Merge remote-tracking branch 'upstream/develop' into expose_exact_hmc…

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GeomScale · Jul 24, 2023 · 81a903d · 81a903d
2 parents f5274f1 + f5440b6
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diff --git a/README.md b/README.md
@@ -131,8 +131,8 @@ model = MetabolicNetwork.from_json('path/to/model_file.json')
 sampler = PolytopeSampler(model)
 A, b, N, N_shift = sampler.get_polytope()
 
-A_rounded, b_rounded, Tr, Tr_shift = sampler.round_polytope(A, b, method="john_postiion")
-A_rounded, b_rounded, Tr, Tr_shift = sampler.round_polytope(A, b, method="isotropic_postiion")
+A_rounded, b_rounded, Tr, Tr_shift = sampler.round_polytope(A, b, method="john_position")
+A_rounded, b_rounded, Tr, Tr_shift = sampler.round_polytope(A, b, method="isotropic_position")
 A_rounded, b_rounded, Tr, Tr_shift = sampler.round_polytope(A, b, method="min_ellipsoid")
 ```
 

diff --git a/dingo/PolytopeSampler.py b/dingo/PolytopeSampler.py
@@ -203,9 +203,10 @@ def generate_steady_states_no_multiphase(
         P = HPolytope(self._A, self._b)
 
         samples = P.generate_samples(method, n, burn_in, thinning, self._parameters["fast_computations"])
+        samples_T = samples.T
 
         steady_states = map_samples_to_steady_states(
-                samples, self._N, self._N_shift
+                samples_T, self._N, self._N_shift
             )
 
         return steady_states
@@ -263,7 +264,8 @@ def sample_from_polytope_no_multiphase(
         except ImportError as e:
             samples = P.generate_samples(method, n, burn_in, thinning, False)
 
-        return samples
+        samples_T = samples.T
+        return samples_T
 
     @staticmethod
     def round_polytope(