From f533dcbeaf9c703d28455a960405e3110fcb4750 Mon Sep 17 00:00:00 2001
From: Kamil Skwarczynski <skwarczynskikamil@gmail.com>
Date: Sun, 1 Sep 2024 15:36:23 +0000
Subject: [PATCH 01/26] minor tweak to cmake to not break CPM

---
 CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index bfb6115f6..fef31ca38 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -340,4 +340,4 @@ if(NOT TARGET uninstall)
 endif()
 
 # KS: Configure the Doxygen input file, this is to ensure whenever we update MaCh3 version Doxyfile will have same version.
-configure_file(${CMAKE_SOURCE_DIR}/cmake/Templates/Doxyfile.in ${CMAKE_SOURCE_DIR}/Doc/Doxyfile @ONLY)
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cmake/Templates/Doxyfile.in ${CMAKE_CURRENT_SOURCE_DIR}/Doc/Doxyfile @ONLY)

From 09e09fcee0afd24b4ed5ba2f0486346386eabbd2 Mon Sep 17 00:00:00 2001
From: Kamil Skwarczynski <skwarczynskikamil@gmail.com>
Date: Mon, 2 Sep 2024 12:30:01 +0000
Subject: [PATCH 02/26] test with new validations CI commence

---
 .github/workflows/CIValidations.yml | 39 +++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)
 create mode 100644 .github/workflows/CIValidations.yml

diff --git a/.github/workflows/CIValidations.yml b/.github/workflows/CIValidations.yml
new file mode 100644
index 000000000..22053059f
--- /dev/null
+++ b/.github/workflows/CIValidations.yml
@@ -0,0 +1,39 @@
+name: Validations CI
+
+# The events that trigger the workflow
+on:
+  pull_request:
+    branches: [ develop ]
+  push:
+    branches: [ feature_CIvalidations ]
+
+permissions:
+  contents: read
+  packages: write
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false  # KS: Prevents cancellation of remaining jobs if one fails
+      matrix:
+        include:
+          - name: SplineValidations
+
+
+    name: Build CI ${{ matrix.name }}
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Getting MaCh3 Container
+      run: docker pull ghcr.io/mach3-software/mach3:alma9latest && docker run --name mach3-container -d ghcr.io/mach3-software/mach3:alma9latest
+
+    - name: Get MaCh3 Validations
+      run: cd /opt/ && git clone https://@github.com/MaCh3Validations-software/MaCh3.git MaCh3Validations && cd MaCh3Validations && mkdir build && cd build && cmake ../ -DMaCh3_Branch=${{ github.head_ref }}
+
+    - name: Install
+      run: make install && source bin/setup.MaCh3.sh && source bin/setup.MaCh3Validations.sh
+
+    - name: Validations
+      run: Apps/${{ matrix.name }}

From 4e6737c0b60e7a7165ec4c5d150df5b48d19ab08 Mon Sep 17 00:00:00 2001
From: Kamil Skwarczynski <skwarczynskikamil@gmail.com>
Date: Mon, 2 Sep 2024 12:32:20 +0000
Subject: [PATCH 03/26] ups

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

diff --git a/.github/workflows/CIValidations.yml b/.github/workflows/CIValidations.yml
index 22053059f..81d9a524d 100644
--- a/.github/workflows/CIValidations.yml
+++ b/.github/workflows/CIValidations.yml
@@ -30,7 +30,7 @@ jobs:
       run: docker pull ghcr.io/mach3-software/mach3:alma9latest && docker run --name mach3-container -d ghcr.io/mach3-software/mach3:alma9latest
 
     - name: Get MaCh3 Validations
-      run: cd /opt/ && git clone https://@github.com/MaCh3Validations-software/MaCh3.git MaCh3Validations && cd MaCh3Validations && mkdir build && cd build && cmake ../ -DMaCh3_Branch=${{ github.head_ref }}
+      run: cd /opt/ && git clone https://@github.com/mach3-software/MaCh3Validations.git MaCh3Validations && cd MaCh3Validations && mkdir build && cd build && cmake ../ -DMaCh3_Branch=${{ github.head_ref }}
 
     - name: Install
       run: make install && source bin/setup.MaCh3.sh && source bin/setup.MaCh3Validations.sh

From 8790ad63abcdf42fb2e58eb29575c05a7a55761a Mon Sep 17 00:00:00 2001
From: Kamil Skwarczynski <skwarczynskikamil@gmail.com>
Date: Mon, 2 Sep 2024 12:37:48 +0000
Subject: [PATCH 04/26] wrong docker command...

