{weatherOz}: an API Client for Australian Weather and Climate Data Resources

bozaah commented 11 months ago

Date accepted: 2024-02-09

Submitting Author Name: Rodrigo Pires

Author Github Handle: !--author1-->@bozaah<!--end-author1--

Other Package Authors Github handles:@adamhsparks, @arhepworth, @jimii19, @syntrix, @becoleary, @HughParsonage, @PaulMelloy, @jonocarroll, @deanmarchiori, @jimjam-slam, @mpadge, @Keith-Pembleton, @maelle

Repository: https://github.com/DPIRD-FSI/weatherOz

Version submitted: v0.0.1

Submission type: Standard

Editor: !--editor-->@ldecicco-USGS<!--end-editor--

Reviewers: @JanLauGe, @rogerssam

Archive: TBD

Version accepted: TBD

Language: en

Paste the full DESCRIPTION file inside a code block below:

Package: weatherOz
Title: An API Client for Australian Weather and Climate Data Resources
Version: 0.0.1
Authors@R: c(
  person(
    given = "Rodrigo",
    family = "Pires",
    role = c("aut", "cre"),
    email = "rodrigo.pires@dpird.wa.gov.au",
    comment = c(ORCID = "0000-0001-7384-6849")
  ),
  person(
    given = "Anna",
    family = "Hepworth",
    role = "aut",
    email = "anna.hepworth@dpird.wa.gov.au",
    comment = c(ORCID = "0000-0003-0204-6347")
  ),
  person(
    given = "Rebecca",
    family = "O'Leary",
    role = "aut",
    email = "bec.oleary@curtin.edu.au"
  ),
  person(
    given = "Jonathan",
    family = "Carroll",
    role = "aut",
    email = "rpkg@jcarroll.com.au",
    comment = c(ORCID = "0000-0002-1404-5264")
  ),
  person(
    given = "James",
    family = "Goldie",
    role = "aut",
    email = "me@jamesgoldie.dev",
    comment = c(ORCID = "0000-0002-5024-6207")
  ),
  person(
    given = "Dean",
    family = "Marchiori",
    role = "aut",
    email = "deanmarchiori@gmail.com"
  ),
  person(
    given = "Paul",
    family = "Melloy",
    role = "aut",
    email = "paul@melloy.com.au",
    comment = c(ORCID = "0000-0003-4253-7167")
  ),
  person(
    given = "Mark",
    family = "Padgham",
    role = "aut",
    email = "mark.padgham@email.com",
    comment = c(ORCID = "0000-0003-2172-5265")
  ),
  person(
    given = "Hugh",
    family = "Parsonage",
    role = "aut",
    email = "hugh.parsonage@gmail.com",
    comment = c(ORCID = "0000-0003-4055-0835")
  ),
  person(
    given = "Keith",
    family = "Pembleton",
    role = "aut",
    email = "keith.pembleton@usq.edu.au",
    comment = c(ORCID = "0000-0002-1896-4516")
  ),
  person(
    given = "Maëlle",
    family = "Salmon",
    role = "ctb",
    email = "maelle.salmon@yahoo.se",
    comment = c(ORCID = "0000-0002-2815-0399",
                "Contributed to debugging a nasty little bug with CI where
                timezones caused tests to fail due to vcr not recognising the
                URL when run outside of Australia/Perth TZ! Suggested the use of
                `withr::local_timzeone()`, see
                <https://github.com/DPIRD-FSI/weatherOz/commit/b052bf91973b8d7e147a39e8938405a64622634b>.")),
  person(
    given = "Jimmy",
    family = "Ng",
    role = "ctb",
    email = "jimmy.ng@dpird.wa.gov.au"
  ),
  person(
    given = "Steve",
    family = "Collins",
    role = "ctb",
    email = "steve.collins@dpird.wa.gov.au",
    comment = c("Designed weatherOz's hex logo.")
  ),
  person(
    given = "Adam H.",
    family = "Sparks",
    email = "adam.sparks@dpird.wa.gov.au",
    role = "aut",
    comment = c(ORCID = "0000-0002-0061-8359")
  ),
  person(given = "Western Australia Agriculture Authority (WAAA)",
         role = c("cph")))
Description: Provides automated downloading, parsing and formatting of weather
    data for Australia through API endpoints provided by the Department of
    Primary Industries and Regional Development (DPIRD) of Western Australia
    and by the Science and Technology Division of the Queensland Government's
    Department of Environment and Science (DES).  As well as the Bureau of
    Meteorology (BOM) of the Australian government precis and coastal
    forecasts, agriculture bulletin data, and downloading and importing radar
    and satellite imagery files.  DPIRD weather data are accessed through public
    APIs provided by DPIRD, <https://www.agric.wa.gov.au/weather-api-20>,
    providing access to weather station data from DPIRD's weather station
    network.  Australia-wide weather data are based on data from the Australian
    Bureau of Meteorology (BOM) data and accessed through SILO (Scientific
    Information for Land Owners) (Jeffery et al., 2001,
    <doi: 10.1016/S1364-8152(01)00008-1>).  DPIRD data are made available under
    a Creative Commons Attribution 3.0 Licence (CC BY 3.0 AU) license
    <https://creativecommons.org/licenses/by/3.0/au/deed.en>.  SILO data are
    released under a  Creative Commons Attribution 4.0 International licence
    (CC BY 4.0) <https://creativecommons.org/licenses/by/4.0/>.  BOM data are
    (c) Australian Government Bureau of Meteorology and released under a
    Creative Commons (CC) Attribution 3.0 licence or Public Access Licence (PAL)
    as appropriate, see <http://www.bom.gov.au/other/copyright.shtml> for
    further details.
URL: https://github.com/DPIRD-FSI/weatherOz/, https://dpird-fsi.github.io/weatherOz/
BugReports: https://github.com/DPIRD-FSI/weatherOz/issues
License: GPL (>= 3)
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Imports: 
    apsimx,
    clock,
    crayon,
    crul,
    curl,
    data.table,
    foreign,
    grDevices,
    jsonlite,
    knitr,
    lubridate,
    magick,
    methods,
    readr (>= 1.1.1),
    stringi,
    stars,
    stats,
    terra,
    utils,
    xml2
Suggests:
    covr,
    dplyr,
    ggplot2,
    ggthemes,
    grid,
    gridExtra,
    mapproj,
    maps,
    mailR,
    rmarkdown,
    spelling,
    testthat (>= 3.0.0),
    vcr (>= 0.6.0),
    vdiffr,
    withr
Config/testthat/edition: 3
Depends: 
    R (>= 4.1.0)
X-schema.org-applicationCategory: Tools
X-schema.org-keywords: dpird, bom, meteorological-data, weather-forecast,
    australia, weather, weather-data, meteorology, western-australia,
    australia-bureau-of-meteorology, western-australia-agriculture
X-schema.org-isPartOf: https://www.agric.wa.gov.au/
VignetteBuilder: knitr
Language: en-US
LazyData: true

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.):
- [x] data retrieval
- [ ] data extraction
- [ ] data munging
- [ ] data deposition
- [ ] data validation and testing
- [ ] 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)

{weatherOz} aims to facilitate access and download weather and climate data for Australia from Australian data sources. Data are sourced from from the Western Australian Department of Primary Industries and Regional Development (DPIRD) and the Scientific Information for Land Owners (SILO) API endpoints and the Australian Government Bureau of Meteorology's (BOM) FTP server.
Who is the target audience and what are scientific applications of this package?

The target audience for this package is researchers, industry stakeholders and endusers who need to find, access and download and analyse weather and climate data from Australian data sources.
Are there other R packages that accomplish the same thing? If so, how does yours differ or meet our criteria for best-in-category?

No available package has the functionality and capabilities to find, access and download weather and climate data for Australia from multiple Australian data sources.

The {bomrang} package, currently archived and unsupported due to Australian Government Bureau of Meteorology (BOM) policy changes, has functionality to source data from BOM. Some of the existing functionality that is permitted by the BOM has been incorporated into {weatherOz}.
(If applicable) Does your package comply with our guidance around Ethics, Data Privacy and Human Subjects Research?

Not applicable.
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.

