show readable error message when applying patch without (extracted) source

easybuild/framework/easyblock.py

@@ -2607,25 +2607,29 @@ def patch_step(self, beginpath=None, patches=None):
             self.log.info("Applying patch %s" % patch['name'])
             trace_msg("applying patch %s" % patch['name'])
 
-            # patch source at specified index (first source if not specified)
-            srcind = patch.get('source', 0)
             # if patch level is specified, use that (otherwise let apply_patch derive patch level)
             level = patch.get('level', None)
             # determine suffix of source path to apply patch in (if any)
             srcpathsuffix = patch.get('sourcepath', patch.get('copy', ''))
             # determine whether 'patch' file should be copied rather than applied
             copy_patch = 'copy' in patch and 'sourcepath' not in patch
 
-            self.log.debug("Source index: %s; patch level: %s; source path suffix: %s; copy patch: %s",
-                           srcind, level, srcpathsuffix, copy_patch)
+            self.log.debug("Patch level: %s; source path suffix: %s; copy patch: %s",
+                           level, srcpathsuffix, copy_patch)
 
             if beginpath is None:
-                try:
-                    beginpath = self.src[srcind]['finalpath']
-                    self.log.debug("Determine begin path for patch %s: %s" % (patch['name'], beginpath))
-                except IndexError as err:
-                    raise EasyBuildError("Can't apply patch %s to source at index %s of list %s: %s",
-                                         patch['name'], srcind, self.src, err)
+                # If the src member is a string we have an extension with a single source.
+                # If that did extract the source beginpath would be set.
+                if isinstance(self.src, str):
+                    raise EasyBuildError("Cannot apply patches if sources were not extracted. "
+                                         "Patch file: " + patch['name'])
+                if self.src:
+                    # Use (extracted) location of first source.
+                    # Other sources will likely not have a reasonable finalpath set.
+                    beginpath = self.src[0]['finalpath']
+                    self.log.debug("Determined begin path for patch %s: %s" % (patch['name'], beginpath))
+                else:
+                    raise EasyBuildError("Can't apply patch %s when there are no sources!", patch['name'])
             else:
                 self.log.debug("Using specified begin path for patch %s: %s" % (patch['name'], beginpath))
 

test/framework/easyblock.py

@@ -2020,26 +2020,30 @@ def test_exclude_path_to_top_of_module_tree(self):
 
     def test_patch_step(self):
         """Test patch step."""
-        test_easyconfigs = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'easyconfigs', 'test_ecs')
-        ec = process_easyconfig(os.path.join(test_easyconfigs, 't', 'toy', 'toy-0.0.eb'))[0]
-        orig_sources = ec['ec']['sources'][:]
+        cwd = os.getcwd()
+
+        testdir = os.path.abspath(os.path.dirname(__file__))
+        test_easyconfigs = os.path.join(testdir, 'easyconfigs', 'test_ecs')
+        ec = process_easyconfig(os.path.join(test_easyconfigs, 't', 'toy', 'toy-0.0.eb'))[0]['ec']
+        orig_sources = ec['sources'][:]
 
         toy_patches = [
             'toy-0.0_fix-silly-typo-in-printf-statement.patch',  # test for applying patch
             ('toy-extra.txt', 'toy-0.0'),  # test for patch-by-copy
         ]
-        self.assertEqual(ec['ec']['patches'], toy_patches)
+        self.assertEqual(ec['patches'], toy_patches)
 
         # test applying patches without sources
-        ec['ec']['sources'] = []
-        eb = EasyBlock(ec['ec'])
+        ec['sources'] = []
+        eb = EasyBlock(ec)
         eb.fetch_step()
         eb.extract_step()
         self.assertErrorRegex(EasyBuildError, '.*', eb.patch_step)
 
         # test actual patching of unpacked sources
-        ec['ec']['sources'] = orig_sources
-        eb = EasyBlock(ec['ec'])
+        ec['sources'] = orig_sources
+        change_dir(cwd)
+        eb = EasyBlock(ec)
         eb.fetch_step()
         eb.extract_step()
         eb.patch_step()
@@ -2051,7 +2055,8 @@ def test_patch_step(self):
 
         # check again with backup of patched files enabled
         update_build_option('backup_patched_files', True)
-        eb = EasyBlock(ec['ec'])
+        change_dir(cwd)
+        eb = EasyBlock(ec)
         eb.fetch_step()
         eb.extract_step()
         eb.patch_step()
@@ -2299,6 +2304,66 @@ def check_ext_start_dir(expected_start_dir, unpack_src=True, parent_startdir=Non
             check_ext_start_dir(self.test_prefix, parent_startdir=self.test_prefix)
             self.assertFalse(self.get_stderr())
 
