Merge pull request ECP-WarpX#7 from RevathiJambunathan/MergingMasterI…

…ntoPulsarBranch_10March

Merging Master branch into PulsarBranch

.github/workflows/source.yml

@@ -1,3 +1,9 @@
+# Copyright 2019-2020 Axel Huebl, Maxence Thevenet
+#
+# This file is part of WarpX.
+#
+# License: BSD-3-Clause-LBNL
+
 name: source
 
 on: [push, pull_request]
@@ -9,6 +15,8 @@ jobs:
 
     steps:
     - uses: actions/checkout@v1
+    - name: Non-ASCII characters
+      run: .github/workflows/source/hasNonASCII
     - name: TABs
       run: .github/workflows/source/hasTabs
     - name: End-of-Line whitespaces
@@ -17,6 +25,8 @@ jobs:
       run: .github/workflows/source/wrongFileNameInExamples
     - name: Examples are tested
       run: .github/workflows/source/inputsNotTested
+    - name: Check that the test matrix for Travis includes all tests
+      run: .github/workflows/source/test_travis_matrix.sh
     - name: Doxygen
       run: |
         sudo apt-get install -y --no-install-recommends doxygen

.github/workflows/source/hasNonASCII

@@ -0,0 +1,41 @@
+#!/usr/bin/env bash
+#
+# Copyright 2016-2020 Axel Huebl
+#
+# License: BSD-3-Clause-LBNL
+
+# Search recursive inside a folder if a shell scripts or batch system files
+# contains non-ASCII characters. This causes problems with some systems.
+# We can also not guarantee that everyone has UTF8 locales installed, so
+# why depend on it.
+#
+# @result 0 if no files are found, else 1
+#
+
+ok=0
+
+pattern="\.c$|\.cpp$|\.F90$|\.h$|\.H$|\.ini$|\.py$|"\
+"\.sh$|\.tex$|\.txt$|\.xml$|\.yml$|"\
+"CMakeLists\.txt|inputs"
+
+for i in $(find . \
+                -not -path "./.git/*"   \
+                -not -path "./.idea/*"  \
+                -not -path "*wp_parse*" \
+                -type f | \
+           grep -P "${pattern}")
+do
+  # non-ASCII test regex via jerrymouse at stackoverflow under CC-By-SA 3.0:
+  #   http://stackoverflow.com/questions/3001177/how-do-i-grep-for-all-non-ascii-characters-in-unix/9395552#9395552
+  result=$(grep --color='always' -P -n "[\x80-\xFF]" $i)
+
+  if [ $? -eq 0 ]
+  then
+    echo "$i contains non-ASCII characters!"
+    echo "$result"
+    ok=1
+  fi
+done
+
+exit $ok
+

.github/workflows/source/test_travis_matrix.sh

@@ -0,0 +1,36 @@
+#! /usr/bin/env sh
+
+set -e
+
+cp .github/workflows/source/travis_matrix.py Regression/
+cd Regression/
+
+# Put the name of all travis tests into a text file
+python prepare_file_travis.py
+grep "\[" travis-tests.ini > travis_all_tests.txt
+
+# Concatenate the names of all elements in Travis matrix into another test file
+WARPX_CI_REGULAR_CARTESIAN=TRUE python prepare_file_travis.py
+grep "\[" travis-tests.ini >  travis_matrix_elements.txt
+WARPX_CI_PSATD=TRUE             python prepare_file_travis.py
+grep "\[" travis-tests.ini >> travis_matrix_elements.txt
+WARPX_CI_PYTHON_MAIN=TRUE       python prepare_file_travis.py
+grep "\[" travis-tests.ini >> travis_matrix_elements.txt
+WARPX_CI_SINGLE_PRECISION=TRUE  python prepare_file_travis.py
+grep "\[" travis-tests.ini >> travis_matrix_elements.txt
+WARPX_CI_RZ_OR_NOMPI=TRUE      python prepare_file_travis.py
+grep "\[" travis-tests.ini >> travis_matrix_elements.txt
+WARPX_CI_QED=TRUE               python prepare_file_travis.py
+grep "\[" travis-tests.ini >> travis_matrix_elements.txt
+
+# Check that the resulting lists are equal
+{
+    python travis_matrix.py &&
+        rm travis_all_tests.txt travis_matrix_elements.txt travis_matrix.py &&
+        echo "test passed" &&
+        exit 0
+} || {
+    rm travis_all_tests.txt travis_matrix_elements.txt travis_matrix.py &&
+        echo "tests failed" &&
+        exit 1
+}

