Add pypy to test matrix (#142)

* Add pypy to test matrix
* catch -> doctest
* tweak CI setup

.ci/run-matrix.sh

@@ -4,6 +4,7 @@ export PATH=/opt-2/gcc-13/bin:$PATH
 export CC=gcc
 export CXX=g++
 #                                     .ci/test-case.sh --asan --python /opt-3/cpython-v3.11.9-asan/bin/python3 /opt-3/sundials-6.7.0-asan
+                                       .ci/test-case.sh        --python /opt-3/pypy3.10-v7.3.15-linux64/bin/python3 /opt-3/sundials-6.7.0-debug
                                        .ci/test-case.sh        --python /opt-3/cpython-v3.11.?-debug/bin/python3 /opt-3/sundials-6.7.0-debug
                                        .ci/test-case.sh        --python /opt-3/cpython-v3.12.2-debug/bin/python3 /opt-3/sundials-6.7.0-debug
 PYCVODES_NO_LAPACK=1 PYCVODES_NO_KLU=1 .ci/test-case.sh        --python /opt-3/cpython-v3.11-apt-deb/bin/python3 /opt-3/sundials-6.7.0-extended

.ci/test-case.sh

@@ -5,8 +5,10 @@ show_help() {
     echo "--native"
     echo "--python <python-exe-path>"
 }
+
 NATIVE=0
 TEST_ASAN=0
+MAKE_TMP_DIR=0
 while [ $# -gt 1 ]; do
     case $1 in
         --native)
@@ -22,12 +24,21 @@ while [ $# -gt 1 ]; do
             TEST_ASAN=1
             shift
             ;;
+        --tmp)
+            MAKE_TMP_DIR=1
+            shift
+            ;;
         *)
             >&2 echo "Unrecognized parameter: $1"
             exit 1
     esac
 done
-
+if [ "$MAKE_TMP_DIR" = 1 ]; then
+    REPO_TMP_DIR=$(mktemp -d)
+    trap 'rm -rf -- "$REPO_TMP_DIR"' EXIT
+    cp -ra . "$REPO_TMP_DIR/."
+    cd "$REPO_TMP_DIR"
+fi
 SUNDBASE=$1
 if [ ! -d "$SUNDBASE/include/sundials" ]; then >&2 echo "No such directory: $SUNDBASE"; exit 1; fi
 if [[ $SUNDBASE =~ *-extended || $SUNDBASE =~ *-single ]]; then
@@ -40,6 +51,7 @@ export LDFLAGS="$LINKLIBS -Wl,--disable-new-dtags -Wl,-rpath,$SUNDBASE/lib -L$SU
 export LD_LIBRARY_PATH=$(compgen -G "/opt-2/llvm-*/lib")
 
 if [ $TEST_ASAN -eq 1 ]; then
+    export CC=clang
     export CXX=clang++
     LIBCXX_ASAN_ROOT=$(compgen -G "/opt-2/libcxx*-asan")
     LIBCXX_ASAN_INCLUDE=${LIBCXX_ASAN_ROOT}/include/c++/v1
@@ -53,7 +65,7 @@ if [ $TEST_ASAN -eq 1 ]; then
     # LD_PRELOAD=$(clang++ --print-file-name=libclang_rt.asan.so)
     export PYTHON="env ASAN_OPTIONS=abort_on_error=1,detect_leaks=0 ${PYTHON:-python3}"
 else
-    export PATH=/opt-2/gcc-13/bin:$PATH
+    export CC=gcc
     export CXX=g++
     if $CXX --version | head -n 1 | grep -E 'g++\.*13\.[0-9]\.[0-9]$'; then exit 1; fi
     export CXXFLAGS="$CXXFLAGS -D_GLIBCXX_DEBUG -D_GLIBCXX_PEDANTIC"

.ci/test-sdist.sh

@@ -11,9 +11,14 @@ env \
     CFLAGS="-isystem $SUNDBASE/include -isystem /usr/include/suitesparse" \
     LDFLAGS="-Wl,--disable-new-dtags -Wl,-rpath,$SUNDBASE/lib -L$SUNDBASE/lib" \
     CC=gcc CXX=g++ pip install ${CI_REPO_NAME}-*.tar.gz
-pip install pytest-flakes pytest-cov matplotlib sphinx numpydoc sphinx-rtd-theme
-../scripts/run_tests.sh --cov ${CI_REPO_NAME} --cov-report html
-../scripts/coverage_badge.py htmlcov/ htmlcov/coverage.svg
-
+python3 -m pytest --pyargs pycvodes
 cd -
-source ./scripts/generate_docs.sh
+env \
+    CFLAGS="-isystem $SUNDBASE/include -isystem /usr/include/suitesparse" \
+    LDFLAGS="-Wl,--disable-new-dtags -Wl,-rpath,$SUNDBASE/lib -L$SUNDBASE/lib" \
+    CC=gcc CXX=g++ python3 setup.py build_ext -i
+
+pip install pytest-flakes pytest-cov matplotlib sphinx numpydoc sphinx-rtd-theme
+./scripts/run_tests.sh --cov ${CI_REPO_NAME} --cov-report html
+./scripts/coverage_badge.py htmlcov/ htmlcov/coverage.svg
+./scripts/generate_docs.sh

