New Person Onboarding

[mikehsu90]

Hello! I am new to RuFaS and today was my first day getting started - I found this getting started onboarding super useful! https://ruminantfarmsystems.github.io/RuFaS/_wiki/onboarding.html

A few notes / questions:

1. In the guide, there's an instruction to place your cursor in the terminal and type in the command: pip install -r requirements.txt but I got an error. Running pip install . instead seems to work - I suspect the presence of a pyproject.toml file makes this possible as there's no requirements.txt file
2. When I run “python main.py” I keep getting the following errors and I am unable to debug:

[14-Oct-2025_Tue_17-48-46.265724][ERROR][freestall] units_key_error. Key 'lactating' not found in the units dictionary for variable 'AnimalModuleReporter.report_milk.milk_data_at_milk_update'.
[14-Oct-2025_Tue_17-48-46.410668][ERROR][freestall] units_key_error. Key 'ammonia_emissions' not found in the units dictionary for variable 'EmissionsEstimator._calculate_homegrown_feed_emissions.homegrown_alfalfa_silage_emissions'.
[14-Oct-2025_Tue_17-48-46.411309][ERROR][freestall] units_key_error. Key 'ammonia_emissions' not found in the units dictionary for variable 'EmissionsEstimator._calculate_homegrown_feed_emissions.homegrown_alfalfa_hay_emissions'.

3. (perhaps related to 2) What is the branch I should be pulling from? main wasn't updated over a year ago, and doesn't have the example files in the onboarding wiki above? Dev is updated more frequently (4 days ago) but has the issue as seen in 2

4. In the Onboarding wiki, Step 8 references a "Step 11" to generate Reports and Graphs, but Step 11 does not exist

5. Can we provide output filters in the Wiki? I tried using Where are the outputs?? #2548 and got some manure graphs but I am unclear if the errors I am getting in 2 is affecting the long report error logs I am also getting. I would love to get a copy of the output filter files that Joseph Waddell used in his video here: https://www.youtube.com/watch?v=A_u2cxla42c

6. Is there a way to see "expected outputs" from the onboarding exercise? That way we can tell if I am setup or I have some underlying issue from the above errors / warnings?

Feel free to re-direct me to another channel or forum for my onboarding questions! Much appreciated, and thanks in advance for your help!

[mikehsu90]

cc @KFosterReed as I found your previous post helpful!

[JoeWaddell]

1. Great flag: we're in the process of updating our onboarding resources, so this is timely! As you worked out, using pip install . is the updated way to install requirements. @ew3361zh helped with this update, so tagging him here in case he has more guidance on this particular bit.
2. I haven't seen this myself, so perhaps if others have run into something similar they can offer guidance.
3. dev is the most updated, but requires the occasional hotfix. main will be the ideal branch in the future, once updated.
4. Another good flag, thank you! While you've likely found it already, for others reading: https://ruminantfarmsystems.github.io/RuFaS/_wiki/Report-Generator.html and https://ruminantfarmsystems.github.io/RuFaS/_wiki/Graph-Generator.html hold the info referenced.
5. I'll need to update the filters I used in that video, as we've made significant progress since (and some variable names have been updated), but in the meantime those in the above two links should provide a good start for anyone looking to build their own. Are there any in particular from the video you were most interested in?
6. Perhaps other developers have a good solution here: I think being able to successfully run the unit tests would be a relatively straightforward way to ensure everything is set up properly, but even that might be overcomplicated, so I'll hold off on guessing and let others chime in.

Glad you've found our resources useful so far, and thanks for the good questions!

[PooyaHekmati]

Thanks for bringing this to our attention @mikehsu90 , issue #2610 tracks the error messages you encountered.

[mikehsu90]

Thank you both - much appreciated! I’ll keep digging through the documentation. Really looking forward to the updated onboarding resources, as I would love to send more folks that way to get them up-to-speed on the model.

@JoeWaddell, I’m exploring how to quantify emissions reductions from shifting to grazing heifers. As a starting point, I’d like to include Grazing, Feed Production, Enteric Fermentation, and Manure Management in the analysis. What would be the best way to set up an initial report that captures all of these?

@PooyaHekmati Thanks for creating the issue! I added a comment to #2610 to help reproduce - let me know if you need anything else!

[JoeWaddell]

So the best way to start is to look through the (long) log of variable names: see the output/logs/freestall_variable_names###.txt file after running a simulation. There you can see every output variable possible! Then searching within that file, you can start to see what is available that hits some keywords (even partial keywords, if things are abbreviated due to length).

It is a little daunting at first, but if you make a list of those that seem like they're of interest, you could start building from there - I start by capturing the variables in different .csv outputs, just to see the raw data prior to any aggregation in e.g. a report filter, and to start organizing things. From there, you can start playing with the aggregation methods in the report functionality! Often I go from raw data then to making graphics, but everyone has their own process!

[mikehsu90]

Thank you! Was able to find the log - there's a LOT of variables, will play around with it!