API+MIN Rename search-dir to search-path

Makes it consistent across all interfaces and documentation.

fixes #70

ChangeLog

@@ -7,14 +7,15 @@ Version 0.9.1+
 	expected
 	* Indices created by bwa and minimap2 are now versioned
 	* arg1 in external modules is no longer always treated as a path
-	* Added expand_searchdir to external modules API (closes #56)
+	* Added expand_searchpath to external modules API (closes #56)
 	* Fixed bug where detection of Fastq encoding was not performed on the second pair
 	* Fix saving fastq sets with --subsample (issue #85)
 	* Add __extra_megahit_args to assemble() (issue #86)
 	* Better error message when user mis-specifies the ngless version string
 	(issue #84)
 	* Support NO_COLOR environment variable (issue #83)
 	* Garbage collection for temporary files (issue #79)
+	* Rename --search-dir to --search-path for consistency with other API
 
 Version 0.9.1 2018-07-17 by luispedro
 	* Add biorxiv citation

NGLess/CmdArgs.hs

@@ -154,7 +154,7 @@ mainArgs = DefaultMode
               <*> optional (strOption $ long "export-json" <> help "File to write JSON representation of script to") -- exportJSON :: Maybe FilePath
               <*> optional (strOption $ long "export-cwl" <> help "File to write CWL wrapper of given script") -- exportCWL :: Maybe FilePath
               <*> switch (long "check-deprecation" <> help "Check if ngless version or any used modules have been deprecated")-- deprecationCheck :: Bool
-              <*> many (strOption $ long "search-dir" <> help "Reference search directories (replace <references> in script)") -- searchPath :: [FilePath]
+              <*> many (strOption $ long "search-path" <> help "Reference search directories (replace <references> in script)") -- searchPath :: [FilePath]
               <*> optional (strOption $ long "index-path" <> help "Index path (directory where indices are stored)") -- indexPath :: Maybe FilePath
               <*> many (strArgument (metavar "ARGV")) -- extraArgs :: [String]
 

NGLess/ExternalModules.hs

@@ -89,7 +89,7 @@ instance Aeson.FromJSON FileType where
 
 data CommandExtra = FlagInfo [T.Text]
             | FileInfo FileType
-            | ExpandSearchDir Bool
+            | ExpandSearchPath Bool
             deriving (Eq, Show)
 
 data CommandArgument = CommandArgument
@@ -127,12 +127,12 @@ instance Aeson.FromJSON CommandArgument where
                     return [ArgCheckSymbol allowed]
                 else return []
         let cargInfo = ArgInformation{..}
-        aexpand <- o .:? "expand_searchdir" .!= False
+        aexpand <- o .:? "expand_searchpath" .!= False
         cargPayload <-
             if
                 | atype `elem` ["option", "flag"] -> liftM FlagInfo <$> ((Just . (:[]) <$> o .: "when-true") <|> o .:? "when-true")
                 | atype `elem` ["readset", "counts", "mappedreadset"] -> (Just . FileInfo <$> Aeson.parseJSON (Aeson.Object o)) <|> return Nothing
-                | atype == "str" -> return $ Just (ExpandSearchDir aexpand)
+                | atype == "str" -> return $ Just (ExpandSearchPath aexpand)
                 | otherwise -> return Nothing
         return CommandArgument{..}
 
@@ -344,7 +344,7 @@ encodeArgument (CommandArgument ai _ payload) (Just v)
             NGLString -> do
                 str <- T.unpack <$> stringOrTypeError "in external module" v
                 case payload of
-                     Just (ExpandSearchDir True) -> fromMaybe str <$> expandPath str
+                     Just (ExpandSearchPath True) -> fromMaybe str <$> expandPath str
                      _ -> return str
             NGLSymbol -> T.unpack <$> symbolOrTypeError "in external module" v
             NGLInteger ->  show <$> integerOrTypeError "in external module" v

docs/sources/command-line-options.md

@@ -38,7 +38,7 @@ of free disk space:
                            Directory where to store temporary files
 
 
-  --search-dir ARG         Reference search directories (replace <references> in
+  --search-path ARG        Reference search directories (replace <references> in
                            script)
   --index-path ARG         Index path (directory where indices are stored)
 

docs/sources/modules.md

@@ -206,13 +206,13 @@ of the output type.
 
 If you plan to make use of [search path expansion](searchpath.html), in order
 for NGLess to expand the argument prior to passing it to the external module
-you need to set ``atype: "str"`` and ``expand_searchdir: true``.
+you need to set ``atype: "str"`` and ``expand_searchpath: true``.
 
         additional:
             -
                 atype: 'str'
                 name: 'reference'
-                expand_searchdir: true
+                expand_searchpath: true
 
 ### Citation
 

docs/sources/whatsnew.rst

@@ -78,7 +78,7 @@ Bugfixes
 - Fixed `lock1
   <http://ngless.embl.de/stdlib.html?highlight=lock1#parallel-module>`__ when
   used with full paths (see `issue #68 <https://github.com/ngless-toolkit/ngless/issues/68>`__)
-- Fix expansion of searchdir with external modules (see `issue #56
+- Fix expansion of searchpath with external modules (see `issue #56
   <https://github.com/ngless-toolkit/ngless/issues/56>`__)
 
 Version 0.8

tests/map_search_path/cmdargs

@@ -1 +1 @@
---search-dir subdirectory
+--search-path subdirectory

tests/map_search_path_multiple/cmdargs

@@ -1 +1 @@
---search-dir subdir1  --search-dir subdir2
+--search-path subdir1  --search-path subdir2

tests/searchdirExternalModule/Modules/test.ngm/0.0/command_path.sh → tests/searchpathExternalModule/Modules/test.ngm/0.0/command_path.sh

@@ -14,7 +14,7 @@ if [ "$2" != "$EXPECTED" ]; then
     exit 1
 fi
 
-EXPECTED="--ref2=../searchdirExternalModule/somedir/input2.fq"
+EXPECTED="--ref2=../searchpathExternalModule/somedir/input2.fq"
 
 if [ "$3" != "$EXPECTED" ]; then
     echo "3nd argument expected '$EXPECTED' saw '$3'"

tests/searchdirExternalModule/Modules/test.ngm/0.0/module.yaml → tests/searchpathExternalModule/Modules/test.ngm/0.0/module.yaml

@@ -2,7 +2,7 @@ version: '0.0.0'
 name: 'Test tool'
 functions:
     -
-        nglName: "testing_searchdir_string"
+        nglName: "testing_searchpath_string"
         arg0: './command_string.sh'
 
         arg1:
@@ -20,22 +20,22 @@ functions:
                 atype: str
 
     -
-        nglName: "testing_searchdir_path"
+        nglName: "testing_searchpath_path"
         arg0: './command_path.sh'
 
         arg1:
             atype: str
-            expand_searchdir: true
+            expand_searchpath: true
 
         additional:
             -
                 name: ref
                 atype: str
-                expand_searchdir: true
+                expand_searchpath: true
             -
                 name: ref2
                 atype: str
-                expand_searchdir: true
+                expand_searchpath: true
             -
                 name: string
                 atype: str

tests/searchpathExternalModule/cmdargs

@@ -0,0 +1 @@
+--search-path location=somedir  --search-path fullpath=../searchpathExternalModule/somedir

tests/searchpathExternalModule/test.ngl

@@ -0,0 +1,5 @@
+ngless '0.0'
+local import "test" version "0.0"
+
+testing_searchpath_path("<location>/input.fq", ref="<location>/input2.fq", ref2="<fullpath>/input2.fq", string="sentence")
+testing_searchpath_string("<location>/input.fq", ref="<location>/input2.fq", ref2="<fullpath>/input2.fq", string="sentence")