Merge pull request #13 from nedtaylor/development

1.3.0
nedtaylor · Mar 13, 2024 · 0d3f02b · 0d3f02b
2 parents 4841b10 + 46606fb
commit 0d3f02b
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diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
@@ -0,0 +1,113 @@
+name: run-cmake-build
+
+on:
+  push:
+    paths:
+      - ".github/workflows/cmake.yml"
+      - "CMakeLists.txt"
+      - "**.f90"
+  pull_request:
+    paths:
+      - ".github/workflows/cmake.yml"
+      - "CMakeLists.txt"
+      - "**.f90"
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: pages
+  cancel-in-progress: false
+
+jobs:
+  build-and-test-cmake-debug:
+    environment:
+      name: github-pages
+    name: Build and test in debug mode
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        compiler: [gcc]
+        version: [13]
+    steps:
+      - name: checkout repo
+        uses: actions/checkout@v4
+
+      - name: actions-setup-cmake
+        uses: jwlawson/actions-setup-cmake@v2.0.1
+        with:
+          cmake-version: '3.24.x'
+
+      - uses: fortran-lang/setup-fortran@v1
+        id: setup-fortran
+        with:
+          compiler: ${{ matrix.compiler }}
+          version: ${{ matrix.version }}
+
+      - name: Install gcovr
+        run: |
+          pip --version
+          pip install gcovr
+          
+      - name: Compile
+        run: |
+          cmake --version
+          gfortran --version
+          mkdir -p build
+          cd build
+          cmake -DCMAKE_BUILD_TYPE=Debug ..
+          make
+          make install
+
+      - name: Test
+        run: |
+          gfortran --version
+          ctest
+          
+  build-and-test-cmake-release:
+    environment:
+      name: github-pages
+    name: Build and test in release mode
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        compiler: [gcc]
+        version: [13]
+    steps:
+      - name: checkout repo
+        uses: actions/checkout@v4
+
+      - name: actions-setup-cmake
+        uses: jwlawson/actions-setup-cmake@v2.0.1
+        with:
+          cmake-version: '3.24.x'
+
+      - uses: fortran-lang/setup-fortran@v1
+        id: setup-fortran
+        with:
+          compiler: ${{ matrix.compiler }}
+          version: ${{ matrix.version }}
+
+      - name: Compile
+        run: |
+          cmake --version
+          gfortran --version
+          mkdir -p build
+          cd build
+          cmake -DCMAKE_BUILD_TYPE=Release ..
+          make
+          make install
+
+      - name: Test
+        run: |
+          gfortran --version
+          ctest
+  
+
diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
@@ -32,12 +32,11 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-latest]
         compiler: [gcc]
         version: [13]
     steps:
       - name: checkout repo
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
       - name: actions-setup-cmake
         uses: jwlawson/actions-setup-cmake@v2.0.1
@@ -63,7 +62,6 @@ jobs:
           cd build
           cmake -DCMAKE_BUILD_TYPE=Debug ..
           make
-          ./test/test_regulariser
           make coverage
 
       - name: Get coverage percentage

diff --git a/.github/workflows/fpm.yml b/.github/workflows/fpm.yml
@@ -35,7 +35,7 @@ jobs:
         version: [13]
     steps:
     - name: checkout repo
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
 
     - uses: fortran-lang/setup-fortran@v1
       id: setup-fortran
@@ -71,7 +71,7 @@ jobs:
 
     steps:
     - name: checkout repo
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
 
     - uses: fortran-lang/setup-fortran@v1
       id: setup-fortran

diff --git a/CHANGELOG b/CHANGELOG
@@ -15,6 +15,31 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Removed
 
+## [1.3.0] - 2024-03-13
+
+### Added
+- batchnorm1d_layer_type (handles both 1D spatial channel data and rank 0 channel data)
+- base_layer submodule file
+- network submodule file
+- Added comments to network and base_layer procedure interfaces
+
+### Changed
+- Improved comment and headers in all source files
+- Improved comments in all test source files
+- Added interfaces within base_layer submodules for ease of readability
+- Added interfaces within network submodules for ease of readability
+- Moved methods of base_layer into submodule
+- Moved methods of network into submodule
+
+### Fixed
+- Remove reference to doc/ directory
+- Fixed typo in example library
+- Fixed example/mnist/src/main.f90 using wrong constants module
+- Fixed cmake isntall path prefix duplication issue
+
+### Removed
+- Deprecate and remove step_decay and lr_reduce_on_plateau procedures
+
 ## [1.2.4] - 2024-03-07
 
