Merge pull request #326 from saraedum/macos

Run tests on macOS in CI

.github/workflows/benchmark.yml

@@ -5,7 +5,7 @@ on:
 
 jobs:
   asv:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
       - uses: actions/checkout@v2
         with:

.github/workflows/conda.yml

@@ -19,12 +19,10 @@ jobs:
       uses: flatsurf/actions/conda-forge-build@main
       with:
         recipe: libflatsurf/recipe
-        channels: flatsurf
     - name: Build pyflatsurf
       uses: flatsurf/actions/conda-forge-build@main
       with:
         recipe: pyflatsurf/recipe
-        channels: flatsurf
     - uses: actions/upload-artifact@v2
       with:
         name: conda-packages

.github/workflows/coverage.yml

@@ -9,7 +9,7 @@ concurrency:
 
 jobs:
   codecov:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
       - uses: actions/checkout@v2
         with: { submodules: recursive, fetch-depth: 0 }

.github/workflows/lint.yml

@@ -9,7 +9,7 @@ concurrency:
 
 jobs:
   clang-format:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
       - uses: actions/checkout@v2
       - uses: DoozyX/clang-format-lint-action@v0.11

.github/workflows/test.yml

@@ -9,17 +9,27 @@ concurrency:
 
 jobs:
   test-libflatsurf:
-    runs-on: ubuntu-20.04
+    runs-on: ${{ matrix.on }}
     strategy:
       matrix:
         include:
-        - target: check
+        - on: ubuntu-22.04
+          target: check
           libflint: '2'
-        - target: check
+        - on: ubuntu-22.04
+          target: check
           libflint: '3'
-        - target: check-valgrind
+        - on: macos-11
+          target: check
           libflint: '2'
-        - target: check-valgrind
+        - on: macos-11
+          target: check
+          libflint: '3'
+        - on: ubuntu-22.04
+          target: check-valgrind
+          libflint: '2'
+        - on: ubuntu-22.04
+          target: check-valgrind
           libflint: '3'
     steps:
       - uses: actions/checkout@v2
@@ -62,24 +72,45 @@ jobs:
       - uses: flatsurf/actions/show-logs@main
         if: ${{ always() }}
   test-pyflatsurf:
-    runs-on: ubuntu-20.04
+    runs-on: ${{ matrix.on }}
     strategy:
       matrix:
         include:
           # No released SageMath supports FLINT 3 yet. So we only test with FLINT 2.
-          - python: "3.8"
+          - on: macos-11
+            python: "3.8"
+            libflint: "2"
+            target: check
+          - on: macos-11
+            python: "3.9"
+            libflint: "2"
+            target: check
+          - on: macos-11
+            python: "3.10"
             libflint: "2"
             target: check
-          - python: "3.9"
+          - on: macos-11
+            python: "3.11"
             libflint: "2"
             target: check
-          - python: "3.10"
+          - on: ubuntu-22.04
+            python: "3.8"
             libflint: "2"
             target: check
-          - python: "3.11"
+          - on: ubuntu-22.04
+            python: "3.9"
             libflint: "2"
             target: check
-          - python: "3.11"
+          - on: ubuntu-22.04
+            python: "3.10"
+            libflint: "2"
+            target: check
+          - on: ubuntu-22.04
+            python: "3.11"
+            libflint: "2"
+            target: check
+          - on: ubuntu-22.04
+            python: "3.11"
             libflint: "2"
             target: check-valgrind
     steps:
@@ -110,6 +141,10 @@ jobs:
           echo "libflint ${{ matrix.libflint }}.*" >> $CONDA_PREFIX/conda-meta/pinned
           mamba env update --quiet -n test -f pyflatsurf/environment.yml
           conda list
+      - name: silence cppyy startup
+        shell: bash -l {0}
+        run: |
+          python -c 'import cppyy'
       - name: make ${{ matrix.target }}
         shell: bash -l {0}
         run: |
@@ -129,7 +164,7 @@ jobs:
       - uses: flatsurf/actions/show-logs@main
         if: ${{ always() }}
   distcheck:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
       - uses: actions/checkout@v2
         with: { submodules: recursive }

asv.conf.json

@@ -41,5 +41,3 @@
   "results_dir": ".asv/results",
   "html_dir": ".asv/html"
 }
-
-

doc/news/macos.rst

@@ -0,0 +1,3 @@
+**Fixed:**
+
+* Fixed tests on macOS. All tests are now automatically run for macOS 11 on GitHub's CI.

libflatsurf/environment.yml

@@ -4,7 +4,6 @@
 name: libflatsurf-build
 channels:
   - conda-forge
-  - defaults
 dependencies:
   - automake
   - benchmark

pyflatsurf/environment.yml

@@ -5,7 +5,6 @@
 name: pyflatsurf-build
 channels:
   - conda-forge
-  - defaults
 dependencies:
   - automake
   - cppyy

pyflatsurf/src/pyflatsurf/__init__.py

@@ -6,7 +6,9 @@
 
 The translation surface coming from a square::
 
