From e2ccc0e9578920204a2c692d9812c909889994d2 Mon Sep 17 00:00:00 2001
From: David John Gagne <davidjohngagne@gmail.com>
Date: Wed, 28 Feb 2024 14:25:39 -0700
Subject: [PATCH 1/7] Added classifier and regression notebook links in docs

---
 docs/source/index.rst                         |  6 +-
 docs/source/install.rst                       | 55 ++++++++++++++++++-
 .../source/notebooks/classifier_example.ipynb |  1 +
 .../source/notebooks/regression_example.ipynb |  1 +
 4 files changed, 60 insertions(+), 3 deletions(-)
 create mode 120000 docs/source/notebooks/classifier_example.ipynb
 create mode 120000 docs/source/notebooks/regression_example.ipynb

diff --git a/docs/source/index.rst b/docs/source/index.rst
index ad0512e..0c6837f 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -9,9 +9,11 @@ Welcome to miles-guess's documentation!
 .. toctree::
    :maxdepth: 2
    :caption: Contents:
-   
-   modules.rst
 
+   install.rst
+   modules.rst
+   notebooks/classifier_example.ipynb
+   notebooks/regression_example.ipynb
 
 Indices and tables
 ==================
diff --git a/docs/source/install.rst b/docs/source/install.rst
index 346209f..8e29f62 100644
--- a/docs/source/install.rst
+++ b/docs/source/install.rst
@@ -1,6 +1,59 @@
 .. install
 
 Install MILES GUESS
--------------------
+===================
+First, set up a base Python environment on
+your system. We highly recommend using miniconda or
+mambaforge to easily install all the dependencies.
+
+To install the stable version of the package:
+
+.. code-block:: bash
+    pip install miles-guess
+
+To use the latest developed version of the package,
+first download :
+
+.. code-block:: bash
+    git clone git@github.com:ai2es/miles-guess.git
+    cd miles-guess
+
+Next, build the environment for the package.
+
+For CPU-based systems:
+
+.. code-block:: bash
+    mamba env create -f environment.yml
+
+For GPU-based systems:
+
+.. code-block:: bash
+    mamba env create -f environment_casper.yml
+
+If you want to install miles-guess directly
+after building your environment run:
+
+.. code-block:: bash
+    pip install .
+
+Keras 3 Installation
+--------------------
+MILES GUESS depends on Keras 3 as its primary
+ML backend and through Keras 3 can support
+tensorflow, pytorch, or jax. The current version
+of tensorflow (2.15) will downgrade keras 3 to
+keras 2.15 upon installation. If you run into
+this issue, reinstall keras 3 by running the
+following command:
+
+.. code-block:: bash
+    pip install --upgrade keras
+
+
+
+
+
+
+
 
 
diff --git a/docs/source/notebooks/classifier_example.ipynb b/docs/source/notebooks/classifier_example.ipynb
new file mode 120000
index 0000000..e614503
--- /dev/null
+++ b/docs/source/notebooks/classifier_example.ipynb
@@ -0,0 +1 @@
+../../../notebooks/classifier_example.ipynb
\ No newline at end of file
diff --git a/docs/source/notebooks/regression_example.ipynb b/docs/source/notebooks/regression_example.ipynb
new file mode 120000
index 0000000..08bc774
--- /dev/null
+++ b/docs/source/notebooks/regression_example.ipynb
@@ -0,0 +1 @@
+../../../notebooks/regression_example.ipynb
\ No newline at end of file

From 500f5091d40f7b9d12c87a5f1422978d8f0dde4f Mon Sep 17 00:00:00 2001
From: David John Gagne <davidjohngagne@gmail.com>
Date: Wed, 28 Feb 2024 16:19:55 -0700
Subject: [PATCH 2/7] Fixed bug.