+    def test_extension_patch_step(self):
+        """Test start dir with extensions."""
+        test_easyconfigs = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'easyconfigs', 'test_ecs')
+        ec = process_easyconfig(os.path.join(test_easyconfigs, 't', 'toy', 'toy-0.0.eb'))[0]['ec']
+
+        cwd = os.getcwd()
+        self.assertExists(cwd)
+
+        def run_extension_step():
+            change_dir(cwd)
+            eb = EasyBlock(ec)
+            # Cleanup build directory
+            if os.path.exists(eb.builddir):
+                remove_dir(eb.builddir)
+            eb.make_builddir()
+            eb.update_config_template_run_step()
+            eb.extensions_step(fetch=True, install=True)
+            return os.path.join(eb.builddir)
+
+        ec['exts_defaultclass'] = 'DummyExtension'
+        ec['exts_list'] = [('toy', '0.0', {'easyblock': 'DummyExtension'})]
+
+        # No patches, no errors
+        with self.mocked_stdout_stderr():
+            run_extension_step()
+            self.assertFalse(self.get_stderr())
+
+        # Patch present, source extracted
+        with ec.disable_templating():
+            ec['exts_list'][0][2]['patches'] = [('toy-extra.txt', 'toy-0.0')]
+            ec['exts_list'][0][2]['unpack_source'] = True
+        with self.mocked_stdout_stderr():
+            builddir = run_extension_step()
+            self.assertTrue(os.path.isfile(os.path.join(builddir, 'toy', 'toy-0.0', 'toy-extra.txt')))
+            self.assertFalse(self.get_stderr())
+
+        # Patch but source not extracted
+        with ec.disable_templating():
+            ec['exts_list'][0][2]['unpack_source'] = False
+        with self.mocked_stdout_stderr():
+            self.assertErrorRegex(EasyBuildError, 'not extracted', run_extension_step)
+            self.assertFalse(self.get_stderr())
+
+        # Patch but no source
+        with ec.disable_templating():
+            ec['exts_list'][0][2]['nosource'] = True
+        with self.mocked_stdout_stderr():
+            self.assertErrorRegex(EasyBuildError, 'no sources', run_extension_step)
+            self.assertFalse(self.get_stderr())
+
+        # Patch without source is possible if the start_dir is set
+        with ec.disable_templating():
+            ec['start_dir'] = '%(builddir)s'
+            ec['exts_list'][0][2]['nosource'] = True
+            ec['exts_list'][0][2]['patches'] = [('toy-extra.txt', '.')]
+        with self.mocked_stdout_stderr():
+            builddir = run_extension_step()
+            self.assertTrue(os.path.isfile(os.path.join(builddir, 'toy-extra.txt')))
+            self.assertFalse(self.get_stderr())
+
     def test_prepare_step(self):
         """Test prepare step (setting up build environment)."""
         test_easyconfigs = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'easyconfigs', 'test_ecs')

test/framework/sandbox/easybuild/easyblocks/generic/dummyextension.py

@@ -28,16 +28,32 @@
 @author: Kenneth Hoste (Ghent University)
 """
 
+from easybuild.framework.easyconfig import CUSTOM
 from easybuild.framework.extensioneasyblock import ExtensionEasyBlock
 
 
 class DummyExtension(ExtensionEasyBlock):
     """Support for building/installing dummy extensions."""
 
+    @staticmethod
+    def extra_options():
+        """Custom easyconfig parameters for dummy extensions."""
+        extra_vars = {
+            'unpack_source': [None, "Unpack sources", CUSTOM],
+        }
+        return ExtensionEasyBlock.extra_options(extra_vars=extra_vars)
+
     def __init__(self, *args, **kwargs):
 
         super(DummyExtension, self).__init__(*args, **kwargs)
 
         # use lowercase name as default value for expected module name, and replace '-' with '_'
         if 'modulename' not in self.options:
             self.options['modulename'] = self.name.lower().replace('-', '_')
+
+    def run(self, unpack_src=False):
+        """Install the dummy extension."""
+        ec_unpack_source = self.cfg.get('unpack_source')
+        if ec_unpack_source is not None:
+            unpack_src = ec_unpack_source
+        super(DummyExtension, self).run(unpack_src)