Open mikemahoney218 opened 3 months ago
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:rocket:
Editor check started
:wave:
Another quick note -- I will not be able to transfer this repository to rOpenSci if accepted. I had asked on Slack and was told by Yani that this was acceptable, though it's only mentioned in the book here. I want to flag this at the start, in case it turns out to be an issue!
git hash: 694d2a5f
Important: All failing checks above must be addressed prior to proceeding
(Checks marked with :eyes: may be optionally addressed.)
Package License: Apache License (>= 2)
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 | 175|
|internal |rsi | 34|
|internal |methods | 3|
|internal |stats | 2|
|internal |tools | 2|
|imports |rlang | 10|
|imports |terra | 10|
|imports |rstac | 5|
|imports |glue | 4|
|imports |future.apply | 2|
|imports |httr | 1|
|imports |sf | 1|
|imports |jsonlite | NA|
|imports |lifecycle | NA|
|imports |proceduralnames | NA|
|imports |tibble | NA|
|suggests |progressr | 1|
|suggests |curl | NA|
|suggests |knitr | NA|
|suggests |rmarkdown | NA|
|suggests |testthat | 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(
names (20), c (19), class (10), lapply (9), length (8), vapply (8), args (6), formals (6), list (6), mget (6), tryCatch (5), file.path (4), for (4), max (4), min (4), options (4), tempfile (4), ifelse (3), url (3), all (2), call (2), character (2), drop (2), eval (2), is.null (2), nrow (2), paste (2), paste0 (2), unlist (2), with (2), col (1), data.frame (1), dirname (1), get (1), grep (1), mapply (1), merge (1), ncol (1), numeric (1), readLines (1), replicate (1), seq_len (1), source (1), str2lang (1), suppressWarnings (1), t (1), tempdir (1), tolower (1), toupper (1), vector (1)
build_progressr (5), spectral_indices (3), extract_urls (2), remap_band_names (2), alos_palsar_mask_function (1), calc_scale_strings (1), calculate_indices (1), check_indices (1), check_type_and_length (1), default_query_function (1), download_web_indices (1), filter_bands (1), filter_platforms (1), get_alos_palsar_imagery (1), get_dem (1), get_landsat_imagery (1), get_naip_imagery (1), get_rescaling_formula (1), get_sentinel1_imagery (1), get_sentinel2_imagery (1), get_stac_data (1), is_pc (1), landsat_mask_function (1), maybe_sign_items (1), set_gdalwarp_extent (1), spectral_indices_url (1)
arg_match (4), caller_env (2), warn (2), exec (1), new_environment (1)
rast (5), sprc (2), crs (1), nlyr (1), predict (1)
assets_url (2), items_datetime (2), stac_search (1)
glue (4)
is (3)
future_lapply (2)
predict (1), setNames (1)
file_ext (1), R_user_dir (1)
user_agent (1)
progressor (1)
st_bbox (1)
base
rsi
rlang
terra
rstac
glue
methods
future.apply
stats
tools
httr
progressr
sf
This package features some noteworthy statistical properties which may need to be clarified by a handling editor prior to progressing.
The package has: - code in R (100% in 15 files) and - 1 authors - 3 vignettes - 5 internal data files - 11 imported packages - 21 exported functions (median 19 lines of code) - 62 non-exported functions in R (median 15 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 | 15| 73.0| | |files_vignettes | 3| 92.4| | |files_tests | 9| 89.6| | |loc_R | 1437| 77.1| | |loc_vignettes | 453| 75.7| | |loc_tests | 853| 84.6| | |num_vignettes | 3| 94.2| | |data_size_total | 26424| 76.4| | |data_size_median | 4831| 74.3| | |n_fns_r | 83| 71.4| | |n_fns_r_exported | 21| 68.8| | |n_fns_r_not_exported | 62| 73.1| | |n_fns_per_file_r | 3| 55.1| | |num_params_per_fn | 7| 85.3| | |loc_per_fn_r | 15| 46.1| | |loc_per_fn_r_exp | 19| 44.7| | |loc_per_fn_r_not_exp | 15| 49.5| | |rel_whitespace_R | 10| 63.3| | |rel_whitespace_vignettes | 32| 76.2| | |rel_whitespace_tests | 13| 73.5| | |doclines_per_fn_exp | 51| 64.2| | |doclines_per_fn_not_exp | 0| 0.0|TRUE | |fn_call_network_size | 36| 59.4| | ---
Click to see the interactive network visualisation of calls between objects in package
goodpractice
