Remove src_postgres

[infotroph]

This is a continuation of PR #2785, which we can no longer update because of an accidentally deleted source branch that turned out to be more hassle to fix than seemed worth it. All the commits from #2785 are contained here and all comments from that discussion thread are now resolved.

Description

• Removed all remaining calls to dplyr::src_postgres, mostly by replacing with PEcAn.DB::db.open() but sometimes with DBI::dbConnect() in places that are run without the PEcAn packages available. Fixes src_postgres needs to be deprecated everywhere #2688
• Converted all bety <- db.open(...); con <- bety$con to con <- db.open(...)
• Converted all bety$con to just bety (or con, in cases where bety was renamed in previous step)
• Converted most existing DBI::dbConnect(...) calls to PEcAn.DB::db.open(...), except in contexts where PEcAn.DB may not be available (e.g. pecanapi demo) or to access non-PEcAn databases (e.g. some examples in DB package)
• Consistently pass all of settings$database$bety into db.open() rather than pick out individual components. Attn @istfer: I believe this should allow port specification to work consistently as requested in src_postgres needs to be deprecated everywhere #2688 (comment)

Motivation and Context

dplyr::src_postgres() is now deprecated and the advice is to instead directly pass a DBI connection into dplyr::tbl(). We've previously replaced a few of these piecemeal, but not systematically (as evidenced by all the places the code was handling both bare con and bety$con).

Review Time Estimate

• Immediately
• Within one week
• When possible

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)

Checklist:

• My change requires a change to the documentation.
• My name is in the list of .zenodo.json
• I have updated the CHANGELOG.md.
• I have updated the documentation accordingly.
• I have read the CONTRIBUTING document.
• I have added tests to cover my changes.
• All new and existing tests passed.

[dlebauer]

Did you update the changelog?-- David

…

-- David LeBauer Director of Data Sciences CALS Comm and Technologies THE UNIVERSITY OF ARIZONA BSRL, 207 1230 N Cherry Ave | Tucson, AZ 85721 Office: 520-621-4381 | Cell: 760-468-8621 ***@***.*** datascience.cals.arizona.edu orcid | twitter | github | linkedin

[infotroph]

Did you update the changelog?
@dlebauer Yes! Thanks for checking. https://github.com/PecanProject/pecan/pull/2881/files#diff-06572a96a58dc510037d5efa622f9bec8519bc1beab13c9f251e97e657a9d4edR13

[istfer]

I guess there isn't much to be done with these hardcoded ones (regarding the port I mean)

[infotroph]

Yeah, these need to be addressed sometime but this refactor was sprawling far enough as it is :p

[infotroph]

@robkooper Can you squash-merge this, please? The commits contain a lot of back and forth that doesn't need to be preserved.

[robkooper]

done