From ba050dabfbb1795073ff9359cb427b3da200578c Mon Sep 17 00:00:00 2001
From: gehbiszumeis <16896724+gehbiszumeis@users.noreply.github.com>
Date: Wed, 27 Oct 2021 16:02:58 +0200
Subject: [PATCH 01/33] new: added to_dict() method to Coregionalize kernel
 class

---
 GPy/kern/src/coregionalize.py | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/GPy/kern/src/coregionalize.py b/GPy/kern/src/coregionalize.py
index d5111c3bf..41ddf8417 100644
--- a/GPy/kern/src/coregionalize.py
+++ b/GPy/kern/src/coregionalize.py
@@ -134,3 +134,18 @@ def gradients_X(self, dL_dK, X, X2=None):
 
     def gradients_X_diag(self, dL_dKdiag, X):
         return np.zeros(X.shape)
+
+    def to_dict(self):
+        """
+        Convert the object into a json serializable dictionary.
+
+        Note: It uses the private method _save_to_input_dict of the parent.
+
+        :return dict: json serializable dictionary containing the needed information to instantiate the object
+        """
+
+        input_dict = super(Coregionalize, self)._save_to_input_dict()
+        input_dict["class"] = "GPy.kern.Coregionalize"
+        input_dict["W"] = self.W.values.tolist()
+        input_dict["kappa"] = self.kappa.values.tolist()
+        return input_dict

From fcb43ce5dd94af96b0e4bcc49755c8d848da9d59 Mon Sep 17 00:00:00 2001
From: gehbiszumeis <16896724+gehbiszumeis@users.noreply.github.com>
Date: Wed, 27 Oct 2021 16:03:31 +0200
Subject: [PATCH 02/33] new: added to_dict() method to MixedNoise likelihood
 class

---
 GPy/likelihoods/mixed_noise.py | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/GPy/likelihoods/mixed_noise.py b/GPy/likelihoods/mixed_noise.py
index db230b134..67102b201 100644
--- a/GPy/likelihoods/mixed_noise.py
+++ b/GPy/likelihoods/mixed_noise.py
@@ -80,3 +80,22 @@ def samples(self, gp, Y_metadata):
             _ysim = np.array([np.random.normal(lik.gp_link.transf(gpj), scale=np.sqrt(lik.variance), size=1) for gpj in gp_filtered.flatten()])
             Ysim[flt,:] = _ysim.reshape(n1,N2)
         return Ysim
+
+    def to_dict(self):
+        """
+        Convert the object into a json serializable dictionary.
+
+        Note: It uses the private method _save_to_input_dict of the parent.
+
+        :return dict: json serializable dictionary containing the needed information to instantiate the object
+        """
+
+        # input_dict = super(MixedNoise, self)._save_to_input_dict()
+        input_dict = {}
+        input_dict["name"] = self.name
+        input_dict["class"] = "GPy.likelihoods.MixedNoise"
+        input_dict["likelihood_list"] = {}
+        for ii in range(len(self.likelihoods_list)):
+            input_dict["likelihood_list"][ii] = self.likelihoods_list[ii].to_dict()
+
+        return input_dict
\ No newline at end of file

From 4de3fdda20abcea2bba678c25eb802686ab47b70 Mon Sep 17 00:00:00 2001
From: gehbiszumeis <16896724+gehbiszumeis@users.noreply.github.com>
Date: Wed, 27 Oct 2021 16:05:24 +0200
Subject: [PATCH 03/33] fix: made Y_metadata dict content serializable

---
 GPy/core/gp.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/GPy/core/gp.py b/GPy/core/gp.py
index 0704c6a6b..5adc8ce47 100644
--- a/GPy/core/gp.py
+++ b/GPy/core/gp.py
@@ -134,9 +134,10 @@ def to_dict(self, save_data=True):
         if self.mean_function is not None:
             input_dict["mean_function"] = self.mean_function.to_dict()
         input_dict["inference_method"] = self.inference_method.to_dict()
-        #FIXME: Assumes the Y_metadata is serializable. We should create a Metadata class
+        # TODO: We should create a Metadata class
         if self.Y_metadata is not None:
-            input_dict["Y_metadata"] = self.Y_metadata
+            # make Y_metadata serializable
+            input_dict["Y_metadata"] = {k: self.Y_metadata[k].tolist() for k in self.Y_metadata.keys()}
         if self.normalizer is not None:
             input_dict["normalizer"] = self.normalizer.to_dict()
         return input_dict

From f79144bf474399ff6feb497424f9d944f878d5ce Mon Sep 17 00:00:00 2001
From: gehbiszumeis <16896724+gehbiszumeis@users.noreply.github.com>
Date: Wed, 27 Oct 2021 16:06:04 +0200
Subject: [PATCH 04/33] fix: typo

---
 GPy/core/parameterization/variational.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/GPy/core/parameterization/variational.py b/GPy/core/parameterization/variational.py
index 1dbd205b4..911c5b3ea 100644
--- a/GPy/core/parameterization/variational.py
+++ b/GPy/core/parameterization/variational.py
@@ -106,7 +106,7 @@ def __init__(self, means=None, variances=None, name='latent space', *a, **kw):
         self.link_parameters(self.mean, self.variance)
         self.num_data, self.input_dim = self.mean.shape
         if self.has_uncertain_inputs():
-            assert self.variance.shape == self.mean.shape, "need one variance per sample and dimenion"
+            assert self.variance.shape == self.mean.shape, "need one variance per sample and dimension"
 
     def set_gradients(self, grad):
         self.mean.gradient, self.variance.gradient = grad

