gittargets: data version control for the targets package

@wlandau

Date accepted: 2022-01-12
Submitting Author Name: Will Landau
Submitting Author Github Handle: @wlandau
Repository: https://github.com/wlandau/gittargets
Version submitted: 0.0.0.9000
Submission type: Standard
Editor: @adamhsparks
Reviewers: @smwindecker, @mdneuzerling

Due date for @smwindecker: 2021-12-20

Due date for @mdneuzerling: 2021-12-28
Archive: TBD
Version accepted: TBD
Language: en

Paste the full DESCRIPTION file inside a code block below:

Package: gittargets
Title: Data Version Control for the Targets Package
Description: Version control systems such as Git help researchers
  track changes and history in data science projects,
  and the 'targets' package (2021, <doi:10.21105/joss.02959>)
  minimizes the computational cost of keeping the latest results
  reproducible and up to date. The 'gittargets' package
  combines these two capabilities. The 'targets' data store
  becomes a version control repository and stays synchronized
  with the Git repository of the source code.
  Users can switch commits and branches
  without invalidating the 'targets' pipeline.
Version: 0.0.0.9000
License: MIT + file LICENSE
URL: https://wlandau.github.io/gittargets/, https://github.com/wlandau/gittargets
BugReports: https://github.com/wlandau/gittargets/issues
Authors@R: c(
  person(
    given = c("William", "Michael"),
    family = "Landau",
    role = c("aut", "cre"),
    email = "will.landau@gmail.com",
    comment = c(ORCID = "0000-0003-1878-3253")
  ),
  person(
    family = "Eli Lilly and Company",
    role = "cph"
  ))
Depends:
  R (>= 3.5.0)
Imports:
  cli (>= 3.0.0),
  data.table (>= 1.12.8),
  gert (>= 1.0.0),
  processx (>= 3.0.0),
  stats,
  targets (>= 0.8.1.9000),
  tibble (>= 3.0.0),
  utils,
  uuid (>= 1.0.0)
Suggests:
  knitr (>= 1.30),
  markdown (>= 1.1),
  rmarkdown (>= 2.4),
  testthat (>= 3.0.0)
Remotes:
  ropensci/targets
SystemRequirements: Git (>= 2.0.0)
Encoding: UTF-8
Language: en-US
VignetteBuilder: knitr
Config/testthat/edition: 3
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.2

Scope

Please indicate which category or categories from our package fit policies this package falls under: (Please check an appropriate box below. If you are unsure, we suggest you make a pre-submission inquiry.):
- data retrieval
- data extraction
- data munging
- data deposition
- workflow automation
- version control
- citation management and bibliometrics
- scientific software wrappers
- field and lab reproducibility tools
- database software bindings
- geospatial data
- text analysis
Explain how and why the package falls under these categories (briefly, 1-2 sentences):

Version control systems such as Git help researchers track changes and history in data science projects, and the targets package minimizes the computational cost of keeping the latest results reproducible and up to date. The gittargets package combines these two capabilities. The targets data store becomes a version control repository and stays synchronized with the Git repository of the source code. Users can switch commits and branches without invalidating the targets pipeline.

Who is the target audience and what are scientific applications of this package?

gittargets is for people who use targets for reproducible analysis pipelines and Git for tracking the code files of those pipelines.

Are there other R packages that accomplish the same thing? If so, how does yours differ or meet our criteria for best-in-category?

Packages gh, gert, git2r, and git2rdata all work with Git from R, but in a way that is more general, less opinionated, and less targets-specific than gittargets. gittargets establishes a separate repository for the targets data that is linked to the project's code repository. This allows the code and data to synchronize without affecting the efficiency or the size of the code repository.

(If applicable) Does your package comply with our guidance around Ethics, Data Privacy and Human Subjects Research?

N/A

If you made a pre-submission inquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted.

N/A

Technical checks

Confirm each of the following by checking the box.

I have read the guide for authors and rOpenSci packaging guide.

This package:

does not violate the Terms of Service of any service it interacts with.
has a CRAN and OSI accepted license.
contains a README with instructions for installing the development version.
includes documentation with examples for all functions, created with roxygen2.
contains a vignette with examples of its essential functions and uses.
has a test suite.
has continuous integration, including reporting of test coverage using services such as Travis CI, Coveralls and/or CodeCov.

Publication options

Do you intend for this package to go on CRAN?
Do you intend for this package to go on Bioconductor?
Do you wish to submit an Applications Article about your package to Methods in Ecology and Evolution? If so:

MEE Options

[n/a] The package is novel and will be of interest to the broad readership of the journal.
[n/a] The manuscript describing the package is no longer than 3000 words.
[n/a] 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)
(Scope: Do consider MEE's Aims and Scope 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

I agree to abide by rOpenSci's Code of Conduct during the review process and in maintaining my package should it be accepted.

