don't add directory that doesn't include any files to $PATH or $LD_LIBRARY_PATH

easybuild/framework/easyblock.py

@@ -93,7 +93,7 @@
 from easybuild.tools.py2vs3 import extract_method_name, string_type
 from easybuild.tools.repository.repository import init_repository
 from easybuild.tools.systemtools import check_linked_shared_libs, det_parallelism, get_shared_lib_ext, use_group
-from easybuild.tools.utilities import INDENT_4SPACES, get_class_for, quote_str
+from easybuild.tools.utilities import INDENT_4SPACES, get_class_for, nub, quote_str
 from easybuild.tools.utilities import remove_unwanted_chars, time2str, trace_msg
 from easybuild.tools.version import this_is_easybuild, VERBOSE_VERSION, VERSION
 
@@ -1429,9 +1429,17 @@ def make_module_req(self):
             note += "for paths are skipped for the statements below due to dry run"
             lines.append(self.module_generator.comment(note))
 
-        # for these environment variables, the corresponding subdirectory must include at least one file
-        keys_requiring_files = set(('PATH', 'LD_LIBRARY_PATH', 'LIBRARY_PATH', 'CPATH',
-                                    'CMAKE_PREFIX_PATH', 'CMAKE_LIBRARY_PATH'))
+        # For these environment variables, the corresponding directory must include at least one file.
+        # The values determine if detection is done recursively, i.e. if it accepts directories where files
+        # are only in subdirectories.
+        keys_requiring_files = {
+            'PATH': False,
+            'LD_LIBRARY_PATH': False,
+            'LIBRARY_PATH': True,
+            'CPATH': True,
+            'CMAKE_PREFIX_PATH': True,
+            'CMAKE_LIBRARY_PATH': True,
+        }
 
         for key, reqs in sorted(requirements.items()):
             if isinstance(reqs, string_type):
@@ -1461,19 +1469,16 @@ def make_module_req(self):
                     if fixed_paths != paths:
                         self.log.info("Fixed symlink lib64 in paths for %s: %s -> %s", key, paths, fixed_paths)
                         paths = fixed_paths
-                # remove duplicate paths
-                # don't use 'set' here, since order in 'paths' is important!
-                uniq_paths = []
-                for path in paths:
-                    if path not in uniq_paths:
-                        uniq_paths.append(path)
-                paths = uniq_paths
+                # remove duplicate paths preserving order
+                paths = nub(paths)
                 if key in keys_requiring_files:
                     # only retain paths that contain at least one file
+                    recursive = keys_requiring_files[key]
                     retained_paths = [
-                        path for path in paths
-                        if os.path.isdir(os.path.join(self.installdir, path))
-                        and dir_contains_files(os.path.join(self.installdir, path))
+                        path
+                        for path, fullpath in ((path, os.path.join(self.installdir, path)) for path in paths)
+                        if os.path.isdir(fullpath)
+                        and dir_contains_files(fullpath, recursive=recursive)
                     ]
                     if retained_paths != paths:
                         self.log.info("Only retaining paths for %s that contain at least one file: %s -> %s",

easybuild/tools/filetools.py

@@ -1096,9 +1096,16 @@ def search_file(paths, query, short=False, ignore_dirs=None, silent=False, filen
     return var_defs, hits
 
 
-def dir_contains_files(path):
-    """Return True if the given directory does contain any file in itself or any subdirectory"""
-    return any(files for _root, _dirs, files in os.walk(path))
+def dir_contains_files(path, recursive=True):
+    """
+    Return True if the given directory does contain any file
+
+    :recursive If False only the path itself is considered, else all subdirectories are also searched
+    """
+    if recursive:
+        return any(files for _root, _dirs, files in os.walk(path))
+    else:
+        return any(os.path.isfile(os.path.join(path, x)) for x in os.listdir(path))
 
 
 def find_eb_script(script_name):

test/framework/easyblock.py

@@ -551,6 +551,25 @@ def test_make_module_req(self):
         else:
             self.assertTrue(False, "Unknown module syntax: %s" % get_module_syntax())
 
+        # If PATH or LD_LIBRARY_PATH contain only folders, do not add an entry
+        sub_lib_path = os.path.join('lib', 'path_folders')
+        sub_path_path = os.path.join('bin', 'path_folders')
+        eb.make_module_req_guess = lambda: {'LD_LIBRARY_PATH': sub_lib_path, 'PATH': sub_path_path}
+        for path in (sub_lib_path, sub_path_path):
+            full_path = os.path.join(eb.installdir, path, 'subpath')
+            os.makedirs(full_path)
+            write_file(os.path.join(full_path, 'any.file'), 'test')
+        txt = eb.make_module_req()
+        if get_module_syntax() == 'Tcl':
+            self.assertFalse(re.search(r"prepend-path\s+LD_LIBRARY_PATH\s+\$%s\n" % sub_lib_path,
+                                       txt, re.M))
+            self.assertFalse(re.search(r"prepend-path\s+PATH\s+\$%s\n" % sub_path_path, txt, re.M))
+        else:
+            assert get_module_syntax() == 'Lua'
+            self.assertFalse(re.search(r'prepend_path\("LD_LIBRARY_PATH", pathJoin\(root, "%s"\)\)\n' % sub_lib_path,
+                                       txt, re.M))
+            self.assertFalse(re.search(r'prepend_path\("PATH", pathJoin\(root, "%s"\)\)\n' % sub_path_path, txt, re.M))
+
         # cleanup
         eb.close_log()
         os.remove(eb.logfile)

test/framework/filetools.py

@@ -2330,21 +2330,26 @@ def makedirs_in_test(*paths):
 
         empty_dir = makedirs_in_test('empty_dir')
         self.assertFalse(ft.dir_contains_files(empty_dir))
+        self.assertFalse(ft.dir_contains_files(empty_dir, recursive=False))
 
         dir_w_subdir = makedirs_in_test('dir_w_subdir', 'sub_dir')
         self.assertFalse(ft.dir_contains_files(dir_w_subdir))
+        self.assertFalse(ft.dir_contains_files(dir_w_subdir, recursive=False))
 
         dir_subdir_file = makedirs_in_test('dir_subdir_file', 'sub_dir_w_file')
         ft.write_file(os.path.join(dir_subdir_file, 'sub_dir_w_file', 'file.h'), '')
         self.assertTrue(ft.dir_contains_files(dir_subdir_file))
+        self.assertFalse(ft.dir_contains_files(dir_subdir_file, recursive=False))
 
         dir_w_file = makedirs_in_test('dir_w_file')
         ft.write_file(os.path.join(dir_w_file, 'file.h'), '')
         self.assertTrue(ft.dir_contains_files(dir_w_file))
+        self.assertTrue(ft.dir_contains_files(dir_w_file, recursive=False))
 
         dir_w_dir_and_file = makedirs_in_test('dir_w_dir_and_file', 'sub_dir')
         ft.write_file(os.path.join(dir_w_dir_and_file, 'file.h'), '')
         self.assertTrue(ft.dir_contains_files(dir_w_dir_and_file))
+        self.assertTrue(ft.dir_contains_files(dir_w_dir_and_file, recursive=False))
 
     def test_find_eb_script(self):
         """Test find_eb_script function."""