Merge branch 'main' into RANS2P2D

.coveragerc

@@ -0,0 +1,13 @@
+[run]
+#plugins = Cython.Coverage # not working for now; excluding cython source below for now
+source = proteus
+omit =
+  */config/*
+  */test_utils/*
+  */tests/*
+  #cythonized modules, not currently showing coverage but tests are running
+  */proteus/WaveTools.py
+  */proteus/BoundaryConditions.py
+  */proteus/SpatialTools.py
+  */proteus/mprans/BoundaryConditions.py
+  */proteus/mprans/SpatialTools.py

.gitmodules

@@ -1,10 +1,10 @@
 [submodule "air-water-vv"]
 	path = air-water-vv
-	url = git://github.com/erdc/air-water-vv.git
+	url = https://github.com/erdc/air-water-vv.git
 	branch = master
 [submodule "stack"]
 	path = stack
-	url = git://github.com/erdc/stack
+	url = https://github.com/erdc/stack
 [submodule "proteus/tests/proteus_tutorial"]
 	path = proteus/tests/proteus_tutorial
-	url = git://github.com/erdc/proteus_tutorial
+	url = https://github.com/erdc/proteus_tutorial

.travis.yml

@@ -1,69 +1,18 @@
-addons:
-  apt:
-    packages:
-    - gfortran
-    - libffi-dev
-    - libssl-dev
-    - python-lzma
-    - python3
-    - doxygen
-    - graphviz
-
-cache:
-  - timeout: 1000
+os: linux
+dist: focal
+language: minimal
 
 notifications:
   email:
     on_success: change
     on_failure: always
 
-after_success:
-  - conda install codecov
-  - codecov
-
 jobs:
   include:
-  - stage: test
-    name: "hashdist linux"
-    os: linux
-    dist: bionic
-    language: python
-    python: 2.7
-    env: TEST_PROFILE="proteus-hashdist"
-    install:
-      - git lfs pull
-      - ./stack/hit/bin/hit init-home
-      - ./stack/hit/bin/hit remote add http://levant.hrwallingford.com/hashdist_src --objects="source"
-      - ./stack/hit/bin/hit remote add http://levant.hrwallingford.com/hashdist_stack --objects="build"
-      - make stack/default.yaml
-      - pushd $HOME
-      - mkdir -p hashdist_src
-      - mkdir -p hashdist_bld
-      - rm -rf .hashdist/src .hashdist/bld
-      - ln -s $HOME/hashdist_src .hashdist/src
-      - ln -s $HOME/hashdist_bld .hashdist/bld
-      - popd
-      - pushd stack
-      - echo $PWD
-      - ls -l
-      - ./hit/bin/hit build -j 2 -v default.yaml
-      - popd
-      - export PATHSAVE=$PATH
-      - export PATH=$PWD/linux/bin:$PATH
-      - export LD_LIBRARY_PATH=$PWD/linux/lib:$LD_LIBRARY_PATH
-      - PROTEUS_OPT="-w -g0 -O2 -UNDEBUG" FC=gfortran CC=mpicc CXX=mpicxx make develop N=2
-      - export SSL_CERT_DIR=/etc/ssl/certs
-    script:
-      - PATH=./linux/bin:$PATH MPLBACKEND=Agg py.test -n 1 --dist=loadfile --forked -v proteus/tests --ignore proteus/tests/POD --ignore proteus/tests/solver_tests/test_nse_RANS2P_step.py --cov=proteus
-      - PATH=./linux/bin:$PATH MPLBACKEND=Agg py.test -n 1 --dist=loadfile --forked -v air-water-vv/Tests/1st_set --cov=proteus
-      - PATH=./linux/bin:$PATH MPLBACKEND=Agg py.test -n 1 --dist=loadfile --forked -v air-water-vv/Tests/2nd_set --cov=proteus
-      - PATH=./linux/bin:$PATH MPLBACKEND=Agg mpiexec -np 2 pytest -v proteus/tests/FSI
   - stage: test
     name: "conda linux"
     os: linux
-    dist: xenial
-    language: python
-    python: 3.7
+    dist: focal
     env: TEST_PROFILE="proteus-conda"
     install:
       - git lfs pull
@@ -77,23 +26,23 @@ jobs:
       - conda info -a
       - conda env create -f environment-dev.yml
       - conda activate proteus-dev
-      - make develop-conda N=1
+      - make develop-conda N=2
     script:
       - export MPLBACKEND="AGG"
-      - py.test -n 1 --dist=loadfile --forked -v proteus/tests --ignore proteus/tests/POD --ignore proteus/tests/solver_tests/test_nse_RANS2P_step.py --cov=proteus
-      - MPLBACKEND=Agg py.test -n 1 --dist=loadfile --forked -v air-water-vv/Tests/1st_set
-      - MPLBACKEND=Agg py.test -n 1 --dist=loadfile --forked -v air-water-vv/Tests/2nd_set
-      - MPLBACKEND=Agg mpiexec -np 2 pytest -v proteus/tests/FSI
+      - py.test -n 1 --forked -v proteus/tests --ignore proteus/tests/POD --ignore proteus/tests/solver_tests/test_nse_RANS2P_step.py
+      - py.test -n 1 --forked -v air-water-vv/Tests/1st_set
+      - py.test -n 1 --forked -v air-water-vv/Tests/2nd_set
+      - py.test -n 1 --forked -v proteus/tests/FSI
     deploy:
       provider: script
       script: bash ./scripts/deploy.sh docs
       skip_cleanup: true
       on:
-        branch: master
+        branch: main
   - stage: test
     name: "conda osx"
     os: osx
-    osx_image: xcode11.3
+    osx_image: xcode13.4
     env: TEST_PROFILE="proteus-conda-osx"
     install:
       - wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh;
@@ -106,9 +55,12 @@ jobs:
       - conda env create -f environment-dev.yml
       - conda activate proteus-dev
       - pip install gmsh
-      - pip install -v -e .
+      - make develop-conda N=2
     script:
       - export MPLBACKEND="AGG"
       - git lfs install
       - git lfs pull
-      - py.test -n 1 --dist=loadfile --forked -v proteus/tests --ignore proteus/tests/solver_tests --ignore proteus/tests/POD --ignore proteus/tests/MeshAdaptPUMI --ignore=proteus/tests/matrix_constructor --ignore=proteus/tests/MoveMeshMonitor --ignore-glob='proteus/tests/periodic/*test_periodic.py' --ignore proteus/tests/solver_tests/test_nse_RANS2P_step.py --ignore proteus/tests/poisson_2d --cov=proteus
+      - py.test -n 1 --forked -v proteus/tests --ignore proteus/tests/solver_tests --ignore proteus/tests/POD --ignore=proteus/tests/MoveMeshMonitor --ignore proteus/tests/periodic
+      - py.test -n 1 --forked -v air-water-vv/Tests/1st_set
+      - py.test -n 1 --forked -v air-water-vv/Tests/2nd_set --ignore air-water-vv/Tests/2nd_set/test_randomWaves.py
+      - py.test -n 1 --forked -v proteus/tests/FSI

