in util.version.py::get_project_path(), consider calling modules (#109)

When derived modules (i.e. viral-classify) are symlinked into viral-core and their versions are read from a VERSION file, only the path to the viral-core version file was used. This changes that behavior, so outer members of the call stack are checked for the presence of VERSION files as well (and if found, the version is read from the first/outermost one found).

(i.e. when calling ./taxon-filter.py --version, with these changes, the version of viral-classify is correctly returned rather than the version of viral-core)

Since this relies on the presence of a VERSION file to find the current "project path", this will fall back to the old behavior if viral-core has a VERSION file and a derived module lacks such a file.

This does not change the behavior where a version file will not be created for a derived module when calling `./symlinked_derived_module.py --version`

Author: tomkinsc

util/version.py

@@ -5,23 +5,57 @@
 __author__ = "dpark@broadinstitute.org"
 __version__ = None
 
+# import built-in
 import subprocess
 import os
 import re
 import time, datetime
 import os.path
+import inspect
+
+# module-level imports
 import util.misc
 
 
-def get_project_path():
-    '''Return the absolute path of the top-level project, assumed to be the
-       parent of the directory containing this script.'''
-    # abspath converts relative to absolute path; expanduser interprets ~
-    path = __file__  # path to this script
+def get_project_path(include_derived_modules=True):
+    '''Return the absolute path of the top-level project,
+       if include_derived_modules==False:
+           path is assumed to be the parent of the directory containing this script.'''
+
+    # obtain path to this script (i.e. the script you're currently reading)
+    path = __file__
+
     path = os.path.expanduser(path)  # interpret ~
-    path = os.path.abspath(path)  # convert to absolute path
+    path = os.path.abspath(path)  # abspath converts relative to absolute path
+
     path = os.path.dirname(path)  # containing directory: util
     path = os.path.dirname(path)  # containing directory: main project dir
+
+    # If we want to be more careful, look at derived Python
+    # modules calling this one, look for a VERSION file to
+    # determine validity of the various containing directories
+    if include_derived_modules:
+        '''
+            find a VERSION file relative to scripts in the Python call stack,
+            looking from the outermost layer (closest to initial invocation)
+            to the innermost call, and use the path of the first VERSION file found.
+
+            This allows a derived module with its own VERSION file
+            to report its versions rather than the core version.
+
+            This falls back to using/finding the core path
+        '''
+        for called_item in inspect.stack()[::-1]:
+           # resolve symlinks so the project_path is relative to the actual location of the invoked script
+           # (i.e. taxon_filter.py --version should resolve viral-classify/VERSION, not viral-core/VERSION)
+            called_item_realpath        = os.path.realpath(called_item.filename)
+            dir_containing_called_item  = os.path.dirname(called_item_realpath)
+            potential_version_file_path = f"{dir_containing_called_item}/VERSION"
+
+            if os.path.isfile(potential_version_file_path):
+                path = dir_containing_called_item
+                break
+
     return path
 
 
@@ -42,7 +76,6 @@ def call_git_describe():
     os.chdir(cwd)
     return ver
 
-
 def release_file():
     return os.path.join(get_project_path(), 'VERSION')