From 4c3c2ac755cb5c0b4e93d93f1806ee2bc9f814f4 Mon Sep 17 00:00:00 2001
From: gehbiszumeis <16896724+gehbiszumeis@users.noreply.github.com>
Date: Fri, 29 Oct 2021 13:32:16 +0200
Subject: [PATCH 05/33] added additional needed parameters to to_dict() method
 for Coregionalize kernel + added _build_from_input dict method

---
 GPy/kern/src/coregionalize.py | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/GPy/kern/src/coregionalize.py b/GPy/kern/src/coregionalize.py
index 41ddf8417..d05f5c6ad 100644
--- a/GPy/kern/src/coregionalize.py
+++ b/GPy/kern/src/coregionalize.py
@@ -146,6 +146,16 @@ def to_dict(self):
 
         input_dict = super(Coregionalize, self)._save_to_input_dict()
         input_dict["class"] = "GPy.kern.Coregionalize"
+        # W and kappa must be serializable
         input_dict["W"] = self.W.values.tolist()
         input_dict["kappa"] = self.kappa.values.tolist()
+        input_dict["output_dim"] = self.output_dim
         return input_dict
+
+    @staticmethod
+    def _build_from_input_dict(kernel_class, input_dict):
+        useGPU = input_dict.pop('useGPU', None)
+        # W and kappa must be converted back to numpy arrays
+        input_dict['W'] = np.array(input_dict['W'])
+        input_dict['kappa'] = np.array(input_dict['kappa'])
+        return Coregionalize(**input_dict)

From 49e272c4493e38fcccef77d3730659891a37f96e Mon Sep 17 00:00:00 2001
From: gehbiszumeis <16896724+gehbiszumeis@users.noreply.github.com>
Date: Fri, 29 Oct 2021 13:33:01 +0200
Subject: [PATCH 06/33] new: added possibility to build MixedNoise likelihood
 from input_dict

---
 GPy/likelihoods/mixed_noise.py | 24 +++++++++++++++++-------
 1 file changed, 17 insertions(+), 7 deletions(-)

diff --git a/GPy/likelihoods/mixed_noise.py b/GPy/likelihoods/mixed_noise.py
index 67102b201..50289e446 100644
--- a/GPy/likelihoods/mixed_noise.py
+++ b/GPy/likelihoods/mixed_noise.py
@@ -91,11 +91,21 @@ def to_dict(self):
         """
 
         # input_dict = super(MixedNoise, self)._save_to_input_dict()
-        input_dict = {}
-        input_dict["name"] = self.name
-        input_dict["class"] = "GPy.likelihoods.MixedNoise"
-        input_dict["likelihood_list"] = {}
+        input_dict = {"name": self.name,
+                      "class": "GPy.likelihoods.MixedNoise",
+                      "likelihoods_list": []}
         for ii in range(len(self.likelihoods_list)):
-            input_dict["likelihood_list"][ii] = self.likelihoods_list[ii].to_dict()
-
-        return input_dict
\ No newline at end of file
+            input_dict["likelihoods_list"].append(self.likelihoods_list[ii].to_dict())
+
+        return input_dict
+
+    @staticmethod
+    def _build_from_input_dict(likelihood_class, input_dict):
+        import copy
+        input_dict = copy.deepcopy(input_dict)
+        # gp_link_dict = input_dict.pop('gp_link_dict')
+        # import GPy
+        # gp_link = GPy.likelihoods.link_functions.GPTransformation.from_dict(gp_link_dict)
+        # input_dict["gp_link"] = gp_link
+        input_dict['likelihoods_list'] = [Likelihood.from_dict(l) for l in input_dict['likelihoods_list']]
+        return likelihood_class(**input_dict)

From a133947b424cbe4f057f816eb387db96d5f8d424 Mon Sep 17 00:00:00 2001
From: gehbiszumeis <16896724+gehbiszumeis@users.noreply.github.com>
Date: Fri, 29 Oct 2021 13:35:13 +0200
Subject: [PATCH 07/33] Y_metadata conversion from serializable to np.array
 when loading from dict

---
 GPy/core/gp.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/GPy/core/gp.py b/GPy/core/gp.py
index 5adc8ce47..62fd43b74 100644
--- a/GPy/core/gp.py
+++ b/GPy/core/gp.py
@@ -163,9 +163,10 @@ def _format_input_dict(input_dict, data=None):
             input_dict["mean_function"] = mean_function
         input_dict["inference_method"] = GPy.inference.latent_function_inference.LatentFunctionInference.from_dict(input_dict["inference_method"])
 
-        #FIXME: Assumes the Y_metadata is serializable. We should create a Metadata class
-        Y_metadata = input_dict.get("Y_metadata")
-        input_dict["Y_metadata"] = Y_metadata
+        # converts Y_metadata from serializable to array. We should create a Metadata class
+        # Y_metadata = input_dict.get("Y_metadata")
+        # input_dict["Y_metadata"] = Y_metadata
+        input_dict["Y_metadata"] = {k: np.array(input_dict['Y_metadata'][k]) for k in input_dict['Y_metadata'].keys()}
 
         normalizer = input_dict.get("normalizer")
         if normalizer is not None:

From 1b8b649878705d76cc23166cddf3009869a23ef7 Mon Sep 17 00:00:00 2001
From: gehbiszumeis <16896724+gehbiszumeis@users.noreply.github.com>
Date: Fri, 29 Oct 2021 14:04:20 +0200
Subject: [PATCH 08/33] fix: rework Y_metadata part for compatibility with
 unittests !minor

