README.CVS

-Preparing the CVS-sources
-=========================
-
-Additional to the software mentioned in README you'll need the
-following programs installed on your system:
-
-  automake >= 1.5
-
-  autoconf >= 2.50
-
-  libtool
-
-Run the script
-
-  ./autogen.sh
-
-to get a ./configure-script.
-
-
-$Id$
-
-

README.md

+<!--
+SPDX-FileCopyrightInfo: Copyright © DUNE Project contributors, see file LICENSE.md in module root
+SPDX-License-Identifier: LicenseRef-GPL-2.0-only-with-DUNE-exception
+-->
+
+DUNE-library
+============
+
+DUNE, the Distributed and Unified Numerics Environment is a modular toolbox
+for solving partial differential equations with grid-based methods.
+
+The main intention is to create slim interfaces allowing an efficient use of
+legacy and/or new libraries. Using C++ techniques DUNE allows one to use very
+different implementation of the same concept (i.e. grid, solver, ...) under
+a common interface with a very low overhead.
+
+DUNE was designed with flexibility in mind. It supports easy discretization
+using methods, like Finite Elements, Finite Volume and also Finite
+Differences. Through separation of data structures DUNE allows fast Linear
+Algebra like provided in the ISTL module, or usage of external libraries
+like BLAS.
+
+This package contains the basic DUNE common classes.
+
+Dependencies
+------------
+
+dune-common depends on the following software packages
+
+- CMake >= 3.16
+- Compiler (C, C++): GNU >= 10 or Clang >= 13
+- Library: GNU libstdc++ >= 10 or Clang libc++ >= 13
+
+Other compilers may also work, but they must support C++20 to the same extent as
+the above. For an overview of the C++20 features supported by these versions, see
+https://en.cppreference.com/w/cpp/compiler_support. For compiling the Python
+bindings, libc++ is not currently supported.
+
+The following software is recommended but optional:
+
+- pkg-config
+- MPI (either OpenMPI, lam, or mpich suffice)
+- Python >= 3.7 (interpreter and development kit for building the python bindings)
+
+For a full explanation of the DUNE installation process please read
+the [installation notes][installation]. The following introduction is meant for
+the impatient.
+
+License
+-------
+
+The DUNE-library and headers are licensed under version 2 of the GNU
+General Public License, with the so-called "runtime exception", as
+follows:
+
+> As a special exception, you may use the DUNE source files as part
+> of a software library or application without restriction.
+> Specifically, if other files instantiate templates or use macros or
+> inline functions from one or more of the DUNE source files, or you
+> compile one or more of the DUNE source files and link them with
+> other files to produce an executable, this does not by itself cause
+> the resulting executable to be covered by the GNU General Public
+> License.  This exception does not however invalidate any other
+> reasons why the executable file might be covered by the GNU General
+> Public License.
+
+This license clones the one of the libstdc++ library. For further
+implications of this library please see their [license page][license]
+
+See the file COPYING for full copying permissions.
+
+Installation
+------------
+
+Short installation instructions can be found in file INSTALL. For the
+full instructions please see [here][installation].
+
+Links
+-----
+
+0. https://www.dune-project.org/installation/installation-faq/
+1. https://dune-project.org/releases/
+2. https://dune-project.org/doc/buildsystem/
+3. https://gcc.gnu.org/onlinedocs/libstdc++/faq.html#faq.license
+
+[installation]: https://www.dune-project.org/installation/installation-buildsrc
+[license]: https://gcc.gnu.org/onlinedocs/libstdc++/faq.html#faq.license

TODO

-- nach perl und makedepend suchen (für undefAllMacros.pl)
-- doxygen configuration files
-- Installation doku in docs
-- operator schnittstelle erweitern, damit man mehr Informationen
-  übergeben kann

autogen.sh

-#!/bin/sh
-# $Id$
-
-# barf on errors
-set -e
-
-# may be used to force a certain automake-version e.g. 1.7
-AMVERS=
-
-DEFAULTCONFOPT=
-
-usage () {
-    echo "Usage: ./autogen.sh [options]"
-    echo "  -i, --intel        use intel compiler"
-    echo "  -g, --gnu          use gnu compiler (default)"
-    echo "  -m, --mpi          use mpicc"
-    echo "  --opts=FILE        use compiler-options from FILE"
-    echo "  -d, --debug        switch debug-opts on"
-    echo "  -n, --nodebug      switch debug-opts off"
-    echo "  -o, --optim        switch optimization on"
-    echo "  -h, --help         you already found this :)"
-}
-
-# no compiler set yet
-COMPSET=0
-for OPT in $* ; do
-
-    set +e
-    # stolen from configure...
-    # when no option is set, this returns an error code
-    arg=`expr "x$OPT" : 'x[^=]*=\(.*\)'`
-    set -e
-
-    case "$OPT" in
-	-i|--intel)   . ./icc.opts ; COMPSET=1 ;;
-	-g|--gnu)     . ./gcc.opts ; COMPSET=1 ;;
-	-m|--mpi)     . ./mpi.opts ; COMPSET=1 ;;
-	--opts=*)
-	    if [ -r $arg ] ; then
-	      echo "reading options from $arg..."
-	      . ./$arg ;
-	      COMPSET=1;
-	    else
-	      echo "Cannot open compiler options file $arg!" ;
-	      exit 1;
-	    fi ;;
-	-d|--debug)   DEBUG=1 ;;
-	-n|--nodebug) DEBUG=0 ;;
-	-o|--optim)   OPTIM=1 ;;
-	-h|--help) usage ; exit 0 ;;
-	# pass unknown opts to ./configure
-	*) CONFOPT="$CONFOPT $OPT" ;;
-    esac
-done
-
-# use the free compiler as default
-if [ "$COMPSET" != "1" ] ; then
-    echo "No compiler set, using GNU compiler as default"
-    . ./gcc.opts
-fi
-
-# create flags
-COMPFLAGS="$FLAGS"
-
-# maybe add debug flag
-if [ "$DEBUG" = "1" ] ; then	
-    COMPFLAGS="$COMPFLAGS $DEBUGFLAGS"
-fi
-
-# maybe add optimization flag
-if [ "$OPTIM" = "1" ] ; then	
-    COMPFLAGS="$COMPFLAGS $OPTIMFLAGS"
-fi
-
-# check if automake-version was set
-if test "x$AMVERS" != x ; then
-  echo Warning: explicitly using automake version $AMVERS
-  # binaries are called automake-$AMVERS
-  AMVERS="-$AMVERS"
-fi
-
-## run autotools
-
-echo "--> libtoolize..."
-# this script won't rewrite the files if they already exist. This is a
-# PITA when you want to upgrade libtool, thus I'm setting --force
-libtoolize --force
-
-# prepare everything
-echo "--> aclocal..."
-aclocal$AMVERS
-
-# applications should provide a config.h for now
-#echo "--> autoheader..."
-#autoheader
-
-echo "--> automake..."
-automake$AMVERS --add-missing
-
-echo "--> autoconf..."
-autoconf
-
-#### start configure with special environment
-
-export CC=$COMP
-export CXX=$CXXCOMP
-export CPP="$COMP -E"
-
-export CFLAGS="$COMPFLAGS"
-export CXXFLAGS="$COMPFLAGS"
-
-./configure $DEFAULTCONFOPT $CONFOPT

