RNApolis 0.4.7__tar.gz → 0.4.9__tar.gz

{rnapolis-0.4.7/src/RNApolis.egg-info → rnapolis-0.4.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: RNApolis
-Version: 0.4.7
+Version: 0.4.9
 Summary: A Python library containing RNA-related bioinformatics functions and classes
 Home-page: https://github.com/tzok/rnapolis-py
 Author: Tomasz Zok

{rnapolis-0.4.7 → rnapolis-0.4.9}/setup.py

@@ -5,7 +5,7 @@ with open("README.md") as f:
 
 setup(
     name="RNApolis",
-    version="0.4.7",
+    version="0.4.9",
     packages=["rnapolis"],
     package_dir={"": "src"},
     author="Tomasz Zok",

{rnapolis-0.4.7 → rnapolis-0.4.9/src/RNApolis.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: RNApolis
-Version: 0.4.7
+Version: 0.4.9
 Summary: A Python library containing RNA-related bioinformatics functions and classes
 Home-page: https://github.com/tzok/rnapolis-py
 Author: Tomasz Zok

{rnapolis-0.4.7 → rnapolis-0.4.9}/src/rnapolis/annotator.py

@@ -9,6 +9,7 @@ from typing import Dict, List, Optional, Set, Tuple
 
 import numpy
 import numpy.typing
+import orjson
 from ordered_set import OrderedSet
 from rnapolis.common import (
     BR,

{rnapolis-0.4.7 → rnapolis-0.4.9}/src/rnapolis/common.py

@@ -704,12 +704,17 @@ class BpSeq:
 
     @cached_property
     def dot_bracket(self):
-        pulp.LpSolverDefault.msg = False
-        return self.convert_to_dot_bracket(pulp.LpSolverDefault)
+        if pulp.HiGHS_CMD().available():
+            solver = pulp.HiGHS_CMD()  # much faster than default
+        else:
+            solver = pulp.LpSolverDefault
+        if solver is not None:
+            solver.msg = False
+        return self.convert_to_dot_bracket(solver)
 
     def convert_to_dot_bracket(self, solver: pulp.LpSolver):
         # if PuLP solvers are not installed, use FCFS
-        if len(pulp.listSolvers(onlyAvailable=True)) == 0:
+        if solver is None:
             return self.fcfs()
 
         # build conflict graph

{rnapolis-0.4.7 → rnapolis-0.4.9}/tests/test_common.py

@@ -121,10 +121,10 @@ def test_pseudoknot_order_assignment():
     assert counter["."] == 1185
     assert counter["("] == 1298
     assert counter["["] == 44
-    assert counter["{"] == 17
-    assert counter["<"] == 7
-    assert counter["A"] == 4
-    assert counter["B"] == 1
+    assert counter["{"] == 18
+    assert counter["<"] == 6
+    assert counter["A"] == 3
+    assert counter["B"] == 2
     assert counter["C"] == 1
     assert counter["D"] == 0