Merge pull request #1281 from cekees/rc1.8.3

1.8.3 release

.gitignore

@@ -81,3 +81,6 @@ proteus/mprans/cRANS3PSed.cpp
 proteus/mprans/cVOF3P.cpp
 proteus/mprans/cVOS3P.cpp
 proteus/superluWrappers.c
+proteus/MeshAdaptPUMI/MeshAdapt.cpp
+proteus/tests/ci/meshNoVessel.edge
+proteus/tests/ci/meshNoVessel.neigh

.gitmodules

@@ -1,3 +0,0 @@
-[submodule "stack"]
-	path = stack
-	url = https://github.com/erdc/stack

.travis.yml

@@ -17,16 +17,20 @@ jobs:
     install:
       - git lfs pull
       - sudo apt-get update
-      - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
-      - bash miniconda.sh -b -p $HOME/miniconda
-      - source "$HOME/miniconda/etc/profile.d/conda.sh"
+      - wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh -O miniforge3.sh;
+      - bash miniforge3.sh -b -p $HOME/miniforge3
+      - source "$HOME/miniforge3/etc/profile.d/conda.sh"
+      - source "$HOME/miniforge3/etc/profile.d/mamba.sh"
       - hash -r
       - conda config --set always_yes yes --set changeps1 no
-      - conda update -q conda
-      - conda info -a
-      - conda env create -f environment-dev.yml
-      - conda activate proteus-dev
-      - PROTEUS_OPT="-g0 -O1" N=2 make develop-conda
+      - mamba init
+      - mamba update -q conda mamba
+      - mamba info -a
+      - mamba env create -f environment-dev.yml
+      - mamba activate proteus-dev
+      - pip install -v . --no-build-isolation --no-binary=":all:"
     script:
       - export MPLBACKEND="AGG"
-      - py.test -n 1 --forked -v proteus/tests --ignore proteus/tests/POD
+      - mkdir test_output
+      - cd test_output
+      - py.test -v --forked --import-mode=importlib ../test

Makefile

@@ -7,12 +7,12 @@ all: develop
 
 SHELL=/usr/bin/env bash
 N ?= 1
-PROTEUS ?= $(shell python3 -c "from __future__ import print_function; import os; print(os.path.realpath(os.getcwd()))")
+PROTEUS ?= $(shell python3 -c "import os; print(os.path.realpath(os.getcwd()))")
 VER_CMD = git log -1 --pretty="%H"
 PROTEUS_BUILD_CMD = python3 setup.py build_ext
-PROTEUS_INSTALL_CMD = pip install -v . #python3 setup.py install
+PROTEUS_INSTALL_CMD = pip3 install --no-deps --no-build-isolation --no-binary=:all: -v . #python3 setup.py install
 PROTEUS_DEVELOP_BUILD_CMD = python3 setup.py build_ext -i
-PROTEUS_DEVELOP_CMD = pip install -v -e . 
+PROTEUS_DEVELOP_CMD = pip3 install --no-deps --no-build-isolation --no-binary=:all: -v -e . 
 #
 ifeq (${N}, 1)
 PROTEUS_BUILD_CMD = python3 -c "print('Letting install handle build_ext')"
@@ -28,6 +28,9 @@ PROTEUS_ARCH ?= $(shell [[ $$(hostname) = centennial* ]] && echo "centennial" ||
 PROTEUS_ARCH ?= $(shell [[ $$(hostname) = thunder* ]] && echo "thunder" || python3 -c "import sys; print(sys.platform)")
 PROTEUS_ARCH ?= $(shell [[ $$(hostname) = gordon* ]] && echo "gordon" || python3 -c "import sys; print(sys.platform)")
 PROTEUS_ARCH ?= $(shell [[ $$(hostname) = conrad* ]] && echo "conrad" || python3 -c "import sys; print(sys.platform)")
+ifdef PROTEUS_PREFIX
+CONDA_PREFIX=''
+endif
 ifdef CONDA_PREFIX
 PROTEUS_ARCH ?= linux
 PROTEUS_PREFIX ?= ${CONDA_PREFIX}
@@ -37,6 +40,7 @@ PROTEUS_PREFIX ?= ${PROTEUS}/${PROTEUS_ARCH}
 PROTEUS_PYTHON ?= ${PROTEUS_PREFIX}/bin/python3
 PROTEUS_VERSION := $(shell ${VER_CMD})
 endif
+
 TEST_MARKER="' '"
 
