Merge pull request #129 from wincowgerDEV/v1.0-prep

v1.0 prep

.Rbuildignore

@@ -6,10 +6,11 @@
 ^\.httr-oauth$
 ^doc$
 ^Meta$
-google-analytics.js
-droptoken.rds
 ^cran-comments\.md$
 ^CRAN-RELEASE$
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+^codecov\.yml$
+^vignettes/spectragryph.*
+^vignettes/advanced.*

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

@@ -1,4 +1,4 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# 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:
@@ -18,7 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
@@ -29,30 +29,31 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - name: Install XQuartz on macOS
+        if: runner.os == 'macOS'
+        run: brew install xquartz --cask
+
+      - 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@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: rcmdcheck
-
-      - uses: r-lib/actions/check-r-package@v1
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Show testthat output
-        if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+      - name: Populate .Renviron with GitHub Secrets
+        run: |
+          echo AWS_ACCESS_KEY_ID="${{ secrets.AWS_ACCESS_KEY_ID }}" >> ~/.Renviron
+          echo AWS_SECRET_ACCESS_KEY="${{ secrets.AWS_SECRET_ACCESS_KEY }}" >> ~/.Renviron
         shell: bash
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true

.github/workflows/test-coverage.yaml

@@ -0,0 +1,50 @@
+# 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: [main, release]
+  pull_request:
+    branches: [main, release]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

.gitignore

@@ -2,9 +2,6 @@
 .Rhistory
 .Rapp.history
 
-# Desktop drive files
-.ini
-
 # Session Data files
 .RData
 
@@ -27,8 +24,11 @@
 # produced PDF vignettes and docs
 vignettes/*.pdf
 inst/doc
-doc
-Meta
+doc/
+Meta/
+
+# Shiny app
+inst/OpenSpecy-shiny-main/
 
 # OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
 .httr-oauth
@@ -48,7 +48,7 @@ Meta
 docs/
 
 # System files
-*.ini
+.ini
 *.swp
 .DS_Store
-docs
+delete.bat

DESCRIPTION

@@ -1,15 +1,19 @@
 Package: OpenSpecy
 Type: Package
 Title: Analyze, Process, Identify, and Share Raman and (FT)IR Spectra
-Version: 0.9.5
-Date: 2022-07-06
-Authors@R: c(person("Win", "Cowger", role = c("cre", "aut"),
+Version: 1.0.0
+Date: 2023-08-29
+Authors@R: c(person("Win", "Cowger", role = c("cre", "aut", "dtc"),
       email = "wincowger@gmail.com",
       comment = c(ORCID = "0000-0001-9226-3104")),
     person("Zacharias", "Steinmetz", role = c("aut"),
-      email = "steinmetz-z@uni-landau.de",
+      email = "z.steinmetz@rptu.de",
       comment = c(ORCID = "0000-0001-6675-5033")),
-    person("Andrew", "Gray", role = c("ctb"),
+    person("Nick", "Leong", role = c("aut"),
+      comment = c(ORCID = "0009-0008-3313-4132")),
+    person("Andrea","Faltynkova", role = c("aut", "dtc"),
+      comment = c(ORCID = "0000-0003-2523-3137")),
+    person("Andrew B", "Gray", role = c("ctb"),
       comment = c(ORCID = "0000-0003-2252-7367")), 
     person("Hannah", "Hapich", role = c("ctb"),
       comment = c(ORCID = "0000-0003-0000-6632")),
@@ -23,18 +27,28 @@ Authors@R: c(person("Win", "Cowger", role = c("cre", "aut"),
       comment = c(ORCID = "0000-0002-7624-711X")),
     person("Sebastian", "Primpke", role = c("ctb", "dtc"),
       comment = c(ORCID = "0000-0001-7633-8524")),
-    person("Orestis", "Herodotou", role = c("ctb", "dtc")))
+    person("Orestis", "Herodotou", role = c("ctb")),
+    person("Mary C", "Norris", role = c("ctb")),
+    person("Christine M", "Knauss", role = c("ctb"), 
+      comment = c(ORCID = "0000-0003-4404-8922")), 
+    person("Aleksandra","Karapetrova", role = c("ctb", "dtc", "rev"),
+      comment = c(ORCID = "0000-0002-9856-1644")),
+    person("Vesna","Teofilovic", role = c("ctb"),
+      comment = c(ORCID = "0000-0002-3557-1482")),
+    person("Laura A. T.","Markley", role = c("ctb"),
+      comment = c(ORCID = "0000-0003-0620-8366")),
+    person("Shreyas","Patankar", role = c("ctb", "dtc")))
 Description: Raman and (FT)IR spectral analysis tool for plastic particles and
     other environmental samples (Cowger et al. 2021,
-    <doi:10.1021/acs.analchem.1c00123>). Supported features include reading
-    spectral data files (.asp, .csv, .jdx, .spc, .spa, .0), Savitzky-Golay
-    smoothing of spectral intensities with smooth_intens(), correcting
-    background noise with subtr_bg() in accordance with Zhao et al. (2007)
-    <doi:10.1366/000370207782597003>, and identifying spectra using an onboard
-    reference library (Cowger et al. 2020, <doi:10.1177/0003702820929064>).
-    Analyzed spectra can be shared with the Open Specy community. A Shiny app is
-    available via run_app() or online at
-    <https://openanalysis.org/openspecy/>.
+    <doi:10.1021/acs.analchem.1c00123>). With read_any(), Open Specy provides a
+    single function for reading individual, batch, or map spectral data files
+    like .asp, .csv, .jdx, .spc, .spa, .0, and .zip. process_spec() simplifies
+    preprocessing spectra, including smoothing, baseline correction,
+    range restriction and flattening, intensity conversions, wavenumber
+    alignment, and min-max normalization. Spectra can be identified in batch
+    using an onboard reference library (Cowger et al. 2020,
+    <doi:10.1177/0003702820929064>) using match_spec(). A Shiny app is available
+    via run_app() or online at <https://openanalysis.org/openspecy/>.
 URL: https://github.com/wincowgerDEV/OpenSpecy-package/,
     http://wincowger.com/OpenSpecy-package/
 BugReports: https://github.com/wincowgerDEV/OpenSpecy-package/issues/
@@ -44,32 +58,37 @@ LazyLoad: true
 LazyData: true
 VignetteBuilder: knitr
 Depends:
-    R (>= 4.0.0)
+    R (>= 4.1.0)
 Imports:
-    dplyr,
-    rlang,
+    methods,
+    data.table,
+    jsonlite,
+    yaml,
     osfr,
+    caTools,
     hyperSpec,
-    hexView,
+    imager,
+    plotly,
     digest,
     signal,
+    glmnet,
     shiny
 Suggests:
     knitr,
     rmarkdown,
-    testthat (>= 3.0.0),
+    testthat (>= 3.1.9),
     config,
+    qs,
     shinyjs,
-    shinythemes,
-    shinyBS,
     shinyWidgets,
+    bs4Dash,
+    dplyr,
     ggplot2,
-    plotly,
-    data.table,
     DT,
     curl,
-    rdrop2, 
+    aws.s3, 
     mongolite,
     loggit
 RoxygenNote: 7.2.3
+Roxygen: list(markdown = TRUE)
 Config/testthat/edition: 3