From 02e450a7ed8d70c38d5f5c0f430515a42b348ced Mon Sep 17 00:00:00 2001
From: Damian Rouson <rouson@lbl.gov>
Date: Sun, 22 Oct 2023 21:55:22 -0700
Subject: [PATCH 01/11] doc(test): fix netCDF_file test comment

---
 test/netCDF_file_test_m.f90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/netCDF_file_test_m.f90 b/test/netCDF_file_test_m.f90
index 56035d396..f01c1b75c 100644
--- a/test/netCDF_file_test_m.f90
+++ b/test/netCDF_file_test_m.f90
@@ -4,7 +4,7 @@
 !! Due to a suspected bug in the Intel ifx compiler, the above C preprocessor macro
 !! effectively eliminates this file's source code when building with an Intel compiler.
 module NetCDF_file_test_m
-  !! Define asymmetric tests and procedures required for reporting results
+  !! Define asymmetric tests for the NetCDF file interface
 
   ! External dependencies
   use assert_m, only : assert

From b024b703b41c649858888e2493f65c5aaae8c6ac Mon Sep 17 00:00:00 2001
From: Damian Rouson <rouson@lbl.gov>
Date: Wed, 25 Oct 2023 12:08:01 -0700
Subject: [PATCH 02/11] feat(hyperparameters): def derived type + json I/O

---
 src/inference_engine/hyperparameters_m.f90 | 49 +++++++++++++++++++
 src/inference_engine/hyperparameters_s.f90 | 54 ++++++++++++++++++++
 test/hyperparameters_test_m.f90            | 57 ++++++++++++++++++++++
 test/main.f90                              |  3 ++
 training_parameters.json                   |  9 ++++
 5 files changed, 172 insertions(+)
 create mode 100644 src/inference_engine/hyperparameters_m.f90
 create mode 100644 src/inference_engine/hyperparameters_s.f90
 create mode 100644 test/hyperparameters_test_m.f90
 create mode 100644 training_parameters.json

diff --git a/src/inference_engine/hyperparameters_m.f90 b/src/inference_engine/hyperparameters_m.f90
new file mode 100644
index 000000000..f0e125ef7
--- /dev/null
+++ b/src/inference_engine/hyperparameters_m.f90
@@ -0,0 +1,49 @@
+module hyperparameters_m
+  use sourcery_m, only : file_t
+  implicit none
+
+  private
+  public :: hyperparameters_t
+  public :: initialization_parameters_t 
+  public :: initialization_t
+
+  type initialization_parameters_t 
+    real spread_
+  end type
+
+  type initialization_t
+    character(len=:), allocatable :: initialization_type_
+    type(initialization_parameters_t) ::  initialization_parameters_
+  end type
+ 
+  type hyperparameters_t
+    private
+    character(len=:), allocatable :: activation_
+    integer  mini_batch_size_
+    integer, allocatable :: nodes_per_layer_(:) 
+    type(initialization_t) initialization_
+  contains
+    procedure :: to_json
+  end type
+
+  interface hyperparameters_t
+
+    pure module function construct_from_json_file(file_) result(hyperparameters)
+      implicit none
+      type(file_t), intent(in) :: file_
+      type(hyperparameters_t) hyperparameters
+    end function
+
+  end interface
+
+  interface
+
+    impure elemental module function to_json(self) result(json_file)
+      implicit none
+      class(hyperparameters_t), intent(in) :: self
+      type(file_t) json_file
+    end function
+
+  end interface
+
+end module
diff --git a/src/inference_engine/hyperparameters_s.f90 b/src/inference_engine/hyperparameters_s.f90
new file mode 100644
index 000000000..29007b92c
--- /dev/null
+++ b/src/inference_engine/hyperparameters_s.f90
@@ -0,0 +1,54 @@
+submodule(hyperparameters_m) hyperparameters_s
+  use assert_m, only : assert, intrinsic_array_t
+  use sourcery_m, only : string_t
+  implicit none
+
+contains
+
+  module procedure construct_from_json_file
+    integer l
+    type(string_t), allocatable :: lines(:)
+
+    lines = file_%lines()
+
+    l = 1
+    call assert(adjustl(lines(l)%string())=="{", 'construct_from_json_file: adjustl(lines(l)%string())=="{"', lines(l)%string())
+
+ !{
+ !     "activation" : "sigmoid",
+ !     "num_mini_batches" : 10,
+ !     "nodes per layer" : [2, 72, 2],
+ !     "initialization" : {
+ !         "type" : "perturbed identity",
+ !         "parameters" : [ { "spread" :  0.05 } ]
+ !      }
+ !}
+
+       
+    l = l + 1
+    call assert(adjustl(lines(l)%string())=="}", 'construct_from_json_file: adjustl(lines(l)%string())=="}"', lines(l)%string())
+  end procedure
+
+  module procedure to_json
+    type(string_t), allocatable :: lines(:)
+    integer, parameter :: outer_object_braces = 2
+    integer, parameter :: num_lines = outer_object_braces
+    integer l
+
+    allocate(lines(num_lines))
+
+    l = 1
+    lines(l) = string_t('{')
+
+    l = l + 1
+    !lines(line) = string_t('        "modelName": "' // &
+                                                   !self%metadata_(findloc(key, "modelName", dim=1))%string() // '",')
+
+
+
+    l = l + 1
+    call assert(l == num_lines, "hyperparameters_s(to_json): l == num_lines", intrinsic_array_t([l,num_lines]))
+    lines(l) = string_t('}')
+  end procedure
+
+end submodule hyperparameters_s
diff --git a/test/hyperparameters_test_m.f90 b/test/hyperparameters_test_m.f90
new file mode 100644
index 000000000..ee7440741
--- /dev/null
+++ b/test/hyperparameters_test_m.f90
@@ -0,0 +1,57 @@
+! Copyright (c), The Regents of the University of California
+! Terms of use are as specified in LICENSE.txt
+module hyperparameters_test_m
+  !! Test hyperparameters_t object I/O and construction
+
+  ! External dependencies
+  use assert_m, only : assert
+  use sourcery_m, only : string_t, test_t, test_result_t
+
+  ! Internal dependencies
+  use hyperparameters_m, only : hyperparameters_t
+
+  implicit none
+
+  private
+  public :: hyperparameters_test_t
+
+  type, extends(test_t) :: hyperparameters_test_t
+  contains
+    procedure, nopass :: subject
+    procedure, nopass :: results
+  end type
+
+contains
+
+  pure function subject() result(specimen)
+    character(len=:), allocatable :: specimen
+    specimen = "A hyperparameters_t object"
+  end function
+
+  function results() result(test_results)
+    type(test_result_t), allocatable :: test_results(:)
+
+    character(len=*), parameter :: longest_description = &
+          "writing and then reading gives input matching output for perturbed identity network"
+
+    associate( &
+      descriptions => &
+        [ character(len=len(longest_description)) :: &
+          "writing and then reading gives input matching output for perturbed identity network" &
+        ], &
+      outcomes => &
+        [ write_then_read_perturbed_identity() & 
+        ] & 
+    )
+      call assert(size(descriptions) == size(outcomes),"hyperparameters_test_m(results): size(descriptions) == size(outcomes)")
+      test_results = test_result_t(descriptions, outcomes)
+    end associate
+       
+  end function
+
+  function write_then_read_perturbed_identity() result(test_passes)
+    logical, allocatable :: test_passes(:)
+    test_passes = [.true.]
+  end function
+
+end module hyperparameters_test_m
\ No newline at end of file
diff --git a/test/main.f90 b/test/main.f90
index af501fd26..0867a6b84 100644
--- a/test/main.f90
+++ b/test/main.f90
@@ -4,11 +4,13 @@ program main
   use inference_engine_test_m, only : inference_engine_test_t  
   use asymmetric_engine_test_m, only : asymmetric_engine_test_t  
   use trainable_engine_test_m, only : trainable_engine_test_t  
+  use hyperparameters_test_m, only : hyperparameters_test_t
   implicit none
 
   type(inference_engine_test_t) inference_engine_test
   type(asymmetric_engine_test_t) asymmetric_engine_test
   type(trainable_engine_test_t) trainable_engine_test
+  type(hyperparameters_test_t) hyperparameters_test
   real t_start, t_finish
 
   integer :: passes=0, tests=0
@@ -18,6 +20,7 @@ program main
   call inference_engine_test%report(passes, tests)
   call asymmetric_engine_test%report(passes, tests)
   call trainable_engine_test%report(passes, tests)
+  call hyperparameters_test%report(passes, tests)
 #ifndef __INTEL_FORTRAN
   block 
     use netCDF_file_test_m, only : netCDF_file_test_t
diff --git a/training_parameters.json b/training_parameters.json
new file mode 100644
index 000000000..37b5701f6
--- /dev/null
+++ b/training_parameters.json
@@ -0,0 +1,9 @@
+{
+     "activation" : "sigmoid",
+     "num_mini_batches" : 10,
+     "nodes per layer" : [2, 72, 2],
+     "initialization" : {
+         "type" : "perturbed identity",
+         "parameters" : [ { "spread" :  0.05 } ]
+      }
+}