No pre-submission inquiry submitted.
Explain reasons for any pkgcheck items which your package is unable to pass.

Currently the {weatherOz} passes all pkgcheck items.

Technical checks

Confirm each of the following by checking the box.

[x] I have read the rOpenSci packaging guide.
[x] I have read the author guide and I expect to maintain this package for at least 2 years or to find a replacement.

This package:

[x] does not violate the Terms of Service of any service it interacts with.
[x] has a CRAN and OSI accepted license.
[x] contains a README with instructions for installing the development version.
[x] includes documentation with examples for all functions, created with roxygen2.
[x] contains a vignette with examples of its essential functions and uses.
[x] has a test suite.
[x] has continuous integration, including reporting of test coverage.

Publication options

[x] 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

- [ ] 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

[x] 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 commented 11 months ago

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

ropensci-review-bot commented 11 months ago

:rocket:

The following problem was found in your submission template:

URL = [https://github.com/DPIRD-FSI/weatherOz] is not valid The package could not be checked because of problems with the URL. Editors: Please ensure these problems are rectified, and then call @ropensci-review-bot check package.

:wave:

bozaah commented 11 months ago

@ropensci-review-bot check package

ropensci-review-bot commented 11 months ago

Thanks, about to send the query.

ropensci-review-bot commented 11 months ago

:rocket:

Editor check started

:wave:

ropensci-review-bot commented 11 months ago

Checks for weatherOz (v0.0.1)

git hash: 7687fb1f

:heavy_check_mark: Package name is available
:heavy_check_mark: has a 'codemeta.json' file.
:heavy_check_mark: has a 'contributing' file.
:heavy_multiplication_x: The following function has no documented return value: [plot,SpatRaster,ANY-method]
:heavy_check_mark: uses 'roxygen2'.
:heavy_check_mark: 'DESCRIPTION' has a URL field.
:heavy_check_mark: 'DESCRIPTION' has a BugReports field.
:heavy_check_mark: Package has at least one HTML vignette
:heavy_multiplication_x: These functions do not have examples: [plot,SpatRaster,ANY-method].
:heavy_check_mark: Package has continuous integration checks.
:heavy_check_mark: Package coverage is 93.6%.
:heavy_check_mark: R CMD check found no errors.
:heavy_check_mark: R CMD check found no warnings.
:eyes: Function names are duplicated in other packages

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

(Checks marked with :eyes: may be optionally addressed.)

Package License: GPL (>= 3)

1. Package Dependencies

Details of Package Dependency Usage (click to open)

The table below tallies all function calls to all packages ('ncalls'), both internal (r-base + recommended, along with the package itself), and external (imported and suggested packages). 'NA' values indicate packages to which no identified calls to R functions could be found. Note that these results are generated by an automated code-tagging system which may not be entirely accurate. |type |package | ncalls| |:----------|:----------|------:| |internal |base | 339| |internal |weatherOz | 11| |imports |data.table | 42| |imports |xml2 | 25| |imports |readr | 13| |imports |stats | 12| |imports |curl | 11| |imports |methods | 10| |imports |lubridate | 8| |imports |foreign | 7| |imports |utils | 6| |imports |crul | 5| |imports |jsonlite | 5| |imports |apsimx | 2| |imports |clock | 2| |imports |crayon | 2| |imports |grDevices | 2| |imports |terra | 2| |imports |magick | 1| |imports |stars | 1| |imports |knitr | NA| |imports |stringi | NA| |suggests |covr | NA| |suggests |dplyr | NA| |suggests |ggplot2 | NA| |suggests |ggthemes | NA| |suggests |grid | NA| |suggests |gridExtra | NA| |suggests |mapproj | NA| |suggests |maps | NA| |suggests |mailR | NA| |suggests |rmarkdown | NA| |suggests |spelling | NA| |suggests |testthat | NA| |suggests |vcr | NA| |suggests |vdiffr | NA| |suggests |withr | NA| |linking_to |NA | NA| Click below for tallies of functions used in each package. Locations of each call within this package may be generated locally by running 's <- pkgstats::pkgstats()', and examining the 'external_calls' table.

base

c (85), lapply (29), list (12), paste (12), tempdir (12), sprintf (11), length (10), mode (10), file.path (9), url (9), as.character (8), names (7), as.integer (6), return (6), parse (5), cbind (4), data.frame (4), for (4), mean (4), substr (4), t (4), character (3), class (3), file (3), grep (3), vapply (3), vector (3), warning (3), which (3), abs (2), agrep (2), attributes (2), by (2), colnames (2), floor (2), gsub (2), options (2), paste0 (2), readLines (2), round (2), seq_len (2), Sys.timezone (2), tolower (2), unlist (2), unname (2), as.Date (1), as.double (1), as.numeric (1), basename (1), ceiling (1), col (1), colMeans (1), date (1), exists (1), find.package (1), grepl (1), if (1), is.na (1), list.files (1), match.arg (1), max (1), merge (1), min (1), nchar (1), range (1), rawToChar (1), rbind (1), setdiff (1), source (1), system.file (1), table (1), try (1), units (1)

data.table

data.table (11), rbindlist (8), setkey (7), as.data.table (4), fcase (4), setorder (4), fread (1), setDT (1), setnames (1), setorderv (1)

xml2

xml_find_first (7), xml_parent (7), xml_attr (5), xml_find_all (5), read_xml (1)

readr

col_character (5), col_double (4), col_integer (3), fwf_cols (1)

stats

df (4), aggregate (3), dt (3), dist (1), end (1)

curl

new_handle (5), curl (4), curl_fetch_memory (2)

weatherOz

parse_coastal_forecast (2), parse_precis_forecast (2), amp_apsim_met (1), definition (1), get_dpird_summaries (1), get_radar (1), get_satellite (1), get_station_metadata (1), try_GET (1)

methods

new (10)

lubridate

time_length (2), days (1), format_ISO8601 (1), interval (1), today (1), year (1), ymd_hms (1)

foreign

read.dbf (7)

utils

data (3), count.fields (1), tail (1), unzip (1)

crul

HttpClient$new (4), Paginator$new (1)

jsonlite

fromJSON (5)

apsimx

read_apsim_met (2)

clock

date_seq (1), duration_minutes (1)

crayon

make_style (2)

grDevices

rgb (2)

terra

rast (2)

magick

image_read (1)

stars

read_stars (1)

**NOTE:** Some imported packages appear to have no associated function calls; please ensure with author that these 'Imports' are listed appropriately.

2. 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 31 files) and - 11 authors - 5 vignettes - 4 internal data files - 20 imported packages - 23 exported functions (median 31 lines of code) - 114 non-exported functions in R (median 31 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 All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by [the `checks_to_markdown()` function](https://docs.ropensci.org/pkgcheck/reference/checks_to_markdown.html) 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 | 31| 89.9| | |files_vignettes | 7| 98.5| | |files_tests | 21| 96.6| | |loc_R | 3471| 92.1| | |loc_vignettes | 1174| 92.8| | |loc_tests | 2381| 95.2|TRUE | |num_vignettes | 5| 97.9|TRUE | |data_size_total | 1490| 61.7| | |data_size_median | 341| 58.2| | |n_fns_r | 137| 83.4| | |n_fns_r_exported | 23| 71.4| | |n_fns_r_not_exported | 114| 86.2| | |n_fns_per_file_r | 3| 49.2| | |num_params_per_fn | 4| 54.6| | |loc_per_fn_r | 31| 77.7| | |loc_per_fn_r_exp | 31| 64.1| | |loc_per_fn_r_not_exp | 31| 79.3| | |rel_whitespace_R | 13| 87.5| | |rel_whitespace_vignettes | 34| 95.3|TRUE | |rel_whitespace_tests | 8| 85.0| | |doclines_per_fn_exp | 67| 77.7| | |doclines_per_fn_not_exp | 0| 0.0|TRUE | |fn_call_network_size | 135| 83.8| | ---

2a. Network visualisation

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

3. `goodpractice` and other checks

Details of goodpractice checks (click to open)

