Updating GH actions (#97)

* CI:true is not default * Updates * Trying out auto script run * Update * bug fix * More updates * Updates * Updates * Updates * Updates * Lots of updates * Even more updates * workflow cleanup * actions bugfix * some gh actions updates * Name change
plantphys · Mar 17, 2022 · a52eb93 · a52eb93
1 parent 1f93a3a
commit a52eb93
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1 +1,3 @@
 ^data-raw$
+^doc$
+^Meta$
diff --git a/.github/workflows/check-standard.yaml → .github/workflows/check-os.yaml b/.github/workflows/check-standard.yaml → .github/workflows/check-os.yaml
@@ -1,13 +1,13 @@
+# Check OS and R releases
 on:
   push:
     branches: [main, master]
   pull_request:
     branches: [main, master]
 
-name: R-CMD-check
+name: R-CMD-check-OS-R
 
 env:
-  R_LIBS_USER: /usr/local/lib/R/site-library
   NCPUS: 2
 
 jobs:
@@ -52,19 +52,19 @@ jobs:
           writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
         shell: Rscript {0}
 
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v2
-        with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-rversion-${{ matrix.config.r }}-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-
-
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::rcmdcheck
           needs: check
-
-      - uses: r-lib/actions/check-r-package@v2
+
+      # rcmdcheck but do not build vignettes
+      - name: Build Check Across OS & R Releases
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--no-build-vignettes"), build_args = c("--no-manual", "--no-build-vignettes"), error_on = "error")
+        shell: Rscript {0}
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@v2
         with:
-          upload-snapshots: true
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check
diff --git a/.github/workflows/check-release.yaml → .github/workflows/check-r-release.yaml b/.github/workflows/check-release.yaml → .github/workflows/check-r-release.yaml
@@ -1,16 +1,16 @@
+# CI to test package on different versions of R, rel-1, rel, rel+1
 on:
   push:
     branches: [main, master]
   pull_request:
     branches: [main, master]
 
-name: R-CMD-check
+name: R-CMD-check-R-release
 
 env:
   R_LIBS_USER: /usr/local/lib/R/site-library
   LC_ALL: en_US.UTF-8
   NCPUS: 2
-  CI: true
 
 jobs:
   R-CMD-check:
@@ -41,6 +41,14 @@ jobs:
           extra-packages: any::rcmdcheck
           needs: check
 
+      # rcmdcheck but do not build vignettes
       - name: Run Fast Build Check Across R Releases
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--ignore-vignettes", "--no-build-vignettes"), build_args = c("--no-manual", "--ignore-vignettes", "--no-build-vignettes"), error_on = "error")
-        shell: Rscript {0}
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--no-build-vignettes"), build_args = c("--no-manual", "--no-build-vignettes"), error_on = "error")
+        shell: Rscript {0}
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@v2
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check
diff --git a/.github/workflows/ci-run_plsr_example.yaml b/.github/workflows/ci-run_plsr_example.yaml
@@ -0,0 +1,57 @@
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: ci-run_PLSR_example
+
+env:
+  R_LIBS_USER: /usr/local/lib/R/site-library
+  LC_ALL: en_US.UTF-8
+  NCPUS: 2
+
+jobs:
+  run-plsr: 
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+
+    strategy:
+      fail-fast: false
+      matrix:
+        R:
+          - "3.6"
+          - "4.0"
+          - "4.1"
+
+    steps:
+      #check out source code
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Install dependencies
+        run: |
+          Rscript -e 'remotes::install_github(repo="TESTgroup-BNL/spectratrait", dependencies=TRUE)'
+
+      # Run R script
+      - name: Run Ely et al. (2019) PLSR Example
+        run: |
+          source("inst/scripts/spectra-trait_ely_leafN_plsr_bootstrap_example.R")
+        shell: Rscript {0}
diff --git a/.github/workflows/ci-weekly.yaml b/.github/workflows/ci-weekly.yaml
@@ -1,39 +1,30 @@
-name: R-CMD-check weekly
+name: R-CMD-check-Weekly
 
 on:
   # every Monday at 4:30 AM
     schedule:
     - cron: '30 4 * * 1'
 
 env:
-  R_LIBS_USER: /usr/local/lib/R/site-library
-  LC_ALL: en_US.UTF-8
   NCPUS: 2
-  CI: true
 
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
 
-    name: ${{ matrix.config.os }} (${{ matrix.config.r }})  
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
 
     strategy:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
-
-          - {os: windows-2022, r: 'release'}
-          # Use 3.6 to trigger usage of RTools35
-          - {os: windows-2022, r: '3.6'}
-
-          # Use older ubuntu to maximise backward compatibility
-          - {os: ubuntu-18.04,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-18.04,   r: 'release'}
-          - {os: ubuntu-18.04,   r: 'oldrel-1'}
-          - {os: ubuntu-18.04,   r: 'oldrel-2'}
-          - {os: ubuntu-18.04,   r: 'oldrel-3'}
-          - {os: ubuntu-18.04,   r: 'oldrel-4'}
+          - {os: macOS-latest,  r: 'oldrel-1'}
+          - {os: macOS-latest,  r: 'release'}
+          - {os: windows-2022,  r: 'oldrel-1'}
+          - {os: windows-2022,  r: 'release'}
+          - {os: ubuntu-latest, r: 'oldrel-1'}
+          - {os: ubuntu-latest, r: 'release'}
+          - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -56,6 +47,14 @@ jobs:
           extra-packages: any::rcmdcheck
           needs: check
 
