From 85726ec4286f6c8bdf20915005651a8e22dd7d6c Mon Sep 17 00:00:00 2001
From: Matthew-Supernaw-NOAA <matthew.supernaw@noaa.gov>
Date: Thu, 12 Oct 2023 15:00:48 -0400
Subject: [PATCH] switched to python

---
 DESCRIPTION | 19 ++++++++-----------
 clean.py    |  8 ++++++++
 clean.sh    |  1 -
 configure   |  2 +-
 run.py      | 35 +++++++++++++++++++++++++++++++++++
 run.sh      | 12 ------------
 6 files changed, 52 insertions(+), 25 deletions(-)
 create mode 100644 clean.py
 delete mode 100755 clean.sh
 create mode 100644 run.py
 delete mode 100755 run.sh

diff --git a/DESCRIPTION b/DESCRIPTION
index b21fee4a..8d0f357c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,22 +1,19 @@
 Package: processR
 Title: Concurrent processing in R
 Version: 1.0
-Authors@R:
+Authors@R: 
     person("Matthew", "Supernaw", , "matthew.supernaw@noaa.gov", role = c("aut", "cre"))
 Description: A multi-process package for R.
 License: GPL (>= 2)
 URL: https://github.com/nmfs-fish-tools/processR
 BugReports: https://github.com/nmfs-fish-tools/processR/issues
-Depends:
-    R (>= 4.0.0)
-Imports: 
-    BH,
-    methods,
-    Rcpp (>= 1.0.10),
-    RInside
-LinkingTo:
-    Rcpp,
-    RInside
+Depends: R (>= 4.0.0)
+Imports: BH, methods, Rcpp (>= 1.0.10), RInside
+LinkingTo: Rcpp, RInside
 Encoding: UTF-8
 RoxygenNote: 7.2.3
 SystemRequirements: C++17
+NeedsCompilation: yes
+Packaged: 2023-10-12 17:23:54 UTC; mattadmin
+Author: Matthew Supernaw [aut, cre]
+Maintainer: Matthew Supernaw <matthew.supernaw@noaa.gov>
diff --git a/clean.py b/clean.py
new file mode 100644
index 00000000..ffbe82de
--- /dev/null
+++ b/clean.py
@@ -0,0 +1,8 @@
+#!/usr/bin/env python3
+
+from pydefs.do_rm import do_rm
+
+do_rm('processRCMake_1.tar.gz')
+do_rm('processRCMake.Rcheck')
+do_rm('_library')
+do_rm('mytest.Rout')
diff --git a/clean.sh b/clean.sh
deleted file mode 100755
index bd55bfb7..00000000
--- a/clean.sh
+++ /dev/null
@@ -1 +0,0 @@
-#!/bin/bash -e 
\ No newline at end of file
diff --git a/configure b/configure
index 9db93000..af2c62d8 100755
--- a/configure
+++ b/configure
@@ -7,7 +7,7 @@ which cmake
 
 RBIN=$(which R)
 
-echo R --version
+echo $(R --version)
 
 RHOME=$(${RBIN} --slave --no-save -e 'cat(R.home())')
 RUSER=$(${RBIN} --slave --no-save -e 'cat(Sys.getenv("R_LIBS_USER"))')
diff --git a/run.py b/run.py
new file mode 100644
index 00000000..1f92e8ba
--- /dev/null
+++ b/run.py
@@ -0,0 +1,35 @@
+#!/usr/bin/env python3
+
+from pydefs.do_call import do_call
+
+import os
+import platform
+import subprocess
+import sys
+
+do_call([sys.executable, 'clean.py'])
+
+if platform.system() == 'Windows':
+  do_call(['where', 'cmake'], fix_message='Install cmake, add cmake to PATH')
+  do_call(['where', 'R'], fix_message='Install R, add R.exe to PATH')
+  do_call(['where', 'sh'], fix_message='Install Rtools, add sh.exe to PATH')
+  do_call(['where', 'g++'], fix_message='Install Rtools, add g++.exe to PATH')
+else:
+  do_call(['which', 'cmake'])
+
+local_library = os.path.join(os.getcwd(), '_library')
+os.mkdir(local_library)
+
+packname = 'ProcessRCMake_1.0.tar.gz'
+
+logfiles = ['00install.out']
+logfiles = [os.path.join('ProcessRCMake.Rcheck', x) for x in logfiles]
+
+do_call(['R', 'CMD', 'build', '.'])
+do_call(['R', 'CMD', 'check', packname], info_files=logfiles)
+do_call(['R', 'CMD', 'INSTALL', '-l', local_library, packname])
+
+result_out = os.path.join(os.getcwd(), 'mytest.Rout')
+os.environ['R_LIBS_USER'] = local_library
+
+
diff --git a/run.sh b/run.sh
deleted file mode 100755
index 554b11e5..00000000
--- a/run.sh
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/bin/bash -e 
-
-set -x
-
-./clean.sh
-
-mkdir _library
-
-R CMD build .
-R CMD INSTALL -l _library processR_0.0.1.tar.gz
-#R CMD BATCH mytest.R || echo "mytest failed"
-