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Rebase minor timing difference from the circuit calculator updates, maybe? Also taking out Black Box unit tests until we finalize integration testing

Preserve CDM property bag objects

See merge request !65

Rebase due to change in preserving gasses to maintain objects rather than delete. Small mathmatical error in this scenario due to this change.

Rebase due to not throwing a uncaught fatal exception when the engine hits irreversable state anymore in the JNI. Now there is one extra time step in the file before a graceful shutdown

Jeff Webb authored Oct 08, 2020 and Aaron Bray committed Oct 16, 2020

(cherry picked from commit 0221c883885032697552b748bc0b7bb3813681f4)

(Or a directory containing 2 csv files)

There is no point in throwing here, there is nobody to catch this, let the Java side worry about Fatal messages

(cherry picked from commit 0cce7ec8)

CDM Clearing

See merge request !64

co-author: Jeff Webb
The original history of the black box implmentation was done on 2.x and merging into 3.x was too painful

Jeff Webb authored Sep 11, 2020 and Aaron Bray committed Sep 14, 2020

Updates to make respiratory able to function standable and without cardiovascular or blood chemistry inputs.

(cherry picked from commit 3deecfdbe8b043aca0bc3cb512f1baec707c906b)

Fix use of protobuf from build

See merge request !63

Use different input files to generate the CMake package configuration
for the build tree and the install tree. This avoids the build tree
trying to refer to our installed copy of protobuf which won't exist if
we haven't been installed. This does require a full copy of protobuf (as
opposed to just the libraries) when we are used from the build tree, but
since we needed that to build, it ought to be available.

Also, fix a small issue in how we check whether we need to use our
internal copy of protobuf.

Optimize data tracking

See merge request !62