.github/workflows/source/travis_matrix.py

@@ -0,0 +1,22 @@
+#! /usr/bin/env python
+
+# Concatenation of tests in each of the 6 elements in Travis matrix
+f = open('./travis_matrix_elements.txt') ; matrix_elements = f.readlines() ; f.close()
+# All tests read by prepare_travis_tests.py
+f = open('./travis_all_tests.txt') ; all_tests = f.readlines() ; f.close()
+
+# Now let's make sure these two are equal
+
+# Remove these elements from both lists, as they are are not test names
+elements_to_remove = ['[main]\n', '[AMReX]\n', '[source]\n', '[extra-PICSAR]\n']
+for element in elements_to_remove:
+    for x in range(matrix_elements.count(element)):
+        matrix_elements.remove(element)
+    for x in range(all_tests.count(element)):
+        all_tests.remove(element)
+
+# Sort lists, and make sure they are equal
+matrix_elements.sort()
+all_tests.sort()
+
+assert( matrix_elements == all_tests )

.lgtm.yml

@@ -1,3 +1,9 @@
+# Copyright 2019 Axel Huebl
+#
+# This file is part of WarpX.
+#
+# License: BSD-3-Clause-LBNL
+
 extraction:
   cpp:
     prepare:

.mailmap

@@ -1,35 +1,47 @@
-Andrew Myers <atmyers@lbl.gov>              Andrew Myers <atmyers2@gmail.com>
-Andrew Myers <atmyers@lbl.gov>              atmyers <atmyers2@gmail.com>
-Aurore Blelly <ablelly@lbl.gov>             ablelly <aurore.blelly@ensta-paristech.fr>
-Aurore Blelly <ablelly@lbl.gov>             ablelly <48810880+ablelly@users.noreply.github.com>
-Axel Huebl <axelhuebl@lbl.gov>              Axel Huebl <axel.huebl@plasma.ninja>
-David Grote <dpgrote@lbl.gov>               grote <dpgrote@lbl.gov>
-David Grote <dpgrote@lbl.gov>               Dave <grote1@llnl.gov>
-David Grote <dpgrote@lbl.gov>               Dave Grote <grote1@llnl.gov>
-David Grote <dpgrote@lbl.gov>               Grote <grote1@n9459722.llnl.gov>
-Edoardo Zoni <ezoni@lbl.gov>                Edoardo Zoni <edoardo.zoni@ipp.mpg.de>
-Ligia Diana Amorim <ldianaamorim@lbl.gov>   L. Diana Amorim <LDianaAmorim@lbl.gov>
-Ligia Diana Amorim <ldianaamorim@lbl.gov>   Diana Amorim <diana@henrivincenti.dhcp.lbl.gov>
-Ligia Diana Amorim <ldianaamorim@lbl.gov>   Ligia Diana Amorim <ligiada@cori01.nersc.gov>
-Ligia Diana Amorim <ldianaamorim@lbl.gov>   Ligia Diana Amorim <ligiada@cori11.nersc.gov>
-Luca Fedeli <luca.fedeli@cea.fr>            Luca Fedeli <luca.fedeli.88@gmail.com>
-Luca Fedeli <luca.fedeli@cea.fr>            lucafedeli88 <luca.fedeli@cea.fr>
-Luca Fedeli <luca.fedeli@cea.fr>            Luca Fedeli <luca@DEB.station>
-Luca Fedeli <luca.fedeli@cea.fr>            Luca Fedeli <luca.fedeli@for.unipi.it>
-Luca Fedeli <luca.fedeli@cea.fr>            Luca <luca@localhost.localdomain>
-Mathieu Lobet <mathieu.lobet@cea.fr>        Mathieu Lobet <mathieu.lobet@gmail.com>
