Feat seqflow recipe

[hannalee2]

Updates

• Added predefined protocols: Seqflow now uses predefined protocols by default, as users rarely provide custom jobs.
• Pump logic update: The pump now starts only when the volume > 0.
• Optional flow rate: Made flow_rate_mlpm optional in run_step to better support heat device and incubation wait cases.
• start_job input handling: Updated start_job to accept either a dictionary or a validated Job object. This fixes an issue where internally unpacking the arguments (**job) would fail if a Job object was passed instead of a dictionary.

Fixed Issues

• Pump: Set self._current_speed_mlpm = 0 when the speed argument is 0.

Merge Checklist

• update the changelog
• bump the version

[micahwoodard]

Should these protocols live somewhere like zookeeper or the local files? Feels weird to have them in the repo

[hannalee2]

That's a great point. These are essentially static baseline protocols that won't change, so having them version-controlled in the repo makes sense for consistency. Xiayin's team receives these protocols from the chemistry team and wants to prevent users from altering them, meaning the files need to stay exactly as they are. I agree that if we need to update them frequently in the future, we can definitely migrate them to Zookeeper or an external store.

If it is only for uder defined01.yml, I will follow up what is this file for.

[hannalee2]

I checked with Xiaoyin, and it turns out user_defined01.yml is treated like protocol files, which is rarely edited.
I will keep it in the protocols/ directory with the others, but I will rename it to something more descriptive so it doesn't look like a local user file. Xiaoyin will rename the file in the future and I will update accordingly.

[hannalee2]

@micahwoodard

After talking with Xiaoyin, he wants to keep a set of template protocols in the repo and store the actual protocols as local files. I think this structure will work well for this case. Let me know what you think. :) Thank you!

seqflow/
├── src/
│ └── seqflow/
│ └── seqflow.py
├── protocols/ <-- Template protocols (User can tests standalone seqflow using this protocols)
└── pyproject.toml

barseq-instrument/
├── src/
│ └── barseq_instrument/
│ └── main.py
├── protocols/ <-- Actual protocols to run
├── configs/ <-- Config file pointing the protocol files
└── pyproject.toml

[micahwoodard]

Would this be better abstracted in the config with this as the override?

[hannalee2]

030a347
Fixed :)