-    >>> from pyflatsurf import Surface, flatsurf
+    >>> from pyflatsurf import Surface, flatsurf  # random output  # we ignore the output because cppyy produces some deprecation warnings
+    ...                                           # doctest: +ELLIPSIS
+    ...
     >>> R2 = flatsurf.Vector['long long']
     >>> square = Surface([[1, 3, 2, -1, -3, -2]], [R2(1, 0), R2(0, 1), R2(1, 1)])
 

pyflatsurf/test/Makefile.am

@@ -6,30 +6,38 @@ EXTRA_DIST = $(TESTS) surfaces.py
 
 AM_TESTS_ENVIRONMENT = . $(builddir)/test-env.sh;
 
-bound.py: test-env.sh
-half_edge.py: test-env.sh
-equivalence_class.py: test-env.sh surfaces.py
-flat_triangulation.py: test-env.sh surfaces.py
-flat_triangulation_combinatorial.py: test-env.sh surfaces.py
-point.py: test-env.sh surfaces.py
-saddle_connections.py: test-env.sh surfaces.py
-vector_renf_elem.py: test-env.sh surfaces.py
-vector_gmp.py: test-env.sh
-deformation.py: test-env.sh surfaces.py
-vertex.py: test-env.sh surfaces.py
-python-doctest.sh: test-env.sh
-sage-doctest.sh: test-env.sh
+bound.py: test-env.sh bin/python
+half_edge.py: test-env.sh bin/python
+equivalence_class.py: test-env.sh surfaces.py bin/python
+flat_triangulation.py: test-env.sh surfaces.py bin/python
+flat_triangulation_combinatorial.py: test-env.sh surfaces.py bin/python
+point.py: test-env.sh surfaces.py bin/python
+saddle_connections.py: test-env.sh surfaces.py bin/python
+vector_renf_elem.py: test-env.sh surfaces.py bin/python
+vector_gmp.py: test-env.sh bin/python
+deformation.py: test-env.sh surfaces.py bin/python
+vertex.py: test-env.sh surfaces.py bin/python
+python-doctest.sh: test-env.sh bin/python
+sage-doctest.sh: test-env.sh bin/python
 
 @VALGRIND_CHECK_RULES@
 
-BUILT_SOURCES = test-env.sh python-doctest.sh sage-doctest.sh
-EXTRA_DIST += test-env.sh.in python-doctest.sh.in sage-doctest.sh.in disable-pytest/pytest.py
-CLEANFILES = test-env.sh python-doctest.sh sage-doctest.sh
+BUILT_SOURCES = test-env.sh bin/python python-doctest.sh sage-doctest.sh
+EXTRA_DIST += test-env.sh.in bin/python.in python-doctest.sh.in sage-doctest.sh.in disable-pytest/pytest.py
+CLEANFILES = test-env.sh bin/python python-doctest.sh sage-doctest.sh
+
+$(builddir)/bin/python: $(srcdir)/bin/python.in Makefile
+	mkdir -p $(builddir)/bin
+	sed -e 's,[@]abs_srcdir[@],$(abs_srcdir),g' -e 's,[@]abs_builddir[@],$(abs_builddir),g' -e 's,[@]pythondir[@],$(pythondir),g' < $< > $@
+	chmod +x $@
+
 $(builddir)/test-env.sh: $(srcdir)/test-env.sh.in Makefile
 	sed -e 's,[@]abs_srcdir[@],$(abs_srcdir),g' -e 's,[@]abs_builddir[@],$(abs_builddir),g' -e 's,[@]pythondir[@],$(pythondir),g' < $< > $@
+
 $(builddir)/python-doctest.sh: $(srcdir)/python-doctest.sh.in Makefile
-	sed -e 's,[@]srcdir[@],$(srcdir),g' < $< > $@
+	sed -e 's,[@]abs_srcdir[@],$(abs_srcdir),g' -e 's,[@]abs_builddir[@],$(abs_builddir),g' < $< > $@
 	chmod +x $@
+
 $(builddir)/sage-doctest.sh: $(srcdir)/sage-doctest.sh.in Makefile
-	sed -e 's,[@]srcdir[@],$(srcdir),g' < $< > $@
+	sed -e 's,[@]abs_srcdir[@],$(abs_srcdir),g' -e 's,[@]abs_builddir[@],$(abs_builddir),g' < $< > $@
 	chmod +x $@

