From 0359205ba0790b8c6350aaecaad6611983d88ae7 Mon Sep 17 00:00:00 2001
From: Tuomas Koskela <t.koskela@ucl.ac.uk>
Date: Wed, 5 Apr 2023 15:17:47 +0100
Subject: [PATCH 01/36] Substitute cppflow submodule with conan package

---
 .gitmodules                    | 3 ---
 cmake_files/dependencies.cmake | 1 +
 conanfile.py                   | 3 +++
 cpp/sopt/CMakeLists.txt        | 2 +-
 cppflow                        | 1 -
 5 files changed, 5 insertions(+), 5 deletions(-)
 delete mode 160000 cppflow

diff --git a/.gitmodules b/.gitmodules
index 4736c48a1..221b57d02 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,6 +1,3 @@
-[submodule "cppflow"]
-	path = cppflow
-	url = git@github.com:UCL/cppflow.git
 [submodule "lexci_models"]
 	path = lexci_models
 	url = git@github.com:astro-informatics/lexci_models.git
diff --git a/cmake_files/dependencies.cmake b/cmake_files/dependencies.cmake
index 91abadda2..3d7216fdf 100644
--- a/cmake_files/dependencies.cmake
+++ b/cmake_files/dependencies.cmake
@@ -51,5 +51,6 @@ endif()
 set(SOPT_MPI ${MPI_FOUND})
 
 if(cppflow)
+  find_package(cppflow)
   find_library(TENSORFLOW_LIB tensorflow REQUIRED)
 endif()
diff --git a/conanfile.py b/conanfile.py
index 8d44861ee..641169cb9 100644
--- a/conanfile.py
+++ b/conanfile.py
@@ -39,6 +39,9 @@ def requirements(self):
         if self.options.logging == 'on':
             self.requires("spdlog/1.9.2")
 
+        if self.options.cppflow == 'on':
+            self.requires("cppflow/2.0.0")
+
     def build_requirements(self):
 
         if self.options.docs == 'on':
diff --git a/cpp/sopt/CMakeLists.txt b/cpp/sopt/CMakeLists.txt
index b44bf2845..11dedc481 100644
--- a/cpp/sopt/CMakeLists.txt
+++ b/cpp/sopt/CMakeLists.txt
@@ -78,7 +78,7 @@ if (cppflow)
   # https://stackoverflow.com/questions/25676277/cmake-target-include-directories-prints-an-error-when-i-try-to-add-the-source
   # Add /usr/local/include for default location of TensorFlow headers
   target_include_directories(sopt PUBLIC
-    $<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/cppflow/include>
+    $<BUILD_INTERFACE:${cppflow_INCLUDE_DIR}>
     $<BUILD_INTERFACE:/usr/local/include>
     $<INSTALL_INTERFACE:cppflow/include/>
     )
diff --git a/cppflow b/cppflow
deleted file mode 160000
index a6d00ccde..000000000
--- a/cppflow
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit a6d00ccdee5a0ccad4b1ac628cdb316cbeef62ef

From 330cd91e3a0d26983528df1d930f7bd3eee292d9 Mon Sep 17 00:00:00 2001
From: Tuomas Koskela <t.koskela@ucl.ac.uk>
Date: Wed, 10 May 2023 13:20:04 +0100
Subject: [PATCH 02/36] Update CI to create cppflow package

---
 .github/workflows/cmake.yml | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
index a19fed6d4..ed0730447 100644
--- a/.github/workflows/cmake.yml
+++ b/.github/workflows/cmake.yml
@@ -132,6 +132,13 @@ jobs:
           ${{ matrix.os }}-${{ matrix.cxx }}
           ${{ matrix.os }}
 
+    - name: Create cppflow package
+      uses: actions/checkout@v3
+      with:
+        repository: UCL/cppflow.git
+        path: cppflow
+      run: conan create ./cppflow/ -pr:h=default -pr:b=default
+
     - name: Conan install on gcc
       if: ${{ contains(matrix.cxx, 'g++-9') }}
       run: conan install ${{github.workspace}} -if ${{github.workspace}}/build -s compiler.libcxx=libstdc++11 --build missing -o mpi=${{matrix.mpi}} -o openmp=${{matrix.omp}} -o cppflow=on -pr:h=default -pr:b=default
@@ -143,7 +150,7 @@ jobs:
     - name: Build
       # Build your program with the given configuration.
       # The Github Actions machines are dual-core so we can build faster using 2 parallel processes
-      run: conan build ${{github.workspace}} -bf ${{github.workspace}}/build 
+      run: conan build ${{github.workspace}} -bf ${{github.workspace}}/build
 
     - name: Test
       working-directory: ${{github.workspace}}/build

From 88c05ed7b120a30db2a28095e38c75ec667289bc Mon Sep 17 00:00:00 2001
From: Tuomas Koskela <t.koskela@ucl.ac.uk>
Date: Wed, 10 May 2023 13:24:41 +0100
Subject: [PATCH 03/36] Add cppflow package in documentation CI

---
 .github/workflows/documentation.yml | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
index 9dfd0f8db..0a77ae4a7 100644
--- a/.github/workflows/documentation.yml
+++ b/.github/workflows/documentation.yml
@@ -12,7 +12,7 @@ on:
         description: 'Run the build with tmate debugging enabled (https://github.com/marketplace/actions/debugging-with-tmate)'
         required: false
         default: false
-    
+
 env:
   CONAN_PRINT_RUN_COMMANDS: 1
   CONAN_REVISIONS_ENABLED: 1
@@ -32,13 +32,13 @@ jobs:
       - name: Setup tmate session
         uses: mxschmitt/action-tmate@v3
         if: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.debug_enabled }}
-          
+
       # Note that we are installing doxygen with apt here, and with conan in the Configure step.
       # This is because there is no easy way of extracting the path to the doxygen executable from conan.
       # the apt installed doxygen is used in the Make Docweb step to build the html files,
       # while the conan installed version is used in the build step.
       # The version we install from apt is older than the 1.9.4 we install from conan, but
-      # it is not causing any issues at the moment. 
+      # it is not causing any issues at the moment.
       - name: Install dependencies
         run: |
           sudo apt update
@@ -56,6 +56,13 @@ jobs:
           version: 2.11.0
           os: linux
 
+    - name: Create cppflow package
+      uses: actions/checkout@v3
+      with:
+        repository: UCL/cppflow.git
+        path: cppflow
+      run: conan create ./cppflow/ -pr:h=default -pr:b=default
+
       - name: Configure
         run: |
           conan install doxygen/1.9.4@#2af713e135f12722e3536808017ba086 --update

From 69c2234363a0689ade313a38a8629954602884b3 Mon Sep 17 00:00:00 2001
From: Tuomas Koskela <t.koskela@ucl.ac.uk>
Date: Wed, 10 May 2023 13:28:34 +0100
Subject: [PATCH 04/36] Split checkout and create into two steps

---
 .github/workflows/cmake.yml         | 4 +++-
 .github/workflows/documentation.yml | 4 +++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
index ed0730447..204898fad 100644
--- a/.github/workflows/cmake.yml
+++ b/.github/workflows/cmake.yml
@@ -132,11 +132,13 @@ jobs:
           ${{ matrix.os }}-${{ matrix.cxx }}
           ${{ matrix.os }}
 
-    - name: Create cppflow package
+    - name: Checkout cppflow repo
       uses: actions/checkout@v3
       with:
         repository: UCL/cppflow.git
         path: cppflow
+
+    - name: Create cppflow package
       run: conan create ./cppflow/ -pr:h=default -pr:b=default
 
     - name: Conan install on gcc
diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
index 0a77ae4a7..2e5d95ffe 100644
--- a/.github/workflows/documentation.yml
+++ b/.github/workflows/documentation.yml
@@ -56,11 +56,13 @@ jobs:
           version: 2.11.0
           os: linux
 
-    - name: Create cppflow package
+    - name: Checkout cppflow repo
       uses: actions/checkout@v3
       with:
         repository: UCL/cppflow.git
         path: cppflow
+
+    - name: Create cppflow package
       run: conan create ./cppflow/ -pr:h=default -pr:b=default
 
       - name: Configure

From 56f541aede551112490acf24e1f8f6759e2bd9e9 Mon Sep 17 00:00:00 2001
From: Tuomas Koskela <t.koskela@ucl.ac.uk>
Date: Wed, 10 May 2023 13:33:12 +0100
Subject: [PATCH 05/36] Fix indentation, add ref to master

