Merge pull request #88 from b-cubed-eu/add-tests

Add tests

.github/CODE_OF_CONDUCT.md

@@ -1,25 +1,126 @@
-# Contributor Code of Conduct
+# Contributor Covenant Code of Conduct
 
-As contributors and maintainers of this project, we pledge to respect all people who 
-contribute through reporting issues, posting feature requests, updating documentation,
-submitting pull requests or patches, and other activities.
+## Our Pledge
 
-We are committed to making participation in this project a harassment-free experience for
-everyone, regardless of level of experience, gender, gender identity and expression,
-sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion.
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
 
-Examples of unacceptable behaviour by participants include the use of sexual language or
-imagery, derogatory comments or personal attacks, trolling, public or private harassment,
-insults, or other unprofessional conduct.
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
 
-Project maintainers have the right and responsibility to remove, edit, or reject comments,
-commits, code, wiki edits, issues, and other contributions that are not aligned to this 
-Code of Conduct. Project maintainers who do not follow the Code of Conduct may be removed 
-from the project team.
+## Our Standards
 
-Instances of abusive, harassing, or otherwise unacceptable behaviour may be reported by 
-opening an issue or contacting one or more of the project maintainers.
+Examples of behavior that contributes to a positive environment for our
+community include:
 
-This Code of Conduct is adapted from the Contributor Covenant 
-(http://contributor-covenant.org), version 1.0.0, available at 
-http://contributor-covenant.org/version/1/0/0/
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at [email protected]. 
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+<https://www.contributor-covenant.org/version/2/1/code_of_conduct.html>.
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][https://github.com/mozilla/inclusion].
+
+For answers to common questions about this code of conduct, see the FAQ at
+<https://www.contributor-covenant.org/faq>. Translations are available at <https://www.contributor-covenant.org/translations>.
+
+[homepage]: https://www.contributor-covenant.org

.github/CONTRIBUTING.md

@@ -1,39 +1,47 @@
-# CONTRIBUTING #
+# Contributing to gcube
 
-### Fixing typos
+This outlines how to propose a change to gcube.
+For a detailed discussion on contributing to this and other tidyverse packages, please see the [development contributing guide](https://rstd.io/tidy-contrib) and our [code review principles](https://code-review.tidyverse.org/).
 
-Small typos or grammatical errors in documentation may be edited directly using the GitHub web interface, so long as the changes are made in the _source_ file.
-E.g. edit a `roxygen2` comment in a `.R` file below `R/`, not in an `.Rd` file below `man/`.
+## Fixing typos
 
-### Prerequisites
+You can fix typos, spelling mistakes, or grammatical errors in the documentation directly using the GitHub web interface, as long as the changes are made in the _source_ file. 
+This generally means you'll need to edit [roxygen2 comments](https://roxygen2.r-lib.org/articles/roxygen2.html) in an `.R`, not a `.Rd` file. 
+You can find the `.R` file that generates the `.Rd` by reading the comment in the first line.
 
-Before you make a substantial pull request, you should always file an issue and make sure someone from the team agrees that it’s a problem. 
-If you’ve found a bug, create an associated issue and illustrate the bug with a minimal [reproducible example](https://www.tidyverse.org/help/#reprex).
+## Bigger changes
+
+If you want to make a bigger change, it's a good idea to first file an issue and make sure someone from the team agrees that it’s needed. 
+If you’ve found a bug, please file an issue that illustrates the bug with a minimal 
+[reprex](https://www.tidyverse.org/help/#reprex) (this will also help you write a unit test, if needed).
+See our guide on [how to create a great issue](https://code-review.tidyverse.org/issues/) for more advice.
 
