Merge pull request #50 from jasenfinch/devel

v0.9.5

Author: jasenfinch

.github/workflows/R-CMD-check.yaml

@@ -5,8 +5,6 @@ on:
     branches: [main, master, devel]
   pull_request:
     branches: [main, master]
-  schedule:
-    - cron: '0 0 * * *'
 
 name: R-CMD-check
 
@@ -40,29 +38,13 @@ jobs:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
-
+      
       - name: Install system dependencies
         if: runner.os == 'Linux'
         run: sudo apt-get install -y libgit2-dev 
-        
+
       - uses: r-lib/actions/setup-r-dependencies@v1
         with:
           extra-packages: rcmdcheck
 
       - uses: r-lib/actions/check-r-package@v1
-
-      - name: Show testthat output
-        if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
-        
-      - name: Test coverage
-        run: covr::codecov()
-        shell: Rscript {0}
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
-        with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check

.github/workflows/pkgdown.yaml

@@ -0,0 +1,39 @@
+# 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
+on:
+  push:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          use-public-rspm: true
+      
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: sudo apt-get install -y libgit2-dev 
+
+      - uses: r-lib/actions/setup-r-dependencies@v1
+        with:
+          extra-packages: pkgdown
+          needs: website
+
+      - name: Deploy package
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'

.github/workflows/test-coverage.yaml

@@ -0,0 +1,34 @@
+# 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
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          use-public-rspm: true
+      
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: sudo apt-get install -y libgit2-dev 
+
+      - uses: r-lib/actions/setup-r-dependencies@v1
+        with:
+          extra-packages: covr
+
+      - name: Test coverage
+        run: covr::codecov()
+        shell: Rscript {0}

.gitignore

@@ -6,3 +6,4 @@ inst/doc
 /doc/
 /Meta/
 Example_project
+docs

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: metaboWorkflows
 Title: Workflow Project Templates for Metabolomics Analyses
-Version: 0.9.4
+Version: 0.9.5
 Authors@R: person("Jasen", "Finch", email = "jsf9@aber.ac.uk", role = c("aut", "cre"))
 Description: Reproducible workflow project templates for metabolomics analyses using the `hrm` <https://jasenfinch.github.io/hrm/> R package ecosystem.
 URL: https://jasenfinch.github.io/metaboWorkflows

NEWS.md

@@ -1,3 +1,7 @@
+# metaboWorkflows 0.9.5
+
+* The correct sample information table is now exported for the pre-treated data.
+
 # metaboWorkflows 0.9.4
 
 * Plotting and summary targets added to the spectral processing module for profiling workflows.

R/targets.R

@@ -349,7 +349,8 @@ pre_treatment_commands <- list(
                                                type = "pre-treated",
                                                outPath = "exports/pre-treated")',
   export_pre_treatment_sample_info = 'metaboMisc::exportSampleInfo(results_pre_treatment,
-                                                                 outPath = "exports/pre-treated")',
+                                                                  type = "pre-treated",
+                                                                  outPath = "exports/pre-treated")',
   plot_PCA = 'metabolyseR::plotPCA(results_pre_treatment,
                                    type = "pre-treated")',
   plot_LDA = 'metabolyseR::plotLDA(results_pre_treatment,

_pkgdown.yml

@@ -1 +1,4 @@
 url: https://jasenfinch.github.io/metaboWorkflows/
+template:
+  bootstrap: 5
+