Merge branch 'release-1.2.1'

.Rbuildignore

@@ -13,6 +13,11 @@ data/genes20k.rda
 data/pan_indrop_matrix_8000cells_18556genes.rda
 data/valuesG1msReduced_treated_K.rda
 data/valuesG1msReduced_treated_MB.rda
+tests/testthat/SC.RData
+tests/testthat/Ndata.RData
+tests/testthat/CTCdataset.rda
+tests/testthat/expdata.RData
+tests/testthat/DATAforDT.RData
 apt.txt
 install.R
 postBuild
@@ -22,4 +27,5 @@ runtime.txt
 .git
 Aux
 binder
-tests
+^\.github$
+tests/

.github/.gitignore

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

.github/workflows/build.yml

@@ -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: [dev, master, release-*]
+  pull_request:
+    branches: [dev, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    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
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

.github/workflows/linter.yml

@@ -0,0 +1,48 @@
+# 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: [dev, master, release-*]
+  pull_request:
+    branches: [dev, master]
+
+name: lint
+
+jobs:
+  lint:
+    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::lintr, local::.
+          needs: lint
+
+      - name: Lint
+        run: |
+          library(lintr)
+          style_rules <- list(
+            T_and_F_symbol_linter(), assignment_linter(), brace_linter(),
+            commas_linter(), commented_code_linter(), todo_comment_linter(),
+            equals_na_linter(),
+            function_left_parentheses_linter(), infix_spaces_linter(),
+            line_length_linter(), whitespace_linter(), object_usage_linter(),
+            absolute_path_linter(),
+            nonportable_path_linter(), pipe_continuation_linter(),
+            semicolon_linter(), seq_linter(), quotes_linter(),
+            spaces_inside_linter(), spaces_left_parentheses_linter(),
+            trailing_blank_lines_linter(), trailing_whitespace_linter(),
+            undesirable_function_linter(), undesirable_operator_linter(),
+            unnecessary_concatenation_linter()
+          )
+          lint_package(linters = style_rules)
+        shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: 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: [dev, master, release-*]
+  pull_request:
+    branches: [dev, master]
+
+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

DESCRIPTION

@@ -1,54 +1,55 @@
 Package: DIscBIO
-Date: 2021-04-28
+Date: 2023-10-09
 Title: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics
-Version: 1.2.0
+Version: 1.2.1
 Authors@R:
-	c(
-		person(
-			given = "Salim",
-			family = "Ghannoum",
-			role = c("aut", "cph"),
-			email = "[email protected]"
-		),
-		person(
-			given = "Alvaro",
-			family = "Köhn-Luque",
-			role = c("aut", "ths"),
-			email = "[email protected]"
-		),
-		person(
-			given = "Waldir",
-			family = "Leoncio",
-			role = c("cre", "aut"),
-			email = "[email protected]"
-		),
-		person(
-			given = "Damiano",
-			family = "Fantini",
-			role = c("ctb")
-		)
-	)
+  c(
+    person(
+      given = "Salim",
+      family = "Ghannoum",
+      role = c("aut", "cph"),
+      email = "[email protected]"
+    ),
+    person(
+      given = "Alvaro",
+      family = "Köhn-Luque",
+      role = c("aut", "ths"),
+      email = "[email protected]"
+    ),
+    person(
+      given = "Waldir",
+      family = "Leoncio",
+      role = c("cre", "aut"),
+      email = "[email protected]"
+    ),
+    person(
+      given = "Damiano",
+      family = "Fantini",
+      role = c("ctb")
+    )
+  )
 Description: An open, multi-algorithmic pipeline for easy, fast and efficient
-	analysis of cellular sub-populations and the molecular signatures that
-	characterize them. The pipeline consists of four successive steps: data
-	pre-processing, cellular clustering with pseudo-temporal ordering, defining
-	differential expressed genes and biomarker identification. More details on
-	Ghannoum et. al. (2021) <doi:10.3390/ijms22031399>. This package implements
-	extensions of the work published by Ghannoum et. al. (2019)
-	<doi:10.1101/700989>.
+  analysis of cellular sub-populations and the molecular signatures that
+  characterize them. The pipeline consists of four successive steps: data
+  pre-processing, cellular clustering with pseudo-temporal ordering, defining
+  differential expressed genes and biomarker identification. More details on
+  Ghannoum et. al. (2021) <doi:10.3390/ijms22031399>. This package implements
+  extensions of the work published by Ghannoum et. al. (2019)
+  <doi:10.1101/700989>.
 License: MIT + file LICENSE
 Encoding: UTF-8
-Imports: methods, TSCAN, boot, httr, mclust, statmod, igraph,
-	RWeka, philentropy, NetIndices, png, grDevices,
-	RColorBrewer, ggplot2, rpart, fpc, cluster, rpart.plot,
-	tsne, AnnotationDbi, org.Hs.eg.db, graphics, stats, utils, impute
+Imports: methods, TSCAN, httr, mclust, statmod, igraph,
+  RWeka, philentropy, NetIndices, png, grDevices,
+  RColorBrewer, ggplot2, rpart, fpc, cluster, rpart.plot,
+  tsne, AnnotationDbi, org.Hs.eg.db, graphics, stats, utils, impute,
+  withr
 Depends:
-	R (>= 4.0), SingleCellExperiment
+  R (>= 4.0), SingleCellExperiment
 Suggests:
-	testthat,
-	Seurat
+  testthat,
+  Seurat
 LazyData: true
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.3
 URL: https://github.com/ocbe-uio/DIscBIO
 BugReports: https://github.com/ocbe-uio/DIscBIO/issues
 Collate:
@@ -86,6 +87,9 @@ Collate:
     'RpartDT.R'
     'RpartEVAL.R'
     'VolcanoPlot.R'
+    'bootstrap.R'
+    'calc_pcareduceres.R'
+    'cross.val.R'
     'customConverters.R'
     'datasets.R'
     'internal-functions-samr-adapted.R'

