Merge pull request #184 from inrae/maj_package

Maj package

DESCRIPTION

@@ -1,10 +1,12 @@
 Package: diades.atlas
 Title: The Diades Atlas Shiny App
-Version: 0.3.2
+Version: 0.3.3
 Authors@R: c(
-    person("Sébastien", "Rochette", , "[email protected]", role = c("cre", "aut"),
+    person("Patrick", "Lambert", , "[email protected]", role = c("cre", "aut"),
+           comment = c(ORCID = "0000-0003-4367-8498")),
+    person("Sébastien", "Rochette", , "[email protected]", role = "aut",
            comment = c(ORCID = "0000-0002-1565-9313")),
-    person("Colin", "Fay", , "[email protected]", role = "aut",
+    person("Colin", "Fay", , "[email protected]", role = c("aut"),
            comment = c(ORCID = "0000-0001-7343-1846")),
     person("Antoine", "Languillaume", , "[email protected]", role = "aut",
            comment = c(ORCID = "0000-0001-9843-5632"))
@@ -58,7 +60,6 @@ Imports:
 Suggests: 
     attempt,
     DiagrammeR (>= 1.0.6.1),
-    DiagrammeRsvg (>= 0.1),
     future,
     knitr (>= 1.34),
     rlang,
@@ -67,8 +68,6 @@ Suggests:
     testthat (>= 3.0.4)
 VignetteBuilder: 
     knitr
-Remotes: 
-    thinkr-open/w3css
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2

Dockerfile

@@ -1,4 +1,4 @@
-FROM rocker/geospatial:4.3.0
+FROM rocker/geospatial:4.4.1
 RUN apt-get update && apt-get install -y  gdal-bin git-core libcairo2-dev libcurl4-openssl-dev libgdal-dev libgeos-dev libgeos++-dev libgit2-dev libicu-dev libpng-dev libpq-dev libproj-dev libssl-dev libudunits2-dev libxml2-dev make pandoc pandoc-citeproc zlib1g-dev && rm -rf /var/lib/apt/lists/*
 
 # RUN echo "options(renv.config.pak.enabled = TRUE, repos = c(CRAN = 'https://packagemanager.rstudio.com/all/__linux__/focal/latest'), download.file.method = 'libcurl', Ncpus = 4)" >> /usr/local/lib/R/etc/Rprofile.site

NEWS.md

@@ -1,3 +1,9 @@
+# diades.atlas 0.3.3
+
+* Upgrade R version in renv.lock
+* Upgrade R package version
+* Fix bad request in page 1
+
 # diades.atlas 0.3.2
 
 * Upgrade R version in renv.lock

R/mod_a_first_fct_map.R

@@ -119,7 +119,7 @@ tm_catchmment <- function(dataContinent) {
   tm_shape(dataContinent) +
     tm_polygons(
       "abundance_interpretation",
-      title = "Status in river catchments (1951-2010)" %>% with_i18("status_in_river_catchments") %>% as.character(),
+      title = "Status in river catchments" %>% with_i18("status_in_river_catchments") %>% as.character(),
       # "<span data-i18n='status_in_river_catchments'>Status in river catchments (1951-2010)</span>",
       palette = c("#FEE0D2", "#FCBBA1", "#A50F15", "#67000D"),
       n = 4,

R/mod_c_third_fct_query_and_plot.R

@@ -50,7 +50,9 @@ get_bv_geoms <- function(bv_ids,
     get_con(session),
     query = sprintf(
       "select basin_id, verysimplified_geom from basin_outlet where basin_id IN %s",
-      dbplyr::translate_sql(!!bv_ids)
+      dbplyr::translate_sql(
+        con = get_con(session), 
+        !!bv_ids)
     )
   )
   basin <- tbl(get_con(session), "basin") %>%

data-raw/bd-page3-climate-change.Rmd

@@ -3,8 +3,10 @@ title: "bd-page3-climate-change"
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{bd-page3-climate-change}
-  %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
+  %\VignetteEngine{knitr::rmarkdown}
+editor_options: 
+  chunk_output_type: console
 ---
 
 ```{r, include = FALSE}
@@ -73,7 +75,7 @@ datasets <- generate_datasets(
   )
 )
 
-species_id <- datasets$species_list[datasets$species_list[["latin_name"]] == "alosa-fallax", "species_id"]
+species_id <- datasets$species_list[datasets$species_list[["latin_name"]] == "Alosa fallax", "species_id"]
 
 scenario <- "rcp85"
 date <- c(1970, 2010)
@@ -106,7 +108,9 @@ get_bv_geoms <- function(bv_ids,
     get_con(session),
     query = sprintf(
       "select basin_id, verysimplified_geom, ccm_name from basin_outlet where basin_id IN %s",
-      dbplyr::translate_sql(!!bv_ids)
+      dbplyr::translate_sql(
+        con = get_con(session), 
+        !!bv_ids)
     )
   )
   basin <- tbl(get_con(session), "basin") %>%