 ### Added

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -46,8 +46,6 @@ if (CMAKE_BUILD_TYPE MATCHES "Debug*" OR CMAKE_BUILD_TYPE MATCHES "Dev*")
         EXECUTABLE ctest
         EXCLUDE "${PROJECT_SOURCE_DIR}/test/*")
   endif()
-  # add coverage compiler flags
-  append_coverage_compiler_flags()
 endif()
 
 # enable testing
@@ -95,6 +93,8 @@ set(LIB_FILES
     mod_loss.f90
     mod_accuracy.f90
     mod_base_layer.f90
+    mod_base_layer_sub.f90
+    mod_batchnorm1d_layer.f90
     mod_batchnorm2d_layer.f90
     mod_batchnorm3d_layer.f90
     mod_conv2d_layer.f90
@@ -117,6 +117,7 @@ set(LIB_FILES
     mod_container_layer.f90
     mod_container_layer_sub.f90
     mod_network.f90
+    mod_network_sub.f90
 )
 foreach(lib ${LIB_FILES})
     list(APPEND PREPENDED_LIB_FILES ${LIB_DIR}/${lib})
@@ -202,8 +203,8 @@ target_link_libraries(${PROJECT_NAME} PUBLIC)
 string(REGEX REPLACE "\\.[^.]*$" ".mod" MODULE_FILES "${SRC_FILES}")
 
 # installation
-install(FILES ${MODULE_DIR}/${MODULE_FILES} DESTINATION ${CMAKE_INSTALL_PREFIX}/include)
-install(TARGETS ${PROJECT_NAME} DESTINATION ${CMAKE_INSTALL_PREFIX}/lib)
+install(FILES ${MODULE_DIR}/${MODULE_FILES} DESTINATION include)
+install(TARGETS ${PROJECT_NAME} DESTINATION lib)
 
 # set compile options based on different build configurations
 target_compile_options(${PROJECT_NAME} PUBLIC "$<$<CONFIG:Release>:${OPTIMFLAGS}>")
@@ -216,5 +217,10 @@ target_compile_options(${PROJECT_NAME} PUBLIC "$<$<CONFIG:Parallel_Dev>:${DEVFLA
 
 # include the build test directory
 if(BUILD_TESTS)
-    add_subdirectory(test)
+  add_subdirectory(test)
 endif()
+
+# add coverage compiler flags
+if (CMAKE_BUILD_TYPE MATCHES "Debug*" OR CMAKE_BUILD_TYPE MATCHES "Dev*")
+  append_coverage_compiler_flags()
+endif()
diff --git a/README.md b/README.md
@@ -29,10 +29,10 @@ ATHENA is distributed with the following directories:
 
 | Directory | Description |
 |---|---|
-|  example/  |    A set of example programs utilising the ATHENA library |
+|  _example/_  |    A set of example programs utilising the ATHENA library |
 |  _src/_ |      Source code  |
 |  _tools/_ |    Additional shell script tools for automating learning  |
-|  test/  |    A set of test programs to check functionality of the library works after compilation |
+|  _test/_  |    A set of test programs to check functionality of the library works after compilation |
 
 
 Documentation
@@ -204,6 +204,7 @@ Files
 |_src/lib/mod_activation.f90_          | generic node activation (transfer) setup  |
 |_src/lib/mod_activation__[_NAME_]_.f90_   | [_NAME_] activation method  |
 |_src/lib/mod_base_layer.f90_          | abstract layer construct type  |
+|_src/lib/mod_base_layer_sub.f90_          | base layer submodule |
 |_src/lib/mod_clipper.f90_             | gradient clipping procedures |
 |_src/lib/mod_constants.f90_           | a set of global constants used in this code  |
 |_src/lib/mod_container.f90_           | layer container construct for handling multiple layers in a network  |
@@ -217,6 +218,7 @@ Files
 |_src/lib/mod_misc.f90_                | miscellaneous procedures  |
 |_src/lib/mod_misc_ml.f90_             | miscellaneous machine learning procedures  |
 |_srcs/lib/mod_network.f90_            | neural network derived type and procedures  |
+|_srcs/lib/mod_network_sub.f90_        | network submodule  |
 |_src/lib/mod_normalisation.f90_       | data normalisation procedures  |
 |_src/lib/mod_optimiser.f90_           | learning optimisation derived type and procedures  |
 |_src/lib/mod_random.f90_              | random number procedures  |

diff --git a/example/example_library/src/mod_constants.f90 b/example/example_library/src/mod_constants.f90
@@ -1,4 +1,4 @@
-module constants_minst
+module constants_mnist
   implicit none
   integer, parameter, public :: real12 = Selected_real_kind(6,37)!(15,307)
   real(real12), parameter, public :: k_b = 1.3806503e-23_real12
@@ -18,4 +18,4 @@ module constants_minst
   real(real12), parameter, public :: INF = huge(0._real12)
   complex(real12), parameter, public :: imag=(0._real12, 1._real12)
   integer, public :: ierror = -1
-end module constants_minst
+end module constants_mnist
diff --git a/example/example_library/src/mod_misc.f90 b/example/example_library/src/mod_misc.f90
@@ -29,8 +29,8 @@
 !!! to_upper         (converts all characters in string to upper case)
 !!! to_lower         (converts all characters in string to lower case)
 !!!#############################################################################
-module misc_minst
-  use constants_minst, only: real12
+module misc_mnist
+  use constants_mnist, only: real12
   implicit none
 