-Mathieu Lobet <mathieu.lobet@cea.fr>        mathieu_lobet <mathieu.lobet@gmail.com>
-Maxence Thevenet <mthevenet@lbl.gov>        MaxThevenet <mthevenet@lbl.gov>
-Maxence Thevenet <mthevenet@lbl.gov>        Maxence Thévenet <mthevenet@lbl.gov>
-Maxence Thevenet <mthevenet@lbl.gov>        mthevenet <mthevenet@lbl.gov>
-Remi Lehe <rlehe@lbl.gov>                   Remi Lehe <remi.lehe@normalesup.org>
-Revathi Jambunathan <rjambunathan@lbl.gov>  RevathiJambunathan <revanathan@gmail.com>
-Revathi Jambunathan <rjambunathan@lbl.gov>  RevathiJambunathan <rjnathan@cori12.nersc.gov>
-Revathi Jambunathan <rjambunathan@lbl.gov>  Revathi Jambunathan <revanathan@login2.summit.olcf.ornl.gov>
-Revathi Jambunathan <rjambunathan@lbl.gov>  Revathi Jambunathan <revanathan@login3.summit.olcf.ornl.gov>
-Revathi Jambunathan <rjambunathan@lbl.gov>  Revathi Jambunathan <revanathan@login4.summit.olcf.ornl.gov>
-Revathi Jambunathan <rjambunathan@lbl.gov>  Revathi Jambunathan <revanathan@login5.summit.olcf.ornl.gov>
-Weiqun Zhang <weiqunzhang@lbl.gov>          Weiqun Zhang <WeiqunZhang@lbl.gov>
-Weiqun Zhang <weiqunzhang@lbl.gov>          WeiqunZhang <WeiqunZhang@lbl.gov
-Yinjian Zhao <yinjianzhao@lbl.gov>          Yin-YinjianZhao <yinjianzhao@lbl.gov>
-Yinjian Zhao <yinjianzhao@lbl.gov>          Yin-YinjianZhao <56095356+Yin-YinjianZhao@users.noreply.github.com>
+Andrew Myers <atmyers@lbl.gov>               Andrew Myers <atmyers2@gmail.com>
+Andrew Myers <atmyers@lbl.gov>               atmyers <atmyers2@gmail.com>
+Aurore Blelly <ablelly@lbl.gov>              ablelly <aurore.blelly@ensta-paristech.fr>
+Aurore Blelly <ablelly@lbl.gov>              ablelly <48810880+ablelly@users.noreply.github.com>
+Axel Huebl <axelhuebl@lbl.gov>               Axel Huebl <axel.huebl@plasma.ninja>
+David Bizzozero <dbizzozero@lbl.gov>         dbizzozero <dbizzozero@users.noreply.github.com>
+David Grote <dpgrote@lbl.gov>                grote <dpgrote@lbl.gov>
+David Grote <dpgrote@lbl.gov>                Dave <grote1@llnl.gov>
+David Grote <dpgrote@lbl.gov>                Dave Grote <grote1@llnl.gov>
+David Grote <dpgrote@lbl.gov>                Grote <grote1@n9459722.llnl.gov>
+Edoardo Zoni <ezoni@lbl.gov>                 Edoardo Zoni <edoardo.zoni@ipp.mpg.de>
+Edoardo Zoni <ezoni@lbl.gov>                 Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
+Glenn Richardson <gtrichardson@berkeley.edu> gtrichardson <gtrichardson@berkeley.edu>
+Jaehong Park <jaehongpark@lbl.gov>           jaehongp <jaehong@jaehongs-mbp-10.attlocal.net>
+Jean-Luc Vay <jlvay@lbl.gov>                 Jean-Luc Vay <jlvay@Jean-Lucs-MacBook-Pro.local>
+Jean-Luc Vay <jlvay@lbl.gov>                 Jean-Luc Vay <jlvay@Jean-Lucs-MBP.dhcp.lbnl.us>