---
 .github/workflows/cmake.yml         |  1 +
 .github/workflows/documentation.yml | 15 ++++++++-------
 2 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
index 204898fad..0314a1a42 100644
--- a/.github/workflows/cmake.yml
+++ b/.github/workflows/cmake.yml
@@ -137,6 +137,7 @@ jobs:
       with:
         repository: UCL/cppflow.git
         path: cppflow
+        ref: master
 
     - name: Create cppflow package
       run: conan create ./cppflow/ -pr:h=default -pr:b=default
diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
index 2e5d95ffe..48a1ca30b 100644
--- a/.github/workflows/documentation.yml
+++ b/.github/workflows/documentation.yml
@@ -56,14 +56,15 @@ jobs:
           version: 2.11.0
           os: linux
 
-    - name: Checkout cppflow repo
-      uses: actions/checkout@v3
-      with:
-        repository: UCL/cppflow.git
-        path: cppflow
+      - name: Checkout cppflow repo
+        uses: actions/checkout@v3
+        with:
+          repository: UCL/cppflow.git
+          path: cppflow
+          ref: master
 
-    - name: Create cppflow package
-      run: conan create ./cppflow/ -pr:h=default -pr:b=default
+      - name: Create cppflow package
+        run: conan create ./cppflow/ -pr:h=default -pr:b=default
 
       - name: Configure
         run: |

From 3397e7bf85a7308b7b6cd1cb0d76b97f7de01c4d Mon Sep 17 00:00:00 2001
From: Tuomas Koskela <t.koskela@ucl.ac.uk>
Date: Wed, 10 May 2023 14:01:39 +0100
Subject: [PATCH 06/36] Add compiler flag for apple-gcc

---
 .github/workflows/cmake.yml | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
index 0314a1a42..e046e1754 100644
--- a/.github/workflows/cmake.yml
+++ b/.github/workflows/cmake.yml
@@ -139,8 +139,15 @@ jobs:
         path: cppflow
         ref: master
 
-    - name: Create cppflow package
-      run: conan create ./cppflow/ -pr:h=default -pr:b=default
+    - name: Create cppflow package on gcc
+      if: ${{ contains(matrix.cxx, 'g++-9') }}
+      run: |
+        conan create ./cppflow/ -pr:h=default -pr:b=default -s compiler.libcxx=libstdc++11
+
+    - name: Create cppflow package on apple-clang
+      if: ${{ contains(matrix.cxx, 'clang++') }}
+      run: |
+        conan create ./cppflow/ -pr:h=default -pr:b=default
 
     - name: Conan install on gcc
       if: ${{ contains(matrix.cxx, 'g++-9') }}

From c726429ac7412d1c717c9cfed5a8767983bd97b0 Mon Sep 17 00:00:00 2001
From: Sarah Jaffa <SJaffa@users.noreply.github.com>
Date: Wed, 10 May 2023 16:18:27 +0100
Subject: [PATCH 07/36] Try adding separate step to save tensorflow path

---
 .github/workflows/cmake.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
index e046e1754..9232621d8 100644
--- a/.github/workflows/cmake.yml
+++ b/.github/workflows/cmake.yml
@@ -102,6 +102,10 @@ jobs:
         version: 2.11.0
         os: darwin
 
+    - name: Add tensorflow path to environment on MacOS
+      if: ${{ contains(matrix.os, 'macos') }}
+      run: echo "LD_LIBRARY_PATH=/usr/local/lib" >> "${GITHUB_ENV}"`
+
     - name: Select Python 3.10
       # otherwise turtlebrowser/get-conan@v1.1 fails on macos-12
       # ref: https://github.com/turtlebrowser/get-conan/issues/4

From a017215b3a79aac4ca729c56204c56faaf336fa5 Mon Sep 17 00:00:00 2001
From: Sarah Jaffa <SJaffa@users.noreply.github.com>
Date: Wed, 10 May 2023 16:30:16 +0100
Subject: [PATCH 08/36] Remove catastrophe apostrophe

---
 .github/workflows/cmake.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
index 9232621d8..b5fe87c1c 100644
--- a/.github/workflows/cmake.yml
+++ b/.github/workflows/cmake.yml
@@ -104,7 +104,7 @@ jobs:
 
     - name: Add tensorflow path to environment on MacOS
       if: ${{ contains(matrix.os, 'macos') }}
-      run: echo "LD_LIBRARY_PATH=/usr/local/lib" >> "${GITHUB_ENV}"`
+      run: echo "LD_LIBRARY_PATH=/usr/local/lib" >> "${GITHUB_ENV}"
 
     - name: Select Python 3.10
       # otherwise turtlebrowser/get-conan@v1.1 fails on macos-12

From fdb03d7c235b0d898444a963add2996197a8666a Mon Sep 17 00:00:00 2001
From: Sarah Jaffa <SJaffa@users.noreply.github.com>
Date: Wed, 10 May 2023 16:45:38 +0100
Subject: [PATCH 09/36] Try without quotes

---
 .github/workflows/cmake.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
index b5fe87c1c..2eea7fda1 100644
--- a/.github/workflows/cmake.yml
+++ b/.github/workflows/cmake.yml
@@ -104,7 +104,7 @@ jobs:
 
     - name: Add tensorflow path to environment on MacOS
       if: ${{ contains(matrix.os, 'macos') }}
-      run: echo "LD_LIBRARY_PATH=/usr/local/lib" >> "${GITHUB_ENV}"
+      run: echo "LD_LIBRARY_PATH=/usr/local/lib" >> ${GITHUB_ENV}
 
     - name: Select Python 3.10
       # otherwise turtlebrowser/get-conan@v1.1 fails on macos-12

From 88ad148b7933efc60448a87cf41a3821701bfa34 Mon Sep 17 00:00:00 2001
From: Sarah Jaffa <SJaffa@users.noreply.github.com>
Date: Wed, 10 May 2023 17:05:52 +0100
Subject: [PATCH 10/36] Try without brackets

---
 .github/workflows/cmake.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
index 2eea7fda1..440ac0ffa 100644
--- a/.github/workflows/cmake.yml
+++ b/.github/workflows/cmake.yml
@@ -104,7 +104,7 @@ jobs:
 
     - name: Add tensorflow path to environment on MacOS
       if: ${{ contains(matrix.os, 'macos') }}
-      run: echo "LD_LIBRARY_PATH=/usr/local/lib" >> ${GITHUB_ENV}
+      run: echo "LD_LIBRARY_PATH=/usr/local/lib" >> $GITHUB_ENV
 
     - name: Select Python 3.10
       # otherwise turtlebrowser/get-conan@v1.1 fails on macos-12

From b80aa531acdffcbaaa9e67347af7602e26c8e1bb Mon Sep 17 00:00:00 2001
From: Sarah Jaffa <SJaffa@users.noreply.github.com>
Date: Wed, 10 May 2023 17:43:51 +0100
Subject: [PATCH 11/36] Move path export to the relevant step

---
 .github/workflows/cmake.yml | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
index 440ac0ffa..5566a0a92 100644
--- a/.github/workflows/cmake.yml
+++ b/.github/workflows/cmake.yml
@@ -102,10 +102,6 @@ jobs:
         version: 2.11.0
         os: darwin
 
-    - name: Add tensorflow path to environment on MacOS
-      if: ${{ contains(matrix.os, 'macos') }}
-      run: echo "LD_LIBRARY_PATH=/usr/local/lib" >> $GITHUB_ENV
-
     - name: Select Python 3.10
       # otherwise turtlebrowser/get-conan@v1.1 fails on macos-12
       # ref: https://github.com/turtlebrowser/get-conan/issues/4
@@ -151,6 +147,7 @@ jobs:
     - name: Create cppflow package on apple-clang
       if: ${{ contains(matrix.cxx, 'clang++') }}
       run: |
+        echo "LD_LIBRARY_PATH=/usr/local/lib" >> $GITHUB_ENV
         conan create ./cppflow/ -pr:h=default -pr:b=default
 
     - name: Conan install on gcc

From a6fb898d2d7870a476877360ee069dc17a720bec Mon Sep 17 00:00:00 2001
From: Sarah Jaffa <SJaffa@users.noreply.github.com>
Date: Wed, 10 May 2023 17:54:50 +0100
Subject: [PATCH 12/36] Try matching TF docs

