loupeR version 1.0.0

Author: esiegel

.github/workflows/check.yml

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+# 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:
+  pull_request:
+    branches: [main]
+
+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: 'release'}
+
+    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: false

.github/workflows/release.yml

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+on:
+  workflow_dispatch:
+    inputs:
+      tag:
+        description: 'Git Tag/Release that we are uploading to'
+        required: true
+
+name: release
+
+permissions:
+  contents: write
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+
+    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: false
+
+      - name: Configure gh for auth
+        env:
+          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
+        run: gh auth setup-git
+
+      - name: Create Exec directory
+        shell: bash
+        run: mkdir exec
+
+      # Copy Louper binaries to the `exec` directory
+      - name: Copy Louper binary to Exec directory (Windows)
+        if: ${{ contains(matrix.config.os, 'windows') }}
+        env:
+          GH_TOKEN: ${{secrets.GITHUB_TOKEN}}
+        run: gh release download ${{ github.event.inputs.tag }} -p 'louper-windows*' -O exec/louper.exe
+      - name: Copy Louper binary to Exec directory (Linux)
+        if: ${{ contains(matrix.config.os, 'ubuntu') }}
+        env:
+          GH_TOKEN: ${{secrets.GITHUB_TOKEN}}
+        run: gh release download ${{ github.event.inputs.tag }} -p 'louper-linux*' -O exec/louper
+      - name: Copy Louper binary to Exec directory (MacOS)
+        if: ${{ contains(matrix.config.os, 'macos') }}
+        env:
+          GH_TOKEN: ${{secrets.GITHUB_TOKEN}}
+        run: gh release download ${{ github.event.inputs.tag }} -p 'louper-macos*' -O exec/louper
+
+      - name: Build R source build
+        shell: bash
+        run: R CMD build .
+
+      - name: Rename source build
+        shell: bash
+        run: mv loupeR*tar.gz loupeR_${{ runner.os }}.tar.gz
+
+      - name: Upload build to release
+        run: gh release upload ${{ github.event.inputs.tag }} loupeR_${{ runner.os }}.tar.gz
+        env:
+          GH_TOKEN: ${{secrets.GITHUB_TOKEN}}

.gitignore

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+.Rproj.user
+.Rhistory
+.Rdata
+.httr-oauth
+.DS_Store

DESCRIPTION

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+Package: loupeR
+Title: Converts Seurat objects to 10x Genomics Loupe files
+Version: 1.0.0
+Authors@R: 
+    person(given = "Eric",
+           family = "Siegel",
+           email = "eric.siegel@10xgenomics.com",
+           role = c("aut", "cre"))
+Description: Converts Seurat objects to 10x Genomics Loupe files.
+    This is a second line to make the package checker not complain.
+License: file LICENSE
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.3.9000
+Suggests: 
+    testthat (>= 3.0.0),
+    Matrix
+Config/testthat/edition: 3
+Imports:
+    methods,
+    Seurat,
+    hdf5r

LICENSE

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+Copyright (c) 2023 10x Genomics
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and
+associated documentation files (the "Software"), to use, copy, modify, and/or merge copies of the
+Software, in both source code and object code format, solely for your internal use, subject to the
+following conditions:
+
+1. The above copyright notice and this permission notice shall be included in all copies or
+substantial portions of the Software.
+
+2. The above rights granted in the Software may be exercised only in connection with a 10x Genomics
+Product (defined below), rightfully purchased from 10x Genomics or an authorized reseller, or data
+generated using such a 10x Genomics Product. A “10X Genomics Product” means, collectively, 10x
+Genomics branded instruments, reagents, consumables, kits, and labware used in accordance with the
+10X Genomics Product Terms and Conditions of Sale or, if applicable, any written contract between
+you and 10x Genomics. The rights granted may also be exercised in connection with other products
+when doing so is an integral part of an experiment where the data is generated primarily using a 10x
+Genomics Product.
+
+3. You agree not to redistribute or sublicense the Software, either in source code or object code
+format.
+
+4. All derivative works, including any modifications of the Software, shall be subject to all of the
+restrictions set forth herein.
+
+5. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT
+NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES
+OR OTHER LIABILITY, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES, WHETHER IN
+AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE,
+THE USE OR INABILITY TO USE, OR OTHER DEALINGS IN THE SOFTWARE (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF
+THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED
+OF THE POSSIBILITY OF SUCH DAMAGES.
+
+You may not use, propagate or modify the Software, or any derivatives thereof, except as expressly
+provided herein. Any attempt otherwise to use, propagate or modify it is void, and will
+automatically terminate your rights under this license.

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(create_bugreport)
+export(create_bugreport_from_seurat)
+export(create_loupe)
+export(create_loupe_from_seurat)
+export(select_assay)
+export(select_clusters)
+export(select_projections)
+export(setup)
+export(validate_clusters)
+export(validate_count_mat)
+export(validate_projections)
+importFrom(Seurat,Assays)
+importFrom(Seurat,GetAssay)
+importFrom(Seurat,Idents)
+importFrom(Seurat,Reductions)
+importFrom(hdf5r,H5File)
+importFrom(hdf5r,H5T_STRING)
+importFrom(methods,is)
+importFrom(utils,download.file)
+importFrom(utils,packageVersion)
+importFrom(utils,sessionInfo)
+importFrom(utils,strcapture)

R/cmd.R

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+#' Create a Loupe file by invoking the external Louper executable
+#'
+#' @param h5path path to the h5 interchange file.
+#' @param output_dir optional directory where the Loupe file will be written
+#' @param output_name optional name of the Loupe file with the extensions not included.
+#' @param executable_path optional path to the louper executable.
+#' @param force optional logical as to whether we should overwrite an already existing file
+#'
+#' @return TRUE on success, FALSE on error
+#'
+#' @noRd
+louper_create_cloupe <- function(
+  h5path,
+  output_dir = NULL,
+  output_name = NULL, 
+  executable_path = NULL,
+  force = FALSE
+) {
+  # default loupe name to `converted.cloupe`
+  if (is.null(output_name)) {
+    output_name <- "converted"
+  }
+  if (is.null(output_dir)) {
+    loupe_path <- sprintf("%s.cloupe", file.path(output_name))
+  } else {
+    loupe_path <- sprintf("%s.cloupe", file.path(output_dir, output_name))
+  }
+
+  h5path <- normalizePath(path.expand(h5path))
+  loupe_path <- suppressWarnings(normalizePath(path.expand(loupe_path)))
+
+  input_flag <- sprintf("--input=%s", h5path)
+  output_flag <- sprintf("--output=%s", loupe_path)
+  args <- c("create", input_flag, output_flag)
+
+  if (file.exists(loupe_path) && !force) {
+    return(err("Loupe file already exists. Set `force = TRUE` to overwrite"))
+  }
+
+  if (force) {
+    args <- c(args, "--force")
+  }
+
+  if (is.null(executable_path)) {
+    executable_path <- find_executable()
+    if (is.null(executable_path)) {
+      return(err("Could not find a valid louper executable.  Please run `setup()`."))
+    }
+  }
+
+  executable_path <- normalizePath(path.expand(executable_path))
+
+  if (!file.exists(executable_path)) {
+    return(err(sprintf("cannot find Louper executable at path: '%s'", executable_path)))
+  }
+
+  status <- system2(command=executable_path, args=args)
+
+  if (status == 0) {
+    return(SUCCESS)
+  } else {
+    return(err(sprintf("Louper executable failed: status code %d", status)))
+  }
+}