-      - uses: r-lib/actions/check-r-package@v2
+      # rcmdcheck but do not build vignettes
+      - name: Build Check Across OS & R Releases
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--no-build-vignettes"), build_args = c("--no-manual", "--no-build-vignettes"), error_on = "error")
+        shell: Rscript {0}
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@v2
         with:
-          upload-snapshots: true
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check
diff --git a/.github/workflows/run_ecosis_pull_example.yaml b/.github/workflows/run_ecosis_pull_example.yaml
@@ -0,0 +1,47 @@
+name: run_ecosis_pull_example
+
+on:
+  schedule:
+    - cron:  '15 1 */5 * *'
+
+env:
+  R_LIBS_USER: /usr/local/lib/R/site-library
+  LC_ALL: en_US.UTF-8
+  NCPUS: 2
+
+jobs:
+  run-plsr: 
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+
+    steps:
+      #check out source code
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Install dependencies
+        run: |
+          Rscript -e 'remotes::install_github(repo="TESTgroup-BNL/spectratrait", dependencies=TRUE)'
+
+      # Run R script
+      - name: Run EcoSIS API Pull Example
+        run: |
+          source("inst/scripts/pull_data_from_ecosis.R")
+        shell: Rscript {0}
diff --git a/.github/workflows/run_plsr_example_auto.yaml b/.github/workflows/run_plsr_example_auto.yaml
@@ -0,0 +1,55 @@
+on:
+  schedule:
+    - cron:  '0 0 */2 * *'
+
+name: run_PLSR_example-auto
+
+env:
+  R_LIBS_USER: /usr/local/lib/R/site-library
+  LC_ALL: en_US.UTF-8
+  NCPUS: 2
+
+jobs:
+  run-plsr: 
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+
+    strategy:
+      fail-fast: false
+      matrix:
+        R:
+          - "3.6"
+          - "4.0"
+          - "4.1"
+
+    steps:
+      #check out source code
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Install dependencies
+        run: |
+          Rscript -e 'remotes::install_github(repo="TESTgroup-BNL/spectratrait", dependencies=TRUE)'
+
+      # Run R script
+      - name: Run Ely et al. (2019) PLSR Example
+        run: |
+          source("inst/scripts/spectra-trait_ely_leafN_plsr_bootstrap_example.R")
+        shell: Rscript {0}
diff --git a/.gitignore b/.gitignore
@@ -44,3 +44,5 @@ rsconnect/
 # MacOSX
 *.DS*
 *._*
+/doc/
+/Meta/
diff --git a/README.md b/README.md
@@ -42,6 +42,9 @@ Finally, to complete the installation you will also need to install the spectrat
 # to install the master branch version
 devtools::install_github(repo = "TESTgroup-BNL/spectratrait", dependencies=TRUE)
 
+# to install the master branch version - with Vignettes (though slower)
+devtools::install_github(repo = "TESTgroup-BNL/spectratrait", dependencies=TRUE, build_vignettes = TRUE)
+
 # to install a specific release, for example release 1.0.5
 devtools::install_github(repo = "TESTgroup-BNL/[email protected]", dependencies=TRUE)
 

diff --git a/inst/docs/sserbin2019_plsr_ex9.pdf b/inst/docs/sserbin2019_plsr_ex9.pdf
diff --git a/inst/scripts/pull_data_from_ecosis.R b/inst/scripts/pull_data_from_ecosis.R
@@ -25,9 +25,7 @@ invisible(lapply(list.of.packages, library, character.only = TRUE))
 
 
 #--------------------------------------------------------------------------------------------------#
-### Setup other functions and options
-# not in
-`%notin%` <- Negate(`%in%`)
+### Setup options
 
 # What is the source dataset from EcoSIS?
 ecosis_id <- "960dbb0c-144e-4563-8117-9e23d14f4aa9"
@@ -107,10 +105,10 @@ trait_data <- sample_info %>%
 head(trait_data)        
 
 # Prepare data for ggplot
-trait_data <- melt(data = trait_data, id.vars = "USDA_Species_Code", measure.vars = c("LMA_g_m2",
-                                                                                      "Cmass_g_g",
-                                                                                      "Nmass_g_g",
-                                                                                      "CN_Ratio"))
+trait_data <- reshape2::melt(data = trait_data, id.vars = "USDA_Species_Code", measure.vars = c("LMA_g_m2",
+                                                                                                "Cmass_g_g",
+                                                                                                "Nmass_g_g",
+                                                                                                "CN_Ratio"))
 head(trait_data)
 
 # Graph the trait data and save a file to the scratch space

diff --git a/inst/scripts/sserbin2019_plsr_ex9.nb.html b/inst/scripts/sserbin2019_plsr_ex9.nb.html
diff --git a/vignettes/ely_etal_ex1.Rmd b/vignettes/ely_etal_ex1.Rmd
@@ -8,6 +8,7 @@ output:
   html_notebook: default
   html_document:
     df_print: paged
+    keep_md: true
   rmarkdown: html_vignette
 vignette: >
   %\VignetteIndexEntry{Spectra-trait PLSR example using leaf-level spectra and leaf nitrogen content (Narea, g/m2) data from eight different crop species growing in a glasshouse at Brookhaven National Laboratory}
-Original file line number
+Diff line change
@@ Expand Up / @@ -44,3 +44,5 @@ rsconnect/ @@
     # MacOSX
     *.DS*
     *._*
+    /doc/
+    /Meta/