 define show_info
@@ -151,6 +155,7 @@ ${PROTEUS_PREFIX}/artifact.json: stack/default.yaml $(shell find stack -type f)
 	@echo "************************"
 	@echo "Dependency build complete"
 	@echo "************************"
+	${PROTEUS_PREFIX}/bin/python -m ensurepip
 
 ${PROTEUS_PREFIX}/bin/proteus_env.sh: ${PROTEUS_PREFIX}/artifact.json
 	@echo "************************"
@@ -166,7 +171,6 @@ install: ${PROTEUS_PREFIX}/bin/proteus_env.sh stack/default.yaml ${PROTEUS_PREFI
 	@echo "Installing..."
 	@echo "************************"
 	$(call show_info)
-	${PROTEUS_ENV} ${PROTEUS_BUILD_CMD}
 	${PROTEUS_ENV} ${PROTEUS_INSTALL_CMD}
 	@echo "************************"
 	@echo "done installing standard extension modules"
@@ -193,7 +197,7 @@ develop: ${PROTEUS_PREFIX}/bin/proteus_env.sh stack/default.yaml ${PROTEUS_PREFI
 	@echo "Installing development version"
 	@echo "************************"
 	$(call show_info)
-	${PROTEUS_ENV} pip install py2gmsh pytest pytest-xdist pytest-cov tables future hypothesis
+	${PROTEUS_ENV} pip3 install py2gmsh pytest pytest-xdist pytest-cov pytest-forked hypothesis
 	${PROTEUS_ENV} ${PROTEUS_DEVELOP_BUILD_CMD}
 	${PROTEUS_ENV} ${PROTEUS_DEVELOP_CMD}
 	@echo "************************"
@@ -217,7 +221,7 @@ develop-conda:
 	@echo "************************************"
 	$(call show_info)
 	${PROTEUS_DEVELOP_CMD}
-	pip install pytest-xdist-forked
+	pip3 install pytest-forked
 	@echo "************************"
 	@echo "Development installation complete"
 	@echo "************************"
@@ -319,7 +323,7 @@ ifdef CONDA_PREFIX
 else
 	source ${PROTEUS_PREFIX}/bin/proteus_env.sh
 endif
-	pip install configparser ipyparallel ipython terminado jupyter ipywidgets ipyleaflet jupyter_dashboards pythreejs rise cesiumpy ipympl sympy transforms3d ipymesh voila ipyvolume ipysheet xonsh[ptk,linux,proctitle] ipytree
+	pip3 install configparser ipyparallel ipython terminado jupyter ipywidgets ipyleaflet jupyter_dashboards pythreejs rise cesiumpy ipympl sympy transforms3d ipymesh voila ipyvolume ipysheet xonsh[ptk,linux,proctitle] ipytree
 	ipcluster nbextension enable --user
 	jupyter nbextension enable --py --sys-prefix ipysheet
 	jupyter nbextension enable --py --sys-prefix widgetsnbextension
@@ -353,7 +357,7 @@ jupyterlab:
 	@echo "************************************"
 	@echo "Enabling jupyter lab"
 	source ${PROTEUS_PREFIX}/bin/proteus_env.sh
-	pip install jupyterlab jupyterlab_latex
+	pip3 install jupyterlab jupyterlab_latex
 	jupyter serverextension enable --py jupyterlab --sys-prefix
 	jupyter serverextension enable --sys-prefix --py jupyterlab_latex
 	jupyter labextension install @jupyter-widgets/jupyterlab-manager

README.md

@@ -9,27 +9,64 @@ rapidly developing computer models and numerical methods.
 
