Make sure anyode headers are distributed (#124)

* run tests for sdist install

* select all for tests

* move flags for compilation

* pass yes-flag to pip-uninstall

* move nogil

* bump commits

* nogil except +

* bjodahimg20dot -> triceratops-3:24

* ci: update paths and env

* exit on first failed test

* -std=c++11 -> -std=c++20

* .so -> EXT_SUFFIX in sysconfig

* avoid package from bdf2 branch

* relax test tolerances

* add appdirs to default requirements

* Bump CI image

* specify branch for AnyODE submodule

* update AnyODE

* relax maxnum steps for CI server

* Add boost to CPLUS_INCLUDE_PATH

* Relax nsteps param for test for CI server

* update CI image

* TST: max_num_test to see if CI failure is resolved

* split test

* run ci tests with 4 GiB RAM?

* handle flaky boost-odeint test

* mark flaky test xfail

* mark actual flaky test flaky

* Python 3 no longer needs to inherit from object

* Set PYTHONPATH during rendering of notebooks?

* matplotlib, kw: linthreshy -> linthresh

* Update matplotlib 3d projection code

* PYTHONPATH shenanigans

Author: bjodah

.ci/run_ci.sh

@@ -9,40 +9,46 @@ if [ ! -e "$SUNDBASE/include/sundials/sundials_config.h" ]; then
     >&2 echo "Not a valid prefix for sundials: $SUNDBASE"
     exit 1
 fi
-
+if [ -e /etc/profile.d/boost.sh ]; then
+    source /etc/profile.d/boost.sh
+    export CPATH=$BOOST_ROOT/include
+fi
+source $(compgen -G "/opt-3/cpython-v3.*-apt-deb/bin/activate")
+python -m pip install --cache-dir $CI_WORKSPACE/cache-ci/pip_cache --upgrade-strategy=eager --upgrade cython "git+https://github.com/bjodah/pycompilation@master#egg=pycompilation"
 # REPO_TEMP_DIR="$(mktemp -d)"
 # trap 'rm -rf -- "$REPO_TEMP_DIR"' EXIT
 # cp -ra . "$REPO_TEMP_DIR/."
 # cd "$REPO_TEMP_DIR"
 
 mkdir -p $HOME/.config/pip/
 echo -e "[global]\nno-cache-dir = false\ndownload-cache = $CI_WORKSPACE/cache-ci/pip_cache" >$HOME/.config/pip/pip.conf
-python3 -m pip install symcxx pysym  # unofficial backends, symengine is tested in the conda build
+python -m pip install mako cython
+python -m pip install --no-build-isolation "git+https://github.com/bjodah/symcxx#egg=symcxx" "git+https://github.com/bjodah/pysym#egg=pysym"  # unofficial backends, symengine is tested in the conda build
 
 # (cd ./tmp/pycvodes;
 SUND_CFLAGS="-isystem $SUNDBASE/include $CFLAGS"
 SUND_LDFLAGS="-Wl,--disable-new-dtags -Wl,-rpath,$SUNDBASE/lib -L$SUNDBASE/lib $LDFLAGS"
-CFLAGS=$SUND_CFLAGS LDFLAGS=$SUND_LDFLAGS python3 -m pip install pycvodes
-
+CFLAGS="$SUND_CFLAGS $CXXFLAGS" CXXFLAGS="$SUND_CFLAGS $CXXFLAGS" LDFLAGS=$SUND_LDFLAGS python -m pip install --no-build-isolation pycvodes
+CPLUS_INCLUDE_PATH="$BOOST_ROOT/include" python -m pip install --no-build-isolation "git+https://github.com/bjodah/pyodeint#egg=pyodeint"
+python -m pip install --no-build-isolation "git+https://github.com/bjodah/pygslodeiv2#egg=pygslodeiv2"
 