CONTRIBUTORS.md

@@ -7,7 +7,7 @@
 
 - Copyright 2017 U.S. Federal Government (in countries where recognized) christopher.e.kees@usace.army.mil
 - Copyright 2017 Chris Kees cekees@gmail.com
-- Copyright 2017 HR Wallingford Limited A.Dimakopoulos@hrwallingford.com
+- Copyright 2017 HR Wallingford Limited angdimak@gmail.com
 - Copyright 2017 Alvin Zhang alv.zhang@gmail.com
 - Copyright 2017 Alistair Bentley alistairbntl@gmail.com
 - Copyright 2017 Steven Mattis steve.a.mattis@gmail.com
@@ -25,6 +25,7 @@
 - Copyright 2019 David Brochart david.brochart@quantstack.net
 - Copyright 2019 Martin Renou martin.renou@quantstack.net
 - Copyright 2019 Eric Tovar eric.j.tovar@usace.army.mil
+- Copyright 2022 Jan Janssen janssen@lanl.gov
 
 **Note for U.S. Federal Employees**
 

Makefile

@@ -101,7 +101,10 @@ clean:
 
 distclean: clean
 	-rm -f stack.done
+ifdef CONDA_PREFIX
+else
 	-rm -rf ${PROTEUS_PREFIX}
+endif
 	-rm -rf build proteus/*.pyc proteus/*.so proteus/*.a proteus/MeshAdaptPUMI/*.so
 	-rm -rf build proteus/mprans/*.pyc proteus/mprans/*.so proteus/mprans/*.a
 	-rm -rf build proteus/richards/*.pyc proteus/richards/*.so proteus/richards/*.a
@@ -115,7 +118,7 @@ stack/hit/bin/hit:
 	cd stack && git submodule update --init
 	@echo "Adding source cache if not done already"
 	-./stack/hit/bin/hit init-home
-	-./stack/hit/bin/hit remote add http://levant.hrwallingford.com/hashdist_src --objects="source"
+	-./stack/hit/bin/hit remote add https://proteus.cee.lsu.edu/hashdist_src --objects="source"
 
 stack:
 	@echo "Updating stack submodule"
@@ -128,7 +131,7 @@ air-water-vv:
 bld_cache: stack/hit/bin/hit
 	@echo "Trying to add build cache for your arch"
 	HASHSTACK_BLD = $(shell lsb_release -ir | python3 -c "import sys; rel=dict((k.split(':')[0].split()[0],k.split(':')[1].strip().replace('.','_').lower()) for k in sys.stdin.readlines()); print('{Distributor}_{Release}'.format(**rel))")
-	./stack/hit/bin/hit remote add http://levant.hrwallingford.com/hashdist_${HASHSTACK_BLD} --objects="build"
+	./stack/hit/bin/hit remote add https://proteus.cee.lsu.edu/hashdist_${HASHSTACK_BLD} --objects="build"
 