---
 .github/workflows/cmake.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
index 5566a0a92..d98f0db21 100644
--- a/.github/workflows/cmake.yml
+++ b/.github/workflows/cmake.yml
@@ -147,7 +147,8 @@ jobs:
     - name: Create cppflow package on apple-clang
       if: ${{ contains(matrix.cxx, 'clang++') }}
       run: |
-        echo "LD_LIBRARY_PATH=/usr/local/lib" >> $GITHUB_ENV
+        echo "LIBRARY_PATH=$LIBRARY_PATH:/usr/local/lib" >> $GITHUB_ENV
+        echo "DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/usr/local/lib" >> $GITHUB_ENV
         conan create ./cppflow/ -pr:h=default -pr:b=default
 
     - name: Conan install on gcc

From 0512c2a32aaf63ce5a841a2cce79aada31218145 Mon Sep 17 00:00:00 2001
From: Sarah Jaffa <SJaffa@users.noreply.github.com>
Date: Wed, 10 May 2023 18:06:58 +0100
Subject: [PATCH 13/36] Try DYLD path

---
 .github/workflows/cmake.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
index d98f0db21..89c86042e 100644
--- a/.github/workflows/cmake.yml
+++ b/.github/workflows/cmake.yml
@@ -147,8 +147,7 @@ jobs:
     - name: Create cppflow package on apple-clang
       if: ${{ contains(matrix.cxx, 'clang++') }}
       run: |
-        echo "LIBRARY_PATH=$LIBRARY_PATH:/usr/local/lib" >> $GITHUB_ENV
-        echo "DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/usr/local/lib" >> $GITHUB_ENV
+        echo "DYLD_LIBRARY_PATH=/usr/local/lib" >> $GITHUB_ENV
         conan create ./cppflow/ -pr:h=default -pr:b=default
 
     - name: Conan install on gcc

From 4ef10bc5c6821af78fc7d290bd99f7ea03f1415b Mon Sep 17 00:00:00 2001
From: Sarah Jaffa <SJaffa@users.noreply.github.com>
Date: Thu, 11 May 2023 10:46:18 +0100
Subject: [PATCH 14/36] cat github env to check

---
 .github/workflows/cmake.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
index 89c86042e..239b108a2 100644
--- a/.github/workflows/cmake.yml
+++ b/.github/workflows/cmake.yml
@@ -147,7 +147,9 @@ jobs:
     - name: Create cppflow package on apple-clang
       if: ${{ contains(matrix.cxx, 'clang++') }}
       run: |
-        echo "DYLD_LIBRARY_PATH=/usr/local/lib" >> $GITHUB_ENV
+        echo "LIBRARY_PATH=$LIBRARY_PATH:/usr/local/lib" >> "$GITHUB_ENV"
+        echo "DYLD_LIBRARY_PATH=/usr/local/lib" >> "$GITHUB_ENV"
+        cat $GITHUB_ENV
         conan create ./cppflow/ -pr:h=default -pr:b=default
 
     - name: Conan install on gcc

From d43f75acd52ce45fd8ff5d85e7c9179fe66d58ae Mon Sep 17 00:00:00 2001
From: Sarah Jaffa <SJaffa@users.noreply.github.com>
Date: Thu, 11 May 2023 11:26:43 +0100
Subject: [PATCH 15/36] Add tmate fail condition and put paths in own step

---
 .github/workflows/cmake.yml | 21 +++++++++++++--------
 1 file changed, 13 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
index 239b108a2..4bf987940 100644
--- a/.github/workflows/cmake.yml
+++ b/.github/workflows/cmake.yml
@@ -67,11 +67,6 @@ jobs:
       with:
         submodules: recursive
 
-   # Enable tmate debugging of manually-triggered workflows if the input option was provided
-    - name: Setup tmate session
-      uses: mxschmitt/action-tmate@v3
-      if: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.debug_enabled }}
-
     - name: Install Dependencies on Ubunutu
       if: ${{ contains(matrix.os, 'ubuntu') }}
       run: |
@@ -139,6 +134,13 @@ jobs:
         path: cppflow
         ref: master
 
+    - name: Add Tensorflow paths to env
+      if: ${{ contains(matrix.cxx, 'clang++') }}
+      run: |
+        echo "LIBRARY_PATH=$LIBRARY_PATH:/usr/local/lib" >> "$GITHUB_ENV"
+        echo "DYLD_LIBRARY_PATH=/usr/local/lib" >> "$GITHUB_ENV"
+        cat $GITHUB_ENV
+
     - name: Create cppflow package on gcc
       if: ${{ contains(matrix.cxx, 'g++-9') }}
       run: |
@@ -147,9 +149,6 @@ jobs:
     - name: Create cppflow package on apple-clang
       if: ${{ contains(matrix.cxx, 'clang++') }}
       run: |
-        echo "LIBRARY_PATH=$LIBRARY_PATH:/usr/local/lib" >> "$GITHUB_ENV"
-        echo "DYLD_LIBRARY_PATH=/usr/local/lib" >> "$GITHUB_ENV"
-        cat $GITHUB_ENV
         conan create ./cppflow/ -pr:h=default -pr:b=default
 
     - name: Conan install on gcc
@@ -170,3 +169,9 @@ jobs:
       # Execute tests defined by the CMake configuration.
       # See https://cmake.org/cmake/help/latest/manual/ctest.1.html for more detail
       run: ctest -C ${{env.BUILD_TYPE}} --output-on-failure
+
+
+    # Enable tmate debugging of manually-triggered workflows if the input option was provided
+    - name: Setup tmate session
+      uses: mxschmitt/action-tmate@v3
+      if: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.debug_enabled && failure() }}

From 882470f36d6abe8e697aaf7be63758ef43de214c Mon Sep 17 00:00:00 2001
From: Sarah Jaffa <SJaffa@users.noreply.github.com>
Date: Thu, 11 May 2023 11:36:06 +0100
Subject: [PATCH 16/36] Updated Mac debug for TF test

---
 .github/workflows/cmake.yml    |  2 +-
 .github/workflows/macdebug.yml | 60 +++++++++++++++++++++++++++-------
 2 files changed, 50 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
index 4bf987940..b2e081306 100644
--- a/.github/workflows/cmake.yml
+++ b/.github/workflows/cmake.yml
@@ -174,4 +174,4 @@ jobs:
     # Enable tmate debugging of manually-triggered workflows if the input option was provided
     - name: Setup tmate session
       uses: mxschmitt/action-tmate@v3
-      if: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.debug_enabled && failure() }}
+      if: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.debug_enabled}}
diff --git a/.github/workflows/macdebug.yml b/.github/workflows/macdebug.yml
index 26f5087f2..41e6e37e6 100644
--- a/.github/workflows/macdebug.yml
+++ b/.github/workflows/macdebug.yml
@@ -28,21 +28,54 @@ jobs:
       CXX: clang++
 
     steps:
-    - uses: actions/checkout@v2
-
-   # Enable tmate debugging of manually-triggered workflows if the input option was provided
-    - name: Setup tmate session
-      uses: mxschmitt/action-tmate@v3
-      if: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.debug_enabled }}
+    - uses: actions/checkout@v3
 
+   
     - name: Install Dependencies on MacOS
-      if: ${{ contains(matrix.os, 'macos') }}
-      run: brew install libtiff open-mpi libyaml ccache conan
+      run: |    
+        brew update
+        brew install libtiff open-mpi libyaml ccache
+        echo "CMAKE_PREFIX_PATH=/usr/local/opt/libomp" >> $GITHUB_ENV
 
-    - name: Conan install on apple-clang
-      if: ${{ contains(matrix.cxx, 'clang++') }}
-      run: conan install ${{github.workspace}} -if ${{github.workspace}}/build --build missing -o mpi=on -o openmp=on
+    - name: Install Tensorflow API on MacOS
+      uses: UCL/install-tensorflow-action@main
+      with:
+        version: 2.11.0
+        os: darwin
+
+    - name: Select Python 3.10
+      # otherwise turtlebrowser/get-conan@v1.1 fails on macos-12
+      # ref: https://github.com/turtlebrowser/get-conan/issues/4
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
+
+    - name: Install Conan
+      id: conan
+      uses: turtlebrowser/get-conan@main
+      with:
+        version: 1.59.0
+    
+    - name: Checkout cppflow repo
+      uses: actions/checkout@v3
+      with:
+        repository: UCL/cppflow.git
+        path: cppflow
+        ref: master
 