---
 GPy/core/gp.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/GPy/core/gp.py b/GPy/core/gp.py
index 62fd43b74..3cfa38ec3 100644
--- a/GPy/core/gp.py
+++ b/GPy/core/gp.py
@@ -164,9 +164,11 @@ def _format_input_dict(input_dict, data=None):
         input_dict["inference_method"] = GPy.inference.latent_function_inference.LatentFunctionInference.from_dict(input_dict["inference_method"])
 
         # converts Y_metadata from serializable to array. We should create a Metadata class
-        # Y_metadata = input_dict.get("Y_metadata")
-        # input_dict["Y_metadata"] = Y_metadata
-        input_dict["Y_metadata"] = {k: np.array(input_dict['Y_metadata'][k]) for k in input_dict['Y_metadata'].keys()}
+        Y_metadata = input_dict.get("Y_metadata")
+        if isinstance(Y_metadata, dict):
+            input_dict["Y_metadata"] = {k: np.array(Y_metadata[k]) for k in Y_metadata.keys()}
+        else:
+            input_dict["Y_metadata"] = Y_metadata
 
         normalizer = input_dict.get("normalizer")
         if normalizer is not None:

From f4409e0f15b8997bd2ed882c1292e339802ebb64 Mon Sep 17 00:00:00 2001
From: gehbiszumeis <16896724+gehbiszumeis@users.noreply.github.com>
Date: Wed, 24 Nov 2021 13:48:51 +0100
Subject: [PATCH 09/33] conda cleanup in appveyors pipeline

---
 appveyor.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/appveyor.yml b/appveyor.yml
index f5faee5cc..085186c38 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -22,6 +22,7 @@ environment:
 
 install:
  - "set PATH=%MINICONDA%;%MINICONDA%\\Scripts;%PATH%"
+ - conda clean --packages
  - conda config --set always_yes yes --set changeps1 no
  - conda update -q conda
  - conda info -a

From 67a481385e52039a0e25776f3a2bcbcccc7c7f2a Mon Sep 17 00:00:00 2001
From: gehbiszumeis <16896724+gehbiszumeis@users.noreply.github.com>
Date: Wed, 24 Nov 2021 14:10:49 +0100
Subject: [PATCH 10/33] conda clean up after conda update

---
 appveyor.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/appveyor.yml b/appveyor.yml
index 085186c38..8554cb546 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -22,9 +22,9 @@ environment:
 
 install:
  - "set PATH=%MINICONDA%;%MINICONDA%\\Scripts;%PATH%"
- - conda clean --packages
  - conda config --set always_yes yes --set changeps1 no
  - conda update -q conda
+ - conda clean --packages
  - conda info -a
  - "conda create -q -n build-environment python=%PYTHON_VERSION% numpy scipy matplotlib"
  - activate build-environment

From 73960b40579eb2e3f0ca28a399ddf5816d8f17c7 Mon Sep 17 00:00:00 2001
From: gehbiszumeis <16896724+gehbiszumeis@users.noreply.github.com>
Date: Wed, 24 Nov 2021 18:14:19 +0100
Subject: [PATCH 11/33] conda clean before conda update

---
 appveyor.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/appveyor.yml b/appveyor.yml
index 8554cb546..a4a248290 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -23,8 +23,8 @@ environment:
 install:
  - "set PATH=%MINICONDA%;%MINICONDA%\\Scripts;%PATH%"
  - conda config --set always_yes yes --set changeps1 no
- - conda update -q conda
  - conda clean --packages
+ - conda update -q conda
  - conda info -a
  - "conda create -q -n build-environment python=%PYTHON_VERSION% numpy scipy matplotlib"
  - activate build-environment

From 7f4ce5f4e59620e7a4159fcc923ef941e7a02252 Mon Sep 17 00:00:00 2001
From: gehbiszumeis <16896724+gehbiszumeis@users.noreply.github.com>
Date: Thu, 25 Nov 2021 08:49:30 +0100
Subject: [PATCH 12/33] try pinning packages for conda

---
 appveyor.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/appveyor.yml b/appveyor.yml
index a4a248290..d029e05c3 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -23,6 +23,7 @@ environment:
 install:
  - "set PATH=%MINICONDA%;%MINICONDA%\\Scripts;%PATH%"
  - conda config --set always_yes yes --set changeps1 no
+ - conda config --add pinned_packages defaults::conda
  - conda clean --packages
  - conda update -q conda
  - conda info -a

From 4567ddfb0bf40e4c581b087105c0a4895574c911 Mon Sep 17 00:00:00 2001
From: gehbiszumeis <16896724+gehbiszumeis@users.noreply.github.com>
Date: Thu, 25 Nov 2021 09:10:23 +0100
Subject: [PATCH 13/33] revert all conda changes

---
 appveyor.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/appveyor.yml b/appveyor.yml
index d029e05c3..f5faee5cc 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -23,8 +23,6 @@ environment:
 install:
  - "set PATH=%MINICONDA%;%MINICONDA%\\Scripts;%PATH%"
  - conda config --set always_yes yes --set changeps1 no
- - conda config --add pinned_packages defaults::conda
- - conda clean --packages
  - conda update -q conda
  - conda info -a
  - "conda create -q -n build-environment python=%PYTHON_VERSION% numpy scipy matplotlib"

From 5f0271776fedcdcf768f5b632825bc1e631207e9 Mon Sep 17 00:00:00 2001
From: gehbiszumeis <16896724+gehbiszumeis@users.noreply.github.com>
Date: Thu, 25 Nov 2021 09:45:46 +0100
Subject: [PATCH 14/33] conda clean all (not only packages)

