feat: add python package stub installer

milescsmith · Aug 11, 2021 · c257f92 · c257f92
1 parent 2b4f4b0
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,16 +4,21 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [2.4.1] - 2020-12-23
+## [2.5.0] - 2020-08-11
+### Added
+  - Added a python stub package to pin package versions
+### Changed
+  - Removed opt-SNE because it hasn't been updated in several years and it is
+    not trivial to install
+
 
+## [2.4.1] - 2020-12-23
 ### Fixed
 - Added missing `@importFrom magrittr %>%` in `PAGA()` header
-
 ### Changed
 - Reformatted `PAGA()` code
 
 
 ## [2.4.0] - 2020-12-23
-
 ### Added
 - Added [PaCMAP](https://github.com/YingfanWang/PaCMAP)
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ReductionWrappers
 Title: Wrapper exposing several Python dimensional reduction tools
-Version: 2.4.0.0000
+Version: 2.5.0
 Authors@R: 
     person(given = "Miles",
            family = "Smith",
@@ -13,14 +13,13 @@ Url: https://github.com/milescsmith/ReductionWrappers
 BugReports: https://github.com/milescsmith/ReductionWrappers/issues
 Depends: R (>= 3.5.0)
 Imports:
-  cowplot,
   rlang,
   reticulate,
   parallel,
   ggplot2,
+  ggpubr,
   glue,
   magrittr,
-  RANN,
   Matrix,
   Seurat,
   SingleCellExperiment,

diff --git a/NAMESPACE b/NAMESPACE
@@ -13,14 +13,11 @@ export(DooptSNE)
 export(PAGA)
 export(PAGAplot)
 export(openTSNE)
-export(optSNE)
 export(pacmap)
 export(phate)
 export(phenograph)
 export(umap)
 importFrom(Matrix,Matrix)
-importFrom(Matrix,sparseMatrix)
-importFrom(RANN,nn2)
 importFrom(Seurat,"Idents<-")
 importFrom(Seurat,AddMetaData)
 importFrom(Seurat,CreateDimReducObject)
@@ -32,14 +29,14 @@ importFrom(SingleCellExperiment,reducedDim)
 importFrom(SingleCellExperiment,reducedDimNames)
 importFrom(SummarizedExperiment,"colData<-")
 importFrom(SummarizedExperiment,colData)
-importFrom(cowplot,theme_cowplot)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,geom_point)
 importFrom(ggplot2,geom_segment)
 importFrom(ggplot2,geom_text)
 importFrom(ggplot2,ggplot)
 importFrom(ggplot2,labs)
 importFrom(ggplot2,scale_color_manual)
+importFrom(ggpubr,theme_pubr)
 importFrom(glue,glue)
 importFrom(magrittr,"%>%")
 importFrom(magrittr,set_colnames)
@@ -49,4 +46,3 @@ importFrom(reticulate,import)
 importFrom(reticulate,py_module_available)
 importFrom(rlang,"%||%")
 importFrom(s2a,convert_to_anndata)
-importFrom(stringr,str_glue)
diff --git a/R/forceatlas2.R b/R/forceatlas2.R
@@ -1,4 +1,4 @@
-#' ForceAtlas2
+#' @title ForceAtlas2
 #'
 #' An R wrapper around the Python implementation of ForceAtlas2 found at
 #' https://github.com/bhargavchippada/forceatlas2
@@ -10,6 +10,9 @@
 #' @param iterations Number of times to iterate the main loop
 #' @param ... Additional arguments to pass to the forceatlas2 object instantiation
 #'
+#' @importFrom reticulate import
+#' @importFrom glue glue
+#' 
 #' @rdname fa2
 #'
 fa2 <- function(init_pos,
@@ -20,37 +23,44 @@ fa2 <- function(init_pos,
   required_modules <- c("fa2","numpy")
   for (i in required_modules) {
     if (!py_module_available(i)) {
-      stop(glue("The {i} module is unavailable.
+      stop(glue::glue("The {i} module is unavailable.
          Please activate the appropriate environment or
          install the module."))
     }
   }
 
-  fa2 <- import(module = "fa2", delay_load = TRUE)
-  np <- import(module = "numpy", delay_load = TRUE)
+  fa2 <- reticulate::import(module = "fa2", delay_load = TRUE)
+  np <- reticulate::import(module = "numpy", delay_load = TRUE)
 
   # shamelessly based from the fantastic Scanpy package
-  forceatlas2 <- fa2$ForceAtlas2(outboundAttractionDistribution=FALSE,  # Dissuade hubs
-                                 linLogMode=FALSE,  # NOT IMPLEMENTED
-                                 adjustSizes=FALSE,  # Prevent overlap (NOT IMPLEMENTED)
-                                 edgeWeightInfluence=1.0,
-                                 # Performance
-                                 jitterTolerance=1.0,  # Tolerance
-                                 barnesHutOptimize=TRUE,
-                                 barnesHutTheta=1.2,
-                                 multiThreaded=FALSE,  # NOT IMPLEMENTED
-                                 # Tuning
-                                 scalingRatio=2.0,
-                                 strongGravityMode=FALSE,
-                                 gravity=1.0,
-                                 # Log
-                                 verbose=TRUE)
+  forceatlas2 <-
+    fa2$ForceAtlas2(
+      outboundAttractionDistribution=FALSE,  # Dissuade hubs
+      linLogMode=FALSE,  # NOT IMPLEMENTED
+      adjustSizes=FALSE,  # Prevent overlap (NOT IMPLEMENTED)
+      edgeWeightInfluence=1.0,
+      # Performance
+      jitterTolerance=1.0,  # Tolerance
+      barnesHutOptimize=TRUE,
+      barnesHutTheta=1.2,
+      multiThreaded=FALSE,  # NOT IMPLEMENTED
+      # Tuning
+      scalingRatio=2.0,
+      strongGravityMode=FALSE,
+      gravity=1.0,
+      # Log
+      verbose=TRUE
+    )
 
-  fa_results <- forceatlas2$forceatlas2(G = adjacencies,
-                                        pos = init_pos,
-                                        iterations = as.integer(iterations))
+  fa_results <-
+   forceatlas2$forceatlas2(
+     G = adjacencies,
+     pos = init_pos,
+     iterations = as.integer(iterations)
+    )
   fa_embeddings <- np$array(fa_results)
   rownames(fa_embeddings) <- rownames(init_pos)
-  colnames(fa_embeddings) <- as.character(glue("fa_{1:ncol(fa_embeddings)}"))
-  return(fa_embeddings)
+  colnames(fa_embeddings) <- as.character(glue::glue("fa_{1:ncol(fa_embeddings)}"))
+
+  fa_embeddings
 }