Remove deprecated manipulation2 (#1208)

* removed removed get_compiled_gene_reaction_rules * added knock_out_model_genes removed find_gene_knockout_reactions from delete.py removed _find_gene_knockout_reactions_fast, _gene_knockout_computation, _get_removed from test_delete.py * Removed references to delete_model_genes() and undelete_model_genes * removed trimmed from model.py since it is no longer used * added deprecation warning * Removed references to delete_model_genes() and undelete_model_genes * fix according to comments * some linting and tidying * fix knock_out_model_genes() * Apply suggestions from code review Co-authored-by: Moritz E. Beber <midnighter@posteo.net> * fix typing and use of set * list comprehension * fixed lint problems * simplified knock_out_model_genes() Added tests to make sure that int and cobra.Gene will work as well Co-authored-by: uri.akavia <uri.akavia@mcgill.ca> Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
opencobra · Apr 29, 2022 · b628572 · b628572
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diff --git a/documentation_builder/faq.ipynb b/documentation_builder/faq.ipynb
@@ -136,7 +136,7 @@
    "source": [
     "That depends on what precisely you mean by delete a gene.\n",
     "\n",
-    "If you want to simulate the model with a gene knockout, use the `cobra.manipulation.delete_model_genes` function. The effects of this function are reversed by `cobra.manipulation.undelete_model_genes`."
+    "If you want to simulate the model with a gene knockout, use the `cobra.manipulation.knock_out_model_genes` function. The effects of this function are reversed when exiting a context."
    ]
   },
   {
@@ -157,7 +157,7 @@
     "model = cobra.test.create_test_model()\n",
     "PGI = model.reactions.get_by_id(\"PGI\")\n",
     "print(\"bounds before knockout:\", (PGI.lower_bound, PGI.upper_bound))\n",
-    "cobra.manipulation.delete_model_genes(model, [\"STM4221\"])\n",
+    "cobra.manipulation.knock_out_model_genes(model, [\"STM4221\"])\n",
     "print(\"bounds after knockouts\", (PGI.lower_bound, PGI.upper_bound))"
    ]
   },

diff --git a/documentation_builder/getting_started.ipynb b/documentation_builder/getting_started.ipynb
@@ -88,11 +88,7 @@
        "                <td>e_coli_core</td>\n",
        "            </tr><tr>\n",
        "                <td><strong>Memory address</strong></td>\n",
-<<<<<<< HEAD
-       "                <td>0x01158878d0</td>\n",
-=======
        "                <td>0x010cb2d358</td>\n",
->>>>>>> origin/devel
        "            </tr><tr>\n",
        "                <td><strong>Number of metabolites</strong></td>\n",
        "                <td>72</td>\n",
@@ -109,11 +105,7 @@
        "          </table>"
       ],
       "text/plain": [
-<<<<<<< HEAD
-       "<Model e_coli_core at 0x1158878d0>"
-=======
        "<Model e_coli_core at 0x10cb2d358>"
->>>>>>> origin/devel
       ]
      },
      "execution_count": 3,
@@ -148,11 +140,7 @@
        "                <td><strong>Name</strong></td><td>L-Glutamate exchange</td>\n",
        "            </tr><tr>\n",
        "                <td><strong>Memory address</strong></td>\n",
-<<<<<<< HEAD
-       "                <td>0x011615e2e8</td>\n",
-=======
        "                <td>0x0117a94898</td>\n",
->>>>>>> origin/devel
        "            </tr><tr>\n",
        "                <td><strong>Stoichiometry</strong></td>\n",
        "                <td>\n",
@@ -170,11 +158,7 @@
        "        "
       ],
       "text/plain": [
-<<<<<<< HEAD
-       "<Reaction EX_glu__L_e at 0x11615e2e8>"
-=======
        "<Reaction EX_glu__L_e at 0x117a94898>"
->>>>>>> origin/devel
       ]
      },
      "execution_count": 4,
@@ -209,31 +193,19 @@
        "                <td><strong>Name</strong></td><td>ATP</td>\n",
        "            </tr><tr>\n",
        "                <td><strong>Memory address</strong></td>\n",
-<<<<<<< HEAD
-       "                <td>0x01160d4630</td>\n",
-=======
        "                <td>0x01179dae48</td>\n",
->>>>>>> origin/devel
        "            </tr><tr>\n",
        "                <td><strong>Formula</strong></td><td>C10H12N5O13P3</td>\n",
        "            </tr><tr>\n",
        "                <td><strong>Compartment</strong></td><td>c</td>\n",
        "            </tr><tr>\n",
        "                <td><strong>In 13 reaction(s)</strong></td><td>\n",
-<<<<<<< HEAD
-       "                    PPS, ADK1, ATPS4r, GLNS, SUCOAS, GLNabc, PGK, ATPM, PPCK, ACKr, PFK, Biomass_Ecoli_core, PYK</td>\n",
-=======
        "                    PPCK, ATPS4r, ADK1, ATPM, GLNS, GLNabc, ACKr, PGK, PPS, PYK, SUCOAS, Biomass_Ecoli_core, PFK</td>\n",
->>>>>>> origin/devel
        "            </tr>\n",
        "        </table>"
       ],
       "text/plain": [
-<<<<<<< HEAD
-       "<Metabolite atp_c at 0x1160d4630>"
-=======
        "<Metabolite atp_c at 0x1179dae48>"
->>>>>>> origin/devel
       ]
      },
      "execution_count": 5,
@@ -302,11 +274,7 @@
        "                <td><strong>Name</strong></td><td>glucose-6-phosphate isomerase</td>\n",
        "            </tr><tr>\n",
        "                <td><strong>Memory address</strong></td>\n",
-<<<<<<< HEAD
-       "                <td>0x0116188e48</td>\n",
-=======
        "                <td>0x0117afacc0</td>\n",
->>>>>>> origin/devel
        "            </tr><tr>\n",
        "                <td><strong>Stoichiometry</strong></td>\n",
        "                <td>\n",
@@ -324,11 +292,7 @@
        "        "
       ],
       "text/plain": [
-<<<<<<< HEAD
-       "<Reaction PGI at 0x116188e48>"
-=======
        "<Reaction PGI at 0x117afacc0>"
->>>>>>> origin/devel
       ]
      },
      "execution_count": 7,
@@ -658,31 +622,19 @@
        "                <td><strong>Name</strong></td><td>ATP</td>\n",
        "            </tr><tr>\n",
        "                <td><strong>Memory address</strong></td>\n",
-<<<<<<< HEAD
-       "                <td>0x01160d4630</td>\n",
-=======
        "                <td>0x01179dae48</td>\n",
->>>>>>> origin/devel
        "            </tr><tr>\n",
        "                <td><strong>Formula</strong></td><td>C10H12N5O13P3</td>\n",
        "            </tr><tr>\n",
        "                <td><strong>Compartment</strong></td><td>c</td>\n",
        "            </tr><tr>\n",
        "                <td><strong>In 13 reaction(s)</strong></td><td>\n",
-<<<<<<< HEAD
-       "                    PPS, ADK1, ATPS4r, GLNS, SUCOAS, GLNabc, PGK, ATPM, PPCK, ACKr, PFK, Biomass_Ecoli_core, PYK</td>\n",
-=======
        "                    PPCK, ATPS4r, ADK1, ATPM, GLNS, GLNabc, ACKr, PGK, PPS, PYK, SUCOAS, Biomass_Ecoli_core, PFK</td>\n",
->>>>>>> origin/devel
        "            </tr>\n",
        "        </table>"
       ],
       "text/plain": [
-<<<<<<< HEAD
-       "<Metabolite atp_c at 0x1160d4630>"
-=======
        "<Metabolite atp_c at 0x1179dae48>"
->>>>>>> origin/devel
       ]
      },
      "execution_count": 19,
@@ -814,17 +766,10 @@
     {
      "data": {
       "text/plain": [
-<<<<<<< HEAD
-       "frozenset({<Reaction Biomass_Ecoli_core at 0x1161337b8>,\n",
-       "           <Reaction G6PDH2r at 0x1160a3a20>,\n",
-       "           <Reaction GLCpts at 0x1160a3da0>,\n",
-       "           <Reaction PGI at 0x116188e48>})"
-=======
        "frozenset({<Reaction Biomass_Ecoli_core at 0x117a71358>,\n",
        "           <Reaction G6PDH2r at 0x117a575f8>,\n",
        "           <Reaction GLCpts at 0x117a9d0f0>,\n",
        "           <Reaction PGI at 0x117afacc0>})"
->>>>>>> origin/devel
       ]
      },
      "execution_count": 24,
@@ -888,11 +833,7 @@
     {
      "data": {
       "text/plain": [
-<<<<<<< HEAD
-       "frozenset({<Gene b4025 at 0x11610a2b0>})"
-=======
        "frozenset({<Gene b4025 at 0x1179cec18>})"
->>>>>>> origin/devel
       ]
      },
      "execution_count": 26,
@@ -920,11 +861,7 @@
        "                <td><strong>Name</strong></td><td>pgi</td>\n",
        "            </tr><tr>\n",
        "                <td><strong>Memory address</strong></td>\n",
-<<<<<<< HEAD
-       "                <td>0x011610a2b0</td>\n",
-=======
        "                <td>0x01179cec18</td>\n",
->>>>>>> origin/devel
        "            </tr><tr>\n",
        "                <td><strong>Functional</strong></td><td>True</td>\n",
        "            </tr><tr>\n",
@@ -934,11 +871,7 @@
        "        </table>"
       ],
       "text/plain": [
-<<<<<<< HEAD
-       "<Gene b4025 at 0x11610a2b0>"
-=======
        "<Gene b4025 at 0x1179cec18>"
->>>>>>> origin/devel
       ]
      },
      "execution_count": 27,
@@ -966,11 +899,7 @@
     {
      "data": {
       "text/plain": [
-<<<<<<< HEAD
-       "frozenset({<Reaction PGI at 0x116188e48>})"
-=======
        "frozenset({<Reaction PGI at 0x117afacc0>})"
->>>>>>> origin/devel
       ]
      },
      "execution_count": 28,
@@ -997,11 +926,7 @@
     {
      "data": {
       "text/plain": [
-<<<<<<< HEAD
-       "frozenset({<Gene eggs at 0x1160245c0>, <Gene spam at 0x116024080>})"
-=======
        "frozenset({<Gene eggs at 0x11793d6d8>, <Gene spam at 0x11793d748>})"
->>>>>>> origin/devel
       ]
      },
      "execution_count": 29,
@@ -1057,11 +982,7 @@
        "                <td><strong>Name</strong></td><td></td>\n",
        "            </tr><tr>\n",
        "                <td><strong>Memory address</strong></td>\n",
-<<<<<<< HEAD
-       "                <td>0x0116024080</td>\n",
-=======
        "                <td>0x011793d748</td>\n",
->>>>>>> origin/devel
        "            </tr><tr>\n",
        "                <td><strong>Functional</strong></td><td>True</td>\n",
        "            </tr><tr>\n",
@@ -1071,11 +992,7 @@
        "        </table>"
       ],
       "text/plain": [
-<<<<<<< HEAD
-       "<Gene spam at 0x116024080>"
-=======
        "<Gene spam at 0x11793d748>"
->>>>>>> origin/devel
       ]
      },
      "execution_count": 31,
@@ -1091,7 +1008,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The `delete_model_genes` function will evaluate the GPR and set the upper and lower bounds to 0 if the reaction is knocked out. This function can preserve existing deletions or reset them using the `cumulative_deletions` flag."
+    "The `knock_out_model_genes` function will evaluate the GPR and set the upper and lower bounds to 0 if the reaction is knocked out."
    ]
   },
   {
@@ -1109,45 +1026,20 @@
     }
    ],
    "source": [
-    "cobra.manipulation.delete_model_genes(\n",
-    "    model, [\"spam\"], cumulative_deletions=True)\n",
+    "cobra.manipulation.knock_out_model_genes(\n",
+    "    model, [\"spam\"])\n",
     "print(\"after 1 KO: %4d < flux_PGI < %4d\" % (pgi.lower_bound, pgi.upper_bound))\n",
     "\n",
-    "cobra.manipulation.delete_model_genes(\n",
-    "    model, [\"eggs\"], cumulative_deletions=True)\n",
+    "cobra.manipulation.knock_out_model_genes(\n",
+    "    model, [\"eggs\"])\n",
     "print(\"after 2 KO:  %4d < flux_PGI < %4d\" % (pgi.lower_bound, pgi.upper_bound))"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The undelete_model_genes can be used to reset a gene deletion"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 33,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "-1000 < pgi < 1000\n"
-     ]
-    }
-   ],
-   "source": [
-    "cobra.manipulation.undelete_model_genes(model)\n",
-    "print(pgi.lower_bound, \"< pgi <\", pgi.upper_bound)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "## Making changes reversibly using models as contexts"
+    "When knocking out model genes in a context, it is reversed when leaving the context."
    ]
   },
   {