+    - name: Add Tensorflow paths to env
+      run: |
+        echo "LIBRARY_PATH=$LIBRARY_PATH:/usr/local/lib" >> "$GITHUB_ENV"
+        echo "DYLD_LIBRARY_PATH=/usr/local/lib" >> "$GITHUB_ENV"
+        cat $GITHUB_ENV
+
+    - name: Create cppflow package on apple-clang
+      run: |
+        conan create ./cppflow/ -pr:h=default -pr:b=default
+    
+    - name: Conan install on apple-clang
+      run: conan install ${{github.workspace}} -if ${{github.workspace}}/build --build missing -o mpi=${{matrix.mpi}} -o openmp=${{matrix.omp}} -o cppflow=on -pr:h=default -pr:b=default
+  
     - name: Build
       # Build your program with the given configuration.
       # The Github Actions machines are dual-core so we can build faster using 2 parallel processes
@@ -53,3 +86,8 @@ jobs:
       # Execute tests defined by the CMake configuration.
       # See https://cmake.org/cmake/help/latest/manual/ctest.1.html for more detail
       run: ctest -C ${{env.BUILD_TYPE}} --output-on-failure
+
+    # Enable tmate debugging of manually-triggered workflows if the input option was provided
+    - name: Setup tmate session
+      uses: mxschmitt/action-tmate@v3
+      if: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.debug_enabled }}

From 56713bb2a1baad80c66476eb47f0e8d4d8746ee2 Mon Sep 17 00:00:00 2001
From: Sarah Jaffa <SJaffa@users.noreply.github.com>
Date: Thu, 11 May 2023 11:44:52 +0100
Subject: [PATCH 17/36] Fix tmate

---
 .github/workflows/macdebug.yml | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/macdebug.yml b/.github/workflows/macdebug.yml
index 41e6e37e6..3e3f18b1f 100644
--- a/.github/workflows/macdebug.yml
+++ b/.github/workflows/macdebug.yml
@@ -69,12 +69,18 @@ jobs:
         echo "DYLD_LIBRARY_PATH=/usr/local/lib" >> "$GITHUB_ENV"
         cat $GITHUB_ENV
 
+    # Enable tmate debugging of manually-triggered workflows if the input option was provided
+    - name: Setup tmate session
+      uses: mxschmitt/action-tmate@v3
+      if: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.debug_enabled }}
+    
+
     - name: Create cppflow package on apple-clang
       run: |
         conan create ./cppflow/ -pr:h=default -pr:b=default
     
     - name: Conan install on apple-clang
-      run: conan install ${{github.workspace}} -if ${{github.workspace}}/build --build missing -o mpi=${{matrix.mpi}} -o openmp=${{matrix.omp}} -o cppflow=on -pr:h=default -pr:b=default
+      run: conan install ${{github.workspace}} -if ${{github.workspace}}/build --build missing -o mpi=off -o openmp=off -o cppflow=on -pr:h=default -pr:b=default
   
     - name: Build
       # Build your program with the given configuration.
@@ -87,7 +93,3 @@ jobs:
       # See https://cmake.org/cmake/help/latest/manual/ctest.1.html for more detail
       run: ctest -C ${{env.BUILD_TYPE}} --output-on-failure
 
-    # Enable tmate debugging of manually-triggered workflows if the input option was provided
-    - name: Setup tmate session
-      uses: mxschmitt/action-tmate@v3
-      if: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.debug_enabled }}

From 2a362fe0d33adc9e65031ec17fc27bad1cacb5f7 Mon Sep 17 00:00:00 2001
From: Sarah Jaffa <SJaffa@users.noreply.github.com>
Date: Thu, 11 May 2023 11:53:55 +0100
Subject: [PATCH 18/36] Tmate triggers on failure

---
 .github/workflows/cmake.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
index b2e081306..368a0f0ee 100644
--- a/.github/workflows/cmake.yml
+++ b/.github/workflows/cmake.yml
@@ -174,4 +174,5 @@ jobs:
     # Enable tmate debugging of manually-triggered workflows if the input option was provided
     - name: Setup tmate session
       uses: mxschmitt/action-tmate@v3
-      if: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.debug_enabled}}
+      if: ${{ failure() }}
+      timeout-minutes: 15

From 65f728133de8df90fac3583032544edf4b9fde35 Mon Sep 17 00:00:00 2001
From: Michael McLeod <michaelmcleod@ucl.ac.uk>
Date: Mon, 22 May 2023 18:03:08 +0100
Subject: [PATCH 19/36] Add g_proximal functions, which return pointers, for
 padmm and primal dual.

---
 cpp/sopt/imaging_padmm.h       | 5 +++++
 cpp/sopt/imaging_primal_dual.h | 1 +
 2 files changed, 6 insertions(+)

diff --git a/cpp/sopt/imaging_padmm.h b/cpp/sopt/imaging_padmm.h
index 1e5dabb92..897581d0c 100644
--- a/cpp/sopt/imaging_padmm.h
+++ b/cpp/sopt/imaging_padmm.h
@@ -83,6 +83,11 @@ class ImagingProximalADMM {
                                                         \
  public:
 
+  proximal::L1<Scalar> * g_proximal()
+  {
+    return &l1_proximal_;
+  }
+
   //! Maximum number of iterations
   SOPT_MACRO(l1_proximal, proximal::L1<Scalar>);
   //! The weighted L2 proximal functioning as g
diff --git a/cpp/sopt/imaging_primal_dual.h b/cpp/sopt/imaging_primal_dual.h
index 963dcc285..1274fce7b 100644
--- a/cpp/sopt/imaging_primal_dual.h
+++ b/cpp/sopt/imaging_primal_dual.h
@@ -94,6 +94,7 @@ class ImagingPrimalDual {
   TYPE NAME##_;                                       \
                                                       \
  public:
+  ImagingPrimalDual * g_proximal(){ return this;}
   //! The l1 prox functioning as f
   SOPT_MACRO(l1_proximal, t_Proximal<Real>);
   //! The l1 prox with weights functioning as f

From 1253cbb1b7efd5c8f1f409117782964c30994745 Mon Sep 17 00:00:00 2001
From: Michael McLeod <michaelmcleod@ucl.ac.uk>
Date: Wed, 31 May 2023 13:06:21 +0100
Subject: [PATCH 20/36] Add complex conversion to tensor method

---
 cpp/sopt/cppflow_utils.cc | 52 ++++++++++++++++++++++++++++++++++++---
 cpp/sopt/cppflow_utils.h  |  4 +++
 2 files changed, 53 insertions(+), 3 deletions(-)

diff --git a/cpp/sopt/cppflow_utils.cc b/cpp/sopt/cppflow_utils.cc
index 2aeee3937..63771489b 100644
--- a/cpp/sopt/cppflow_utils.cc
+++ b/cpp/sopt/cppflow_utils.cc
@@ -4,9 +4,13 @@
 #include <cppflow/cppflow.h>
 #include "cppflow/ops.h"
 #include "cppflow/model.h"
+#include <stdexcept>
 
 namespace sopt {
 namespace cppflowutils {
+
+  const double imaginary_threshold = 1e-5;
+
     cppflow::tensor convert_image_to_tensor(Image<double> const &image, int image_rows, int image_cols){
         // Convert the Sopt::Image of doubles(wrapper for Eigen::Array) to a cppflow::tensor of floats
         // TODO: Make types template parameters
@@ -16,7 +20,7 @@ namespace cppflowutils {
         std::vector<float> input_values(image_rows*image_cols, 1);
         for (int i = 0; i < image.rows(); ++i) {
             for (int j = 0; j < image.cols(); ++j) {
-            input_values[j*image_cols+i] = image(i,j);
+              input_values[j*image_cols+i] = image(i,j);
             }
         }
 
@@ -26,16 +30,58 @@ namespace cppflowutils {
         return input_tensor;
     }
 
+  cppflow::tensor convert_image_to_tensor(Image<std::complex<double>> const &image, int image_rows, int image_cols) {
+    // Convert the Sopt::Image of complex (wrapper for Eigen::Array) to a cppflow::tensor of floats
+    // Only takes the real part for processing, on the assumption that the imaginary part is negligible.
+    // If ratio of imaginary part to real part is greater than the threshold then this will throw an exception.
+    // TODO: Make types template parameters
+    // create a vector of the right shape (model expects extra dimensions on start and end)
+    std::vector<int64_t> input_shape = {1, image_rows, image_cols, 1};
+
+    std::vector<float> input_values(image_rows*image_cols, 1);
+
+    for (int i = 0; i < image.rows(); ++i) {
+        for (int j = 0; j < image.cols(); ++j) {
+          if(std::abs(image(i,j).imag())/std::abs(image(i,j).real()) > cppflowutils::imaginary_threshold)
+          {
+            throw std::runtime_error("Cannot convert to tensorflow format: imaginary component of image is non-negligible.");
+          }
+          input_values[j*image_cols+i] = image(i,j).real();
+        }
+    }
+
+    // create a tensor from vector
+    cppflow::tensor input_tensor(input_values, input_shape);
+    return input_tensor;
+  }
+
   // Convert an image stored in a sopt::Vector<double> to a cppflow::tensor of floats
   cppflow::tensor convert_image_to_tensor(sopt::Vector<double> const &image, int image_rows, int image_cols) {
 
-    std::vector<float> values(&image[0], image.data()+image.size());
-    cppflow::tensor input_tensor(values, {1, image_rows, image_cols, 1});
+    std::vector<float> input_values(&image[0], image.data()+image.size());
+    cppflow::tensor input_tensor(input_values, {1, image_rows, image_cols, 1});
 
     return input_tensor;
 
   }
 
+  // Convert an image stored in a sopt::Vector<double> to a cppflow::tensor of floats
+  cppflow::tensor convert_image_to_tensor(sopt::Vector<std::complex<double>> const &image, int image_rows, int image_cols) {
+
+    std::vector<float> input_values(image_rows);
+    for(int i = 0; i < image_rows; i++)
+    {
+      if(std::abs(image(i).imag())/std::abs(image(i).real()) > cppflowutils::imaginary_threshold)
+      {
+        throw std::runtime_error("Cannot conver to tensorflow format: imaginary component of image vector is non negligible.");
+      }
+      input_values[i] = image(i).real();
+    }
+    cppflow::tensor input_tensor(input_values, {1, image_rows, image_cols, 1});
+
+    return input_tensor;
+  }
+
   // Convert model output in a std::vector into a sopt::Image (2D Eigen::Array)
   Eigen::Map<Eigen::Array<double, Eigen::Dynamic, Eigen::Dynamic>> convert_tensor_to_image(std::vector<float> model_output, int image_rows, int image_cols){
     // convert tensor of floats to Eigen::Array of doubles
diff --git a/cpp/sopt/cppflow_utils.h b/cpp/sopt/cppflow_utils.h
index 332d6efc6..4987657f4 100644
--- a/cpp/sopt/cppflow_utils.h
+++ b/cpp/sopt/cppflow_utils.h
@@ -5,13 +5,17 @@
 #include "sopt/types.h"
 #include <cppflow/cppflow.h>
 #include "cppflow/ops.h"
+#include <complex>
 
 namespace sopt {
 namespace cppflowutils {
+
 //! Converts a sopt::Image to a cppflow::tensor
 cppflow::tensor convert_image_to_tensor(sopt::Image<double> const &image, int image_rows, int image_cols);
+cppflow::tensor convert_image_to_tensor(sopt::Image<std::complex<double>> const &image, int image_rows, int image_cols);
 //! Converts a sopt::Vector to a cppflow::tensor
 cppflow::tensor convert_image_to_tensor(sopt::Vector<double> const &image, int image_rows, int image_cols);
+cppflow::tensor convert_image_to_tensor(sopt::Vector<std::complex<double>> const &image, int image_rows, int image_cols);
 
 //! Convert a cppflow:tensor to an Eigen::Array
 Eigen::Map<Eigen::Array<double, Eigen::Dynamic, Eigen::Dynamic>> convert_tensor_to_image(std::vector<float> model_output, int image_rows, int image_cols);

From 62476f9e2ebcc325b176bce21fedc06e70c72ee4 Mon Sep 17 00:00:00 2001
From: Tuomas Koskela <t.koskela@ucl.ac.uk>
Date: Wed, 31 May 2023 13:42:36 +0100
Subject: [PATCH 21/36] Try adding CMAKE_PREFIX_PATH to env

---
 .github/workflows/cmake.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
index 368a0f0ee..01836309a 100644
--- a/.github/workflows/cmake.yml
+++ b/.github/workflows/cmake.yml
@@ -139,6 +139,7 @@ jobs:
       run: |
         echo "LIBRARY_PATH=$LIBRARY_PATH:/usr/local/lib" >> "$GITHUB_ENV"
         echo "DYLD_LIBRARY_PATH=/usr/local/lib" >> "$GITHUB_ENV"
+        echo "CMAKE_PREFIX_PATH=/usr/local/lib" >> $GITHUB_ENV
         cat $GITHUB_ENV
 
     - name: Create cppflow package on gcc

From 2c8e216146401a395bc7b843d923ee405ce2291e Mon Sep 17 00:00:00 2001
From: Tuomas Koskela <t.koskela@ucl.ac.uk>
Date: Wed, 31 May 2023 13:59:40 +0100
Subject: [PATCH 22/36] Patch g++ to the right version

---
 .github/workflows/cmake.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
index fbe443f56..cf6793f3c 100644
--- a/.github/workflows/cmake.yml
+++ b/.github/workflows/cmake.yml
@@ -143,7 +143,7 @@ jobs:
         cat $GITHUB_ENV
 
     - name: Create cppflow package on gcc
-      if: ${{ contains(matrix.cxx, 'g++-9') }}
+      if: ${{ contains(matrix.cxx, 'g++-10') }}
       run: |
         conan create ./cppflow/ -pr:h=default -pr:b=default -s compiler.libcxx=libstdc++11
 

From c823c1d39a9521ca99886263055961672ae36a3b Mon Sep 17 00:00:00 2001
From: Michael McLeod <michaelmcleod@ucl.ac.uk>
Date: Wed, 31 May 2023 15:06:49 +0100
Subject: [PATCH 23/36] Fix assertion in example

---
 cpp/sopt/gradient_operator.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cpp/sopt/gradient_operator.h b/cpp/sopt/gradient_operator.h
index 5094ef773..906aea5dc 100644
--- a/cpp/sopt/gradient_operator.h
+++ b/cpp/sopt/gradient_operator.h
@@ -49,7 +49,7 @@ template <class T>
 LinearTransform<Vector<T>> gradient_operator(const t_int rows, const t_int cols) {
   return LinearTransform<Vector<T>>(
       [rows, cols](Vector<T> &out, Vector<T> const &x) {
-        assert(x.size() = rows * cols * 2);
+        assert(x.size() == rows * cols * 2);
         out = diff2d_adjoint(x, rows, cols) / 2.;
         assert(out.size() == rows * cols);
       },

From f700c8e0ef58c7c80b6b142988584f8a61237521 Mon Sep 17 00:00:00 2001
From: Tuomas Koskela <t.koskela@ucl.ac.uk>
Date: Wed, 31 May 2023 15:26:53 +0100
Subject: [PATCH 24/36] Skip brew update. Test cppflow build fix

---
 .github/workflows/cmake.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
index cf6793f3c..254102eb4 100644
--- a/.github/workflows/cmake.yml
+++ b/.github/workflows/cmake.yml
@@ -78,7 +78,7 @@ jobs:
       run: |
         # Skip brew update until https://github.com/actions/setup-python/issues/577 is fixed
         # Seems to be working, alghough the issue is still open
-        brew update
+        #brew update
         brew install libtiff open-mpi libyaml ccache
         echo "CMAKE_PREFIX_PATH=/usr/local/opt/libomp" >> $GITHUB_ENV
 
@@ -132,7 +132,7 @@ jobs:
       with:
         repository: UCL/cppflow.git
         path: cppflow
-        ref: master
+        ref: tk/macos-build-fix
 
     - name: Add Tensorflow paths to env
       if: ${{ contains(matrix.cxx, 'clang++') }}

From d6496e3d3ca40bddbfd7a8641afcd7c7cb944ffc Mon Sep 17 00:00:00 2001
From: Tuomas Koskela <t.koskela@ucl.ac.uk>
Date: Wed, 31 May 2023 16:22:56 +0100
Subject: [PATCH 25/36] Remove extra paths from env

---
 .github/workflows/cmake.yml | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
index 254102eb4..d69d35f12 100644
--- a/.github/workflows/cmake.yml
+++ b/.github/workflows/cmake.yml
@@ -134,13 +134,13 @@ jobs:
         path: cppflow
         ref: tk/macos-build-fix
 