From fd2cc996fe0f99cd1471b95ce4f75509371e241c Mon Sep 17 00:00:00 2001
From: Damian Rouson <rouson@lbl.gov>
Date: Sun, 29 Oct 2023 20:13:09 -0700
Subject: [PATCH 03/11] refac: update sourcery depency version to 4.4.0

---
 fpm.toml                                      |  2 +-
 .../activation_strategy_m.f90                 |  2 +-
 src/inference_engine/hyperparameters_m.f90    | 26 ++-----
 src/inference_engine/hyperparameters_s.f90    | 76 +++++++++----------
 src/inference_engine/inference_engine_m_.f90  |  3 +-
 src/inference_engine/inference_engine_s.f90   |  6 +-
 .../network_configuration_m.f90               | 39 ++++++++++
 .../network_configuration_s.f90               | 54 +++++++++++++
 src/inference_engine/neuron_m.f90             |  2 +-
 src/inference_engine/neuron_s.f90             |  8 +-
 src/inference_engine/relu_m.f90               |  2 +-
 src/inference_engine/sigmoid_m.f90            |  2 +-
 src/inference_engine/step_m.f90               |  2 +-
 src/inference_engine/swish_m.f90              |  2 +-
 test/asymmetric_engine_test_m.f90             |  4 +-
 test/inference_engine_test_m.f90              |  5 +-
 test/netCDF_file_test_m.f90                   |  4 +-
 training_parameters.json                      |  9 ---
 18 files changed, 153 insertions(+), 95 deletions(-)
 create mode 100644 src/inference_engine/network_configuration_m.f90
 create mode 100644 src/inference_engine/network_configuration_s.f90
 delete mode 100644 training_parameters.json

diff --git a/fpm.toml b/fpm.toml
index 3042622a5..bdc742364 100644
--- a/fpm.toml
+++ b/fpm.toml
@@ -6,5 +6,5 @@ maintainer = "rouson@lbl.gov"
 
 [dependencies]
 assert = {git = "https://github.com/sourceryinstitute/assert", tag = "1.5.0"}
-sourcery = {git = "https://github.com/sourceryinstitute/sourcery", tag = "3.9.1"}
+sourcery = {git = "https://github.com/sourceryinstitute/sourcery", tag = "4.4.0"}
 netcdf-interfaces = {git = "https://github.com/rouson/netcdf-interfaces.git", branch = "implicit-interfaces"}
diff --git a/src/inference_engine/activation_strategy_m.f90 b/src/inference_engine/activation_strategy_m.f90
index cdb464852..dd888ee7c 100644
--- a/src/inference_engine/activation_strategy_m.f90
+++ b/src/inference_engine/activation_strategy_m.f90
@@ -4,7 +4,7 @@ module activation_strategy_m
 
   ! External dependencies
   use kind_parameters_m, only : rkind
-  use string_m, only : string_t
+  use sourcery_m, only : string_t
   implicit none
 
   private
diff --git a/src/inference_engine/hyperparameters_m.f90 b/src/inference_engine/hyperparameters_m.f90
index f0e125ef7..dea9e6580 100644
--- a/src/inference_engine/hyperparameters_m.f90
+++ b/src/inference_engine/hyperparameters_m.f90
@@ -1,34 +1,22 @@
 module hyperparameters_m
-  use sourcery_m, only : file_t
+  use sourcery_m, only : string_t, file_t
   implicit none
 
   private
   public :: hyperparameters_t
-  public :: initialization_parameters_t 
-  public :: initialization_t
 
-  type initialization_parameters_t 
-    real spread_
-  end type
-
-  type initialization_t
-    character(len=:), allocatable :: initialization_type_
-    type(initialization_parameters_t) ::  initialization_parameters_
-  end type
- 
   type hyperparameters_t
     private
-    character(len=:), allocatable :: activation_
-    integer  mini_batch_size_
-    integer, allocatable :: nodes_per_layer_(:) 
-    type(initialization_t) initialization_
+    integer :: mini_batches_ = 10
+    real :: learning_rate_ = 1.5
+    character(len=:), allocatable :: optimizer_
   contains
     procedure :: to_json
   end type
 
   interface hyperparameters_t
 
-    pure module function construct_from_json_file(file_) result(hyperparameters)
+    pure module function from_json(file_) result(hyperparameters)
       implicit none
       type(file_t), intent(in) :: file_
       type(hyperparameters_t) hyperparameters
@@ -38,10 +26,10 @@ pure module function construct_from_json_file(file_) result(hyperparameters)
 
   interface
 
-    impure elemental module function to_json(self) result(json_file)
+    pure module function to_json(self) result(lines)
       implicit none
       class(hyperparameters_t), intent(in) :: self
-      type(file_t) json_file
+      type(string_t), allocatable :: lines(:)
     end function
 
   end interface
diff --git a/src/inference_engine/hyperparameters_s.f90 b/src/inference_engine/hyperparameters_s.f90
index 29007b92c..c1f9aae94 100644
--- a/src/inference_engine/hyperparameters_s.f90
+++ b/src/inference_engine/hyperparameters_s.f90
@@ -1,54 +1,50 @@
 submodule(hyperparameters_m) hyperparameters_s
-  use assert_m, only : assert, intrinsic_array_t
-  use sourcery_m, only : string_t
+  use assert_m, only : assert
   implicit none
 
+  character(len=*), parameter :: mini_batches_key  = "mini-batches"
+  character(len=*), parameter :: learning_rate_key = "learning rate"
+  character(len=*), parameter :: optimizer_key     = "optimizer"
+
 contains
 
-  module procedure construct_from_json_file
-    integer l
+  module procedure from_json
     type(string_t), allocatable :: lines(:)
+    integer l
+    logical hyperparameters_key_found 
 
     lines = file_%lines()
-
-    l = 1
-    call assert(adjustl(lines(l)%string())=="{", 'construct_from_json_file: adjustl(lines(l)%string())=="{"', lines(l)%string())
-
- !{
- !     "activation" : "sigmoid",
- !     "num_mini_batches" : 10,
- !     "nodes per layer" : [2, 72, 2],
- !     "initialization" : {
- !         "type" : "perturbed identity",
- !         "parameters" : [ { "spread" :  0.05 } ]
- !      }
- !}
-
-       
-    l = l + 1
-    call assert(adjustl(lines(l)%string())=="}", 'construct_from_json_file: adjustl(lines(l)%string())=="}"', lines(l)%string())
+    hyperparameters_key_found = .false.
+
+    loop_through_file: &
+    do l=1,size(lines)
+      if (lines(l)%get_json_key() == "hyperparameters") then
+        hyperparameters_key_found = .true.
+        hyperparameters%mini_batches_  = lines(l+1)%get_json_value(string_t(mini_batches_key), mold=0)
+        hyperparameters%learning_rate_ = lines(l+2)%get_json_value(string_t(learning_rate_key), mold=0.)
+        hyperparameters%optimizer_ = lines(l+3)%get_json_value(string_t(optimizer_key), mold=string_t(""))
+        return
+      end if
+    end do loop_through_file
+
+    call assert(hyperparameters_key_found, "hyperparameters_s(from_json): hyperparameters_found")
   end procedure
 
   module procedure to_json
-    type(string_t), allocatable :: lines(:)
-    integer, parameter :: outer_object_braces = 2
-    integer, parameter :: num_lines = outer_object_braces
-    integer l
-
-    allocate(lines(num_lines))
-
-    l = 1
-    lines(l) = string_t('{')
-
-    l = l + 1
-    !lines(line) = string_t('        "modelName": "' // &
-                                                   !self%metadata_(findloc(key, "modelName", dim=1))%string() // '",')
-
-
-
-    l = l + 1
-    call assert(l == num_lines, "hyperparameters_s(to_json): l == num_lines", intrinsic_array_t([l,num_lines]))
-    lines(l) = string_t('}')
+    character(len=*), parameter :: indent = repeat(" ",ncopies=4)
+    integer, parameter :: max_digits = 12
+    character(len=max_digits) mini_batches_string, learning_rate_string
+
+    write(mini_batches_string,*) self%mini_batches_
+    write(learning_rate_string,*) self%learning_rate_
+
+    lines = [ &
+      string_t(indent // '"hyperparameters": {'), &
+      string_t(indent // indent // '"' // mini_batches_key  // '": '  // mini_batches_string   ), &
+      string_t(indent // indent // '"' // learning_rate_key // '": '  // learning_rate_string  ), &
+      string_t(indent // indent // '"' // optimizer_key     // '": "' // self%optimizer_ // '"'), &
+      string_t(indent // '}') &
+    ]
   end procedure
 
