Eric R. Scott

macOS now uses Zsh as default shell

2

### How could the content be improved? It would be good to mention Zsh early on in the episode now that it is the [default shell](https://support.apple.com/guide/terminal/change-the-default-shell-trml113/mac) on macOS. For example,...

`src_dbi()` has been superseded/deprecated

1

https://github.com/datacarpentry/R-ecology-lesson/blob/ac8b94ee5d1a806a85280093a497cf433e08ba32/05-r-and-databases.Rmd#L110 According to the documentation `dbplyr::src_dbi()` is superseded and `dplyr::src_dbi()` is deprecated. Looking at the `dbplyr` documentation, it looks like the recommended way to do this is with `DBI::dbListTables(mammals)`

Broken link and missing documentation for `cos_solar_zenith_angle()`

2

### Bug Description The documentation for `cos_solar_zenith_angle()`, an exported function in `PEcAn.data.atmosphere` has only a 1 sentence description that points the user to what is now a spam gambling website....

Improve CONTRIBUTING.md

7

The contents of CONTRIBUTING is mostly generic about getting started with git and github. This should contain things like: - How to write tests for functions that need BETY -...

Use DB mocking for tests that require BETY?

3

## Description Tests for some packages fail in environments without access to BETYdb. E.g. [PEcAn.BIOCRO](https://github.com/r-universe/pecanproject/actions/runs/3353111973/jobs/5584238472). ## Proposed Solution I'm familiar with "webmocking", where requests to an API are stored and...

Use `options()` for project-level settings like `write`

1

## Description I'll use `settings$database$bety$write` as an example, but this likely applies to other settings. Currently, the `settings` object, or pieces of it, get passed down to functions to determine...

Uninformative error when machine id isn't registered in BETY

1

### Bug Description If the hostname in pecan.xml isn't registered in BETY, then `prepare.settings()` errors with the following: ``` Error in postgresqlExecStatement(conn, statement, ...) : RPosgreSQL error: could not Retrieve...

Add keywords to DESCRIPTION files

3

[r-universe](https://pecanproject.r-universe.dev/ui#packages) pulls tags for PEcAn packages from the GitHub repo tags. BUT we can also supply package-specific tags in DESCRIPTION files by adding `X-schema.org-keywords:` For example: https://github.com/ropensci/elastic/blob/master/DESCRIPTION Let's use this...

wrong dimensions assigned for some variables by `model2netcdf.ED2()`

2

### Bug Description Consistently get warnings from `ncvar_put()` like: >[1] "ncvar_put: warning: you asked to write 6912 values, but the passed data array has 12288 entries!" I think this is...

Only write params with priors and/or data to config.xml

8

## Description Testing out what happens when PEcAn.ED2 doesn't write default constants to config.xml. An extreme fix for #3124 ## Motivation and Context Would simplify PEcAn.ED2 code a lot and...