Merge pull request #3974 from boegel/post_install_patches

add support for post-install patches

Author: lexming

easybuild/framework/easyblock.py

@@ -454,13 +454,17 @@ def fetch_patches(self, patch_specs=None, extension=False, checksums=None):
         Add a list of patches.
         All patches will be checked if a file exists (or can be located)
         """
+        post_install_patches = []
         if patch_specs is None:
-            patch_specs = self.cfg['patches']
+            # if no patch_specs are specified, use all pre-install and post-install patches
+            post_install_patches = self.cfg['postinstallpatches']
+            patch_specs = self.cfg['patches'] + post_install_patches
 
         patches = []
         for index, patch_spec in enumerate(patch_specs):
 
             patch_info = create_patch_info(patch_spec)
+            patch_info['postinstall'] = patch_spec in post_install_patches
 
             force_download = build_option('force_download') in [FORCE_DOWNLOAD_ALL, FORCE_DOWNLOAD_PATCHES]
             path = self.obtain_file(patch_info['name'], extension=extension, force_download=force_download)
@@ -2230,7 +2234,7 @@ def fetch_step(self, skip_checksums=False):
             self.dry_run_msg("\nList of patches:")
 
         # fetch patches
-        if self.cfg['patches']:
+        if self.cfg['patches'] + self.cfg['postinstallpatches']:
             if isinstance(self.cfg['checksums'], (list, tuple)):
                 # if checksums are provided as a list, first entries are assumed to be for sources
                 patches_checksums = self.cfg['checksums'][len(self.cfg['sources']):]
@@ -2402,11 +2406,15 @@ def extract_step(self):
             else:
                 raise EasyBuildError("Unpacking source %s failed", src['name'])
 
-    def patch_step(self, beginpath=None):
+    def patch_step(self, beginpath=None, patches=None):
         """
         Apply the patches
         """
-        for patch in self.patches:
+        if patches is None:
+            # if no patches are specified, use all non-post-install patches
+            patches = [p for p in self.patches if not p['postinstall']]
+
+        for patch in patches:
             self.log.info("Applying patch %s" % patch['name'])
             trace_msg("applying patch %s" % patch['name'])
 
@@ -2821,13 +2829,25 @@ def run_post_install_commands(self, commands=None):
                     raise EasyBuildError("Invalid element in 'postinstallcmds', not a string: %s", cmd)
                 run_cmd(cmd, simple=True, log_ok=True, log_all=True)
 
+    def apply_post_install_patches(self, patches=None):
+        """
+        Apply post-install patch files that are specified via the 'postinstallpatches' easyconfig parameter.
+        """
+        if patches is None:
+            patches = [p for p in self.patches if p['postinstall']]
+
+        self.log.debug("Post-install patches to apply: %s", patches)
+        if patches:
+            self.patch_step(beginpath=self.installdir, patches=patches)
+
     def post_install_step(self):
         """
         Do some postprocessing
         - run post install commands if any were specified
         """
 
         self.run_post_install_commands()
+        self.apply_post_install_patches()
 
         self.fix_shebang()
 

easybuild/framework/easyconfig/default.py

@@ -114,6 +114,7 @@
     'preinstallopts': ['', 'Extra prefix options for installation.', BUILD],
     'pretestopts': ['', 'Extra prefix options for test.', BUILD],
     'postinstallcmds': [[], 'Commands to run after the install step.', BUILD],
+    'postinstallpatches': [[], 'Patch files to apply after running the install step.', BUILD],
     'required_linked_shared_libs': [[], "List of shared libraries (names, file names, or paths) which must be "
                                         "linked in all installed binaries/libraries", BUILD],
     'runtest': [None, ('Indicates if a test should be run after make; should specify argument '

test/framework/sandbox/sources/toy/toy-0.0_fix-README.patch

@@ -0,0 +1,5 @@
+--- README.old	2022-03-01 14:28:43.000000000 +0100
++++ README	2022-03-01 14:29:01.000000000 +0100
+@@ -1 +1 @@
+-TOY
++toy 0.0, a toy test program

test/framework/toy_build.py

@@ -3721,6 +3721,25 @@ def test_toy_ignore_test_failure(self):
         self.assertTrue("Build succeeded (with --ignore-test-failure) for 1 out of 1" in stdout)
         self.assertFalse(stderr)
 
+    def test_toy_post_install_patches(self):
+        """
+        Test use of post-install patches
+        """
+        test_ecs = os.path.join(os.path.dirname(__file__), 'easyconfigs', 'test_ecs')
+        toy_ec = os.path.join(test_ecs, 't', 'toy', 'toy-0.0.eb')
+
+        test_ec_txt = read_file(toy_ec)
+        test_ec_txt += "\npostinstallpatches = ['toy-0.0_fix-README.patch']"
+        test_ec = os.path.join(self.test_prefix, 'test.eb')
+        write_file(test_ec, test_ec_txt)
+
+        self.test_toy_build(ec_file=test_ec)
+
+        toy_installdir = os.path.join(self.test_installpath, 'software', 'toy', '0.0')
+        toy_readme_txt = read_file(os.path.join(toy_installdir, 'README'))
+        # verify whether patch indeed got applied
+        self.assertEqual(toy_readme_txt, "toy 0.0, a toy test program\n")
+
 
 def suite():
     """ return all the tests in this file """