 end submodule hyperparameters_s
diff --git a/src/inference_engine/inference_engine_m_.f90 b/src/inference_engine/inference_engine_m_.f90
index cbab99256..358d59a93 100644
--- a/src/inference_engine/inference_engine_m_.f90
+++ b/src/inference_engine/inference_engine_m_.f90
@@ -2,9 +2,8 @@
 ! Terms of use are as specified in LICENSE.txt
 module inference_engine_m_
   !! Define an abstraction that supports inference operationsn on a neural network
-  use string_m, only : string_t
   use activation_strategy_m, only : activation_strategy_t
-  use file_m, only : file_t
+  use sourcery_m, only : file_t, string_t
   use kind_parameters_m, only : rkind
   use tensor_m, only : tensor_t
   use differentiable_activation_strategy_m, only :differentiable_activation_strategy_t
diff --git a/src/inference_engine/inference_engine_s.f90 b/src/inference_engine/inference_engine_s.f90
index 559ef29ab..9e03b08df 100644
--- a/src/inference_engine/inference_engine_s.f90
+++ b/src/inference_engine/inference_engine_s.f90
@@ -1,16 +1,14 @@
 ! Copyright (c), The Regents of the University of California
 ! Terms of use are as specified in LICENSE.txt
 submodule(inference_engine_m_) inference_engine_s
-  use assert_m, only : assert
-  use intrinsic_array_m, only : intrinsic_array_t
+  use assert_m, only : assert, intrinsic_array_t
   use step_m, only : step_t
   use swish_m, only : swish_t
   use sigmoid_m, only : sigmoid_t
   use relu_m, only : relu_t
   use layer_m, only : layer_t
   use neuron_m, only : neuron_t
-  use file_m, only : file_t
-  use formats_m, only : separated_values
+  use sourcery_m, only : separated_values
   implicit none
 
   interface assert_consistency
diff --git a/src/inference_engine/network_configuration_m.f90 b/src/inference_engine/network_configuration_m.f90
new file mode 100644
index 000000000..6f057e7a6
--- /dev/null
+++ b/src/inference_engine/network_configuration_m.f90
@@ -0,0 +1,39 @@
+module network_configuration_m
+  use sourcery_m, only : file_t
+  implicit none
+
+  private
+  public :: network_configuration_t
+  
+  type network_configuration_t
+    private
+    type(string_t) activation_function_
+    integer, allocatable :: nodes_per_layer_(:)
+    logical skip_connections_
+  contains
+    procedure :: to_json
+  end type
+
+  end type
+
+  interface network_configuration_t
+
+    elemental module function from_json(file_) result(network_configuration)
+      implicit none
+      type(file_t), intent(in) :: file_
+      type(network_configuration_t) network_configuration
+    end function
+
+  end interface
+
+  interface
+
+    elemental module function to_json(self) result(json_file)
+      implicit none
+      class(network_configuration_t), intent(in) :: self
+      type(file_t) json_file
+    end function
+
+  end interface
+
+end module
diff --git a/src/inference_engine/network_configuration_s.f90 b/src/inference_engine/network_configuration_s.f90
new file mode 100644
index 000000000..43249fcc4
--- /dev/null
+++ b/src/inference_engine/network_configuration_s.f90
@@ -0,0 +1,54 @@
+submodule(network_configuration_m) network_configuration_s
+  use assert_m, only : assert
+  use sourcery_m, only : string_t
+  implicit none
+
+  character(len=*), parameter :: activation_function_key = "activation function"
+  character(len=*), parameter :: nodes_per_layer_key     = "nodes per layer"
+  character(len=*), parameter :: skip_connections_key    = "skip connections"
+
+contains
+
+  module procedure from_json
+    type(string_t), allocatable :: lines(:)
+    integer l
+    logical network configuration_key_found 
+
+    lines = file_%lines()
+    network configuration_key_found = .false.
+
+    loop_through_file: &
+    do l=1,size(lines)
+      if (line(l)%get_key() == "network configuration") then
+        network configuration_key_found = .true.
+        self%activation_function_ = line(l+1)%get_json_value(activation_function_key, mold=string(""))
+        self%nodes_per_layer_     = line(l+2)%get_json_value(nodes_per_layer_key    , mold=[integer::])
+        self%skip_connections_    = line(l+2)%get_json_value(skip_connetions_key    , mold=.true.)
+        return
+      end if
+    end do loop_through_file
+
+    call assert(network configuration_found, "network configuration_s(from_json): network configuration_found")
+  end procedure
+
+  module procedure to_json
+    character(len=:), parameter :: indent = repeat(" ",ncopies=4)
+    integer, parameter :: max_digits = 12, max_length=5
+    character(len=max_digits) activation_function_string, nodes_per_layer_string, skip_connections_string
+    character(len=max_length) skip_connections_string
+    
+
+    write(activation_function_string,*) self%activation_function_
+    write(nodes_per_layer_string    ,*) self%nodes_per_layer_
+    write(skip_connections_string   ,*) merge("true ","false", self%skip_connections_)
+
+    lines = [ &
+      string_t(indent // '"network configuration":  {'), &
+      string_t(indent // indent // '"' // activation_function_key //'": '  // activation_function_string    ), &
+      string_t(indent // indent // '"' // nodes_per_layer_key     //'": '  // nodes_per_layer_string        ), &
+      string_t(indent // indent // '"' // skip_connections_key    //'": "' // skip_connections_string // '"'), &
+      string_t(indent // '}') &
+    ]
+  end procedure
+
+end submodule network_configuration_s
diff --git a/src/inference_engine/neuron_m.f90 b/src/inference_engine/neuron_m.f90
index 03bf2a54a..dca1c45e5 100644
--- a/src/inference_engine/neuron_m.f90
+++ b/src/inference_engine/neuron_m.f90
@@ -1,7 +1,7 @@
 ! Copyright (c), The Regents of the University of California
 ! Terms of use are as specified in LICENSE.txt
 module neuron_m
-  use string_m, only : string_t
+  use sourcery_m, only : string_t
   use kind_parameters_m, only : rkind
   implicit none
 
diff --git a/src/inference_engine/neuron_s.f90 b/src/inference_engine/neuron_s.f90
index 2b25bd7fc..115675af3 100644
--- a/src/inference_engine/neuron_s.f90
+++ b/src/inference_engine/neuron_s.f90
@@ -11,11 +11,11 @@
     character(len=:), allocatable :: line
     integer i
 
-    call assert(adjustl(neuron_lines(start)%string())=='{', "read_json: neuron object start", neuron_lines(start)%string())
+    call assert(adjustl(neuron_lines(start)%string())=='{', "neuron_s(construct): neuron object start",neuron_lines(start)%string())
 
     line = neuron_lines(start+1)%string()
     associate(colon => index(line, ":"))
-      call assert(adjustl(line(:colon-1))=='"weights"', "read_json: neuron weights", line)
+      call assert(adjustl(line(:colon-1))=='"weights"', "neuron_s(construct): neuron weights", line)
       associate(opening_bracket => colon + index(line(colon+1:), "["))
         associate(closing_bracket => opening_bracket + index(line(opening_bracket+1:), "]"))
           associate(commas => count("," == [(line(i:i), i=opening_bracket+1,closing_bracket-1)]))
@@ -30,12 +30,12 @@
 
     line = neuron_lines(start+2)%string()
     associate(colon => index(line, ":"))
-      call assert(adjustl(line(:colon-1))=='"bias"', "read_json: neuron bias", line)
+      call assert(adjustl(line(:colon-1))=='"bias"', "neuron_s(construct): neuron bias", line)
       read(line(colon+1:), fmt=*) neuron%bias_
     end associate
 
     line = adjustl(neuron_lines(start+3)%string())
-    call assert(line(1:1)=='}', "read_json: neuron object end", line)
+    call assert(line(1:1)=='}', "neuron_s(construct): neuron object end", line)
     line = adjustr(neuron_lines(start+3)%string())
     if (line(len(line):len(line)) == ",") neuron%next = construct(neuron_lines, start+4)
 
diff --git a/src/inference_engine/relu_m.f90 b/src/inference_engine/relu_m.f90
index 2108e7a78..0fae43e22 100644
--- a/src/inference_engine/relu_m.f90
+++ b/src/inference_engine/relu_m.f90
@@ -3,7 +3,7 @@
 module relu_m
   use differentiable_activation_strategy_m, only : differentiable_activation_strategy_t
   use kind_parameters_m, only : rkind
-  use string_m, only : string_t
+  use sourcery_m, only : string_t
   implicit none
 
   private
diff --git a/src/inference_engine/sigmoid_m.f90 b/src/inference_engine/sigmoid_m.f90
index d66324560..3f27b3c81 100644
--- a/src/inference_engine/sigmoid_m.f90
+++ b/src/inference_engine/sigmoid_m.f90
@@ -3,7 +3,7 @@
 module sigmoid_m
   use differentiable_activation_strategy_m, only : differentiable_activation_strategy_t
   use kind_parameters_m, only : rkind
-  use string_m, only : string_t
+  use sourcery_m, only : string_t
   implicit none
 
   private
diff --git a/src/inference_engine/step_m.f90 b/src/inference_engine/step_m.f90
index e3661770c..297a99473 100644
--- a/src/inference_engine/step_m.f90
+++ b/src/inference_engine/step_m.f90
@@ -3,7 +3,7 @@
 module step_m
   use activation_strategy_m, only : activation_strategy_t
   use kind_parameters_m, only : rkind
-  use string_m, only : string_t
+  use sourcery_m, only : string_t
   implicit none
 
   private
diff --git a/src/inference_engine/swish_m.f90 b/src/inference_engine/swish_m.f90
index d0c24c64e..64edac8dd 100644
--- a/src/inference_engine/swish_m.f90
+++ b/src/inference_engine/swish_m.f90
@@ -3,7 +3,7 @@
 module swish_m
   use differentiable_activation_strategy_m, only : differentiable_activation_strategy_t
   use kind_parameters_m, only : rkind
-  use string_m, only : string_t
+  use sourcery_m, only : string_t
   implicit none
 
   private
diff --git a/test/asymmetric_engine_test_m.f90 b/test/asymmetric_engine_test_m.f90
index 9b1f8e9bb..932f07b9b 100644
--- a/test/asymmetric_engine_test_m.f90
+++ b/test/asymmetric_engine_test_m.f90
@@ -5,9 +5,7 @@ module asymmetric_engine_test_m
 
