Merge pull request #176 from inbo/dev_nextrelease

Release n2khab 0.10.0

.Rbuildignore

@@ -10,3 +10,4 @@ pkgdown/
 ^appveyor\.yml$
 ^\.zenodo\.json$
 ^\.github$
+^CODE_OF_CONDUCT\.md$

.github/CONTRIBUTING.md

@@ -101,31 +101,30 @@ This is the structure of the [repo]:
 ├── n2khab.Rproj        <- Main RStudio project file.
 ├── NAMESPACE
 ├── NEWS.md             <- The changelog.
-└── README.md
+└── README.md           <- The package homepage.
 ```
 
 ### Coding tools
 
 When writing functions for `n2khab`:
 
-- please use `tidyverse`, `sf` and `raster` packages for data reading.
-Discover the human-friendly way of coding a data processing pipeline through the use of [pipes](https://r4ds.had.co.nz/pipes.html)!
+- please use `sf` and `terra` packages for reading geospatial data.
 Organise data in R in a [tidy](https://r4ds.had.co.nz/tidy-data.html#tidy-data-1) way in order to avoid troubles later on.
 Recommended resources to get started are:
     - [R for Data Science](https://r4ds.had.co.nz/)
     - [Geocomputation with R](https://geocompr.robinlovelace.net)
-    - [R packages](https://r-pkgs.org/) (by Hadley Wickham and Jenny Bryan)
+    - [R packages](https://r-pkgs.org/)
     - [`vignette("rd-formatting", package = "roxygen2")`](https://roxygen2.r-lib.org/articles/formatting.html) for documentation syntax.
     Or use markdown support in function documentation after adding the `@md` tag.
 - have a quick look at the [tidyverse style guide](https://style.tidyverse.org/).
 There you see how to style object, variable and function names, as well as the documentation.
 At least keep in mind: **use lower case and 'snake_case'** for object, variable and function names.
-- if your function returns a dataframe, use `dplyr::as_tibble()` to return it as a tibble instead.
-A tibble is a dataframe that makes working in the tidyverse a little [easier](https://r4ds.had.co.nz/tibbles.html).
+- if your function returns a data frame, use `dplyr::as_tibble()` to return it as a tibble instead.
+A tibble is a data frame that makes working in the tidyverse a little [easier](https://r4ds.had.co.nz/tibbles.html).
 - functions that read or process data should return data as much as possible internationalized:
     - availability of English names for types, environmental pressures, ...
     Other languages can be accommodated as well;
-    - English names for table headings (dataframe variables).
+    - English names for table headings (data frame variables).
 
 
 ### How to contribute code? 

.zenodo.json

@@ -4,26 +4,26 @@
     "license": "GPL-3.0",
     "upload_type": "software",
     "access_right": "open",
-    "version": "0.9.1",
+    "version": "0.10.0",
     "creators": [
         {
             "name": "Vanderhaeghe, Floris",
-            "affiliation": "Research Institute for Nature and Forest",
+            "affiliation": "Research Institute for Nature and Forest (INBO)",
             "orcid": "0000-0002-6378-6229"
         },
         {
             "name": "Westra, Toon",
-            "affiliation": "Research Institute for Nature and Forest",
+            "affiliation": "Research Institute for Nature and Forest (INBO)",
             "orcid": "0000-0003-2478-9459"
         },
         {
             "name": "Herr, Cécile",
-            "affiliation": "Research Institute for Nature and Forest",
+            "affiliation": "Research Institute for Nature and Forest (INBO)",
             "orcid": "0000-0002-2833-6046"
         },
         {
             "name": "Van Calster, Hans",
-            "affiliation": "Research Institute for Nature and Forest",
+            "affiliation": "Research Institute for Nature and Forest (INBO)",
             "orcid": "0000-0001-8595-8426"
         }
     ],

CODE_OF_CONDUCT.md

@@ -0,0 +1,126 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+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.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* 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 floris.vanderhaeghe@inbo.be. 
+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

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: n2khab
 Title: Providing Preprocessed Reference Data for Flemish Natura 2000 Habitat Analyses
-Version: 0.9.1
+Version: 0.10.0
 Authors@R: c(
     person("Floris", "Vanderhaeghe", email = "floris.vanderhaeghe@inbo.be", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-6378-6229")), 
     person("Toon", "Westra", email = "toon.westra@inbo.be", role = c("aut"), comment = c(ORCID = "0000-0003-2478-9459")), 
@@ -54,15 +54,19 @@ Suggests:
     jsonlite,
     knitr,
     mapview,
+    n2khabmon,
     openssl,