---
 appveyor.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/appveyor.yml b/appveyor.yml
index f5faee5cc..1f2b2501d 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -23,6 +23,7 @@ environment:
 install:
  - "set PATH=%MINICONDA%;%MINICONDA%\\Scripts;%PATH%"
  - conda config --set always_yes yes --set changeps1 no
+ - conda clean --all
  - conda update -q conda
  - conda info -a
  - "conda create -q -n build-environment python=%PYTHON_VERSION% numpy scipy matplotlib"

From cd783a111313ad20b359580017e2a5ef58f6832b Mon Sep 17 00:00:00 2001
From: gehbiszumeis <16896724+gehbiszumeis@users.noreply.github.com>
Date: Thu, 25 Nov 2021 10:38:38 +0100
Subject: [PATCH 15/33] use conda update anaconda

---
 appveyor.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/appveyor.yml b/appveyor.yml
index 1f2b2501d..782e75f90 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -23,8 +23,8 @@ environment:
 install:
  - "set PATH=%MINICONDA%;%MINICONDA%\\Scripts;%PATH%"
  - conda config --set always_yes yes --set changeps1 no
- - conda clean --all
- - conda update -q conda
+ - conda update anaconda
+# - conda update -q conda
  - conda info -a
  - "conda create -q -n build-environment python=%PYTHON_VERSION% numpy scipy matplotlib"
  - activate build-environment

From 9c9dfb23e037f860242799e34847d6ea37a475ba Mon Sep 17 00:00:00 2001
From: gehbiszumeis <16896724+gehbiszumeis@users.noreply.github.com>
Date: Thu, 25 Nov 2021 10:58:54 +0100
Subject: [PATCH 16/33] pin conda package

---
 appveyor.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/appveyor.yml b/appveyor.yml
index 782e75f90..63074f123 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -22,9 +22,9 @@ environment:
 
 install:
  - "set PATH=%MINICONDA%;%MINICONDA%\\Scripts;%PATH%"
- - conda config --set always_yes yes --set changeps1 no
- - conda update anaconda
-# - conda update -q conda
+ - conda config --set always_yes yes --set changeps1 no --add pinned_packages defaults::conda
+ - conda clean --all
+ - conda update -q conda
  - conda info -a
  - "conda create -q -n build-environment python=%PYTHON_VERSION% numpy scipy matplotlib"
  - activate build-environment

From 289a15c8c539ce897a4dfeef383bd283ce094914 Mon Sep 17 00:00:00 2001
From: gehbiszumeis <16896724+gehbiszumeis@users.noreply.github.com>
Date: Thu, 25 Nov 2021 11:02:34 +0100
Subject: [PATCH 17/33] pin conda package

---
 appveyor.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/appveyor.yml b/appveyor.yml
index 63074f123..18ff37a56 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -22,7 +22,8 @@ environment:
 
 install:
  - "set PATH=%MINICONDA%;%MINICONDA%\\Scripts;%PATH%"
- - conda config --set always_yes yes --set changeps1 no --add pinned_packages defaults::conda
+ - conda config --set always_yes yes --set changeps1 no
+ - conda config --add pinned_packages defaults::conda
  - conda clean --all
  - conda update -q conda
  - conda info -a

From 4d9f9e8276922f9d85f25a2d5f7939800d39abf8 Mon Sep 17 00:00:00 2001
From: gehbiszumeis <16896724+gehbiszumeis@users.noreply.github.com>
Date: Thu, 25 Nov 2021 11:18:25 +0100
Subject: [PATCH 18/33] try installing charset-normalizer beforehand

---
 appveyor.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/appveyor.yml b/appveyor.yml
index 18ff37a56..39433a900 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -23,8 +23,7 @@ environment:
 install:
  - "set PATH=%MINICONDA%;%MINICONDA%\\Scripts;%PATH%"
  - conda config --set always_yes yes --set changeps1 no
- - conda config --add pinned_packages defaults::conda
- - conda clean --all
+ - conda install charset-normalizer
  - conda update -q conda
  - conda info -a
  - "conda create -q -n build-environment python=%PYTHON_VERSION% numpy scipy matplotlib"

From 517108a0665e8ace346a5a7d3ad39143fa654261 Mon Sep 17 00:00:00 2001
From: gehbiszumeis <16896724+gehbiszumeis@users.noreply.github.com>
Date: Thu, 25 Nov 2021 11:25:28 +0100
Subject: [PATCH 19/33] try to get from conda-forge

---
 appveyor.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/appveyor.yml b/appveyor.yml
index 39433a900..85f5ef9c2 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -23,7 +23,7 @@ environment:
 install:
  - "set PATH=%MINICONDA%;%MINICONDA%\\Scripts;%PATH%"
  - conda config --set always_yes yes --set changeps1 no
- - conda install charset-normalizer
+ - conda config --prepend channels conda-forge
  - conda update -q conda
  - conda info -a
  - "conda create -q -n build-environment python=%PYTHON_VERSION% numpy scipy matplotlib"

From 0dc988b4ba38b7bc8f7cdedf9cfc44cee98f7349 Mon Sep 17 00:00:00 2001
From: gehbiszumeis <16896724+gehbiszumeis@users.noreply.github.com>
Date: Thu, 25 Nov 2021 11:35:50 +0100
Subject: [PATCH 20/33] revert all conda changes

---
 appveyor.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/appveyor.yml b/appveyor.yml
index 85f5ef9c2..f5faee5cc 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -23,7 +23,6 @@ environment:
 install:
  - "set PATH=%MINICONDA%;%MINICONDA%\\Scripts;%PATH%"
  - conda config --set always_yes yes --set changeps1 no
- - conda config --prepend channels conda-forge
  - conda update -q conda
  - conda info -a
  - "conda create -q -n build-environment python=%PYTHON_VERSION% numpy scipy matplotlib"

From cd6e9b58e806a6c432ceefeac88b10bd129e1c75 Mon Sep 17 00:00:00 2001
From: Peter Paul Kiefer <ppk42@users.noreply.github.com>
Date: Thu, 25 Nov 2021 18:49:55 +0100
Subject: [PATCH 21/33] Try to fix the conda update challange.

