re-run cython to support Python 3.10 + misc patches from the Debian package

.travis.yml

@@ -21,22 +21,9 @@ matrix:
   fast_finish: true
   include:
 
-    - os: linux
-      python: "3.4"
-      # Tell travis we want debian trusty
-      sudo: required
-      dist: trusty
-      env:
-        - TESTATTR="'not huge and not known_failing'"
-      addons:
-        apt:
-          packages:
-            - astyle
-            - cppcheck
-            - enchant
 
     - os: linux
-      python: "3.5"
+      python: "3.6"
       # Tell travis we want debian trusty
       sudo: required
       dist: trusty
@@ -50,10 +37,9 @@ matrix:
             - enchant
 
     - os: linux
-      python: "3.6"
+      python: "3.10"
       # Tell travis we want debian trusty
       sudo: required
-      dist: trusty
       env:
         - TESTATTR="'not huge and not known_failing'"
       addons:
@@ -63,6 +49,7 @@ matrix:
             - cppcheck
             - enchant
 
+
     - os: osx
       language: generic
       osx_image: xcode7.3

MANIFEST.in

@@ -1,5 +1,5 @@
 include ChangeLog ez_setup.py IDEAS Makefile README.md setup.cfg
-include versioneer.py MANIFEST.in CITATION CONTRIBUTING.md Doxyfile.in
+include versioneer.py MANIFEST.in CITATION Doxyfile.in
 include LICENSE TODO .ycm_extra_conf.py authors.csv
 recursive-include lib *.hh *.cc [Mm]akefile* get_version.py
 recursive-include khmer *.hh

Makefile

@@ -62,7 +62,7 @@ INCLUDESTRING=$(shell gcc -E -x c++ - -v < /dev/null 2>&1 >/dev/null \
 INCLUDEOPTS=$(shell gcc -E -x c++ - -v < /dev/null 2>&1 >/dev/null \
 	    | grep '^ /' | grep -v cc1plus | awk '{print "-I" $$1 " "}')
 
-PYINCLUDE=$(shell python -c "import sysconfig; \
+PYINCLUDE=$(shell python3 -c "import sysconfig; \
             flags = ['-I' + sysconfig.get_path('include'), \
             '-I' + sysconfig.get_path('platinclude')]; print(' '.join(flags))")
 
@@ -83,8 +83,8 @@ else
 	TESTATTR ?= 'not known_failing and not jenkins and not huge and not linux'
 endif
 
-MODEXT=$(shell python -c \
-       "import sysconfig;print(sysconfig.get_config_var('SO'))")
+MODEXT=$(shell python3 -c \
+       "import sysconfig;print(sysconfig.get_config_var('EXT_SUFFIX'))")
 EXTENSION_MODULE = khmer/_khmer$(MODEXT)
 CY_MODULES = $($(wildcard khmer/_oxli/*.pyx): .pyx=.$(MODEXT))
 
@@ -147,7 +147,7 @@ clean: FORCE
 
 debug: FORCE
 	export CFLAGS="-pg -fprofile-arcs -D_GLIBCXX_DEBUG_PEDANTIC \
-		-D_GLIBCXX_DEBUG -DDEBUG_ASSEMBLY=1 -DDEBUG_FILTERS=1"; python setup.py build_ext --debug \
+		-D_GLIBCXX_DEBUG -DDEBUG_ASSEMBLY=1 -DDEBUG_FILTERS=1"; python3 setup.py build_ext --debug \
 		--inplace
 
 ## doc         : render documentation in HTML
@@ -263,7 +263,7 @@ diff-cover.html: coverage-gcovr.xml coverage.xml
 		--html-report diff-cover.html
 
 pytests.xml: FORCE
-	py.test --junitxml=$@ -m ${TESTATTR}
+	python3 -m pytest --junitxml=$@ -m ${TESTATTR}
 
 ## doxygen     : generate documentation of the C++ and Python code
 # helpful packages: doxygen graphviz
@@ -308,7 +308,7 @@ libtest: FORCE
 ## test        : run the khmer test suite
 test: FORCE
 	./setup.py develop
-	py.test -m ${TESTATTR}
+	python3 -m pytest -m ${TESTATTR}
 
 sloccount.sc: $(CPPSOURCES) $(PYSOURCES) $(wildcard tests/*.py) Makefile
 	sloccount --duplicates --wide --details include src khmer scripts tests \
@@ -324,7 +324,7 @@ coverity-build:
 		export PATH=${PATH}:${cov_analysis_dir}/bin; \
 		cov-build --dir cov-int --c-coverage gcov \
 			--disable-gcov-arg-injection make coverage-debug; \
-		cov-capture --dir cov-int --c-coverage gcov python -m pytest \
+		cov-capture --dir cov-int --c-coverage gcov python3 -m pytest \
 			-m $(TESTATTR) ; \
 		cov-import-scm --dir cov-int --scm git 2>/dev/null; \
 	else echo 'bin/cov-build does not exist in $$cov_analysis_dir: '\
@@ -377,18 +377,18 @@ list-author-emails:
 
 list-citation:
 	git log --format='%aN,%aE' | sort -u | grep -v -F -f author-skips.txt > authors.csv
-	python sort-authors-list.py
+	python3 sort-authors-list.py
 
 ## cpp-demos   : run programs demonstrating access to the (unstable) C++ API
 cpp-demos: sharedobj
 	cd examples/c++-api/ && make all run
 
 ## py-demos    : run programs demonstrating access to the Python API
 py-demos: sharedobj
-	python examples/python-api/exact-counting.py
-	python examples/python-api/bloom.py
-	python examples/python-api/consume.py examples/c++-api/reads.fastq
-	python examples/python-api/mask.py
+	python3 examples/python-api/exact-counting.py
+	python3 examples/python-api/bloom.py
+	python3 examples/python-api/consume.py examples/c++-api/reads.fastq
+	python3 examples/python-api/mask.py
 
 COMMIT ?= $(shell git rev-parse HEAD)
 SLUG ?= $(TRAVIS_PULL_REQUEST_SLUG)