---
 mlguess/keras/models_deprecated.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/mlguess/keras/models_deprecated.py b/mlguess/keras/models_deprecated.py
index 4b26c96..0473e45 100644
--- a/mlguess/keras/models_deprecated.py
+++ b/mlguess/keras/models_deprecated.py
@@ -9,7 +9,7 @@
 from tensorflow.keras.layers import Dense, LeakyReLU, GaussianNoise, Dropout
 from tensorflow.keras.optimizers import Adam, SGD
 from mlguess.keras.layers import DenseNormalGamma, DenseNormal
-from mlguess.keras.losses import EvidentialRegressionLoss, EvidentialRegressionCoupledLoss, GaussianNLL
+from mlguess.keras.losses import EvidentialRegressionLoss, EvidentialRegressionCoupledLoss, gaussian_nll
 from mlguess.keras.losses import DirichletEvidentialLoss
 from mlguess.keras.callbacks import ReportEpoch
 from imblearn.under_sampling import RandomUnderSampler
@@ -597,7 +597,7 @@ def build_neural_network(self, inputs, outputs):
             inputs (int): Number of input predictor variables
             outputs (int): Number of output predictor variables
         """
-        self.loss = GaussianNLL
+        self.loss = gaussian_nll
 
         nn_input = Input(shape=(inputs,), name="input")
         nn_model = nn_input

From 34493f3ba3b240225ab80339d8c4b2dc9b3fb204 Mon Sep 17 00:00:00 2001
From: David John Gagne <davidjohngagne@gmail.com>
Date: Thu, 29 Feb 2024 10:28:06 -0700
Subject: [PATCH 3/7] Updated docs and environment.

---
 docs/source/install.rst | 14 ++++++++++++++
 environment.yml         |  2 +-
 environment_casper.yml  |  2 +-
 pyproject.toml          |  8 +++++---
 4 files changed, 21 insertions(+), 5 deletions(-)

diff --git a/docs/source/install.rst b/docs/source/install.rst
index 8e29f62..4e50240 100644
--- a/docs/source/install.rst
+++ b/docs/source/install.rst
@@ -2,6 +2,14 @@
 
 Install MILES GUESS
 ===================
+
+MILES GUESS supports Python 3.8 to 3.11. Support
+for newer versions of Python depends on the choice
+of deep learning model backend.
+
+The primary ML library dependency is keras 3. Install one
+of the keras 3 backends (tensorflow, pytorch, or jax).
+
 First, set up a base Python environment on
 your system. We highly recommend using miniconda or
 mambaforge to easily install all the dependencies.
@@ -9,12 +17,14 @@ mambaforge to easily install all the dependencies.
 To install the stable version of the package:
 
 .. code-block:: bash
+
     pip install miles-guess
 
 To use the latest developed version of the package,
 first download :
 
 .. code-block:: bash
+
     git clone git@github.com:ai2es/miles-guess.git
     cd miles-guess
 
@@ -23,17 +33,20 @@ Next, build the environment for the package.
 For CPU-based systems:
 
 .. code-block:: bash
+
     mamba env create -f environment.yml
 
 For GPU-based systems:
 
 .. code-block:: bash
+
     mamba env create -f environment_casper.yml
 
 If you want to install miles-guess directly
 after building your environment run:
 
 .. code-block:: bash
+
     pip install .
 
 Keras 3 Installation
@@ -47,6 +60,7 @@ this issue, reinstall keras 3 by running the
 following command:
 