See: https://community.intel.com/t5/Intel-Distribution-for-Python/Conda-update-Conda-fails/td-p/1126174

It is just a try for a different context/(conda version).
---
 appveyor.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/appveyor.yml b/appveyor.yml
index f5faee5cc..451fa4f40 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -23,6 +23,7 @@ environment:
 install:
  - "set PATH=%MINICONDA%;%MINICONDA%\\Scripts;%PATH%"
  - conda config --set always_yes yes --set changeps1 no
+ - conda install charset-normalizer -f
  - conda update -q conda
  - conda info -a
  - "conda create -q -n build-environment python=%PYTHON_VERSION% numpy scipy matplotlib"

From 9c0c1676923a5086ed684dc6928b0e751d73839d Mon Sep 17 00:00:00 2001
From: Peter Paul Kiefer <ppk42@users.noreply.github.com>
Date: Thu, 25 Nov 2021 19:24:52 +0100
Subject: [PATCH 22/33] Still fixing build error on appveyor

I also use a newer miniconda version for greater python versions.
---
 appveyor.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/appveyor.yml b/appveyor.yml
index 451fa4f40..261e50f05 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -10,11 +10,11 @@ environment:
     - PYTHON_VERSION: 3.6
       MINICONDA: C:\Miniconda36-x64
     - PYTHON_VERSION: 3.7
-      MINICONDA: C:\Miniconda36-x64
+      MINICONDA: C:\Miniconda37-x64
     - PYTHON_VERSION: 3.8
-      MINICONDA: C:\Miniconda36-x64
+      MINICONDA: C:\Miniconda38-x64
     - PYTHON_VERSION: 3.9
-      MINICONDA: C:\Miniconda36-x64
+      MINICONDA: C:\Miniconda38-x64
 
 #configuration:
 #  - Debug

From 62f88ff0f19b527ee80c9ddf82c6ec4d0d448ddc Mon Sep 17 00:00:00 2001
From: Peter Paul Kiefer <ppk42@users.noreply.github.com>
Date: Thu, 25 Nov 2021 19:33:07 +0100
Subject: [PATCH 23/33] Update appveyor.yml

Thinking it over it decided to use miniconda38 for all python versions unless python 3.5.
---
 appveyor.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/appveyor.yml b/appveyor.yml
index 261e50f05..e69bb64e4 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -8,9 +8,9 @@ environment:
     - PYTHON_VERSION: 3.5
       MINICONDA: C:\Miniconda35-x64
     - PYTHON_VERSION: 3.6
-      MINICONDA: C:\Miniconda36-x64
+      MINICONDA: C:\Miniconda38-x64
     - PYTHON_VERSION: 3.7
-      MINICONDA: C:\Miniconda37-x64
+      MINICONDA: C:\Miniconda38-x64
     - PYTHON_VERSION: 3.8
       MINICONDA: C:\Miniconda38-x64
     - PYTHON_VERSION: 3.9
@@ -23,7 +23,6 @@ environment:
 install:
  - "set PATH=%MINICONDA%;%MINICONDA%\\Scripts;%PATH%"
  - conda config --set always_yes yes --set changeps1 no
- - conda install charset-normalizer -f
  - conda update -q conda
  - conda info -a
  - "conda create -q -n build-environment python=%PYTHON_VERSION% numpy scipy matplotlib"

From 77ea10b752b74ed8e382f9c14bdad98e2dfd764f Mon Sep 17 00:00:00 2001
From: gehbiszumeis <16896724+gehbiszumeis@users.noreply.github.com>
Date: Fri, 26 Nov 2021 09:19:57 +0100
Subject: [PATCH 24/33] revert miniconda versioning changes

---
 appveyor.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/appveyor.yml b/appveyor.yml
index e69bb64e4..f5faee5cc 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -8,13 +8,13 @@ environment:
     - PYTHON_VERSION: 3.5
       MINICONDA: C:\Miniconda35-x64
     - PYTHON_VERSION: 3.6
-      MINICONDA: C:\Miniconda38-x64
+      MINICONDA: C:\Miniconda36-x64
     - PYTHON_VERSION: 3.7
-      MINICONDA: C:\Miniconda38-x64
+      MINICONDA: C:\Miniconda36-x64
     - PYTHON_VERSION: 3.8
-      MINICONDA: C:\Miniconda38-x64
+      MINICONDA: C:\Miniconda36-x64
     - PYTHON_VERSION: 3.9
-      MINICONDA: C:\Miniconda38-x64
+      MINICONDA: C:\Miniconda36-x64
 
 #configuration:
 #  - Debug

From c84d968f2a7dce2ef44315b6b9f024f05bc07b08 Mon Sep 17 00:00:00 2001
From: gehbiszumeis <16896724+gehbiszumeis@users.noreply.github.com>
Date: Fri, 26 Nov 2021 09:20:24 +0100
Subject: [PATCH 25/33] adjust GPy version in appveyor.yml

