Merge pull request #32 from stemangiola/aws

Support remote repository urls

Author: multimeric

.Rbuildignore

@@ -3,3 +3,4 @@
 ^dev
 ^\.github$
 ^LICENSE\.md$
+^README\.Rmd$

.github/workflows/check-bioc.yml

@@ -95,22 +95,26 @@ jobs:
           install.packages('remotes')
           saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
         shell: Rscript {0}
+      
+      - name: Cache assay data
+        uses: actions/cache@v3
+        with:
+          key: ${{ runner.os }}-hca-harmonised
+          path: ~/.cache/hca_harmonised
 
       - name: Cache R packages
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
         uses: actions/cache@v2
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2
 
       - name: Cache R packages on Linux
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
         uses: actions/cache@v2
         with:
           path: /home/runner/work/_temp/Library
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2
 
       - name: Install Linux system dependencies
         if: runner.os == 'Linux'

DESCRIPTION

@@ -5,31 +5,40 @@ Version: 0.1.0
 Authors@R: c(person("Stefano", "Mangiola", email = "[email protected]",
                   role = c("aut", "cre"))
                   )
-Description: Queries the Human Cell Atlas.
-License: GPL (>= 3)
+Description: Provides access to a copy of the Human Cell Atlas, but with 
+    harmonised metadata. This allows for uniform querying across numerous 
+    datasets within the Atlas using common fields such as cell type, tissue 
+    type, and patient ethnicity. Usage involves first querying the metadata
+    table for cells of interest, and then downloading the corresponding cells 
+    into a SingleCellExperiment object. 
+License: GPL-3
 Depends:
-    R (>= 4.1.0)
+    R (>= 4.2.0)
 Imports:
     dplyr,
     SummarizedExperiment,
     SingleCellExperiment,
     tidySingleCellExperiment,
-    purrr,
+    purrr (>= 1.0.0),
     BiocGenerics,
     glue,
     HDF5Array,
     DBI,
     RSQLite,
-    magrittr,
+    rappdirs,
+    httr,
+    cli,
     assertthat,
     SeuratObject,
     Seurat,
     methods,
-    rlang
+    rlang,
+    stats
 Suggests:
     here,
     stringr,
     tidyseurat,
+    zellkonverter,
     scMerge,
     DelayedArray,
     openssl,
@@ -38,15 +47,24 @@ Suggests:
     SingleR,
     tools,
     rmarkdown,
-    zellkonverter,
     dbplyr,
     knitr,
     testthat
 Biarch: true
-biocViews: AssayDomain, Infrastructure, RNASeq, DifferentialExpression, GeneExpression, Normalization, Clustering, QualityControl, Sequencing, Transcription, Transcriptomics
+biocViews: 
+    AssayDomain,
+    Infrastructure,
+    RNASeq,
+    DifferentialExpression,
+    GeneExpression,
+    Normalization,
+    Clustering,
+    QualityControl,
+    Sequencing,
+    Transcription,
+    Transcriptomics
 Encoding: UTF-8
-LazyData: true
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 LazyDataCompression: xz
 URL: https://github.com/stemangiola/HCAquery
 BugReports: https://github.com/stemangiola/HCAquery/issues

NAMESPACE

@@ -13,19 +13,37 @@ importFrom(RSQLite,SQLite)
 importFrom(Seurat,as.Seurat)
 importFrom(SeuratObject,as.sparse)
 importFrom(SingleCellExperiment,SingleCellExperiment)
+importFrom(SingleCellExperiment,simplifyToSCE)
 importFrom(SummarizedExperiment,"assayNames<-")
 importFrom(SummarizedExperiment,colData)
 importFrom(assertthat,assert_that)
+importFrom(assertthat,has_name)
+importFrom(cli,cli_abort)
+importFrom(cli,cli_alert_info)
+importFrom(cli,cli_alert_success)
 importFrom(dplyr,as_tibble)
 importFrom(dplyr,filter)
+importFrom(dplyr,full_join)
 importFrom(dplyr,pull)
 importFrom(dplyr,tbl)
+importFrom(dplyr,tibble)
+importFrom(dplyr,transmute)
 importFrom(glue,glue)
-importFrom(magrittr,equals)
+importFrom(httr,GET)
+importFrom(httr,modify_url)
+importFrom(httr,parse_url)
+importFrom(httr,progress)
+importFrom(httr,stop_for_status)
+importFrom(httr,write_disk)
 importFrom(methods,as)
+importFrom(purrr,imap)
+importFrom(purrr,keep)
 importFrom(purrr,map)
 importFrom(purrr,map_int)
+importFrom(purrr,pmap_chr)
 importFrom(purrr,reduce)
-importFrom(purrr,when)
+importFrom(purrr,transpose)
+importFrom(rappdirs,user_cache_dir)
 importFrom(rlang,.data)
+importFrom(stats,setNames)
 importFrom(tidySingleCellExperiment,inner_join)

NEWS.md

@@ -0,0 +1,3 @@
+# HCAquery 0.1.0
+
+* Added a `NEWS.md` file to track changes to the package.