 .. code-block:: bash
+
     pip install --upgrade keras
 
 
diff --git a/environment.yml b/environment.yml
index d47f0cd..f3b8769 100644
--- a/environment.yml
+++ b/environment.yml
@@ -2,7 +2,7 @@ name: guess
 channels:
   - conda-forge
 dependencies:
-  - python=3.10
+  - python=3.11
   - numpy<1.24
   - scipy
   - matplotlib
diff --git a/environment_casper.yml b/environment_casper.yml
index 64debc4..0563423 100644
--- a/environment_casper.yml
+++ b/environment_casper.yml
@@ -3,7 +3,7 @@ channels:
   - conda-forge
   - nvidia
 dependencies:
-  - python=3.10
+  - python=3.11
   - numpy=1.23.*
   - scipy
   - matplotlib
diff --git a/pyproject.toml b/pyproject.toml
index 7008802..67f0267 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "miles-guess"
-authors = [{name = "John Schreck, David John Gagne, Charlie Becker, Gabrielle Gantos", email = "miles@ucar.edu"}]
+authors = [{name = "John Schreck, David John Gagne, Charlie Becker, Gabrielle Gantos", email = "milescore@ucar.edu"}]
 readme = "README.md"
 license = {file = "LICENSE"}
 dynamic = ["version"]
@@ -36,12 +36,14 @@ dependencies = [
     ]
 
 [project.optional-dependencies]
-tensorflow = ["tensorflow>=2.12"]
+tensorflow = ["tensorflow==2.16.0rc0"]
 
-tensorflow_gpu = ["tensorflow[and-cuda]"]
+tensorflow_gpu = ["tensorflow[and-cuda]==2.16.0rc0"]
 
 torch = ["torch"]
 
+jax = ["jax"]
+
 
 
 [tool.setuptools]

From de804f24461e1597cde110521341de1a189dfe7e Mon Sep 17 00:00:00 2001
From: David John Gagne <davidjohngagne@gmail.com>
Date: Thu, 29 Feb 2024 10:34:12 -0700
Subject: [PATCH 4/7] Updated modules

---
 docs/source/index.rst   |  2 +-
 docs/source/mlguess.rst |  1 +
 docs/source/modules.rst | 10 +++++++---
 3 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/docs/source/index.rst b/docs/source/index.rst
index 0c6837f..023ce9b 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -11,7 +11,7 @@ Welcome to miles-guess's documentation!
    :caption: Contents:
 
    install.rst
-   modules.rst
+   mlguess.rst
    notebooks/classifier_example.ipynb
    notebooks/regression_example.ipynb
 
diff --git a/docs/source/mlguess.rst b/docs/source/mlguess.rst
index 4fa79cd..2a6618a 100644
--- a/docs/source/mlguess.rst
+++ b/docs/source/mlguess.rst
@@ -8,6 +8,7 @@ Subpackages
    :maxdepth: 4
 
    mlguess.keras
+   mlguess.tests
    mlguess.torch
 
 Submodules
diff --git a/docs/source/modules.rst b/docs/source/modules.rst
index 3ca959a..ca24a9a 100644
--- a/docs/source/modules.rst
+++ b/docs/source/modules.rst
@@ -1,7 +1,11 @@
-mlguess
-=======
+applications
+============
 
 .. toctree::
    :maxdepth: 4
 
-   mlguess
+   evaluate_ptype
+   train_classifier_ptype
+   train_evidential_SL
+   train_gaussian_SL
+   train_mlp_SL

From 2feced13ce5a071e6e1d335d27b8bbba188c5a89 Mon Sep 17 00:00:00 2001
From: David John Gagne <davidjohngagne@gmail.com>
Date: Thu, 29 Feb 2024 10:34:41 -0700
Subject: [PATCH 5/7] Update removal of modules

---
 docs/source/modules.rst | 11 -----------
 1 file changed, 11 deletions(-)
 delete mode 100644 docs/source/modules.rst

diff --git a/docs/source/modules.rst b/docs/source/modules.rst
deleted file mode 100644
index ca24a9a..0000000
--- a/docs/source/modules.rst
+++ /dev/null
@@ -1,11 +0,0 @@
-applications
-============
-
-.. toctree::
-   :maxdepth: 4
-
-   evaluate_ptype
-   train_classifier_ptype
-   train_evidential_SL
-   train_gaussian_SL
-   train_mlp_SL

From 5ecb8989e942538c26c7a514f1fc26f7685c318d Mon Sep 17 00:00:00 2001
From: David John Gagne <davidjohngagne@gmail.com>
Date: Thu, 29 Feb 2024 10:42:56 -0700
Subject: [PATCH 6/7] Edits to docs