---
 appveyor.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/appveyor.yml b/appveyor.yml
index f5faee5cc..b62f8b7d8 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -3,7 +3,7 @@ environment:
     secure: 8/ZjXFwtd1S7ixd7PJOpptupKKEDhm2da/q3unabJ00=
   COVERALLS_REPO_TOKEN:
     secure: d3Luic/ESkGaWnZrvWZTKrzO+xaVwJWaRCEP0F+K/9DQGPSRZsJ/Du5g3s4XF+tS
-  gpy_version: 1.9.9
+  gpy_version: 1.10.0
   matrix:
     - PYTHON_VERSION: 3.5
       MINICONDA: C:\Miniconda35-x64

From a63306423df5886270d40903454bdbce028a73a3 Mon Sep 17 00:00:00 2001
From: Peter Paul Kiefer <dafisppk@gmail.com>
Date: Sat, 27 Nov 2021 16:03:10 +0100
Subject: [PATCH 26/33] 1st attempt bring the appveyor build to life again

---
 appveyor.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/appveyor.yml b/appveyor.yml
index f5faee5cc..dd89a2c47 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -8,13 +8,13 @@ environment:
     - PYTHON_VERSION: 3.5
       MINICONDA: C:\Miniconda35-x64
     - PYTHON_VERSION: 3.6
-      MINICONDA: C:\Miniconda36-x64
+      MINICONDA: C:\Miniconda3-x64
     - PYTHON_VERSION: 3.7
-      MINICONDA: C:\Miniconda36-x64
+      MINICONDA: C:\Miniconda3-x64
     - PYTHON_VERSION: 3.8
-      MINICONDA: C:\Miniconda36-x64
+      MINICONDA: C:\Miniconda3-x64
     - PYTHON_VERSION: 3.9
-      MINICONDA: C:\Miniconda36-x64
+      MINICONDA: C:\Miniconda3-x64
 
 #configuration:
 #  - Debug

From 299b3b023ac209f1fb449f1927eca1f0c4225b1d Mon Sep 17 00:00:00 2001
From: Peter Paul Kiefer <dafisppk@gmail.com>
Date: Sun, 28 Nov 2021 10:00:24 +0100
Subject: [PATCH 27/33] #955 fixing ci build on appveyor

After bringing the miniconda env to work again, the wrong matplotlib version was used. This commit should fix that.
---
 appveyor.yml |  3 ++-
 setup.py     | 12 ++++++++----
 2 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/appveyor.yml b/appveyor.yml
index dd89a2c47..4768a3fa9 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -25,7 +25,8 @@ install:
  - conda config --set always_yes yes --set changeps1 no
  - conda update -q conda
  - conda info -a
- - "conda create -q -n build-environment python=%PYTHON_VERSION% numpy scipy matplotlib"
+# github issue #955: freez build versions of numpy, scipy and matplotlib
+ - "conda create -q -n build-environment python=%PYTHON_VERSION% numpy=1.19.2 scipy=1.5.2 matplotlib=3.3.4"
  - activate build-environment
  # We need wheel installed to build wheels
  - python -m pip install wheel
diff --git a/setup.py b/setup.py
index 73bfc0356..261a7c908 100644
--- a/setup.py
+++ b/setup.py
@@ -117,11 +117,13 @@ def ismac():
 except ModuleNotFoundError:
     ext_mods = []
 
-install_requirements = ['numpy>=1.7', 'six', 'paramz>=0.9.0', 'cython>=0.29']
+# #955
+install_requirements = ['numpy==1.19.2', 'six', 'paramz>=0.9.0', 'cython>=0.29']
 if sys.version_info < (3, 6):
     install_requirements += ['scipy>=1.3.0,<1.5.0']
 else:
-    install_requirements += ['scipy>=1.3.0']
+    # #955
+    install_requirements += ['scipy==1.5.2']
 
 setup(name = 'GPy',
       version = __version__,
@@ -168,13 +170,15 @@ def ismac():
       include_package_data = True,
       py_modules = ['GPy.__init__'],
       test_suite = 'GPy.testing',
-      setup_requires = ['numpy>=1.7'],
+      # #955
+      setup_requires = ['numpy == 1.19.2'],
       install_requires = install_requirements,
       extras_require = {'docs':['sphinx'],
                         'optional':['mpi4py',
                                     'ipython>=4.0.0',
                                     ],
-                        'plotting':['matplotlib >= 3.0',
+                        #matplotlib Version see github issue #955
+                        'plotting':['matplotlib == 3.3.4',
                                     'plotly >= 1.8.6'],
                         'notebook':['jupyter_client >= 4.0.6',
                                     'ipywidgets >= 4.0.3',

From a93c4ace5f884db4f55e0faffd9f3287d5e86f35 Mon Sep 17 00:00:00 2001
From: Peter Paul Kiefer <dafisppk@gmail.com>
Date: Sun, 28 Nov 2021 10:25:18 +0100
Subject: [PATCH 28/33] #955 Fix CI build