and other checks#### 3a. Continuous Integration Badges [![R-CMD-check.yaml](https://github.com/Permian-Global-Research/rsi/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/Permian-Global-Research/rsi/actions) **GitHub Workflow Results** | id|name |conclusion |sha | run_number|date | |----------:|:--------------------------|:----------|:------|----------:|:----------| | 8486854009|Lock Threads |success |694d2a | 156|2024-03-30 | | 8482543797|pages build and deployment |success |1de384 | 65|2024-03-29 | | 8482287996|pkgdown |success |694d2a | 135|2024-03-29 | | 8482287992|R-CMD-check |success |694d2a | 131|2024-03-29 | | 8482287990|R-CMD-check-hard |success |694d2a | 131|2024-03-29 | | 8482287998|test-coverage |success |694d2a | 131|2024-03-29 | --- #### 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/) ERROR: Test Coverage Failed #### Cyclocomplexity with [cyclocomp](https://github.com/MangoTheCat/cyclocomp) The following functions have cyclocomplexity >= 15: function | cyclocomplexity --- | --- get_stac_data | 44 stack_rasters | 28 check_type_and_length | 25 #### Static code analyses with [lintr](https://github.com/jimhester/lintr) [lintr](https://github.com/jimhester/lintr) found the following 127 potential issues: message | number of times --- | --- Avoid library() and require() calls in packages | 4 Lines should not be more than 80 characters. | 123
:heavy_multiplication_x: The following 2 function names are duplicated in other packages: - - `calculate_indices` from ClusterStability - - `sign_planetary_computer` from rstac
|package |version | |:--------|:--------| |pkgstats |0.1.3.11 | |pkgcheck |0.1.2.21 |
Processing may not proceed until the items marked with :heavy_multiplication_x: have been resolved.
Guessing covr fails due to not setting my custom is_covr
environment variable:
https://github.com/Permian-Global-Research/rsi/commit/c62e6e9aa08c06a54094edc6c3df994260d8aa17
This environment variable is used to skip a test on my covr CI. The tl;dr is that rsi executes some code in a minimal environment to protect against malicious code downloaded from the internet, which prevents covr from injecting its tracking inside of that minimal environment. I still want the file to be tested (and the other pieces of the file to be counted in coverage), though, so I wrapped the local environment section in nocov
and added this environment variable.
You can see my code coverage report at https://app.codecov.io/gh/Permian-Global-Research/rsi and my CI workflow for this at https://github.com/Permian-Global-Research/rsi/blob/main/.github/workflows/test-coverage.yaml
@ropensci-review-bot assign @jhollist as editor
Assigned! @jhollist is now the editor
@mikemahoney218 Been swamped these last few days. I will work on digging through this today and tomorrow and get back to you soon and should hopefully be ready to start finding reviewers.
I am looking forward to this review. Does look like an interesting package!
No worries, and thanks for the update!
@ropensci-review-bot check rsi
I'm sorry human, I don't understand that. You can see what commands I support by typing:
@ropensci-review-bot help
@ropensci-review-bot check package
Thanks, about to send the query.
:rocket:
Editor check started
:wave:
Just want to flag that I'm still expecting (your version of) covr to fail, due to https://github.com/ropensci/software-review/issues/636#issuecomment-2028086514
The core issue is that calculate_indices()
is basically intended to run code from a random site on the internet -- a trusted site, but still a security risk. As such, that downloaded code is run inside a minimal environment that prevents injecting any unexpected code or functions. Unfortunately, covr works by injecting unexpected functions into your source code, and then counting how many times its functions get run -- then calculate_indices()
doesn't allow those to execute, causing the function to fail.
As a result, I toggle the tests that hit this code path using a custom is_covr
variable, which isn't set by your covr check (because I just made it up, I don't know of a supported way to do this) and so your covr check fails.
I don't want to disable the whole .R file from covr, because covr can instrument the rest of the file, and I don't want to drop these tests (or make them off by default) because I'd like R CMD check
to check this function. I've got a live coverage report running via GHA and hopefully viewable at:
https://app.codecov.io/gh/Permian-Global-Research/rsi?branch=main
git hash: e71186f2
Important: All failing checks above must be addressed prior to proceeding
(Checks marked with :eyes: may be optionally addressed.)