+Jean-Luc Vay <jlvay@lbl.gov>                 Jean-Luc Vay <jlvay@jlvay2.lbl.gov>
+Junmin Gu <jgu@lbl.gov>                      guj <guj@users.noreply.github.com>
+Ligia Diana Amorim <ldianaamorim@lbl.gov>    L. Diana Amorim <LDianaAmorim@lbl.gov>
+Ligia Diana Amorim <ldianaamorim@lbl.gov>    Diana Amorim <diana@henrivincenti.dhcp.lbl.gov>
+Ligia Diana Amorim <ldianaamorim@lbl.gov>    Ligia Diana Amorim <ligiada@cori01.nersc.gov>
+Ligia Diana Amorim <ldianaamorim@lbl.gov>    Ligia Diana Amorim <ligiada@cori11.nersc.gov>
+Lixin Ge <lge@slac.stanford.edu>             lixin <lge@slac.stanford.edu>
+Luca Fedeli <luca.fedeli@cea.fr>             Luca Fedeli <luca.fedeli.88@gmail.com>
+Luca Fedeli <luca.fedeli@cea.fr>             lucafedeli88 <luca.fedeli@cea.fr>
+Luca Fedeli <luca.fedeli@cea.fr>             Luca Fedeli <luca@DEB.station>
+Luca Fedeli <luca.fedeli@cea.fr>             Luca Fedeli <luca.fedeli@for.unipi.it>
+Luca Fedeli <luca.fedeli@cea.fr>             Luca <luca@localhost.localdomain>
+Kevin Gott <kngott@lbl.gov>                  kngott <30483578+kngott@users.noreply.github.com>
+Mathieu Lobet <mathieu.lobet@cea.fr>         Mathieu Lobet <mathieu.lobet@gmail.com>
+Mathieu Lobet <mathieu.lobet@cea.fr>         mathieu_lobet <mathieu.lobet@gmail.com>
+Maxence Thevenet <mthevenet@lbl.gov>         MaxThevenet <mthevenet@lbl.gov>
+Maxence Thevenet <mthevenet@lbl.gov>         Maxence Thévenet <mthevenet@lbl.gov>
+Maxence Thevenet <mthevenet@lbl.gov>         mthevenet <mthevenet@lbl.gov>
+Remi Lehe <rlehe@lbl.gov>                    Remi Lehe <remi.lehe@normalesup.org>
+Revathi Jambunathan <rjambunathan@lbl.gov>   RevathiJambunathan <revanathan@gmail.com>
+Revathi Jambunathan <rjambunathan@lbl.gov>   RevathiJambunathan <rjnathan@cori12.nersc.gov>
+Revathi Jambunathan <rjambunathan@lbl.gov>   Revathi Jambunathan <revanathan@login2.summit.olcf.ornl.gov>
+Revathi Jambunathan <rjambunathan@lbl.gov>   Revathi Jambunathan <revanathan@login3.summit.olcf.ornl.gov>
+Revathi Jambunathan <rjambunathan@lbl.gov>   Revathi Jambunathan <revanathan@login4.summit.olcf.ornl.gov>
+Revathi Jambunathan <rjambunathan@lbl.gov>   Revathi Jambunathan <revanathan@login5.summit.olcf.ornl.gov>
+Revathi Jambunathan <rjambunathan@lbl.gov>   Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com>
+Revathi Jambunathan <rjambunathan@lbl.gov>   Revathi Jambunathan <rjnathan@cori12.nersc.gov>
+Weiqun Zhang <weiqunzhang@lbl.gov>           Weiqun Zhang <WeiqunZhang@lbl.gov>
+Weiqun Zhang <weiqunzhang@lbl.gov>           WeiqunZhang <WeiqunZhang@lbl.gov
+Yinjian Zhao <yinjianzhao@lbl.gov>           Yin-YinjianZhao <yinjianzhao@lbl.gov>
+Yinjian Zhao <yinjianzhao@lbl.gov>           Yin-YinjianZhao <56095356+Yin-YinjianZhao@users.noreply.github.com>

