Add/remove methods in shim types

Author: bentsherman

src/main/java/nextflow/script/types/shim/List.java

@@ -35,11 +35,13 @@ public interface List<E> extends Iterable<E> {
         Collates the list into a list of sub-lists of length `size`. If `keepRemainder` is `true`, any remaining elements are included as a partial sub-list, otherwise they are excluded.
     """)
     List<List<E>> collate(int size, boolean keepRemainder);
+    List<List<E>> collate(int size);
 
     @Description("""
         Collates the list into a list of sub-lists of length `size`, stepping through the list `step` elements for each sub-list. If `keepRemainder` is `true`, any remaining elements are included as a partial sub-list, otherwise they are excluded.
     """)
     List<List<E>> collate(int size, int step, boolean keepRemainder);
+    List<List<E>> collate(int size, int step);
 
     @Description("""
         Returns the first value in the list that satisfies the given condition.

src/main/java/nextflow/script/types/shim/Path.java

@@ -33,11 +33,6 @@ public interface Path {
 
     // file attributes
 
-    @Description("""
-        Returns `true` if the file exists.
-    """)
-    boolean exists();
-
     @Constant("baseName")
     @Description("""
         Gets the file name without its extension, e.g. `/some/path/file.tar.gz` -> `file.tar`.
@@ -56,12 +51,6 @@ public interface Path {
     """)
     String getName();
 
-    @Constant("simpleName")
-    @Description("""
-        Gets the file name without any extension, e.g. `/some/path/file.tar.gz` -> `file`.
-    """)
-    String getSimpleName();
-
     @Constant("parent")
     @Description("""
         Gets the file parent path, e.g. `/some/path/file.txt` -> `/some/path`.
@@ -74,6 +63,17 @@ public interface Path {
     """)
     String getScheme();
 
+    @Constant("simpleName")
+    @Description("""
+        Gets the file name without any extension, e.g. `/some/path/file.tar.gz` -> `file`.
+    """)
+    String getSimpleName();
+
+    @Description("""
+        Returns `true` if the file exists.
+    """)
+    boolean exists();
+
     @Description("""
         Returns `true` if the file is a directory.
     """)
@@ -131,22 +131,11 @@ Returns the file last modified timestamp in Unix time (i.e. milliseconds since J
 
     // reading
 
-    @Description("""
-        Iterates over the file, applying the specified closure to each byte.
-    """)
-    void eachByte(Consumer<Byte> action);
-
     @Description("""
         Iterates over the file, applying the specified closure to each line.
     """)
     void eachLine(Consumer<String> action);
 
-    @Constant("bytes")
-    @Description("""
-        Returns the file content as a byte array.
-    """)
-    byte[] getBytes();
-
     @Constant("text")
     @Description("""
         Returns the file content as a string.
@@ -165,11 +154,6 @@ Returns the file last modified timestamp in Unix time (i.e. milliseconds since J
     """)
     void append(String text);
 
-    @Description("""
-        Writes a byte array to a file. Equivalent to setting the `bytes` property.
-    """)
-    void setBytes(byte[] bytes);
-
     @Description("""
         Writes text to a file. Equivalent to setting the `text` property.
     """)
@@ -202,16 +186,6 @@ Returns the file last modified timestamp in Unix time (i.e. milliseconds since J
     """)
     String getPermissions();
 
-    @Description("""
-        Returns the first-level elements (files and directories) of a directory as a list of strings.
-    """)
-    List<String> list();
-
-    @Description("""
-        Returns the first-level elements (files and directories) of a directory as a list of Paths.
-    """)
-    List<Path> listFiles();
-
     @Description("""
         Creates a directory at the given path, returning `true` if the directory is created successfully, and `false` otherwise.
     """)
@@ -247,35 +221,28 @@ Returns the file last modified timestamp in Unix time (i.e. milliseconds since J
     """)
     boolean setPermissions(int owner, int group, int other);
 
-    @Description("""
-        Iterates through first-level directories only.
-    """)
-    void eachDir(Consumer<Path> action);
-
-    @Description("""
-        Iterates through directories whose names match the given filter.
-    """)
-    void eachDirMatch(String nameFilter, Consumer<Path> action);
+    // listing and traversing directories
 
     @Description("""
-        Iterates through directories depth-first (regular files are ignored).
+        Iterates through first-level files and directories.
     """)
-    void eachDirRecurse(Consumer<Path> action);
+    void eachFile(Consumer<Path> action);
 
     @Description("""
-        Iterates through first-level files and directories.
+        Iterates through files and directories depth-first.
     """)
-    void eachFile(Consumer<Path> action);
+    void eachFileRecurse(Consumer<Path> action);
 
     @Description("""
-        Iterates through files and directories whose names match the given filter.
+        Returns the first-level elements (files and directories) in a directory.
     """)
-    void eachFileMatch(String nameFilter, Consumer<Path> action);
+    List<Path> listDirectory();
 
+    @Deprecated
     @Description("""
-        Iterates through files and directories depth-first.
+        Returns the first-level elements (files and directories) in a directory.
     """)
-    void eachFileRecurse(Consumer<Path> action);
+    List<Path> listFiles();
 
     // splitting