 
 ```bash
-conda install proteus -c conda-forge
+mamba install proteus -c conda-forge
 ```
 
 For a development installation, you want to install Proteus's dependencies and compile Proteus from source:
 
 ```bash
-conda env create -f environment-dev.yml
-conda activate proteus-dev
-make develop-conda # or pip install -v -e .
+mamba env create -f environment-dev.yml #environment-dev-up.yml to try unpinned dependencies
+mamba activate proteus-dev
+pip install -v -e .
 ```
 
-You can also build proteus and dependencies from source (without conda) with 
+# HPC Installation
 
-```bash
-make develop
-make test
+For installation on high performance environments you may want to install Proteus's dependencies from source as well. We recommend using the PETSc build system to install most of the dependencies. The following is general outline:
+
+Create a basic python environment you can install into:
+
+```
+mamba env create -f petsc-dev.yml
+mamba activate petsc-dev
+```
+
+or
+
+```
+python -m venv petsc-dev
+pip install setuptools make cmake cython swig pybind11 numpy
+```
+
+Next, build petsc from source
+
+```
+bash scripts/petsc_config_linux_conda_seq.sh #see https://petsc.org/release/install/
+```
+
+Next, build additional C++ dependencies and install into environment prefix (e.g $CONDA_PREFIX or $VIRTUAL_ENV)
+
+https://github.com/projectchrono/chrono #>=9.0.1, with python bindings
+https://github.com/scorec/core #>=2.2.8, shared, python bindinds not needed
+https://github.com/xtensor-stack/xtl
+https://github.com/xtensor-stack/xtensor
+https://github.com/xtensor-stack/xtensor-python
+
+Finally, locally build and install remaining python dependencies into environment
+
+```
+CC=mpicc CXX=mpicxx MPI_DIR=$MPI_ROOT pip install -v mpi4py==3.1.6 --no-build-isolation --no-binary=:all:
+PETSC_DIR=$CONDA_PREFIX PETSC_ARCH="" pip install -v ../petsc/src/binding/petsc4py --no-build-isolation --no-binary=:all:
+HDF5_MPI=ON HDF5_DIR=${CONDA_PREFIX} CC=mpicc CXX=mpicxx pip install -v h5py --no-build-isolation --no-binary=:all: #note h5py depends on mpi4py for this config
+CC=mpicc CXX=mpicxx pip install -v . --no-build-isolation --no-binary=:all:
 ```
 
-See https://github.com/erdc/proteus/wiki/How-to-Build-Proteus for more information on building the entire stack.
+Some optional packages can be installed with pip/mamba: py2gmsh, memory_profiler, scipy, pytest.
+
+See https://github.com/erdc/proteus/wiki/How-to-Build-Proteus for old information on building the entire stack.
 
 # Developer Information
 
 The source code, wiki, and issue tracker are on GitHub at
+
 https://github.com/erdc/proteus.

docs/Doxyfile

@@ -38,7 +38,7 @@ PROJECT_NAME           = proteus
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 1.8.2.dev0
+PROJECT_NUMBER         = 1.8.3
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

docs/source/conf.py

@@ -450,4 +450,4 @@ def linkcode_resolve(domain, info):
 #    "exhaleExecutesDoxygen": True,
 #    #"exhaleUseDoxyfile": True,
 #    "exhaleDoxygenStdin":    exhaleDoxygenStdin
-#}
+#}

environment-dev-up.yml

@@ -1,4 +1,4 @@
-name: proteus-dev-up-240321