.readthedocs.yml

@@ -1,4 +1,9 @@
+# Copyright 2019-2020 Axel Huebl, Maxence Thevenet
+#
+# This file is part of WarpX.
+#
+# License: BSD-3-Clause-LBNL
+
 requirements_file: Docs/requirements.txt
 
 formats:
-    - htmlzip

.travis.yml

@@ -1,28 +1,44 @@
+# Copyright 2018-2019 Axel Huebl, David Grote, Luca Fedeli
+# Maxence Thevenet, Remi Lehe
+#
+# This file is part of WarpX.
+#
+# License: BSD-3-Clause-LBNL
+
 dist: xenial
 language: c++
 sudo: true
+cache: pip
 
 env:
   matrix:
-    - WARPX_TEST_DIM=3 HAS_QED=FALSE
-    - WARPX_TEST_DIM=RZ HAS_QED=FALSE
-    - WARPX_TEST_DIM=2 HAS_QED=FALSE
-    - HAS_QED=TRUE
+    - WARPX_CI_REGULAR_CARTESIAN=TRUE
+    - WARPX_CI_PSATD=TRUE
+    - WARPX_CI_PYTHON_MAIN=TRUE
+    - WARPX_CI_SINGLE_PRECISION=TRUE
+    - WARPX_CI_RZ_OR_NOMPI=TRUE
+    - WARPX_CI_QED=TRUE
 
 before_install:
     - sudo apt-get update
-    - sudo apt-get install -y gcc gfortran g++ openmpi-bin libopenmpi-dev libfftw3-dev libfftw3-mpi-dev
-    # Install miniconda and python dependencies
-    - wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
-    - bash Miniconda3-latest-Linux-x86_64.sh -b
-    - export PATH=/home/travis/miniconda3/bin:$PATH
-    - pip install --upgrade pip && pip install numpy scipy matplotlib mpi4py cython
-    - pip install git+https://github.com/yt-project/yt.git
+    - sudo apt-get install -y gcc gfortran g++ openmpi-bin libopenmpi-dev libfftw3-dev libfftw3-mpi-dev libhdf5-openmpi-dev pkg-config make python3 python3-pip python3-setuptools
+      # xenial misses "libadios-openmpi-dev"
+    - sudo update-alternatives --install /usr/bin/python python /usr/bin/python3 2
+    - sudo update-alternatives --set python /usr/bin/python3
+
+install:
+    - python -m pip install --upgrade pip
+    - python -m pip install --upgrade cmake cython matplotlib mpi4py numpy scipy
+    - export CEI_CMAKE="/home/travis/.local/bin/cmake"
+    - python -m pip install --upgrade git+https://github.com/yt-project/yt.git
+    - sudo curl -L -o /usr/local/bin/cmake-easyinstall https://git.io/JvLxY && sudo chmod a+x /usr/local/bin/cmake-easyinstall
 
 script:
     - export FFTW_HOME=/usr/
-    - export OMP_NUM_THREADS=1
+
     # Run the tests on the current commit
     - export WARPX_TEST_COMMIT=$TRAVIS_COMMIT
+
     # Run the script that prepares the test environment and runs the tests
+    - export OMP_NUM_THREADS=1
     - ./run_test.sh