 ### Pull request process
 
-*  We recommend that you create a Git branch for each pull request (PR).  
-*  Look at the GitHub Actions build status before and after making changes.
-The `README` should contain badges for any continuous integration services used by the package.  
-*  We require the `tidyverse` [style guide](http://style.tidyverse.org).
-You can use the [`styler`](https://CRAN.R-project.org/package=styler) package to apply these styles, but please don't restyle code that has nothing to do with your PR.  
-*  We use [`roxygen2`](https://cran.r-project.org/package=roxygen2).  
-*  We use [`testthat`](https://cran.r-project.org/package=testthat). 
-Contributions with test cases included are easier to accept.  
-*  For user-facing changes, add a bullet to the top of `NEWS.md` below the current development version header describing the changes made followed by your GitHub username, and links to relevant issue(s)/PR(s).
+*   Fork the package and clone onto your computer. If you haven't done this before, we recommend using `usethis::create_from_github("b-cubed-eu/gcube", fork = TRUE)`.
+
+*   Install all development dependencies with `devtools::install_dev_deps()`, and then make sure the package passes R CMD check by running `devtools::check()`. 
+    If R CMD check doesn't pass cleanly, it's a good idea to ask for help before continuing. 
+*   Create a Git branch for your pull request (PR). We recommend using `usethis::pr_init("brief-description-of-change")`.
+
+*   Make your changes, commit to git, and then create a PR by running `usethis::pr_push()`, and following the prompts in your browser.
+    The title of your PR should briefly describe the change.
+    The body of your PR should contain `Fixes #issue-number`.
 
-### Code of Conduct
+*  For user-facing changes, add a bullet to the top of `NEWS.md` (i.e. just below the first header). Follow the style described in <https://style.tidyverse.org/news.html>.
 
-Please note that this project is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md). 
-By contributing to this project you agree to abide by its terms.
+### Code style
 
-### Prefer to Email? 
+*   New code should follow the tidyverse [style guide](https://style.tidyverse.org). 
+    You can use the [styler](https://CRAN.R-project.org/package=styler) package to apply these styles, but please don't restyle code that has nothing to do with your PR.  
 
-Email the person listed as maintainer in the `DESCRIPTION` file of this repo.
+*  We use [roxygen2](https://cran.r-project.org/package=roxygen2), with [Markdown syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/rd-formatting.html), for documentation.  
 
-Though note that private discussions over email don't help others - of course
-email is totally warranted if it's a sensitive problem of any kind.
+*  We use [testthat](https://cran.r-project.org/package=testthat) for unit tests. 
+   Contributions with test cases included are easier to accept.  
 
-### Thanks for contributing!
+## Code of Conduct
 
-This contributing guide is adapted from the `tidyverse` contributing guide available at https://raw.githubusercontent.com/r-lib/usethis/master/inst/templates/tidy-contributing.md 
+Please note that the gcube project is released with a
+[Contributor Code of Conduct](CODE_OF_CONDUCT.md). By contributing to this
+project you agree to abide by its terms.

.github/workflows/check_on_branch.yml

@@ -17,4 +17,4 @@ jobs:
     permissions:
       contents: read
     steps:
-      - uses: inbo/actions/check_pkg@checklist-0.3.7
+      - uses: inbo/actions/check_pkg@main

.github/workflows/check_on_main.yml

@@ -16,4 +16,4 @@ jobs:
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: inbo/actions/check_pkg@checklist-0.3.7
+      - uses: inbo/actions/check_pkg@main

.zenodo.json

@@ -1,6 +1,6 @@
 {
   "title": "gcube: Simulating Biodiversity Data Cubes",
-  "version": "0.1.0",
+  "version": "0.2.0",
   "license": "MIT",
   "upload_type": "software",
   "description": "<p>Simulation framework for biodiversity data cubes.<\/p>",

CITATION.cff

@@ -25,4 +25,4 @@ abstract: "Simulation framework for biodiversity data cubes."
 identifiers:
 - type: url
   value: https://b-cubed-eu.github.io/gcube/
-version: 0.1.0
+version: 0.2.0

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: gcube
 Title: Simulating Biodiversity Data Cubes
-Version: 0.1.0
+Version: 0.2.0
 Authors@R: c(
     person("Ward", "Langeraert", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-5900-8109", affiliation = "Research Institute for Nature and Forest (INBO)")),
@@ -40,7 +40,6 @@ URL: https://github.com/b-cubed-eu/gcube,
 BugReports: https://github.com/b-cubed-eu/gcube/issues
 Imports:
     assertthat,
-    cli,
     dplyr,
     gstat,
     methods,