-    - name: Add Tensorflow paths to env
-      if: ${{ contains(matrix.cxx, 'clang++') }}
-      run: |
-        echo "LIBRARY_PATH=$LIBRARY_PATH:/usr/local/lib" >> "$GITHUB_ENV"
-        echo "DYLD_LIBRARY_PATH=/usr/local/lib" >> "$GITHUB_ENV"
-        echo "CMAKE_PREFIX_PATH=/usr/local/lib" >> $GITHUB_ENV
-        cat $GITHUB_ENV
+    # - name: Add Tensorflow paths to env
+    #   if: ${{ contains(matrix.cxx, 'clang++') }}
+    #   run: |
+    #     echo "LIBRARY_PATH=$LIBRARY_PATH:/usr/local/lib" >> "$GITHUB_ENV"
+    #     echo "DYLD_LIBRARY_PATH=/usr/local/lib" >> "$GITHUB_ENV"
+    #     echo "CMAKE_PREFIX_PATH=/usr/local/lib" >> $GITHUB_ENV
+    #     cat $GITHUB_ENV
 
     - name: Create cppflow package on gcc
       if: ${{ contains(matrix.cxx, 'g++-10') }}

From 379967f17fe53bafb1632d36d5b3ee0a898e1597 Mon Sep 17 00:00:00 2001
From: Tuomas Koskela <t.koskela@ucl.ac.uk>
Date: Wed, 31 May 2023 16:31:29 +0100
Subject: [PATCH 26/36] Debug before conan create

---
 .github/workflows/cmake.yml | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
index d69d35f12..927ecd269 100644
--- a/.github/workflows/cmake.yml
+++ b/.github/workflows/cmake.yml
@@ -142,6 +142,14 @@ jobs:
     #     echo "CMAKE_PREFIX_PATH=/usr/local/lib" >> $GITHUB_ENV
     #     cat $GITHUB_ENV
 
+
+
+    # Enable tmate debugging of manually-triggered workflows if the input option was provided
+    - name: Setup tmate session
+      uses: mxschmitt/action-tmate@v3
+      if: ${{ failure() }}
+      timeout-minutes: 15
+
     - name: Create cppflow package on gcc
       if: ${{ contains(matrix.cxx, 'g++-10') }}
       run: |
@@ -170,10 +178,3 @@ jobs:
       # Execute tests defined by the CMake configuration.
       # See https://cmake.org/cmake/help/latest/manual/ctest.1.html for more detail
       run: ctest -C ${{env.BUILD_TYPE}} --output-on-failure
-
-
-    # Enable tmate debugging of manually-triggered workflows if the input option was provided
-    - name: Setup tmate session
-      uses: mxschmitt/action-tmate@v3
-      if: ${{ failure() }}
-      timeout-minutes: 15

From 02e3cd332c0579fa9de32ebaea9c9030ecdb2906 Mon Sep 17 00:00:00 2001
From: Tuomas Koskela <t.koskela@ucl.ac.uk>
Date: Wed, 31 May 2023 17:03:06 +0100
Subject: [PATCH 27/36] Clean up debugging

---
 .github/workflows/cmake.yml | 24 +++++-------------------
 1 file changed, 5 insertions(+), 19 deletions(-)

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
index 927ecd269..50ece194a 100644
--- a/.github/workflows/cmake.yml
+++ b/.github/workflows/cmake.yml
@@ -76,12 +76,14 @@ jobs:
     - name: Install Dependencies on MacOS
       if: ${{ contains(matrix.os, 'macos') }}
       run: |
-        # Skip brew update until https://github.com/actions/setup-python/issues/577 is fixed
-        # Seems to be working, alghough the issue is still open
-        #brew update
         brew install libtiff open-mpi libyaml ccache
         echo "CMAKE_PREFIX_PATH=/usr/local/opt/libomp" >> $GITHUB_ENV
 
+    # Enable tmate debugging of manually-triggered workflows if the input option was provided
+    - name: Setup tmate session
+      uses: mxschmitt/action-tmate@v3
+      if: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.debug_enabled }}
+
     - name: Install Tensorflow API on Ubuntu
       # TODO could this be combined with mac version somehow? if/else?
       if: ${{ contains(matrix.os, 'ubuntu') }}
@@ -134,22 +136,6 @@ jobs:
         path: cppflow
         ref: tk/macos-build-fix
 
-    # - name: Add Tensorflow paths to env
-    #   if: ${{ contains(matrix.cxx, 'clang++') }}
-    #   run: |
-    #     echo "LIBRARY_PATH=$LIBRARY_PATH:/usr/local/lib" >> "$GITHUB_ENV"
-    #     echo "DYLD_LIBRARY_PATH=/usr/local/lib" >> "$GITHUB_ENV"
-    #     echo "CMAKE_PREFIX_PATH=/usr/local/lib" >> $GITHUB_ENV
-    #     cat $GITHUB_ENV
-
-
-
-    # Enable tmate debugging of manually-triggered workflows if the input option was provided
-    - name: Setup tmate session
-      uses: mxschmitt/action-tmate@v3
-      if: ${{ failure() }}
-      timeout-minutes: 15
-
     - name: Create cppflow package on gcc
       if: ${{ contains(matrix.cxx, 'g++-10') }}
       run: |

From c881f7eac046310a5f7a8926376583749e1c6fb2 Mon Sep 17 00:00:00 2001
From: Tuomas Koskela <t.koskela@ucl.ac.uk>
Date: Wed, 31 May 2023 17:07:23 +0100
Subject: [PATCH 28/36] Checkout cppflow master

---
 .github/workflows/cmake.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
index 50ece194a..6b50ef6c6 100644
--- a/.github/workflows/cmake.yml
+++ b/.github/workflows/cmake.yml
@@ -134,7 +134,7 @@ jobs:
       with:
         repository: UCL/cppflow.git
         path: cppflow
-        ref: tk/macos-build-fix
+        ref: master
 
     - name: Create cppflow package on gcc
       if: ${{ contains(matrix.cxx, 'g++-10') }}

From 54a12ccfc8c015358deb9bdd50ad1ec93c3d29d2 Mon Sep 17 00:00:00 2001
From: Michael McLeod <michaelmcleod@ucl.ac.uk>
Date: Thu, 1 Jun 2023 15:30:40 +0100
Subject: [PATCH 29/36] Fix type problem causing seg fault in proximal weights

---
 cpp/sopt/l1_g_proximal.h | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/cpp/sopt/l1_g_proximal.h b/cpp/sopt/l1_g_proximal.h
index 7be3febf6..0bb32dcab 100644
--- a/cpp/sopt/l1_g_proximal.h
+++ b/cpp/sopt/l1_g_proximal.h
@@ -49,7 +49,9 @@ class L1GProximal : public GProximal<SCALAR> {
 
   // Return the norm associated with this implementation
   Real proximal_norm(t_Vector const &x) const override {
-    return sopt::l1_norm(static_cast<t_Vector>(Psi().adjoint() * x), l1_proximal_weights());
+    auto &weights = l1_proximal_weights();
+    auto input = static_cast<t_Vector>(Psi().adjoint() * x);
+    return sopt::l1_norm(input, weights);
   }
 
   // Return g_proximal as a lambda function. Used in operator() in base class.
@@ -97,7 +99,7 @@ class L1GProximal : public GProximal<SCALAR> {
   SOPT_MACRO(positivity_constraint, bool);
   SOPT_MACRO(real_constraint, bool);
   SOPT_MACRO(nu, Real);
-  SOPT_MACRO(weights, t_Vector);
+  SOPT_MACRO(weights, Vector<t_real>);
 #undef SOPT_MACRO
 
   //! Analysis operator Ψ

From 42915449b815f9a52147a42455b5353dc70c97df Mon Sep 17 00:00:00 2001
From: Tuomas Koskela <t.koskela@ucl.ac.uk>
Date: Tue, 13 Jun 2023 16:44:27 +0100
Subject: [PATCH 30/36] We can debug in the cmake workflow