#### 3a. Continuous Integration Badges [![tic](https://github.com/DPIRD-FSI/weatherOz/workflows/tic/badge.svg)](https://github.com/DPIRD-FSI/weatherOz/actions) **GitHub Workflow Results** | id|name |conclusion |sha | run_number|date | |----------:|:--------------------------|:----------|:------|----------:|:----------| | 5689124046|pages build and deployment |success |134efe | 165|2023-07-28 | | 5689093279|tic |success |ddf7ed | 533|2023-07-28 | --- #### 3b. `goodpractice` results #### `R CMD check` with [rcmdcheck](https://r-lib.github.io/rcmdcheck/) rcmdcheck found no errors, warnings, or notes #### Test coverage with [covr](https://covr.r-lib.org/) Package coverage: 93.62 #### Cyclocomplexity with [cyclocomp](https://github.com/MangoTheCat/cyclocomp) The following functions have cyclocomplexity >= 15: function | cyclocomplexity --- | --- get_dpird_summaries | 16 find_nearby_stations | 15 #### Static code analyses with [lintr](https://github.com/jimhester/lintr) [lintr](https://github.com/jimhester/lintr) found the following 18 potential issues: message | number of times --- | --- Avoid library() and require() calls in packages | 2 Lines should not be more than 80 characters. | 16

4. Other Checks

Details of other checks (click to open)

:heavy_multiplication_x: The following function name is duplicated in other packages: - - `get_station_metadata` from stationaRy

Package Versions

|package |version | |:--------|:-------| |pkgstats |0.1.3.4 | |pkgcheck |0.1.2.1 |

Editor-in-Chief Instructions:

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

bozaah commented 11 months ago

Thank you! We have addressed the✖️ issues: dealt with terra::plot() export, reduced complexity of get_dpird_summaries() and find_nearby_stations(), and we expect that users should be aware of get_station_metadata() if loading both weatherOz and stationaRy. Users can use :: to select a function from the intended package and/or utilities such as the {conflicted} package.

@ropensci-review-bot check package

bozaah commented 11 months ago

@ropensci-review-bot check package

ropensci-review-bot commented 11 months ago

Thanks, about to send the query.

ropensci-review-bot commented 11 months ago

:rocket:

Editor check started

:wave:

ropensci-review-bot commented 11 months ago

Checks for weatherOz (v0.0.1.9000)

git hash: 00bb71e0

:heavy_check_mark: Package name is available
:heavy_check_mark: has a 'codemeta.json' file.
:heavy_check_mark: has a 'contributing' file.
:heavy_check_mark: uses 'roxygen2'.
:heavy_check_mark: 'DESCRIPTION' has a URL field.
:heavy_check_mark: 'DESCRIPTION' has a BugReports field.
:heavy_check_mark: Package has at least one HTML vignette
:heavy_check_mark: All functions have examples.
:heavy_check_mark: Package has continuous integration checks.
:heavy_check_mark: Package coverage is 93.6%.
:heavy_check_mark: R CMD check found no errors.
:heavy_check_mark: R CMD check found no warnings.
:eyes: Function names are duplicated in other packages

(Checks marked with :eyes: may be optionally addressed.)

Package License: GPL (>= 3)

1. Package Dependencies

Details of Package Dependency Usage (click to open)

The table below tallies all function calls to all packages ('ncalls'), both internal (r-base + recommended, along with the package itself), and external (imported and suggested packages). 'NA' values indicate packages to which no identified calls to R functions could be found. Note that these results are generated by an automated code-tagging system which may not be entirely accurate. |type |package | ncalls| |:----------|:----------|------:| |internal |base | 340| |internal |weatherOz | 11| |imports |data.table | 45| |imports |xml2 | 25| |imports |readr | 13| |imports |stats | 12| |imports |curl | 11| |imports |methods | 10| |imports |lubridate | 8| |imports |foreign | 7| |imports |utils | 6| |imports |crul | 5| |imports |jsonlite | 5| |imports |apsimx | 2| |imports |clock | 2| |imports |crayon | 2| |imports |grDevices | 2| |imports |terra | 2| |imports |magick | 1| |imports |stars | 1| |imports |knitr | NA| |imports |stringi | NA| |suggests |covr | NA| |suggests |dplyr | NA| |suggests |ggplot2 | NA| |suggests |ggthemes | NA| |suggests |grid | NA| |suggests |gridExtra | NA| |suggests |mapproj | NA| |suggests |maps | NA| |suggests |mailR | NA| |suggests |rmarkdown | NA| |suggests |spelling | NA| |suggests |testthat | NA| |suggests |vcr | NA| |suggests |vdiffr | NA| |suggests |withr | NA| |linking_to |NA | NA| Click below for tallies of functions used in each package. Locations of each call within this package may be generated locally by running 's <- pkgstats::pkgstats()', and examining the 'external_calls' table.

base

c (86), lapply (29), list (12), paste (12), tempdir (12), sprintf (11), length (10), mode (10), url (10), file.path (9), as.character (8), names (7), as.integer (6), return (6), parse (5), cbind (4), data.frame (4), for (4), mean (4), substr (4), t (4), character (3), class (3), file (3), grep (3), vapply (3), vector (3), warning (3), which (3), abs (2), agrep (2), attributes (2), by (2), colnames (2), floor (2), gsub (2), options (2), paste0 (2), readLines (2), round (2), seq_len (2), Sys.timezone (2), tolower (2), unlist (2), as.Date (1), as.double (1), as.numeric (1), basename (1), ceiling (1), col (1), colMeans (1), date (1), exists (1), find.package (1), grepl (1), if (1), is.na (1), list.files (1), match.arg (1), max (1), merge (1), min (1), nchar (1), range (1), rawToChar (1), rbind (1), setdiff (1), source (1), system.file (1), table (1), try (1), units (1), unname (1)

data.table

data.table (11), setkey (9), rbindlist (8), setorder (5), as.data.table (4), fcase (4), fread (1), setDT (1), setnames (1), setorderv (1)

xml2

xml_find_first (7), xml_parent (7), xml_attr (5), xml_find_all (5), read_xml (1)

readr

col_character (5), col_double (4), col_integer (3), fwf_cols (1)

stats

df (4), aggregate (3), dt (3), dist (1), end (1)

curl

new_handle (5), curl (4), curl_fetch_memory (2)

weatherOz

parse_coastal_forecast (2), parse_precis_forecast (2), amp_apsim_met (1), get_dpird_summaries (1), get_radar (1), get_satellite (1), get_station_metadata (1), silo_daily_values (1), try_GET (1)

methods

new (10)

lubridate

time_length (2), days (1), format_ISO8601 (1), interval (1), today (1), year (1), ymd_hms (1)

foreign

read.dbf (7)

utils

data (3), count.fields (1), tail (1), unzip (1)

crul

HttpClient$new (4), Paginator$new (1)

jsonlite

fromJSON (5)

apsimx

read_apsim_met (2)

clock

date_seq (1), duration_minutes (1)

crayon

make_style (2)

grDevices

rgb (2)

terra

rast (2)

magick

image_read (1)

stars

read_stars (1)

**NOTE:** Some imported packages appear to have no associated function calls; please ensure with author that these 'Imports' are listed appropriately.