---
 docs/source/conf.py                |  2 +-
 docs/source/mlguess.tests.rst      | 45 ++++++++++++++++++++
 mlguess/torch/regression_losses.py | 66 +++++++++++++++---------------
 3 files changed, 79 insertions(+), 34 deletions(-)
 create mode 100644 docs/source/mlguess.tests.rst

diff --git a/docs/source/conf.py b/docs/source/conf.py
index b58173f..ff20911 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -9,7 +9,7 @@
 project = 'miles-guess'
 copyright = '2024, MILES Group'
 author = 'MILES Group'
-release = '0.1'
+release = '2024.1.1'
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
diff --git a/docs/source/mlguess.tests.rst b/docs/source/mlguess.tests.rst
new file mode 100644
index 0000000..a5c21cf
--- /dev/null
+++ b/docs/source/mlguess.tests.rst
@@ -0,0 +1,45 @@
+mlguess.tests package
+=====================
+
+Submodules
+----------
+
+mlguess.tests.test\_environment module
+--------------------------------------
+
+.. automodule:: mlguess.tests.test_environment
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mlguess.tests.test\_layers module
+---------------------------------
+
+.. automodule:: mlguess.tests.test_layers
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mlguess.tests.test\_models module
+---------------------------------
+
+.. automodule:: mlguess.tests.test_models
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mlguess.tests.test\_pit module
+------------------------------
+
+.. automodule:: mlguess.tests.test_pit
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: mlguess.tests
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/mlguess/torch/regression_losses.py b/mlguess/torch/regression_losses.py
index 067f841..e93f6c0 100644
--- a/mlguess/torch/regression_losses.py
+++ b/mlguess/torch/regression_losses.py
@@ -4,9 +4,9 @@
 import torch
 import torch.nn.functional as F
 
-
 tol = torch.finfo(torch.float32).eps
 
+
 def nig_nll(y, gamma, v, alpha, beta):
     """Implements Normal Inverse Gamma-Negative Log Likelihood for
        Deep Evidential Regression
@@ -16,13 +16,14 @@ def nig_nll(y, gamma, v, alpha, beta):
     """
     two_blambda = 2 * beta * (1 + v) + tol
     nll = 0.5 * torch.log(np.pi / (v + tol)) \
-            - alpha * torch.log(two_blambda + tol) \
-            + (alpha + 0.5) * torch.log(v * (y - gamma) ** 2 + two_blambda + tol) \
-            + torch.lgamma(alpha) \
-            - torch.lgamma(alpha + 0.5)
+          - alpha * torch.log(two_blambda + tol) \
+          + (alpha + 0.5) * torch.log(v * (y - gamma) ** 2 + two_blambda + tol) \
+          + torch.lgamma(alpha) \
+          - torch.lgamma(alpha + 0.5)
 
     return nll
 
+
 def nig_reg(y, gamma, v, alpha):
     """Implements Normal Inverse Gamma Regularizer for Deep Evidential
        Regression
@@ -34,6 +35,7 @@ def nig_reg(y, gamma, v, alpha):
     evi = 2 * v + alpha
     return error * evi
 
+
 def evidential_regression_loss(y, pred, coef=1.0):
     """Implements Evidential Regression Loss for Deep Evidential
        Regression
@@ -67,17 +69,18 @@ def modified_mse(gamma, nu, alpha, beta, target, reduction='mean'):
     Returns:
         [FloatTensor]: The loss value. 
     """
-    mse = (gamma-target)**2
+    mse = (gamma - target) ** 2
     c = get_mse_coef(gamma, nu, alpha, beta, target).detach()
-    mod_mse = mse*c
-    
-    if reduction == 'mean': 
+    mod_mse = mse * c
+
+    if reduction == 'mean':
         return mod_mse.mean()
     elif reduction == 'sum':
         return mod_mse.sum()
     else:
         return mod_mse
 