   ! External dependencies
   use assert_m, only : assert
-  use string_m, only : string_t
-  use test_m, only : test_t
-  use test_result_m, only : test_result_t
+  use sourcery_m, only : string_t, test_t, test_result_t
 
   ! Internal dependencies
   use inference_engine_m, only : inference_engine_t, tensor_t
diff --git a/test/inference_engine_test_m.f90 b/test/inference_engine_test_m.f90
index 7f66aa333..44f40a25b 100644
--- a/test/inference_engine_test_m.f90
+++ b/test/inference_engine_test_m.f90
@@ -6,10 +6,7 @@ module inference_engine_test_m
   ! External dependencies
   use assert_m, only : assert
   use kind_parameters_m, only : rkind
-  use string_m, only : string_t
-  use test_m, only : test_t
-  use test_result_m, only : test_result_t
-  use file_m, only : file_t
+  use sourcery_m, only : string_t, test_t, test_result_t, file_t
 
   ! Internal dependencies
   use inference_engine_m, only : inference_engine_t, tensor_t, difference_t
diff --git a/test/netCDF_file_test_m.f90 b/test/netCDF_file_test_m.f90
index f01c1b75c..6cbfc84c8 100644
--- a/test/netCDF_file_test_m.f90
+++ b/test/netCDF_file_test_m.f90
@@ -8,9 +8,7 @@ module NetCDF_file_test_m
 
   ! External dependencies
   use assert_m, only : assert
-  use string_m, only : string_t
-  use test_m, only : test_t
-  use test_result_m, only : test_result_t
+  use sourcery_m, only : string_t, test_t, test_result_t
   use netcdf, only : &
      nf90_create, nf90_def_dim, nf90_def_var, nf90_enddef, nf90_put_var, nf90_inquire_dimension, & ! functions
      nf90_close, nf90_open, nf90_inq_varid, nf90_get_var, nf90_inquire_variable, &
diff --git a/training_parameters.json b/training_parameters.json
deleted file mode 100644
index 37b5701f6..000000000
--- a/training_parameters.json
+++ /dev/null
@@ -1,9 +0,0 @@
-{
-     "activation" : "sigmoid",
-     "num_mini_batches" : 10,
-     "nodes per layer" : [2, 72, 2],
-     "initialization" : {
-         "type" : "perturbed identity",
-         "parameters" : [ { "spread" :  0.05 } ]
-      }
-}

From 0c95d20f4525a73f487f7eae7fc5a6012b9fafc4 Mon Sep 17 00:00:00 2001
From: Damian Rouson <rouson@lbl.gov>
Date: Tue, 31 Oct 2023 07:58:16 -0700
Subject: [PATCH 04/11] test(hyperparameters): add unit test & finish type

---
 src/inference_engine/hyperparameters_m.f90    | 20 ++++++-
 src/inference_engine/hyperparameters_s.f90    | 34 ++++++++----
 .../network_configuration_m.f90               | 39 --------------
 .../network_configuration_s.f90               | 54 -------------------
 src/inference_engine_m.f90                    |  1 +
 test/hyperparameters_test_m.f90               | 21 +++++---
 6 files changed, 58 insertions(+), 111 deletions(-)
 delete mode 100644 src/inference_engine/network_configuration_m.f90
 delete mode 100644 src/inference_engine/network_configuration_s.f90

diff --git a/src/inference_engine/hyperparameters_m.f90 b/src/inference_engine/hyperparameters_m.f90
index dea9e6580..174545008 100644
--- a/src/inference_engine/hyperparameters_m.f90
+++ b/src/inference_engine/hyperparameters_m.f90
@@ -12,13 +12,23 @@ module hyperparameters_m
     character(len=:), allocatable :: optimizer_
   contains
     procedure :: to_json
+    procedure :: equals
+    generic :: operator(==) => equals
   end type
 
   interface hyperparameters_t
 
-    pure module function from_json(file_) result(hyperparameters)
+    pure module function from_json(lines) result(hyperparameters)
       implicit none
-      type(file_t), intent(in) :: file_
+      type(string_t), intent(in) :: lines(:)
+      type(hyperparameters_t) hyperparameters
+    end function
+
+    pure module function from_components(mini_batches, learning_rate, optimizer) result(hyperparameters)
+      implicit none
+      integer, intent(in) :: mini_batches
+      real, intent(in) :: learning_rate
+      character(len=*), intent(in) :: optimizer
       type(hyperparameters_t) hyperparameters
     end function
 
@@ -32,6 +42,12 @@ pure module function to_json(self) result(lines)
       type(string_t), allocatable :: lines(:)
     end function
 
+    elemental module function equals(lhs, rhs) result(lhs_equals_rhs)
+      implicit none
+      class(hyperparameters_t), intent(in) :: lhs, rhs
+      logical lhs_equals_rhs
+    end function
+
   end interface
 
 end module
diff --git a/src/inference_engine/hyperparameters_s.f90 b/src/inference_engine/hyperparameters_s.f90
index c1f9aae94..aadab89ed 100644
--- a/src/inference_engine/hyperparameters_s.f90
+++ b/src/inference_engine/hyperparameters_s.f90
@@ -8,15 +8,31 @@
 
 contains
 
+  module procedure from_components
+    hyperparameters%mini_batches_ = mini_batches
+    hyperparameters%learning_rate_ = learning_rate
+    hyperparameters%optimizer_ = optimizer
+  end procedure 
+
+  module procedure equals
+
+    real, parameter :: tolerance = 1.E-08
+
+    call assert(allocated(lhs%optimizer_) .and. allocated(rhs%optimizer_), "hyperparameters_s(equals): allocated optimizers")
+
+    lhs_equals_rhs = &
+      lhs%mini_batches_ == rhs%mini_batches_ .and. &
+      lhs%optimizer_ == rhs%optimizer_ .and. &
+      abs(lhs%learning_rate_ - rhs%learning_rate_) <= tolerance
+     
+  end procedure 
+
   module procedure from_json
-    type(string_t), allocatable :: lines(:)
     integer l
     logical hyperparameters_key_found 
 
-    lines = file_%lines()
     hyperparameters_key_found = .false.
 
-    loop_through_file: &
     do l=1,size(lines)
       if (lines(l)%get_json_key() == "hyperparameters") then
         hyperparameters_key_found = .true.
@@ -25,24 +41,24 @@
         hyperparameters%optimizer_ = lines(l+3)%get_json_value(string_t(optimizer_key), mold=string_t(""))
         return
       end if
-    end do loop_through_file
+    end do
 
     call assert(hyperparameters_key_found, "hyperparameters_s(from_json): hyperparameters_found")
   end procedure
 
   module procedure to_json
     character(len=*), parameter :: indent = repeat(" ",ncopies=4)
-    integer, parameter :: max_digits = 12
-    character(len=max_digits) mini_batches_string, learning_rate_string
+    integer, parameter :: max_width= 18
+    character(len=max_width) mini_batches_string, learning_rate_string
 
     write(mini_batches_string,*) self%mini_batches_
     write(learning_rate_string,*) self%learning_rate_
 
