0,0 +1,49 @@
+name: macOS Older Python Wheels
+
+on: [push, pull_request]
+
+jobs:
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [macos-11]
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: actions/setup-python@v3
+        name: Install Python
+        with:
+          python-version: '3.9'
+
+      - name: Install cibuildwheel
+        run: |
+          python -m pip install cibuildwheel
+
+      - name: Build wheels
+        run: |
+          python -m cibuildwheel --output-dir wheelhouse
+        env:
+          # Skip Python 2.7, 3.5, 3.11, 32 bit Linux, and PyPy
+          CIBW_SKIP: cp27-* cp35-* cp38-* cp39-* cp310-* cp311-* pp*
+          CIBW_ARCHS_MACOS: x86_64
+          CIBW_BEFORE_BUILD: >
+            pip install cython FXrays low_index sphinx sphinx_rtd_theme &&
+            pip install --pre --extra-index-url https://test.pypi.org/simple cypari &&
+            pip install git+https://github.com/3-manifolds/PLink &&
+            pip install git+https://github.com/3-manifolds/snappy_manifolds &&
+            pip install git+https://github.com/3-manifolds/Spherogram
+          CIBW_BEFORE_TEST: >
+            pip install cython low_index &&
+            pip install --pre --extra-index-url https://test.pypi.org/simple cypari &&
+            pip install git+https://github.com/3-manifolds/PLink &&
+            pip install git+https://github.com/3-manifolds/snappy_manifolds &&
+            pip install git+https://github.com/3-manifolds/Spherogram
+          CIBW_TEST_COMMAND: python -m snappy.test --skip-modern-opengl
+
+      - uses: actions/upload-artifact@v3
+        with:
+          name: snappy_macos_older_wheels
+          path: ./wheelhouse/*.whl
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -9,8 +9,7 @@ jobs:
     runs-on: ubuntu-jammy
     strategy:
       matrix:
-        version: [9.3, 9.4, 9.5, 9.6, 9.7, 9.8]
-
+        version: [9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 10.0]
     container:
       image: ghcr.io/sagemath/sage/sage-ubuntu-jammy-standard-with-targets:${{ matrix.version }}
       options: --user root
@@ -42,7 +41,7 @@ jobs:
       - name: Install snappy
         run: |
           cd /__w/SnapPy/SnapPy
-          sage -pip install wheel FXrays
+          sage -pip install wheel FXrays sphinx_rtd_theme
           sage -python setup.py pip_install
 
       - name: Do the tests

diff --git a/.github/workflows/windows.yml b/.github/workflows/windows.yml
@@ -11,12 +11,12 @@ jobs:
         os: [windows-latest]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v3
         name: Install Python
         with:
-          python-version: '3.8'
+          python-version: '3.9'
 
       - name: Install cibuildwheel
         run: |
@@ -29,20 +29,20 @@ jobs:
           # Skip Python 2.7, 3.5, 3.11, and PyPy
           CIBW_SKIP: cp27-* cp35-* pp*
           CIBW_BEFORE_BUILD: >
-            pip install cython sphinx FXrays &&
-            pip install --index-url https://test.pypi.org/simple cypari &&
+            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 git+https://github.com/3-manifolds/low_index
+            pip install git+https://github.com/3-manifolds/Spherogram
           CIBW_BEFORE_TEST: >
-            pip install cython &&
+            pip install cython 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 &&
-            pip install git+https://github.com/3-manifolds/low_index
+            pip install git+https://github.com/3-manifolds/Spherogram
           CIBW_TEST_COMMAND: python -m snappy.test --skip-modern-opengl
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
         with:
+          name: snappy_windows_wheels
           path: ./wheelhouse/*.whl
diff --git a/cython/SnapPy.pxi b/cython/SnapPy.pxi
@@ -306,7 +306,7 @@ cdef extern from "triangulation.h":
         c_TetShape   *shape[2]
         c_VertexCrossSections *cross_section
         EdgeClass *edge_class[6]
-        
+
     ctypedef struct c_Triangulation "Triangulation":
         c_Tetrahedron  tet_list_begin
         c_Tetrahedron  tet_list_end
@@ -568,6 +568,7 @@ cdef extern from "SnapPea.h":
     extern Boolean cusp_is_fillable(c_Triangulation *manifold, int cusp_index) except *
     extern Boolean is_closed_manifold(c_Triangulation *manifold) except *
     extern c_GroupPresentation *fundamental_group(c_Triangulation *manifold, Boolean simplify_presentation, Boolean fillings_may_affect_generators, Boolean minimize_number_of_generators, Boolean try_hard_to_shorten_relators) except *
+    extern c_GroupPresentation *compute_unsimplified_presentation(c_Triangulation *manifold) except *
     extern int fg_get_num_generators(c_GroupPresentation *group) except *
     extern int fg_get_num_orig_gens(c_GroupPresentation *group) except *
     extern Boolean fg_integer_fillings(c_GroupPresentation *group) except *
@@ -747,7 +748,7 @@ cdef extern from "addl_code.h":
     extern void free_cusp_equation(int* equation)
     extern c_Triangulation*    triangulate_link_complement_from_file(char* file_name, char *path)  except *
     extern c_Triangulation* fibered_manifold_associated_to_braid(int numStrands, int braidLength, int* word)  except *
-    extern void set_tet_shapes(c_Triangulation* manifold, Complex* filled_shapes, Complex* complete_shapes) 
+    extern void set_tet_shapes(c_Triangulation* manifold, Complex* filled_shapes, Complex* complete_shapes)
     extern void set_target_holonomy(c_Triangulation* manifold, int theCuspIndex, Complex theTarget, int theRecomputeFlag)
     extern c_Triangulation* DT2Triangulation(char* c_link_record)
     extern void choose_gen_tetrahedron_info(c_Triangulation* manifold, int tet_index, int *generator_path, int *face0_gen, int *face1_gen, int *face2_gen, int *face3_gen, Complex *corner0, Complex *corner1, Complex *corner2, Complex *corner3, int *neighbor0_idx, int *neighbor1_idx, int *neighbor2_idx, int *neighbor3_idx, int *perm0, int *perm1, int *perm2, int *perm3)
@@ -760,43 +761,43 @@ cdef extern from "isomorphism_signature.h":
     extern c_Triangulation* triangulation_from_isomorphism_signature(char *isoSig)
 
