* screenconstraint more robust against nans and flags

* Clean up this PR

* ...and some whitespace fixes

* Use local isfinite
Co-authored-by: Maaike Mevius <mevius@lof006.control.lofar>
Co-authored-by: André Offringa <offringa@gmail.com>

* Separate and optimize pipeline build steps; Add coverage to test step

* Move src copy out of base image; remove env extensions

* Use a dymanic tag for the base image

* Define base tag and fix test step

* Remove wrong slash

* Exclude build from coverage

* WIP test filter coverage

* Use ninja for testing

* Use correct ninja package

* Optimize coverage files; Add more threads for dp3 build

Convert applycalh5 test to boost test

Add averager boost test

Add boost unit test to tUVWFlagger

Add boost unit test to tUpsample

Boostify baselineaverager

Boostify demixer (not working) and filter

Boostify h5par, medflagger and gridinterpolate

Boostify ndppp, preflagger and median

WIP boostify PSet

Boostify scaledata and stationadder

Remove cout in uvwflagger test

Change unsigned int to rownr_t in tests

Update/Fix tPSet

Fix UVW pointer to out-of-scope data.

Use CPU_COUNT instead of CPU_ISSET.

Valgrind complained about reading unitialized data here.

tUVWFlagger: Namespace updates

Add BOOST_FAIL case; Remove commented code and cout in tests

Remove unused parameters; remove unused test; add boost check to uvw test 8

Initialise vectors

Remove most using namespace x

tApplyCal namespace updates

Replace BOOST_CHECK(true)

use data range for repetitive tests

Remove last using namespace in tests

Rename tNDPPP -> tDPPP

Use single constant for number of channels.

tScaleData: Remove unused 'using casacore::Complex'.

tPSet: Use BOOST_CHECK_THROW; Use unique_ptr for input.

Refactor tStationAdder structure

- Use BOOST_CHECK_THROW
- Move test code inside BOOST_XXXX_TEST_CASE
- Use std::make_shared for steps

Boostify tInterpolateStep

Move and rename tInterpolate(Step).cc

Simplify tInterpolate

- Avoid using entire casacore namespace.
- Replace casacore vectors by std::vector.

tPSet: Replace scoping by separate tests

Remove unused includes

* Remove empty yaml keys; Fix ApplyBeam reference

* Remove double step step

* Add the missing doc types

* Baseline description now mentions the most common example

Also, there's an error in the Filter description.

* Minor doc fixes

* Skip invalid antennas in RotationAndDiagonalConstraint::Apply
* Let CMake manage C++ standard version
* Make phase referencing optional in RotationAndDiagonalConstraint
* Add test without phase reference.
Also add BOOST_DATA_TEST_CASE support to CMakeLists.txt
* Rename doPhaseReference -> doRotationReference
* Also rename phasereference in parset for RotAndDiag
* Add docs for phasereference and rotationreference
* Use false as default rotationreference setting.
* DDECal.yml: Use code style for mode=...
Co-authored-by: Maik Nijhuis <maik.nijhuis@triopsys.nl>

* Remove unused DPInput::ShPtr
* Add CMAKE_CXX_FLAGS_CUSTOM so one can use -Werror locally
* Add explicit fall through comments

The astron webserver apparently blocks the url "/inc"

Move documentation from https://www.astron.nl/lofarwiki/doku.php?id=public:user_software:documentation:ndppp to the source code. User docs are deployed to www.astron.nl/citt/DP3 .

Add design document

* Add .gitlab-ci.yml

* Change docker image name

* Make project name lowercase

* Add . in docker build command

* Add docker file for doxygen; CI attempt #1

* Make standalone CMakeLists.txt for docs

* Build doc outside docker

* Install and use ninja

* Make doxygen run without compiler

* Use docker:stable instead of alpine

* Do not build doxygen in docker

* Build no-lofar variant

* Remove travis configuration

* Remove unused docker image for doc

* De-duplicate DOCKER_IMAGE
Co-authored-by: Maik Nijhuis <maik.nijhuis@triopsys.nl>

* Change comments for Doxygen

Change the comments in the UVWFlagger to be compatible with Doxygen

* Change comments for Doxygen

Changed the comments in DPPP and AOFlaggerStep to be consistent with Doxyxen

* Replace nonstandard //# by // in license comments

* Replace //# by // at namespace ends

* Replace //# by ///< after variables

* Doxygenize DPPP/GridInterpolate.h

* Remove forward declaration comments

* Remove "//# Data members" comments

* Replace/remove remaining //# comments

* Replace // by /// in headers

* Fix ///< immediately after member definitions

* Tweak Doxygon output

Update header files in IDFPredict, ParmDB, PythonDPPP, SPWCombine and TestDynDPPP

* Update doxygen for AOFlagger and Blob directories

* Complete Doxygen for DPPP dir

* Fix groups for Doxygen

* Update doxygen for files in Common/

* Add missing gpl

* Update doxygen / add license headers for DDECal

* Doxygen cleanup

Replaced <group>, <src>, <srcblock>, <note> and other unsupported tags with their Doxygen variants

* Fix the class doxygen description

* Fix doxygen references and bad tags.

* Remove NDPPP group, use EXTRACT_ALL=yes
Co-authored-by: Lars Krombeen <krombeen@fs5.cm.cluster>
Co-authored-by: Lars Krombeen <lars.krombeen@cgi.com>

Set the README as the main page on the Doxygen output

Use binaries in Travis

Since travis/Github supports Ubuntu 20.04 now, casacore and aoflagger are available from debian.

* Check version of AOFlagger

This is in preparation of AOFlagger's 3.0 release, for which its API will change. By checking
inside CMake, the user is presented with an AOFlagger version error instead of
compilation errors once we switch. Also removes an unnecessary search for SIGC++

Build doxygen documentation

[ci skip]

[ci skip]

Make CMake smarter about finding python3

Add step for setting beam keywords

This is useful after a predict (with DP3 or image based with e.g. wsclean) in which no consideration of the beam was applied.
In that case, the visibilities are "corrected" for
the beam towards an arbitrary direction. If one source is predicted, it is as if the beam is corrected for in that direction.
This step makes that possible, and e.g. to unapply/corrupt for the beam after having predicted/fted the visibilities afterwards.

This fixes #236.

Fixes #231 .

* Fix compilation with g++ 10

g++ 10 is slightly stricter on what headers to include. Test with e.g. "CXX=/usr/bin/g++-10 cmake ../".

* Fix Travis using latest ubuntu

Travis 'suddenly' failed because a newer Ubuntu version is used now.

* Fix finding of Boost Python

Change check for pre-64bit rownrs to casacore 3.4