-python3 setup.py sdist
-PKG_VERSION=$(python3 setup.py --version)
+python setup.py sdist
+PKG_VERSION=$(python setup.py --version)
 export PYODESYS_CVODE_FLAGS=$SUND_CFLAGS
 export PYODESYS_CVODE_LDFLAGS=$SUND_LDFLAGS
-(cd dist/; python3 -m pip install "$PKG_NAME-$PKG_VERSION.tar.gz[all]"; python3 -m pytest --pyargs $PKG_NAME)
-python3 -m pip uninstall --yes $PKG_NAME
-python3 -m pip install -e .[all]
-python3 -m pytest -xv -k test_integrate_chained_robertson pyodesys/tests/test_robertson.py
+(cd dist/; python -m pip install "$PKG_NAME-$PKG_VERSION.tar.gz[all]"; python -m pytest -v -x --pyargs $PKG_NAME)
+python -m pip uninstall --yes $PKG_NAME
+python -m pip install -e .[all]
+python -m pytest -xv -k test_integrate_chained_robertson pyodesys/tests/test_robertson.py
 export PYTHONHASHSEED=$(python3 -c "import random; print(random.randint(1,2**32-1))")
-PYTHON="python3 -R" ./scripts/run_tests.sh --cov $PKG_NAME --cov-report html
+PYTHON="python -R" ./scripts/run_tests.sh --cov $PKG_NAME --cov-report html
 
-./scripts/render_notebooks.sh
-(cd $PKG_NAME/tests; jupyter nbconvert --log-level=INFO --to=html --ExecutePreprocessor.enabled=True --ExecutePreprocessor.timeout=600 *.ipynb)
+( export PYTHONPATH=$(pwd); ./scripts/render_notebooks.sh; cd $PKG_NAME/tests; jupyter nbconvert --log-level=INFO --to=html --ExecutePreprocessor.enabled=True --ExecutePreprocessor.timeout=600 *.ipynb )
 ./scripts/generate_docs.sh
 
 # Test package without any 3rd party libraries that are in extras_require:
-python3 -m pip install virtualenv
-python3 -m virtualenv venv
+python -m pip install virtualenv
+python -m virtualenv venv
 git archive -o dist/$PKG_NAME-head.zip HEAD  # test pip installable zip (symlinks break)
 set +u
-(source ./venv/bin/activate; cd dist/; python3 -m pip install pytest $PKG_NAME-head.zip; python3 -m pytest --pyargs $PKG_NAME)
+(source ./venv/bin/activate; cd dist/; python -m pip install pytest $PKG_NAME-head.zip; python -m pytest --pyargs $PKG_NAME)

.gitmodules

@@ -1,3 +1,4 @@
 [submodule "external/anyode"]
 	path = external/anyode
 	url = https://github.com/bjodah/anyode
+        branch = master

.woodpecker.yaml

@@ -1,76 +1,79 @@
+variables:
+  - &ci_image 'cont-reg.bjodah.se:443/bjodah/triceratops-4:25'
+
 when:
   - event: [push]
 
 steps:
 
   - name: restore-cache
-    image: bjodah/bjodahimg20dot:21.8.a
+    image: *ci_image
     commands:
       - curl ftp://${CI_REPO_NAME}:$${ARTIFACTS_PASS}@$${FTP_SERVER}/cache/cache-ci.tar | tar -C / x || mkdir -p $CI_WORKSPACE/cache-ci/pip_cache
     secrets: [ ARTIFACTS_PASS, FTP_SERVER ]
     when:
      - event: push
        repo: bjodah/pyodesys
 
-  - name: test-sund-5.7.0-rel
+  - name: test-sund-6.7.0-rel
     depends_on: restore-cache
-    image: bjodah/bjodahimg20dot:21.8.a
+    image: *ci_image
     environment:
-      - CC=gcc-11
-      - CXX=g++-11
+      - CC=gcc-14
+      - CXX=g++-14
+      - CXXFLAGS=-std=c++20
       - OMP_NUM_THREADS=1
       - ANYODE_NUM_THREADS=2
-      - CPLUS_INCLUDE_PATH=/usr/include/suitesparse:/opt/boost-1.77.0/include
+      - CPLUS_INCLUDE_PATH=/usr/include/suitesparse:/opt-3/boost-1.88.0/include
       - LIBRARY_PATH=/usr/lib/x86_64-linux-gnu
       - LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu
-      - SUNDBASE=/opt/sundials-5.7.0-release
+      - SUNDBASE=/opt-3/sundials-6.7.0-release
     commands:
-      - cp -ra $CI_WORKSPACE /tmp/test-sund-5.7.0-rel
-      - cd /tmp/test-sund-5.7.0-rel
-      - python3 -m pip install --cache-dir $CI_WORKSPACE/cache-ci/pip_cache --upgrade-strategy=eager --upgrade cython https://github.com/bjodah/pycompilation/archive/master.tar.gz
-      - bash -c "ulimit -v 2048000; .ci/run_ci.sh pyodesys $SUNDBASE"
+      - cp -ra $CI_WORKSPACE /tmp/test-sund-6.7.0-rel
+      - cd /tmp/test-sund-6.7.0-rel
+      - bash -lc "ulimit -v 2048000; .ci/run_ci.sh pyodesys $SUNDBASE"
       - ./scripts/prepare_deploy.sh
       - bash -c '[[ $(python3 setup.py --version) =~ ^[0-9]+.* ]]'
-      - cp -ra /tmp/test-sund-5.7.0-rel/deploy $CI_WORKSPACE/
+      - cp -ra /tmp/test-sund-6.7.0-rel/deploy $CI_WORKSPACE/
 