@ropensci-review-bot

Thanks for submitting to rOpenSci, our editors and @ropensci-review-bot will reply soon. Type @ropensci-review-bot help for help.

🚀

Error: Issue template has no 'repourl'

👋

Missing values: author1, repourl

Sorry about that, should be fixed now.

@ropensci-review-bot

@ropensci-review-bot check package

Thanks, about to send the query.

🚀

Editor check started

👋

Checks for gittargets (v0.0.0.9000)

git hash: b6eadc4b

✔️ Package name is available
✔️ has a 'CITATION' file.
✔️ has a 'codemeta.json' file.
✔️ has a 'contributing' file.
✔️ uses 'roxygen2'.
✔️ 'DESCRIPTION' has a URL field.
✔️ 'DESCRIPTION' has a BugReports field.
✔️ Package has at least one HTML vignette
✔️ All functions have examples.
✔️ Package has continuous integration checks.
✖️ Package coverage is 13.3% (should be at least 75%).
✔️ R CMD check found no errors.
✔️ R CMD check found no warnings.

Important: All failing checks above must be addressed prior to proceeding

Package License: MIT + file LICENSE

1. Statistical Properties

This package features some noteworthy statistical properties which may need to be clarified by a handling editor prior to progressing.

Details of statistical properties (click to open)

The package has:

code in R (100% in 15 files) and
1 authors
1 vignette
no internal data file
9 imported packages
9 exported functions (median 23 lines of code)
94 non-exported functions in R (median 6 lines of code)

Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages
The following terminology is used:

loc = "Lines of Code"
fn = "function"
exp/not_exp = exported / not exported

The final measure (fn_call_network_size) is the total number of calls between functions (in R), or more abstract relationships between code objects in other languages. Values are flagged as "noteworthy" when they lie in the upper or lower 5th percentile.

measure	value	percentile	noteworthy
files_R	15	70.6
files_vignettes	0	0.0	TRUE
files_tests	17	94.1
loc_R	663	53.5
loc_tests	417	68.5
num_vignettes	1	60.7
n_fns_r	103	71.7
n_fns_r_exported	9	38.9
n_fns_r_not_exported	94	76.9
n_fns_per_file_r	4	51.7
num_params_per_fn	4	54.3
loc_per_fn_r	7	23.4
loc_per_fn_r_exp	23	54.1
loc_per_fn_r_not_exp	6	29.1
rel_whitespace_R	6	24.3
rel_whitespace_tests	7	76.1
doclines_per_fn_exp	62	74.1
doclines_per_fn_not_exp	0	0.0	TRUE
fn_call_network_size	123	80.4

1a. Network visualisation

Click to see the interactive network visualisation of calls between objects in package

2. `goodpractice` and other checks

Details of goodpractice and other checks (click to open)

3a. Continuous Integration Badges

GitHub Workflow Results

name	conclusion	sha	date
check	success	b6eadc	2021-11-17
cover	success	b6eadc	2021-11-17
lint	success	b6eadc	2021-11-17
pkgdown	success	b6eadc	2021-11-17

3b. `goodpractice` results

`R CMD check` with rcmdcheck

rcmdcheck found no errors, warnings, or notes

Test coverage with covr

Package coverage: 13.35

The following files are not completely covered by tests:

file	coverage
R/tar_git_checkout.R	0%
R/tar_git_init.R	0%
R/tar_git_log.R	0%
R/tar_git_ok.R	0%
R/tar_git_snapshot.R	0%
R/tar_git_status_code.R	0%
R/tar_git_status_data.R	0%
R/tar_git_status_targets.R	0%
R/tar_git_status.R	0%
R/utils_assert.R	0%
R/utils_git.R	30.77%

Cyclocomplexity with cyclocomp

No functions have cyclocomplexity >= 15

Static code analyses with lintr

lintr found no issues with this package!

Package Versions

package	version
pkgstats	0.0.2.72
pkgcheck	0.0.2.107

Editor-in-Chief Instructions:

Processing may not proceed until the items marked with ✖️ have been resolved.

gittargets requires command line Git in order for git-lfs to work (related: r-lib/gert#160). The majority of tests will automatically be skipped if tar_git_ok() returns FALSE. Is there still a path forward?

Yeah, that makes sense. I'll get started on getting this moving.

@wlandau

And I'll check out why coverage might have failed tomorrow, although git is definitely installed. @wlandau Nothing you need to worry about, thanks.

Edit: For the record, @wlandau helped debug there, and the bot checks now give coverage of 100% 🚀 💯

Thank you both!

Related: I have not been able to correctly set up Git on the Windows GitHub Actions for gittargets. I tried a bunch of different approaches, but I still get errors claiming I need to configure git config --global user.name and git config --global user.email. The other runners appear to work just fine though, including the one that checks coverage.

