Merge pull request #48 from PaulSt/pip

work on new pip install

.github/workflows/Dockerfile

@@ -2,24 +2,16 @@ FROM ubuntu:latest
 
 WORKDIR /home/app
 
-RUN apt-get update && DEBIAN_FRONTEND="noninteractive" apt-get -y install vim python3 python3-pip python3-distutils python3-tk libpython3-dev libxmu-dev tk-dev tcl-dev cmake git g++ libglu1-mesa-dev libblas-dev liblapack-dev
+RUN apt-get update && DEBIAN_FRONTEND="noninteractive" apt-get -y install vim python3 python3-pip python3-distutils git #python3-tk libpython3-dev libxmu-dev tk-dev tcl-dev cmake g++ libglu1-mesa-dev libblas-dev liblapack-dev
 
-#RUN pip install ngsolve ngstrefftz
+RUN pip install ngsolve 
+RUN pip install ngstrefftz 
 
-RUN apt-get update
-RUN apt-get update
-RUN apt-get install -y software-properties-common
-RUN add-apt-repository universe
-RUN add-apt-repository ppa:ngsolve/nightly -y
-RUN apt-get install ngsolve -y
-
-ENV PYTHONPATH=/usr/lib/python3/dist-packages/
-ENV NETGENDIR=/usr/bin/
+#ENV PYTHONPATH=/usr/lib/python3/dist-packages/
+#ENV NETGENDIR=/usr/bin/
+ENV PYTHONPATH=$PYTHONPATH:/usr/local/lib/python3.10/site-packages/
 
 RUN git clone --recursive https://github.com/PaulSt/NGSTrefftz /home/app/ngstrefftz
-RUN cmake -B/home/app/ngstrefftz/make -S/home/app/ngstrefftz/src
-RUN make -C/home/app/ngstrefftz/make
-RUN make -C/home/app/ngstrefftz/make install
 
 RUN apt-get install npm nodejs -y
 RUN pip3 install jupyter_contrib_nbextensions
@@ -42,3 +34,12 @@ RUN cd /home/app/ngstrefftz/external_dependencies/ngstents/tentswebgui && ./buil
 RUN cd /home/app/ngstrefftz/external_dependencies/ngstents/tentswebgui && pip3 install .
 RUN jupyter nbextension install --py tentswebgui
 RUN jupyter nbextension enable --py tentswebgui
+
+##RUN pip3 install jupyter
+RUN pip3 install jupyter_contrib_nbextensions
+RUN pip3 install jupyter_nbextensions_configurator
+RUN pip3 install RISE
+RUN pip3 install ipywidgets
+RUN jupyter contrib nbextension install 
+#RUN cd /home/app/ngstents/tentswebgui && pip3 install --user .
+

.github/workflows/build.yml

@@ -91,56 +91,55 @@ jobs:
         #if: ${{ failure() }}
         #uses: mxschmitt/action-tmate@v3
 
-  pypi-test:
+  pypi:
     needs: [ubuntu]
     runs-on: ubuntu-latest
+    container:
+      image: quay.io/pypa/manylinux2014_x86_64:latest
     steps:
-      - name: install pkgs
-        run: |
-             sudo apt-get update && DEBIAN_FRONTEND="noninteractive" sudo apt-get -y install vim python3 python3-pip python3-distutils python3-tk libpython3-dev libxmu-dev tk-dev tcl-dev cmake git g++ libglu1-mesa-dev libblas-dev liblapack-dev
-             sudo apt-get install -y software-properties-common
-             sudo add-apt-repository universe
-             sudo add-apt-repository ppa:ngsolve/nightly -y
-             sudo apt-get install ngsolve -y
-      - name: set path
-        run: |
-             echo "PYTHONPATH=/usr/lib/python3/dist-packages/" >> $GITHUB_ENV
-             echo "NETGENDIR=/usr/bin/" >> $GITHUB_ENV
       - uses: actions/checkout@v2
         with:
           submodules: 'True'
-      - name: Update pip and Install setuptools
-        run: |
-          python3 -m pip install --upgrade pip
-          python3 -m pip install setuptools
-      - name: Package ngstrefftz sources for PyPI
-        run: python3 setup.py sdist
-      - name: pip install ngstrefftz
-        run: pip install dist/*
+          path: 'NGSTrefftz'
+          fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
+      - name: build pip
+        run: cd NGSTrefftz/.github/workflows && sh build_pip.sh
+      - name: Publish source distribution to PyPI
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}
+          packages_dir: NGSTrefftz/wheelhouse/
+          #repository_url: https://test.pypi.org/legacy/
 