Freezing numpy and scipy was a bad idea.
I freeze matplotlib  dependend  on the python version only.
---
 appveyor.yml |  9 +++++++--
 setup.py     | 13 ++++++-------
 2 files changed, 13 insertions(+), 9 deletions(-)

diff --git a/appveyor.yml b/appveyor.yml
index 4768a3fa9..6bf3333cf 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -7,14 +7,19 @@ environment:
   matrix:
     - PYTHON_VERSION: 3.5
       MINICONDA: C:\Miniconda35-x64
+      MPL_VERSION: 3.0.0
     - PYTHON_VERSION: 3.6
       MINICONDA: C:\Miniconda3-x64
+      MPL_VERSION: 3.3.4
     - PYTHON_VERSION: 3.7
       MINICONDA: C:\Miniconda3-x64
+      MPL_VERSION: 3.3.4
     - PYTHON_VERSION: 3.8
       MINICONDA: C:\Miniconda3-x64
+      MPL_VERSION: 3.3.4
     - PYTHON_VERSION: 3.9
       MINICONDA: C:\Miniconda3-x64
+      MPL_VERSION: 3.3.4
 
 #configuration:
 #  - Debug
@@ -25,8 +30,8 @@ install:
  - conda config --set always_yes yes --set changeps1 no
  - conda update -q conda
  - conda info -a
-# github issue #955: freez build versions of numpy, scipy and matplotlib
- - "conda create -q -n build-environment python=%PYTHON_VERSION% numpy=1.19.2 scipy=1.5.2 matplotlib=3.3.4"
+# github issue #955: freeze build version of matplotlib
+ - "conda create -q -n build-environment python=%PYTHON_VERSION% numpy scipy matplotlib=%MPL_VERSION%"
  - activate build-environment
  # We need wheel installed to build wheels
  - python -m pip install wheel
diff --git a/setup.py b/setup.py
index 261a7c908..b79a0d12a 100644
--- a/setup.py
+++ b/setup.py
@@ -117,13 +117,13 @@ def ismac():
 except ModuleNotFoundError:
     ext_mods = []
 
-# #955
-install_requirements = ['numpy==1.19.2', 'six', 'paramz>=0.9.0', 'cython>=0.29']
+install_requirements = ['numpy>=1.7', 'six', 'paramz>=0.9.0', 'cython>=0.29']
+matplotlib_version = 'matplotlib==3.3.4'
 if sys.version_info < (3, 6):
     install_requirements += ['scipy>=1.3.0,<1.5.0']
+    matplotlib_version = 'matplotlib==3.0.0'
 else:
-    # #955
-    install_requirements += ['scipy==1.5.2']
+    install_requirements += ['scipy>=1.3.0']
 
 setup(name = 'GPy',
       version = __version__,
@@ -170,15 +170,14 @@ def ismac():
       include_package_data = True,
       py_modules = ['GPy.__init__'],
       test_suite = 'GPy.testing',
-      # #955
-      setup_requires = ['numpy == 1.19.2'],
+      setup_requires = ['numpy>=1.7'],
       install_requires = install_requirements,
       extras_require = {'docs':['sphinx'],
                         'optional':['mpi4py',
                                     'ipython>=4.0.0',
                                     ],
                         #matplotlib Version see github issue #955
-                        'plotting':['matplotlib == 3.3.4',
+                        'plotting':[matplotlib_version,
                                     'plotly >= 1.8.6'],
                         'notebook':['jupyter_client >= 4.0.6',
                                     'ipywidgets >= 4.0.3',

From 23aae96152c9a2b530b80613044571cea8549959 Mon Sep 17 00:00:00 2001
From: gehbiszumeis <16896724+gehbiszumeis@users.noreply.github.com>
Date: Wed, 1 Dec 2021 10:06:01 +0100
Subject: [PATCH 29/33] add: built_from_dict method for White Kernel

---
 GPy/kern/src/static.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/GPy/kern/src/static.py b/GPy/kern/src/static.py
index e02513378..a854fe416 100644
--- a/GPy/kern/src/static.py
+++ b/GPy/kern/src/static.py
@@ -68,6 +68,11 @@ def to_dict(self):
         input_dict = super(White, self)._save_to_input_dict()
         input_dict["class"] = "GPy.kern.White"
         return input_dict
+
+    @staticmethod
+    def _build_from_input_dict(kernel_class, input_dict):
+        useGPU = input_dict.pop('useGPU', None)
+        return White(**input_dict)
     
     def K(self, X, X2=None):
         if X2 is None:

From 5c587e91b9a0f185c8caea5abf0e48d7e9220f35 Mon Sep 17 00:00:00 2001
From: gehbiszumeis <16896724+gehbiszumeis@users.noreply.github.com>
Date: Tue, 14 Dec 2021 15:08:13 +0100
Subject: [PATCH 30/33] docstring typo fix

---
 GPy/models/sparse_gp_coregionalized_regression.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/GPy/models/sparse_gp_coregionalized_regression.py b/GPy/models/sparse_gp_coregionalized_regression.py
index 2a19d52cb..c5a8a6005 100644
--- a/GPy/models/sparse_gp_coregionalized_regression.py
+++ b/GPy/models/sparse_gp_coregionalized_regression.py
@@ -28,7 +28,7 @@ class SparseGPCoregionalizedRegression(SparseGP):
 
     :param name: model name
     :type name: string
-    :param W_rank: number tuples of the corregionalization parameters 'W' (see coregionalize kernel documentation)
+    :param W_rank: number tuples of the coregionalization parameters 'W' (see coregionalize kernel documentation)
     :type W_rank: integer
     :param kernel_name: name of the kernel
     :type kernel_name: string

From ebad34a118f5e85b92d42f3b5e72399f9741d43b Mon Sep 17 00:00:00 2001
From: gehbiszumeis <16896724+gehbiszumeis@users.noreply.github.com>
Date: Thu, 23 Dec 2021 09:18:26 +0100
Subject: [PATCH 31/33] to and & from_dict method for periodic kernel

