Bdf2

.ci/run_ci.sh

@@ -14,41 +14,46 @@ if [ -e /etc/profile.d/boost.sh ]; then
     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"
+python3 -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
-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
+
+echo -e "[global]\nno-cache-dir = false\ndownload-cache = $CI_WORKSPACE/cache-ci/pip_cache" >$HOME/.config/pip/pip.conf  # CI_WORKSPACE or pwd?
+python3 -m pip install mako cython
+python3 -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
+python3 -m pip install "git+https://github.com/bjodah/sym@jun21#egg=sym"
+
 
 # (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 $CXXFLAGS" CXXFLAGS="$SUND_CFLAGS $CXXFLAGS" LDFLAGS=$SUND_LDFLAGS python -m pip install --no-build-isolation pycvodes
-CPLUS_INCLUDE_PATH="$BOOST_ROOT/include" python -m pip install --no-build-isolation "git+https://github.com/bjodah/pyodeint#egg=pyodeint"
-python -m pip install --no-build-isolation "git+https://github.com/bjodah/pygslodeiv2#egg=pygslodeiv2"
+git clean -xfd # -e tmp/
+
+CFLAGS="$SUND_CFLAGS $CXXFLAGS" CXXFLAGS="$SUND_CFLAGS $CXXFLAGS" LDFLAGS=$SUND_LDFLAGS python3 -m pip install --no-build-isolation "git+https://github.com/bjodah/pycvodes@may21#egg=pycvodes"
+python3 -m pip install --no-build-isolation "git+https://github.com/bjodah/pyodeint@sep21#egg=pyodeint"
+python3 -m pip install --no-build-isolation "git+https://github.com/bjodah/pygslodeiv2#egg=pygslodeiv2"
 
-python setup.py sdist
-PKG_VERSION=$(python setup.py --version)
+python3 setup.py sdist
+PKG_VERSION=$(python3 setup.py --version)
 export PYODESYS_CVODE_FLAGS=$SUND_CFLAGS
 export PYODESYS_CVODE_LDFLAGS=$SUND_LDFLAGS
-(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 $PKG_NAME
-python -m pip install -e .[all]
-python -m pytest -xv -k test_integrate_chained_robertson pyodesys/tests/test_robertson.py
+(cd dist/; python3 -m pip install "$PKG_NAME-$PKG_VERSION.tar.gz[all]"; python3 -m pytest -v -x --pyargs $PKG_NAME)
+python3 -m pip uninstall --yes $PKG_NAME
+python3 -m pip install -e .[all]
+python3 -m pytest -xv -k test_integrate_chained_robertson pyodesys/tests/test_robertson.py
 export PYTHONHASHSEED=$(python3 -c "import random; print(random.randint(1,2**32-1))")
-PYTHON="python -R" ./scripts/run_tests.sh --cov $PKG_NAME --cov-report html
+PYTHON="python3 -R" ./scripts/run_tests.sh --cov $PKG_NAME --cov-report html
 
 ( 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:
-python -m pip install virtualenv
-python -m virtualenv venv
+python3 -m pip install virtualenv
+python3 -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/; python -m pip install pytest $PKG_NAME-head.zip; python -m pytest --pyargs $PKG_NAME)
+(source ./venv/bin/activate; cd dist/; python3 -m pip install pytest $PKG_NAME-head.zip; python3 -m pytest --pyargs $PKG_NAME)

.woodpecker.yaml

@@ -26,7 +26,7 @@ steps:
     environment:
       CC: gcc-14
       CXX: g++-14
-      CXXFLAGS: -std=c++20
+      CXXFLAGS: -std=c++20 -DBOOST_UBLAS_TYPE_CHECK=0 -DNDEBUG
       OMP_NUM_THREADS: 1
       ANYODE_NUM_THREADS: 2
       CPLUS_INCLUDE_PATH: /usr/include/suitesparse:/opt-4/boost-1.91.0-release/include
@@ -48,7 +48,7 @@ steps:
     environment:
       CC: gcc-14
       CXX: g++-14
-      CXXFLAGS: -std=c++20
+      CXXFLAGS: -std=c++20 -DBOOST_UBLAS_TYPE_CHECK=0 -DNDEBUG
       OMP_NUM_THREADS: 1
       ANYODE_NUM_THREADS: 2
       CPLUS_INCLUDE_PATH: /usr/include/suitesparse:/opt-4/boost-1.91.0-release/include

CHANGES.rst

@@ -1,3 +1,7 @@
+v0.14.6
+=======
+- Bump dependencies
+
 v0.14.5
 =======
 - Update setup.yp

