Feature/GitHub actions (#27)

* edit rbuildignore

* Update pkgdown, fix vignette, prevent call to non-existent object in applyFilt

* remove docs

* remove visNetwork from dependencies

* add datadr back to workflows temporarily to appease site building
set pak version in pkgdown action

.Rbuildignore

@@ -8,3 +8,4 @@ pkgdown-template
 docs
 data-raw
 ^scratchwork$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

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

@@ -0,0 +1,57 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: master
+  pull_request:
+    branches: master
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ubuntu-latest
+
+    # runs-on: ${{ matrix.config.os }}
+    # 
+    # name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    # 
+    # strategy:
+    #   fail-fast: false
+    #   matrix:
+    #     config:
+    #       - {os: macos-latest,   r: 'release'}
+    #       - {os: windows-latest, r: 'release'}
+    #       - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+    #       - {os: ubuntu-latest,   r: 'release'}
+    #       - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - 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@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+          pak-version: devel # See https://github.com/r-lib/actions/issues/559
+
+      - uses: r-lib/actions/check-r-package@v2
+        env:
+          '_R_CHECK_LIMIT_CORES_': 'warn'
+        with:
+          upload-snapshots: true
+          args: 'c("--no-manual")'
+          build_args: 'c("--no-manual")'
+          error-on: '"error"'

.github/workflows/pkgdown.yaml

@@ -0,0 +1,49 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: master
+  pull_request:
+    branches: master
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+          pak-version: devel # See https://github.com/r-lib/actions/issues/559
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE, examples = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: |
+          github.event_name == 'release' ||
+          (github.event_name == 'workflow_dispatch' && github.ref == 'refs/heads/master')
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/test-coverage.yaml

@@ -0,0 +1,30 @@
+# 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: master
+  pull_request:
+    branches: 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@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: covr
+
+      - name: Test coverage
+        run: covr::codecov()
+        shell: Rscript {0}

.gitignore

@@ -4,6 +4,8 @@
 # Session Data files
 .RData
 .DS_Store
+# Output from site building
+docs
 # Example code in package build process
 *-Ex.R
 # Output files from R CMD build
@@ -16,6 +18,7 @@
 # produced vignettes
 vignettes/*.html
 vignettes/*.pdf
+vignettes/*.R
 # OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
 .httr-oauth
 # knitr and R markdown default cache directories

DESCRIPTION

@@ -25,7 +25,6 @@ Imports:
     tidyr,
     reshape2,
     vegan,
-    visNetwork,
     data.table,
     ggplot2,
     lazyeval,
@@ -34,15 +33,17 @@ Imports:
     readr
 Suggests:
     MetaCycData,
+    datadr,
     knitr,
     rmarkdown,
-    datadr,
-    trelliscope,
     foreach,
     doParallel,
     testthat,
     purrr,
     viridis,
     DT
+Remotes:
+    github::delta-rho/datadr,
+    github::EMSL-Computing/MetaCycData
 VignetteBuilder: knitr
 RoxygenNote: 7.2.3

R/applyFilt.R

@@ -129,7 +129,7 @@ applyFilt.massFilt <- function(filter_object, msObj, min_mass = 200, max_mass =
     if(length(min_mass) != 1) stop("min_mass must be of length 1")
     if(length(max_mass) != 1) stop("max_mass must be of length 1")
 
-    edata_cname <- getEDataColName(ftmsObj)
+    edata_cname <- getEDataColName(msObj)
 
     mass_info <- filter_object[,"Mass"]
 

README.md

@@ -1,6 +1,8 @@
 # ftmsRanalysis
-[![Build Status](https://travis-ci.org/EMSL-Computing/ftmsRanalysis.svg?branch=master)](https://travis-ci.org/EMSL-Computing/ftmsRanalysis)
+<!-- badges: start -->
+[![R-CMD-check](https://github.com/EMSL-Computing/ftmsRanalysis/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/EMSL-Computing/ftmsRanalysis/actions/workflows/R-CMD-check.yaml)
 [![Coverage Status](https://codecov.io/github/EMSL-Computing/ftmsRanalysis/coverage.svg?branch=master)](https://codecov.io/github/EMSL-Computing/ftmsRanalysis?branch=master)
+<!-- badges: end -->
 
 This R package provides functionality for data formatting, preprocessing, filtering, exploratory data analysis and visualization of fourier transform (FT) mass spectrometry (MS) data. 
 

_pkgdown.yml

@@ -1,5 +1,4 @@
 template:
-  path: "pkgdown-template"
   params:
     bootswatch: cosmo
 #title: FT-MS Data Analysis in R
@@ -99,6 +98,10 @@ reference:
   - '`getInstrumentType`'
   - '`getModuleName`'
   - '`getVanKrevelenCategoryBounds`'
+- title: CoreMS to ftmsRanalysis conversion
+  contents:
+  - 'coreMSDataToFtmsData'
+  - 'as.CoreMSData'
 - title: Column name methods
   desc: Methods to get the column name used to store various meta data values
   contents:
@@ -145,6 +148,69 @@ reference:
   - '`ftms12T_edata`'
   - '`ftms12T_emeta`'
   - '`ftms12T_fdata`'
+- title: internal
+  desc: Other functions
+  contents:
+  - calc_aroma
+  - calc_dbe
+  - calc_element_ratios
+  - calc_gibbs
+  - calc_kendrick
+  - calc_nosc
+  - conf_filter
+  - conf_filter_dt
+  - filter_worker
+  - getGroupComparisonSummaryFunctionNames
+  - getPrincipalCoordinates
+  - gtest.standard
+  - heatmap
+  - mass_error_plot
+  - numPeaksPlot
+  - one_factor_change
+  - parse_mf
+  - plot.CoreMSData
+  - plot.confFilt
+  - plotlyHeatmap
+  - read_CoreMS_data
+  - setAromaColName
+  - setBS1ColName
+  - setBS2ColName
+  - setBS3ColName
+  - setCarbonColName
+  - setCompoundColName
+  - setDBEAIColName
+  - setDBEColName
+  - setDBEValenceDF
+  - setDBEoColName
+  - setEDataColName
+  - setElCompColName
+  - setExtractionColName
+  - setFDataColName
+  - setGibbsColName
+  - setHCRatioColName
+  - setHydrogenColName
+  - setIsotopicColName
+  - setKendrickDefectColName
+  - setKendrickMassColName
+  - setMFColName
+  - setMFNameColName
+  - setMassColName
+  - setModAromaColName
+  - setModuleColName
+  - setModuleNodeColName
+  - setNCRatioColName
+  - setNOSCColName
+  - setNPRatioColName
+  - setNitrogenColName
+  - setOCRatioColName
+  - setOxygenColName
+  - setPCRatioColName
+  - setPhosphorusColName
+  - setReactionColName
+  - setSulfurColName
+  - transformation_counts
+  - unique_mf_assignment
+  - vector_replace
 
 github:
   - icon: fa-github