+
 def get_mse_coef(gamma, nu, alpha, beta, y):
     """
     Return the coefficient of the MSE loss for each prediction.
@@ -100,7 +103,7 @@ def get_mse_coef(gamma, nu, alpha, beta, y):
     nu_eff = check_mse_efficiency_nu(gamma, nu, alpha, beta, y)
     delta = (gamma - y).abs()
     min_bound = torch.min(nu_eff, alpha_eff).min()
-    c = (min_bound.sqrt()/(delta + tol)).detach()
+    c = (min_bound.sqrt() / (delta + tol)).detach()
     return torch.clip(c, min=False, max=1.)
 
 
@@ -123,7 +126,7 @@ def check_mse_efficiency_alpha(nu, alpha, beta):
         where f => the NLL loss (BayesianDTI.loss.MarginalLikelihood)
     
     """
-    right = (torch.exp((torch.digamma(alpha+0.5)-torch.digamma(alpha))) - 1)*2*beta*(1+nu) / (nu + 1e-8)
+    right = (torch.exp((torch.digamma(alpha + 0.5) - torch.digamma(alpha))) - 1) * 2 * beta * (1 + nu) / (nu + 1e-8)
     return right.detach()
 
 
@@ -161,9 +164,10 @@ class EvidentialMarginalLikelihood(torch.nn.modules.loss._Loss):
     Reference: https://www.mit.edu/~amini/pubs/pdf/deep-evidential-regression.pdf
     Source: https://github.com/deargen/MT-ENet/tree/468822188f52e517b1ee8e386eea607b2b7d8829
     """
+
     def __init__(self, size_average=None, reduce=None, reduction: str = 'mean'):
         super(EvidentialMarginalLikelihood, self).__init__(size_average, reduce, reduction)
-    
+
     def forward(self, gamma: torch.Tensor, nu: torch.Tensor, alpha: torch.Tensor, beta: torch.Tensor,
                 target: torch.Tensor) -> torch.Tensor:
         """
@@ -176,25 +180,21 @@ def forward(self, gamma: torch.Tensor, nu: torch.Tensor, alpha: torch.Tensor, be
             
         Return:
             (Tensor) Negative log marginal likelihood of EvidentialNet
-                p(y|m) = Student-t(y; gamma, (beta(1+nu))/(nu*alpha) , 2*alpha)
-                then, the negative log likelihood is (CAUTION QUITE COMPLEX!)
-                NLL = -log(p(y|m)) =
-                    log(3.14/nu)*0.5 - alpha*log(2*beta*(1 + nu)) + (alpha + 0.5)*log( nu(target - gamma)^2 + 2*beta(1 + nu) )
-                    + log(GammaFunc(alpha)/GammaFunc(alpha + 0.5))
+
         """
         pi = torch.tensor(np.pi)
-        x1 = torch.log(pi/(nu + tol))*0.5
-        x2 = -alpha*torch.log(2.*beta*(1.+ nu) + tol)
-        x3 = (alpha + 0.5)*torch.log( nu*(target - gamma)**2 + 2.*beta*(1. + nu) + tol)
+        x1 = torch.log(pi / (nu + tol)) * 0.5
+        x2 = -alpha * torch.log(2. * beta * (1. + nu) + tol)
+        x3 = (alpha + 0.5) * torch.log(nu * (target - gamma) ** 2 + 2. * beta * (1. + nu) + tol)
         x4 = torch.lgamma(alpha + tol) - torch.lgamma(alpha + 0.5 + tol)
-        if self.reduction == 'mean': 
+        if self.reduction == 'mean':
             return (x1 + x2 + x3 + x4).mean()
         elif self.reduction == 'sum':
             return (x1 + x2 + x3 + x4).sum()
         else:
             return x1 + x2 + x3 + x4
 
-    
+
 class EvidenceRegularizer(torch.nn.modules.loss._Loss):
     """
     Regularization for the regression prior network.
@@ -203,10 +203,11 @@ class EvidenceRegularizer(torch.nn.modules.loss._Loss):
     Reference: https://www.mit.edu/~amini/pubs/pdf/deep-evidential-regression.pdf
     Source: https://github.com/deargen/MT-ENet/tree/468822188f52e517b1ee8e386eea607b2b7d8829
     """
+
     def __init__(self, size_average=None, reduce=None, reduction: str = 'mean', factor=0.1):
         super(EvidenceRegularizer, self).__init__(size_average, reduce, reduction)
         self.factor = factor
-    
+
     def forward(self, gamma: torch.Tensor, nu: torch.Tensor, alpha: torch.Tensor,
                 target: torch.Tensor) -> torch.Tensor:
         """
@@ -218,17 +219,15 @@ def forward(self, gamma: torch.Tensor, nu: torch.Tensor, alpha: torch.Tensor,
 
         Return:
             (Tensor) prior network regularization
-            Loss = |y - gamma|*(2*nu + alpha) * factor
-            
         """
-        loss_value =  torch.abs(target - gamma)*(2*nu + alpha) * self.factor
-        if self.reduction == 'mean': 
+        loss_value = torch.abs(target - gamma) * (2 * nu + alpha) * self.factor
+        if self.reduction == 'mean':
             return loss_value.mean()
         elif self.reduction == 'sum':
             return loss_value.sum()
         else:
             return loss_value
-    
+
 
 class GaussianNLL(torch.nn.modules.loss._Loss):
     """
@@ -237,15 +236,16 @@ class GaussianNLL(torch.nn.modules.loss._Loss):
     Reference: https://www.mit.edu/~amini/pubs/pdf/deep-evidential-regression.pdf
     Source: https://github.com/deargen/MT-ENet/tree/468822188f52e517b1ee8e386eea607b2b7d8829
     """
+
     def __init__(self, size_average=None, reduce=None, reduction: str = 'mean'):
         super(GaussianNLL, self).__init__(size_average, reduce, reduction)
-    
+
     def forward(self, input_mu: torch.Tensor, input_std: torch.Tensor,
                 target: torch.Tensor) -> torch.Tensor:
-        x1 = 0.5*torch.log(2*np.pi*input_std*input_std)
-        x2 = 0.5/(input_std**2)*((target - input_mu)**2)
-        
+        x1 = 0.5 * torch.log(2 * np.pi * input_std * input_std)
+        x2 = 0.5 / (input_std ** 2) * ((target - input_mu) ** 2)
+
         if self.reduction == 'mean':
             return torch.mean(x1 + x2)
         elif self.reduction == 'sum':
-            return torch.sum(x1 + x2)
\ No newline at end of file
+            return torch.sum(x1 + x2)

From 528a84bca2773f422601d8b443311acc10b92dba Mon Sep 17 00:00:00 2001
From: David John Gagne <davidjohngagne@gmail.com>
Date: Thu, 29 Feb 2024 10:45:05 -0700
Subject: [PATCH 7/7] Updated env and workflow

---
 .github/workflows/python-package-conda.yml | 3 ---
 environment.yml                            | 2 +-
 2 files changed, 1 insertion(+), 4 deletions(-)

diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml
index 61bc64c..4eaaa9c 100644
--- a/.github/workflows/python-package-conda.yml
+++ b/.github/workflows/python-package-conda.yml
@@ -16,9 +16,6 @@ jobs:
       with:
         environment-file: environment.yml
         activate-environment: test
-        create-args: >-
-          python=3.10
-          numpy
     - shell: bash -l {0}
       run: |
         pip install --upgrade keras
diff --git a/environment.yml b/environment.yml
index 7f73fb5..0915416 100644
--- a/environment.yml
+++ b/environment.yml
@@ -2,7 +2,7 @@ name: guess
 channels:
   - conda-forge
 dependencies:
-  - python=3.11
+  - python=3.10
   - numpy<1.24
   - scipy
   - matplotlib