     raster (>= 3.6-3),
     readxl,
     rmarkdown,
+    terra,
     testthat (>= 3.0.0),
     tidyverse,
     tools,
     units,
     utils,
     withr
+Remotes:
+    inbo/n2khabmon
 VignetteBuilder: knitr
 Config/testthat/edition: 3

NAMESPACE

@@ -7,7 +7,9 @@ export(download_zenodo)
 export(expand_types)
 export(fileman_folders)
 export(fileman_up)
+export(locate_n2khab_data)
 export(md5sum)
+export(n2khab_options)
 export(read_GRTSmh)
 export(read_GRTSmh_base4frac)
 export(read_GRTSmh_diffres)
@@ -80,6 +82,8 @@ importFrom(purrr,map_lgl)
 importFrom(rlang,.data)
 importFrom(rlang,na_lgl)
 importFrom(rprojroot,find_root)
+importFrom(rprojroot,find_root_file)
+importFrom(rprojroot,has_dir)
 importFrom(rprojroot,is_git_root)
 importFrom(rprojroot,is_rstudio_project)
 importFrom(sf,"st_crs<-")
@@ -101,9 +105,8 @@ importFrom(stringr,str_split)
 importFrom(stringr,str_squish)
 importFrom(stringr,str_sub)
 importFrom(stringr,str_to_title)
-importFrom(tidyr,gather)
 importFrom(tidyr,nest)
-importFrom(tidyr,spread)
+importFrom(tidyr,tribble)
 importFrom(tidyr,unnest)
 importFrom(utils,packageDescription)
 importFrom(utils,packageVersion)

NEWS.md

@@ -1,3 +1,29 @@
+# n2khab 0.10.0 (2023-12-01)
+
+## Breaking change
+
+`read_GRTSmh()`, `read_GRTSmh_base4frac()`, `read_GRTSmh_diffres()` and `read_raster_runif()` now return a `SpatRaster` object from {[terra](https://rspatial.github.io/terra)} by default (#173).
+Previous behaviour using {raster} can still be restored; see below.
+However do note that {raster} is a legacy package and {terra} is its successor.
+
+## New feature
+
+The package can be configured using `options()` or corresponding environment variables.
+Current configuration state is returned by `n2khab_options()`.
+See `?n2khab_options` for information on package configuration.
+
+Two settings are now available:
+
+- optionally use {raster} instead of {terra} (#173);
+- optionally set a custom `n2khab_data` path, affecting all functions that need this path (#174).
+
+## Deprecated functions
+
+`read_schemes()` and `read_scheme_types()` were moved to a new package {[n2khabmon](https://inbo.github.io/n2khabmon)}.
+In {n2khab} they are still functional but deprecated, and will eventually disappear (#175).
+The accompanying data sources `schemes` and `scheme_types` have moved to {n2khabmon}.
+{n2khab} 0.10.0 will be the minimum version required by {n2khabmon}.
+
 # n2khab 0.9.1 (2023-11-24)
 
 - Added workaround for a note during package installation ([d300e4a](https://github.com/inbo/n2khab/commit/d300e4a)).
@@ -26,7 +52,7 @@ These data sources have not changed since previous release.
 
 # n2khab 0.7.0 (2022-05-23)
 
-- Upgrade most [vc-formatted](https://ropensci.github.io/git2rdata) data sources to the format of **git2rdata** version 0.4.0. In this version, files not optimized for version control (but rather for readability), are saved as csv instead of tsv files. For **n2khab**, this applies to the `types` and `env_pressures` data sources. Since it is expected that this upgrade is not compatible with older **git2rdata** versions, the version dependency for **git2rdata** has been updated (#161).
+- Upgrade most [vc-formatted](https://ropensci.github.io/git2rdata) data sources to the format of {git2rdata} version 0.4.0. In this version, files not optimized for version control (but rather for readability), are saved as csv instead of tsv files. For {n2khab}, this applies to the `types` and `env_pressures` data sources. Since it is expected that this upgrade is not compatible with older {git2rdata} versions, the version dependency for {git2rdata} has been updated (#161).
 - `scheme_types` data source: update typegroup membership of type `7210` in scheme `GW_03.3` (#161).
 
 # n2khab 0.6.0 (2022-02-03)
@@ -176,5 +202,5 @@ Further, a number of smaller fixes and enhancements were made.
 This package is the successor of the 'n2khabutils' package.
 Previous to commit `c8608d9`, the code was part of the [n2khab-monitoring](https://github.com/inbo/n2khab-monitoring) repo (formerly 'n2khab-inputs'), where the original version history remains stored.
 At that time, the package was called 'n2khabutils'.
-As a convenience, the **n2khab** repo still holds the rewritten (shrinked) package history from before commit `c8608d9`, as defined by the related files and folders.
+As a convenience, the {n2khab} repo still holds the rewritten (shrinked) package history from before commit `c8608d9`, as defined by the related files and folders.
 See [this](https://github.com/inbo/n2khab-monitoring/issues/28) issue in the 'n2khab-monitoring' repo, where the migration is documented.