bin/CMakeLists.txt

+# SPDX-FileCopyrightInfo: Copyright © DUNE Project contributors, see file LICENSE.md in module root
+# SPDX-License-Identifier: LicenseRef-GPL-2.0-only-with-DUNE-exception
+
+install(PROGRAMS
+  dune-add-spdx
+  dune-ctest
+  duneproject
+  dunecontrol
+  dunepackaging.py
+  dune-git-whitespace-hook
+  DESTINATION ${CMAKE_INSTALL_BINDIR})

bin/dune-add-spdx

+#! /usr/bin/env python3
+# SPDX-FileCopyrightInfo: Copyright © DUNE Project contributors, see file LICENSE.md in module root
+# SPDX-License-Identifier: LicenseRef-GPL-2.0-only-with-DUNE-exception
+
+import argparse
+import dataclasses
+import errno
+import logging
+import re
+
+# REUSE-IgnoreStart
+parser = argparse.ArgumentParser(
+    description='add SPDX header to DUNE project modules'
+)
+parser.add_argument(
+    '--license', '-l', dest='license',
+    help='SPDX license name',
+    default='LicenseRef-GPL-2.0-only-with-DUNE-exception',
+)
+parser.add_argument(
+    '--copyright', '-c', dest='copyright',
+    help='copyright information',
+    default='Copyright © DUNE Project contributors, see file LICENSE.md in module root',
+)
+parser.add_argument(
+    '--like', dest='like',
+    help='handle files like a file named like this',
+),
+parser.add_argument(
+    '--log', dest='log',
+    help='set log level',
+),
+parser.add_argument(
+    'files', nargs='+',
+    help='files to add copyright and license headers to',
+)
+
+
+@dataclasses.dataclass
+class Rule:
+    pattern: str
+    prefix: str = ""
+    suffix: str = ""
+    line_prefix: str = ""
+    line_suffix: str = ""
+    use_license_file: bool = False
+    skip_lines: re.Pattern = None
+
+    def match(self, filename) -> bool:
+        return bool(re.search(self.pattern, filename))
+
+
+rules = [
+    Rule(
+        pattern=r"\.(?:c|cc|cc\.in|h|hh|hh\.in|ct|ht|t|geo)$|config\.h\.cmake$",
+        line_prefix="// ",
+    ),
+    Rule(
+        pattern=r"\.(?:rst|rst\.in)$",
+        prefix="::\n",
+        line_prefix="  ",
+        suffix="\n",
+    ),
+    Rule(
+        pattern=r"\.bib$",
+        line_prefix="@Comment ",
+        suffix="\n",
+    ),
+    Rule(
+        pattern=r"\.dgf$",
+        line_prefix="% ",
+        skip_lines=re.compile("^DGF"),
+    ),
+    Rule(
+        pattern=r"\.tex$",
+        line_prefix="% ",
+        suffix="\n",
+    ),
+    Rule(
+        pattern=r"(?:\.amc|\.cmake|\.cmake\.in|\.gitignore|\.ini|\.pc\.in"
+                r"|\.pl|\.py|\.py\.in|\.sh|\.toml|\.toml\.in|\.yml"
+                r"|CMakeLists.txt|Doxylocal|dune.module|MANIFEST\.in)$",
+        line_prefix="# ",
+        suffix="\n",
+    ),
+    Rule(
+        pattern=r"/doxygen/.*\.txt$",
+        line_prefix="// ",
+        suffix="\n",
+    ),
+    Rule(
+        pattern=r"(?:\.md|INSTALL)$",
+        prefix="<!--\n",
+        suffix="-->\n\n",
+    ),
+    Rule(
+        pattern=r"\.(?:cel|eps|fig|pdf|png|svg|vrt)$",
+        use_license_file=True,
+    ),
+    Rule(
+        # gmsh's MSH file format support comments via unknown sections
+        # ($Comment ... $EndComment), but DUNE does not handle that.
+        # Reference: https://gmsh.info/doc/texinfo/gmsh.html#MSH-file-format
+        pattern=r"\.msh",
+        use_license_file=True,
+    ),
+]
+
+
+skip_lines = re.compile(r'-\*-|vi(?:m)?:|^#!')
+
+
+class Notice:
+    def __init__(self, copyright, license):
+        self.copyright = f'SPDX-FileCopyrightInfo: {copyright}'
+        self.license = f'SPDX-License-Identifier: {license}'
+
+    def match(self, lines) -> bool:
+        pattern = re.compile(f'(?:{re.escape(self.copyright)}|{re.escape(self.license)})')
+        return any(pattern.search(line) for line in lines)
+
+
+def rule_for_file(filename) -> Rule:
+    for rule in rules:
+        if rule.match(filename):
+            return rule
+    return None
+
+
+def line_for_notice(lines, rule: Rule) -> int:
+    for index, line in enumerate(lines):
+        if not skip_lines.search(line) \
+           and (rule.skip_lines is None or not rule.skip_lines.search(line)):
+            return index
+    return len(lines)
+
+
+def apply_rule_to_file(filename, rule: Rule, notice: Notice):
+    if rule.use_license_file:
+        try:
+            with open(f"{filename}.license", "xt") as fh:
+                logging.debug(f"{filename}: create separate .license file")
+                print(notice.copyright, file=fh)
+                print(notice.license, file=fh)
+        except OSError as e:
+            if e.errno == errno.EEXIST:
+                logging.info(f"{filename}: separate .license file already exists")
+            else:
+                raise
+    else:
+        with open(filename, "rt") as fh:
+            lines = fh.readlines()
+        if notice.match(lines):
+            logging.info(f"{filename}: already contains a notice")
+            return
+        index = line_for_notice(lines, rule)
+        logging.debug(f"{filename}: Will insert notice at line {index}")
+        if rule.suffix:
+            lines.insert(index, rule.suffix)
+        lines.insert(index, f"{rule.line_prefix}{notice.license}{rule.line_suffix}\n")
+        lines.insert(index, f"{rule.line_prefix}{notice.copyright}{rule.line_suffix}\n")
+        if rule.prefix:
+            lines.insert(index, rule.prefix)
+        with open(filename, "wt") as fh:
+            print(*lines, sep='', end='', file=fh)
+
+
+if __name__ == '__main__':
+    args = parser.parse_args()
+    if args.log:
+        logging.basicConfig(level=getattr(logging, args.log.upper()))
+    notice = Notice(args.copyright, args.license)
+    for filename in args.files:
+        logging.debug(f"Processing {filename}")
+        if args.like:
+            rule = rule_for_file(args.like)
+        else:
+            rule = rule_for_file(filename)
+        if rule is None:
+            logging.warning(f"{filename}: No rule found for this file. Add a rule or try --like.")
+            continue
+        apply_rule_to_file(filename, rule, notice)
+
+
+# add-spdx() {
+#     local file line_prefix prefix suffix
+#     local copying_file="LICENSE.md"
+#     local license="LicenseRef-GPL-2.0-only-with-DUNE-exception"
+#     xxlicense="LGPL-2.1-or-later"
+#     for file in "$@"; do
+#         prefix=""
+#         line_prefix=""
+#         suffix=""
+#         license_file="${file}"
+#         case "${file}" in
+#             *.cc|*.hh|*config.h.cmake|*.cc.in|*.ct|*.ht|*.t) line_prefix="// " ;;
+#             */doxygen/*.txt) line_prefix="// "; suffix=$'\n' ;;
+#             *CMakeLists.txt|*.py|*.gitignore|*.yml|*Doxylocal|*.toml|*.pc.in|*dune.module|*.cmake|*.ini) line_prefix="# "; suffix=$'\n' ;;
+#             *.md|*INSTALL) prefix=$'<!--\n'; suffix=$'\n-->\n' ;;
+#             *.tex) line_prefix="% "; suffix=$'\n' ;;
+#             *.svg|*.png|*.eps|*.pdf) license_file="${file}.license"; file="" ;;
+#         esac
+#
+#         ed ${file} <<EOT
+# 0i
+# ${prefix}${line_prefix}SPDX-FileCopyrightText: Copyright © DUNE Project contributors, see file ${copying_file} in module root
+# ${line_prefix}SPDX-License-Identifier: ${license}${suffix}
+# .
+# w ${license_file}
+# q
+# EOT
+#     done
+# }
+# REUSE-IgnoreEnd

