Globals fix (#35)

* replaced globals() with a dictionary * increment version * --version only outputs version number
FowlerLab · Apr 7, 2020 · a9c8165 · a9c8165
1 parent b663d79
commit a9c8165
Show file tree

Hide file tree

Showing 7 changed files with 83 additions and 16 deletions.
diff --git a/docs/conf.py b/docs/conf.py
@@ -53,7 +53,7 @@
 # The short X.Y version.
 version = '1.3'
 # The full version, including alpha/beta/rc tags.
-release = '1.3.0'
+release = '1.3.1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/enrich2/gui/configurator.py b/enrich2/gui/configurator.py
@@ -15,11 +15,27 @@
 from ..experiment import Experiment
 from ..condition import Condition
 from ..selection import Selection
+from ..barcode import BarcodeSeqLib
+from ..barcodevariant import BcvSeqLib
+from ..barcodeid import BcidSeqLib
+from ..basic import BasicSeqLib
+from ..idonly import IdOnlySeqLib
 from ..overlap import OverlapSeqLib
 from ..seqlib import SeqLib
 from ..storemanager import SCORING_METHODS, LOGR_METHODS
 
 
+#: map class names to class definitions to avoid use of globals()
+SEQLIB_CLASSES = {
+    "BarcodeSeqLib": BarcodeSeqLib,
+    "BcvSeqLib": BcvSeqLib,
+    "BcidSeqLib": BcidSeqLib,
+    "BasicSeqLib": BasicSeqLib,
+    "IdOnlySeqLib": IdOnlySeqLib,
+    "OverlapSeqLib": OverlapSeqLib,
+}
+
+
 def write_json(d, handle):
     """
     Write the contents of dictionary *d* to an open file *handle* in json format.
@@ -358,8 +374,7 @@ def menu_open(self):
                 elif is_selection(cfg):
                     obj = Selection()
                 elif is_seqlib(cfg):
-                    sltype = seqlib_type(cfg)
-                    obj = globals()[sltype]()
+                    obj = SEQLIB_CLASSES[seqlib_type(cfg)]()
                 else:
                     tkMessageBox.showerror(None, "Unrecognized config format.")
                     return

diff --git a/enrich2/gui/create_root_dialog.py b/enrich2/gui/create_root_dialog.py
@@ -3,7 +3,28 @@
 import ttk
 import tkSimpleDialog
 from .dialog_elements import FileEntry, StringEntry, DEFAULT_COLUMNS
-from .create_seqlib_dialog import seqlib_label_text
+from .create_seqlib_dialog import SEQLIB_LABEL_TEXT
+from ..barcode import BarcodeSeqLib
+from ..barcodevariant import BcvSeqLib
+from ..barcodeid import BcidSeqLib
+from ..basic import BasicSeqLib
+from ..idonly import IdOnlySeqLib
+from ..overlap import OverlapSeqLib
+from ..selection import Selection
+from ..experiment import Experiment
+
+
+#: map class names to class definitions to avoid use of globals()
+ELEMENT_CLASSES = {
+    "BarcodeSeqLib": BarcodeSeqLib,
+    "BcvSeqLib": BcvSeqLib,
+    "BcidSeqLib": BcidSeqLib,
+    "BasicSeqLib": BasicSeqLib,
+    "IdOnlySeqLib": IdOnlySeqLib,
+    "OverlapSeqLib": OverlapSeqLib,
+    "Selection": Selection,
+    "Experiment": Experiment,
+}
 
 
 class CreateRootDialog(tkSimpleDialog.Dialog):
@@ -60,10 +81,10 @@ def body(self, master):
 
         label = ttk.Label(element_types, text="SeqLib")
         label.grid(column=0, row=5, sticky="w")
-        for i, k in enumerate(seqlib_label_text.keys()):
+        for i, k in enumerate(SEQLIB_LABEL_TEXT.keys()):
             rb = ttk.Radiobutton(
                 element_types,
-                text=seqlib_label_text[k],
+                text=SEQLIB_LABEL_TEXT[k],
                 variable=self.element_tkstring,
                 value=k,
             )
@@ -93,7 +114,7 @@ def apply(self):
 
         # create the object
         try:
-            self.element = globals()[self.element_tkstring.get()]()
+            self.element = ELEMENT_CLASSES[self.element_tkstring.get()]()
         except KeyError:
             raise KeyError(
                 "Unrecognized element type '{}'".format(self.element_tkstring.get())

diff --git a/enrich2/gui/create_seqlib_dialog.py b/enrich2/gui/create_seqlib_dialog.py
@@ -3,9 +3,15 @@
 import ttk
 import tkSimpleDialog
 from collections import OrderedDict
+from ..barcode import BarcodeSeqLib
+from ..barcodevariant import BcvSeqLib
+from ..barcodeid import BcidSeqLib
+from ..basic import BasicSeqLib
+from ..idonly import IdOnlySeqLib
+from ..overlap import OverlapSeqLib
 