---
 GPy/kern/src/periodic.py                   | 25 ++++++++++++++++++++++
 GPy/models/gp_coregionalized_regression.py |  2 +-
 2 files changed, 26 insertions(+), 1 deletion(-)

diff --git a/GPy/kern/src/periodic.py b/GPy/kern/src/periodic.py
index 3a7a515e3..d97c92341 100644
--- a/GPy/kern/src/periodic.py
+++ b/GPy/kern/src/periodic.py
@@ -40,6 +40,13 @@ def f(x):
             return alpha*np.cos(omega*x + phase)
         return f
 
+    def _save_to_input_dict(self):
+        input_dict = super(Periodic, self)._save_to_input_dict()
+        input_dict["variance"] = self.variance.values.tolist()
+        input_dict["lengthscale"] = self.lengthscale.values.tolist()
+        input_dict["period"] = self.period.values.tolist()
+        return input_dict
+
     @silence_errors
     def _cos_factorization(self, alpha, omega, phase):
         r1 = np.sum(alpha*np.cos(phase),axis=1)[:,None]
@@ -200,6 +207,24 @@ def parameters_changed(self):
         self.G = self.Gram_matrix()
         self.Gi = np.linalg.inv(self.G)
 
+    def to_dict(self):
+        """
+        Convert the object into a json serializable dictionary.
+
+        Note: It uses the private method _save_to_input_dict of the parent.
+
+        :return dict: json serializable dictionary containing the needed information to instantiate the object
+        """
+
+        input_dict = super(PeriodicMatern32, self)._save_to_input_dict()
+        input_dict["class"] = "GPy.kern.PeriodicMatern32"
+        return input_dict
+
+    @staticmethod
+    def _build_from_input_dict(kernel_class, input_dict):
+        useGPU = input_dict.pop('useGPU', None)
+        return kernel_class(**input_dict)
+
     def Gram_matrix(self):
         La = np.column_stack((self.a[0]*np.ones((self.n_basis,1)),self.a[1]*self.basis_omega,self.a[2]*self.basis_omega**2))
         Lo = np.column_stack((self.basis_omega,self.basis_omega,self.basis_omega))
diff --git a/GPy/models/gp_coregionalized_regression.py b/GPy/models/gp_coregionalized_regression.py
index 6604f6348..4662ab419 100644
--- a/GPy/models/gp_coregionalized_regression.py
+++ b/GPy/models/gp_coregionalized_regression.py
@@ -23,7 +23,7 @@ class GPCoregionalizedRegression(GP):
     :type likelihoods_list: None | a list GPy.likelihoods
     :param name: model name
     :type name: string
-    :param W_rank: number tuples of the corregionalization parameters 'W' (see coregionalize kernel documentation)
+    :param W_rank: number tuples of the coregionalization parameters 'W' (see coregionalize kernel documentation)
     :type W_rank: integer
     :param kernel_name: name of the kernel
     :type kernel_name: string

From aa9a2ee3600b0fc55f7b39fe8f7ecfa94af2c30a Mon Sep 17 00:00:00 2001
From: gehbiszumeis <16896724+gehbiszumeis@users.noreply.github.com>
Date: Wed, 19 Jan 2022 15:15:19 +0100
Subject: [PATCH 32/33] typo fix

---
 GPy/core/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/GPy/core/__init__.py b/GPy/core/__init__.py
index 08659add0..8b5226681 100644
--- a/GPy/core/__init__.py
+++ b/GPy/core/__init__.py
@@ -63,7 +63,7 @@ def randomize(self, rand_gen=None, *args, **kwargs):
     Make this draw from the prior if one exists, else draw from given random generator
 
     :param rand_gen: np random number generator which takes args and kwargs
-    :param flaot loc: loc parameter for random number generator
+    :param float loc: loc parameter for random number generator
     :param float scale: scale parameter for random number generator
     :param args, kwargs: will be passed through to random number generator
     """

From f161325f626240a83031f4b8a80579f09513b478 Mon Sep 17 00:00:00 2001
From: gehbiszumeis <16896724+gehbiszumeis@users.noreply.github.com>
Date: Wed, 23 Feb 2022 16:19:49 +0100
Subject: [PATCH 33/33] saving W_rank variable in from_dict method for
 Coregionalization kernels + typo fix

---
 GPy/kern/src/coregionalize.py | 1 +
 GPy/util/multioutput.py       | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/GPy/kern/src/coregionalize.py b/GPy/kern/src/coregionalize.py
index d05f5c6ad..a5a72bb04 100644
--- a/GPy/kern/src/coregionalize.py
+++ b/GPy/kern/src/coregionalize.py
@@ -150,6 +150,7 @@ def to_dict(self):
         input_dict["W"] = self.W.values.tolist()
         input_dict["kappa"] = self.kappa.values.tolist()
         input_dict["output_dim"] = self.output_dim
+        input_dict["rank"] = self.rank
         return input_dict
 
     @staticmethod
diff --git a/GPy/util/multioutput.py b/GPy/util/multioutput.py
index 912278388..0b1772e28 100644
--- a/GPy/util/multioutput.py
+++ b/GPy/util/multioutput.py
@@ -75,7 +75,7 @@ def ICM(input_dim, num_outputs, kernel, W_rank=1,W=None,kappa=None,name='ICM'):
     :num_outputs: Number of outputs
     :param kernel: kernel that will be multiplied by the coregionalize kernel (matrix B).
     :type kernel: a GPy kernel
-    :param W_rank: number tuples of the corregionalization parameters 'W'
+    :param W_rank: number tuples of the coregionalization parameters 'W'
     :type W_rank: integer
     """
     if kernel.input_dim != input_dim: