Update to R 4.4 & renv 3.19

.dockerignore

@@ -0,0 +1,5 @@
+.github
+.git
+.Rproj.user
+renv/
+scpcaTools.Rproj

.github/workflows/build-docker.yaml

@@ -43,7 +43,6 @@ jobs:
       - name: Build full image
         uses: docker/build-push-action@v5
         with:
-          context: "{{defaultContext}}:docker"
           tags: ${{ steps.meta.outputs.tags }}
           push: ${{ github.event_name == 'push' }}
           cache-from: type=registry,ref=${{ env.REGISTRY }}/${{ env.REGISTRY_USER }}/scpcatools:buildcache
@@ -93,7 +92,6 @@ jobs:
       - name: Build and push image
         uses: docker/build-push-action@v5
         with:
-          context: "{{defaultContext}}:docker"
           target: ${{ matrix.target }}
           push: ${{ github.event_name == 'push' }}
           tags: ${{ steps.meta.outputs.tags }}

docker/Dockerfile → Dockerfile

@@ -1,36 +1,37 @@
 ##########################
 # Build the slim image target first --------------------------------------------
-FROM bioconductor/r-ver:3.18 AS slim
+FROM bioconductor/r-ver:3.19 AS slim
 LABEL maintainer="[email protected]"
 LABEL org.opencontainers.image.title "scpcatools-slim"
 LABEL org.opencontainers.image.source https://github.com/AlexsLemonade/scpcaTools
 
 #### R packages
 # Use renv for R packages
 ENV RENV_CONFIG_CACHE_ENABLED FALSE
-RUN Rscript -e "install.packages(c('remotes', 'renv'))"
+RUN Rscript -e "install.packages(c('renv'))"
 
-COPY renv_slim.lock renv.lock
+COPY docker/renv_slim.lock renv.lock
 # restore renv and remove cache files
 RUN Rscript -e 'renv::restore()' && \
   rm -rf ~/.cache/R/renv && \
   rm -rf /tmp/downloaded_packages && \
   rm -rf /tmp/Rtmp*
 
-# bust cache if needed
-ADD "https://api.github.com/repos/AlexsLemonade/scpcaTools/commits?per_page=1" latest_commit
+
 # Install scpcaTools package (& test loading)
-RUN Rscript -e "remotes::install_github('AlexsLemonade/scpcaTools', upgrade = 'never'); \
-  require(scpcaTools)"
+COPY . scpcaTools
+RUN R CMD INSTALL scpcaTools/
+RUN Rscript -e "require(scpcaTools)"
 
-CMD [ "R" ]
+# restore slim renv
+COPY docker/renv_slim.lock renv.lock
 
 ##########################
 # Add Seurat support target ----------------------------------------------------
 FROM slim AS seurat
 LABEL org.opencontainers.image.title "scpcatools-seurat"
 
-COPY renv_seurat.lock renv.lock
+COPY docker/renv_seurat.lock renv.lock
 RUN Rscript -e 'renv::restore()' && \
   rm -rf ~/.cache/R/renv && \
   rm -rf /tmp/downloaded_packages && \
@@ -42,7 +43,7 @@ RUN Rscript -e 'renv::restore()' && \
 FROM slim AS reports
 LABEL org.opencontainers.image.title "scpcatools-reports"
 
-COPY renv_reports.lock renv.lock
+COPY docker/renv_reports.lock renv.lock
 RUN Rscript -e 'renv::restore()' && \
   rm -rf ~/.cache/R/renv && \
   rm -rf /tmp/downloaded_packages && \
@@ -54,7 +55,7 @@ RUN Rscript -e 'renv::restore()' && \
 FROM slim AS anndata
 LABEL org.opencontainers.image.title "scpcatools-anndata"
 
-COPY renv_zellkonverter.lock renv.lock
+COPY docker/renv_zellkonverter.lock renv.lock
 RUN Rscript -e 'renv::restore()' && \
   rm -rf ~/.cache/R/renv && \
   rm -rf /tmp/downloaded_packages && \
@@ -67,7 +68,7 @@ RUN Rscript -e "proc <- basilisk::basiliskStart(env = zellkonverter::zellkonvert
   basilisk.utils::cleanConda()"
 
 #### Python packages
-COPY requirements_anndata.txt requirements.txt
+COPY docker/requirements_anndata.txt requirements.txt
 RUN pip install --no-cache-dir -r requirements.txt
 
 
@@ -76,7 +77,7 @@ RUN pip install --no-cache-dir -r requirements.txt
 FROM anndata AS scvi
 LABEL org.opencontainers.image.title "scpcatools-scvi"
 
-COPY requirements_scvi.txt requirements.txt
+COPY docker/requirements_scvi.txt requirements.txt
 RUN pip install --no-cache-dir -r requirements.txt
 
 
@@ -91,6 +92,6 @@ RUN Rscript -e 'renv::restore()' && \
   rm -rf /tmp/downloaded_packages && \
   rm -rf /tmp/Rtmp*
 
-COPY requirements.txt requirements.txt
+COPY docker/requirements.txt requirements.txt
 
 RUN pip install --no-cache-dir -r requirements.txt

R/integrate_sces.R

@@ -3,7 +3,7 @@
 
 #' Integrate a merged set of SingleCellExperiment objects using a specified
 #'  integration method. The final SCE object will contain an additional reducedDim
-#'  entitled `{integration_method}_PCA`. All original SCE assays are retained.
+#'  entitled `\{integration_method\}_PCA`. All original SCE assays are retained.
 #'  `fastMNN` integration uses all default setting, but additional parameters can be supplied.
 #'  `harmony` integration uses existing PCs, but additional parameters can be supplied.
 #'
@@ -27,7 +27,7 @@
 #' @param ... Any additional parameters to be passed to the given integration method
 #'
 #' @return An updated merged SCE object containing a new reduced dimension named
-#'   `{integration_method}_PCA` containing the corrected PCs. In the case of `fastMNN`
+#'   `\{integration_method\}_PCA` containing the corrected PCs. In the case of `fastMNN`
 #'   integration, the SCE also includes a corrected expression assay (`fastMNN_corrected`)
 #'
 #' @import SingleCellExperiment

R/merge_sce_list.R

@@ -18,9 +18,9 @@
 #'    unique cell barcode.
 #'  - Of the original colData columns, only column names provided in the argument
 #'    `retain_coldata_cols` will be retained.
-#'  - The resulting colData row names will be be prefixed with `{sce_name-}`.
+#'  - The resulting colData row names will be be prefixed with `\{sce_name-\}`.
 #'  - The resulting rowData slot column names will be appended with the given
-#'    SCE's name, as `{sce_name}-{column_name}` except for columns whose names
+#'    SCE's name, as `\{sce_name\}-\{column_name\}` except for columns whose names
 #'    are indicated to preserve with the `preserve_rowdata_cols` argument.
 #'
 #'  SCE altExp contents are modified or retained as follows:
@@ -30,7 +30,7 @@
 #'    the argument `retain_altexp_coldata_cols`, as specified for each named
 #'    altExp will be retained.
 #'  - The resulting rowData slot column names will be appended with the given
-#'    SCE's name, as `{sce_name}-{column_name}` except for columns whose names
+#'    SCE's name, as `\{sce_name\}-\{column_name\}` except for columns whose names
 #'    are indicated to preserve with the `preserve_altexp_rowdata_cols` argument.
 #'
 #'