-  pypi-publish:
-    needs: [pypi-test]
+  pypi-src:
+    needs: [ubuntu]
     runs-on: ubuntu-latest
-    if: github.event_name == 'release' && github.event.action == 'created' #startsWith(github.ref, 'refs/tags/v') # && github.event_name == 'push' 
     steps:
       - uses: actions/checkout@v2
         with:
           submodules: 'True'
+      - name: install pkgs
+        run: |
+             sudo apt-get update && DEBIAN_FRONTEND="noninteractive" sudo apt-get -y install vim python3 python3-pip python3-distutils python3-tk libpython3-dev libxmu-dev tk-dev tcl-dev cmake git g++ libglu1-mesa-dev libblas-dev liblapack-dev
+             pip install ngsolve
       - name: Update pip and Install setuptools
         run: |
           python3 -m pip install --upgrade pip
           python3 -m pip install setuptools
       - name: Package ngstrefftz sources for PyPI
         run: python3 setup.py sdist
+      - name: pip install ngstrefftz
+        run: pip install dist/*
       - name: Publish source distribution to PyPI
         uses: pypa/gh-action-pypi-publish@master
+        if: github.event_name == 'release' && github.event.action == 'created' #startsWith(github.ref, 'refs/tags/v') # && github.event_name == 'push' 
         with:
           skip_existing: true
           user: __token__
           password: ${{ secrets.PYPI_API_TOKEN }}
 
   docker:
-    needs: [ubuntu]
+    needs: [ubuntu,pypi]
     runs-on: ubuntu-latest
     if: github.event_name == 'release' && github.event.action == 'created'
     steps:

.github/workflows/build_pip.sh

@@ -0,0 +1,44 @@
+#! /bin/bash
+set -e
+yum -y update
+yum -y install ninja-build fontconfig-devel tk-devel tcl-devel libXmu-devel mesa-libGLU-devel ccache
+
+py=/opt/python/cp39-cp39/bin/python
+$py fix_auditwheel_policy.py
+cd ../..
+
+git config --global --add safe.directory '*'
+
+export ORIGINAL_PATH="$PATH"
+
+for pyversion in 38 39 310
+do
+    export PYDIR="/opt/python/cp${pyversion}-cp${pyversion}/bin"
+    export PATH="$ORIGINAL_PATH:$PYDIR"
+    #echo $PYDIR
+    #$PYDIR/pip install -U pytest-check numpy wheel scikit-build mkl==2021.* mkl-devel==2021.*
+    #$PYDIR/pip install netgen-mesher
+    #NETGENDIR=/opt/_internal/cpython-3.9.13/bin
+
+    #rm -rf /home/app/ngstrefftz/make
+    rm -rf _skbuild
+    $PYDIR/pip install ngsolve
+
+    $PYDIR/pip wheel -vvv .
+    auditwheel repair ngstrefftz*.whl
+    rm -rf *.whl
+    $PYDIR/pip uninstall -y ngsolve
+    $PYDIR/pip uninstall -y netgen-mesher
+
+    # avx2 build:
+    rm -rf _skbuild
+    $PYDIR/pip install ngsolve-avx2
+    NETGEN_ARCH=avx2 $PYDIR/pip wheel -vvv .
+    auditwheel repair ngstrefftz*.whl
+    rm -rf *.whl
+    $PYDIR/pip uninstall -y ngsolve-avx2
+    $PYDIR/pip uninstall -y netgen-mesher-avx2
+done
+
+$PYDIR/pip install -U twine
+#$PYDIR/twine upload wheelhouse/*manylinux*.whl

