* This image is multi-stage. Each stage tailored for one stage on the pipeline
* Final image has a much less weight due to copying binaries to a new image and downloading essential dependencies.

* This changes allow to import and use targets by just finding the dune-copasi library. No dune library required for downstream project.
* The testing library may be used as a subfolder or as a dune-copasi downstream project.
* The config file is installed so that non-dune users may just include the config definitions without re-generation of the file.
* Python project not setup. It is not doing anything anyways.
* Updated dune module requirements to 2.7
* Adds basic information for CMake packaging

Now targets seem to be importable in a very simple manner.

The old installation procedure was not very good wrt folder destination. Now, /opt/dune/ is suggested to host the final files

CMake 3.13 seems to have a problem with this. Here, the targets are not set up at all according to the cache variables and only set up targets will be compiled and installed

That's because TIFF images are clamped instead of zeroed when evaluated outside its domain

Liam Keegan authored 4 years ago and Santiago Ospina De Los Ríos committed 4 years ago

* fix pixel index rounding bug
* remove offset instead of adding it
* clamp invalid indices to nearest valid pixel instead of returning zero

Santiago Ospina De Los Ríos authored 4 years ago and Santiago Ospina De Los Ríos committed 4 years ago

* When intersection is a boundary, there is no outside entity and segfault is thrown. That's fixed here by checking if it has a neighbor entity.
* After some review, the skip method interface was modified to return bool instead of passing bool reference. This should not affect branches that do not support skip methods.

Santiago Ospina De Los Ríos authored 4 years ago and Santiago Ospina De Los Ríos committed 4 years ago

If this function is consumed by another program by 
a library, macOS llvm complains that it cannot override 
weak variable at run time.

Santiago Ospina De Los Ríos authored 4 years ago and Santiago Ospina De Los Ríos committed 4 years ago

When the Dune::Copasi::Impl namespace was introduced, the compiler complains that this line has not a clear namespace reference

Santiago Ospina De Los Ríos authored 4 years ago and Santiago Ospina De Los Ríos committed 4 years ago

If the compartment names happen to not be ordered in the same way as their indices, this could introduce a parsing error.

Santiago Ospina De Los Ríos authored 4 years ago and Santiago Ospina De Los Ríos committed 4 years ago

* Some typos are fixed
* The boundary subsection of the new membranes is fixed

Santiago Ospina De Los Ríos authored 4 years ago and Santiago Ospina De Los Ríos committed 4 years ago

This was introduced by mistake some time ago. It was not ready, and never evolved to anything concrete.