reorganize R scripts

wtroy2 · Jun 17, 2020 · b3b5bd3 · b3b5bd3
1 parent 9031a2d
commit b3b5bd3
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Showing 14 changed files with 13 additions and 13 deletions.
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -4,4 +4,4 @@ include *.txt
 include mapdamage/seqtk/kseq.h
 include mapdamage/seqtk/README.md
 include mapdamage/seqtk/seqtk.c
-recursive-include mapdamage/Rscripts *.r
+recursive-include mapdamage/r *.r
diff --git a/mapdamage/Rscripts/common.r → mapdamage/r/common.r b/mapdamage/Rscripts/common.r → mapdamage/r/common.r
diff --git a/mapdamage/Rscripts/lengths.R → mapdamage/r/lengths.r b/mapdamage/Rscripts/lengths.R → mapdamage/r/lengths.r
diff --git a/mapdamage/Rscripts/mapDamage.R → mapdamage/r/mapDamage.r b/mapdamage/Rscripts/mapDamage.R → mapdamage/r/mapDamage.r
diff --git a/mapdamage/Rscripts/stats/data.R → mapdamage/r/stats/data.r b/mapdamage/Rscripts/stats/data.R → mapdamage/r/stats/data.r
diff --git a/mapdamage/Rscripts/stats/function.R → mapdamage/r/stats/function.r b/mapdamage/Rscripts/stats/function.R → mapdamage/r/stats/function.r
diff --git a/mapdamage/Rscripts/stats/main.R → mapdamage/r/stats/main.r b/mapdamage/Rscripts/stats/main.R → mapdamage/r/stats/main.r
@@ -6,19 +6,19 @@ suppressPackageStartupMessages(library(gam))
 suppressPackageStartupMessages(library(RcppGSL))
 
 #Miscellaneous functions
-source("function.R")
+source("function.r")
 
 #Prior and proposal distributions for the parameters
-source("priorPropose.R")
+source("priorPropose.r")
 
 #Update functions for the gibbs sampler
-source("postConditonal.R")
+source("postConditonal.r")
 
 #functions for the grid search
-source("start.R")
+source("start.r")
 
 #functions for loading the data
-source("data.R")
+source("data.r")
 
 
 #######################################################

diff --git a/mapdamage/Rscripts/stats/postConditonal.R → mapdamage/r/stats/postConditonal.r b/mapdamage/Rscripts/stats/postConditonal.R → mapdamage/r/stats/postConditonal.r
@@ -1,5 +1,5 @@
 # The posterior conditional function utilized by the
-# Gibbs sampler in function.R. They have all the
+# Gibbs sampler in function.r. They have all the
 # same form maybe they should be implemented in a
 # smarter way.
 

diff --git a/mapdamage/Rscripts/stats/priorPropose.R → mapdamage/r/stats/priorPropose.r b/mapdamage/Rscripts/stats/priorPropose.R → mapdamage/r/stats/priorPropose.r
diff --git a/mapdamage/Rscripts/stats/runGeneral.R → mapdamage/r/stats/runGeneral.r b/mapdamage/Rscripts/stats/runGeneral.R → mapdamage/r/stats/runGeneral.r
@@ -84,4 +84,4 @@ use_bw_theme <- getArgument("USE_BW_THEME", as.logical)
 #
 #######################################################
 
-source("main.R")
+source("main.r")
diff --git a/mapdamage/Rscripts/stats/start.R → mapdamage/r/stats/start.r b/mapdamage/Rscripts/stats/start.R → mapdamage/r/stats/start.r
diff --git a/mapdamage/rscript.py b/mapdamage/rscript.py
@@ -18,7 +18,7 @@ def misincorporation_plot(options):
     logger.info("Saving misincorporation plot to '%s'", output)
 
     return _rscript_call(
-        Path("mapDamage.R"),
+        Path("mapDamage.r"),
         COMP=fcomp,
         PDFOUT=output,
         AROUND=options.refplot,
@@ -43,7 +43,7 @@ def length_distribution_plot(options):
     logger.info("Saving length distribution plot to '%s'", output)
 
     return _rscript_call(
-        Path("lengths.R"),
+        Path("lengths.r"),
         LGDIST=flength,
         PDFOUT=output,
         MISINCORP=fmut,
@@ -76,7 +76,7 @@ def perform_bayesian_estimates(options):
     folder = options.folder.absolute()
 
     return _rscript_call(
-        Path("stats") / "runGeneral.R",
+        Path("stats") / "runGeneral.r",
         GRID_ITER=options.rand,
         BURN_IN=options.burn,
         ADJUST_ITER=options.adjust,
@@ -97,7 +97,7 @@ def perform_bayesian_estimates(options):
 
 
 def _rscript_call(filepath, **kwargs):
-    cwd = Path(resource_filename("mapdamage", "Rscripts")) / filepath.parent
+    cwd = Path(resource_filename("mapdamage", "r")) / filepath.parent
     command = ["Rscript", filepath.name]
     for item in sorted(kwargs.items()):
         command.append("%s=%s" % item)

diff --git a/mapdamage/seqtk.cpython-36m-x86_64-linux-gnu.so b/mapdamage/seqtk.cpython-36m-x86_64-linux-gnu.so
diff --git a/setup.py b/setup.py
@@ -30,7 +30,7 @@ def run(self):
     version="2.2.0",
     author="Aurélien Ginolhac, Mikkel Schubert, Hákon Jónsson",
     packages=["mapdamage"],
-    package_data={"mapdamage": ["Rscripts/*.R", "Rscripts/stats/*.R", "tests/*"]},
+    package_data={"mapdamage": ["r/*.r", "r/stats/*.r", "tests/*"]},
     entry_points={"console_scripts": ["mapDamage=mapdamage.main:entry_point"]},
     url="https://github.com/ginolhac/mapDamage",
     license="LICENSE.txt",