Merge 442a201 into b56f653

scprep/run/__init__.py

@@ -1,5 +1,6 @@
 from .dyngen import DyngenSimulate
 from .r_function import install_bioconductor
+from .r_function import install_github
 from .r_function import RFunction
 from .slingshot import Slingshot
 from .splatter import SplatSimulate

scprep/run/dyngen.py

@@ -2,6 +2,17 @@
 
 import pandas as pd
 
+_install_dyngen = r_function.RFunction(
+    args="""lib=.libPaths()[1], dependencies=NA,
+            repos='http://cran.rstudio.com', verbose=TRUE""",
+    body="""
+       install.packages(c("dynwrap", "dyngen"),
+                        lib=lib,
+                        repos=repos,
+                        dependencies=dependencies)
+    """,
+)
+
 _get_backbones = r_function.RFunction(
     setup="""
         library(dyngen)
@@ -95,13 +106,10 @@
 def install(
     lib=None,
     dependencies=None,
-    update=False,
     repos="http://cran.us.r-project.org",
-    build_vignettes=False,
-    force=False,
     verbose=True,
 ):
-    """Install Dyngen Github repository.
+    """Install Dyngen from CRAN.
 
     Parameters
     ----------
@@ -114,37 +122,22 @@ def install(
         When False, installs no dependencies.
         When None/NA, installs all packages specified under "Depends", "Imports"
         and "LinkingTo".
-    update: string or boolean, optional (default: False)
-        One of "default", "ask", "always", or "never". "default"
-        Respects R_REMOTES_UPGRADE variable if set, falls back to "ask" if unset.
-        "ask" prompts the user for which out of date packages to upgrade.
-        For non-interactive sessions "ask" is equivalent to "always".
-        TRUE and FALSE also accepted, correspond to "always" and "never" respectively.
     repos: string, optional (default: "http://cran.us.r-project.org"):
         R package repository.
-    build_vignettes: boolean, optional (default: False)
-        Builds Github vignettes.
-    force: boolean, optional (default: False)
-        Forces installation even if remote state has not changed since previous install.
     verbose: boolean, optional (default: True)
         Install script verbosity.
     """
-    r_function.install_github(
-        repo="dynverse/dynwrap",
-        update=update,
-        lib=lib,
-        dependencies=dependencies,
-        repos=repos,
-        verbose=verbose,
-    )
 
-    r_function.install_github(
-        repo="dynverse/dyngen",
-        update=update,
-        lib=lib,
-        dependencies=dependencies,
+    kwargs = {}
+    if lib is not None:
+        kwargs["lib"] = lib
+    if dependencies is not None:
+        kwargs["dependencies"] = dependencies
+
+    _install_dyngen(
         repos=repos,
         verbose=verbose,
+        **kwargs,
     )
 
 

test/test_run.py

@@ -44,43 +44,46 @@ def test_install_bioc():
         )
 
     def test_install_github_lib():
-        scprep.run.dyngen.install(verbose=False)
+        scprep.run.install_github("twitter/AnomalyDetection", verbose=False)
         fun = scprep.run.RFunction(
             body="""
             packages <- installed.packages()
-            'dyngen' %in% packages
+            'AnomalyDetection' %in% packages
             """
         )
 
         assert fun()
 
     def test_install_github_dependencies_None():
-        scprep.run.dyngen.install(verbose=False)
+        scprep.run.install_github("twitter/AnomalyDetection", verbose=False)
         fun = scprep.run.RFunction(
             body="""
             if (!require("pacman", quietly=TRUE)) {
                 install.packages("pacman",
                 repos='http://cran.rstudio.com')
             }
 
-            deps <- pacman::p_depends(dyngen)[c("Depends","Imports","LinkingTo")]
+            deps <- pacman::p_depends(AnomalyDetection, local=TRUE)[c("Depends",
+                    "Imports","LinkingTo")]
             all(unname(unlist(deps)) %in% installed.packages()[, "Package"])
             """
         )
 
         assert fun()
 
     def test_install_github_dependencies_True():
-        scprep.run.dyngen.install(verbose=False, dependencies=True)
+        scprep.run.install_github(
+            "twitter/AnomalyDetection", verbose=False, dependencies=True
+        )
         fun = scprep.run.RFunction(
             body="""
             if (!require("pacman", quietly=TRUE)) {
                 install.packages("pacman",
                 repos='http://cran.rstudio.com')
             }
 
-            deps <- pacman::p_depends(dyngen)[c("Depends","Imports","LinkingTo",
-                    "Suggests")]
+            deps <- pacman::p_depends(AnomalyDetection, local=TRUE)[c("Depends",
+                    "Imports","LinkingTo","Suggests")]
             deps <- unname(unlist(deps))
             installed <- installed.packages()[, "Package"]
             success <- all(deps %in% installed)
@@ -294,6 +297,54 @@ class TestDyngen(unittest.TestCase):
         def setUpClass(self):
             scprep.run.dyngen.install(verbose=False)
 
+        def test_install_dyngen_lib(self):
+            scprep.run.dyngen.install(verbose=False)
+            fun = scprep.run.RFunction(
+                body="""
+                packages <- installed.packages()
+                'dyngen' %in% packages
+                """
+            )
+
+            assert fun()
+
+        def test_install_dyngen_dependencies_None(self):
+            scprep.run.dyngen.install(verbose=False)
+            fun = scprep.run.RFunction(
+                body="""
+                if (!require("pacman", quietly=TRUE)) {
+                    install.packages("pacman",
+                    repos='http://cran.rstudio.com')
+                }
+
+                deps <- pacman::p_depends(dyngen)[c("Depends","Imports","LinkingTo")]
+                all(unname(unlist(deps)) %in% installed.packages()[, "Package"])
+                """
+            )
+
+            assert fun()
+
+        def test_install_dyngen_dependencies_True(self):
+            scprep.run.dyngen.install(verbose=False, dependencies=True)
+            fun = scprep.run.RFunction(
+                body="""
+                if (!require("pacman", quietly=TRUE)) {
+                    install.packages("pacman",
+                    repos='http://cran.rstudio.com')
+                }
+
+                deps <- pacman::p_depends(dyngen)[c("Depends","Imports","LinkingTo",
+                        "Suggests")]
+                deps <- unname(unlist(deps))
+                installed <- installed.packages()[, "Package"]
+                success <- all(deps %in% installed)
+                list(success=success, deps=deps, installed=installed)
+                """
+            )
+
+            result = fun()
+            assert result["success"], result
+
         def test_dyngen_backbone_not_in_list(self):
             utils.assert_raises_message(
                 ValueError,