.github/workflows/fix_auditwheel_policy.py

@@ -0,0 +1,41 @@
+import json
+
+policy_file = "/opt/_internal/pipx/venvs/auditwheel/lib/python3.9/site-packages/auditwheel/policy/manylinux-policy.json"
+data = json.load(open(policy_file))
+# todo: read libs from netgen.libs directory and remove hashes from names, then add just libmkl_rt.so.1
+additional_libs = [
+        "libGLU.so.1",
+        "libGLX.so.0",
+        "libGLdispatch.so.0",
+        "libOpenGL.so.0",
+        "libXmu.so.6",
+        "libbz2.so.1.0.6",
+        "libcsg.so",
+        "libcsgvis.so",
+        "libfontconfig.so.1.11.1",
+        "libfreetype.so.6.14.0",
+        "libgeom2d.so",
+        "libgeom2dvis.so",
+        "libgui.so",
+        "libinterface.so",
+        "libmesh.so",
+        "libmkl_rt.so.1",
+        "libngcore.so",
+        "libnggui.so",
+        "libnglib.so",
+        "libocc.so",
+        "libpng15.so.15.13.0",
+        "libstl.so",
+        "libstlvis.so",
+        "libtcl8.so",
+        "libtk8.so",
+        "libuuid.so.1.3.0",
+        "libvisual.so",
+        "libz.so.1.2.7",
+        ]
+
+for entry in data:
+    if 'manylinux' in entry['name']:
+        entry['lib_whitelist'] += additional_libs
+
+json.dump(data, open(policy_file, 'w'))

Dockerfile

@@ -1,12 +1,12 @@
 FROM paulstdocker/ngstrefftz:latest
 
-#RUN pip3 install jupyter
-RUN pip3 install jupyter_contrib_nbextensions
-RUN pip3 install jupyter_nbextensions_configurator
-RUN pip3 install RISE
-RUN pip3 install ipywidgets
-RUN jupyter contrib nbextension install 
-#RUN cd /home/app/ngstents/tentswebgui && pip3 install --user .
+##RUN pip3 install jupyter
+#RUN pip3 install jupyter_contrib_nbextensions
+#RUN pip3 install jupyter_nbextensions_configurator
+#RUN pip3 install RISE
+#RUN pip3 install ipywidgets
+#RUN jupyter contrib nbextension install 
+##RUN cd /home/app/ngstents/tentswebgui && pip3 install --user .
 
 ARG NB_USER=jovyan
 ARG NB_UID=1000
@@ -26,8 +26,8 @@ RUN jupyter nbextensions_configurator enable --user
 RUN jupyter nbextension enable --user codefolding/main 
 RUN jupyter nbextension enable --user --py tentswebgui
 
-WORKDIR /home/${NB_USER}
-
-COPY . ${HOME}
+#WORKDIR /home/${NB_USER}
+#COPY . ${HOME}
+WORKDIR /home/app/ngstrefftz/docs/notebooks
 
 CMD ["jupyter", "notebook", "--port=8888", "--no-browser", "--ip=0.0.0.0", "--allow-root" ]  

DockerfileML

@@ -0,0 +1,5 @@
+FROM quay.io/pypa/manylinux2014_x86_64
+USER root
+COPY . /home/app/ngstrefftz
+WORKDIR /home/app/ngstrefftz
+#RUN chmod +x build_pip.sh && ./build_pip.sh

docs/notebooks/twavetents.ipynb

@@ -15,8 +15,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from ngstents._pytents import TentSlab\n",
     "from ngstrefftz import TWave\n",
+    "from ngstents._pytents import TentSlab\n",
     "from ngsolve.TensorProductTools import *\n",
     "from netgen.geom2d import unit_square\n",
     "from ngsolve import *\n",

setup.py

@@ -15,6 +15,7 @@
 import os
 import re
 import subprocess
+
 def get_version():
     """
     Gets the current version number.
@@ -93,6 +94,11 @@ def build_extension(self, ext):
         cmake_args = ['-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=' + extdir,
                       '-DPYTHON_EXECUTABLE=' + sys.executable,
                       '-DCMAKE_CXX_COMPILER=ngscxx']
+        if 'PYDIR' in os.environ:
+            cmake_args += [f'-DCMAKE_PREFIX_PATH={os.environ["PYDIR"]}/..']
+            cmake_args += [f'-DPYTHON_EXECUTABLE={os.environ["PYDIR"]}/python3']
+            cmake_args += [f'-DPYTHON_LIBRARY={os.environ["PYDIR"]}/../lib']
+            cmake_args += [f'-DPYTHON_INCLUDE_DIR={os.environ["PYDIR"]}/../include']
         cfg = 'Debug' if self.debug else 'Release'
         build_args = ['--config', cfg]
         cmake_args += ['-DCMAKE_BUILD_TYPE=' + cfg]
@@ -110,26 +116,37 @@ def build_extension(self, ext):
         # subprocess.check_call(['mkdir', 'ngstents'], cwd=self.build_lib)
         # subprocess.check_call(['mv', '_pytents.so', 'ngstents'], cwd=self.build_lib)
 