 
@@ -1766,4 +1766,4 @@ pure function to_lower(buffer) result(lower)
   end function to_lower
 !!!#####################################################
 
-end module misc_minst
+end module misc_mnist
diff --git a/example/example_library/src/mod_read_mnist.f90 b/example/example_library/src/mod_read_mnist.f90
@@ -1,5 +1,5 @@
 module read_mnist
-  use constants_minst, only: real12
+  use constants_mnist, only: real12
   use athena, only: pad_data
   implicit none
 
@@ -13,7 +13,7 @@ module read_mnist
 !!! read mnist dataset
 !!!#############################################################################
   subroutine read_mnist_db(file,images,labels,kernel_size,image_size,padding_method)
-    use misc_minst, only: icount
+    use misc_mnist, only: icount
     implicit none
     integer :: i, j, k, Reason, unit
     integer :: num_samples, num_pixels, t_kernel_size = 1

diff --git a/example/mnist/src/main.f90 b/example/mnist/src/main.f90
@@ -8,7 +8,7 @@ program mnist_example
   use omp_lib
 #endif
   use athena
-  use constants, only: real12
+  use constants_mnist, only: real12
   use read_mnist, only: read_mnist_db
   use inputs
 

diff --git a/example/mnist_3D/src/main.f90 b/example/mnist_3D/src/main.f90
@@ -8,7 +8,7 @@ program mnist_test
   use omp_lib
 #endif
   use athena
-  use constants_minst, only: real12
+  use constants_mnist, only: real12
   use read_mnist, only: read_mnist_db
   use inputs
 

diff --git a/example/mnist_bn/src/main.f90 b/example/mnist_bn/src/main.f90
@@ -8,7 +8,7 @@ program mnist_example
   use omp_lib
 #endif
   use athena
-  use constants_minst, only: real12
+  use constants_mnist, only: real12
   use read_mnist, only: read_mnist_db
   use inputs
 

diff --git a/example/mnist_drop/src/main.f90 b/example/mnist_drop/src/main.f90
@@ -8,7 +8,7 @@ program mnist_test
   use omp_lib
 #endif
   use athena
-  use constants_minst, only: real12
+  use constants_mnist, only: real12
   use read_mnist, only: read_mnist_db
   use inputs
 

diff --git a/example/simple/src/main.f90 b/example/simple/src/main.f90
@@ -1,6 +1,6 @@
 program simple
   use athena
-  use constants_minst, only: real12, pi
+  use constants_mnist, only: real12, pi
 
   implicit none
 

diff --git a/example/sine/src/main.f90 b/example/sine/src/main.f90
@@ -1,6 +1,6 @@
 program sine
   use athena
-  use constants_minst, only: real12, pi
+  use constants_mnist, only: real12, pi
 
   implicit none
 

diff --git a/fpm.toml b/fpm.toml
@@ -1,5 +1,5 @@
 name = "athena"
-version = "1.2.4"
+version = "1.3.0"
 license = "MIT"
 author = "Ned Thaddeus Taylor"
 maintainer = "n.t.taylor@exeter.ac.uk"

diff --git a/src/athena.f90 b/src/athena.f90
@@ -1,7 +1,10 @@
 !!!#############################################################################
 !!! Code written by Ned Thaddeus Taylor
-!!! Code part of the ARTEMIS group (Hepplestone research group)
-!!! Think Hepplestone, think HRG
+!!! Code part of the ATHENA library - a feedforward neural network library
+!!!#############################################################################
+!!! module contains all publicly available types and procedures within the ...
+!!! ... ATHENA library
+!!! No other types or procedures should be needed to be accessed by the user
 !!!#############################################################################
 module athena
   use misc_ml, only: shuffle, split, pad_data
@@ -50,6 +53,7 @@ module athena
   use input4d_layer,   only: input4d_layer_type
 
   !! batch normalisation layer types
+  use batchnorm1d_layer, only: batchnorm1d_layer_type, read_batchnorm1d_layer
   use batchnorm2d_layer, only: batchnorm2d_layer_type, read_batchnorm2d_layer
   use batchnorm3d_layer, only: batchnorm3d_layer_type, read_batchnorm3d_layer