.woodpecker.yaml

@@ -1,30 +1,64 @@
 when:
-  - event: [pull_request, tag, cron, push]
+  - event: [push]  # pull_request, tag, cron, 
 
 steps:
-  - name: build-and-test-asan
-    image: cont-reg.bjodah.se:443/bjodah/triceratops-3:14
+  - name: pypy
+    image: cont-reg.bjodah.se:443/bjodah/triceratops-3:16
+    commands:
+      - .ci/test-case.sh --tmp --python /opt-3/pypy3.10-v7.3.15-linux64/bin/python3 /opt-3/sundials-6.7.0-debug
+
+  - name: py3.11-dbg
+    image: cont-reg.bjodah.se:443/bjodah/triceratops-3:16
+    commands:
+      - .ci/test-case.sh --tmp --python /opt-3/cpython-v3.11.?-debug/bin/python3 /opt-3/sundials-6.7.0-debug
+
+  - name: py3.12-dbg
+    image: cont-reg.bjodah.se:443/bjodah/triceratops-3:16
+    commands:
+      - .ci/test-case.sh --tmp --python /opt-3/cpython-v3.12.2-debug/bin/python3 /opt-3/sundials-6.7.0-debug
+
+  - name: py3.11-extended
+    image: cont-reg.bjodah.se:443/bjodah/triceratops-3:16
+    environment:
+      - PYCVODES_NO_LAPACK=1
+      - PYCVODES_NO_KLU=1
+    commands:
+      - .ci/test-case.sh --tmp --python /opt-3/cpython-v3.11-apt-deb/bin/python3 /opt-3/sundials-6.7.0-extended
+
+  - name: py3.12-single
+    image: cont-reg.bjodah.se:443/bjodah/triceratops-3:16
+    environment:
+      - PYCVODES_NO_LAPACK=1
+      - PYCVODES_NO_KLU=1
+    commands:
+      - .ci/test-case.sh --tmp --python /opt-3/cpython-v3.12.2-release/bin/python3 /opt-3/sundials-6.7.0-single
+
+  - name: sdist-and-docs
+    image: cont-reg.bjodah.se:443/bjodah/triceratops-3:16
     environment:
       - PYCVODES_STRICT=1
       - LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu
-      - LLVM_ROOT=/opt-2/llvm-18
     commands:
       #- git fetch -tq
       # - bash -c '[[ $(python3 setup.py --version 2>/dev/null) =~ ^[0-9]+.* ]]'
-      - .ci/run-matrix.sh
       - .ci/test-sdist.sh
       - ./scripts/prepare_deploy.sh
-      - if grep "DO-NOT-MERGE!" -R . --exclude ".woodpecker.yml"; then exit 1; fi
-
+      - if grep "DO-NOT-MERGE!" -R . --exclude ".woodpecker.yaml"; then exit 1; fi
+    depends_on:
+      - pypy
+      - py3.11-dbg
+      - py3.12-dbg
+      - py3.11-extended
+      - py3.12-single
 
   - name: deploy-public-html
-    image: cont-reg.bjodah.se:443/bjodah/triceratops-3:14
+    image: cont-reg.bjodah.se:443/bjodah/triceratops-3:16
     commands:
-      - tar -C ./deploy/public_html czf pycovdes-${CI_COMMIT_BRANCH}.tar.gz .
-      - curl -T pycovdes-${CI_COMMIT_BRANCH}.tar.gz ftp://pycovdes:$${ARTIFACTS_PASS}@$${FTP_SERVER}/public_html/
+      - tar -C ./deploy/public_html -czf pycvodes-${CI_COMMIT_BRANCH}.tar.gz .
+      - curl -T pycvodes-${CI_COMMIT_BRANCH}.tar.gz ftp://pycvodes:$${ARTIFACTS_PASS}@$${FTP_SERVER}/public_html/
     secrets: [ ARTIFACTS_PASS, FTP_SERVER ]
     when:
      - event: push
-       repo: github.com/bjodah/pycovdes
+       repo: bjodah/pycvodes
     depends_on:
-      - build-and-test
+      - sdist-and-docs

pycvodes/include/sundials_cxx.hpp

@@ -1,7 +1,10 @@
 #pragma once
-#include <cstring> // std::memcpy
 #include <nvector/nvector_serial.h>  /* serial N_Vector types, fcts., macros */
 #include <sundials/sundials_config.h>
+#include <stdexcept>
+#include <cstring> // std::memcpy
+#include <vector>
+
 namespace sundials_cxx {
 #if SUNDIALS_VERSION_MAJOR >= 3
     const int version_major = SUNDIALS_VERSION_MAJOR;

pycvodes/tests/test_cvodes_numpy.py

@@ -13,6 +13,15 @@
 )
 
