Merge branch 'release/4.3.3'

.Rbuildignore

@@ -20,11 +20,14 @@ cran-comments.md
 ^R/osmose-plot4d\.R$
 ^R/ex_osmose-plot\.R$
 ^R/osmose\.netcdf\.R$
-^R/update_config\.R$
 ^R/osmose\.maps\.R$
 ^R/osmose2R\.R$
 ^data-raw$
-^inst/java$
-java/target
-java/.classpath
-java/.vscode
+^inst/java/.*\.zip$
+^java/target$
+^java/.classpath$
+^java/.vscode$
+^osmose.Rcheck$
+^RELEASE.md$
+^.vscode$
+^.*ipynb.*$

.github/workflows/java-compile.yml

@@ -18,11 +18,27 @@ jobs:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - uses: actions/checkout@v2
 
-      - name: Set up JDK 1.8
+      # extracts the list of lfs file identifiers
+      - name: Create LFS file list
+        run: git lfs ls-files -l | cut -d' ' -f1 | sort > .lfs-assets-id
+
+      # restore the LFS cache
+      - name: Restore LFS cache
+        uses: actions/cache@v2
+        id: lfs-cache
+        with:
+          path: .git/lfs
+          key: ${{ runner.os }}-lfs-${{ hashFiles('.lfs-assets-id') }}-v1
+
+      # Pull LFS files
+      - name: Git LFS Pull
+        run: git lfs pull
+
+      - name: Set up JDK 11
         uses: actions/setup-java@v1
         with:
-          java-version: 1.8
-      
+          java-version: 11
+
       - name: Cache Maven dependencies
         id: maven-dep
         uses: actions/cache@v2
@@ -31,13 +47,12 @@ jobs:
         with:
             path: ~/.m2/repository
             key: ${{ runner.os }}-build-${{ env.cache-name }}-${{ hashFiles('**/*.jar') }}
-            restore-keys: | 
+            restore-keys: |
                 ${{ runner.os }}-build-${{ env.cache-name }}-
                 ${{ runner.os }}-build-
                 ${{ runner.os }}-
 
       - name: Compile Java code
-        run:  | 
-            cd java 
+        run:  |
             mvn build-helper:remove-project-artifact
-            mvn -B package
+            mvn -B package -DskipTests=true

.github/workflows/r-compile.yml

@@ -19,34 +19,30 @@ jobs:
       - uses: actions/checkout@v2
 
       - name: R install
-        uses: r-lib/actions/setup-r@master
-            
+        uses: r-lib/actions/setup-r@v2
+
       - name: Install NetCDF and Latex
-        run: sudo apt-get update && sudo apt-get install -yq libnetcdf-dev texlive-latex-base texlive-fonts-recommended texlive-fonts-extra
+        run:  sudo apt-get install -yq libnetcdf-dev texlive-latex-base texlive-fonts-recommended texlive-fonts-extra
 
       - name: Cache R dependencies
         id: r-dep
         uses: actions/cache@v2
         env:
-            cache-name: r-dep-modules
+            cache-name: r-dep-modules-v2
         with:
             path: /home/runner/work/_temp/Library
             key: ${{ runner.os }}-build-${{ env.cache-name }}-${{ hashFiles('**/DESCRIPTION') }}
-            restore-keys: | 
-                ${{ runner.os }}-build-${{ env.cache-name }}-
-                ${{ runner.os }}-build-
-                ${{ runner.os }}-
 
       - name: Install Osmose dependencies
         if: steps.r-dep.outputs.cache-hit != 'true'
-        run: install.packages(c("rlist", "knitr", "rmarkdown", "stringr", "ncdf4", "mgcv", "fields"), repos="http://cran.us.r-project.org")
+        run: install.packages(c("rlist", "knitr", "rmarkdown", "stringr", "ncdf4", "mgcv", "ggplot2", "spam", "viridis", "fields", "R.utils", "calibrar"), repos="http://cran.us.r-project.org")
         shell: Rscript {0}
 
       - name: Build Osmose without vignettes
-        run: R CMD build --no-build-vignettes .
+        run:  R CMD build --no-build-vignettes .
 
       - name: Check Osmose without vignettes
         run: |
             file=`ls *tar.gz`
             echo $file
-            R CMD check --as-cran --ignore-vignettes ${file} 
+            R CMD check --as-cran --ignore-vignettes ${file}

.gitignore

@@ -1,6 +1,13 @@
 # History files
 .Rhistory
 .Rapp.history
+.RData
+
+# doc/**/*.puml
+
+**/**ipynb**
+**/*~lock*
+
 
 # Example code in package build process
 *-Ex.R
@@ -24,6 +31,7 @@ vignettes/*.pdf
 
 inst/extdata/Rplots.pdf
 inst/extdata/plot_test.R
+**/osmose-Ex*
 
 inst/extdata/eec/make_netcdf_mask.R
 *.swp
@@ -35,8 +43,14 @@ inst/doc
 /vignettes/plot_method_cache
 /vignettes/create_run_read_cache
 
+java/target
 target
-**sh
+
+doc/_static/javadoc
+doc/_static/puml
+
+
+check.sh
 **.html
 build
 dist
@@ -46,4 +60,32 @@ nbproject
 **.Rcheck
 
 **/nbactions.xml
+**/.classpath
+**/.settings
+**/.project
+**/*jar-with-dependencies.jar
+
+**/*.ipynb
+
+# doc
+**/_build
+**/eec_4.3.0
+**/gog
+**/*calib_demo*
+doc/osmose/_static/plot_step_chart.pdf
+doc/odd_des/submodel/mort/_static/fishing-period.pdf
+doc/odd_des/submodel/mort/_static/size_ratio.pdf
+doc/odd_des/submodel/_static/gom.pdf
+doc/odd_des/submodel/_static/size_ratio.pdf
+doc/odd_des/submodel/_static/vb.pdf
+doc/**/_static/*svg
+**.log
+**.aux
 
+**/verif_fisheries*.png
+doc/rosmose/_static/*png
+**/_static/**/*.png
+random_drift.pdf
+random_drift.svg
+/*.sh
+doc/bioen_odd_des/submodel/_static/repfonct_bioen.pdf