diff --git a/release-notes/next-release.md b/release-notes/next-release.md
@@ -2,6 +2,10 @@
 
 ## New features
 
+Added knock_out_model_genes to simulate knock-outs, setting
+reaction bounds of effected reactions to zero and returning a list
+of reactions that were knocked-out. Replaces delete_model_genes and undelete_model_genes
+since it is context sensitive.
 Improve reading of matlab models, which will include metaboilte
 and reaction annotations.
 
@@ -24,7 +28,15 @@ test_gpr_that_needs_two_replacements()
 
 ## Deprecated features
 
+Deprecated delete_model_genes, undelete_model_genes.
+
 ## Backwards incompatible changes
 
+removed find_gene_knockout_reactions from delete.py
+
+removed _find_gene_knockout_reactions_fast, 
+_gene_knockout_computation, _get_removed 
+from test_delete.py
 Removed pymatlib direct transfer of models to matlab process. 
 Please use save_matlab_model() and then read the model in matlab.
+
diff --git a/src/cobra/core/gene.py b/src/cobra/core/gene.py
@@ -18,7 +18,7 @@
 from ast import parse as ast_parse
 from copy import deepcopy
 from keyword import kwlist
-from typing import TYPE_CHECKING, FrozenSet, Iterable, Optional, Set, Tuple, Union
+from typing import FrozenSet, Iterable, Optional, Set, Tuple, Union
 from warnings import warn
 
 import sympy.logic.boolalg as spl
@@ -30,9 +30,6 @@
 from cobra.util.util import format_long_string
 
 
-if TYPE_CHECKING:
-    from cobra import Model
-
 # TODO - When https://github.com/symengine/symengine.py/issues/334 is resolved,
 #  change sympy.Symbol (above in imports) to optlang.symbolics.Symbol
 

diff --git a/src/cobra/core/model.py b/src/cobra/core/model.py
@@ -93,9 +93,6 @@ def __init__(self, id_or_model=None, name=None):
             self._solver = id_or_model.solver
         else:
             Object.__init__(self, id_or_model, name=name)
-            self._trimmed = False
-            self._trimmed_genes = []
-            self._trimmed_reactions = {}
             self.genes = DictList()
             self.reactions = DictList()  # A list of cobra.Reactions
             self.metabolites = DictList()  # A list of cobra.Metabolites

diff --git a/src/cobra/manipulation/__init__.py b/src/cobra/manipulation/__init__.py
@@ -1,12 +1,10 @@
 from .annotate import add_SBO
 from .delete import (
     delete_model_genes,
-    find_gene_knockout_reactions,
-    get_compiled_gene_reaction_rules,
+    knock_out_model_genes,
     prune_unused_metabolites,
     prune_unused_reactions,
     remove_genes,
-    undelete_model_genes,
 )
 from .modify import escape_ID, rename_genes
 from .validate import check_mass_balance, check_metabolite_compartment_formula