-  - name: test-sund-5.7.0-extended
+  - name: test-sund-6.7.0-extended
     depends_on: restore-cache
-    image: bjodah/bjodahimg20dot:21.8.a
+    image: *ci_image
     environment:
-      - CC=gcc-11
-      - CXX=g++-11
+      - CC=gcc-14
+      - CXX=g++-14
+      - CXXFLAGS=-std=c++20
       - OMP_NUM_THREADS=1
       - ANYODE_NUM_THREADS=2
-      - CPLUS_INCLUDE_PATH=/usr/include/suitesparse:/opt/boost-1.77.0/include
+      - CPLUS_INCLUDE_PATH=/usr/include/suitesparse:/opt-3/boost-1.88.0/include
       - LIBRARY_PATH=/usr/lib/x86_64-linux-gnu
       - LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu
-      - SUNDBASE=/opt/sundials-5.7.0-extended
+      - SUNDBASE=/opt-3/sundials-6.7.0-extended
       - PYCVODES_NO_LAPACK=1
       - PYCVODES_NO_KLU=1
     commands:
-      - cp -ra $CI_WORKSPACE/ /tmp/test-sund-5.7.0-extended
-      - cd /tmp/test-sund-5.7.0-extended
-      - python3 -m pip install --cache-dir $CI_WORKSPACE/cache-ci/pip_cache --upgrade-strategy=eager --upgrade cython
-      - bash -c "ulimit -v 2048000; .ci/run_ci.sh pyodesys $SUNDBASE"
+      - cp -ra $CI_WORKSPACE/ /tmp/test-sund-6.7.0-extended
+      - cd /tmp/test-sund-6.7.0-extended
+      - bash -lc "ulimit -v 4096000; .ci/run_ci.sh pyodesys $SUNDBASE"
       - ./scripts/grep-for-merge-blocking-token.sh
       - ./scripts/grep-for-binary-data.sh
 
   - name: rebuild-cache
-    image: bjodah/bjodahimg20dot:21.8.a
+    image: *ci_image
     commands:
       - find $CI_WORKSPACE/cache-ci/ -type f -mtime +90 -exec rm {} \;
       - tar cf cache-ci.tar $CI_WORKSPACE/cache-ci/
       - curl -T cache-ci.tar ftp://${CI_REPO_NAME}:$${ARTIFACTS_PASS}@$${FTP_SERVER}/cache/
     secrets: [ ARTIFACTS_PASS, FTP_SERVER ]
     depends_on:
-      - test-sund-5.7.0-rel
+      - test-sund-6.7.0-rel
 
   - name: deploy-public-html
-    image: bjodah/bjodahimg20dot:21.8.a
+    image: *ci_image
     commands:
       - tar -C deploy/public_html -czf ${CI_REPO_NAME}-${CI_COMMIT_BRANCH}.tar.gz .
       - curl -T ${CI_REPO_NAME}-${CI_COMMIT_BRANCH}.tar.gz ftp://${CI_REPO_NAME}:$${ARTIFACTS_PASS}@$${FTP_SERVER}/public_html/
     secrets: [ ARTIFACTS_PASS, FTP_SERVER ]
     depends_on:
-      - test-sund-5.7.0-rel
+      - test-sund-6.7.0-rel
 