 
-seqlib_label_text = OrderedDict(
+SEQLIB_LABEL_TEXT = OrderedDict(
     [
         ("BcvSeqLib", "Barcoded Variant"),
         ("BcidSeqLib", "Barcoded Identifier"),
@@ -16,6 +22,16 @@
     ]
 )
 
+#: map class names to class definitions to avoid use of globals()
+SEQLIB_CLASSES = {
+    "BarcodeSeqLib": BarcodeSeqLib,
+    "BcvSeqLib": BcvSeqLib,
+    "BcidSeqLib": BcidSeqLib,
+    "BasicSeqLib": BasicSeqLib,
+    "IdOnlySeqLib": IdOnlySeqLib,
+    "OverlapSeqLib": OverlapSeqLib,
+}
+
 
 class CreateSeqLibDialog(tkSimpleDialog.Dialog):
     """
@@ -31,10 +47,10 @@ def body(self, master):
         message = ttk.Label(master, text="SeqLib type:")
         message.grid(column=0, row=0)
 
-        for i, k in enumerate(seqlib_label_text.keys()):
+        for i, k in enumerate(SEQLIB_LABEL_TEXT.keys()):
             rb = ttk.Radiobutton(
                 master,
-                text=seqlib_label_text[k],
+                text=SEQLIB_LABEL_TEXT[k],
                 variable=self.element_tkstring,
                 value=k,
             )
@@ -57,6 +73,6 @@ def buttonbox(self):
 
     def apply(self):
         try:
-            self.element_type = globals()[self.element_tkstring.get()]
+            self.element_type = SEQLIB_CLASSES[self.element_tkstring.get()]
         except KeyError:
             raise KeyError("Unrecognized element type.")
diff --git a/enrich2/main.py b/enrich2/main.py
@@ -40,7 +40,7 @@
 __author__ = "Alan F Rubin"
 __copyright__ = "Copyright 2016-2020, Alan F Rubin"
 __license__ = "BSD-3-Clause"
-__version__ = "1.3.0"
+__version__ = "1.3.1"
 __maintainer__ = "Alan F Rubin"
 __email__ = "alan.rubin@wehi.edu.au"
 
@@ -98,7 +98,7 @@ def main_cmd():
 
     # add support for semantic version checking
     parser.add_argument(
-        "--version", action="version", version="%(prog)s {}".format(__version__)
+        "--version", action="version", version="{}".format(__version__)
     )
 
     # add analysis options

diff --git a/enrich2/selection.py b/enrich2/selection.py
@@ -1,6 +1,10 @@
 from __future__ import print_function
+from .barcode import BarcodeSeqLib
 from .barcodevariant import BcvSeqLib
 from .barcodeid import BcidSeqLib
+from .basic import BasicSeqLib
+from .idonly import IdOnlySeqLib
+from .overlap import OverlapSeqLib
 from .config_check import seqlib_type
 from .storemanager import StoreManager
 import os
@@ -25,6 +29,17 @@
 from .dataframe import singleton_dataframe
 
 
+#: map class names to class definitions to avoid use of globals()
+SEQLIB_CLASSES = {
+    "BarcodeSeqLib": BarcodeSeqLib,
+    "BcvSeqLib": BcvSeqLib,
+    "BcidSeqLib": BcidSeqLib,
+    "BasicSeqLib": BasicSeqLib,
+    "IdOnlySeqLib": IdOnlySeqLib,
+    "OverlapSeqLib": OverlapSeqLib,
+}
+
+
 def regression_apply(row, timepoints, weighted):
     """
     :py:meth:`pandas.DataFrame.apply` apply function for calculating 
@@ -148,7 +163,7 @@ def configure(self, cfg, configure_children=True):
                 if libtype is None:
                     raise ValueError("Unrecognized SeqLib config")
                 elif libtype in ("BcvSeqLib", "BcidSeqLib"):
-                    lib = globals()[libtype]()
+                    lib = SEQLIB_CLASSES[libtype]()
                     # don't re-parse the barcode maps if possible
                     mapfile = lib_cfg["barcodes"]["map file"]
                     if mapfile in self.barcode_maps.keys():
@@ -160,7 +175,7 @@ def configure(self, cfg, configure_children=True):
                 else:
                     # requires that the SeqLib derived classes be imported into the
                     # module namespace using "from x import y" style
-                    lib = globals()[libtype]()
+                    lib = SEQLIB_CLASSES[libtype]()
                     lib.configure(lib_cfg)
                     self.add_child(lib)
 

diff --git a/setup.py b/setup.py
@@ -3,7 +3,7 @@
 
 setup(
     name="Enrich2",
-    version="1.3.0",
+    version="1.3.1",
 
     packages=find_packages(),