There's a ton of documentation on the importers, but it doesn't say much 
about how data actually gets from the extractor into beancount.  The only 
thing I can find is a sentence that mentions that bean-extract "produces 
some Beancount input text to be moved to your input file".
 

Is the process of adding data to your Beancount input file intended to be a 
manual copy/paste one?


Correct. Eg: "Putting it All Together into a Workflow 
<https://reds-rants.netlify.app/personal-finance/putting-it-all-together-into-a-workflow/>
"
 

If for some reason you need to re-import some data that you'd already 
imported and added to your beancount input file, is it your responsibility 
to manually go find the records in the input file that came from that 
import, remove them, and replace them with the new import data?  Is there 
some method or tool for tracking or managing how the beancount input file 
is composed from all the sources?


The ingest code has a function to identify duplicates that you can 
use/adapt.
 

Let's say you run Beancount and it makes some decisions for you -- for 
example, matching asset sales with corresponding lots for cap gains 
computation.  You use these to file your taxes.  How do you make a record 
of those decisions and enforce that a later run of Beancount doesn't change 
them (e.g., if next tax year you switch to a different booking method)?


You get to declare lot matching in your file (FIFO, NONE, STRICT, etc.). As 
long as the Beancount code doesn't change its output (and it shouldn't), 
it'll produce the same output given the same input.

The more general problem here is one of snapshotting your accounts. 
Beancount is best used by software engineers, and thus, version control 
(git), tagging, and such work well. I generate a tax reference output file 
for each year 
<https://reds-rants.netlify.app/personal-finance/computing-taxes-with-beancount/>,
 
and occasionally re-generate and compare with the reference to ensure 
nothing's changed.

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