+name: proteus-dev-up-240912
 channels:
   - conda-forge
   - defaults
@@ -8,7 +8,7 @@ dependencies:
   - make
   - setuptools
   - cython
-  - daetk
+  - pybind11
   - hdf5 =*=*mpich*
   - h5py =*=*mpich*
   - metis
@@ -20,40 +20,33 @@ dependencies:
   - parmetis
   - petsc4py
   - petsc
-  - scorec
   - superlu
   - superlu_dist
+  - scorec >=2.2.8
   - triangle
-  - pychrono
+  - pychrono >=9.0.1
   - gmsh
   - matplotlib
   - mpi4py
-  - pytables
   - pytest
   - pytest-cov
   - pytest-xdist
   - scipy
   - tetgen
   - ncurses
   - python
-  - future
   - ipyparallel
-  - pillow
   - xtensor-python
   - git-lfs
   - eigen
   - zoltan
   - hypre
-  - mumps-mpi
-  - numexpr
-  - ptscotch
-  - scalapack
   - tbb
   - zipp
   - parso
   - pycparser
   - ipython
   - decorator
   - cffi
-  - netcdf4
-  - jupyterlab
+  - jupyterlab
+  - openmp

environment-dev.yml

@@ -5,54 +5,46 @@ channels:
 dependencies:
   - pip =24.0
   - compilers =1.7.0
-  - make =4.3
-  - setuptools =69.2.0
-  - cython =3.0.9
-  - daetk =1.0.1
+  - make =4.4.1
+  - setuptools =73.0.1
+  - cython =3.0.11
   - hdf5 =1.14.3=*mpich*
-  - h5py =3.10.0=*mpich*
+  - h5py =3.11.0=*mpich*
   - metis =5.1.0
-  - mpich =4.2.0
-  - mpich-mpicc =4.2.0
-  - mpich-mpicxx =4.2.0
-  - numpy =1.26.4
-  - openblas =0.3.26
+  - mpich =4.2.2
+  - mpich-mpicc =4.2.2
+  - mpich-mpicxx =4.2.2
+  - numpy =2.1.1
+  - openblas =0.3.28
   - parmetis =4.0.3
-  - petsc4py =3.20.5
-  - petsc =3.20.5
-  - scorec =2.2.7
+  - petsc4py =3.21.5
+  - petsc =3.21.5
+  - scorec =2.2.8
   - superlu =5.2.2
-  - superlu_dist =8.2.1
+  - superlu_dist =9.0.0
   - triangle =1.6
-  - pychrono =7.0.0
+  - pychrono =9.0.1
   - gmsh =4.12.2
-  - matplotlib =3.8.3
-  - mpi4py =3.1.5
-  - pytables =3.9.2
-  - pytest =8.1.1
-  - pytest-cov =4.1.0
-  - pytest-xdist =3.5.0
-  - scipy =1.12.0
+  - matplotlib =3.9.2
+  - mpi4py =4.0.0
+  - pytest =8.3.3
+  - pytest-cov =5.0.0
+  - pytest-xdist =3.6.1
+  - pytest-forked
+  - scipy =1.14.1
   - tetgen =1.6.0
-  - ncurses =6.4.20240210
-  - python =3.10.14
-  - future =1.0.0
-  - ipyparallel =8.7.0
-  - pillow =10.2.0
+  - ncurses =6.5
+  - python =3.12.5
   - xtensor-python = 0.27.0
   - git-lfs =3.5.1
   - eigen =3.4.0
   - zoltan =3.901
-  - hypre =2.28.0
-  - mumps-mpi =5.6.2
-  - numexpr =2.9.0
-  - ptscotch =7.0.4
+  - hypre =2.31.0
+  - mumps-mpi =5.7.3
   - scalapack =2.2.0
-  - tbb =2021.11.0
-  - zipp =3.17.0
-  - parso =0.8.3
-  - pycparser =2.21
-  - ipython =8.22.2
-  - decorator =5.1.1
-  - cffi =1.16.0
-  - sympy =1.12
+  - tbb =2021.13.0
+  - zipp =3.20.1
+  - parso =0.8.4
+  - pycparser =2.22
+  - cffi =1.17.1
+  - sympy =1.13.2

environment-petsc-dev.yml

@@ -0,0 +1,15 @@
+name: petsc-dev
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - pip
+  - setuptools
+  - make
+  - cmake
+  - cython
+  - swig
+  - numpy
+  - pybind11
+  - openblas
+  - tetgen

petsc-dev.yml

@@ -0,0 +1,16 @@
+name: petsc-dev
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - compilers
+  - python
+  - numpy
+  - setuptools
+  - pip
+  - make
+  - cmake
+  - cython
+  - swig
+  - ncurses
+  - xtensor-python