From d910766a77d34f7d340fb7ac0a19589a7dbfa24a Mon Sep 17 00:00:00 2001
From: Mirek Kratochvil <miroslav.kratochvil@uni.lu>
Date: Fri, 14 Oct 2022 10:42:56 +0200
Subject: [PATCH 1/2] remove `polish` parameter specific to osqp

---
 docs/src/examples/08_pfba.jl | 2 --
 docs/src/examples/13_moma.jl | 6 +++---
 2 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/docs/src/examples/08_pfba.jl b/docs/src/examples/08_pfba.jl
index 209b6c82d..c10fbfd02 100644
--- a/docs/src/examples/08_pfba.jl
+++ b/docs/src/examples/08_pfba.jl
@@ -43,7 +43,6 @@ fluxes = parsimonious_flux_balance_analysis_dict(
     Clarabel.Optimizer;
     modifications = [
         silence, # optionally silence the optimizer (Clarabel is very verbose by default)
-        change_optimizer_attribute("polish", true), # tell Clarabel to invest time into improving the precision of the solution
         change_constraint("R_EX_glc__D_e"; lb = -12, ub = -12), # fix glucose consumption rate
     ],
 )
@@ -70,7 +69,6 @@ flux_vector = parsimonious_flux_balance_analysis_vec(
     ],
     qp_modifications = [
         change_optimizer(Clarabel.Optimizer), # now switch to Clarabel (Tulip wouldn't be able to finish the computation)
-        change_optimizer_attribute("polish", true), # get an accurate solution, see Clarabel's documentation
         silence, # and make it quiet.
     ],
 )
diff --git a/docs/src/examples/13_moma.jl b/docs/src/examples/13_moma.jl
index 82d3439c9..21b9bef00 100644
--- a/docs/src/examples/13_moma.jl
+++ b/docs/src/examples/13_moma.jl
@@ -28,7 +28,7 @@ using Clarabel
 reference_flux = flux_balance_analysis_dict(
     model,
     Clarabel.Optimizer;
-    modifications = [silence, change_optimizer_attribute("polish", true)],
+    modifications = [silence],
 )
 
 # As the change here, we manually knock out CYTBD reaction:
@@ -41,7 +41,7 @@ flux_summary(
         changed_model,
         reference_flux,
         Clarabel.Optimizer;
-        modifications = [silence, change_optimizer_attribute("polish", true)],
+        modifications = [silence],
     ),
 )
 
@@ -52,6 +52,6 @@ flux_summary(
     flux_balance_analysis_dict(
         changed_model,
         Clarabel.Optimizer;
-        modifications = [silence, change_optimizer_attribute("polish", true)],
+        modifications = [silence],
     ),
 )

From f66abed0bee73fad97f70181caa512b04b6cbd51 Mon Sep 17 00:00:00 2001
From: exaexa <exaexa@users.noreply.github.com>
Date: Fri, 14 Oct 2022 09:32:02 +0000
Subject: [PATCH 2/2] automatic formatting

triggered by @exaexa on PR #681
---
 docs/src/examples/13_moma.jl | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/docs/src/examples/13_moma.jl b/docs/src/examples/13_moma.jl
index 21b9bef00..200ccd07d 100644
--- a/docs/src/examples/13_moma.jl
+++ b/docs/src/examples/13_moma.jl
@@ -25,11 +25,8 @@ using Clarabel
 
 # We will need a reference solution, which represents the original state of the
 # organism before the change.
-reference_flux = flux_balance_analysis_dict(
-    model,
-    Clarabel.Optimizer;
-    modifications = [silence],
-)
+reference_flux =
+    flux_balance_analysis_dict(model, Clarabel.Optimizer; modifications = [silence])
 
 # As the change here, we manually knock out CYTBD reaction:
 changed_model = change_bound(model, "R_CYTBD", lower = 0.0, upper = 0.0);