Deprecate corneto.K for corneto.opt

saezlab · May 9, 2024 · d88006e · d88006e
1 parent 8f50d0b
commit d88006e
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Showing 3 changed files with 33 additions and 12 deletions.
diff --git a/corneto/__init__.py b/corneto/__init__.py
@@ -1,12 +1,15 @@
 import sys
+import warnings
 
 from corneto import _plotting as pl
 from corneto._constants import *
 from corneto._graph import Attr, Attributes, EdgeType, Graph
 from corneto._util import info
 from corneto.backend import DEFAULT_BACKEND, DEFAULT_SOLVER, available_backends
-from corneto.backend import DEFAULT_BACKEND as K
-from corneto.backend import DEFAULT_BACKEND as ops
+
+# from corneto.backend import DEFAULT_BACKEND as K  # deprecate
+# from corneto.backend import DEFAULT_BACKEND as ops  # deprecate
+from corneto.backend import DEFAULT_BACKEND as opt
 from corneto.backend._base import HammingLoss as hamming_loss
 from corneto.backend._base import Indicator, NonZeroIndicator
 
@@ -19,6 +22,25 @@
 )
 from corneto.utils import Attr, Attributes
 
+
+class DeprecatedBackend:
+    def __init__(self, backend):
+        self._backend = backend
+
+    def __getattr__(self, attr):
+        warnings.warn(
+            "'corneto.K' and 'corneto.ops' are deprecated and will be removed in a future version. Use 'corneto.opt' instead.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
+        return getattr(self._backend, attr)
+
+
+# Wrapping the backend instance with the DeprecatedBackend
+K = DeprecatedBackend(opt)
+ops = DeprecatedBackend(opt)
+
+
 __all__ = [
     "Attr",
     "EdgeType",

diff --git a/corneto/backend/_base.py b/corneto/backend/_base.py
@@ -381,16 +381,7 @@ def direction(self) -> Direction:
         return self._direction
 
     def copy(self) -> "ProblemDef":
-        # TODO: Fix copy! add tests
-        return ProblemDef(
-            self._backend,
-            self._constraints,
-            self._objectives,
-            self._expressions,
-            self._weights,
-            self._direction,
-            self._graph,
-        )
+        raise NotImplementedError()
 
     def _add(self, other: Any, inplace: bool = False):
         if isinstance(other, ProblemDef):

diff --git a/docs/tutorials/context-specific-metabolic-omics.ipynb b/docs/tutorials/context-specific-metabolic-omics.ipynb
@@ -12,6 +12,14 @@
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    "metadata": {},
    "outputs": [
+    {
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+      "text/plain": []
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
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