     lines = [ &
       string_t(indent // '"hyperparameters": {'), &
-      string_t(indent // indent // '"' // mini_batches_key  // '": '  // mini_batches_string   ), &
-      string_t(indent // indent // '"' // learning_rate_key // '": '  // learning_rate_string  ), &
-      string_t(indent // indent // '"' // optimizer_key     // '": "' // self%optimizer_ // '"'), &
+      string_t(indent // indent // '"' // mini_batches_key  // '" : '  // mini_batches_string   ), &
+      string_t(indent // indent // '"' // learning_rate_key // '" : '  // learning_rate_string  ), &
+      string_t(indent // indent // '"' // optimizer_key     // '" : "' // self%optimizer_ // '"'), &
       string_t(indent // '}') &
     ]
   end procedure
diff --git a/src/inference_engine/network_configuration_m.f90 b/src/inference_engine/network_configuration_m.f90
deleted file mode 100644
index 6f057e7a6..000000000
--- a/src/inference_engine/network_configuration_m.f90
+++ /dev/null
@@ -1,39 +0,0 @@
-module network_configuration_m
-  use sourcery_m, only : file_t
-  implicit none
-
-  private
-  public :: network_configuration_t
-  
-  type network_configuration_t
-    private
-    type(string_t) activation_function_
-    integer, allocatable :: nodes_per_layer_(:)
-    logical skip_connections_
-  contains
-    procedure :: to_json
-  end type
-
-  end type
-
-  interface network_configuration_t
-
-    elemental module function from_json(file_) result(network_configuration)
-      implicit none
-      type(file_t), intent(in) :: file_
-      type(network_configuration_t) network_configuration
-    end function
-
-  end interface
-
-  interface
-
-    elemental module function to_json(self) result(json_file)
-      implicit none
-      class(network_configuration_t), intent(in) :: self
-      type(file_t) json_file
-    end function
-
-  end interface
-
-end module
diff --git a/src/inference_engine/network_configuration_s.f90 b/src/inference_engine/network_configuration_s.f90
deleted file mode 100644
index 43249fcc4..000000000
--- a/src/inference_engine/network_configuration_s.f90
+++ /dev/null
@@ -1,54 +0,0 @@
-submodule(network_configuration_m) network_configuration_s
-  use assert_m, only : assert
-  use sourcery_m, only : string_t
-  implicit none
-
-  character(len=*), parameter :: activation_function_key = "activation function"
-  character(len=*), parameter :: nodes_per_layer_key     = "nodes per layer"
-  character(len=*), parameter :: skip_connections_key    = "skip connections"
-
-contains
-
-  module procedure from_json
-    type(string_t), allocatable :: lines(:)
-    integer l
-    logical network configuration_key_found 
-
-    lines = file_%lines()
-    network configuration_key_found = .false.
-
-    loop_through_file: &
-    do l=1,size(lines)
-      if (line(l)%get_key() == "network configuration") then
-        network configuration_key_found = .true.
-        self%activation_function_ = line(l+1)%get_json_value(activation_function_key, mold=string(""))
-        self%nodes_per_layer_     = line(l+2)%get_json_value(nodes_per_layer_key    , mold=[integer::])
-        self%skip_connections_    = line(l+2)%get_json_value(skip_connetions_key    , mold=.true.)
-        return
-      end if
-    end do loop_through_file
-
-    call assert(network configuration_found, "network configuration_s(from_json): network configuration_found")
-  end procedure
-
-  module procedure to_json
-    character(len=:), parameter :: indent = repeat(" ",ncopies=4)
-    integer, parameter :: max_digits = 12, max_length=5
-    character(len=max_digits) activation_function_string, nodes_per_layer_string, skip_connections_string
-    character(len=max_length) skip_connections_string
-    
-
-    write(activation_function_string,*) self%activation_function_
-    write(nodes_per_layer_string    ,*) self%nodes_per_layer_
-    write(skip_connections_string   ,*) merge("true ","false", self%skip_connections_)
-
-    lines = [ &
-      string_t(indent // '"network configuration":  {'), &
-      string_t(indent // indent // '"' // activation_function_key //'": '  // activation_function_string    ), &
-      string_t(indent // indent // '"' // nodes_per_layer_key     //'": '  // nodes_per_layer_string        ), &
-      string_t(indent // indent // '"' // skip_connections_key    //'": "' // skip_connections_string // '"'), &
-      string_t(indent // '}') &
-    ]
-  end procedure
-
-end submodule network_configuration_s
diff --git a/src/inference_engine_m.f90 b/src/inference_engine_m.f90
index 81e3614f9..fd3bcdfc9 100644
--- a/src/inference_engine_m.f90
+++ b/src/inference_engine_m.f90
@@ -15,5 +15,6 @@ module inference_engine_m
  use swish_m, only : swish_t
  use tensor_m, only : tensor_t
  use trainable_engine_m, only : trainable_engine_t
+ use hyperparameters_m, only : hyperparameters_t
  implicit none
 end module
diff --git a/test/hyperparameters_test_m.f90 b/test/hyperparameters_test_m.f90
index ee7440741..f2d1f65b4 100644
--- a/test/hyperparameters_test_m.f90
+++ b/test/hyperparameters_test_m.f90
@@ -5,7 +5,8 @@ module hyperparameters_test_m
 
   ! External dependencies
   use assert_m, only : assert
-  use sourcery_m, only : string_t, test_t, test_result_t
+  use sourcery_m, only : string_t, test_t, test_result_t, file_t
+  use inference_engine_m, only : hyperparameters_t
 
   ! Internal dependencies
   use hyperparameters_m, only : hyperparameters_t
@@ -32,15 +33,15 @@ function results() result(test_results)
     type(test_result_t), allocatable :: test_results(:)
 
     character(len=*), parameter :: longest_description = &
-          "writing and then reading gives input matching output for perturbed identity network"
+          "component-wise construction followed by conversion to and from JSON"
 
     associate( &
       descriptions => &
         [ character(len=len(longest_description)) :: &
-          "writing and then reading gives input matching output for perturbed identity network" &
+          "component-wise construction followed by conversion to and from JSON" &
         ], &
       outcomes => &
-        [ write_then_read_perturbed_identity() & 
+        [ write_then_read_hyperparameters() & 
         ] & 
     )
       call assert(size(descriptions) == size(outcomes),"hyperparameters_test_m(results): size(descriptions) == size(outcomes)")
@@ -49,9 +50,15 @@ function results() result(test_results)
        
   end function
 
-  function write_then_read_perturbed_identity() result(test_passes)
-    logical, allocatable :: test_passes(:)
-    test_passes = [.true.]
+  function write_then_read_hyperparameters() result(test_passes)
+    logical test_passes
+
+    associate(hyperparameters => hyperparameters_t(mini_batches=5, learning_rate=1., optimizer = "stochastic gradient descent"))
+      associate(from_json => hyperparameters_t(hyperparameters%to_json()))
+        test_passes = hyperparameters == from_json
+      end associate
+    end associate
+
   end function
 
 end module hyperparameters_test_m
\ No newline at end of file

From 829b967c3cc446aac2671006366bf7c87e4f629e Mon Sep 17 00:00:00 2001
From: Damian Rouson <rouson@lbl.gov>
Date: Tue, 31 Oct 2023 10:26:04 -0700
Subject: [PATCH 05/11] feat(network_configuration): add type & JSON I/O

---
 .../network_configuration_m.f90               | 53 +++++++++++++++
 .../network_configuration_s.f90               | 68 +++++++++++++++++++
 src/inference_engine_m.f90                    |  1 +
 test/main.f90                                 |  3 +
 test/network_configuration_test_m.f90         | 65 ++++++++++++++++++
 5 files changed, 190 insertions(+)
 create mode 100644 src/inference_engine/network_configuration_m.f90
 create mode 100644 src/inference_engine/network_configuration_s.f90
 create mode 100644 test/network_configuration_test_m.f90