2. 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 31 files) and - 11 authors - 5 vignettes - 4 internal data files - 20 imported packages - 22 exported functions (median 28 lines of code) - 118 non-exported functions in R (median 31 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 All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by [the `checks_to_markdown()` function](https://docs.ropensci.org/pkgcheck/reference/checks_to_markdown.html) 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 | 31| 89.9| | |files_vignettes | 7| 98.5| | |files_tests | 21| 96.6| | |loc_R | 3475| 92.1| | |loc_vignettes | 1219| 93.1| | |loc_tests | 2381| 95.2|TRUE | |num_vignettes | 5| 97.9|TRUE | |data_size_total | 1490| 61.7| | |data_size_median | 341| 58.2| | |n_fns_r | 140| 83.9| | |n_fns_r_exported | 22| 70.1| | |n_fns_r_not_exported | 118| 86.7| | |n_fns_per_file_r | 3| 49.3| | |num_params_per_fn | 4| 54.6| | |loc_per_fn_r | 30| 76.5| | |loc_per_fn_r_exp | 28| 60.2| | |loc_per_fn_r_not_exp | 31| 79.3| | |rel_whitespace_R | 13| 87.6| | |rel_whitespace_vignettes | 32| 95.3|TRUE | |rel_whitespace_tests | 8| 85.0| | |doclines_per_fn_exp | 74| 82.4| | |doclines_per_fn_not_exp | 0| 0.0|TRUE | |fn_call_network_size | 138| 84.1| | ---

2a. Network visualisation

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

3. `goodpractice` and other checks

Details of goodpractice checks (click to open)

#### 3a. Continuous Integration Badges [![tic](https://github.com/DPIRD-FSI/weatherOz/workflows/tic/badge.svg)](https://github.com/DPIRD-FSI/weatherOz/actions) **GitHub Workflow Results** | id|name |conclusion |sha | run_number|date | |----------:|:--------------------------|:----------|:------|----------:|:----------| | 5710706833|pages build and deployment |success |479b90 | 173|2023-07-31 | | 5710485651|tic |success |00bb71 | 556|2023-07-31 | | 5704197703|Update tic |failure |d40571 | 19|2023-07-30 | --- #### 3b. `goodpractice` results #### `R CMD check` with [rcmdcheck](https://r-lib.github.io/rcmdcheck/) rcmdcheck found no errors, warnings, or notes #### Test coverage with [covr](https://covr.r-lib.org/) Package coverage: 93.58 #### Cyclocomplexity with [cyclocomp](https://github.com/MangoTheCat/cyclocomp) No functions have cyclocomplexity >= 15 #### Static code analyses with [lintr](https://github.com/jimhester/lintr) [lintr](https://github.com/jimhester/lintr) found the following 17 potential issues: message | number of times --- | --- Avoid library() and require() calls in packages | 2 Lines should not be more than 80 characters. | 15

4. Other Checks

Details of other checks (click to open)

:heavy_multiplication_x: The following function name is duplicated in other packages: - - `get_station_metadata` from stationaRy

Package Versions

|package |version | |:--------|:-------| |pkgstats |0.1.3.4 | |pkgcheck |0.1.2.1 |

Editor-in-Chief Instructions:

This package is in top shape and may be passed on to a handling editor

noamross commented 10 months ago

@ropensci-review-bot assign @ldecicco-USGS as editor

ropensci-review-bot commented 10 months ago

Assigned! @ldecicco-USGS is now the editor

ldecicco-USGS commented 9 months ago

Editor checks:

[x] Documentation: The package has sufficient documentation available online (README, pkgdown docs) to allow for an assessment of functionality and scope without installing the package. In particular,
- [x] Is the case for the package well made?
- [x] Is the reference index page clear (grouped by topic if necessary)?
- [x] Are vignettes readable, sufficiently detailed and not just perfunctory?
[x] Fit: The package meets criteria for fit and overlap.
[x] Installation instructions: Are installation instructions clear enough for human users?
[x] Tests: If the package has some interactivity / HTTP / plot production etc. are the tests using state-of-the-art tooling?
[x] Contributing information: Is the documentation for contribution clear enough e.g. tokens for tests, playgrounds?
[x] License: The package has a CRAN or OSI accepted license.
[x] Project management: Are the issue and PR trackers in a good shape, e.g. are there outstanding bugs, is it clear when feature requests are meant to be tackled?

Editor comments

I installed it and ran the examples and things seemed to work and make sense on a very high level.

ldecicco-USGS commented 9 months ago

@ropensci-review-bot seeking reviewers

ropensci-review-bot commented 9 months ago

Please add this badge to the README of your package repository:

[![Status at rOpenSci Software Peer Review](https://badges.ropensci.org/598_status.svg)](https://github.com/ropensci/software-review/issues/598)

Furthermore, if your package does not have a NEWS.md file yet, please create one to capture the changes made during the review process. See https://devguide.ropensci.org/releasing.html#news

ldecicco-USGS commented 9 months ago

@ropensci-review-bot assign @JanLauGe as reviewer

ropensci-review-bot commented 9 months ago

@JanLauGe added to the reviewers list. Review due date is 2023-09-28. Thanks @JanLauGe for accepting to review! Please refer to our reviewer guide.

rOpenSci’s community is our best asset. We aim for reviews to be open, non-adversarial, and focused on improving software quality. Be respectful and kind! See our reviewers guide and code of conduct for more.

ropensci-review-bot commented 9 months ago

@JanLauGe: If you haven't done so, please fill this form for us to update our reviewers records.

bozaah commented 9 months ago

Dear @ldecicco-USGS, Thank you for taking up the editor role for our package. I appreciate yours and @JanLauGe's time working on this.

I am writing to mention that I will be on leave until the first week of November so I will be somehow slow and/or unresponsive to queries from you and the package reviewers. I will address the comments and necessary edits upon my return. Thank you!

ropensci-review-bot commented 9 months ago

:calendar: @JanLauGe you have 2 days left before the due date for your review (2023-09-28).

JanLauGe commented 8 months ago

Apologies for the delay in getting this off the ground. I'd love to kick this off this week if that is still okay with everybody?

ldecicco-USGS commented 7 months ago

@JanLauGe, I'm not sure why I didn't get the last notification - but if you are still up for a review, that would be fantastic. I have a couple of leads on a second reviewer @bozaah - so let's get the ball rolling again!

ldecicco-USGS commented 7 months ago

@ropensci-review-bot assign @rogerssam as reviewer

ropensci-review-bot commented 7 months ago

@rogerssam added to the reviewers list. Review due date is 2023-12-19. Thanks @rogerssam for accepting to review! Please refer to our reviewer guide.

rOpenSci’s community is our best asset. We aim for reviews to be open, non-adversarial, and focused on improving software quality. Be respectful and kind! See our reviewers guide and code of conduct for more.

ropensci-review-bot commented 7 months ago

@rogerssam: If you haven't done so, please fill this form for us to update our reviewers records.

rogerssam commented 7 months ago

@ropensci-review-bot check package

ropensci-review-bot commented 7 months ago

Thanks, about to send the query.

ropensci-review-bot commented 7 months ago

:rocket:

The following problem was found in your submission template:

HTML variable [due-dates-list] is missing Editors: Please ensure these problems with the submission template are rectified. Package checks have been started regardless.

:wave:

ropensci-review-bot commented 7 months ago

Checks for weatherOz (v0.0.1.9000)

git hash: 435648d0

:heavy_check_mark: Package name is available
:heavy_check_mark: has a 'codemeta.json' file.
:heavy_check_mark: has a 'contributing' file.
:heavy_check_mark: uses 'roxygen2'.
:heavy_check_mark: 'DESCRIPTION' has a URL field.
:heavy_check_mark: 'DESCRIPTION' has a BugReports field.
:heavy_check_mark: Package has at least one HTML vignette
:heavy_check_mark: All functions have examples.
:heavy_check_mark: Package has continuous integration checks.
:heavy_check_mark: Package coverage is 96.6%.
:heavy_check_mark: R CMD check found no errors.
:heavy_check_mark: R CMD check found no warnings.
:eyes: Function names are duplicated in other packages

(Checks marked with :eyes: may be optionally addressed.)