bin/dune-ctest

+#! /usr/bin/env python3
+# SPDX-FileCopyrightInfo: Copyright © DUNE Project contributors, see file LICENSE.md in module root
+# SPDX-License-Identifier: LicenseRef-GPL-2.0-only-with-DUNE-exception
+#
+# Wrapper around CTest for DUNE
+#
+# CTest returns with an error status not only when tests failed, but also
+# when tests were only skipped.  This wrapper checks the log and returns
+# successfully if no tests failed; skipped tests do not result in an error.
+# This behaviour is needed in a continuous integration environment, when
+# building binary packages or in other cases where the testsuite should be
+# run automatically.
+#
+# Moreover, this script also converts the XML test report generated by CTest
+# into a JUnit report file that can be consumed by a lot of reporting
+# software.
+#
+# Author: Ansgar Burchardt <Ansgar.Burchardt@tu-dresden.de>
+# Author: Steffen Müthing <steffen.muething@iwr.uni-heidelberg.de> (for the JUnit part)
+
+import errno
+import glob
+import os.path
+import shutil
+import subprocess
+import sys
+import xml.etree.ElementTree as et
+from pathlib import Path
+import os
+import re
+
+
+class CTestParser:
+
+    def findCTestOutput(self):
+        files = glob.glob("Testing/*/Test.xml")
+        if len(files) != 1:
+            fn = files.join(", ")
+            raise Exception("Found multiple CTest output files: {}".format(files.join(", ")))
+        return files[0]
+
+    def printTest(self,test,output=None):
+        status = test.get("Status")
+        name = test.find("Name").text
+        fullName = test.find("FullName").text
+        if output is not None:
+            output = test.find("Results").find("Measurement").find("Value").text
+
+        print("======================================================================")
+        print("Name:      {}".format(name))
+        print("FullName:  {}".format(fullName))
+        print("Status:    {}".format(status.upper()))
+        if output:
+            print("Output:")
+            for line in output.splitlines():
+                print("          ", line)
+        print()
+
+    def __init__(self,junitpath=None):
+        self.inputpath = self.findCTestOutput()
+        if junitpath is None:
+            if "CI_PROJECT_DIR" in os.environ:
+                buildroot = Path(os.environ["CI_PROJECT_DIR"])
+                # create a slug from the project name
+                name = os.environ["CI_PROJECT_NAME"].lower()
+                name = re.sub(r"[^-a-z0-9]","-",name);
+                junitbasename = "{}-".format(name)
+            else:
+                buildroot = Path.cwd()
+                junitbasename = ""
+            junitdir = buildroot / "junit"
+            junitdir.mkdir(parents=True,exist_ok=True)
+            self.junitpath = junitdir / "{}cmake.xml".format(junitbasename)
+        else:
+            self.junitpath = Path(junitpath)
+            junitdir = junitpath.resolve().parent
+            junitdir.mkdir(parents=True,exist_ok=True)
+        self.tests = 0
+        self.passed = 0
+        self.failures = 0
+        self.skipped = 0
+        self.errors = 0
+        self.skipped = 0
+        self.time = 0.0
+
+    def createJUnitSkeleton(self):
+        self.testsuites = et.Element("testsuites")
+        self.testsuite = et.SubElement(self.testsuites,"testsuite")
+        self.properties = et.SubElement(self.testsuite,"properties")
+
+    def fillJUnitStatistics(self):
+        self.testsuite.set("name","cmake")
+        self.testsuite.set("tests",str(self.tests))
+        self.testsuite.set("disabled","0")
+        self.testsuite.set("errors",str(self.errors))
+        self.testsuite.set("failures",str(self.failures))
+        self.testsuite.set("skipped",str(self.skipped))
+        self.testsuite.set("time",str(self.time))
+
+    def processTest(self,test):
+        testcase = et.SubElement(self.testsuite,"testcase")
+        testcase.set("name",test.find("Name").text)
+        testcase.set("assertions","1")
+        testcase.set("classname","cmake")
+        time = test.find("./Results/NamedMeasurement[@name='Execution Time']/Value")
+        if time is not None:
+            self.time += float(time.text)
+            testcase.set("time",time.text)
+        self.tests += 1
+        outcome = test.get("Status")
+        if outcome == "passed":
+            testcase.set("status","passed")
+            self.passed += 1
+        elif outcome == "failed":
+            self.failures += 1
+            testcase.set("status","failure")
+            failure = et.SubElement(testcase,"failure")
+            failure.set("message","program execution failed")
+            failure.text = test.find("./Results/Measurement/Value").text
+            self.printTest(test)
+        elif outcome == "notrun":
+            # This does not exit on older CMake versions, so work around that
+            try:
+                status = test.find("./Results/NamedMeasurement[@name='Completion Status']/Value").text
+                if status == "SKIP_RETURN_CODE=77":
+                    self.skipped += 1
+                    et.SubElement(testcase,"skipped")
+                elif status == "Required Files Missing":
+                    self.errors += 1
+                    error = et.SubElement(testcase,"error")
+                    error.set("message","compilation failed")
+                    error.set("type","compilation error")
+                    self.printTest(test,output="Compilation error")
+                else:
+                    error = et.SubElement(testcase,"error")
+                    error.set("message","unknown error during test execution")
+                    error.set("type","unknown")
+                    error.text = test.find("./Results/Measurement/Value").text
+                    self.errors += 1
+                    self.printTest(test)
+            except AttributeError:
+                output_tag = test.find("./Results/Measurement/Value")
+                if output_tag is not None:
+                    msg = output_tag.text
+                    if "skipped" in msg:
+                        self.skipped += 1
+                        et.SubElement(testcase,"skipped")
+                    elif "Unable to find required file" in msg:
+                        self.errors += 1
+                        error = et.SubElement(testcase,"error")
+                        error.set("message","compilation failed")
+                        error.set("type","compilation error")
+                        self.printTest(test,output="Compilation error")
+                    else:
+                        error = et.SubElement(testcase,"error")
+                        error.set("message","unknown error during test execution")
+                        error.set("type","unknown")
+                        error.text = msg
+                        self.errors += 1
+                        self.printTest(test)
+                else:
+                    error = et.SubElement(testcase,"error")
+                    error.set("message","unknown error during test execution")
+                    error.set("type","unknown")
+                    error.text = "no message"
+                    self.errors += 1
+                    self.printTest(test)
+
+        output_tag = test.find("./Results/Measurement/Value")
+        if output_tag is not None:
+            out = et.SubElement(testcase,"system-out")
+            out.text = output_tag.text
+
+    def process(self):
+
+        with open(self.inputpath, "r", encoding="utf-8") as fh:
+            tree = et.parse(fh)
+
+        root = tree.getroot()
+
+        self.createJUnitSkeleton()
+
+        for test in root.findall(".//Testing/Test"):
+            self.processTest(test)
+
+        self.fillJUnitStatistics()
+
+        with self.junitpath.open("wb") as fh:
+            fh.write(et.tostring(self.testsuites,encoding="utf-8"))
+            print("JUnit report for CTest results written to {}".format(self.junitpath))
+
+        return self.errors + self.failures
+
+
+def runCTest(argv=[]):
+    cmd = ["ctest",
+           "--output-on-failure",
+           "--dashboard", "ExperimentalTest",
+           "--no-compress-output",
+    ]
+    cmd.extend(argv)
+    subprocess.call(cmd)
+
+def checkDirectory():
+    if not os.path.exists("CMakeCache.txt"):
+        raise Exception("ERROR: dune-ctest must be run in a cmake build directory")
+
+def removeCTestOutput():
+    try:
+        shutil.rmtree("Testing")
+    except OSError as e:
+        if e.errno != errno.ENOENT:
+            raise
+
+def main():
+    try:
+        checkDirectory()
+        removeCTestOutput()
+        runCTest(argv=sys.argv[1:])
+        parser = CTestParser()
+        errors = parser.process()
+        status = 0 if errors == 0 else 1
+        sys.exit(status)
+    except Exception as e:
+        print("Internal error: {}".format(e))
+        sys.exit(127)
+
+if __name__ == "__main__":
+    main()

