Add github action (#2)

* add github action

* add Dockerfile

* ignore BBSoptions

* missing imports

* roxygenise

* error on error

.Rbuildignore

@@ -1,3 +1,5 @@
 ^velociraptor\.Rproj$
 ^\.Rproj\.user$
 ^LICENSE\.md$
+^\.github$
+^\.BBSoptions$

.github/.gitignore

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

.github/workflows/bioc_pkg.yml

@@ -0,0 +1,80 @@
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+name: build-check-deploy
+
+jobs:
+  build_check_deploy:
+    runs-on: ubuntu-latest
+    container: bioconductor/bioconductor_docker:devel
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v1
+        with:
+          path: /usr/local/lib/R/site-library
+          key: ${{ runner.os }}-r-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-r-1-
+
+      # This lets us augment with additional dependencies
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        env:
+          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
+        run: |
+          Rscript -e "remotes::install_github('r-hub/sysreqs')"
+          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
+          sudo -s eval "$sysreqs"
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories(), Ncpu = 2L)
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "error", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Publish to Registry
+        if: github.event_name == 'push' && github.ref == 'refs/heads/master'
+        uses: elgohr/Publish-Docker-Github-Action@master
+        with:
+          name: docker.pkg.github.com/${{ github.repository }}/master:latest
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+          registry: docker.pkg.github.com
+
+      - name: Build pkgdown
+        if: github.event_name == 'push' && github.ref == 'refs/heads/master'
+        run: |
+           PATH=$PATH:$HOME/bin/ Rscript -e 'BiocManager::install("pkgdown"); pkgdown::build_site(".")'
+
+      # deploy needs rsync? Seems so.
+      - name: Install deploy dependencies
+        if: github.event_name == 'push' && github.ref == 'refs/heads/master'
+        run: |
+          apt-get update && apt-get -y install rsync
+
+      - name: Deploy 🚀
+        if: github.event_name == 'push' && github.ref == 'refs/heads/master'
+        uses: JamesIves/github-pages-deploy-action@releases/v3
+        with:
+          ACCESS_TOKEN: ${{ secrets.ACCESS_TOKEN }}
+          BRANCH: gh-pages # The branch the action should deploy to.
+          FOLDER: docs # The folder the action should deploy.

DESCRIPTION

@@ -8,6 +8,7 @@ Depends:
     SummarizedExperiment
 Imports:
     methods,
+    BiocGenerics,
     reticulate,
     S4Vectors,
     DelayedArray,

Dockerfile

@@ -0,0 +1,9 @@
+FROM bioconductor/bioconductor_docker:devel
+
+WORKDIR /home/rstudio
+
+COPY --chown=rstudio:rstudio . /home/rstudio/
+
+RUN apt-get update && apt-get install -y libglpk-dev && apt-get clean && rm -rf /var/lib/apt/lists/*
+
+RUN Rscript -e "devtools::install('.', dependencies=TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE)"

NAMESPACE

@@ -4,7 +4,11 @@ export(scvelo)
 exportMethods(scvelo)
 import(SummarizedExperiment)
 import(basilisk)
+import(methods)
+importFrom(BiocGenerics,sizeFactors)
+importFrom(DelayedArray,is_sparse)
 importFrom(S4Vectors,DataFrame)
+importFrom(S4Vectors,make_zero_col_DFrame)
 importFrom(basilisk,BasiliskEnvironment)
 importFrom(reticulate,import)
 importFrom(scuttle,normalizeCounts)

R/scvelo.R

@@ -31,13 +31,13 @@
 #'
 #' For consistency with other Bioconductor packages, we perform scaling normalization, log-transformation and subsetting
 #' before starting the velocity calculations with \pkg{scvelo}.
-#' This allows us to guarantee that, e.g., the spliced log-expression matrix of HVGs is the same as that used in other 
+#' This allows us to guarantee that, e.g., the spliced log-expression matrix of HVGs is the same as that used in other
 #' applications like clustering or trajectory reconstruction.
 #' Nonetheless, one can set \code{use.theirs=TRUE} to directly use the entire \pkg{scvelo} normalization and filtering pipeline.
-#' 
+#'
 #' Upon first use, this function will instantiate a conda environment containing the \pkg{scvelo} package.
-#' 
-#' @return 
+#'
+#' @return
 #' A \linkS4class{SummarizedExperiment} is returned containing the output of the velocity calculations.
 #' TODO: SOME DOCUMENTATION REQUIRED.
 #'
@@ -51,24 +51,24 @@
 #' unspliced <- counts(sce2)
 #'
 #' out <- scvelo(list(spliced, unspliced))
-#' 
+#'
 #' @author Aaron Lun
 #' @name scvelo
 NULL
 