@ropensci-review-bot

@ropensci-review-bot assign @adamhsparksas editor

@ropensci-review-bot

@ropensci-review-bot assign @adamhsparks as editor

@adamhsparks

@adamhsparks Sorry about that! Done.

@wlandau

Well done, @wlandau! Thanks for this new package submission to rOpenSci. I'm guessing you know the drill now. If you need assistance with anything, please let me know.

@adamhsparks

Amazing! Thanks @adamhsparks for facilitating the process and thanks @smwindecker and @mdneuzerling for the reviews! gittargets is in much better shape now, especially regarding documentation.

@adamhsparks, would you be willing to grant me admin permissions at https://github.com/ropensci/gittargets? The rOpenSci transfer process still removes that on my end.

@ropensci-review-bot

Ah, sorry I didn't see this:

After transfer write a comment @ropensci-review-bot finalize transfer of where is the repo/package name. This will give you admin access back.

@ropensci-review-bot

@ropensci-review-bot finalize transfer gittargets

@ropensci-review-bot

@ropensci-review-bot finalize transfer

@ropensci-review-bot

@ropensci-review-bot finalize transfer of gittargets

Transfer completed. The gittargets team is now owner of the repository

I still do not have admin permissions. Did I need to add myself to the gittargets team in advance?

Other than that, I believe all the to-dos are now complete.

@wlandau

@wlandau I've now added you to that team. You hadn't received any invitation to it beforehands, correct? Thanks for the bug catching. 🙏

@maelle

Thanks, @maelle! I did not receive an invitation before, but I do have admin permissions now.

Very minor: on my end, it looks like the rOpenSci README badge still says "Under Review". Are these badges still supported?

@wlandau

Sorry @wlandau, our badge server went to sleep a month ago without anybody realising - I've re-enabled it, so it should update soon.

Thanks Mark! Looks to be fixed.

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gittargets: data version control for the targets package #486

Due date for @mdneuzerling: 2021-12-28
Archive: TBD
Version accepted: TBD
Language: en

Scope

Technical checks

Publication options

Code of conduct

Checks for gittargets (v0.0.0.9000)

1. Statistical Properties

1a. Network visualisation

2. `goodpractice` and other checks

3a. Continuous Integration Badges

3b. `goodpractice` results

`R CMD check` with rcmdcheck

Test coverage with covr

Cyclocomplexity with cyclocomp

Static code analyses with lintr

Editor-in-Chief Instructions:

49 remaining items

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gittargets: data version control for the targets package #486

Description

Due date for @mdneuzerling: 2021-12-28 Archive: TBD Version accepted: TBD Language: en

Scope

Technical checks

Publication options

Code of conduct

Activity

ropensci-review-bot commented on Nov 17, 2021

ropensci-review-bot commented on Nov 17, 2021

ropensci-review-bot commented on Nov 17, 2021

wlandau commented on Nov 17, 2021

ldecicco-USGS commented on Nov 17, 2021

ropensci-review-bot commented on Nov 17, 2021

ropensci-review-bot commented on Nov 17, 2021

ropensci-review-bot commented on Nov 17, 2021

Checks for gittargets (v0.0.0.9000)

1. Statistical Properties

1a. Network visualisation

2. goodpractice and other checks

3a. Continuous Integration Badges

3b. goodpractice results

R CMD check with rcmdcheck

Test coverage with covr

Cyclocomplexity with cyclocomp

Static code analyses with lintr

Editor-in-Chief Instructions:

wlandau commented on Nov 17, 2021

ldecicco-USGS commented on Nov 17, 2021

mpadge commented on Nov 17, 2021

wlandau commented on Nov 17, 2021

ldecicco-USGS commented on Nov 18, 2021

ldecicco-USGS commented on Nov 18, 2021

49 remaining items

mdneuzerling commented on Jan 12, 2022

adamhsparks commented on Jan 12, 2022

wlandau commented on Jan 12, 2022

wlandau commented on Jan 12, 2022

wlandau commented on Jan 12, 2022

wlandau commented on Jan 12, 2022

wlandau commented on Jan 12, 2022

ropensci-review-bot commented on Jan 12, 2022

wlandau commented on Jan 12, 2022

wlandau commented on Jan 12, 2022

maelle commented on Jan 13, 2022

wlandau commented on Jan 13, 2022

wlandau commented on Jan 18, 2022

mpadge commented on Jan 18, 2022

wlandau commented on Jan 19, 2022

Metadata

Metadata

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Labels

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Development

Issue actions

Due date for @mdneuzerling: 2021-12-28
Archive: TBD
Version accepted: TBD
Language: en

2. `goodpractice` and other checks

3b. `goodpractice` results

`R CMD check` with rcmdcheck