diff --git a/src/inference_engine/network_configuration_m.f90 b/src/inference_engine/network_configuration_m.f90
new file mode 100644
index 000000000..f86eb637e
--- /dev/null
+++ b/src/inference_engine/network_configuration_m.f90
@@ -0,0 +1,53 @@
+module network_configuration_m
+  use sourcery_m, only : string_t, file_t
+  implicit none
+
+  private
+  public :: network_configuration_t
+
+  type network_configuration_t
+    private
+    logical :: skip_connections_ = .false.
+    integer, allocatable :: nodes_per_layer_(:)
+    character(len=:), allocatable :: activation_function_
+  contains
+    procedure :: to_json
+    procedure :: equals
+    generic :: operator(==) => equals
+  end type
+
+  interface network_configuration_t
+
+    pure module function from_json(lines) result(network_configuration)
+      implicit none
+      type(string_t), intent(in) :: lines(:)
+      type(network_configuration_t) network_configuration
+    end function
+
+    pure module function from_components(skip_connections, nodes_per_layer, activation_function) result(network_configuration)
+      implicit none
+      logical, intent(in) :: skip_connections
+      integer, intent(in) :: nodes_per_layer(:)
+      character(len=*), intent(in) :: activation_function
+      type(network_configuration_t) network_configuration
+    end function
+
+  end interface
+
+  interface
+
+    pure module function to_json(self) result(lines)
+      implicit none
+      class(network_configuration_t), intent(in) :: self
+      type(string_t), allocatable :: lines(:)
+    end function
+
+    elemental module function equals(lhs, rhs) result(lhs_equals_rhs)
+      implicit none
+      class(network_configuration_t), intent(in) :: lhs, rhs
+      logical lhs_equals_rhs
+    end function
+
+  end interface
+
+end module
diff --git a/src/inference_engine/network_configuration_s.f90 b/src/inference_engine/network_configuration_s.f90
new file mode 100644
index 000000000..66cebec50
--- /dev/null
+++ b/src/inference_engine/network_configuration_s.f90
@@ -0,0 +1,68 @@
+submodule(network_configuration_m) network_configuration_s
+  use assert_m, only : assert
+  use sourcery_m, only : csv
+  implicit none
+
+  character(len=*), parameter :: skip_connections_key  = "skip connections"
+  character(len=*), parameter :: nodes_per_layer_key = "nodes per layer"
+  character(len=*), parameter :: activation_function_key     = "activation function"
+
+contains
+
+  module procedure from_components
+    network_configuration%skip_connections_ = skip_connections
+    network_configuration%nodes_per_layer_ = nodes_per_layer
+    network_configuration%activation_function_ = activation_function
+  end procedure 
+
+  module procedure equals
+
+    call assert(allocated(lhs%activation_function_) .and. allocated(rhs%activation_function_), "network_configuration_s(equals): allocated activation_functions")
+
+    lhs_equals_rhs = &
+      lhs%skip_connections_ .eqv. rhs%skip_connections_ .and. &
+      lhs%activation_function_ == rhs%activation_function_ .and. &
+      all(lhs%nodes_per_layer_ == rhs%nodes_per_layer_)
+     
+  end procedure 
+
+  module procedure from_json
+    integer l
+    logical network_configuration_key_found 
+
+    network_configuration_key_found = .false.
+
+    do l=1,size(lines)
+      if (lines(l)%get_json_key() == "network configuration") then
+        network_configuration_key_found = .true.
+        network_configuration%skip_connections_  = lines(l+1)%get_json_value(string_t(skip_connections_key), mold=.true.)
+        network_configuration%nodes_per_layer_ = lines(l+2)%get_json_integer_array(string_t(nodes_per_layer_key), mold=[0,1])
+        network_configuration%activation_function_ = lines(l+3)%get_json_value(string_t(activation_function_key), mold=string_t(""))
+        return
+      end if
+    end do
+
+    call assert(network_configuration_key_found, "network_configuration_s(from_json): network_configuration_found")
+  end procedure
+
+  module procedure to_json
+    character(len=*), parameter :: indent = repeat(" ",ncopies=4)
+    integer, parameter :: max_logical_width= 6, char_per_elem = 10, brackets = 2
+    character(len=max_logical_width) skip_connections_string
+    character(len=:), allocatable :: nodes_per_layer_string
+
+    allocate(character(len=size(self%nodes_per_layer_)*char_per_elem + brackets) :: nodes_per_layer_string)
+
+    write(skip_connections_string,*) trim(merge("true ","false",self%skip_connections_))
+    write(nodes_per_layer_string, csv) self%nodes_per_layer_
+
+    lines = [ &
+      string_t(indent // '"network configuration": {'), &
+      string_t(indent // indent // '"' // skip_connections_key  // '" : '  // skip_connections_string   ), &
+      string_t(indent // indent // '"' // nodes_per_layer_key // '" : ['  // trim(nodes_per_layer_string) // ']'  ), &
+      string_t(indent // indent // '"' // activation_function_key     // '" : "' // self%activation_function_ // '"'), &
+      string_t(indent // '}') &
+    ]
+  end procedure
+
+end submodule network_configuration_s
diff --git a/src/inference_engine_m.f90 b/src/inference_engine_m.f90
index fd3bcdfc9..94b1d4a1e 100644
--- a/src/inference_engine_m.f90
+++ b/src/inference_engine_m.f90
@@ -16,5 +16,6 @@ module inference_engine_m
  use tensor_m, only : tensor_t
  use trainable_engine_m, only : trainable_engine_t
  use hyperparameters_m, only : hyperparameters_t
+ use network_configuration_m, only : network_configuration_t
  implicit none
 end module
diff --git a/test/main.f90 b/test/main.f90
index 0867a6b84..c90821cb4 100644
--- a/test/main.f90
+++ b/test/main.f90
@@ -5,12 +5,14 @@ program main
   use asymmetric_engine_test_m, only : asymmetric_engine_test_t  
   use trainable_engine_test_m, only : trainable_engine_test_t  
   use hyperparameters_test_m, only : hyperparameters_test_t
+  use network_configuration_test_m, only : network_configuration_test_t
   implicit none
 
   type(inference_engine_test_t) inference_engine_test
   type(asymmetric_engine_test_t) asymmetric_engine_test
   type(trainable_engine_test_t) trainable_engine_test
   type(hyperparameters_test_t) hyperparameters_test
+  type(network_configuration_test_t) network_configuration_test
   real t_start, t_finish
 
   integer :: passes=0, tests=0
@@ -21,6 +23,7 @@ program main
   call asymmetric_engine_test%report(passes, tests)
   call trainable_engine_test%report(passes, tests)
   call hyperparameters_test%report(passes, tests)
+  call network_configuration_test%report(passes, tests)
 #ifndef __INTEL_FORTRAN
   block 
     use netCDF_file_test_m, only : netCDF_file_test_t
diff --git a/test/network_configuration_test_m.f90 b/test/network_configuration_test_m.f90
new file mode 100644
index 000000000..1c6c2cbd8
--- /dev/null
+++ b/test/network_configuration_test_m.f90
@@ -0,0 +1,65 @@
+! Copyright (c), The Regents of the University of California
+! Terms of use are as specified in LICENSE.txt
+module network_configuration_test_m
+  !! Test network_configuration_t object I/O and construction
+
+  ! External dependencies
+  use assert_m, only : assert
+  use sourcery_m, only : string_t, test_t, test_result_t, file_t
+  use inference_engine_m, only : network_configuration_t
+
+  ! Internal dependencies
+  use network_configuration_m, only : network_configuration_t
+
+  implicit none
+
+  private
+  public :: network_configuration_test_t
+
+  type, extends(test_t) :: network_configuration_test_t
+  contains
+    procedure, nopass :: subject
+    procedure, nopass :: results
+  end type
+
+contains
+
+  pure function subject() result(specimen)
+    character(len=:), allocatable :: specimen
+    specimen = "A network_configuration_t object"
+  end function
+
+  function results() result(test_results)
+    type(test_result_t), allocatable :: test_results(:)
+
+    character(len=*), parameter :: longest_description = &
+          "component-wise construction followed by conversion to and from JSON"
+
+    associate( &
+      descriptions => &
+        [ character(len=len(longest_description)) :: &
+          "component-wise construction followed by conversion to and from JSON" &
+        ], &
+      outcomes => &
+        [ write_then_read_network_configuration() & 
+        ] & 
+    )
+      call assert(size(descriptions) == size(outcomes),"network_configuration_test_m(results): size(descriptions) == size(outcomes)")
+      test_results = test_result_t(descriptions, outcomes)
+    end associate
+       
+  end function
+
+  function write_then_read_network_configuration() result(test_passes)
+    logical test_passes
+
+    associate(constructed_from_components=> &
+      network_configuration_t(skip_connections=.false., nodes_per_layer=[2,72,2], activation_function="sigmoid"))
+      associate(constructed_from_json => network_configuration_t(constructed_from_components%to_json()))
+        test_passes = constructed_from_components == constructed_from_json 
+      end associate
+    end associate
+
+  end function
+
+end module network_configuration_test_m
\ No newline at end of file

From e629617b31b66ddcd9286c498b705b8c4bb4f30f Mon Sep 17 00:00:00 2001
From: Damian Rouson <rouson@lbl.gov>
Date: Tue, 31 Oct 2023 12:33:13 -0700
Subject: [PATCH 06/11] feat(example): add print-sample-input-file.f90

---
 example/print-sample-input-file.f90 | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 example/print-sample-input-file.f90

diff --git a/example/print-sample-input-file.f90 b/example/print-sample-input-file.f90
new file mode 100644
index 000000000..b8cc6922a
--- /dev/null
+++ b/example/print-sample-input-file.f90
@@ -0,0 +1,24 @@
+program print_sample_input_file
+  use inference_engine_m, only : hyperparameters_t, network_configuration_t
+  implicit none
+
+  associate(params => hyperparameters_t(mini_batches=10, learning_rate=1.5, optimizer = "adam"))
+    associate(net_conf=> network_configuration_t(skip_connections=.false., nodes_per_layer=[2,72,2], activation_function="sigmoid"))
+      associate(params_json => params%to_json(), net_json => net_conf%to_json())
+        print *,"{"
+        block 
+          integer line
+          do line = 1, size(params_json)
+            print *, (params_json(line)%string())
+          end do
+          do line = 1, size(net_json)
+            print *, (net_json(line)%string())
+          end do
+        end block
+        print *,"}"
+      end associate
+    end associate
+  end associate
+
+
+end program

From cda51ee9e201c6be72e70f5259ea3ae73455e13c Mon Sep 17 00:00:00 2001
From: Damian Rouson <rouson@lbl.gov>
Date: Tue, 31 Oct 2023 16:30:55 -0700
Subject: [PATCH 07/11] fix(network_configuration): update dependency

This commit updates the sourcery library dependency to version
4.4.2, which resolves a generic interface disambiguation bug that
blocked the network_configuration_t unit test from passing.
---
 fpm.toml                                         | 2 +-
 src/inference_engine/network_configuration_s.f90 | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/fpm.toml b/fpm.toml
index bdc742364..128595586 100644
--- a/fpm.toml
+++ b/fpm.toml
@@ -6,5 +6,5 @@ maintainer = "rouson@lbl.gov"
 
