patch: add workdir option (#5501)

* patch: add working_dir option
* added documentation

lib/spack/docs/packaging_guide.rst

@@ -1304,6 +1304,36 @@ It's generally easier to just structure your patch file so that it
 applies cleanly with ``-p1``, but if you're using a patch you didn't
 create yourself, ``level`` can be handy.
 
+"""""""""""""""
+``working_dir``
+"""""""""""""""
+
+This tells spack where to run the ``patch`` command.  By default,
+the working directory is the source path of the stage (``.``).
+However, sometimes patches are made with respect to a subdirectory
+and this is where the working directory comes in handy. Internally,
+the working directory is given to ``patch`` via the ``-d`` option.
+Let's take the example patch from above and assume for some reason,
+it can only be downloaded in the following form:
+
+.. code-block:: diff
+   :linenos:
+
+   --- a/romio/adio/ad_lustre/ad_lustre_rwcontig.c 2013-12-10 12:05:44.806417000 -0800
+   +++ b/romio/adio/ad_lustre/ad_lustre_rwcontig.c 2013-12-10 11:53:03.295622000 -0800
+   @@ -8,7 +8,7 @@
+     *   Copyright (C) 2008 Sun Microsystems, Lustre group
+     \*/
+
+   -#define _XOPEN_SOURCE 600
+   +//#define _XOPEN_SOURCE 600
+    #include <stdlib.h>
+    #include <malloc.h>
+    #include "ad_lustre.h"
+
+Hence, the patch needs to applied in the ``src/mpi`` subdirectory, and the
+``working_dir='src/mpi'`` option would exactly do that.
+
 ^^^^^^^^^^^^^^^^^^^^^
 Patch functions
 ^^^^^^^^^^^^^^^^^^^^^

lib/spack/spack/directives.py

@@ -410,7 +410,7 @@ def _execute_provides(pkg):
 
 
 @directive('patches')
-def patch(url_or_filename, level=1, when=None, **kwargs):
+def patch(url_or_filename, level=1, when=None, working_dir=".", **kwargs):
     """Packages can declare patches to apply to source.  You can
     optionally provide a when spec to indicate that a particular
     patch should only be applied when the package's spec meets
@@ -421,6 +421,7 @@ def patch(url_or_filename, level=1, when=None, **kwargs):
         level (int): patch level (as in the patch shell command)
         when (Spec): optional anonymous spec that specifies when to apply
             the patch
+        working_dir (str): dir to change to before applying
 
     Keyword Args:
         sha256 (str): sha256 sum of the patch, used to verify the patch
@@ -437,7 +438,8 @@ def _execute_patch(pkg_or_dep):
         # patch to the existing list.
         cur_patches = pkg_or_dep.patches.setdefault(when_spec, [])
         cur_patches.append(
-            Patch.create(pkg_or_dep, url_or_filename, level, **kwargs))
+            Patch.create(pkg_or_dep, url_or_filename, level,
+                         working_dir, **kwargs))
 
     return _execute_patch
 

lib/spack/spack/patch.py

@@ -56,7 +56,7 @@ class Patch(object):
     """
 
     @staticmethod
-    def create(pkg, path_or_url, level=1, **kwargs):
+    def create(pkg, path_or_url, level=1, working_dir=".", **kwargs):
         """
         Factory method that creates an instance of some class derived from
         Patch
@@ -65,23 +65,25 @@ def create(pkg, path_or_url, level=1, **kwargs):
             pkg: package that needs to be patched
             path_or_url: path or url where the patch is found
             level: patch level (default 1)
+            working_dir (str): dir to change to before applying (default '.')
 
         Returns:
             instance of some Patch class
         """
         # Check if we are dealing with a URL
         if '://' in path_or_url:
-            return UrlPatch(path_or_url, level, **kwargs)
+            return UrlPatch(path_or_url, level, working_dir, **kwargs)
         # Assume patches are stored in the repository
-        return FilePatch(pkg, path_or_url, level)
+        return FilePatch(pkg, path_or_url, level, working_dir)
 
-    def __init__(self, path_or_url, level):
+    def __init__(self, path_or_url, level, working_dir):
         # Check on level (must be an integer > 0)
         if not isinstance(level, int) or not level >= 0:
             raise ValueError("Patch level needs to be a non-negative integer.")
         # Attributes shared by all patch subclasses
         self.path_or_url = path_or_url
         self.level = level
+        self.working_dir = working_dir
         # self.path needs to be computed by derived classes
         # before a call to apply
         self.path = None
@@ -99,13 +101,14 @@ def apply(self, stage):
         patch = which("patch", required=True)
         with working_dir(stage.source_path):
             # Use -N to allow the same patches to be applied multiple times.
-            patch('-s', '-p', str(self.level), '-i', self.path)
+            patch('-s', '-p', str(self.level), '-i', self.path,
+                  "-d", self.working_dir)
 
 
 class FilePatch(Patch):
     """Describes a patch that is retrieved from a file in the repository"""
-    def __init__(self, pkg, path_or_url, level):
-        super(FilePatch, self).__init__(path_or_url, level)
+    def __init__(self, pkg, path_or_url, level, working_dir):
+        super(FilePatch, self).__init__(path_or_url, level, working_dir)
 
         pkg_dir = os.path.dirname(absolute_path_for_package(pkg))
         self.path = os.path.join(pkg_dir, path_or_url)
@@ -123,8 +126,8 @@ def sha256(self):
 
 class UrlPatch(Patch):
     """Describes a patch that is retrieved from a URL"""
-    def __init__(self, path_or_url, level, **kwargs):
-        super(UrlPatch, self).__init__(path_or_url, level)
+    def __init__(self, path_or_url, level, working_dir, **kwargs):
+        super(UrlPatch, self).__init__(path_or_url, level, working_dir)
         self.url = path_or_url
 
         self.archive_sha256 = None