 
+def _get_refcount_None():
+    if hasattr(sys, 'getrefcount'):
+        gc.collect()
+        gc.collect()
+        return sys.getrefcount(None)
+    else:  # e.g. pypy
+        return 0
+
+
 def test_config_env():
     # This test is useful for e.g. out-of-tree conda-recipes (e.g. conda-forge) where variables
     # are set manually (and could otherwise be forgotten unless tests fail).
@@ -822,10 +831,7 @@ def j(t, y, Jmat, dfdt=None, fy=None):
         k = 0
         for jiter in range(nIter):
             if jiter == 1:
-                gc.collect()
-                gc.collect()
-                nNone1 = sys.getrefcount(None)
-
+                nNone1 = _get_refcount_None()
             t0 = k
             tend = k + 1 # so let the step to be 1 second
             k+=1
@@ -840,5 +846,5 @@ def j(t, y, Jmat, dfdt=None, fy=None):
             y_prev2 = yout.T[1][-1]
         gc.collect()
         gc.collect()
-        nNone2 = sys.getrefcount(None)
-        assert -10 < nNone1 - nNone2 < 10
+        nNone2 = _get_refcount_None()
+        assert -nIter//10 < nNone1 - nNone2 < nIter//10

tests/.gitignore

@@ -1,4 +1,5 @@
-catch.hpp
+doctest.h
+doctest.o
 test_cvodes_anyode
 test_cvodes_cxx
 test_sundials_cxx
@@ -8,6 +9,5 @@ test_cvodes_anyode_autorestart
 test_cvodes_anyode_svd
 test_tough_case
 test_cvodes_anyode_quad
-catch.o
 test_cvodes_anyode_jtimes
 test_cvodes_anyode_sparse

tests/Makefile

@@ -50,22 +50,22 @@ else
 endif
 
 clean:
-	$(RM) catch.o
+	$(RM) doctest.o
 	$(RM) $(TARGETS)
 	if [ -f test_cvodes_anyode_parallel ] ; then rm test_cvodes_anyode_parallel ; fi;
 
-test_%: test_%.cpp ../pycvodes/include/cvodes_cxx.hpp catch.o
-	$(CXX) $(CXXFLAGS) $(INCLUDE) $(DEFINES) -o $@ $< catch.o $(LDFLAGS)
+test_%: test_%.cpp ../pycvodes/include/cvodes_cxx.hpp doctest.o
+	$(CXX) $(CXXFLAGS) $(INCLUDE) $(DEFINES) -o $@ $< doctest.o $(LDFLAGS)
 
-test_cvodes_anyode_parallel: test_cvodes_anyode_parallel.cpp ../pycvodes/include/cvodes_*.hpp catch.o
+test_cvodes_anyode_parallel: test_cvodes_anyode_parallel.cpp ../pycvodes/include/cvodes_*.hpp doctest.o
 ifeq ($(CXX),clang++-6.0)
 	@echo "skipping openmp when using clang"
 else
-	$(CXX) $(CXXFLAGS) $(OPENMP_FLAG) $(INCLUDE) $(DEFINES) -o $@ $< catch.o $(LDFLAGS) $(OPENMP_LIB)
+	$(CXX) $(CXXFLAGS) $(OPENMP_FLAG) $(INCLUDE) $(DEFINES) -o $@ $< doctest.o $(LDFLAGS) $(OPENMP_LIB)
 endif
 
-catch.hpp: catch.hpp.bz2
+doctest.h: doctest.h.bz2
 	bzcat $< >$@
 
-catch.o: catch.cpp catch.hpp
+doctest.o: doctest.cpp doctest.h
 

tests/doctest.cpp

@@ -0,0 +1,2 @@
+#define DOCTEST_CONFIG_IMPLEMENT_WITH_MAIN
+#include "doctest.h"

tests/doctest.h.url

@@ -0,0 +1 @@
+https://github.com/doctest/doctest/releases/download/v2.4.11/doctest.h

tests/test_cvodes_anyode.cpp

@@ -1,9 +1,9 @@
 // C++11 source code.
-#include "catch.hpp"
+#include "doctest.h"
 #include "cvodes_anyode.hpp"
 #include "testing_utils.hpp"
 