 [dependencies]
 assert = {git = "https://github.com/sourceryinstitute/assert", tag = "1.5.0"}
-sourcery = {git = "https://github.com/sourceryinstitute/sourcery", tag = "4.4.0"}
+sourcery = {git = "https://github.com/sourceryinstitute/sourcery", tag = "4.4.2"}
 netcdf-interfaces = {git = "https://github.com/rouson/netcdf-interfaces.git", branch = "implicit-interfaces"}
diff --git a/src/inference_engine/network_configuration_s.f90 b/src/inference_engine/network_configuration_s.f90
index 66cebec50..9f93d8d47 100644
--- a/src/inference_engine/network_configuration_s.f90
+++ b/src/inference_engine/network_configuration_s.f90
@@ -36,7 +36,7 @@
       if (lines(l)%get_json_key() == "network configuration") then
         network_configuration_key_found = .true.
         network_configuration%skip_connections_  = lines(l+1)%get_json_value(string_t(skip_connections_key), mold=.true.)
-        network_configuration%nodes_per_layer_ = lines(l+2)%get_json_integer_array(string_t(nodes_per_layer_key), mold=[0,1])
+        network_configuration%nodes_per_layer_ = lines(l+2)%get_json_value(string_t(nodes_per_layer_key), mold=[integer::])
         network_configuration%activation_function_ = lines(l+3)%get_json_value(string_t(activation_function_key), mold=string_t(""))
         return
       end if

From de39ecbb61319319b3bb392dd02066e84838f83a Mon Sep 17 00:00:00 2001
From: Damian Rouson <rouson@lbl.gov>
Date: Tue, 31 Oct 2023 17:43:04 -0700
Subject: [PATCH 08/11] refac(hyperparams|net_conf):rm unused dependencies

---
 src/inference_engine/hyperparameters_m.f90       | 2 +-
 src/inference_engine/network_configuration_m.f90 | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/inference_engine/hyperparameters_m.f90 b/src/inference_engine/hyperparameters_m.f90
index 174545008..35eb5156a 100644
--- a/src/inference_engine/hyperparameters_m.f90
+++ b/src/inference_engine/hyperparameters_m.f90
@@ -1,5 +1,5 @@
 module hyperparameters_m
-  use sourcery_m, only : string_t, file_t
+  use sourcery_m, only : string_t
   implicit none
 
   private
diff --git a/src/inference_engine/network_configuration_m.f90 b/src/inference_engine/network_configuration_m.f90
index f86eb637e..30e85cf0d 100644
--- a/src/inference_engine/network_configuration_m.f90
+++ b/src/inference_engine/network_configuration_m.f90
@@ -1,5 +1,5 @@
 module network_configuration_m
-  use sourcery_m, only : string_t, file_t
+  use sourcery_m, only : string_t
   implicit none
 
   private

From 628de786eee92b9ea5814b0e13fdc834fe4ea9fb Mon Sep 17 00:00:00 2001
From: Damian Rouson <rouson@lbl.gov>
Date: Tue, 31 Oct 2023 18:44:28 -0700
Subject: [PATCH 09/11] feat(training_configuration_t): add type, JSON I/O

---
 src/inference_engine/hyperparameters_s.f90    |  6 +-
 .../network_configuration_s.f90               |  6 +-
 .../training_configuration_m.f90              | 53 +++++++++++++++
 .../training_configuration_s.f90              | 49 +++++++++++++
 src/inference_engine_m.f90                    |  5 +-
 test/main.f90                                 |  3 +
 test/training_configuration_test_m.f90        | 68 +++++++++++++++++++
 7 files changed, 182 insertions(+), 8 deletions(-)
 create mode 100644 src/inference_engine/training_configuration_m.f90
 create mode 100644 src/inference_engine/training_configuration_s.f90
 create mode 100644 test/training_configuration_test_m.f90

diff --git a/src/inference_engine/hyperparameters_s.f90 b/src/inference_engine/hyperparameters_s.f90
index aadab89ed..31e67b64b 100644
--- a/src/inference_engine/hyperparameters_s.f90
+++ b/src/inference_engine/hyperparameters_s.f90
@@ -56,9 +56,9 @@
 
     lines = [ &
       string_t(indent // '"hyperparameters": {'), &
-      string_t(indent // indent // '"' // mini_batches_key  // '" : '  // mini_batches_string   ), &
-      string_t(indent // indent // '"' // learning_rate_key // '" : '  // learning_rate_string  ), &
-      string_t(indent // indent // '"' // optimizer_key     // '" : "' // self%optimizer_ // '"'), &
+      string_t(indent // indent // '"' // mini_batches_key  // '" : '  // trim(adjustl(mini_batches_string))  // "," ), &
+      string_t(indent // indent // '"' // learning_rate_key // '" : '  // trim(adjustl(learning_rate_string)) // "," ), &
+      string_t(indent // indent // '"' // optimizer_key     // '" : "' // trim(adjustl(self%optimizer_     )) // '"'), &
       string_t(indent // '}') &
     ]
   end procedure
diff --git a/src/inference_engine/network_configuration_s.f90 b/src/inference_engine/network_configuration_s.f90
index 9f93d8d47..99a810aa4 100644
--- a/src/inference_engine/network_configuration_s.f90
+++ b/src/inference_engine/network_configuration_s.f90
@@ -58,9 +58,9 @@
 
     lines = [ &
       string_t(indent // '"network configuration": {'), &
-      string_t(indent // indent // '"' // skip_connections_key  // '" : '  // skip_connections_string   ), &
-      string_t(indent // indent // '"' // nodes_per_layer_key // '" : ['  // trim(nodes_per_layer_string) // ']'  ), &
-      string_t(indent // indent // '"' // activation_function_key     // '" : "' // self%activation_function_ // '"'), &
+      string_t(indent // indent // '"' // skip_connections_key    // '" : '  // trim(adjustl(skip_connections_string  )) //  ','), &
+      string_t(indent // indent // '"' // nodes_per_layer_key     // '" : [' // trim(adjustl(nodes_per_layer_string   )) // '],'), &
+      string_t(indent // indent // '"' // activation_function_key // '" : "' // trim(adjustl(self%activation_function_)) // '"' ), &
       string_t(indent // '}') &
     ]
   end procedure
diff --git a/src/inference_engine/training_configuration_m.f90 b/src/inference_engine/training_configuration_m.f90
new file mode 100644
index 000000000..300990289
--- /dev/null
+++ b/src/inference_engine/training_configuration_m.f90
@@ -0,0 +1,53 @@
+module training_configuration_m
+  use sourcery_m, only : string_t, file_t
+  use hyperparameters_m, only : hyperparameters_t
+  use network_configuration_m, only : network_configuration_t
+  implicit none
+
+  private
+  public :: training_configuration_t
+
+  type, extends(file_t) :: training_configuration_t
+    private
+    type(hyperparameters_t) hyperparameters_
+    type(network_configuration_t) network_configuration_
+  contains
+    procedure :: to_json
+    procedure :: equals
+    generic :: operator(==) => equals
+  end type
+
+  interface training_configuration_t
+
+    module function from_components(hyperparameters, network_configuration) result(training_configuration)
+      implicit none
+      type(hyperparameters_t), intent(in) :: hyperparameters
+      type(network_configuration_t), intent(in) :: network_configuration
+      type(training_configuration_t) training_configuration
+    end function
+
+    module function from_file(file_object) result(training_configuration)
+      implicit none
+      type(file_t), intent(in) :: file_object
+      type(training_configuration_t) training_configuration
+    end function
+
+  end interface
+
+  interface
+
+    pure module function to_json(self) result(json_lines)
+      implicit none
+      class(training_configuration_t), intent(in) :: self
+      type(string_t), allocatable :: json_lines(:)
+    end function
+
+    elemental module function equals(lhs, rhs) result(lhs_eq_rhs)
+      implicit none
+      class(training_configuration_t), intent(in) :: lhs, rhs
+      logical lhs_eq_rhs
+    end function
+
+  end interface
+
+end module
diff --git a/src/inference_engine/training_configuration_s.f90 b/src/inference_engine/training_configuration_s.f90
new file mode 100644
index 000000000..29382a665
--- /dev/null
+++ b/src/inference_engine/training_configuration_s.f90
@@ -0,0 +1,49 @@
+submodule(training_configuration_m) training_configuration_s
+  use assert_m, only : assert
+  implicit none
+
+  character(len=*), parameter :: header="{", footer="}", separator = ","
+
+contains
+
+  module procedure from_components
+
+    training_configuration%hyperparameters_ = hyperparameters
+    training_configuration%network_configuration_ = network_configuration
+    training_configuration%file_t = file_t([ &
+      string_t(header), &
+      training_configuration%hyperparameters_%to_json(), &
+      string_t(separator), &
+      training_configuration%network_configuration_%to_json(), &
+      string_t(footer) &
+    ])
+  end procedure
+
+  module procedure from_file
+    integer, parameter :: hyperparameters_start=2, hyperparameters_end=6, separator_line=7   ! line numbers
+    integer, parameter :: net_config_start=8, net_config_end=12                         ! line numbers
+    integer, parameter :: file_start=hyperparameters_start-1, file_end=net_config_end+1 ! line numbers
+
+    training_configuration%file_t = file_object
+
+    associate(lines => training_configuration%file_t%lines())
+      call assert(trim(adjustl(lines(file_start)%string()))==header,"training_configuration_s(from_file): header",lines(file_start))
+      training_configuration%hyperparameters_ = hyperparameters_t(lines(hyperparameters_start:hyperparameters_end))
+      call assert(trim(adjustl(lines(separator_line)%string()))==separator,"training_configuration_s(from_file): separator", &
+        lines(file_start))
+      training_configuration%network_configuration_= network_configuration_t(lines(net_config_start:net_config_end))
+      call assert(trim(adjustl(lines(file_end)%string()))==footer, "training_configuration_s(from_file): footer", lines(file_end))
+    end associate
+  end procedure
+
+  module procedure to_json
+    json_lines = self%lines()
+  end procedure
+
+  module procedure equals
+    lhs_eq_rhs = &
+      lhs%hyperparameters_ == rhs%hyperparameters_ .and. &
+      lhs%network_configuration_ == rhs%network_configuration_
+  end procedure
+
+end submodule training_configuration_s
diff --git a/src/inference_engine_m.f90 b/src/inference_engine_m.f90
index 94b1d4a1e..081eb3773 100644
--- a/src/inference_engine_m.f90
+++ b/src/inference_engine_m.f90
@@ -4,18 +4,19 @@ module inference_engine_m
  !! Specify the user-facing modules, derived types, and type parameters
  use activation_strategy_m, only : activation_strategy_t
  use differentiable_activation_strategy_m, only : differentiable_activation_strategy_t
+ use hyperparameters_m, only : hyperparameters_t
  use input_output_pair_m, only : input_output_pair_t, shuffle
  use inference_engine_m_, only : inference_engine_t, difference_t
  use kind_parameters_m, only : rkind
  use mini_batch_m, only : mini_batch_t
  use NetCDF_file_m, only : NetCDF_file_t 
+ use network_configuration_m, only : network_configuration_t
  use relu_m, only : relu_t
  use sigmoid_m, only : sigmoid_t
  use step_m, only : step_t
  use swish_m, only : swish_t
  use tensor_m, only : tensor_t
  use trainable_engine_m, only : trainable_engine_t
- use hyperparameters_m, only : hyperparameters_t
- use network_configuration_m, only : network_configuration_t
+ use training_configuration_m, only : training_configuration_t
  implicit none
 end module
diff --git a/test/main.f90 b/test/main.f90
index c90821cb4..cc3f840fd 100644
--- a/test/main.f90
+++ b/test/main.f90
@@ -6,6 +6,7 @@ program main
   use trainable_engine_test_m, only : trainable_engine_test_t  
   use hyperparameters_test_m, only : hyperparameters_test_t
   use network_configuration_test_m, only : network_configuration_test_t
+  use training_configuration_test_m, only : training_configuration_test_t
   implicit none
 