Package License: Apache License (>= 2)
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 | 175|
|internal |rsi | 34|
|internal |methods | 3|
|internal |stats | 2|
|internal |tools | 2|
|imports |rlang | 10|
|imports |terra | 10|
|imports |rstac | 5|
|imports |glue | 4|
|imports |future.apply | 2|
|imports |httr | 1|
|imports |sf | 1|
|imports |jsonlite | NA|
|imports |lifecycle | NA|
|imports |proceduralnames | NA|
|imports |tibble | NA|
|suggests |progressr | 1|
|suggests |curl | NA|
|suggests |knitr | NA|
|suggests |rmarkdown | NA|
|suggests |testthat | 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(
names (20), c (19), class (10), lapply (9), length (8), vapply (8), args (6), formals (6), list (6), mget (6), tryCatch (5), file.path (4), for (4), max (4), min (4), options (4), tempfile (4), ifelse (3), url (3), all (2), call (2), character (2), drop (2), eval (2), is.null (2), nrow (2), paste (2), paste0 (2), unlist (2), with (2), col (1), data.frame (1), dirname (1), get (1), grep (1), mapply (1), merge (1), ncol (1), numeric (1), readLines (1), replicate (1), seq_len (1), source (1), str2lang (1), suppressWarnings (1), t (1), tempdir (1), tolower (1), toupper (1), vector (1)
build_progressr (5), spectral_indices (3), extract_urls (2), remap_band_names (2), alos_palsar_mask_function (1), calc_scale_strings (1), calculate_indices (1), check_indices (1), check_type_and_length (1), default_query_function (1), download_web_indices (1), filter_bands (1), filter_platforms (1), get_alos_palsar_imagery (1), get_dem (1), get_landsat_imagery (1), get_naip_imagery (1), get_rescaling_formula (1), get_sentinel1_imagery (1), get_sentinel2_imagery (1), get_stac_data (1), is_pc (1), landsat_mask_function (1), maybe_sign_items (1), set_gdalwarp_extent (1), spectral_indices_url (1)
arg_match (4), caller_env (2), warn (2), exec (1), new_environment (1)
rast (5), sprc (2), crs (1), nlyr (1), predict (1)
assets_url (2), items_datetime (2), stac_search (1)
glue (4)
is (3)
future_lapply (2)
predict (1), setNames (1)
file_ext (1), R_user_dir (1)
user_agent (1)
progressor (1)
st_bbox (1)
base
rsi
rlang
terra
rstac
glue
methods
future.apply
stats
tools
httr
progressr
sf
This package features some noteworthy statistical properties which may need to be clarified by a handling editor prior to progressing.
The package has: - code in R (100% in 15 files) and - 1 authors - 3 vignettes - 5 internal data files - 11 imported packages - 21 exported functions (median 19 lines of code) - 62 non-exported functions in R (median 15 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 | 15| 73.0| | |files_vignettes | 3| 92.4| | |files_tests | 9| 89.6| | |loc_R | 1437| 77.1| | |loc_vignettes | 499| 78.0| | |loc_tests | 853| 84.6| | |num_vignettes | 3| 94.2| | |data_size_total | 26424| 76.4| | |data_size_median | 4831| 74.3| | |n_fns_r | 83| 71.4| | |n_fns_r_exported | 21| 68.8| | |n_fns_r_not_exported | 62| 73.1| | |n_fns_per_file_r | 3| 55.1| | |num_params_per_fn | 7| 85.3| | |loc_per_fn_r | 15| 46.1| | |loc_per_fn_r_exp | 19| 44.7| | |loc_per_fn_r_not_exp | 15| 49.5| | |rel_whitespace_R | 10| 63.3| | |rel_whitespace_vignettes | 33| 79.8| | |rel_whitespace_tests | 13| 73.5| | |doclines_per_fn_exp | 51| 64.2| | |doclines_per_fn_not_exp | 0| 0.0|TRUE | |fn_call_network_size | 36| 59.4| | ---
Click to see the interactive network visualisation of calls between objects in package
goodpractice
and other checks#### 3a. Continuous Integration Badges [![R-CMD-check.yaml](https://github.com/Permian-Global-Research/rsi/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/Permian-Global-Research/rsi/actions) **GitHub Workflow Results** | id|name |conclusion |sha | run_number|date | |----------:|:--------------------------|:----------|:------|----------:|:----------| | 8572262292|Commands |skipped |bc9e46 | 46|2024-04-05 | | 8639486278|Lock Threads |success |e71186 | 168|2024-04-11 | | 8575408691|pages build and deployment |success |f75519 | 69|2024-04-05 | | 8575285598|pkgdown |success |e71186 | 140|2024-04-05 | | 8575285595|R-CMD-check |success |e71186 | 135|2024-04-05 | | 8575285599|R-CMD-check-hard |success |e71186 | 135|2024-04-05 | | 8575285597|test-coverage |success |e71186 | 135|2024-04-05 | --- #### 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/) ERROR: Test Coverage Failed #### Cyclocomplexity with [cyclocomp](https://github.com/MangoTheCat/cyclocomp) The following functions have cyclocomplexity >= 15: function | cyclocomplexity --- | --- get_stac_data | 44 stack_rasters | 28 check_type_and_length | 25 #### Static code analyses with [lintr](https://github.com/jimhester/lintr) [lintr](https://github.com/jimhester/lintr) found the following 127 potential issues: message | number of times --- | --- Avoid library() and require() calls in packages | 4 Lines should not be more than 80 characters. | 123
:heavy_multiplication_x: The following 2 function names are duplicated in other packages: - - `calculate_indices` from ClusterStability - - `sign_planetary_computer` from rstac
|package |version | |:--------|:--------| |pkgstats |0.1.3.11 | |pkgcheck |0.1.2.21 |
Processing may not proceed until the items marked with :heavy_multiplication_x: have been resolved.