Package License: GPL (>= 3)

1. Package Dependencies

Details of Package Dependency Usage (click to open)

The table below tallies all function calls to all packages ('ncalls'), both internal (r-base + recommended, along with the package itself), and external (imported and suggested packages). 'NA' values indicate packages to which no identified calls to R functions could be found. Note that these results are generated by an automated code-tagging system which may not be entirely accurate. |type |package | ncalls| |:----------|:----------|------:| |internal |base | 348| |internal |weatherOz | 10| |imports |data.table | 45| |imports |xml2 | 25| |imports |readr | 13| |imports |stats | 12| |imports |curl | 11| |imports |methods | 10| |imports |lubridate | 8| |imports |foreign | 7| |imports |utils | 6| |imports |crul | 5| |imports |jsonlite | 5| |imports |apsimx | 2| |imports |clock | 2| |imports |crayon | 2| |imports |grDevices | 2| |imports |terra | 2| |imports |magick | 1| |imports |stars | 1| |imports |knitr | NA| |imports |stringi | NA| |suggests |covr | NA| |suggests |dplyr | NA| |suggests |ggplot2 | NA| |suggests |ggthemes | NA| |suggests |grid | NA| |suggests |gridExtra | NA| |suggests |mapproj | NA| |suggests |maps | NA| |suggests |mailR | NA| |suggests |rmarkdown | NA| |suggests |spelling | NA| |suggests |testthat | NA| |suggests |vcr | NA| |suggests |vdiffr | NA| |suggests |withr | NA| |linking_to |NA | NA| Click below for tallies of functions used in each package. Locations of each call within this package may be generated locally by running 's <- pkgstats::pkgstats()', and examining the 'external_calls' table.

base

c (90), lapply (29), length (12), list (12), paste (12), tempdir (12), mode (11), sprintf (11), url (10), file.path (9), as.character (8), names (7), as.integer (6), round (6), parse (5), cbind (4), data.frame (4), for (4), mean (4), return (4), substr (4), t (4), vector (4), character (3), class (3), file (3), grep (3), vapply (3), warning (3), which (3), abs (2), agrep (2), attributes (2), by (2), colnames (2), floor (2), gsub (2), options (2), paste0 (2), readLines (2), seq_len (2), Sys.timezone (2), tolower (2), unlist (2), as.Date (1), as.double (1), as.numeric (1), basename (1), ceiling (1), col (1), colMeans (1), date (1), find.package (1), grepl (1), is.na (1), list.files (1), match.arg (1), max (1), merge (1), min (1), nchar (1), range (1), rawToChar (1), rbind (1), setdiff (1), source (1), system.file (1), table (1), try (1), units (1), unname (1)

data.table

data.table (11), setkey (9), rbindlist (8), setorder (5), as.data.table (4), fcase (4), fread (1), setDT (1), setnames (1), setorderv (1)

xml2

xml_find_first (7), xml_parent (7), xml_attr (5), xml_find_all (5), read_xml (1)

readr

col_character (5), col_double (4), col_integer (3), fwf_cols (1)

stats

df (4), aggregate (3), dt (3), dist (1), end (1)

curl

new_handle (5), curl (4), curl_fetch_memory (2)

methods

new (10)

weatherOz

parse_coastal_forecast (2), parse_precis_forecast (2), amp_apsim_met (1), get_dpird_summaries (1), get_radar (1), get_satellite (1), silo_daily_values (1), try_GET (1)

lubridate

time_length (2), days (1), format_ISO8601 (1), interval (1), today (1), year (1), ymd_hms (1)

foreign

read.dbf (7)

utils

data (3), count.fields (1), tail (1), unzip (1)

crul

HttpClient$new (4), Paginator$new (1)

jsonlite

fromJSON (5)

apsimx

read_apsim_met (2)

clock

date_seq (1), duration_minutes (1)

crayon

make_style (2)

grDevices

rgb (2)

terra

rast (2)

magick

image_read (1)

stars

read_stars (1)

**NOTE:** Some imported packages appear to have no associated function calls; please ensure with author that these 'Imports' are listed appropriately.

2. 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 32 files) and - 11 authors - 5 vignettes - 4 internal data files - 20 imported packages - 22 exported functions (median 29 lines of code) - 122 non-exported functions in R (median 30 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 All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by [the `checks_to_markdown()` function](https://docs.ropensci.org/pkgcheck/reference/checks_to_markdown.html) 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 | 32| 90.5| | |files_vignettes | 7| 98.5| | |files_tests | 21| 96.6| | |loc_R | 3566| 92.5| | |loc_vignettes | 1181| 92.9| | |loc_tests | 2396| 95.2|TRUE | |num_vignettes | 5| 97.9|TRUE | |data_size_total | 1490| 61.7| | |data_size_median | 341| 58.2| | |n_fns_r | 144| 84.4| | |n_fns_r_exported | 22| 70.1| | |n_fns_r_not_exported | 122| 87.2| | |n_fns_per_file_r | 3| 49.2| | |num_params_per_fn | 4| 54.6| | |loc_per_fn_r | 30| 76.5| | |loc_per_fn_r_exp | 30| 62.7| | |loc_per_fn_r_not_exp | 30| 79.1| | |rel_whitespace_R | 13| 88.0| | |rel_whitespace_vignettes | 34| 95.3|TRUE | |rel_whitespace_tests | 8| 85.1| | |doclines_per_fn_exp | 74| 82.4| | |doclines_per_fn_not_exp | 0| 0.0|TRUE | |fn_call_network_size | 144| 84.7| | ---

2a. Network visualisation

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

3. `goodpractice` and other checks

Details of goodpractice checks (click to open)

#### 3a. Continuous Integration Badges [![tic](https://github.com/DPIRD-FSI/weatherOz/workflows/tic/badge.svg)](https://github.com/DPIRD-FSI/weatherOz/actions) **GitHub Workflow Results** | id|name |conclusion |sha | run_number|date | |----------:|:--------------------------|:----------|:------|----------:|:----------| | 7017953196|pages build and deployment |success |e142b0 | 298|2023-11-28 | | 7017551355|tic |failure |435648 | 767|2023-11-28 | | 6993334698|Update tic |failure |8d8131 | 36|2023-11-26 | --- #### 3b. `goodpractice` results #### `R CMD check` with [rcmdcheck](https://r-lib.github.io/rcmdcheck/) rcmdcheck found no errors, warnings, or notes #### Test coverage with [covr](https://covr.r-lib.org/) Package coverage: 96.56 #### Cyclocomplexity with [cyclocomp](https://github.com/MangoTheCat/cyclocomp) No functions have cyclocomplexity >= 15 #### Static code analyses with [lintr](https://github.com/jimhester/lintr) [lintr](https://github.com/jimhester/lintr) found the following 16 potential issues: message | number of times --- | --- Avoid library() and require() calls in packages | 2 Lines should not be more than 80 characters. | 14

4. Other Checks

Details of other checks (click to open)

:heavy_multiplication_x: The following function name is duplicated in other packages: - - `get_station_metadata` from stationaRy

Package Versions

|package |version | |:--------|:--------| |pkgstats |0.1.3.9 | |pkgcheck |0.1.2.11 |

Editor-in-Chief Instructions:

This package is in top shape and may be passed on to a handling editor

rogerssam commented 7 months ago

HI all, here is my review.

Package Review

Please check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide

Briefly describe any working relationship you have (had) with the package authors.
- No working relationship with authors to date.
☒ As the reviewer I confirm that there are no conflicts of interest for me to review this work (if you are unsure whether you are in conflict, please speak to your editor before starting your review).

Documentation

The package includes all the following forms of documentation:

☒ A statement of need: clearly stating problems the software is designed to solve and its target audience in README
☒ Installation instructions: for the development version of package and any non-standard dependencies in README
☒ Vignette(s): demonstrating major functionality that runs successfully locally
☒ Function Documentation: for all exported functions
☒ Examples: (that run successfully locally) for all exported functions
☒ Community guidelines: including contribution guidelines in the README or CONTRIBUTING, and DESCRIPTION with URL, BugReports and Maintainer (which may be autogenerated via Authors@R).

Functionality

☒ Installation: Installation succeeds as documented.
☒ Functionality: Any functional claims of the software been confirmed.
☒ Performance: Any performance claims of the software been confirmed.
☒ Automated tests: Unit tests cover essential functions of the package and a reasonable range of inputs and conditions. All tests pass on the local machine.
☒ Packaging guidelines: The package conforms to the rOpenSci packaging guidelines.

Estimated hours spent reviewing: 6

☒ Should the author(s) deem it appropriate, I agree to be acknowledged as a package reviewer (“rev” role) in the package DESCRIPTION file.