---
 .github/workflows/macdebug.yml | 95 ----------------------------------
 1 file changed, 95 deletions(-)
 delete mode 100644 .github/workflows/macdebug.yml

diff --git a/.github/workflows/macdebug.yml b/.github/workflows/macdebug.yml
deleted file mode 100644
index 3e3f18b1f..000000000
--- a/.github/workflows/macdebug.yml
+++ /dev/null
@@ -1,95 +0,0 @@
-name: MacOSDebug
-
-on:
-  workflow_dispatch:
-    inputs:
-      debug_enabled:
-        description: 'Run the build with tmate debugging enabled (https://github.com/marketplace/actions/debugging-with-tmate)'
-        required: false
-        default: false
-
-env:
-  # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
-  BUILD_TYPE: Release
-  OMP_NUM_THREADS: 2
-  CONAN_PRINT_RUN_COMMANDS: 1
-  CONAN_CPU_COUNT: 2
-
-jobs:
-  build:
-    name: macos-clang-debug
-    # The CMake configure and build commands are platform agnostic and should work equally
-    # well on Windows or Mac.  You can convert this to a matrix build if you need
-    # cross-platform coverage.
-    # See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix
-    runs-on: macos-11
-    env:
-      CC: clang
-      CXX: clang++
-
-    steps:
-    - uses: actions/checkout@v3
-
-   
-    - name: Install Dependencies on MacOS
-      run: |    
-        brew update
-        brew install libtiff open-mpi libyaml ccache
-        echo "CMAKE_PREFIX_PATH=/usr/local/opt/libomp" >> $GITHUB_ENV
-
-    - name: Install Tensorflow API on MacOS
-      uses: UCL/install-tensorflow-action@main
-      with:
-        version: 2.11.0
-        os: darwin
-
-    - name: Select Python 3.10
-      # otherwise turtlebrowser/get-conan@v1.1 fails on macos-12
-      # ref: https://github.com/turtlebrowser/get-conan/issues/4
-      uses: actions/setup-python@v4
-      with:
-        python-version: '3.10'
-
-    - name: Install Conan
-      id: conan
-      uses: turtlebrowser/get-conan@main
-      with:
-        version: 1.59.0
-    
-    - name: Checkout cppflow repo
-      uses: actions/checkout@v3
-      with:
-        repository: UCL/cppflow.git
-        path: cppflow
-        ref: master
-
-    - name: Add Tensorflow paths to env
-      run: |
-        echo "LIBRARY_PATH=$LIBRARY_PATH:/usr/local/lib" >> "$GITHUB_ENV"
-        echo "DYLD_LIBRARY_PATH=/usr/local/lib" >> "$GITHUB_ENV"
-        cat $GITHUB_ENV
-
-    # Enable tmate debugging of manually-triggered workflows if the input option was provided
-    - name: Setup tmate session
-      uses: mxschmitt/action-tmate@v3
-      if: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.debug_enabled }}
-    
-
-    - name: Create cppflow package on apple-clang
-      run: |
-        conan create ./cppflow/ -pr:h=default -pr:b=default
-    
-    - name: Conan install on apple-clang
-      run: conan install ${{github.workspace}} -if ${{github.workspace}}/build --build missing -o mpi=off -o openmp=off -o cppflow=on -pr:h=default -pr:b=default
-  
-    - name: Build
-      # Build your program with the given configuration.
-      # The Github Actions machines are dual-core so we can build faster using 2 parallel processes
-      run: conan build ${{github.workspace}} -bf ${{github.workspace}}/build
-
-    - name: Test
-      working-directory: ${{github.workspace}}/build
-      # Execute tests defined by the CMake configuration.
-      # See https://cmake.org/cmake/help/latest/manual/ctest.1.html for more detail
-      run: ctest -C ${{env.BUILD_TYPE}} --output-on-failure
-

From 32ecc275df2db6fc7553abfc79df1c779e917567 Mon Sep 17 00:00:00 2001
From: Michael McLeod <michaelmcleod@ucl.ac.uk>
Date: Wed, 14 Jun 2023 10:52:59 +0100
Subject: [PATCH 31/36] Restore MPI communicators for FB algorithm

---
 cpp/sopt/imaging_forward_backward.h | 5 +++--
 cpp/sopt/l1_g_proximal.h            | 8 ++++++++
 cpp/sopt/l2_forward_backward.h      | 2 +-
 3 files changed, 12 insertions(+), 3 deletions(-)

diff --git a/cpp/sopt/imaging_forward_backward.h b/cpp/sopt/imaging_forward_backward.h
index 6bfb60267..2d813dafa 100644
--- a/cpp/sopt/imaging_forward_backward.h
+++ b/cpp/sopt/imaging_forward_backward.h
@@ -125,6 +125,7 @@ class ImagingForwardBackward {
 #ifdef SOPT_MPI
   //! Communicator for summing objective_function
   SOPT_MACRO(obj_comm, mpi::Communicator);
+  SOPT_MACRO(adjoint_space_comm, mpi::Communicator);
 #endif
 
 #undef SOPT_MACRO
@@ -205,7 +206,7 @@ class ImagingForwardBackward {
 
   //! \brief Proximal of the L2 ball
   //! \details Non-const version to setup the object.
-  t_Gradient &l2_graident() { return l2_gradient_; }
+  t_Gradient &l2_gradient() { return l2_gradient_; }
 
   //! Helper function to set-up default residual convergence function
   ImagingForwardBackward<Scalar> &residual_convergence(Real const &tolerance) {
@@ -316,7 +317,7 @@ bool ImagingForwardBackward<SCALAR>::objective_convergence(mpi::Communicator con
   if (scalvar.relative_tolerance() <= 0e0) return true;
   auto const current = obj_comm.all_sum_all<t_real>(
 	((gamma() > 0) ? g_proximal_->proximal_norm(x)
-       * gamma() : 0) + std::pow(sopt::l2_norm(residual), 2) / (2 * sigma() * sigma()));
+       * gamma() : 0) + std::pow(sopt::l2_norm(residual), 2) / (2 * sigma_ * sigma_));
   return scalvar(current);
 };
 #endif
diff --git a/cpp/sopt/l1_g_proximal.h b/cpp/sopt/l1_g_proximal.h
index 0bb32dcab..e19d7fb83 100644
--- a/cpp/sopt/l1_g_proximal.h
+++ b/cpp/sopt/l1_g_proximal.h
@@ -15,6 +15,10 @@
 #include "sopt/g_proximal.h"
 #include "sopt/l1_proximal.h"
 
+#ifdef SOPT_MPI
+ #include "sopt/mpi/communicator.h"
+#endif
+
 namespace sopt {
 namespace algorithm {
 
@@ -100,6 +104,10 @@ class L1GProximal : public GProximal<SCALAR> {
   SOPT_MACRO(real_constraint, bool);
   SOPT_MACRO(nu, Real);
   SOPT_MACRO(weights, Vector<t_real>);
+#ifdef SOPT_MPI
+  SOPT_MACRO(adjoint_space_comm, mpi::Communicator);
+  SOPT_MACRO(direct_space_comm, mpi::Communicator);
+#endif
 #undef SOPT_MACRO
 
   //! Analysis operator Ψ
diff --git a/cpp/sopt/l2_forward_backward.h b/cpp/sopt/l2_forward_backward.h
index 2d60e092b..7d6eefd7f 100644
--- a/cpp/sopt/l2_forward_backward.h
+++ b/cpp/sopt/l2_forward_backward.h
@@ -206,7 +206,7 @@ class L2ForwardBackward {
   t_Proximal<Vector<Real>> &l2_proximal_weighted() { return l2_proximal_weighted_; }
   //! \brief Proximal of the L2 ball
   //! \details Non-const version to setup the object.
-  t_Gradient &l2_graident() { return l2_gradient_; }
+  t_Gradient &l2_gradient() { return l2_gradient_; }
 
   //! Helper function to set-up default residual convergence function
   L2ForwardBackward<Scalar> &residual_convergence(Real const &tolerance) {

From 39f957ae94f864bf391f5fd6f721adf97ec84671 Mon Sep 17 00:00:00 2001
From: Sarah Jaffa <SJaffa@users.noreply.github.com>
Date: Wed, 14 Jun 2023 11:53:39 +0100
Subject: [PATCH 32/36] Updated install instructions for cppflow conan package

---
 README.md | 74 +++++++++++++++++++++++++++++++++----------------------
 1 file changed, 44 insertions(+), 30 deletions(-)

diff --git a/README.md b/README.md
index a4ebc8024..138c3da71 100644
--- a/README.md
+++ b/README.md
@@ -29,6 +29,7 @@ Dependencies installation
 - [GCC](https://gcc.gnu.org) v7.3.0 GNU compiler for `C++`.
 - [UCL/GreatCMakeCookOff](https://github.com/UCL/GreatCMakeCookOff) Collection of `CMake` recipes. Downloaded automatically if absent.
 - [OpenMP](http://openmp.org/wp/) v4.8.4 (Trusty) - Optional - Speeds up some of the operations.
+- [Cppflow](https://github.com/UCL/cppflow) - Optional - A warpper for the Tensorflow C API allowing us to read Tensorflow models into SOPT. Needed if you are using a learned prior.
 - [Conan](https://docs.conan.io/en/latest/installation.html) - C++ package manager which installs the following:
   - [Eigen3](http://eigen.tuxfamily.org/index.php?title=Main_Page) v3.2.0 (Trusty) Modern `C++` linear algebra. Downloaded automatically if absent.
   - [spdlog](https://github.com/gabime/spdlog) v* - Optional - Logging library. Downloaded automatically if
@@ -42,45 +43,58 @@ Dependencies installation
 Installing and building SOPT
 ----------------------------
 
-You can build **SOPT** entirely from the source code. Once the mandatory dependencies are present, `git clone` from the [GitHub repository](https://github.com/astro-informatics/sopt):
+You can build **SOPT** entirely from the source code.
 
