From 09a00fd74fbbae3f1037c74cda0ab46a79dce0fe Mon Sep 17 00:00:00 2001
From: GuillaumeG <guipagui@gmail.com>
Date: Mon, 4 Mar 2024 14:25:16 +0100
Subject: [PATCH] fix(deps): update libs (#13)

* fix(deps): update libs

* styles(cameobrs): super-linter

* chore(github): update deps
---
 recipes/meta.yaml                                    | 12 ++++--------
 recipes/workflow.yaml                                |  7 +++----
 .../deterministic/flux_variability_based.py          | 12 +++---------
 .../unit/test_strain_design_deterministic.py         |  4 ++--
 4 files changed, 12 insertions(+), 23 deletions(-)

diff --git a/recipes/meta.yaml b/recipes/meta.yaml
index 571176d..71418dd 100644
--- a/recipes/meta.yaml
+++ b/recipes/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "straindesign" %}
-{% set version = "3.1.0" %}
+{% set version = "3.2.3" %}
 
 package:
   name: {{ name }}
@@ -16,14 +16,13 @@ build:
 requirements:
   build:
     - pip
-    - python
+    - python>=3.8
     - pyyaml
     - setuptools
   run:
     - biopython
     - blessings
-    - click
-    - cobra>=0.24
+    - cobra>=0.29
     - escher
     - future
     - gnomic
@@ -31,14 +30,11 @@ requirements:
     - IProgress
     - lazy-object-proxy
     - plotly
-    - python
-    - markupsafe
+    - python>=3.8
     - networkx
     - numexpr
-    - numpy<1.24 # Related to https://github.com/numpy/numpy/pull/22607
     - openbabel
     - openpyxl
-    - optlang
     - ordered-set
     - palettable
     - pandas
diff --git a/recipes/workflow.yaml b/recipes/workflow.yaml
index 36d477e..b30dc54 100644
--- 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
index 1ab386a..69c832d 100644
--- a/src/cameobrs/strain_design/deterministic/flux_variability_based.py
+++ b/src/cameobrs/strain_design/deterministic/flux_variability_based.py
@@ -360,11 +360,7 @@ def run(
         ].values
 
         if self.normalize_ranges_by is not None:
-            logger.debug(
-                self.reference_flux_ranges.loc[
-                    self.normalize_ranges_by,
-                ]
-            )
+            logger.debug(self.reference_flux_ranges.loc[self.normalize_ranges_by,])
             # The most obvious flux to normalize by is the biomass reaction
             # flux. This is probably always greater than zero. Just in case
             # the model is defined differently or some other normalizing
@@ -435,7 +431,7 @@ 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 +876,7 @@ 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"]
 
@@ -1114,7 +1110,6 @@ def run(
                 exclude_ids.append(reaction)
 
         with TimeMachine() as tm:
-
             tm(do=int, undo=partial(setattr, model, "objective", model.objective))
             tm(do=int, undo=partial(setattr, target, "lower_bound", target.lower_bound))
             tm(do=int, undo=partial(setattr, target, "upper_bound", target.upper_bound))
@@ -1228,7 +1223,6 @@ def __init__(
         *args,
         **kwargs,
     ):
-
         super(FSEOFResult, self).__init__(
             self._generate_designs(reference, enforced_levels, reaction_results),
             *args,
diff --git a/tests/cameobrs/unit/test_strain_design_deterministic.py b/tests/cameobrs/unit/test_strain_design_deterministic.py
index 91347cc..bb02daf 100644
--- 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