Merge pull request #52 from sigven/bundle_update_2023

v2.0rc - 2024

Author: sigven

.Rbuildignore

@@ -2,18 +2,13 @@
 ^\.Rproj\.user$
 ^\.bumpversion\.cfg$
 ^\.github$
-
+^examples
 ^data-raw$
 ^LICENSE\.md$
-
 ^conda$
-^cpsr_classification\.pdf$
-^cpsr_classification\.png$
-^cpsr_superpanel_0\.6\.2\.xlsx$
-^cpsr_views\.png$
 ^docs$
-^example\.vcf\.gz$
-^example\.vcf\.gz.tbi$
 ^pkgdown/_pkgdown\.yml$
 ^pkgdown$
 ^_pkgdown\.yml$
+^\.pre-commit-config\.yaml$
+^vignettes$

.bumpversion.cfg

@@ -1,7 +1,11 @@
 [bumpversion]
-current_version = 1.0.1
+current_version = 1.0.1.9016
 commit = True
 tag = False
+parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\.(?P<dev>\d+))?
+serialize = 
+	{major}.{minor}.{patch}.{dev}
+	{major}.{minor}.{patch}
 
 [bumpversion:file:DESCRIPTION]
 search = Version: {current_version}

.github/workflows/build_conda.yaml

@@ -4,12 +4,12 @@ on:
   push:
     branches:
       - master
-      - dev
+      - bundle_update_2023
 env:
   atoken: ${{ secrets.ANACONDA_UPLOAD_TOKEN }}
   recipe_path: conda/recipe
   env_yml_path: conda/env/yml
-  VERSION: '1.0.1' # versioned by bump2version
+  VERSION: '1.0.1.9016' # versioned by bump2version
 jobs:
   build_conda_pkgs:
     # When merging to one of the branches above and the commit message matches
@@ -19,25 +19,31 @@ jobs:
     defaults:
       run:
         shell: bash -l {0}
-
     steps:
       - name: Checkout code
-        uses: actions/checkout@v2
-      - name: Set up Mambaforge
-        uses: conda-incubator/setup-miniconda@v2
+        uses: actions/checkout@v4
+      - name: Micromamba setup
+        uses: mamba-org/setup-micromamba@v1
         with:
-          miniforge-variant: Mambaforge
-          miniforge-version: 4.11.0-0
-          show-channel-urls: true
-          auto-activate-base: false
-          activate-environment: condabuild
-          environment-file: conda/condabuild_env.yml
-          use-mamba: true
-      - name: Build + upload cpsr conda pkg
+          environment-file: ${{ env.env_yml_path }}/condabuild_env.yml
+      - name: 🐍 Conda pkg build and upload
         run: |
           conda mambabuild ${recipe_path}/cpsr -c pcgr -c conda-forge -c bioconda --token ${atoken}
+      - name: 🔖 Tag creation
+        uses: actions/github-script@v7
+        with:
+          script: |
+            const the_tag_name = 'refs/tags/v' + process.env.VERSION
+            github.rest.git.createRef({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              ref: the_tag_name,
+              sha: context.sha
+            })
 
   pkgdown_site:
+    # only build pkgdown site on master
+    if: github.ref_name == 'master'
     name: Deploy pkgdown website
     runs-on: ubuntu-latest
     needs: build_conda_pkgs
@@ -46,34 +52,17 @@ jobs:
         shell: bash -l {0}
     steps:
       - name: Checkout code
-        uses: actions/checkout@v2
-      - name: Set up miniconda
-        uses: conda-incubator/setup-miniconda@v2
+        uses: actions/checkout@v4
+      - name: Micromamba setup
+        uses: mamba-org/setup-micromamba@v1
         with:
-          auto-update-conda: true
-          auto-activate-base: true
-          activate-environment: ""
-          mamba-version: "*"
-          channels: "pcgr,conda-forge,bioconda"
-      - name: Install conda packages
-        run: mamba env create -n pkgdown -f ${env_yml_path}/pkgdown.yml
+          environment-file: ${{ env.env_yml_path }}/pkgdown.yml
       - name: Publish pkgdown website
         run: |
             git config --local user.email "[email protected]"
             git config --local user.name "GitHub Actions"
-            conda activate pkgdown
+            micromamba activate pkgdown
             printf "cpsr version:\n"
             Rscript -e "packageVersion('cpsr')"
-            Rscript -e "pkgdown::deploy_to_branch(pkg = '.', commit_message = paste(pkgdown:::construct_commit_message('.'), '- see https://sigven.github.io/cpsr/'), branch = 'gh-pages', new_process = FALSE)"
+            Rscript -e "pkgdown::deploy_to_branch(pkg = '.', commit_message = 'Built CPSR website: https://sigven.github.io/cpsr/', branch = 'gh-pages', new_process = FALSE)"
 
-      - name: Create tag
-        uses: actions/github-script@v5
-        with:
-          script: |
-            const the_tag_name = 'refs/tags/v' + process.env.VERSION
-            github.rest.git.createRef({
-              owner: context.repo.owner,
-              repo: context.repo.repo,
-              ref: the_tag_name,
-              sha: context.sha
-            })

.gitignore

@@ -40,3 +40,6 @@ vignettes/*.pdf
 
 /outputs
 docs
+inst/doc
+
+data-raw/variant_classification

DESCRIPTION

@@ -1,8 +1,7 @@
 Package: cpsr
 Type: Package
 Title: Cancer Predisposition Sequencing Reporter (CPSR)
-Version: 1.0.1
-Date: 2022-11-11
+Version: 1.0.1.9016
 Authors@R:
     c(person(given = "Sigve",
              family = "Nakken",
@@ -27,27 +26,35 @@ Description: CPSR is a computational workflow that interprets germline variants
              predisposition and inherited cancer syndromes.
 License: MIT + file LICENSE
 biocViews:
-Remotes: github::sigven/pcgr/pcgrr@master
+Remotes: github::sigven/pcgr/pcgrr
 Imports:
     assertable,
     assertthat,
+    bslib,
+    crosstalk,
     dplyr,
+    DT,
     ggplot2,
-    log4r,
-    magrittr,
+    glue,
+    htmltools,
+    openxlsx2,
     pcgrr,
+    quarto,
+    readr,
     rlang,
-    scales,
+    shiny,
     stringr,
+    stringi,
     tidyr
 Depends:
     R (>= 4.0)
 Suggests:
-    testthat,
-    devtools,
     BSgenome.Hsapiens.UCSC.hg19,
-    BSgenome.Hsapiens.UCSC.hg38
+    BSgenome.Hsapiens.UCSC.hg38,
+    knitr,
+    rmarkdown
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.1
+RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE)
+VignetteBuilder: knitr

LICENSE

@@ -1,2 +1,2 @@
-YEAR: 2022
+YEAR: 2024
 COPYRIGHT HOLDER: Sigve Nakken

LICENSE.md

@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright (c) 2022 Sigve Nakken
+Copyright (c) 2024 Sigve Nakken
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

NAMESPACE

@@ -1,15 +1,21 @@
 # Generated by roxygen2: do not edit by hand
 
+export(append_cpg_properties)
+export(assign_classification)
 export(assign_pathogenicity_evidence)
-export(assign_variant_tiers)
-export(detect_cancer_traits_clinvar)
-export(determine_pathogenicity_classification)
+export(bs_icon2)
+export(check_variant2cancer_phenotype)
+export(combine_novel_and_preclassified)
+export(exclude_vars_by_maf)
+export(exclude_vars_non_cancer)
+export(exclude_vars_noncoding)
 export(generate_cpsr_report)
-export(get_germline_biomarkers)
 export(get_insilico_prediction_statistics)
 export(get_max_rows_pr_datatable)
+export(load_germline_snv_indel)
+export(plot_summary_statistics)
+export(plot_virtual_panels)
 export(retrieve_secondary_calls)
-export(summary_donut_chart)
-importFrom(magrittr,"%>%")
+export(write_cpsr_output)
 importFrom(rlang,":=")
 importFrom(rlang,.data)

