Modify only_adjacent_edges to rely on overlapping locations only (#602)

* example to reproduce, should change to grouping by overlap only for only_adjacent_edges (drop support for partial overlap)

* suppress known test warnings

* change how only_adjacent_edges works, now it wont work for partial overhangs, but work properly in other cases

* remove comment

* fix assembly_uses_only_adjacent_edges

* better solution with partially_digested_seqs_in_restriction_ligation_assembly

* fix partially_digested_seqs_in_restriction_ligation_assembly to handle pre-cut inputs and add decicated test for this

* Add inversion assembly support for single-input recombination (#603)

* remove comment

* first version working with two examples

* keep back-compatibility and add deprecation warnings

* added tests

* add recombinase_assembly

* add history validations to test to ensure inversion is correctly validated

* update replay_products for recombinase

* restore only_adjacent_edges=True in restriction_ligation_assembly

* fix tests + copilot feedback

Author: manulera

docs/notebooks/hackathon_copenhagen_2025.ipynb

@@ -908,9 +908,9 @@
     }
    ],
    "source": [
-    "from pydna.assembly2 import homologous_recombination_excision\n",
+    "from pydna.assembly2 import homologous_recombination_excision_or_inversion\n",
     "\n",
-    "products = homologous_recombination_excision(transformed_genome, limit=10)\n",
+    "products = homologous_recombination_excision_or_inversion(transformed_genome, limit=10)\n",
     "\n",
     "print(products[0].seq)\n",
     "print(products[1].seq)"
@@ -977,7 +977,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.11"
+   "version": "3.12.2"
   }
  },
  "nbformat": 4,

docs/notebooks/history.ipynb

@@ -57,9 +57,9 @@
     "    ligation_assembly,\n",
     "    gateway_assembly,\n",
     "    homologous_recombination_integration,\n",
-    "    homologous_recombination_excision,\n",
+    "    homologous_recombination_excision_or_inversion,\n",
     "    cre_lox_integration,\n",
-    "    cre_lox_excision,\n",
+    "    cre_lox_excision_or_inversion,\n",
     "    pcr_assembly,\n",
     "    crispr_integration,\n",
     ")\n",
@@ -320,7 +320,7 @@
     "insert = Dseqrecord(f\"{homology}gggg{homology}\")\n",
     "integration_product, *_ = homologous_recombination_integration(genome, [insert], 20)\n",
     "\n",
-    "excision_product, *_ = homologous_recombination_excision(integration_product, 20)\n",
+    "excision_product, *_ = homologous_recombination_excision_or_inversion(integration_product, 20)\n",
     "\n",
     "genome.name = \"genome\"\n",
     "insert.name = \"insert\"\n",
@@ -367,7 +367,7 @@
     "a = Dseqrecord(f\"cccccc{LOXP_SEQUENCE}aaaaa\")\n",
     "b = Dseqrecord(f\"{LOXP_SEQUENCE}bbbbb\", circular=True)\n",
     "integration_product, *_ = cre_lox_integration(a, [b])\n",
-    "excision_product, *_ = cre_lox_excision(integration_product)\n",
+    "excision_product, *_ = cre_lox_excision_or_inversion(integration_product)\n",
     "\n",
     "a.name = \"genome\"\n",
     "b.name = \"plasmid\"\n",

pytest.ini

@@ -0,0 +1,13 @@
+[pytest]
+filterwarnings =
+    ignore:Partial overlaps can return wrong products.*:UserWarning
+    ignore:Some recombination products were discarded because they had off-target cuts.*:UserWarning
+    ignore:The user_assembly_design function is experimental and may change in future versions.*:FutureWarning
+    ignore:Increasing length of locus line to allow long name.*:
+    ignore:Feature qualifier key.*:Bio.BiopythonWarning
+    ignore:Truncated LOCUS line found - is this correct\?.*:Bio.BiopythonWarning
+    ignore:LOCUS line is wrongly formatted, we used a more permissive parser.*:UserWarning
+    ignore:The primer_screen module is experimental.*:FutureWarning
+
+markers =
+    mpl_image_compare