NAMESPACE

@@ -23,8 +23,6 @@ export(simulate_timeseries)
 import(assertthat)
 import(dplyr)
 import(sf)
-importFrom(cli,cli_abort)
-importFrom(cli,cli_warn)
 importFrom(gstat,gstat)
 importFrom(gstat,vgm)
 importFrom(methods,formalArgs)

NEWS.md

@@ -1,3 +1,10 @@
+# gcube 0.2.0
+
+*	Improve function checks with `stopifnot()` and the [assertthat](https://CRAN.R-project.org/package=assertthat) package.
+*	Add missing unit tests.
+*	Set repo status to active.
+* Use tidy contributing and code of conduct.
+
 # gcube 0.1.0
 
 * Create data cube for multiple species using `purrr::pmap()`.
@@ -9,7 +16,7 @@
 
 # gcube 0.0.1
 
-* Add [`checklist`](https://inbo.github.io/checklist/) infrastructure.
+* Add [checklist](https://inbo.github.io/checklist/) infrastructure.
 
 # gcube 0.0.0
 

R/add_coordinate_uncertainty.R

@@ -14,7 +14,7 @@
 #' @export
 #'
 #' @import sf
-#' @importFrom cli cli_abort
+#' @importFrom stats setNames
 #'
 #' @family main
 #'
@@ -49,52 +49,30 @@
 add_coordinate_uncertainty <- function(
     observations,
     coords_uncertainty_meters = 25) {
+  ### Start checks
+  # 1. Check input type and length
+  # Check if observations is an sf object
+  stopifnot("`observations` must be an sf object with POINT geometry." =
+              inherits(observations, "sf") &&
+              sf::st_geometry_type(observations,
+                                   by_geometry = FALSE) == "POINT")
 
-  ## checks
-  ## is it sf object
-  if (!inherits(observations, "sf")) {
-    cli::cli_abort(c(
-      "{.var observations}  must be an object of class 'sf'",
-      "x" = paste(
-        "You've supplied an object of class {.cls {class(observations)}}"
-      )
-    ))
-  }
-  ## check if coords_uncertainty_meters is numeric
-  if (!is.numeric(coords_uncertainty_meters)) {
-    cli::cli_abort(
-      "{.var coords_uncertainty_meters must be a numeric value}"
-    )
-  }
+  # Check if coords_uncertainty_meters is numeric
+  stopifnot("`coords_uncertainty_meters` must be  numeric vector." =
+              is.numeric(coords_uncertainty_meters))
 
-  ## is geometry type POINT?
-  is_point <- sf::st_geometry_type(observations, by_geometry = FALSE) == "POINT"
-  if (!is_point) {
-    cli::cli_abort(c(
-      "{.var observations} must be a 'sf' object with POINT geometry",
-      paste("x" = "You've supplied an 'sf' object of geometry type {.cls",
-            "{sf::st_geometry_type(observations, by_geometry = FALSE)}}")
-      )
-    )
-   }
-
-  ## number of points in sf object and the coords_uncertainty_meters must be the
-  ## same when coords_uncertainty_meters is larger than 1
-  if (length(coords_uncertainty_meters) != 1) {
+  # 2. Other checks
+  # Number of observations and values in coords_uncertainty_meters must be the
+  # same when number of values is larger than 1
+  if (length(coords_uncertainty_meters) > 1) {
     size_match <- length(coords_uncertainty_meters) == nrow(observations)
-
-    if (!size_match) {
-      cli::cli_abort(
-        c(
-          paste("{.var coords_uncertainty_meters} has diferent length than the",
-                "number of rows in {.var observations}"),
-          "x" = paste("You've supplied {.var coords_uncertainty_meters} of",
-                      "length {length(coords_uncertainty_meters)}",
-                      "but {.var observations} has {nrow(observations)} rows.")
-        )
-     )
-    }
+    error_message <- paste(
+      "Number of values in `coords_uncertainty_meters` differs from the number",
+      "of observations."
+    )
+    do.call(stopifnot, stats::setNames(list(size_match), error_message))
   }
+  ### End checks
 
   observations$coordinateUncertaintyInMeters <- coords_uncertainty_meters