bin/dune-git-whitespace-hook

+#!/bin/sh
+# dune-git-whitespace-hook
+# DO NOT TOUCH THE PRECEDING LINE
+# It is used by dunecontrol to enable automatic updates of the whitespace hook
+#
+# SPDX-FileCopyrightInfo: Copyright © DUNE Project contributors, see file LICENSE.md in module root
+# SPDX-License-Identifier: LicenseRef-GPL-2.0-only-with-DUNE-exception
+#
+# DUNE pre-commit hook to enforce whitespace policy
+# This hook prevents adding lines with trailing whitespace and or tab characters
+# in line indentation for certain files (see the TRAILING_WHITESPACE_DEFAULT and
+# TAB_IN_INDENT_DEFAULT variables below for the default sets of files that will
+# be checked).
+# You can tell the hook which files should be inspected by setting the Git
+# configuration variables "hooks.whitespace.trailing" and "hooks.whitespace.tabinindent".
+# Those variables should contain valid Perl regular expressions. The names of modified
+# files will be matched against those regexes.
+
+# git-diff-index needs a valid commit to compare to
+if git rev-parse --verify HEAD >/dev/null 2>&1
+then
+	against=HEAD
+else
+	# Initial commit: diff against an empty tree object
+	against=4b825dc642cb6eb9a060e54bf8d69288fbee4904
+fi
+
+
+# By default, we disallow trailing whitespace for the following files, but the check for C/C++ and CMake sources
+# happens in the tab-in-indent check to avoid confusing users with duplicate error messages
+TRAILING_WHITESPACE_DEFAULT='^(dune\.module|README|README\.SVN|COPYING|INSTALL|TODO)$|^[^/]*(\.md|\.pc\.in)$|^doc/.*\.md$'
+
+# By default, we disallow tabs in indents and trailing whitespace in C/C++ and CMake source files
+TAB_IN_INDENT_DEFAULT='(^|/)CMakeLists\.txt$|(\.cpp|\.hpp|\.cc|\.hh|\.c|\.h|\.cmake|\.sh|\.py)$'
+
+# Get user preferences
+TRAILING_WHITESPACE_FILES=$(git config hooks.whitespace.trailing)
+
+# Set default regex for disallowing trailing whitespace if the user did not set anything.
+# We need to check the return value of git-config to distinguish the case
+# when the user set an empty value
+if [ $? -ne 0 ];
+then
+  TRAILING_WHITESPACE_FILES="$TRAILING_WHITESPACE_DEFAULT"
+fi
+
+
+TAB_IN_INDENT_FILES=$(git config hooks.whitespace.tabinindent)
+
+# Set default regex for disallowing tabs if the user did not set anything.
+# We need to check the return value of git-config to distinguish the case
+# when the user set an empty value
+if [ $? -ne 0 ];
+then
+  TAB_IN_INDENT_FILES="$TAB_IN_INDENT_DEFAULT"
+fi
+
+
+# Unfortunately, we have to mess directly with the repository config file,
+# as git won't honor a custom config file specified by GIT_CONFIG
+
+# backup repository-local user setting for core.whitespace
+USER_WHITESPACE=$(git config --local --get core.whitespace)
+if [ $? -ne 0 ];
+then
+  USER_HAS_CUSTOM_WHITESPACE=0
+else
+  USER_HAS_CUSTOM_WHITESPACE=1
+fi
+
+# Figure out how to call xargs to make sure it won't invoke its argument with
+# an empty argument list. BSD xargs will not do that by default, while GNU xargs
+# needs -r to do the same. So we start by checking whether xargs does the right
+# thing without options. Now there could be other obscure versions of xargs out
+# there (on clusters etc.) that behave in yet another way, so we try with -r as
+# well. If that fails, we throw a big error message at the user.
+
+# In the following line, xargs should not call false, so the return value should be 0.
+echo "" | xargs false
+
+if [ $? -ne 0 ]; then
+  # Let's try with -r
+  echo "" | xargs -r false
+  if [ $? -ne 0 ]; then
+    # Houston, we have a problem
+    if [ -z "$DUNE_WHITESPACE_IGNORE_XARGS" ]; then
+      echo "You seem to be lacking a version of xargs that is compatible to either BSD or GNU!" 1>&2
+      echo "Please file a bug report at http://dune-project.org about this issue with your exact operating system type and version!" 1>&2
+      echo "You can still use this hook by setting the environment variable DUNE_WHITESPACE_IGNORE_XARGS to 1, but please be aware" 1>&2
+      echo "that the hook might create false positives." 1>&2
+      echo "==============================================================" 1>&2
+      echo "Aborting the commit..." 1>&2
+      exit 99
+    else
+      SILENTXARGS=xargs
+    fi
+  else
+    SILENTXARGS="xargs -r"
+  fi
+else
+  SILENTXARGS=xargs
+fi
+
+
+fail=0
+done=0
+
+do_cleanup()
+{
+
+  if [ $done -ne 1 ];
+  then
+    echo "Error while executing whitespace checking pre-commit hook!" 1>&2
+    echo "There might still be whitespace errors in your commit!" 1>&2
+  fi
+
+  if [ $USER_HAS_CUSTOM_WHITESPACE -eq 1 ];
+  then
+    git config --replace-all core.whitespace "$USER_WHITESPACE"
+  else
+    git config --unset core.whitespace
+  fi
+
+  # be nice and let the commit go through if something went wrong along the
+  # way and we did not record a failure
+  exit $fail
+}
+
+trap do_cleanup EXIT
+
+# set custom value
+git config --replace-all core.whitespace trailing-space
+
+if [ -z "$TRAILING_WHITESPACE_FILES" ];
+then
+  git diff-index --check --cached $against --
+  result=$?
+else
+  export TRAILING_WHITESPACE_FILES
+  git diff-index --cached --name-only $against                  \
+    | perl -ne 'print if /$ENV{TRAILING_WHITESPACE_FILES}/'     \
+    | $SILENTXARGS git diff-index --check --cached $against --
+  result=$?
+fi
+
+if [ $result -ne 0 ];
+then
+  fail=1
+fi
+
+git config --replace-all core.whitespace trailing-space,tab-in-indent
+
+if [ -z "$TAB_IN_INDENT_FILES" ];
+then
+  git diff-index --check --cached $against --
+  result=$?
+else
+  export TAB_IN_INDENT_FILES
+  git diff-index --cached --name-only $against                  \
+    | perl -ne 'print if /$ENV{TAB_IN_INDENT_FILES}/'           \
+    | $SILENTXARGS git diff-index --check --cached $against --
+  result=$?
+fi
+
+if [ $result -ne 0 ];
+then
+  fail=1
+fi
+
+done=1
+
+# trap will call the cleanup code