Review Comments

Overall the package appears to be well developed, robust and meets a need of providing access to weather data in Australia. Some additional comments:

Checking for the example API key is a nice UX touch.
The vignettes are clear, and show a good demonstration of the functionality of the package.
The main functions follow a clear convention, which provides obvious entry points for new users.
Great to see near complete test coverage.
I am familiar with the difference between patched point and data drills from the SILO data, but I expect new users would not be, so perhaps the titles of those functions could be expanded? For example Get DataDrill (Gridded) Weather Data From SILO and Get PatchedPoint (Station) Weather Data From SILO or similar. I think it makes sense to have the function names matching the SILO API, but I think the titles could provide a little more clarity. I also realise that the detail is available within the function documentation, however that’s an extra step for users to find the right function that they need.
A point to note is that despite the SILO function manual pages stating a character input is required for station code, they work perfectly fine with other data types (e.g. numeric, even list(008137) works!). I think this is good, but perhaps the documentation should be updated to clarify that numerics are acceptable, as it's not technically expected behaviour based on the docs?

In the current state, I think the package is very good and perfectly usable, however below are some additional suggestions for improvements. I will add some issues on the repo for consideration by the authors.

I wonder if it’s worth including some sort of validation on the api_key (email) input to the SILO functions? Obviously email address validation is not trivial but at present entry of abc as the api_key/email is valid input. Some obvious errors are caught by SILO (e.g. ---@...) but others are not. I will leave it as a decision for the authors.
I think it would be useful for the get_station_metadata() function to have the ability to return a single station metadata, rather than just all of them. There could be a station argument set to "all" by default.

Overall, great work, and I will be personally using it shortly for some of my work!

Thanks, Sam Rogers

bozaah commented 6 months ago

Dear @ldecicco-USGS, We have addressed the feedback from @rogerssam which we appreciate a lot. We also took on board the comments regarding the name of functions requesting SILO data and the documentation on the data types accepted as station_code by the SILO functions. We will address those once we receive the review from @JanLauGe if that is acceptable. Much appreciated, Rodrigo.

ropensci-review-bot commented 6 months ago

:calendar: @rogerssam you have 2 days left before the due date for your review (2023-12-19).

JanLauGe commented 6 months ago

Package Review

Briefly describe any working relationship you have (had) with the package authors. No working relationship with authors to date.
[x] As the reviewer I confirm that there are no conflicts of interest for me to review this work (if you are unsure whether you are in conflict, please speak to your editor before starting your review).

Documentation

The package includes all the following forms of documentation:

[x] A statement of need: clearly stating problems the software is designed to solve and its target audience in README
[x] Installation instructions: for the development version of package and any non-standard dependencies in README
[x] Vignette(s): demonstrating major functionality that runs successfully locally
[x] Function Documentation: for all exported functions
[x] Examples: (that run successfully locally) for all exported functions
[x] Community guidelines: including contribution guidelines in the README or CONTRIBUTING, and DESCRIPTION with URL, BugReports and Maintainer (which may be autogenerated via Authors@R).

Functionality

[x] Installation: Installation succeeds as documented.
[ ] Functionality: Any functional claims of the software been confirmed. I have not tested all functions yet due to getting stuck with the unit tests.
[x] Performance: Any performance claims of the software been confirmed.
[ ] Automated tests: Unit tests cover essential functions of the package and a reasonable range of inputs and conditions. All tests pass on the local machine. Currently I'm getting test errors on my local machine. Happy to work with you to figure out what is going on.
[x] Packaging guidelines: The package conforms to the rOpenSci packaging guidelines.

Estimated hours spent reviewing: 5

[x] Should the author(s) deem it appropriate, I agree to be acknowledged as a package reviewer ("rev" role) in the package DESCRIPTION file.

Additional comments:

this check for whether the API key has been provided currently doesn't work with the examples because both NULL and an empty string resulting from Sys.getenv("DPIRD_API_KEY") passes the test. That means that if a new user just uses the function from the example they end up with a relatively cryptic error. Can you add a test or conditition for NULL and empty string?
I agree with @rogerssam that email address validation would be a good addition. To play it safe, the package could produce a message() when detecting an invalid email address instead of stop()-ing with an error. Example of an email address validation regex.
Running tests required installing the vcr package for me which is not listed as dependency.
Currently some tests are failing for me locally (iOS). I'm attaching the test report below.

...
trying URL 'ftp://ftp.bom.gov.au/anon/gen/fwo/IDW14199.xml'
Content type 'unknown' length 546501 bytes (533 KB)
==================================================
file downloaded to:/var/folders/43/c5m9cb696l7fgnfsls66r1f400th2k/T//RtmpbdumdW/file6cd638754f36.gif
file downloaded to:/var/folders/43/c5m9cb696l7fgnfsls66r1f400th2k/T//RtmpbdumdW/file6cd61da37f2f.gif
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 396 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-get_dpird_summaries.R:235:15'): get_dpird_summaries() returns hourly values ──
Error: 

================================================================================
An HTTP request has been made that vcr does not know how to handle:
GET https://api.dpird.wa.gov.au/v2/weather/stations/summaries/hourly?stationCode=BI&startDateTime=2017-10-28&endDateTime=2017-11-01&interval=hourly&select=stationCode%2CstationName%2Cperiod%2Cwind&group=all&includeClosed=false&api_key=<<<dpird_api_key>>>&offset=0&limit=74
vcr is currently using the following cassette:
  - <local path redacted>/weatherOz/tests/fixtures/dpird_summaries_hourly.json
    - record_mode: once
    - match_requests_on: method, uri

yabellini commented 6 months ago

Hi @rogerssam, @arhepworth, @syntrix, @becoleary. rOpenSci Community Manager here.
If you want to join our Slack, I can send an invitation. Please share with me what email you want to use. You can write me to yabellini@ropensci.org. Thank you!

ldecicco-USGS commented 5 months ago

Thanks so much @JanLauGe! If you aren't on the rOpenSci slack, please see @yabellini 's message above

ldecicco-USGS commented 5 months ago

@ropensci-review-bot submit review https://github.com/ropensci/software-review/issues/598#issuecomment-18659958772 time 5

ropensci-review-bot commented 5 months ago

Error: That url is not pointing to a reviewer comment in this issue

ldecicco-USGS commented 5 months ago

@ropensci-review-bot submit review https://github.com/ropensci/software-review/issues/598#issuecomment-1865995877 time 5

ropensci-review-bot commented 5 months ago

Logged review for JanLauGe (hours: 5)

ldecicco-USGS commented 5 months ago

@ropensci-review-bot submit review https://github.com/ropensci/software-review/issues/598#issuecomment-1832968340 time 6

ropensci-review-bot commented 5 months ago

Logged review for rogerssam (hours: 6)

ropensci-review-bot commented 5 months ago

@bozaah, @adamhsparks, @arhepworth, @jimii19, @syntrix, @becoleary, @HughParsonage, @PaulMelloy, @jonocarroll, @deanmarchiori, @jimjam-slam, @mpadge, @Keith-Pembleton, @maelle: please post your response with @ropensci-review-bot submit response <url to issue comment> if you haven't done so already (this is an automatic reminder).

Here's the author guide for response. https://devguide.ropensci.org/authors-guide.html

bozaah commented 5 months ago

Thank you for your comments and feedback. I am working through the changes and should have my reply by Thursday. Much appreciated, Rodrigo

bozaah commented 5 months ago

Thank you for your time reviewing {weatherOz} @JanLauGe and @rogerssam, we appreciate that. Your comments have helped us improve the package and hopefully the user experience with {weatherOz}. I have collated the responses to the points you have raised below:

We have added an email validation check as suggested. Functions will still return an error and stop if a valid api_key is not provided. Closed issue 49 with commit 3dfba0b.
We have maintained SILO functionality with the same names (i.e., get_data_drill() and get_patched_point()). As noted, the function documentation is clear on the API endpoints queried and there is also the SILO vignette which details the functionality and has additional information on the endpoints, variables and query output types. We believe this provides the user a clear view of the functionality.
We have added a check to functions that required the station_code argument (i.e., get_dpird_extremes(), get_dpird_minute(), get_dpird_summaries(), get_patched_point() and get_patched_point_apsim()) so that only a character string type is accepted. commit ae26fe9.
Added functionality to get_station_metadata() so that it returns the metadata for only one station if required. Closed issue 51 with commit 8166c92.
Added check to the functions that require the api_key argument (i.e., get_dpird_*(), get_data_drill*(), get_patched_point*(), find_nearby_stations() and get_station_metadata()) so that missing, empty or null returns an error. commit f86b949.
We have listed {vcr} in the Suggests section of the DESCRIPTION as noted in the rOpenSci HTTP testing in R book. We are happy to adjust that if there is better way to address this.
The test error @JanLauGe is due to the date range used in the query (and consequently saved into the {vcr} cassete). The DPIRD endpoint with hourly data (and also 15min and 30min intervals) only accepts dates up to the 1st day of the last year (in 2024 this is 2023-01-01). The function help describes this limitation when the interval argument is shorter than daily. I have updated the testthat.R and saved a new {vcr} cassete to reflect that and I have no errors on my current checks/tests. Thank you for picking this up!