+import netgen.version
+import ngsolve
+netgen_name = netgen.config.NETGEN_PYTHON_PACKAGE_NAME
+avx2 = netgen_name.replace('netgen-mesher', '') # keep -avx2 suffix
+name = 'ngstrefftz' + avx2
+install_requires = [ 'ngsolve'+avx2+'>='+ngsolve.__version__ ]
+
+if sys.argv[1] == "sdist":
+    package_data = {"ngstrefftz": ["*"
+                                ,"../test/*"
+                                ,"../external_dependencies/ngstents/*"\
+                                ,"../external_dependencies/ngstents/src/*"\
+                                ,"../external_dependencies/ngstents/py/*"\
+                                ]}
+    name += "-src"
+else:
+    package_data = {}
+
 setup(
-    name='ngstrefftz',
+    name=name,
     version=str(get_version()),
     author='Paul Stocker',
     author_email='[email protected]',
     description='NGSTrefftz is an add-on to NGSolve for Trefftz methods.',
     long_description='NGSTrefftz provides a framework to implement Trefftz finite element spaces for NGSolve, with several Trefftz spaces already implemented. Additionally, Trefftz-DG on tent-pitched meshes for the acoustic wave equation is implemented using meshes provided by ngstents. Furthermore, the package includes an implementation of the embedded Trefftz method.',
     url="https://github.com/PaulSt/ngstrefftz",
+    install_requires=install_requires,
     ext_modules=[CMakeExtension('ngstrefftz_py','src')],
     cmdclass=dict(build_ext=CMakeBuild),
     packages=["ngstrefftz"],
     package_dir={"ngstrefftz": "src"},
-    package_data={"ngstrefftz": ["*"
-                                ,"../test/*"
-                                ,"../external_dependencies/ngstents/*"\
-                                ,"../external_dependencies/ngstents/src/*"\
-                                ,"../external_dependencies/ngstents/py/*"\
-                                ]},
     python_requires='>=3.5',
-    # install_requires=[
-       # 'NGSolve>=6.2',
-    # ]
+    package_data=package_data,
 )

test/tents.py

@@ -16,7 +16,7 @@ def SolveWaveTents(initmesh, order, c, t_step):
     >>> order = 4
     >>> SetNumThreads(4)
     >>> c = 1
-    >>> t_step = 2/sqrt(3)
+    >>> t_step = 0.5
     >>> meshes=[ Mesh(SegMesh(4,0,math.pi)), Mesh(unit_square.GenerateMesh(maxh = 0.4)) , Mesh(unit_cube.GenerateMesh(maxh = 1))]
     >>> for initmesh in meshes:
     ...    for maxh in range(3):
@@ -25,14 +25,14 @@ def SolveWaveTents(initmesh, order, c, t_step):
     ...            initmesh.Refine()
     ...        else:
     ...            initmesh=Mesh(SegMesh(initmesh.ne*2,0,1))
-    0.14...
+    0.12...
     ...e-05
     ...e-06
     0.01...
-    0.002...
+    0.001...
     0.0001...
     0.1...
-    0.06...
+    0.05...
     0.003...
 
     same example with Neumann boundary conditions
@@ -46,11 +46,11 @@ def SolveWaveTents(initmesh, order, c, t_step):
     ...            initmesh.Refine()
     ...        else:
     ...            initmesh=Mesh(SegMesh(initmesh.ne*2,0,1))
-    0.14...
+    0.12...
     ...e-05
     ...e-06
-    0.01...
-    0.002...
+    0.0...
+    0.001...
     0.0001...
     0.1...
     0.05...
@@ -216,7 +216,7 @@ def SolveWaveTentsFO(initmesh, order, c, t_step):
     ...     SolveWaveTentsFO(initmesh, order, c, t_step) # doctest:+ELLIPSIS
     ...     initmesh.Refine()
     0.01...
-    0.002...
+    0.00...
     0.0001...
     """