bin/dunepackaging.py

+#!/usr/bin/env python3
+# SPDX-FileCopyrightInfo: Copyright © DUNE Project contributors, see file LICENSE.md in module root
+# SPDX-License-Identifier: LicenseRef-GPL-2.0-only-with-DUNE-exception
+
+try:
+    import skbuild
+except ImportError:
+    print("skbuild needed for packaging, run 'pip install scikit-build'")
+    import sys
+    sys.exit(0)
+
+import sys, os, io, getopt, re, shutil
+import importlib, subprocess
+import email.utils
+from datetime import date
+
+# make sure that 'metadata' is taken from the current `dune-common` folder
+# and not some installed version which might be different from the one I'm
+# packaging (by mistake). The path to `packagemetadata.py` needs to be
+# added to the python path (to work here) and to the environment so that a
+# later call to `python setup.py` also works.
+here = os.path.dirname(os.path.abspath(__file__))
+mods = os.path.join(here, "..", "python", "dune")
+sys.path.append(mods)
+pythonpath  = mods + ":" + os.environ.get('PYTHONPATH','.')
+os.environ['PYTHONPATH'] = pythonpath
+try:
+    from packagemetadata import metaData
+except ImportError:
+    # not calling from within a dune-common source module so use installed
+    # version after all
+    from dune.packagemetadata import metaData
+
+def main(argv):
+
+    repositories = ["gitlab", "testpypi", "pypi"]
+    def usage():
+        return 'usage: dunepackaging.py [--upload <'+"|".join(repositories)+'> | -c | --clean | --version <version> | --onlysdist | --bdist_conda]'
+
+    try:
+        opts, args = getopt.getopt(argv, "hc", ["upload=", "clean", "version=", "onlysdist", "bdist_conda"])
+    except getopt.GetoptError:
+        print(usage())
+        sys.exit(2)
+
+    upload = False
+    repository = "gitlab"
+    clean = False
+    version = None
+    onlysdist = False
+    bdistconda = False
+    for opt, arg in opts:
+        if opt == '-h':
+            print(usage())
+            sys.exit(2)
+        elif opt in ("--upload"):
+            upload = True
+            if arg != '':
+                repository = arg
+                if repository not in repositories:
+                    print("Specified repository must be one of: " + " ".join(repositories))
+                    sys.exit(2)
+        elif opt in ("-c", "--clean"):
+            clean = True
+        elif opt in ("--version"):
+            version = arg
+        elif opt in ("--onlysdist"):
+            onlysdist = True
+        elif opt in ("--bdist_conda"):
+            onlysdist  = True
+            bdistconda = True
+
+    # Remove generated files
+    def removeFiles():
+        import glob
+        files = ['MANIFEST', 'dist', '_skbuild', '__pycache__']
+        print("Remove generated files: " + ", ".join(files))
+        remove = ['rm', '-rf'] + files
+        subprocess.call(remove)
+        # checkout setup.py and pyproject.toml
+        checkout = ['git', 'checkout', 'setup.py', 'pyproject.toml']
+        subprocess.call(checkout)
+
+    if clean:
+        removeFiles()
+        sys.exit(0)
+
+    data, cmake_flags = metaData(version, dependencyCheck=False)
+
+    if version is None:
+        version = data.version
+
+    # Generate setup.py
+    print("Generate setup.py")
+    f = open("setup.py", "w")
+    f.write("""#
+# DO NOT MODIFY THIS FILE!
+# This file is autogenerated by the `dunepackaging.py` script and
+# only used for the pypi dune packages. This file will not be included in
+# the build directory.
+#
+# See https://www.dune-project.org/dev/adding_python/ for docs on
+# Python packaging for Dune modules.
+#
+""")
+    f.write("import os, sys\n")
+    if data.name == 'dune-common':
+        f.write("here = os.path.dirname(os.path.abspath(__file__))\n")
+        f.write("mods = os.path.join(here, \"python\", \"dune\")\n")
+        f.write("sys.path.append(mods)\n\n")
+    f.write("try:\n")
+    f.write("    from dune.packagemetadata import metaData\n")
+    f.write("except ImportError:\n")
+    f.write("    from packagemetadata import metaData\n")
+    f.write("from skbuild import setup\n")
+
+    f.write("setup(**metaData('"+version+"')[1])\n")
+    f.close()
+
+    # Generate pyproject.toml
+    print("Generate pyproject.toml")
+    f = open("pyproject.toml", "w")
+    f.write("""#
+# DO NOT MODIFY THIS FILE!
+# This file is autogenerated by the `dunepackaging.py` script and
+# only used for the pypi dune packages. This file will not be included in
+# the build directory.
+#
+# See https://www.dune-project.org/dev/adding_python/ for docs on
+# Python packaging for Dune modules.
+#
+# This is uses the `Python-Requires` field in the `dune.modules` file to
+# populate the `requires` entry. Additional packages needed for the package
+# build should be added in the `dune.modules`. These packages will then also be
+# included in the package install from source.
+#
+""")
+    requires = data.asPythonRequirementString(data.depends + data.python_requires)
