From b3635b3cc35489dd45c654de263df9401c3baf8e Mon Sep 17 00:00:00 2001
From: Matthias Koenig <konigmatt@googlemail.com>
Date: Mon, 22 Mar 2021 00:30:14 +0100
Subject: [PATCH] Fix #101, bugfix parameter fitting

---
 release-notes/next-release.md   |  2 ++
 src/sbmlsim/fit/optimization.py | 11 +++++++++++
 src/sbmlsim/serialization.py    |  2 +-
 3 files changed, 14 insertions(+), 1 deletion(-)

diff --git a/release-notes/next-release.md b/release-notes/next-release.md
index 96f3727a..6f7831d5 100644
--- a/release-notes/next-release.md
+++ b/release-notes/next-release.md
@@ -2,6 +2,7 @@
 - breaking changes in units handling
 - bugfix plotting `dimensionless` units in labels
 - remove deprecated `distrib` and `sampling` functionality.
+- fixed typo in sensitivity
 
 **parameter fitting**
 - refactoring parameter fitting
@@ -18,3 +19,4 @@
   - ‘arctan’ : rho(z) = arctan(z). Limits a maximum loss on a single residual, has properties similar to ‘cauchy’.
 - figures closing in reports (#88)
 - improved parameter fitting plots and results (#32)
+- bugfix all NaN errors (#101)
diff --git a/src/sbmlsim/fit/optimization.py b/src/sbmlsim/fit/optimization.py
index 354efe54..4c0076bf 100644
--- a/src/sbmlsim/fit/optimization.py
+++ b/src/sbmlsim/fit/optimization.py
@@ -346,6 +346,7 @@ def initialize(
                     # Changes to baseline, which is the first point
                     y_ref = y_ref - y_ref[0]
 
+                # --- errors on data ---
                 # Use errors for weighting (tries SD and falls back on SE)
                 y_ref_err = None
                 if data_ref.y_sd is not None:
@@ -356,6 +357,10 @@ def initialize(
                     y_ref_err_type = "SE"
                 else:
                     y_ref_err_type = None
+                # handle special case of all NaN
+                if np.all(np.isnan(y_ref_err)):
+                    y_ref_err = None
+                    y_ref_err_type = None
 
                 # handle missing data (0.0 and NaN)
                 if y_ref_err is not None:
@@ -363,8 +368,14 @@ def initialize(
                     y_ref_err[(y_ref_err == 0.0)] = np.NAN
                     if np.all(np.isnan(y_ref_err)):
                         # handle special case of all NaN errors
+                        logger.warning(
+                            f"Errors are all NaN '{sid}.{mapping_id}' y data: "
+                            f"'{y_ref_err}'"
+                        )
                         y_ref_err = None
+                        y_ref_err_type = None
                     else:
+                        # FIXME: this must be based on coefficient of variation
                         # some NaNs could exist (err is maximal error of all points)
                         y_ref_err[np.isnan(y_ref_err)] = np.nanmax(y_ref_err)
 
diff --git a/src/sbmlsim/serialization.py b/src/sbmlsim/serialization.py
index c85c9d18..9cde069c 100644
--- a/src/sbmlsim/serialization.py
+++ b/src/sbmlsim/serialization.py
@@ -57,7 +57,7 @@ def default(self, o):
 
         if hasattr(o, "to_dict"):
             # custom serializer
-            print(type(o))
+            # print(type(o))
             if isinstance(o, type):
                 print(o.__name__)
             return o.to_dict()