examples/_native_override_chemical_kinetics.ipynb

@@ -58,7 +58,7 @@
     "            axes[0].axvline(result.xout[-1], linestyle='--', label='t = %.4f' % result.xout[-1])\n",
     "        result.plot(ax=axes[0])\n",
     "        result.plot(ax=axes[1], deriv=True)\n",
-    "        axes[1].set_yscale('symlog', linthreshy=1e-9)\n",
+    "        axes[1].set_yscale('symlog', linthresh=1e-9)\n",
     "        axes[1].axhline(1e-9, linestyle='--')\n",
     "        axes[1].axhline(-1e-9, linestyle='--')\n",
     "        for ax in axes:\n",

examples/_nonlinear_3body_system.ipynb

@@ -99,7 +99,7 @@
    "outputs": [],
    "source": [
     "fig1 = plt.figure()\n",
-    "ax = fig1.gca(projection='3d')\n",
+    "ax = fig1.add_subplot(projection='3d')\n",
     "ax.plot(*res.yout[:, 0:3].T, alpha=1.0, color='r')\n",
     "ax.plot(*res.yout[:, 3:6].T, alpha=1.0, color='g')\n",
     "ax.plot(*res.yout[:, 6:9].T, alpha=1.0, color='b')"

examples/_radiolysis.ipynb

@@ -51,7 +51,7 @@
     "    plot_kw = dict(legend=dict(loc='center left', prop={'size': 8}), xscale='log')\n",
     "    for r, axcol in zip(res, axes.T):\n",
     "        r.plot(ax=axcol[0], yscale='log', title_info=2, **plot_kw)\n",
-    "        r.plot(ax=axcol[1], deriv=True, yscale='symlog;linthreshy=1e-9', **plot_kw)\n",
+    "        r.plot(ax=axcol[1], deriv=True, yscale='symlog;linthresh=1e-9', **plot_kw)\n",
     "        r.plot_invariant_violations(ax=axcol[2], **plot_kw)\n",
     "        for ax in axcol:\n",
     "            ax.set_xlim([1e-13, 1e-3])\n",

examples/lorenz.ipynb

@@ -84,7 +84,7 @@
     "    xout, yout, info = odesystem.integrate(\n",
     "        10, y0, dict(sigma=sigma, rho=rho, beta=beta),\n",
     "        integrator='cvode', nsteps=5000)\n",
-    "    ax = fig.gca(projection='3d')\n",
+    "    ax = fig.add_subplot(projection='3d')\n",
     "    for lines in stack:\n",
     "        lines[0].set_alpha(0.6*lines[0].get_alpha())\n",
     "    stack.append(ax.plot(*yout.T, alpha=1.0, color='g'))\n",

external/anyode

@@ -25,7 +25,7 @@ class RecoverableError(Exception):
     pass
 
 
-class ODESys(object):
+class ODESys:
     """ Object representing an ODE system.
 
     ``ODESys`` provides unified interface to:

pyodesys/core.py

@@ -8,6 +8,7 @@
 import os
 import shutil
 import sys
+import sysconfig
 import tempfile
 
 import numpy as np
@@ -39,13 +40,13 @@
 
 _compile_kwargs = {
     'options': ['warn', 'pic', 'fast', 'openmp'],
-    'std': 'c++11',
+    'std': 'c++20',
     'include_dirs': [np.get_include(), pkg_resources.resource_filename(__name__, 'sources')],
     'libraries': [],
     'cplus': True,
 }
 
-_ext_suffix = '.so'  # sysconfig.get_config_var('EXT_SUFFIX')
+_ext_suffix = sysconfig.get_config_var('EXT_SUFFIX')
 _obj_suffix = '.o'  # os.path.splitext(_ext_suffix)[0] + '.o'  # '.obj'
 
 
@@ -90,7 +91,7 @@ def __init__(self, odesys, *args, **kwargs):
         self.namespace_extend = kwargs.pop('namespace_extend', {})
         self.tempdir_basename = '_pycodeexport_pyodesys_%s' % self.__class__.__name__
         self.obj_files = self.obj_files + ('%s%s' % (self.wrapper_name, _obj_suffix),)
-        self.so_file = '%s%s' % (self.wrapper_name, '.so')
+        self.so_file = '%s%s' % (self.wrapper_name, _ext_suffix)
         _wrapper_src = pkg_resources.resource_filename(
             __name__, 'sources/%s.pyx' % self.wrapper_name)
         if cachedir is None: