Add TS1 mechanism configuration and initial condtions to the examples

[carl-drews]

Added the following files to examples:
Directory of C:\2024\MusicBox\music-box-interactive-api\interactive\api\static\examples\TS1

08/01/2024 05:19 PM

.
08/01/2024 05:19 PM ..
08/01/2024 05:02 PM 67 config.json
08/01/2024 05:02 PM 7,627 initial_conditions.csv
08/01/2024 05:02 PM 160,424 reactions.json
08/01/2024 05:02 PM 33,014 species.json
4 File(s) 201,132 bytes
2 Dir(s) 198,050,938,880 bytes free

Use Docker to verify that the JSON files are retrievable, for example:
http://localhost:8000/api/load-example?example=TS1

[K20shores]

This is almost correct. The top level folder needs to have a my_config.json, like the other three examples have. You should (I hope) be able to run your command line music box client on any of the examples by pointing them to the top level folder of any of the examples

[mattldawson]

Just noticed the tests are failing - is this something unrelated to this PR?

[carl-drews]

I don't know why the checks are failing; it looks like the docker-compose command is not found.

TS1 and CHAPMAN run to completion and produce output.
FLOW_TUBE does not run because of differences among FLOW_* macros. See Slack.
FULL_GAS_PHASE does not run because of "description". See Slack.

[carl-drews]

Ready for another round of reviews after addressing requests. Note that TS1 will not run without this python change in music_box.py on about line 721. The addresses a gap in the ordered sequencing:

        rate_constants = {}
        for rate in curr_conditions.reaction_rates:

            if (rate.reaction.reaction_type == "PHOTOLYSIS"):
                key = "PHOTO." + rate.reaction.name
            elif (rate.reaction.reaction_type == "LOSS"):
                key = "LOSS." + rate.reaction.name
            elif (rate.reaction.reaction_type == "EMISSION"):
                key = "EMIS." + rate.reaction.name
            rate_constants[key] = rate.rate

        **ordered_rate_constants = (len(rate_constants.keys()) + 1) * [0.0]   # bogus + 1**

[K20shores]

The test failure is nothing to do with the code added here, and something with the action. I fixed it in #422

[boulderdaze]

Looks good! Thank you for addressing them!

[carl-drews]

Formatted with indent = 2 spaces.

[carl-drews]

TS1 is ready for further development (restore initial conditions).