pyflatsurf/test/bin/python.in

@@ -0,0 +1,42 @@
+#!/bin/sh
+
+# Run Python 3 with environment variables set so that local headers and
+# libraries in this repository are used when running tests.
+
+# Usually, one would do this setup as part of test-env.sh, i.e.,
+# AM_TESTS_ENVIRONMENT. However, macOS drops DYLD_LIBRARY_PATH whenever a
+# shebang is followed, so we actually need to execute the Python binary
+# directly and pass a script to it as a parameter to keep DYLD_LIBRARY_PATH
+# alive.
+
+# Disable warnings on macOS with FLINT 2.8.4, see https://github.com/conda-forge/libflint-feedstock/issues/26
+export EXTRA_CLING_ARGS="-Wno-macro-redefined $EXTRA_CLING_ARGS"
+
+# Resolve #include <flatsurf/*.hpp> relative to libflatsurf in the source tree and
+# resolve #include "local.h" relative to libflatsurf/flatsurf in the build tree.
+export EXTRA_CLING_ARGS="-I@abs_srcdir@/../../libflatsurf -I@abs_builddir@/../../libflatsurf/flatsurf $EXTRA_CLING_ARGS"
+
+# Load libflatsurf.so from our build tree.
+export LD_LIBRARY_PATH="@abs_builddir@/../../libflatsurf/src/.libs/:$LD_LIBRARY_PATH"
+
+# Load libflatsurf.dylib from our build tree.
+export DYLD_LIBRARY_PATH="@abs_builddir@/../../libflatsurf/src/.libs/:$DYLD_LIBRARY_PATH"
+
+# Load pyflatsurf from our source tree.
+export PYTHONPATH="@abs_srcdir@/../src/:$PYTHONPATH:@pythondir@"
+
+# Support libasan loading when our library has been built with -fsanitize=address.
+if [ ! -z "$FLATSURF_LD_PRELOAD" ]; then
+  export LD_PRELOAD="$FLATSURF_LD_PRELOAD:$LD_PRELOAD"
+fi
+
+# Support libasan loading on macOS when our library has been built with -fsanitize=address.
+if [ ! -z "$FLATSURF_DYLD_INSERT_LIBRARIES" ]; then
+  if [ -z "$DYLD_INSERT_LIBRARIES" ]; then
+    export DYLD_INSERT_LIBRARIES="$FLATSURF_DYLD_INSERT_LIBRARIES"
+  else
+    export DYLD_INSERT_LIBRARIES="$FLATSURF_DYLD_INSERT_LIBRARIES:$DYLD_INSERT_LIBRARIES"
+  fi
+fi
+
+exec python3 $@

pyflatsurf/test/bound.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/env python
 
 ######################################################################
 # This file is part of flatsurf.

pyflatsurf/test/deformation.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/env python
 
 ######################################################################
 # This file is part of flatsurf.

pyflatsurf/test/equivalence_class.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/env python
 
 ######################################################################
 # This file is part of flatsurf.

pyflatsurf/test/flat_triangulation.py

@@ -1,4 +1,5 @@
-#!/usr/bin/env python3
+#!/usr/bin/env python
+
 ######################################################################
 # This file is part of flatsurf.
 #

pyflatsurf/test/flat_triangulation_combinatorial.py

@@ -1,4 +1,5 @@
-#!/usr/bin/env python3
+#!/usr/bin/env python
+
 ######################################################################
 # This file is part of flatsurf.
 #

pyflatsurf/test/flow_decomposition.py

@@ -1,5 +1,4 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
+#!/usr/bin/env python
 
 ######################################################################
 # This file is part of flatsurf.

pyflatsurf/test/half_edge.py

@@ -1,5 +1,4 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
+#!/usr/bin/env python
 
 ######################################################################
 # This file is part of flatsurf.

pyflatsurf/test/point.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/env python
 
 ######################################################################
 # This file is part of flatsurf.

pyflatsurf/test/python-doctest.sh.in

@@ -3,8 +3,8 @@
 ######################################################################
 #  This file is part of flatsurf.
 #
-#        Copyright (C) 2019 Vincent Delecroix
-#        Copyright (C) 2019 Julian Rüth
+#        Copyright (C)      2019 Vincent Delecroix
+#        Copyright (C) 2019-2024 Julian Rüth
 #
 #  flatsurf is free software: you can redistribute it and/or modify
 #  it under the terms of the GNU Lesser General Public License as published by
@@ -22,5 +22,10 @@
 
 set -ex
 
-TARGETS=`grep -l '>>>' @srcdir@/../src/pyflatsurf/*.py`
-pytest -vv --doctest-modules $TARGETS
+# We cannot run pytest directly since it would be invoked through its shebang
+# which makes macOS sanitize some environment variables. Instead, we go through
+# our bin/python wrapper to set the necessary environment variables and invoke
+# the Python binary to run pytest which keeps our environment intact on macOS.
+
+IGNORE=`grep -L '>>>' @abs_srcdir@/../src/pyflatsurf/*.py | awk '{ print "--ignore=" $0 }'`
+python -m pytest --verbose --doctest-modules $IGNORE '@abs_srcdir@/../src/pyflatsurf' $@

pyflatsurf/test/saddle_connections.py

@@ -1,5 +1,4 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
+#!/usr/bin/env python
 
 ######################################################################
 # This file is part of flatsurf.