NAMESPACE

@@ -46,7 +46,6 @@ importFrom(NetIndices,GenInd)
 importFrom(RColorBrewer,brewer.pal)
 importFrom(RWeka,J48)
 importFrom(TSCAN,TSCANorder)
-importFrom(boot,boot)
 importFrom(cluster,clusGap)
 importFrom(cluster,maxSE)
 importFrom(cluster,silhouette)
@@ -143,3 +142,6 @@ importFrom(utils,download.file)
 importFrom(utils,read.table)
 importFrom(utils,write.csv)
 importFrom(utils,write.table)
+importFrom(withr,local_options)
+importFrom(withr,with_options)
+importFrom(withr,with_par)

NEWS.md

@@ -1,31 +1,35 @@
-This file documents the changes between stable releases of DIscBIO.
+# DIscBIO 1.2.1
 
-# Version 1.2.0
+* Fixed integration and unit tests (issue #22, #37)
+* Improved coding style (issue #38)
+* Removed dependency on `boot` (issue 26)
 
-- Added support for retrying to retrieve URLs (issue #29)
-- Removed duplicated (legacy) function
-- Improved detection of duplicated data on `NetAnalysis()`
-- Improved I/O behavior
-- Improved validation
-- Bug fixes
+# DIscBIO 1.2.0
 
-# Version 1.1.0
+* Added support for retrying to retrieve URLs (issue #29)
+* Removed use of duplicated (legacy) function _on unit tests only_
+* Improved detection of duplicated data on `NetAnalysis()`
+* Improved I/O behavior
+* Improved validation
+* Bug fixes
 
-- Added support for more gene types
-- Improved I/O behavior
-- Updated Binder notebooks
+# DIscBIO 1.1.0
 
-# Version 1.0.1
+* Added support for more gene types
+* Improved I/O behavior
+* Updated Binder notebooks
 
-- Bug fixes
-- Updated Binder notebook
+# DIscBIO 1.0.1
 
-# Version 1.0.0
+* Bug fixes
+* Updated Binder notebook
+
+# DIscBIO 1.0.0
 
 Contains several changes from the [original work](https://github.com/SystemsBiologist/PSCAN), the most relevant of which are listed below:
 
-- Several functions have been enhanced with a `quiet` argument to suppress intermediate output (essential to obtain cleaner output in batch scripts and unit tests)
-- Functions have been isolated into their own R files
-- Function and package documentation were added
-- Test datasets were compressed to occupy less disk space
-- Bugs have been fixed
+* Several functions have been enhanced with a `quiet` argument to suppress intermediate output (essential to obtain cleaner output in batch scripts and unit tests)
+* Functions have been isolated into their own R files
+* Function and package documentation were added
+* Test datasets were compressed to occupy less disk space
+* Bugs have been fixed