[r] rename CellCensus to cellxgene.census

.github/workflows/r-check.yml

@@ -1,4 +1,4 @@
-name: R CellCensus package checks
+name: R cellxgene.census package checks
 
 on:
   pull_request:
@@ -18,16 +18,16 @@ jobs:
           extra-repositories: https://tiledb-inc.r-universe.dev
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          working-directory: ./api/r/CellCensus
+          working-directory: ./api/r/cellxgene.census
           extra-packages: any::rcmdcheck, any::styler
           needs: check
           # Disable dependency caching so long as we depend on bleeding-edge
           # builds of tiledbsoma from r-universe. Its DESCRIPTION version
           # number isn't routinely updated to invalidate our cache.
           cache: false
       - name: styler
-        run: Rscript -e 'library("styler"); style_pkg("api/r/CellCensus", dry="fail")'
+        run: Rscript -e 'library("styler"); style_pkg("api/r/cellxgene.census", dry="fail")'
       - uses: r-lib/actions/check-r-package@v2
         with:
-          working-directory: ./api/r/CellCensus
+          working-directory: ./api/r/cellxgene.census
           args: 'c("--no-manual", "--as-cran")'

api/r/CellCensus/.Rbuildignore → api/r/cellxgene.census/.Rbuildignore

@@ -1,4 +1,4 @@
-^CellCensus\.Rproj$
+^cellxgene.census\.Rproj$
 ^\.Rproj\.user$
 ^LICENSE\.md$
 ^_pkgdown\.yml$

api/r/CellCensus/DESCRIPTION → api/r/cellxgene.census/DESCRIPTION

@@ -1,15 +1,15 @@
-Package: CellCensus
+Package: cellxgene.census
 Title: CZ CELLxGENE Discover Cell Census
 Version: 0.0.0.9000
 Authors@R: 
     person("Chan Zuckerberg Initiative", email = "[email protected]",
            role = c("aut", "cre", "cph", "fnd"))
 Description: API to facilitate the use of the CZ CELLxGENE Discover Cell 
   Census. For more information about the API and the project visit
-  https://github.com/chanzuckerberg/cell-census/
+  https://github.com/chanzuckerberg/cellxgene-census/
 License: MIT + file LICENSE
-URL: https://github.com/chanzuckerberg/cell-census
-BugReports: https://github.com/chanzuckerberg/cell-census/issues
+URL: https://github.com/chanzuckerberg/cellxgene-census
+BugReports: https://github.com/chanzuckerberg/cellxgene-census/issues
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3

api/r/CellCensus/R/get_helpers.R → api/r/cellxgene.census/R/get_helpers.R

@@ -1,6 +1,6 @@
 #' Read the feature dataset presence matrix.
 #'
-#' @param census The census object, usually returned by `CellCensus::open_soma()`.
+#' @param census The census object, usually returned by `cellxgene.census::open_soma()`.
 #' @param organism The organism to query, usually one of `Homo sapiens` or `Mus musculus`
 #' @param measurement_name The measurement object to query. Defaults to `RNA`.
 #'
@@ -18,7 +18,7 @@ get_presence_matrix <- function(census, organism, measurement_name = "RNA") {
 #' Convenience wrapper around `SOMAExperimentAxisQuery`, to build and execute a
 #' query, and return it as a `Seurat` object.
 #'
-#' @param census The census object, usually returned by `CellCensus::open_soma()`.
+#' @param census The census object, usually returned by `cellxgene.census::open_soma()`.
 #' @param organism The organism to query, usually one of `Homo sapiens` or `Mus musculus`
 #' @param measurement_name The measurement object to query. Defaults to `RNA`.
 #' @param X_name The `X` layer to query. Defaults to `raw`.

api/r/CellCensus/README.md → api/r/cellxgene.census/README.md

@@ -13,12 +13,12 @@ Also see the [Python API](https://chanzuckerberg.github.io/cellxgene-census/).
 
 ## Installation
 
-You can install the development version of cellxgene.census from [GitHub](https://github.com/) with:
+You can install the development version of `cellxgene.census` from [GitHub](https://github.com/) with:
 
 ``` r
 # install.packages("devtools")
-devtools::install_github("chanzuckerberg/cellxgene-census/api/r/CellCensus")
-print(CellCensus::open_soma())
+devtools::install_github("chanzuckerberg/cellxgene-census/api/r/cellxgene.census")
+print(cellxgene.census::open_soma())
 ```
 
 (minimal apt dependencies: r-base cmake git)
@@ -28,7 +28,7 @@ print(CellCensus::open_soma())
 This is a basic example which shows you how to solve a common problem:
 
 ``` r
-library(CellCensus)
+library(cellxgene.census)
 ## basic example code
 ```
 

api/r/CellCensus/tests/testthat.R → api/r/cellxgene.census/tests/testthat.R

@@ -7,6 +7,6 @@
 # * https://testthat.r-lib.org/reference/test_package.html#special-files
 
 library(testthat)
-library(CellCensus)
+library(cellxgene.census)
 
-test_check("CellCensus")
+test_check("cellxgene.census")

api/r/CellCensus/vignettes/census_datasets.Rmd → api/r/cellxgene.census/vignettes/census_datasets.Rmd

@@ -25,7 +25,7 @@ https://github.com/chanzuckerberg/cell-census/blob/main/api/python/notebooks/api
 Each Cell Census contains a top-level data frame itemizing the datasets contained therein. You can read this `SOMADataFrame` into an [Arrow Table](https://arrow.apache.org/docs/r/reference/Table.html):
 
 ```{r}
-census <- CellCensus::open_soma()
+census <- cellxgene.census::open_soma()
 census_datasets <- census$get("census_info")$get("datasets")$read()
 print(census_datasets)
 ```
@@ -80,12 +80,12 @@ dataset_seurat <- expt_query$to_seurat(c(counts = "raw"))
 print(dataset_seurat)
 ```
 
-You can also use the `CellCensus::get_source_h5ad_uri()` API to fetch a URI pointing to the H5AD associated with this `dataset_id`. This is the same H5AD you can download from the CELLxGENE Portal, and may contain additional data-submitter provided information which was not included in the Cell Census.
+You can also use the `cellxgene.census::get_source_h5ad_uri()` API to fetch a URI pointing to the H5AD associated with this `dataset_id`. This is the same H5AD you can download from the CELLxGENE Portal, and may contain additional data-submitter provided information which was not included in the Cell Census.
 
 The "locator" returned by this API will include a URI and additional information that may be necessary to use the URI (eg, the S3 region).
 
 ```{r}
-CellCensus::get_source_h5ad_uri("0bd1a1de-3aee-40e0-b2ec-86c7a30c7149")
+cellxgene.census::get_source_h5ad_uri("0bd1a1de-3aee-40e0-b2ec-86c7a30c7149")
 ```
 
-The `CellCensus::download_source_h5ad()` API downloads the H5AD to a local file, which can then be used in R using [SeuratDisk's anndata converter](https://mojaveazure.github.io/seurat-disk/articles/convert-anndata.html).
+The `cellxgene.census::download_source_h5ad()` API downloads the H5AD to a local file, which can then be used in R using [SeuratDisk's anndata converter](https://mojaveazure.github.io/seurat-disk/articles/convert-anndata.html).