+    requires = list(set(requires)) # make requirements unique
+    minimal = ["pip", "setuptools", "wheel", "scikit-build", "cmake>=3.16", "ninja", "requests"]
+    requires += [r for r in minimal if not any([a.startswith(r) for a in requires])]
+    requires.sort()
+    f.write("[build-system]\n")
+    f.write("requires = "+requires.__str__()+"\n")
+    f.write("build-backend = 'setuptools.build_meta'\n")
+    f.close()
+
+    # Create source distribution and upload to repository
+    python = sys.executable
+    if upload or onlysdist:
+        print("Remove dist")
+        remove = ['rm', '-rf', 'dist']
+        subprocess.call(remove)
+
+        # check if we have scikit-build
+        import importlib
+        if importlib.util.find_spec("skbuild") is None:
+            print("Please install the pip package 'scikit-build' to build the source distribution.")
+            sys.exit(2)
+
+        # append hash of current git commit to README
+        shutil.copy('README.md', 'tmp_README.md')
+        githash = ['git', 'rev-parse', 'HEAD']
+        hash = subprocess.check_output(githash, encoding='UTF-8')
+        with open("README.md", "a") as f:
+            f.write("\n\ngit-" + hash)
+
+        print("Create source distribution")
+        # make sure setup.py/pyproject.toml are tracked by git so that
+        # they get added to the package by scikit
+        gitadd = ['git', 'add', 'setup.py', 'pyproject.toml']
+        subprocess.call(gitadd)
+        # run sdist
+        build = [python, 'setup.py', 'sdist']
+        subprocess.call(build, stdout=subprocess.DEVNULL)
+        # undo the above git add
+        gitreset = ['git', 'reset', 'setup.py', 'pyproject.toml']
+        subprocess.call(gitreset)
+
+        # restore README.md
+        shutil.move('tmp_README.md', 'README.md')
+
+        if not onlysdist:
+            # check if we have twine
+            import importlib
+            if importlib.util.find_spec("twine") is None:
+                print("Please install the pip package 'twine' to upload the source distribution.")
+                sys.exit(2)
+
+            twine = [python, '-m', 'twine', 'upload']
+            twine += ['--repository', repository]
+            twine += ['dist/*']
+            subprocess.call(twine)
+
+            removeFiles()
+
+        # create conda package meta.yaml (experimental)
+        if bdistconda:
+            import hashlib
+            remove = ['rm', '-rf', 'dist/'+data.name]
+            subprocess.call(remove)
+            mkdir  = ['mkdir', 'dist/'+data.name ]
+            subprocess.call(mkdir)
+
+            print("Create bdist_conda (experimental)")
+            distfile = 'dist/'+data.name+'-'+version+'.tar.gz'
+            datahash = ''
+            with open(distfile, "rb") as include:
+                source = include.read()
+                datahash = hashlib.sha256( source ).hexdigest()
+
+            print("Generate ",'dist/'+data.name+'/meta.yaml')
+            f = open('dist/'+data.name+'/meta.yaml', "w")
+            f.write('{% set name = "' + data.name + '" %}\n')
+            f.write('{% set version = "' + version + '" %}\n')
+            f.write('{% set hash = "' + datahash + '" %}\n\n')
+            f.write('package:\n')
+            f.write('  name: "{{ name|lower }}"\n')
+            f.write('  version: "{{ version }}"\n\n')
+            f.write('source:\n')
+            f.write('  path: ../{{ name }}-{{ version }}/\n')
+            f.write('  sha256: {{ hash }}\n\n')
+            f.write('build:\n')
+            f.write('  number: 1\n')
+            if 'TMPDIR' in os.environ:
+                f.write('  script_env:\n')
+                f.write('    - TMPDIR=' + os.environ['TMPDIR'] +'\n')
+            f.write('  script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv "\n\n')
+            f.write('requirements:\n')
+
+            requirements = ['pip', 'python', 'mkl', 'tbb', 'intel-openmp',
+                            'libgcc-ng', 'libstdcxx-ng', 'gmp', 'scikit-build',
+                            'mpi4py', 'matplotlib', 'numpy', 'scipy', 'ufl']
+
+            for dep in data.depends:
+                requirements += [dep[0]]
+
+            f.write('  host:\n')
+            for dep in requirements:
+                f.write('    - ' + dep + '\n')
+
+            f.write('\n')
+            f.write('  run:\n')
+            for dep in requirements:
+                f.write('    - ' + dep + '\n')
+
+            f.write('\n')
+            f.write('test:\n')
+            f.write('  imports:\n')
+            f.write('    - ' + data.name.replace('-','.') + '\n\n')
+            f.write('about:\n')
+            f.write('  home: '+data.url+'\n')
+            f.write('  license: GPLv2 with linking exception.\n')
+            f.write('  license_family: GPL\n')
+            f.write('  summary: '+data.description+'\n')
+            f.close()
+
+if __name__ == "__main__":
+    main(sys.argv[1:])