I am currently running the checks and tests locally on MacOS and Windows. I have also updated the Github CI/tic workflows and I am hopeful it will work. I have added @JanLauGe and @rogerssam to the list of authors commit a00dbba Again, thank you for your feedback, I am sure users will benefit from your comments!

I will create a PR so that @adamhsparks can check for issues I might have missed (or created) while editing {weatherOz} in line with your feedback. We will also update the NEWS.md with the most recent changes once the merge is accepted.

Please let me know if there is anything else you would like us to take a look or rectify.

Thank you!

bozaah commented 5 months ago

@ropensci-review-bot check package

ropensci-review-bot commented 5 months ago

Thanks, about to send the query.

ropensci-review-bot commented 5 months ago

:rocket:

Editor check started

:wave:

ropensci-review-bot commented 5 months ago

Checks for weatherOz (v0.0.1.9000)

git hash: 08139af0

:heavy_check_mark: Package name is available
:heavy_check_mark: has a 'codemeta.json' file.
:heavy_check_mark: has a 'contributing' file.
:heavy_check_mark: uses 'roxygen2'.
:heavy_check_mark: 'DESCRIPTION' has a URL field.
:heavy_check_mark: 'DESCRIPTION' has a BugReports field.
:heavy_check_mark: Package has at least one HTML vignette
:heavy_check_mark: All functions have examples.
:heavy_check_mark: Package has continuous integration checks.
:heavy_multiplication_x: Package coverage failed
:heavy_multiplication_x: R CMD check found 1 error.
:heavy_check_mark: R CMD check found no warnings.
:eyes: Function names are duplicated in other packages

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

(Checks marked with :eyes: may be optionally addressed.)

Package License: GPL (>= 3)

1. Package Dependencies

Details of Package Dependency Usage (click to open)

The table below tallies all function calls to all packages ('ncalls'), both internal (r-base + recommended, along with the package itself), and external (imported and suggested packages). 'NA' values indicate packages to which no identified calls to R functions could be found. Note that these results are generated by an automated code-tagging system which may not be entirely accurate. |type |package | ncalls| |:----------|:----------|------:| |internal |base | 350| |internal |weatherOz | 10| |imports |data.table | 45| |imports |xml2 | 25| |imports |readr | 13| |imports |stats | 12| |imports |curl | 11| |imports |methods | 10| |imports |lubridate | 8| |imports |foreign | 7| |imports |utils | 6| |imports |crul | 5| |imports |jsonlite | 5| |imports |apsimx | 2| |imports |clock | 2| |imports |crayon | 2| |imports |grDevices | 2| |imports |terra | 2| |imports |magick | 1| |imports |stars | 1| |imports |knitr | NA| |imports |stringi | NA| |suggests |covr | NA| |suggests |dplyr | NA| |suggests |ggplot2 | NA| |suggests |ggthemes | NA| |suggests |grid | NA| |suggests |gridExtra | NA| |suggests |mapproj | NA| |suggests |maps | NA| |suggests |mailR | NA| |suggests |rmarkdown | NA| |suggests |spelling | NA| |suggests |testthat | NA| |suggests |vcr | NA| |suggests |vdiffr | NA| |suggests |withr | NA| |linking_to |NA | NA| Click below for tallies of functions used in each package. Locations of each call within this package may be generated locally by running 's <- pkgstats::pkgstats()', and examining the 'external_calls' table.

base

c (90), lapply (30), length (12), list (12), paste (12), tempdir (12), mode (11), sprintf (11), url (10), file.path (9), as.character (8), names (7), as.integer (6), round (6), parse (5), cbind (4), data.frame (4), for (4), mean (4), return (4), substr (4), t (4), vector (4), character (3), class (3), file (3), grep (3), unlist (3), vapply (3), warning (3), which (3), abs (2), agrep (2), attributes (2), by (2), colnames (2), floor (2), gsub (2), options (2), paste0 (2), readLines (2), seq_len (2), Sys.timezone (2), tolower (2), as.Date (1), as.double (1), as.numeric (1), basename (1), ceiling (1), col (1), colMeans (1), date (1), find.package (1), grepl (1), is.na (1), list.files (1), match.arg (1), max (1), merge (1), min (1), nchar (1), range (1), rawToChar (1), rbind (1), setdiff (1), source (1), system.file (1), table (1), try (1), units (1), unname (1)

data.table

data.table (11), setkey (9), rbindlist (8), setorder (5), as.data.table (4), fcase (4), fread (1), setDT (1), setnames (1), setorderv (1)

xml2

xml_find_first (7), xml_parent (7), xml_attr (5), xml_find_all (5), read_xml (1)

readr

col_character (5), col_double (4), col_integer (3), fwf_cols (1)

stats

df (4), aggregate (3), dt (3), dist (1), end (1)

curl

new_handle (5), curl (4), curl_fetch_memory (2)

methods

new (10)

weatherOz

parse_coastal_forecast (2), parse_precis_forecast (2), amp_apsim_met (1), get_dpird_summaries (1), get_radar (1), get_satellite (1), silo_daily_values (1), try_GET (1)

lubridate

time_length (2), days (1), format_ISO8601 (1), interval (1), today (1), year (1), ymd_hms (1)

foreign

read.dbf (7)

utils

data (3), count.fields (1), tail (1), unzip (1)

crul

HttpClient$new (4), Paginator$new (1)

jsonlite

fromJSON (5)

apsimx

read_apsim_met (2)

clock

date_seq (1), duration_minutes (1)

crayon

make_style (2)

grDevices

rgb (2)

terra

rast (2)

magick

image_read (1)

stars

read_stars (1)

**NOTE:** Some imported packages appear to have no associated function calls; please ensure with author that these 'Imports' are listed appropriately.

2. 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 32 files) and - 11 authors - 5 vignettes - 4 internal data files - 20 imported packages - 22 exported functions (median 30 lines of code) - 124 non-exported functions in R (median 30 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 All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by [the `checks_to_markdown()` function](https://docs.ropensci.org/pkgcheck/reference/checks_to_markdown.html) 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 | 32| 90.5| | |files_vignettes | 7| 98.5| | |files_tests | 21| 96.6| | |loc_R | 3594| 92.5| | |loc_vignettes | 1181| 92.9| | |loc_tests | 2459| 95.4|TRUE | |num_vignettes | 5| 97.9|TRUE | |data_size_total | 1476| 61.7| | |data_size_median | 341| 58.2| | |n_fns_r | 146| 84.6| | |n_fns_r_exported | 22| 70.1| | |n_fns_r_not_exported | 124| 87.5| | |n_fns_per_file_r | 3| 49.3| | |num_params_per_fn | 4| 54.6| | |loc_per_fn_r | 30| 76.5| | |loc_per_fn_r_exp | 30| 63.0| | |loc_per_fn_r_not_exp | 30| 78.2| | |rel_whitespace_R | 13| 88.2| | |rel_whitespace_vignettes | 34| 95.3|TRUE | |rel_whitespace_tests | 8| 85.1| | |doclines_per_fn_exp | 74| 81.9| | |doclines_per_fn_not_exp | 0| 0.0|TRUE | |fn_call_network_size | 148| 85.0| | ---

2a. Network visualisation

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

3. `goodpractice` and other checks

Details of goodpractice checks (click to open)

