Release version 4.0.0 (#653)

Includes: * Established code as a standalone package * Align variables (column names) with Darwin Core, Dublin Core, and the Ecological Trait-data Standard * Allowing more metadata to be associated with individual trait measurements instead of traits or the dataset (e.g. life stage, replicates, entity type) * Rework context, so that multiple context properties can be read in * Reworked identifiers, including 5 separate context property identifiers and location id * Add source_id, such that individual rows of data can be attributed to a specific source * Merge different date fields into `collection_date` * Work from two separate vocabulary workshops merged in (`Seed Traits` & `Whole Plant and Leaf Vegetative Traits`). Also some work realigning traits related to fire response. * Rename other traits to have more consistent naming * Added entity_type, reflecting the entity being measured * Added scraped data from online floras for 7 traits related to plant growth form. For `plant_growth_form` and `woodiness` manually gap-filled from the taxonomic literature to have complete data coverage * Reworked how taxonomic names are processed, such that submitted taxon names are now aligning to the most specific taxon name possible, with separate columns for `family`; `genus`; `binomial`; `trinomial`, filled in as appropriate. * New taxonomic updates added, based on updated algorithms that do a much better job of capturing phrase names and submitted taxon names that include notes. In addition, algorithms automatically identify names that can only be aligned to genus. * Removed taxon matching code from austraits.build (to become part of a separate package) * Add database metadata into the build process
traitecoevo · Nov 27, 2022 · 442206a · 442206a
1 parent 08b89e5
commit 442206a
Show file tree

Hide file tree

Showing 678 changed files with 306,739 additions and 122,884 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,6 +1,11 @@
 ^\.github$
 ^\.rstudio$
-^\.remake$
+^.*\.remake$
+^remake.yml$
+^_targets$
+^\.local$
+^\.cache$
+^\.config$
 ^README\.Rmd$
 ^data$
 ^docs$
@@ -9,7 +14,15 @@
 ^todo$
 ^export$
 ^config$
-^.rstudio$
-^remake.yml$
+^.*ignore$
+^docs$
+^.*\.Rproj$
+^\.Rproj\.user$
+Dockerfile$
+_pkgdown.yml$
+^codecov\.yml$
+^.*code-.*$
+^tmp.*$
+^tests/build$
 ^doc$
 ^Meta$
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -1,9 +1,11 @@
 # Workflow derived from https://github.com/r-lib/actions/tree/master/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+# https://github.com/r-lib/actions/tree/v2-branch/check-r-package
+
 on:
   push:
     branches: [main, master, develop]
-  
+
   pull_request:
     branches: [main, master, develop]
 
@@ -28,23 +30,24 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: rcmdcheck
+          extra-packages: local::., any::rcmdcheck, any::covr
+          needs: check
 
-      - name: Run tests
-        run: testthat::test_dir("tests/testthat")
-        shell: Rscript {0}
-
-      - uses: r-lib/actions/check-r-package@v1
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          args: 'c("--no-manual", "--as-cran")'
+          error-on: '"error"'
+          check-dir: '"check"'
 
       - name: Show testthat output
         if: always()
@@ -57,3 +60,24 @@ jobs:
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: check
+
+      - name: Test build infrastructure
+        run: |
+          library(austraits.build)
+          source("scripts/custom.R")
+          testthat::test_dir("tests/build/")
+        shell: Rscript {0}
+
+      - name: Benchmark
+        run: |
+          library(austraits.build)
+          source("scripts/custom.R")
+          source("scripts/benchmark.R")
+          run_benchmark()
+        shell: Rscript {0}
+
+      - name: Test coverage
+        run: |
+          library(austraits.build)
+          covr::codecov(quiet=FALSE, type = "all")
+        shell: Rscript {0}
diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
diff --git a/.github/workflows/check-build.yml b/.github/workflows/check-build.yml
@@ -22,36 +22,25 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@master
-
-      - uses: r-lib/actions/setup-pandoc@master
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r@v2
+
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Restore R package cache
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - uses: r-lib/actions/setup-r-dependencies@v1
+          extra-packages: local::.
 
-      - name: Test build infrastructure
-        run: testthat::test_dir("tests/build/")
+      - name: check sources
+        run: |
+          library(austraits.build)
+          source("scripts/custom.R")
+          dataset_test(dir("data"))
         shell: Rscript {0}
 