bin/find_modules.py

+# SPDX-FileCopyrightInfo: Copyright © DUNE Project contributors, see file LICENSE.md in module root
+# SPDX-License-Identifier: LicenseRef-GPL-2.0-only-with-DUNE-exception
+
+try:
+    from dune.common.module import resolve_dependencies, resolve_order, select_modules
+
+except ImportError:
+    import os
+    here = os.path.dirname(os.path.abspath(__file__))
+    mods = os.path.join(os.path.dirname(here), "python", "dune", "common")
+    if os.path.exists(os.path.join(mods, "module.py")):
+        import sys
+        sys.path.append(mods)
+        from module import resolve_dependencies, resolve_order, select_modules
+    else:
+        raise
+
+print("Found Modules:")
+print("--------------")
+modules, _ = select_modules()
+for description in modules.values():
+    print(repr(description))
+    print()
+
+print()
+print("Resolved Dependencies:")
+print("----------------------")
+deps = resolve_dependencies(modules)
+for mod_name, mod_deps in deps.items():
+    print(mod_name + ": " + " ".join(mod_deps))
+
+print()
+print("Build Order:")
+print("------------")
+print(" ".join(resolve_order(deps)))

bin/rebuild-dune-pypi.sh

+#!/bin/bash
+# SPDX-FileCopyrightInfo: Copyright © DUNE Project contributors, see file LICENSE.md in module root
+# SPDX-License-Identifier: LicenseRef-GPL-2.0-only-with-DUNE-exception
+#
+# This script builds a Python package index on gitlab.dune-project.org. Such an
+# index is necessary as a drop-in replacement for PyPI in continuous integration,
+# when runners operate with restricted network access.
+#
+# Running this script requires the following prerequisites to be met:
+# * Go to Gitlab Profile/Setting/Access Tokens and create a personal API access token with
+#   at least the `write_registry` and 'api' scope.
+# * Export your token with `export TWINE_PASSWORD=<token>`
+#
+
+# This script exits upon errors
+set -e
+
+# We authenticate with a personal Gitlab API token. You are expected to
+# have set TWINE_PASSWORD to your API token when calling this script.
+export TWINE_USERNAME=__token__
+
+# Make sure that TWINE_PASSWORD was set
+# export TWINE_PASSWORD=...
+if [ -z "$TWINE_PASSWORD" ]
+then
+  echo "TWINE_PASSWORD was not set!"
+  exit 1
+fi
+
+# Create a temporary directory as workspace for this script
+TMPDIR=$(mktemp -d)
+pushd $TMPDIR
+
+python3 -m venv env
+source env/bin/activate
+python -m pip install pip-download twine
+
+pip-download -d $(pwd)/downloads \
+  # dune-common \
+  # dune-geometry \
+  # dune-grid \
+  # dune-istl \
+  # dune-localfunctions \
+  # dune-alugrid \
+  # dune-fem \
+  pyparsing \
+  mpi4py \
+  wheel \
+  setuptools \
+  jinja2 \
+  portalocker \
+  fenics-ufl==2019.1.0 \
+  matplotlib \
+  scipy \
+  pip>=21 \
+  ninja \
+  sortedcontainers
+
+
+# Upload the packages to the index
+for filename in downloads/*
+do
+  # NB: The 133 here is the Gitlab project ID of dune-common.
+  python -m twine upload --verbose --skip-existing --repository-url https://gitlab.dune-project.org/api/v4/projects/133/packages/pypi $filename
+done
+
+# Clean up the temporary directory
+popd
+rm -rf $TMPDIR