 cygwin_bootstrap.done: stack/scripts/setup_cygstack.py stack/scripts/cygstack.txt
 	python3 stack/scripts/setup_cygstack.py stack/scripts/cygstack.txt
@@ -194,6 +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
 	${PROTEUS_ENV} ${PROTEUS_DEVELOP_BUILD_CMD}
 	${PROTEUS_ENV} ${PROTEUS_DEVELOP_CMD}
 	@echo "************************"
@@ -354,9 +358,9 @@ endif
 	printf "c.LocalEngineSetLauncher.engine_cmd = ['python', '-m', 'ipyparallel.engine']\n" >> ${HOME}/.ipython/profile_mpi/ipcluster_config.py
 	printf "c.MPIEngineSetLauncher.engine_cmd = ['python', '-m', 'ipyparallel.engine']\n" >> ${HOME}/.ipython/profile_mpi/ipcluster_config.py
 ifdef CONDA_PREFIX
-	cd ${CONDA_PREFIX}/lib/python3.7/site-packages/notebook/static/components/react && wget https://unpkg.com/react-dom@16/umd/react-dom.production.min.js
+	cd ${CONDA_PREFIX}/lib/python3.9/site-packages/notebook/static/components/react && wget https://unpkg.com/react-dom@16/umd/react-dom.production.min.js
 else
-	cd linux/lib/python3.7/site-packages/notebook/static/components/react && wget https://unpkg.com/react-dom@16/umd/react-dom.production.min.js
+	cd linux/lib/python3.9/site-packages/notebook/static/components/react && wget https://unpkg.com/react-dom@16/umd/react-dom.production.min.js
 endif
 
 jupyterlab:

README.md

@@ -1,20 +1,12 @@
-# Proteus: Computational Methods and Simulation Toolkit [![Build Status](https://travis-ci.com/erdc/proteus.svg?branch=master)](https://travis-ci.com/erdc/proteus) [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/erdc/proteus_tutorial/master?filepath=index.ipynb)  [![DOI](https://zenodo.org/badge/2212385.svg)](https://zenodo.org/badge/latestdoi/2212385)
+# Proteus: Computational Methods and Simulation Toolkit [![Build Status](https://travis-ci.com/erdc/proteus.svg?branch=main)](https://travis-ci.com/erdc/proteus) [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/erdc/proteus_tutorial/master?filepath=index.ipynb)  [![DOI](https://zenodo.org/badge/2212385.svg)](https://zenodo.org/badge/latestdoi/2212385)
 
 
 Proteus (http://proteustoolkit.org) is a Python package for
 rapidly developing computer models and numerical methods.
 
 # Installation
 
-The recommended way is the following:
 
-```bash
-make develop
-make test
-```
-https://github.com/erdc/proteus/wiki/How-to-Build-Proteus
-
-However, we are transitioning to a conda-based environment. Proteus can be installed with:
 
 ```bash
 conda install proteus -c conda-forge
@@ -25,9 +17,18 @@ For a development installation, you want to install Proteus's dependencies and c
 ```bash
 conda env create -f environment-dev.yml
 conda activate proteus-dev
-pip install -v -e .
+make develop-conda # or pip install -v -e .
+```
+
+You can also build proteus and dependencies from source (without conda) with 
+
+```bash
+make develop
+make test
 ```
 
+See https://github.com/erdc/proteus/wiki/How-to-Build-Proteus for more information on building the entire stack.
+
 # Developer Information
 
 The source code, wiki, and issue tracker are on GitHub at

codecov.yml

@@ -0,0 +1,3 @@
+ignore:
+  - "proteus/tests"
+  - "proteus/scripts"

docker/conda/Dockerfile

@@ -14,7 +14,7 @@ ENV F90 mpif90
 RUN rm -rf proteus && \
     git clone https://github.com/erdc/proteus && \
     cd proteus && \
-    git checkout master && \
+    git checkout main && \
     pip install -v -e . && \ 
     rm -rf build && \
     rm -rf air-water-vv && \

docker/hashdist/Dockerfile

@@ -14,7 +14,7 @@ ENV F90 mpif90
 RUN rm -rf proteus && \
     git clone https://github.com/erdc/proteus && \
     cd proteus && \
-    git checkout master && \
+    git checkout main && \
     git submodule update --init --recursive && \
     make PROTEUS_OPT="-DNDEBUG -g0 -O0" N=1 develop && \
     rm -rf air-water-vv && \

docker/jupyter/Dockerfile

@@ -14,7 +14,7 @@ ENV F90 mpif90
 RUN rm -rf proteus && \
     git clone https://github.com/erdc/proteus && \
     cd proteus && \
-    git checkout master && \
+    git checkout main && \
     git submodule update --init --recursive && \
     make PROTEUS_OPT="-DNDEBUG -g0 -O2" N=2 develop && \
     CC=gcc CXX=g++ ./linux/bin/pip3 install matplotlib && \

docs/Doxyfile

@@ -38,7 +38,8 @@ PROJECT_NAME           = proteus
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 1.7.5.dev0
+PROJECT_NUMBER         = 1.8.1
+
 # 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
 # quick idea about the purpose of the project. Keep the description short.