Merge pull request #3067 from akesandgren/handle_patches_in_extensions_better

Handle patches in extensions more like normal patches.

Author: boegel

easybuild/framework/easyblock.py

@@ -453,8 +453,8 @@ def fetch_patches(self, patch_specs=None, extension=False, checksums=None):
                 raise EasyBuildError('No file found for patch %s', patch_spec)
 
         if extension:
-            self.log.info("Fetched extension patches: %s" % patches)
-            return [patch['path'] for patch in patches]
+            self.log.info("Fetched extension patches: %s", patches)
+            return patches
         else:
             self.log.info("Added patches: %s" % self.patches)
 
@@ -544,6 +544,7 @@ def fetch_extension_sources(self, skip_checksums=False):
 
                                 if not skip_checksums:
                                     for patch in ext_patches:
+                                        patch = patch['path']
                                         # report both MD5 and SHA256 checksums,
                                         # since both are valid default checksum types
                                         for checksum_type in (CHECKSUM_TYPE_MD5, CHECKSUM_TYPE_SHA256):
@@ -553,6 +554,7 @@ def fetch_extension_sources(self, skip_checksums=False):
                                     # verify checksum (if provided)
                                     self.log.debug('Verifying checksums for extension patches...')
                                     for idx, patch in enumerate(ext_patches):
+                                        patch = patch['path']
                                         checksum = self.get_checksum_for(checksums[1:], filename=patch, index=idx)
                                         if verify_checksum(patch, checksum):
                                             self.log.info('Checksum for extension patch %s verified', patch)
@@ -3484,8 +3486,8 @@ def make_checksum_lines(checksums, indent_level):
                         print_msg(" * %s: %s" % (src_fn, checksum), log=_log)
                         ext_checksums.append((src_fn, checksum))
                     for ext_patch in ext.get('patches', []):
-                        patch_fn = os.path.basename(ext_patch)
-                        checksum = compute_checksum(ext_patch, checksum_type)
+                        patch_fn = os.path.basename(ext_patch['path'])
+                        checksum = compute_checksum(ext_patch['path'], checksum_type)
                         print_msg(" * %s: %s" % (patch_fn, checksum), log=_log)
                         ext_checksums.append((patch_fn, checksum))
 

easybuild/framework/extensioneasyblock.py

@@ -32,7 +32,7 @@
 from easybuild.framework.easyconfig import CUSTOM
 from easybuild.framework.extension import Extension
 from easybuild.tools.build_log import EasyBuildError
-from easybuild.tools.filetools import apply_patch, change_dir, extract_file
+from easybuild.tools.filetools import change_dir, extract_file
 from easybuild.tools.utilities import remove_unwanted_chars, trace_msg
 
 
@@ -110,10 +110,7 @@ def run(self, unpack_src=False):
                 change_dir(self.start_dir)
 
         # patch if needed
-        if self.patches:
-            for patchfile in self.patches:
-                if not apply_patch(patchfile, self.ext_dir):
-                    raise EasyBuildError("Applying patch %s failed", patchfile)
+        EasyBlock.patch_step(self, beginpath=self.ext_dir)
 
     def sanity_check_step(self, exts_filter=None, custom_paths=None, custom_commands=None):
         """

test/framework/easyconfig.py

@@ -463,7 +463,10 @@ def test_extensions_templates(self):
         # check whether template values were resolved correctly in Extension instances that were created/used
         toy_ext = eb.ext_instances[0]
         self.assertEqual(os.path.basename(toy_ext.src), 'toy-0.0-py3-test.tar.gz')
-        self.assertEqual(toy_ext.patches, [os.path.join(self.test_prefix, toy_patch_fn)])
+        patches = []
+        for patch in toy_ext.patches:
+            patches.append(patch['path'])
+        self.assertEqual(patches, [os.path.join(self.test_prefix, toy_patch_fn)])
         expected = {
             'patches': ['toy-0.0_fix-silly-typo-in-printf-statement.patch'],
             'prebuildopts': 'gcc -O2 toy.c -o toy-0.0 && mv toy-0.0 toy #',

test/framework/toy_build.py

@@ -1132,6 +1132,33 @@ def test_toy_patches(self):
         archived_patch_file = os.path.join(repositorypath, 'toy', 'toy-0.0_fix-silly-typo-in-printf-statement.patch')
         self.assertTrue(os.path.isfile(archived_patch_file))
 
+    def test_toy_extension_patches(self):
+        """Test install toy that includes extensions with patches."""
+        test_ecs = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs', 'test_ecs')
+        toy_ec = os.path.join(test_ecs, 't', 'toy', 'toy-0.0.eb')
+        toy_ec_txt = read_file(toy_ec)
+
+        # create file that we'll copy via 'patches'
+        write_file(os.path.join(self.test_prefix, 'test.txt'), 'test123')
+
+        test_ec = os.path.join(self.test_prefix, 'test.eb')
+        test_ec_txt = '\n'.join([
+            toy_ec_txt,
+            'exts_list = [',
+            '   ("bar", "0.0", {',
+            '       "buildopts": " && ls -l test.txt",',
+            '       "patches": [',
+            '           "bar-0.0_fix-silly-typo-in-printf-statement.patch",',  # normal patch
+            '           ("bar-0.0_fix-very-silly-typo-in-printf-statement.patch", 0),',  # patch with patch level
+            '           ("test.txt", "."),',  # file to copy to build dir (not a real patch file)
+            '       ],',
+            '   }),',
+            ']',
+        ])
+        write_file(test_ec, test_ec_txt)
+
+        self.test_toy_build(ec_file=test_ec)
+
     def test_toy_module_fulltxt(self):
         """Strict text comparison of generated module file."""
         self.test_toy_tweaked()