       - name: build austraits
-        run: remake::make()
+        run: |
+          library(austraits.build)
+          source("scripts/custom.R")
+          remake::make()
         shell: Rscript {0}
-
-      - name: Archive artifacts
-        uses: actions/upload-artifact@v2
-        with:
-          name: austraits
-          path: export/data/curr/austraits.rds
+
diff --git a/.gitignore b/.gitignore
@@ -7,9 +7,11 @@ temp
 *.zip
 *.rds
 *.rda
-man/*
 .RData
 .Rhistory
+.cache/
+.local/
+.config/
 *.Rproj
 tmp*
 reports
@@ -27,3 +29,5 @@ doc
 Meta
 config/APC/*
 config/NSL/*
+/doc/
+/Meta/
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,76 +1,63 @@
-Type: Compendium
+Type: Package
 Package: austraits.build
-Title: Raw data and code used to build the AusTraits compilation
-Version: 3.0.2
+Title: Package used to build an AusTraits data resource
+Version: 0.9.0
 Maintainer: Daniel Falster <[email protected]>
 Authors@R: c(
     person(given = "Daniel", family = "Falster", role = c("cre", "aut"), email = "[email protected]", comment = c(ORCID = "0000-0002-9814-092X")),
+    person(given = "Elizabeth", family = "Wenk", role = c("cur", "aut"),  comment = c(ORCID = "0000-0001-5640-5910")),
     person(given = "Rachael", family = "Gallagher", role = c("aut", "cur"), comment = c(ORCID = "0000-0002-4680-8115")),
-    person(given = "Elizabeth", family = "Wenk", role = c("cur", "aut")),
-    person(given = "Ian", family = "Wright", role = c("aut")),
-    person(given = "Sam", family = "Andrew", role = c("aut")),
     person(given = "Gary", family = "Truong", role = c("ctb")),
-    person(given = "Caitlin", family = "Baxter", role = c("aut")),
     person(given = "Stuart", family = "Allen", role = c("ctb")),
-    person(given = "James", family = "Lawson", role = c("ctb")),
     person("ARDC", role = c("fnd")),
     person("ARC", role = c("fnd"))
     )
-Description: AusTraits is an open-source platform for 
-    ongoing compilation and distribution of data on the traits of Australian 
-    plant species. Data have been assembled from diverse sources, describing 
-    more than 300 plant traits and over 25k taxa. This repository contains all
-    the information needed to build the resource from different sources, i.e.
-    harmonise the different datasets into a common structure,
-    with common variable names, units and structure. Also included are the functions
-    we use to help with adding new studies. For mroe information on the project 
-    https://austraits.org
+Description: This package enbales harmonising of data from diverse sources. The code was originally built to support AusTraits,  an open-source compilation of data on the traits of Australian plant species. For more information on AusTraits go to https://austraits.org.
 BugReports: https://github.com/traitecoevo/austraits.build/issues
 URL: http://traitecoevo.github.io/austraits.build/
-License: BSD2 + file LICENSE
-Depends: 
-    R (>= 3.6.1),
+License: BSD_2_clause + file LICENCE
+Depends:
+    R (>= 3.6.0),
     base,
-    stringr,
-    tidyr,
     dplyr,
-    readr,
-    purrr,
     lubridate,
-    testthat
+    readr,
+    stringr,
+    tidyr
 Imports:
-    magrittr,   
     crayon,
-    RefManageR,
-    rmarkdown,
-    knitr,
-    remake,
-    desc,
     git2r,
-    yaml,
-    storr,
     kableExtra,
-    rprojroot,
-    forcats,
-    ggplot2,
-    ggbeeswarm,
-    gridExtra,
-    leaflet,
-    scales,
-    testthat
+    magrittr,
+    purrr,
+    RefManageR,
+    remake,
+    rlang,
+    rmarkdown,
+    stringi,
+    styler,
+    testthat,
+    tibble,
+    whisker,
+    yaml
 Suggests:
+    austraits,
+    leaflet,
+    ggbeeswarm,
+    bibtex,
+    knitr,
+    bench,
     devtools,
-    pkgdown,
-    whisker,
     markdown,
-    googledrive,
+    rprojroot,
+    pkgdown,
     rcrossref,
     zip,
-    bench
+    covr
 Remotes:
+    traitecoevo/austraits@develop,
     richfitz/remake
 Encoding: UTF-8
-LazyData: true
 VignetteBuilder: knitr
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.1
 Config/testthat/edition: 3
diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-FROM rocker/verse:3.6.1
+FROM rocker/verse:4.1.2
 LABEL maintainer="Daniel Falster"
 LABEL email="[email protected]"
 
@@ -38,7 +38,7 @@ COPY ./DESCRIPTION ${HOME}
 
 RUN chown -R ${NB_USER} ${HOME}
 
-RUN R --quiet -e "options(repos = list(CRAN = 'http://mran.revolutionanalytics.com/snapshot/2020-01-01/')); devtools::install_deps(upgrade = 'never')"
+RUN R --quiet -e "options(repos = list(CRAN = 'http://mran.revolutionanalytics.com/snapshot/2022-05-01/')); devtools::install_deps(upgrade = 'never')"
 
 RUN echo "options(remake.verbose.noop=FALSE)" >> /usr/local/lib/R/etc/Rprofile.site