-TEST_CASE( "decay_adaptive", "[simple_adaptive]" ) {
+TEST_CASE( "decay_adaptive" ) {
     Decay odesys(1.0);
     std::vector<int> root_indices;
     int td = 1;
@@ -24,7 +24,7 @@ TEST_CASE( "decay_adaptive", "[simple_adaptive]" ) {
     free(xyout);
 }
 
-TEST_CASE( "decay_adaptive_ew_ele", "[simple_adaptive]" ) {
+TEST_CASE( "decay_adaptive_ew_ele" ) {
     Decay odesys(1.0);
     std::vector<int> root_indices;
     int td = 1;
@@ -65,7 +65,7 @@ TEST_CASE( "decay_adaptive_ew_ele", "[simple_adaptive]" ) {
     free(ew_ele);
 }
 
-TEST_CASE( "decay_predefined_ew_ele", "[simple_predefined]" ) {
+TEST_CASE( "decay_predefined_ew_ele" ) {
     Decay odesys(1.0);
     int nt = 37;
     realtype t0=0, tend=4.0;
@@ -108,7 +108,7 @@ TEST_CASE( "decay_predefined_ew_ele", "[simple_predefined]" ) {
     REQUIRE( odesys.current_info.nfo_int["n_steps"] < 997 );
 }
 
-TEST_CASE( "decay_adaptive_get_dx_max", "[simple_adaptive]" ) {
+TEST_CASE( "decay_adaptive_get_dx_max" ) {
     Decay odesys(1.0);
     realtype y0 = 1.0;
     std::vector<int> root_indices;
@@ -130,7 +130,7 @@ TEST_CASE( "decay_adaptive_get_dx_max", "[simple_adaptive]" ) {
 }
 
 
-TEST_CASE( "decay_adaptive_dx_max", "[simple_adaptive]" ) {
+TEST_CASE( "decay_adaptive_dx_max" ) {
     Decay odesys(1.0);
     realtype y0 = 1.0;
     std::vector<int> root_indices;

tests/test_cvodes_anyode_autorestart.cpp

@@ -1,4 +1,4 @@
-#include "catch.hpp"
+#include "doctest.h"
 #include <math.h>
 #include <vector>
 #include "anyode/anyode.hpp"
@@ -7,7 +7,7 @@
 #include "cetsa_case.hpp"
 
 
-TEST_CASE( "adaptive_autorestart", "[simple_adaptive]" ) {
+TEST_CASE( "adaptive_autorestart" ) {
     std::vector<realtype> p = {{298.15, 39390, -135.3, 18010, 44960, 48.2, 65919.5, -93.8304, 1780, 3790, 57.44, 19700, -157.4}};
     OdeSys odesys(&p[0]);
     int td = 1;

tests/test_cvodes_anyode_jtimes.cpp

@@ -1,11 +1,11 @@
-#include "catch.hpp"
+#include "doctest.h"
 #include <math.h>
 #include <vector>
 #include "anyode/anyode.hpp"
 #include "cvodes_anyode.hpp"
 #include "cetsa_case_iterative.hpp"
 
-TEST_CASE( "adaptive_tricky_svd_no_jac_no_prec", "[simple_adaptive]" ) {
+TEST_CASE( "adaptive_tricky_svd_no_jac_no_prec" ) {
     std::vector<realtype> p = {{321.14999999999998, 39390, -135.30000000000001, 18010, 44960, 48.200000000000003,
                               49320, -114.59999999999999, 1780, -34400.547966379738, -2.865040967667511,
                               93065.338440593958, 5.7581184659305222}};

tests/test_cvodes_anyode_parallel.cpp

@@ -1,9 +1,9 @@
 // C++11 source code.
-#include "catch.hpp"
+#include "doctest.h"
 #include "cvodes_anyode_parallel.hpp"
 #include "testing_utils.hpp"
 
-TEST_CASE( "decay_adaptive", "[multi_adaptive]" ) {
+TEST_CASE( "decay_adaptive" ) {
     std::vector<realtype> k {{ 2.0, 3.0}};
     Decay odesys1(k[0]);
     Decay odesys2(k[1]);
@@ -44,7 +44,7 @@ TEST_CASE( "decay_adaptive", "[multi_adaptive]" ) {
     free(xyout_arr);
 }
 
-TEST_CASE( "decay_predefined", "[multi_predefined]" ) {
+TEST_CASE( "decay_predefined" ) {
     std::vector<realtype> k {{ 2.0, 3.0}};
     Decay odesys1(k[0]);
     Decay odesys2(k[1]);