#### 3a. Continuous Integration Badges [![tic](https://github.com/DPIRD-FSI/weatherOz/workflows/tic/badge.svg)](https://github.com/DPIRD-FSI/weatherOz/actions) **GitHub Workflow Results** | id|name |conclusion |sha | run_number|date | |----------:|:----------|:----------|:------|----------:|:----------| | 7738192426|tic |success |e0defb | 13|2024-02-01 | | 7683305424|Update tic |failure |08139a | 45|2024-01-28 | --- #### 3b. `goodpractice` results #### `R CMD check` with [rcmdcheck](https://r-lib.github.io/rcmdcheck/) R CMD check generated the following error: 1. checking tests ... Running ‘spelling.R’ Comparing ‘spelling.Rout’ to ‘spelling.Rout.save’ ... OK Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: ▆ 1. ├─vcr::use_cassette(...) at test-get_dpird_summaries.R:282:13 2. │ └─cassette$call_block(...) 3. └─weatherOz::get_dpird_summaries(...) at test-get_dpird_summaries.R:284:15 ── Error ('test-get_dpird_summaries.R:337:15'): get_dpird_summaries() returns 15min values ── Error: Start date is too early. Data in 15 and 30 min intervals are only available from the the 1st day of 2023. Backtrace: ▆ 1. ├─vcr::use_cassette(...) at test-get_dpird_summaries.R:335:13 2. │ └─cassette$call_block(...) 3. └─weatherOz::get_dpird_summaries(...) at test-get_dpird_summaries.R:337:15 [ FAIL 2 | WARN 0 | SKIP 0 | PASS 396 ] Error: Test failures Execution halted R CMD check generated the following test_fail: 1. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(weatherOz) Attaching package: 'weatherOz' The following object is masked from 'package:graphics': plot The following object is masked from 'package:base': plot > > test_check("weatherOz") trying URL 'ftp://ftp.bom.gov.au/anon/gen/fwo/IDQ60604.xml' Content type 'unknown' length 10795 bytes (10 KB) ================================================== trying URL 'ftp://ftp.bom.gov.au/anon/gen/fwo/IDN65176.xml' Content type 'unknown' length 12961 bytes (12 KB) ================================================== trying URL 'ftp://ftp.bom.gov.au/anon/gen/fwo/IDD65176.xml' Content type 'unknown' length 5705 bytes ================================================== trying URL 'ftp://ftp.bom.gov.au/anon/gen/fwo/IDS65176.xml' Content type 'unknown' length 12682 bytes (12 KB) ================================================== trying URL 'ftp://ftp.bom.gov.au/anon/gen/fwo/IDT65176.xml' Content type 'unknown' length 8863 bytes ================================================== trying URL 'ftp://ftp.bom.gov.au/anon/gen/fwo/IDV65176.xml' Content type 'unknown' length 5229 bytes ================================================== trying URL 'ftp://ftp.bom.gov.au/anon/gen/fwo/IDW65176.xml' Content type 'unknown' length 12009 bytes (11 KB) ================================================== trying URL 'ftp://ftp.bom.gov.au/anon/gen/fwo/IDN11001.xml' Content type 'unknown' length 29052 bytes (28 KB) ================================================== trying URL 'ftp://ftp.bom.gov.au/anon/gen/fwo/IDN11001.xml' Content type 'unknown' length 29052 bytes (28 KB) ================================================== trying URL 'ftp://ftp.bom.gov.au/anon/gen/fwo/IDD11030.xml' Content type 'unknown' length 21417 bytes (20 KB) ================================================== trying URL 'ftp://ftp.bom.gov.au/anon/gen/fwo/IDQ11290.xml' Content type 'unknown' length 46064 bytes (44 KB) ================================================== trying URL 'ftp://ftp.bom.gov.au/anon/gen/fwo/IDS11072.xml' Content type 'unknown' length 30551 bytes (29 KB) ================================================== trying URL 'ftp://ftp.bom.gov.au/anon/gen/fwo/IDT12329.xml' Content type 'unknown' length 31044 bytes (30 KB) ================================================== trying URL 'ftp://ftp.bom.gov.au/anon/gen/fwo/IDV10200.xml' Content type 'unknown' length 15601 bytes (15 KB) ================================================== trying URL 'ftp://ftp.bom.gov.au/anon/gen/fwo/IDW11160.xml' Content type 'unknown' length 41082 bytes (40 KB) ================================================== Found 7 header lines Found 15 comment lines Found 22 skip lines Found 0 constants Found 7 header lines Found 16 comment lines Found 23 skip lines Found 0 constants trying URL 'ftp://ftp.bom.gov.au/anon/gen/fwo/IDQ11295.xml' Content type 'unknown' length 563696 bytes (550 KB) ================================================== trying URL 'ftp://ftp.bom.gov.au/anon/gen/fwo/IDN11060.xml' Content type 'unknown' length 719715 bytes (702 KB) ================================================== trying URL 'ftp://ftp.bom.gov.au/anon/gen/fwo/IDN11060.xml' Content type 'unknown' length 719715 bytes (702 KB) ================================================== trying URL 'ftp://ftp.bom.gov.au/anon/gen/fwo/IDD10207.xml' Content type 'unknown' length 475232 bytes (464 KB) ================================================== trying URL 'ftp://ftp.bom.gov.au/anon/gen/fwo/IDS10044.xml' Content type 'unknown' length 277565 bytes (271 KB) ================================================== trying URL 'ftp://ftp.bom.gov.au/anon/gen/fwo/IDT16710.xml' Content type 'unknown' length 350117 bytes (341 KB) ================================================== trying URL 'ftp://ftp.bom.gov.au/anon/gen/fwo/IDV10753.xml' Content type 'unknown' length 401781 bytes (392 KB) ================================================== trying URL 'ftp://ftp.bom.gov.au/anon/gen/fwo/IDW14199.xml' Content type 'unknown' length 544359 bytes (531 KB) ================================================== file downloaded to:/tmp/RtmpZroZZl/file7c337561e271.gif file downloaded to:/tmp/RtmpZroZZl/file7c331b4bc44e.gif [ FAIL 2 | WARN 0 | SKIP 0 | PASS 396 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-get_dpird_summaries.R:284:15'): get_dpird_summaries() returns 30min values ── Error: Start date is too early. Data in 15 and 30 min intervals are only available from the the 1st day of 2023. Backtrace: ▆ 1. ├─vcr::use_cassette(...) at test-get_dpird_summaries.R:282:13 2. │ └─cassette$call_block(...) 3. └─weatherOz::get_dpird_summaries(...) at test-get_dpird_summaries.R:284:15 ── Error ('test-get_dpird_summaries.R:337:15'): get_dpird_summaries() returns 15min values ── Error: Start date is too early. Data in 15 and 30 min intervals are only available from the the 1st day of 2023. Backtrace: ▆ 1. ├─vcr::use_cassette(...) at test-get_dpird_summaries.R:335:13 2. │ └─cassette$call_block(...) 3. └─weatherOz::get_dpird_summaries(...) at test-get_dpird_summaries.R:337:15 [ FAIL 2 | WARN 0 | SKIP 0 | PASS 396 ] Error: Test failures Execution halted R CMD check generated the following check_fail: 1. rcmdcheck_tests_pass #### Test coverage with [covr](https://covr.r-lib.org/) ERROR: Test Coverage Failed #### Cyclocomplexity with [cyclocomp](https://github.com/MangoTheCat/cyclocomp) No functions have cyclocomplexity >= 15 #### Static code analyses with [lintr](https://github.com/jimhester/lintr) [lintr](https://github.com/jimhester/lintr) found the following 16 potential issues: message | number of times --- | --- Avoid library() and require() calls in packages | 2 Lines should not be more than 80 characters. | 14

4. Other Checks

Details of other checks (click to open)

:heavy_multiplication_x: The following function name is duplicated in other packages: - - `get_station_metadata` from stationaRy

Package Versions

|package |version | |:--------|:--------| |pkgstats |0.1.3.9 | |pkgcheck |0.1.2.13 |

Editor-in-Chief Instructions:

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

ldecicco-USGS commented 5 months ago

Thanks for your response @bozaah! @JanLauGe and @rogerssam let us know if you are happy with the authors response to your reviews and if there's any others aspects you have comments on (I have faith that @bozaah will get the final checks noted by review-bot sorted out)

ropensci / software-review