@mikemahoney218 Thanks for the update. And as you expected the bot checks fail. I am not too worried about that given you have good coverage and can demonstrate it with the codecov reports. We will want to make sure that this coverage is reported out in the repositories README. You may already be doing that, I just haven't checked yet!
Stay tuned, I am working on this today and tomorrow and expect to move on to finding reviewers shortly after that!
I think we are ready to pass on to reviewers! Nice Job!
Only one very small request:
I like to see a more upfront CONTRIBUTING. I always get lost trying to find them when embedded inside .github
. A simple link to that file should suffice!
Also, I have no concerns about the tests failing on the bot. You have implemented them well, the coverage is good, and the badge makes it easy to find.
@ropensci-review-bot seeking reviewers
Please add this badge to the README of your package repository:
[![Status at rOpenSci Software Peer Review](https://badges.ropensci.org/636_status.svg)](https://github.com/ropensci/software-review/issues/636)
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
Added the link to CONTRIBUTING!
@ropensci-review-bot assign @mdsumner as reviewer
@mdsumner added to the reviewers list. Review due date is 2024-05-09. Thanks @mdsumner 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.
@mdsumner: If you haven't done so, please fill this form for us to update our reviewers records.
@ropensci-review-bot set due date for @mdsumner to 2024-05-24
Review due date for @mdsumner is now 24-May-2024
@mikemahoney218 Just wanted to quickly touch base. I am still working on finding a 2nd reviewer. Hopefully I will hear back with a positive response soon from my latest inquiry. Sorry for the delay!
@ropensci-review-bot set due date for @mdsumner to 2024-06-19
Review due date for @mdsumner is now 19-June-2024
@ropensci-review-bot assign @OldLipe as reviewer
@OldLipe added to the reviewers list. Review due date is 2024-07-03. Thanks @OldLipe 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.
@OldLipe: If you haven't done so, please fill this form for us to update our reviewers records.
Submitting Author Name: Mike Mahoney Submitting Author Github Handle: !--author1-->@mikemahoney218<!--end-author1-- Repository: https://github.com/Permian-Global-Research/rsi/ Version submitted: Submission type: Standard Editor: !--editor-->@jhollist<!--end-editor-- Reviewers: @mdsumner, @OldLipe
Due date for @mdsumner: 2024-06-19 Due date for @OldLipe: 2024-07-03Archive: TBD Version accepted: TBD Language: en
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.):
Explain how and why the package falls under these categories (briefly, 1-2 sentences):
This package supports (spatial) data retrieval from APIs implementing the OGC STAC API standard, processing the downloaded data (including automated masking, compositing and rescaling) computing spectral indices from those data, and wrangling the outputs into formats useful for modeling and visualization.
Anyone with a need to download and process spatial data, particularly remote sensing data, particularly satellite-based earth observation rasters. We've used rsi to automate the entire data preparation process of forest carbon and structure models (not yet published), but the package is broadly useful to anyone working in Earth surface modeling.
Yes:
There are a few minor things that I think rsi does better than other approaches (we sign items right before each one is downloaded, for instance, whereas some other packages sign items before starting to download the entire set, meaning the signature can expire causing large downloads to fail), but this difference I think is mostly a matter of taste. I'm very familiar with local GDAL, terra, and sf, and so rsi tries to get users back to working with local GDAL, terra, and sf as fast as possible.
NA
NA
pkgcheck
items which your package is unable to pass.~I have never successfully gotten the CI item to be a check, and I have no idea why. I'm using the standard
usethis
functions to structure my CI, for what it's worth!~ Apparently this is a local-only issue.I addressed failing covr in https://github.com/ropensci/software-review/issues/636#issuecomment-2028086514
Technical checks
Confirm each of the following by checking the box.
This package:
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