add numpy, mpi4py to required packages

remove some python 2 related code and fixed up some other issues
pointed out by Timo
deprecated old compatibility file - move Python 3 code to dune.common.utility

FieldVector/Matrix classes with low dimension

add all flags to pybind11 modules

move bin files and cmake modules from dune-python
add sphinx support from dune-python

Make the comments a tiny bit more meaningful.

Add the 'Suggests' field, to make it more obvious that optional
dependencies are possible.

Ansgar Burchardt authored 5 years ago and Christoph Grüninger committed 5 years ago

The name git-whitespace-hook is a bit too generic for a DUNE-specific
tool.

Autotools is gone quite some time now. No need to keep this tools.

Apparently, this option has been around since 2009, but somehow
it never made it into the man page and the output of -h.

'configure' is an old alias for 'cmake', back from the
good old AutoTools days.

As it turns out, older versions of CTest do not output a "Completion Status" for
tests that were not run, so we need a fallback. The only place for information
is the test output, which we parse for certain key phrases to detect tests that
were skipped or had missing requirements (typically due to compilation
failures).

The build directory does not really work here, because it will just be called
build-cmake. So extract it from the CI_PROJECT_NAME variable and normalize that.

- dune-ctest now writes a JUnit XML result file to Testing/cmake.xml. This can
  be picked up by GitLab for better error reporting.
- Right now, tests that fail because compilation failed are not detected as an
  error. This is fixed now.

Fixes:
- Use unambiguous truth values (Closes: #134)
- When checking with pkg-config, look for the dependency rather than the last
  module from the list of found modules

Modernizations:
- Scope variables
- Use a simple `if` rather than a loop to check for presence of a depency in
  list of existing modules
- Make sure the function does not depend on the status of the `-e` option, or
  whether it is called from within the condition of an `if` or a `||` or `&&`.

Documentation:
- Document calling convention for the function and assumptions on the
  parameters.

As a shell script, duneproject is not covered by the scripts preventing tabs
in indentation (or simply was exempt from the Great Reformatting).  Also, the
tab width was inconsistent.

This expands all tabs and uses a consistent indentation of 2.  It also
instructs both emacs and vi to use these settings, since their default
indentation for shell scripts seems to differ.

CTest already prints the messages once.

Closes: #126

Markus Blatt authored 7 years ago and Christoph Grüninger committed 7 years ago

The script uses dune_enable_all_packages which has issues with older
CMake versions.

- For the files that should only occur in the toplevel directory, make sure to
  only match them in the toplevel directory.  This allows having them in an
  imported header only library in some subdirectory.
  + For files such as `.cc` or `.hh` that are matched by extension, there is
    no sane generic way to not check them when they are imported from
    somewhere else, so you'll still have to do something special, sorry.
- For files that are matched by name, make sure that name matches the full
  basename of the file, not just a suffix.
- Pass the regular expressions to perl in a safe way so they can contain
  arbitrary character without arcane quoting.  This mostly applies to the path
  separator '/'.

It is now possible to pass -D...=... flags to CMake via configure-opts.
Bash- / Autotools-style variables like CC=.. or MPICC=.. are no longer
support in configure-opts.

Autotools are history, no need to check for libraries built by libtool.

Pardiso isn't supported anymore by dune-istl.

up to now a CMAKE_MODULE_PATH environment variable was properly considered
and appended to the cmake parameters. This did not work for an environment
variable specified in the opts file. This patch makes the behaviour
consistent between shell environment and opts file variables.

(fixes #25)

When dunecontrol update fails the module name no longer has
underscores instead of hyphens.

This fixes #78

* dune-common requires CMake 2.8.12 anyway
* confusing option
* better remove line by hand after module created