-``` bash
-git clone https://github.com/astro-informatics/sopt.git
-```
 
-Then, the program can be built with standard `CMake` command:
 
-``` bash
-cd /path/to/code
-mkdir build
-cd build
-conan install .. --build missing
-conan build ..
-```
+1. If you are using a learned prior you must install teh Tensorflow C API and `cppflow package:
+    - Install [TensorFlow C API](https://www.tensorflow.org/install/lang_c)
+    - Clone the UCL fork of cppflow and create a conan package using
 
-To install in directory `INSTALL_FOLDER`, add the following options to the conan build command:
+        ``` bash
+        git clone git@github.com:UCL/cppflow.git
+        conan create ./cppflow/ -pr:h=default -pr:b=default
+        ```
 
-``` bash
-conan build .. -bf INSTALL_FOLDER -if .
-```
+1. Once the mandatory dependencies are present, `git clone` from the [GitHub repository](https://github.com/astro-informatics/sopt):
 
-CMake build options should be passed as options to `conan install` using the `-o` flag with a value `on` or `off`. Possible options are
+    ``` bash
+    git clone https://github.com/astro-informatics/sopt.git
+    ```
 
-- tests (default on)
-- benchmarks (default off)
-- examples (default on)
-- logging (default on)
-- openmp (default on)
-- mpi (default on)
-- docs (default off)
-- coverage (default off)
+1. Then, the program can be built using conan:
 
-For example, to build with both MPI and OpenMP off you would use
+    ``` bash
+    cd /path/to/code
+    mkdir build
+    cd build
+    conan install .. --build missing
+    conan build ..
+    ```
 
-``` bash
-conan install .. --build missing -o openmp=off -o mpi=off
-conan build ..
-```
+    - To install in directory `INSTALL_FOLDER`, add the following options to the conan build command:
+
+        ``` bash
+        conan build .. -bf INSTALL_FOLDER -if .
+        ```
+
+    - CMake build options should be passed as options to `conan install` using the `-o` flag with a value `on` or `off`. Possible options are
+
+    - tests (default on)
+    - benchmarks (default off)
+    - examples (default on)
+    - logging (default on)
+    - openmp (default on)
+    - mpi (default on)
+    - docs (default off)
+    - coverage (default off)
+
+        For example, to build with both MPI and OpenMP off you would use
+
+        ``` bash
+        conan install .. --build missing -o openmp=off -o mpi=off
+        conan build ..
+        ```
 
 Common errors
 -------

From 983f80de6f3992febc12a31b7a5fa197980161ed Mon Sep 17 00:00:00 2001
From: Tuomas Koskela <t.koskela@ucl.ac.uk>
Date: Wed, 14 Jun 2023 16:19:01 +0100
Subject: [PATCH 33/36] Fix typo

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 138c3da71..b828ec41d 100644
--- a/README.md
+++ b/README.md
@@ -47,7 +47,7 @@ You can build **SOPT** entirely from the source code.
 
 
 
-1. If you are using a learned prior you must install teh Tensorflow C API and `cppflow package:
+1. If you are using a learned prior you must install the Tensorflow C API and `cppflow` package:
     - Install [TensorFlow C API](https://www.tensorflow.org/install/lang_c)
     - Clone the UCL fork of cppflow and create a conan package using
 

From fc664f2efab3ea6dded114e9e3451b51dc370dde Mon Sep 17 00:00:00 2001
From: Tuomas Koskela <t.koskela@ucl.ac.uk>
Date: Wed, 14 Jun 2023 16:20:01 +0100
Subject: [PATCH 34/36] Add cppflow option

---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index b828ec41d..61ec5c438 100644
--- a/README.md
+++ b/README.md
@@ -88,6 +88,7 @@ You can build **SOPT** entirely from the source code.
     - mpi (default on)
     - docs (default off)
     - coverage (default off)
+	- cppflow (default off)
 
         For example, to build with both MPI and OpenMP off you would use
 

From bbbc5adbe63ecec1e75e8f212353474ad078b4cb Mon Sep 17 00:00:00 2001
From: Michael McLeod <michaelmcleod@ucl.ac.uk>
Date: Wed, 14 Jun 2023 17:21:09 +0100
Subject: [PATCH 35/36] Change from relative to absolute threshold for
 imaginary component of image

---
 cpp/sopt/cppflow_utils.cc | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/cpp/sopt/cppflow_utils.cc b/cpp/sopt/cppflow_utils.cc
index 63771489b..90c8dd10f 100644
--- a/cpp/sopt/cppflow_utils.cc
+++ b/cpp/sopt/cppflow_utils.cc
@@ -9,7 +9,8 @@
 namespace sopt {
 namespace cppflowutils {
 
-  const double imaginary_threshold = 1e-5;
+  // arbitrary constant for imaginary part of image vectors. 
+  const double imaginary_threshold = 1e-10;
 
     cppflow::tensor convert_image_to_tensor(Image<double> const &image, int image_rows, int image_cols){
         // Convert the Sopt::Image of doubles(wrapper for Eigen::Array) to a cppflow::tensor of floats
@@ -42,7 +43,7 @@ namespace cppflowutils {
 
     for (int i = 0; i < image.rows(); ++i) {
         for (int j = 0; j < image.cols(); ++j) {
-          if(std::abs(image(i,j).imag())/std::abs(image(i,j).real()) > cppflowutils::imaginary_threshold)
+          if(std::abs(image(i,j).real()) > cppflowutils::imaginary_threshold)
           {
             throw std::runtime_error("Cannot convert to tensorflow format: imaginary component of image is non-negligible.");
           }
@@ -71,7 +72,7 @@ namespace cppflowutils {
     std::vector<float> input_values(image_rows);
     for(int i = 0; i < image_rows; i++)
     {
-      if(std::abs(image(i).imag())/std::abs(image(i).real()) > cppflowutils::imaginary_threshold)
+      if(std::abs(image(i).real()) > cppflowutils::imaginary_threshold)
       {
         throw std::runtime_error("Cannot conver to tensorflow format: imaginary component of image vector is non negligible.");
       }

From 976872f2b55fdefd38d88af24726381b62a05b63 Mon Sep 17 00:00:00 2001
From: Tuomas Koskela <t.koskela@ucl.ac.uk>
Date: Wed, 21 Jun 2023 13:53:57 +0100
Subject: [PATCH 36/36] Update README.md

Add conan profiles to install instructions
---
 README.md | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 61ec5c438..360066c67 100644
--- a/README.md
+++ b/README.md
@@ -55,6 +55,8 @@ You can build **SOPT** entirely from the source code.
         git clone git@github.com:UCL/cppflow.git
         conan create ./cppflow/ -pr:h=default -pr:b=default
         ```
+      Note that conan requires you to specify the host (h) and the build (b) profiles on the command
+      line (`-pr:h=default -pr:b=default`), if you haven't defined them in your conan profile.
 
 1. Once the mandatory dependencies are present, `git clone` from the [GitHub repository](https://github.com/astro-informatics/sopt):
 
@@ -68,7 +70,7 @@ You can build **SOPT** entirely from the source code.
     cd /path/to/code
     mkdir build
     cd build
-    conan install .. --build missing
+    conan install .. --build missing -pr:h=default -pr:b=default
     conan build ..
     ```
 
@@ -93,7 +95,7 @@ You can build **SOPT** entirely from the source code.
         For example, to build with both MPI and OpenMP off you would use
 
         ``` bash
-        conan install .. --build missing -o openmp=off -o mpi=off
+        conan install .. --build missing -o openmp=off -o mpi=off -pr:h=default -pr:b=default
         conan build ..
         ```