Mac python wheels

.github/workflows/clang_format_check.yaml

@@ -10,6 +10,6 @@ jobs:
         - name: Fetch repository
           uses: actions/checkout@v1
         - name: Install packages
-          run: sudo apt-get install python3-venv
+          run: sudo apt-get update && sudo apt-get install python3-venv
         - name: check_clang_format
           run: ci/check_clang_format.sh

.github/workflows/coverage_test.yaml

@@ -14,7 +14,7 @@ jobs:
             - name: Get submodules
               run: git submodule update --init --force --recursive
             - name: Install packages
-              run: sudo apt-get install build-essential libhdf5-dev lcov
+              run: sudo apt-get update && sudo apt-get install build-essential libhdf5-dev lcov
             - name: Build and run unittests
               run: ci/coverage_test.sh
             - name: Upload Coverage to Coveralls

ci/python_test.sh

@@ -2,21 +2,22 @@
 
 set -euxo pipefail
 
-VENV=build/venv-python-test
+VENV=$(pwd)/build/venv-python-test/
 
 if [[ ! -d "$VENV" ]]; then
     # We use virtualenv instead of venv for python2 tests
     pip install virtualenv
     virtualenv "$VENV"
 fi
 
-set +u  # ignore errors in virtualenv's activate
-source "$VENV/bin/activate"
-set -u
+BIN=$VENV/bin/
 
-pip install --upgrade pip
+$BIN/pip -v install --upgrade pip setuptools wheel
 
 # install
-pip install .
-pip install nose
-nosetests python
+$BIN/pip -v install --force .
+$BIN/pip install nose
+
+# prevent the $REPO_ROOT/libsonata/ directory from interfering with the tests
+cd python
+$BIN/nosetests -s -v

libsonata/__init__.py

@@ -0,0 +1,19 @@
+# Needed so that mac wheels properly delocate:
+#  https://github.com/matthew-brett/delocate/issues/22
+
+from libsonata._libsonata import (EdgePopulation,
+                                  EdgeStorage,
+                                  ElementsDataFrame,
+                                  ElementsReportPopulation,
+                                  ElementsReportReader,
+                                  NodePopulation,
+                                  NodeStorage,
+                                  Selection,
+                                  SomasDataFrame,
+                                  SomasReportPopulation,
+                                  SomasReportReader,
+                                  SonataError,
+                                  SpikePopulation,
+                                  SpikeReader,
+                                  version,
+                                  )

python/CMakeLists.txt

@@ -9,7 +9,7 @@ endif()
 pybind11_add_module(sonata_python SYSTEM bindings.cpp)
 
 set_target_properties(sonata_python PROPERTIES
-    OUTPUT_NAME "libsonata"
+    OUTPUT_NAME "_libsonata"
 )
 
 target_link_libraries(sonata_python

python/bindings.cpp

@@ -360,7 +360,7 @@ void bindReportReader(py::module& m, const std::string& prefix) {
 }
 
 
-PYBIND11_MODULE(libsonata, m) {
+PYBIND11_MODULE(_libsonata, m) {
     py::class_<Selection>(m,
                           "Selection",
                           "ID sequence in the form convenient for querying attributes")

setup.py

@@ -156,7 +156,7 @@ def run(self):
     author="BlueBrain Project, EPFL",
     author_email="[email protected]",
     classifiers=[],
-    ext_modules=[CMakeExtension("libsonata")],
+    ext_modules=[CMakeExtension("libsonata._libsonata")],
     cmdclass=lazy_dict(
         build_ext=CMakeBuild,
         test_ext=CMakeBuild,
@@ -166,5 +166,8 @@ def run(self):
     zip_safe=False,
     setup_requires=setup_requires,
     install_requires=install_requires,
-    use_scm_version=True,
+    use_scm_version={"local_scheme": "no-local-version",
+                     },
+    packages=['libsonata',
+              ],
 )