Merge pull request #98 from pauldmccarthy/mnt/no-compile-numpy

Mnt/no compile numpy

.ci/build_wheels.sh

@@ -2,10 +2,6 @@
 
 set -e
 
-# Make sure cython is available on all platforms
-# Numpy is required to build the test modules
-export CIBW_BEFORE_BUILD="pip install cython numpy"
-
 # Make sure zlib headers are available on linux
 export CIBW_BEFORE_ALL_LINUX="yum install -y zlib-devel || apt-get install -y zlib1g-dev || apk add zlib-dev || true"
 
@@ -16,15 +12,26 @@ export CIBW_ENVIRONMENT_WINDOWS="ZLIB_HOME='$ZLIB_HOME'"
 # Run quick test suite on built wheels.
 export CIBW_TEST_REQUIRES="cython pytest numpy nibabel"
 
-# Disable pypy builds
-export CIBW_SKIP="pp*"
+# Disable pypy builds (reasons for doing this have been lost to
+# history [GHA logs of failing builds deleted]).
+#
+# Disable musllinux builds until numpy binaries are available (as
+# compiling numpy takes too long, and causes GHA jobs to time out).
+export CIBW_SKIP="pp* *musllinux*"
+
+# Skip i686/aarch64 tests - I have experienced hangs on these
+# platforms, which I traced to a trivial numpy operation -
+# "numpy.linalg.det(numpy.eye(3))". This occurs when numpy has
+# to be compiled from source during the build, so can be
+# re-visited if/when numpy is avaialble on all platforms.
+export CIBW_TEST_SKIP="*i686* *aarch64*"
 
 # Pytest makes it *very* awkward to run tests
 # from an installed package, and still find/
 # interpret a conftest.py file correctly.
-echo '#!/usr/bin/env bash'                                          >  testcmd
-echo 'cp $1/setup.cfg .'                                            >> testcmd
-echo 'python -m indexed_gzip.tests -c setup.cfg -m "not slow_test"' >> testcmd
+echo '#!/usr/bin/env bash'                                               >  testcmd
+echo 'cp $1/pyproject.toml .'                                            >> testcmd
+echo 'python -m indexed_gzip.tests -c pyproject.toml -m "not slow_test"' >> testcmd
 chmod a+x testcmd
 
 export CIBW_TEST_COMMAND="bash {project}/testcmd {project}"
@@ -34,7 +41,6 @@ export CIBW_TEST_COMMAND="bash {project}/testcmd {project}"
 python -m pip install cibuildwheel
 python -m cibuildwheel --output-dir ./dist
 
-
 # Disable py27 builds on windows
 export CIBW_BUILD="cp27-mac* cp27-*linux*"
 python -m pip install cibuildwheel==1.*

CHANGELOG.md

@@ -1,12 +1,12 @@
 # `indexed_gzip` changelog
 
 
-## 1.6.11 (April 13th 2022)
+## 1.6.12 (April 14th 2022)
 
 
 * Changed the default read buffer size used by the `IndexedGzipFile` class
   (#90).
-* Update to wheel building procedure (#92,#93,#95,#96,#97).
+* Update to wheel building procedure (#92,#93,#95,#96,#97,#98).
 * Aded `pyproject.toml` to declare build-time requirements (#94).
 
 

indexed_gzip/__init__.py

@@ -19,4 +19,4 @@
 """
 
 
-__version__ = '1.6.11'
+__version__ = '1.6.12'

pyproject.toml

@@ -1,2 +1,14 @@
 [build-system]
 requires = ["setuptools >= 40.8.0", "wheel", "cython", "numpy"]
+
+[tool.pytest.ini_options]
+testpaths = [
+    "indexed_gzip/tests"
+]
+addopts = "-v"
+markers = [
+    "zran_test:         Test the zran.c library",
+    "indexed_gzip_test: Test the indexed_gzip library",
+    "nibabel_test:      Test interaction between indexed_gzip and nibabel/numpy",
+    "slow_test:         Test which takes a long time"
+]