fix(deps): update libs

brsynth · Mar 4, 2024 · 9fb7532 · 9fb7532
1 parent 3d27ca8
commit 9fb7532
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Showing 3 changed files with 7 additions and 8 deletions.
diff --git a/recipes/workflow.yaml b/recipes/workflow.yaml
@@ -1,4 +1,4 @@
-name: test
+name: straindesign-local
 channels:
   - conda-forge
   - plotly
@@ -8,7 +8,7 @@ dependencies:
   - biopython
   - blessings
   - click
-  - cobra>=0.24
+  - cobra
   - conda-build
   - escher
   - future
@@ -20,10 +20,9 @@ dependencies:
   - markupsafe
   - networkx
   - numexpr
-  - numpy<1.24 # Related to https://github.com/numpy/numpy/pull/22607
+  - numpy
   - openbabel
   - openpyxl
-  - optlang
   - ordered-set
   - palettable
   - pandas

diff --git a/src/cameobrs/strain_design/deterministic/flux_variability_based.py b/src/cameobrs/strain_design/deterministic/flux_variability_based.py
@@ -435,7 +435,7 @@ def run(
                 results = list(view.map(func_obj, self.grid.iterrows()))
 
         solutions = dict(
-            (tuple(point.iteritems()), fva_result) for (point, fva_result) in results
+            (tuple(point.items()), fva_result) for (point, fva_result) in results
         )
 
         for sol in solutions.values():
@@ -880,7 +880,7 @@ def _display_on_map_static(self, index, map_name, palette="RdYlBu", **kwargs):
             reaction_data[numpy.isposinf(reaction_data)] = reaction_data.max()
             reaction_data[numpy.isneginf(reaction_data)] = reaction_data.min()
 
-            reaction_data = dict(reaction_data.iteritems())
+            reaction_data = dict(reaction_data.items())
             reaction_data["max"] = numpy.abs(values).max()
             reaction_data["min"] = -reaction_data["max"]
 

diff --git a/tests/cameobrs/unit/test_strain_design_deterministic.py b/tests/cameobrs/unit/test_strain_design_deterministic.py
@@ -207,11 +207,11 @@ def test_result_is_correct(self, glpk_growth_coupling_potential):
         fva = cameobrs.flux_variability_analysis(
             model, fraction_of_optimum=1, remove_cycles=False, reactions=["PFL"]
         )
-        assert fva["lower_bound"][0] <= 0 <= fva["upper_bound"][0]
+        assert fva["lower_bound"].iloc[0] <= 0 <= fva["upper_bound"].iloc[0]
         with model:
             for knockout in knockouts:
                 model.reactions.get_by_id(knockout).knock_out()
             fva = cameobrs.flux_variability_analysis(
                 model, fraction_of_optimum=1, remove_cycles=False, reactions=["PFL"]
             )
-            assert abs(fva["lower_bound"][0]) > 4
+            assert abs(fva["lower_bound"].iloc[0]) > 4