 cdef extern from "ptolemy_types.h":
-     ctypedef char* Two_identified_variables[2]
+    ctypedef char* Two_identified_variables[2]
+
+    ctypedef struct Identification_of_variables:
+        int num_identifications
+        Two_identified_variables *variables
+        int *signs
+        int *powers
 
-     ctypedef struct Identification_of_variables:
-         int num_identifications
-         Two_identified_variables *variables
-         int *signs
-         int *powers
+    extern void free_identification_of_variables(Identification_of_variables id)
 
-     extern void free_identification_of_variables(Identification_of_variables id)
-
-     ctypedef struct Integer_matrix_with_explanations:
-         int **entries
-         int num_rows
-         int num_cols
-         char **explain_row
-         char **explain_column
+    ctypedef struct Integer_matrix_with_explanations:
+        int **entries
+        int num_rows
+        int num_cols
+        char **explain_row
+        char **explain_column
 
-     extern void free_integer_matrix_with_explanations(Integer_matrix_with_explanations m)
+    extern void free_integer_matrix_with_explanations(Integer_matrix_with_explanations m)
 
-     extern int number_of_edges(c_Triangulation *manifold)
+    extern int number_of_edges(c_Triangulation *manifold)
 
 cdef extern from "change_peripheral_curves_nonorientable.h":
-     extern c_FuncResult change_peripheral_curves_nonorientable( c_Triangulation *manifold, MatrixInt22 change_matrices[])
+    extern c_FuncResult change_peripheral_curves_nonorientable( c_Triangulation *manifold, MatrixInt22 change_matrices[])
 
 cdef extern from "gluing_equations_pgl.h":
-     extern void get_edge_gluing_equations_pgl(c_Triangulation *manifold, Integer_matrix_with_explanations *m, int N)
-     extern void get_face_gluing_equations_pgl(c_Triangulation *manifold, Integer_matrix_with_explanations *m, int N)
-     extern void get_internal_gluing_equations_pgl(c_Triangulation *manifold, Integer_matrix_with_explanations *m, int N)
-     extern void get_cusp_equations_pgl(c_Triangulation *manifold, Integer_matrix_with_explanations *m, int N, int cusp_num, int m, int l)
+    extern void get_edge_gluing_equations_pgl(c_Triangulation *manifold, Integer_matrix_with_explanations *m, int N)
+    extern void get_face_gluing_equations_pgl(c_Triangulation *manifold, Integer_matrix_with_explanations *m, int N)
+    extern void get_internal_gluing_equations_pgl(c_Triangulation *manifold, Integer_matrix_with_explanations *m, int N)
+    extern void get_cusp_equations_pgl(c_Triangulation *manifold, Integer_matrix_with_explanations *m, int N, int cusp_num, int m, int l)
 
 cdef extern from "ptolemy_equations.h":
-     extern void get_ptolemy_equations_identified_coordinates(c_Triangulation *manifold, Identification_of_variables *id, int N, int* obstruction_class)
-     extern void get_ptolemy_equations_identified_face_classes(c_Triangulation *manifold, Identification_of_variables *id)
-     extern void get_ptolemy_equations_action_by_decoration_change(c_Triangulation *manifold, int N, Integer_matrix_with_explanations *m)
-     extern void get_ptolemy_equations_boundary_map_3(c_Triangulation *manifold, Integer_matrix_with_explanations *m)
-     extern void get_ptolemy_equations_boundary_map_2(c_Triangulation *manifold, Integer_matrix_with_explanations *m)
-     extern void get_ptolemy_equations_boundary_map_1(c_Triangulation *manifold, Integer_matrix_with_explanations *m)
+    extern void get_ptolemy_equations_identified_coordinates(c_Triangulation *manifold, Identification_of_variables *id, int N, int* obstruction_class)
+    extern void get_ptolemy_equations_identified_face_classes(c_Triangulation *manifold, Identification_of_variables *id)
+    extern void get_ptolemy_equations_action_by_decoration_change(c_Triangulation *manifold, int N, Integer_matrix_with_explanations *m)
+    extern void get_ptolemy_equations_boundary_map_3(c_Triangulation *manifold, Integer_matrix_with_explanations *m)
+    extern void get_ptolemy_equations_boundary_map_2(c_Triangulation *manifold, Integer_matrix_with_explanations *m)
+    extern void get_ptolemy_equations_boundary_map_1(c_Triangulation *manifold, Integer_matrix_with_explanations *m)
 
 cdef extern from "inline.h":
     pass
diff --git a/cython/core/abelian_group.pyx b/cython/core/abelian_group.pyx
@@ -142,6 +142,7 @@ cdef class PresentationMatrix():
     A sparse representation of the presentation matrix of an abelian group.
     """
     cdef rows, cols, _row_support, _col_support, _entries, _units, dead_columns
+
     def __init__(self, rows, cols):
         self.rows = rows
         self.cols = cols