 #' @importFrom S4Vectors DataFrame
 #' @importFrom scuttle normalizeCounts
-.scvelo <- function(x, subset.row=NULL, log.norm=FALSE, 
-    sf.spliced=NULL, sf.unspliced=NULL, 
-    use.theirs=FALSE, 
+.scvelo <- function(x, subset.row=NULL, log.norm=FALSE,
+    sf.spliced=NULL, sf.unspliced=NULL,
+    use.theirs=FALSE,
     mode=c('steady_state', 'deterministic', 'stochastic', 'dynamical'),
     get.velocities=TRUE)
 {
     spliced <- x[[1]]
     unspliced <- x[[2]]
     if (!identical(as.integer(dim(spliced)), as.integer(dim(unspliced)))) {
         stop("matrices in 'x' must have the same dimensions")
-    } 
+    }
 
     # Can't be bothered figuring this out.
     if (log.norm && use.theirs) {
@@ -88,8 +88,8 @@ NULL
     }
 
     mode <- match.arg(mode)
-    output <- basiliskRun(env=velo.env, fun=.run_scvelo, 
-        spliced=spliced, unspliced=unspliced, 
+    output <- basiliskRun(env=velo.env, fun=.run_scvelo,
+        spliced=spliced, unspliced=unspliced,
         use.theirs=use.theirs, mode=mode)
 
     output
@@ -108,7 +108,7 @@ NULL
     if (use.theirs) {
         scv$pp$filter_and_normalize(adata)
     }
-    scv$pp$moments(adata) 
+    scv$pp$moments(adata)
 
     if (mode=="dynamical") {
         scv$tl$recover_dynamics(adata)
@@ -118,9 +118,10 @@ NULL
     scv$tl$velocity_graph(adata)
     scv$tl$velocity_pseudotime(adata)
 
-    .scvelo_anndata2sce(adata) 
+    .scvelo_anndata2sce(adata)
 }
 
+#' @importFrom S4Vectors make_zero_col_DFrame
 .scvelo_anndata2sce <- function(adata) {
     assays <- .extractor_python_dict(adata$layers, c("Mu", "Ms", "velocity"), single=TRUE)
     rowdata <- .extractor_python_dict(adata$obs, names(adata$obs))
@@ -155,9 +156,10 @@ setMethod("scvelo", "ANY", .scvelo)
 
 #' @export
 #' @rdname scvelo
-setMethod("scvelo", "SummarizedExperiment", function(x, ..., 
-    assay.spliced="counts", assay.unspliced="unspliced", 
-    sf.spliced=sizeFactors(x), sf.unspliced=NULL) 
+#' @importFrom BiocGenerics sizeFactors
+setMethod("scvelo", "SummarizedExperiment", function(x, ...,
+    assay.spliced="counts", assay.unspliced="unspliced",
+    sf.spliced=sizeFactors(x), sf.unspliced=NULL)
 {
     x <- list(assay(x, assay.spliced), assay(x, assay.unspliced))
     scvelo(x, ..., size.factors=size.factors)

README.md

@@ -0,0 +1,27 @@
+
+# velociraptor
+
+<!-- badges: start -->
+[![R build status](https://github.com/kevinrue/velociraptor/workflows/build-check-deploy/badge.svg)](https://github.com/kevinrue/velociraptor/actions)
+<!-- badges: end -->
+
+The goal of velociraptor is to ...
+
+## Installation
+
+You can install the released version of velociraptor from [GitHub](https://github.com/kevinrue/velociraptor) with:
+
+``` r
+install.packages("remotes")
+remotes::install_github("kevinrue/velociraptor")
+```
+
+## Example
+
+This is a basic example which shows you how to solve a common problem:
+
+``` r
+library(velociraptor)
+## basic example code
+```
+