correct dependency to snakemake

setup.py

@@ -4,6 +4,11 @@
 """The setup script."""
 
 from setuptools import setup, find_packages
+import sys
+
+if sys.version_info < (3, 5):
+    print("At least Python 3.5 is required.\n", file=sys.stderr)
+    exit(1)
 
 with open('README.rst') as readme_file:
     readme = readme_file.read()
@@ -15,8 +20,7 @@
     'Click>=6.0',
     'click-log',
     'PyYAML>=4.2b1',
-    'snakemake>=3.13.2',
-    # TODO: put package requirements here
+    'snakemake>=5.5.1',
 ]
 
 setup_requirements = [
@@ -54,12 +58,6 @@
         'Development Status :: 2 - Pre-Alpha',
         'Intended Audience :: Developers',
         'Natural Language :: English',
-        "Programming Language :: Python :: 2",
-        'Programming Language :: Python :: 2.6',
-        'Programming Language :: Python :: 2.7',
-        'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.3',
-        'Programming Language :: Python :: 3.4',
         'Programming Language :: Python :: 3.5',
     ],
     test_suite='tests',

tox.ini

@@ -1,13 +1,14 @@
 [tox]
-envlist = py26, py27, py33, py34, py35, flake8
+envlist = py35, flake8
+# py26, py27, py33, py3i4
 
 [travis]
 python =
     3.5: py35
-    3.4: py34
-    3.3: py33
-    2.7: py27
-    2.6: py26
+#    3.4: py34
+#    3.3: py33
+#    2.7: py27
+#    2.6: py26
 
 [testenv:flake8]
 basepython=python

wbuild/.wBuild/wBuildParser.R

@@ -1,3 +1,12 @@
+for(p in c("stringr", "yaml", "magrittr", "gsubfn"))
+	if(!requireNamespace(p, quietly=TRUE))
+		install.packages(p)
+library(stringr)
+library(methods)
+library(yaml)
+library(magrittr)
+library(gsubfn)
+
 parseWBHeader = function(filename, ...)
 {
 	addWildCards = list(...)
@@ -6,7 +15,6 @@ parseWBHeader = function(filename, ...)
 		filename = snakemake@input[['RScript']]
 	}
 
-	library(stringr)
 	wbPD = 'Output/ProcessedData'
 	wildcards = list(
 			`wbPD` = 'Output/ProcessedData',
@@ -17,11 +25,7 @@ parseWBHeader = function(filename, ...)
 	wildcards = c(wildcards,addWildCards)
 	if(!exists('snakemake') || snakemake@rule == 'WB')
 	{
-		library(methods)
-		library(yaml)
-		library(magrittr)
-		library(gsubfn)
-
+
 		wb = readLines(filename)%>%str_subset("^#'")%>%str_replace("^#'",'')%>%paste0(collapse='\n')%>%
 				str_replace("\\n---(.|\\n)*",'')%>%yaml.load%>%`[[`('wb')
 
@@ -120,4 +124,4 @@ wbRead = function(name)
 		return(wbReadRDS(name))
 	}
 	stop('Could not determine format of ', snakemake@input[[name]])
-}
+}

wbuild/.wBuild/wBuildParser2.R

@@ -1,36 +1,53 @@
+for(p in c("stringr", "gsubfn"))
+	if(!requireNamespace(p, quietly=TRUE))
+		install.packages(p)
 library(stringr)
 library(gsubfn)
-parseWBHeader2 = function(file, wildcards = list(), debug = T)
-{
+
+parseWBHeader2 <- function(file, wildcards=list(), debug=TRUE, options=c(),
+                    rerun=FALSE){
+
 	# Are we interactive or in real snakemake run?
-	if(exists('snakemake')&&is.null(snakemake@config[['wbDump']]))
-	{
+	if(exists('snakemake') && is.null(snakemake@config[['wbDump']]) &&
+	        !isTRUE(rerun)){
 		return (snakemake)
 	}
+
 	#' Create dependency file
-	system2('python',c('.wBuild/wbParse.py',file))
+	system2('python', c('.wBuild/wbParse.py',file))
+
 	#' Replace wildcards if necessary
-	if(length(wildcards)>0)
-	{
-		names(wildcards) = paste0('{',names(wildcards),'}')
-		dependencyfile = readLines('.wBuild.depend')
-		dependencyfile_wild  <- gsubfn('\\{[^\\}]+\\}', wildcards,dependencyfile)
+	if(length(wildcards) > 0){
+		wildcards2rep <- rep(wildcards, each=2)
+		names(wildcards2rep) <- paste0(
+                c('{', '{{'), names(wildcards2rep), c('}', '}}'))
+		dependencyfile <- readLines('.wBuild.depend')
+		dependencyfile_wild <- gsubfn(
+                '\\{+[^\\}]+\\}+', wildcards2rep, dependencyfile)
 		writeLines(dependencyfile_wild, con=".wBuild.depend")
 	}
+
 	#' Extract rule name (1st in file)
 	dependencyfile = readLines('.wBuild.depend')
 	rule_name = str_extract(dependencyfile,'(?<=rule )[A-z0-9_]*')
 	rule_name = rule_name[!is.na(rule_name)][1]
-
-	if(debug==T)
-	{
+
+	if(isTRUE(debug)){
 		writeLines(dependencyfile)
 	}
+
 	#' Run snakemake to dump snakemake object, dumps some error yet
-	system2('snakemake',c(rule_name,'--config','wbDump=T','--nolock','--latency-wait','0','-q','-F','--allowed-rules',rule_name,'--mode','2'))
+	system2('snakemake', c(rule_name, '--config', 'wbDump=T', '--nolock',
+            '--latency-wait', '0', '-q', '-F', '--allowed-rules', rule_name,
+            '--mode', '2', options))
 	#' Read snakemake object in
-	snakemake <<- readRDS('.wBuild/snakemake.dump')
+	ans <- readRDS('.wBuild/snakemake.dump')
+	slot(ans, "wildcards", check=FALSE) <- wildcards
+
+	snakemake <<- ans
 }
+
+
 #
 #parseWBHeader2('Scripts/Analysis1/010_BasicInput/020_BasicInput.R',debug=F)
 #parseWBHeader2(file ='Scripts/Analysis1/050_PythonCode/030_AnalysisTemplate.R',list(id='anton'))

wbuild/utils.py

@@ -275,6 +275,8 @@ def __init__(self):
                     self.path = p
                     break
         else:
+            if type(self.path) is list:
+                self.path=self.path[0]
             self.path=os.path.abspath(self.path)
 
         # this is taken from the snakemake main file