Add rworkflows

.github/workflows/lint.yaml

@@ -10,7 +10,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:

.github/workflows/rworkflows.yml

@@ -0,0 +1,60 @@
+name: rworkflows
+'on':
+  push:
+    branches: 
+    - main 
+    - rworkflows
+  pull_request:
+    branches:
+    - main
+    - rworkflows
+jobs:
+  rworkflows:
+    permissions:
+      contents: write
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    container: ${{ matrix.config.cont }}
+    strategy:
+      fail-fast: ${{ false }}
+      matrix:
+        config:
+        - os: ubuntu-latest
+          bioc: devel
+          r: auto
+          cont: bioconductor/bioconductor_docker:devel
+          rspm: https://packagemanager.rstudio.com/cran/__linux__/latest/release
+        - os: ubuntu-latest
+          bioc: release
+          r: auto
+          cont: bioconductor/bioconductor_docker:latest 
+          http-user-agent: 'release'
+        - os: macOS-latest
+          bioc: release
+          r: auto
+          cont: ~
+          rspm: ~
+        - os: windows-latest
+          bioc: release
+          r: auto
+          cont: ~
+          rspm: ~
+    steps:
+    - uses: neurogenomics/rworkflows@master
+      with:
+        run_bioccheck: ${{ true }}
+        run_rcmdcheck: ${{ true }}
+        as_cran: ${{ false }}
+        run_vignettes: ${{ true }}
+        has_testthat: ${{ true }}
+        run_covr: ${{ true }}
+        run_pkgdown: ${{ true }}
+        has_runit: ${{ false }}
+        has_latex: ${{ false }}
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run_docker: ${{ false }}
+        docker_user: username
+        DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
+        runner_os: ${{ runner.os }}
+        cache_version: cache-v1
+        enable_act: ${{ false }}

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: anndataR
 Title: AnnData interoperability in R
-Version: 0.0.0.9000
+Version: 0.99.0
 Authors@R: c(
     person("Robrecht", "Cannoodt", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-3641-729X", github = "rcannood")),
@@ -46,4 +46,4 @@ Config/Needs/website: pkgdown, tibble, knitr, rprojroot, stringr, readr,
 Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE, r6 = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.2.3.9000

NAMESPACE

@@ -5,6 +5,7 @@ export(dummy_data)
 export(from_Seurat)
 export(from_SingleCellExperiment)
 export(read_h5ad)
+export(setup_conda)
 export(to_HDF5AnnData)
 export(to_InMemory)
 export(to_Seurat)

NEWS.md

@@ -1,5 +1,17 @@
+# anndataR 0.99.0
+
+## New features
+
+- Add `rworkflows` CI.
+- Update *lint.yaml* to use `actions/checkout@v4` (which has less issues).
+- New function `setup_conda` automatically installs miniconda 
+  and sets up conda env: #97
+- Change version to Bioc-recommended devel version: 0.99.0
+
 # anndataR 0.1.0
 
+## New features
+
 Initial release of anndataR, providing support for working with AnnData objects in R.
 
 Feature list:

R/setup_conda.R

@@ -0,0 +1,29 @@
+#' Setup conda
+#' 
+#' Install miniconda and setup a conda env to use python dependencies.
+#' @inheritParams reticulate::install_miniconda
+#' @inheritParams reticulate::py_install
+#' @inheritDotParams reticulate::py_install
+#' @returns Null
+#' 
+#' @export
+#' @examples
+#' \dontrun{
+#' setup_conda()
+#' }
+setup_conda <- function(path = reticulate::miniconda_path(),
+                        update = TRUE, 
+                        force = FALSE,
+                        packages = c("anndata", "scanpy"),
+                        ...){
+
+  requireNamespace("reticulate")
+  if(!reticulate::py_module_available(module = "anndata")){
+    reticulate::install_miniconda(path = path, 
+                                  update = update, 
+                                  force = force)
+    reticulate::py_install(packages = packages, 
+                           pip = TRUE,
+                           ...)
+  } 
+}