cmake/CMakeLists.txt

+# SPDX-FileCopyrightInfo: Copyright © DUNE Project contributors, see file LICENSE.md in module root
+# SPDX-License-Identifier: LicenseRef-GPL-2.0-only-with-DUNE-exception
+
+add_subdirectory(modules)
+add_subdirectory(scripts)
+add_subdirectory(test)
\ No newline at end of file

cmake/modules/AddBLASLapackFlags.cmake

+# SPDX-FileCopyrightInfo: Copyright © DUNE Project contributors, see file LICENSE.md in module root
+# SPDX-License-Identifier: LicenseRef-GPL-2.0-only-with-DUNE-exception
+
+# Defines the functions to use BLAS/Lapack
+#
+# .. cmake_function:: add_dune_blas_lapack_flags
+#
+#    .. cmake_param:: targets
+#       :positional:
+#       :single:
+#       :required:
+#
+#       A list of targets to use BLAS/Lapack with.
+#
+include_guard(GLOBAL)
+
+include(FeatureSummary)
+set_package_properties("BLAS" PROPERTIES
+  DESCRIPTION "fast linear algebra routines")
+set_package_properties("LAPACK" PROPERTIES
+  DESCRIPTION "fast linear algebra routines")
+
+# register HAVE_BLAS and HAVE_LAPACK for config.h
+set(HAVE_BLAS ${BLAS_FOUND})
+set(HAVE_LAPACK ${LAPACK_FOUND})
+
+# register Lapack library as dune package
+if(HAVE_LAPACK)
+  dune_register_package_flags(LIBRARIES "${LAPACK_LIBRARIES}")
+
+  include(CMakePushCheckState)
+  cmake_push_check_state()
+  set(CMAKE_REQUIRED_LIBRARIES ${LAPACK_LIBRARIES})
+  check_function_exists("dsyev_" LAPACK_NEEDS_UNDERLINE)
+  cmake_pop_check_state()
+elseif(HAVE_BLAS)
+  dune_register_package_flags(LIBRARIES "${BLAS_LIBRARIES}")
+endif()
+
+# add function to link against the BLAS/Lapack library
+function(add_dune_blas_lapack_flags _targets)
+  foreach(_target ${_targets})
+    if(LAPACK_FOUND)
+      target_link_libraries(${_target} PUBLIC ${LAPACK_LIBRARIES})
+    elseif(BLAS_FOUND)
+      target_link_libraries(${_target} PUBLIC ${BLAS_LIBRARIES})
+    endif()
+  endforeach(_target)
+endfunction(add_dune_blas_lapack_flags)

cmake/modules/AddGMPFlags.cmake

+# SPDX-FileCopyrightInfo: Copyright © DUNE Project contributors, see file LICENSE.md in module root
+# SPDX-License-Identifier: LicenseRef-GPL-2.0-only-with-DUNE-exception
+
+# Defines the functions to use GMP
+#
+# .. cmake_function:: add_dune_gmp_flags
+#
+#    .. cmake_param:: targets
+#       :positional:
+#       :single:
+#       :required:
+#
+#       A list of targets to use GMP with.
+#
+include_guard(GLOBAL)
+
+# set HAVE_GMP for the config.h file
+set(HAVE_GMP ${GMP_FOUND})
+
+# register all GMP related flags
+if(GMP_FOUND)
+  dune_register_package_flags(
+    LIBRARIES GMP::gmpxx
+    COMPILE_DEFINITIONS "HAVE_GMP=1"
+  )
+endif()
+
+# add function to link against the GMP library
+function(add_dune_gmp_flags _targets)
+  if(GMP_FOUND)
+    foreach(_target ${_targets})
+      target_link_libraries(${_target} PUBLIC GMP::gmpxx)
+      target_compile_definitions(${_target} PUBLIC HAVE_GMP=1)
+    endforeach(_target ${_targets})
+  endif(GMP_FOUND)
+endfunction(add_dune_gmp_flags)

cmake/modules/AddMETISFlags.cmake

+# SPDX-FileCopyrightInfo: Copyright © DUNE Project contributors, see file LICENSE.md in module root
+# SPDX-License-Identifier: LicenseRef-GPL-2.0-only-with-DUNE-exception
+
+# Defines the functions to use METIS
+#
+# .. cmake_function:: add_dune_metis_flags
+#
+#    .. cmake_param:: targets
+#       :positional:
+#       :single:
+#       :required:
+#
+#       A list of targets to use METIS with.
+#
+include_guard(GLOBAL)
+
+# register HAVE_METIS for config.h
+set(HAVE_METIS ${METIS_FOUND})
+
+set(METIS_COMPILE_DEFINITIONS)
+if(HAVE_METIS)
+  list(APPEND METIS_COMPILE_DEFINITIONS "HAVE_METIS=1")
+endif()
+if(HAVE_SCOTCH_METIS)
+  list(APPEND METIS_COMPILE_DEFINITIONS "HAVE_SCOTCH_METIS=1")
+endif()
+
+# register METIS library as dune package
+if(METIS_FOUND)
+  dune_register_package_flags(LIBRARIES METIS::METIS
+    COMPILE_DEFINITIONS ${METIS_COMPILE_DEFINITIONS})
+endif()
+
+# Add function to link targets against METIS library
+function(add_dune_metis_flags _targets)
+  if(METIS_FOUND)
+    foreach(_target ${_targets})
+      target_link_libraries(${_target} PUBLIC METIS::METIS)
+      target_compile_definitions(${_target} PUBLIC ${METIS_COMPILE_DEFINITIONS})
+    endforeach(_target)
+  endif()
+endfunction(add_dune_metis_flags _targets)