   type(inference_engine_test_t) inference_engine_test
@@ -13,6 +14,7 @@ program main
   type(trainable_engine_test_t) trainable_engine_test
   type(hyperparameters_test_t) hyperparameters_test
   type(network_configuration_test_t) network_configuration_test
+  type(training_configuration_test_t) training_configuration_test
   real t_start, t_finish
 
   integer :: passes=0, tests=0
@@ -24,6 +26,7 @@ program main
   call trainable_engine_test%report(passes, tests)
   call hyperparameters_test%report(passes, tests)
   call network_configuration_test%report(passes, tests)
+  call training_configuration_test%report(passes, tests)
 #ifndef __INTEL_FORTRAN
   block 
     use netCDF_file_test_m, only : netCDF_file_test_t
diff --git a/test/training_configuration_test_m.f90 b/test/training_configuration_test_m.f90
new file mode 100644
index 000000000..3701a6ad5
--- /dev/null
+++ b/test/training_configuration_test_m.f90
@@ -0,0 +1,68 @@
+! Copyright (c), The Regents of the University of California
+! Terms of use are as specified in LICENSE.txt
+module training_configuration_test_m
+  !! Test training_configuration_t object I/O and construction
+
+  ! External dependencies
+  use assert_m, only : assert
+  use sourcery_m, only : string_t, test_t, test_result_t, file_t
+  use inference_engine_m, only : training_configuration_t, hyperparameters_t, network_configuration_t
+
+  ! Internal dependencies
+  use training_configuration_m, only : training_configuration_t
+
+  implicit none
+
+  private
+  public :: training_configuration_test_t
+
+  type, extends(test_t) :: training_configuration_test_t
+  contains
+    procedure, nopass :: subject
+    procedure, nopass :: results
+  end type
+
+contains
+
+  pure function subject() result(specimen)
+    character(len=:), allocatable :: specimen
+    specimen = "A training_configuration_t object"
+  end function
+
+  function results() result(test_results)
+    type(test_result_t), allocatable :: test_results(:)
+
+    character(len=*), parameter :: longest_description = &
+          "component-wise construction followed by conversion to and from JSON"
+
+    associate( &
+      descriptions => &
+        [ character(len=len(longest_description)) :: &
+          "component-wise construction followed by conversion to and from JSON" &
+        ], &
+      outcomes => &
+        [ construct_and_convert_to_and_from_json() & 
+        ] & 
+    )
+      call assert(size(descriptions) == size(outcomes),"training_configuration_test_m(results): size(descriptions)==size(outcomes)")
+      test_results = test_result_t(descriptions, outcomes)
+    end associate
+       
+  end function
+
+  function construct_and_convert_to_and_from_json() result(test_passes)
+    logical test_passes
+
+
+    associate(training_configuration => training_configuration_t( &
+      hyperparameters_t(mini_batches=5, learning_rate=1., optimizer = "adam"), &
+      network_configuration_t(skip_connections=.false., nodes_per_layer=[2,72,2], activation_function="sigmoid") &
+    ))
+      associate(from_json => training_configuration_t(file_t(training_configuration%to_json())))
+        test_passes = training_configuration == from_json
+      end associate
+    end associate
+
+  end function
+
+end module training_configuration_test_m
\ No newline at end of file

From 8b71baeb6e5d344f89a4855d58dc4df080d0576b Mon Sep 17 00:00:00 2001
From: Damian Rouson <rouson@lbl.gov>
Date: Tue, 31 Oct 2023 18:45:06 -0700
Subject: [PATCH 10/11] feat(exampl): add print-training-configuration.f90

replaces print-sample-input-file.f90
---
 example/print-sample-input-file.f90      | 24 ------------------------
 example/print-training-configuration.f90 | 15 +++++++++++++++
 2 files changed, 15 insertions(+), 24 deletions(-)
 delete mode 100644 example/print-sample-input-file.f90
 create mode 100644 example/print-training-configuration.f90

diff --git a/example/print-sample-input-file.f90 b/example/print-sample-input-file.f90
deleted file mode 100644
index b8cc6922a..000000000
--- a/example/print-sample-input-file.f90
+++ /dev/null
@@ -1,24 +0,0 @@
-program print_sample_input_file
-  use inference_engine_m, only : hyperparameters_t, network_configuration_t
-  implicit none
-
-  associate(params => hyperparameters_t(mini_batches=10, learning_rate=1.5, optimizer = "adam"))
-    associate(net_conf=> network_configuration_t(skip_connections=.false., nodes_per_layer=[2,72,2], activation_function="sigmoid"))
-      associate(params_json => params%to_json(), net_json => net_conf%to_json())
-        print *,"{"
-        block 
-          integer line
-          do line = 1, size(params_json)
-            print *, (params_json(line)%string())
-          end do
-          do line = 1, size(net_json)
-            print *, (net_json(line)%string())
-          end do
-        end block
-        print *,"}"
-      end associate
-    end associate
-  end associate
-
-
-end program
diff --git a/example/print-training-configuration.f90 b/example/print-training-configuration.f90
new file mode 100644
index 000000000..c002286c2
--- /dev/null
+++ b/example/print-training-configuration.f90
@@ -0,0 +1,15 @@
+program print_training_configuration
+  !! Demonstrate how to construct and print a training_configuration_t object
+  use inference_engine_m, only : training_configuration_t, hyperparameters_t, network_configuration_t
+  use sourcery_m, only : file_t
+  implicit none
+
+  associate(training_configuration => training_configuration_t( &
+    hyperparameters_t(mini_batches=10, learning_rate=1.5, optimizer = "adam"), &
+    network_configuration_t(skip_connections=.false., nodes_per_layer=[2,72,2], activation_function="sigmoid") &
+  ))
+    associate(json_file => file_t(training_configuration%to_json()))
+      call json_file%write_lines()
+    end associate
+  end associate
+end program

From d93e16811d93b4a535ff09101c1fbcdc2224efff Mon Sep 17 00:00:00 2001
From: Damian Rouson <rouson@lbl.gov>
Date: Tue, 31 Oct 2023 19:13:17 -0700
Subject: [PATCH 11/11] feat(fpm): update sourcery dependency version

---
 fpm.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/fpm.toml b/fpm.toml
index 128595586..f8274f992 100644
--- a/fpm.toml
+++ b/fpm.toml
@@ -6,5 +6,5 @@ maintainer = "rouson@lbl.gov"
 
 [dependencies]
 assert = {git = "https://github.com/sourceryinstitute/assert", tag = "1.5.0"}
-sourcery = {git = "https://github.com/sourceryinstitute/sourcery", tag = "4.4.2"}
+sourcery = {git = "https://github.com/sourceryinstitute/sourcery", tag = "4.4.3"}
 netcdf-interfaces = {git = "https://github.com/rouson/netcdf-interfaces.git", branch = "implicit-interfaces"}