examples/_const_step_size.ipynb

@@ -3,9 +3,17 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%load_ext autoreload\n",
+    "%autoreload 2"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
    "outputs": [],
    "source": [
     "from itertools import product, repeat\n",
@@ -15,21 +23,19 @@
     "from pyodesys import ODESys\n",
     "from pyodesys.integrators import (RK4_example_integrator, EulerForward_example_integrator,\n",
     "                                  EulerBackward_example_integrator, Trapezoidal_example_integrator,\n",
-    "                                  Midpoint_example_integrator)\n",
+    "                                  Midpoint_example_integrator, BDF2FVC_example_integrator)\n",
     "from pyodesys.tests.bateman import bateman_full\n",
     "%matplotlib inline"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "choice = RadioButtons(\n",
-    "    options=['decay', 'sine'],\n",
+    "    options=['sine', 'decay'],\n",
     "    description='Case:',\n",
     "    disabled=False\n",
     ")\n",
@@ -39,9 +45,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "if choice.value == 'decay':\n",
@@ -69,57 +73,80 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def demo(integrator, slc=slice(None)):\n",
+    "    xout1 = np.linspace(x0, xend, n0+1)[slc]\n",
+    "    res1 = odesys.integrate(xout1, y0, p, first_step=xend/n0, integrator=integrator)\n",
+    "\n",
+    "    fig, axes = plt.subplots(1, 2, figsize=(14, 4))\n",
+    "    fig.suptitle(integrator.__name__)\n",
+    "    res1.plot(ls=('-',), ax=axes[0])\n",
+    "    axes[0].set_title(\"values\")\n",
+    "\n",
+    "    xplt = np.linspace(xout1[0], xout1[-1])\n",
+    "    yref1 = ref(res1.xout)\n",
+    "    res1.plot(x=xplt, y=ref(xplt), ls=(':',), ax=axes[0])\n",
+    "    res1.plot(y=res1.yout - yref1, ax=axes[1])\n",
+    "    axes[1].set_title(\"errors\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
    "outputs": [],
    "source": [
-    "xout1 = np.linspace(x0, xend, n0 + 1)\n",
-    "res1 = odesys.integrate(xout1, y0, p, first_step=xend/n0, integrator=EulerForward_example_integrator)\n",
-    "yref1 = ref(res1.xout)\n",
-    "fig, axes = plt.subplots(1, 2, figsize=(14, 4))\n",
-    "res1.plot(ls=('-',), ax=axes[0])\n",
-    "xplt = np.linspace(x0, xend)\n",
-    "res1.plot(x=xplt, y=ref(xplt), ls=(':',), ax=axes[0])\n",
-    "res1.plot(y=res1.yout - yref1, ax=axes[1])"
+    "demo(EulerForward_example_integrator, slc=slice(0,13))"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "demo(BDF2FVC_example_integrator, slc=slice(0,13))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
    "outputs": [],
    "source": [
     "def plot_order_of_convergence(Integrator, nruns=6):\n",
-    "    res, nruns = [], 7\n",
+    "    res = []\n",
     "    for i in range(nruns):\n",
     "        n = n0 * 2**i\n",
     "        x = np.linspace(0, 1, n)\n",
     "        res.append(odesys.integrate(x, y0, p, integrator=Integrator))\n",
     "\n",
-    "    vals = {}\n",
+    "    vals, refs = {}, {}\n",
     "    for ix, iy in product(range(n0), range(len(y0))):\n",
     "        vals[ix, iy] = [res[i].yout[ix*(2**i), iy] for i in range(nruns)]\n",
+    "        refs[ix, iy] = [ref(res[i].xout)[ix*(2**i), iy] for i in range(nruns)]\n",
     "\n",
-    "    logn = np.log(n0 * 2**np.arange(nruns))\n",
+    "    lgn = np.log10([len(r.xout) for r in res])\n",
     "    fig, axes = plt.subplots(1, len(y0), figsize=(14, 4))\n",
+    "    fig.suptitle(Integrator.__name__)\n",
     "    for iy, ax in enumerate(axes):\n",
     "        for ix in range(1, n0):\n",
-    "            lnabserr = np.log(np.abs(np.array(vals[ix, iy]) - yref1[ix, iy]))\n",
-    "            ax.plot(logn, lnabserr, '.-', c=(ix/n0, 0, 0))\n",
-    "        popt = np.polyfit(logn, lnabserr, 1)\n",
-    "        ax.plot(logn[[0,-1]], np.polyval(popt, logn[[0,-1]]), label='y=%.2f x %+.2f' % tuple(popt))\n",
-    "        ax.legend()"
+    "            lgabserr = np.log10(np.abs(np.array(vals[ix, iy]) - refs[ix, iy]))\n",
+    "            ax.plot(lgn, lgabserr, '.-', c=(ix/n0, 0, 0))\n",
+    "        popt = np.polyfit(lgn, lgabserr, 1)\n",
+    "        ax.plot(lgn[[0,-1]], np.polyval(popt, lgn[[0,-1]]), label='err_y%d(n)=%.2f x %+.2f' % ((iy,)+tuple(popt)))\n",
+    "        ax.legend()\n",
+    "        ax.set_xlabel(r'$\\lg{n_\\mathrm{t}}$')\n",
+    "        ax.set_ylabel(r'$\\lg{|e|}$')\n",
+    "        ax.set_ylim([-13, 2])"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "plot_order_of_convergence(EulerForward_example_integrator)"
@@ -128,10 +155,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": false,
-    "scrolled": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "plot_order_of_convergence(EulerBackward_example_integrator)"
@@ -140,9 +164,16 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "plot_order_of_convergence(BDF2FVC_example_integrator)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
    "outputs": [],
    "source": [
     "plot_order_of_convergence(Midpoint_example_integrator)"
@@ -151,9 +182,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "plot_order_of_convergence(Trapezoidal_example_integrator)"
@@ -162,16 +191,32 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "plot_order_of_convergence(RK4_example_integrator)"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
+  "@webio": {
+   "lastCommId": null,
+   "lastKernelId": null
+  },
   "kernelspec": {
    "display_name": "Python 3",
    "language": "python",
@@ -187,16 +232,17 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.5.2"
+   "version": "3.8.1+"
   },
+  "name": "_const_step_size.ipynb",
   "widgets": {
    "state": {
     "7d4a5a6f8d584513bb39fffa7cdc282a": {
-     "views": [
-      {
-       "cell_index": 1
-      }
-     ]
+     "views": {
+      "cell_index": [
+       1
+      ]
+     }
     }
    },
    "version": "1.2.0"