ropensci / SymbiotaR2

SymbiotaR2: an R package for accessing and downloading from Symbiota2 portals
MIT License
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Draft ROpenSci Checklist #7

Closed akoontz11 closed 4 years ago

akoontz11 commented 4 years ago

Below is the demo ROpenSci issue list. Let me know what looks incorrect. The 3 items I'm unsure on are:

  1. Package categories,
  2. The technical checkbox for continuous integration (CI)? We didn't reference the usethis package at all, or Travis--but my understanding in this area is limited.
  3. Confirmation that we intend for this package to go onto CRAN afterwards? I ask because the testing section on the ROpenSci dev guide talks about a skip_on_cran() command that we'll seem to need if we are to submit there...

Submitting Author: Austin Koontz (@akoontz11 )
Repository: https://github.com/pearselab/SymbiotaR2 Version submitted: 0.0.1 Editor: TBD
Reviewer 1: TBD
Reviewer 2: TBD
Archive: TBD
Version accepted: TBD


Package: SymbiotaR2
Type: Package
Title: Downloading data from Symbiota2 portals into R
Version: 0.0-1
Authors@R: c(person("Austin", "Koontz", email = "austin.koontz@usu.edu", role = c("aut", "cre")),
    person("William D.", "Pearse", email = "will.pearse@gmail.com", role ="aut", comment=c(ORCID="0000-0002-6241-3164")))
Maintainer: Austin Koontz <austin.koontz@usu.edu>
Description: Download data from Symbiota2 portals using Symbiota's
    API. Covers the Checklists, Collections, Crowdsource, Exsiccati,
    Glossary, ImageProcessor, Key, Media, Occurrence, Reference, Taxa,
    Traits, and UserRoles API families. Each Symbiota2 portal owner
    can load their own plugins (and modified code), and so this
    package may not cover every possible API endpoint from a given
    Symbiota2 instance.
License: MIT + file LICENSE
URL: https://github.com/pearselab/SymbiotaR2
BugReports: https://github.com/pearselab/SymbiotaR2/issues
VignetteBuilder: knitr
LazyLoad: yes
Suggests:
    knitr (>= 1.23),
    testthat (>= 2.0.0),
    vcr (>= 0.3.0)  
Imports:
    httr (>= 1.0.0),
    xml2 (>= 1.2.0),
    rjson (>= 0.2.20),
    fs (>= 1.2.6)
Encoding: UTF-8
RoxygenNote: 7.0.2

Scope

The primary purpose of SymbiotaR2 is to allow users to pull objects from the specified Symbiota2 database portal into an R environment. It does this by wrapping each of the default API calls made available on the Symbiota2 portal of interest.

The target audiences includes anyone interested in using R to analyze biological specimen data made available through the Symbiota2 content management system. Potential scientific applications include comparing biological trait data between different lineages, analyzing phenological data, and biodiversity research generally.

No R packages have been developed for the updated code structure provided by Symbiota2.

Technical checks

Confirm each of the following by checking the box. This package:

Publication options

JOSS Options - [x] The package has an **obvious research application** according to [JOSS's definition](https://joss.readthedocs.io/en/latest/submitting.html#submission-requirements). - [x] The package contains a `paper.md` matching [JOSS's requirements](https://joss.readthedocs.io/en/latest/submitting.html#what-should-my-paper-contain) with a high-level description in the package root or in `inst/`. - [ ] The package is deposited in a long-term repository with the DOI: - (*Do not submit your package separately to JOSS*)
MEE Options - [ ] The package is novel and will be of interest to the broad readership of the journal. - [ ] The manuscript describing the package is no longer than 3000 words. - [ ] You intend to archive the code for the package in a long-term repository which meets the requirements of the journal (see [MEE's Policy on Publishing Code](http://besjournals.onlinelibrary.wiley.com/hub/journal/10.1111/(ISSN)2041-210X/journal-resources/policy-on-publishing-code.html)) - (*Scope: Do consider MEE's [Aims and Scope](http://besjournals.onlinelibrary.wiley.com/hub/journal/10.1111/(ISSN)2041-210X/aims-and-scope/read-full-aims-and-scope.html) for your manuscript. We make no guarantee that your manuscript will be within MEE scope.*) - (*Although not required, we strongly recommend having a full manuscript prepared when you submit here.*) - (*Please do not submit your package separately to Methods in Ecology and Evolution*)

Code of conduct

willpearse commented 4 years ago

I've added "data retrieval" to the categories. We will have Travis-CI (running now, although it will fail because not all the tests work). Once that's up and running, I'll setup Coveralls. I'll show you how I do that once it's done; it's fiddly... We don't need to worry about the skip_on_cran stuff because we're using vcr to circumvent that.

akoontz11 commented 4 years ago

Closing this issue, as official ROpenSci Checklist exists.