R/bsicons.R

@@ -0,0 +1,92 @@
+# Copied from https://github.com/rstudio/bsicons/blob/f7dca31/R/icons.R
+icon_info_mini <- list(
+  name = c(
+    "bullseye",
+    "check-square"
+  ),
+  contents = c(
+    "<path d=\"M8 15A7 7 0 1 1 8 1a7 7 0 0 1 0 14zm0 1A8 8 0 1 0 8 0a8 8 0 0 0 0 16z\"></path>\n<path d=\"M8 13A5 5 0 1 1 8 3a5 5 0 0 1 0 10zm0 1A6 6 0 1 0 8 2a6 6 0 0 0 0 12z\"></path>\n<path d=\"M8 11a3 3 0 1 1 0-6 3 3 0 0 1 0 6zm0 1a4 4 0 1 0 0-8 4 4 0 0 0 0 8z\"></path>\n<path d=\"M9.5 8a1.5 1.5 0 1 1-3 0 1.5 1.5 0 0 1 3 0z\"></path>",
+    "<path d=\"M14 1a1 1 0 0 1 1 1v12a1 1 0 0 1-1 1H2a1 1 0 0 1-1-1V2a1 1 0 0 1 1-1h12zM2 0a2 2 0 0 0-2 2v12a2 2 0 0 0 2 2h12a2 2 0 0 0 2-2V2a2 2 0 0 0-2-2H2z\"></path>\n<path d=\"M10.97 4.97a.75.75 0 0 1 1.071 1.05l-3.992 4.99a.75.75 0 0 1-1.08.02L4.324 8.384a.75.75 0 1 1 1.06-1.06l2.094 2.093 3.473-4.425a.235.235 0 0 1 .02-.022z\"></path>"
+  )
+)
+
+#' Use Bootstrap icons (as inline SVG)
+#'
+#' Copied from https://github.com/rstudio/bsicons.
+#' @param name The name of the Bootstrap icon. Whitespace is replaced with `-`
+#'   (that way, `"arrow up"` can be used to refer to the "actual name" of
+#'   `"arrow-up"`). For a searchable list of names, see <https://icons.getbootstrap.com/>
+#' @param size Any valid CSS unit defining both the height and width of the
+#'   icon.
+#' @param class Additional CSS classes to add to the `<svg>` element. Consider
+#'   providing Bootstrap 5+ utility classes (e.g., `text-success`) here to
+#'   stylize the icon (but also note that those utility classes will only work
+#'   when Bootstrap 5+ is on the page).
+#' @param title If provided (highly recommended), `a11y` defaults to `"sem"`,
+#'   meaning the title is used for on-hover text and screen reader
+#'   announcements.
+#' @param a11y Cases that distinguish the role of the icon and inform which
+#'   accessibility attributes to be used. Icons can either be `"deco"`
+#'   (decorative, the default case), `"sem"` (semantic), `"none"` (no
+#'   accessibility features). The default, `"auto"`, resolves to `"sem"` if a
+#'   `title` is provided (and `"deco"` otherwise).
+#' @param ... additional CSS properties (e.g., `margin`, `position`, etc.)
+#'   placed on the `<svg>` tag.
+#'
+#' @return An [htmltools::HTML()] string containing the SVG icon.
+#' @export
+bs_icon2 <- function(name, size = "1em", class = NULL, title = NULL,
+                     a11y = c("auto", "deco", "sem", "none"), ...) {
+  if (length(name) != 1) {
+    rlang::abort("The number of icons specified in `name` must be 1.")
+  }
+
+  "%||%" <- function(x, y) {
+    if (is.null(x)) y else x
+  }
+
+  name <- sub("\\s+", "-", tolower(name))
+  idx <- match(name, tolower(icon_info_mini$name))
+  stopifnot(!is.na(idx))
+  svg_children <- icon_info_mini$contents[idx]
+  size <- htmltools::validateCssUnit(size)
+  style_attr <- paste0(
+    "height:", size, ";",
+    "width:", size, ";",
+    "fill:currentColor;",
+    # Better default vertical positioning of icons in a inline context (inspired by fontawesome::fa())
+    "vertical-align:-0.125em;",
+    htmltools::css(...)
+  )
+
+  # Generate accessibility attributes if either of
+  # the "deco" or "sem" cases are chosen
+  a11y <- rlang::arg_match(a11y)
+  a11y_attrs <- ""
+
+  if (a11y == "auto") {
+    a11y <- if (is.null(title)) "deco" else "sem"
+  }
+
+  if (a11y == "deco") {
+    a11y_attrs <- 'aria-hidden="true" role="img" '
+  } else if (a11y == "sem") {
+    title <- title %||% name
+    a11y_attrs <- sprintf(
+      'aria-label="%s" role="img" ',
+      htmltools::htmlEscape(title, attribute = TRUE)
+    )
+  }
+
+  res <- sprintf(
+    '<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 16 16" class="bi bi-%s %s" style="%s" %s>%s%s</svg>',
+    name,
+    paste(class, collapse = " "),
+    style_attr,
+    a11y_attrs,
+    if (is.null(title)) "" else paste0("<title>", htmltools::htmlEscape(title), "</title>"),
+    svg_children
+  )
+
+  htmltools::browsable(htmltools::HTML(res))
+}