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

diff --git a/.github/workflows/CIValidations.yml b/.github/workflows/CIValidations.yml
index 81d9a524d..3edbb7e65 100644
--- a/.github/workflows/CIValidations.yml
+++ b/.github/workflows/CIValidations.yml
@@ -27,7 +27,7 @@ jobs:
     - uses: actions/checkout@v3
 
     - name: Getting MaCh3 Container
-      run: docker pull ghcr.io/mach3-software/mach3:alma9latest && docker run --name mach3-container -d ghcr.io/mach3-software/mach3:alma9latest
+      run: docker pull ghcr.io/mach3-software/mach3:alma9latest && docker run -it --name mach3-container ghcr.io/mach3-software/mach3:alma9latest
 
     - name: Get MaCh3 Validations
       run: cd /opt/ && git clone https://@github.com/mach3-software/MaCh3Validations.git MaCh3Validations && cd MaCh3Validations && mkdir build && cd build && cmake ../ -DMaCh3_Branch=${{ github.head_ref }}

From f3ebe7c681b6aed5fe96bac36570621905c07da0 Mon Sep 17 00:00:00 2001
From: Kamil Skwarczynski <skwarczynskikamil@gmail.com>
Date: Mon, 2 Sep 2024 12:52:02 +0000
Subject: [PATCH 05/26] maybe now

---
 .github/workflows/CIValidations.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/CIValidations.yml b/.github/workflows/CIValidations.yml
index 3edbb7e65..4d5ee8b7f 100644
--- a/.github/workflows/CIValidations.yml
+++ b/.github/workflows/CIValidations.yml
@@ -14,21 +14,21 @@ permissions:
 jobs:
   build:
     runs-on: ubuntu-latest
+
+    name: Validations CI ${{ matrix.name }}
+
     strategy:
-      fail-fast: false  # KS: Prevents cancellation of remaining jobs if one fails
+      fail-fast: false  # Prevents cancellation of remaining jobs if one fails
       matrix:
         include:
           - name: SplineValidations
 
-
-    name: Build CI ${{ matrix.name }}
+    container:
+      image: ghcr.io/mach3-software/mach3:alma9latest
 
     steps:
     - uses: actions/checkout@v3
 
-    - name: Getting MaCh3 Container
-      run: docker pull ghcr.io/mach3-software/mach3:alma9latest && docker run -it --name mach3-container ghcr.io/mach3-software/mach3:alma9latest
-
     - name: Get MaCh3 Validations
       run: cd /opt/ && git clone https://@github.com/mach3-software/MaCh3Validations.git MaCh3Validations && cd MaCh3Validations && mkdir build && cd build && cmake ../ -DMaCh3_Branch=${{ github.head_ref }}
 

From 616f40806011679b702a4d7497842c919731d110 Mon Sep 17 00:00:00 2001
From: Kamil Skwarczynski <skwarczynskikamil@gmail.com>
Date: Mon, 2 Sep 2024 12:55:47 +0000
Subject: [PATCH 06/26] debug

---
 .github/workflows/CIValidations.yml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/CIValidations.yml b/.github/workflows/CIValidations.yml
index 4d5ee8b7f..790611d8d 100644
--- a/.github/workflows/CIValidations.yml
+++ b/.github/workflows/CIValidations.yml
@@ -29,8 +29,11 @@ jobs:
     steps:
     - uses: actions/checkout@v3
 
+    - name: Debug Branch Name
+      run: echo "Current Branch: ${{ github.head_ref }}"
+
     - name: Get MaCh3 Validations
-      run: cd /opt/ && git clone https://@github.com/mach3-software/MaCh3Validations.git MaCh3Validations && cd MaCh3Validations && mkdir build && cd build && cmake ../ -DMaCh3_Branch=${{ github.head_ref }}
+      run: cd /opt/ && git clone https://@github.com/mach3-software/MaCh3Validations.git MaCh3Validations && cd MaCh3Validations && mkdir build && cd build && cmake ../ -DMaCh3_Branch="${{ github.head_ref }}"
 
     - name: Install
       run: make install && source bin/setup.MaCh3.sh && source bin/setup.MaCh3Validations.sh

From 0b0b6e9e67ccb93dec93d2d5bc4e2ff8f5898814 Mon Sep 17 00:00:00 2001
From: Kamil Skwarczynski <skwarczynskikamil@gmail.com>
Date: Mon, 2 Sep 2024 13:00:35 +0000
Subject: [PATCH 07/26] github treats push different to PR...

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

diff --git a/.github/workflows/CIValidations.yml b/.github/workflows/CIValidations.yml
index 790611d8d..8bad612f1 100644
--- a/.github/workflows/CIValidations.yml
+++ b/.github/workflows/CIValidations.yml
@@ -30,10 +30,10 @@ jobs:
     - uses: actions/checkout@v3
 
     - name: Debug Branch Name
-      run: echo "Current Branch: ${{ github.head_ref }}"
+      run: echo "Current Branch: ${{ github.ref }}"
 
     - name: Get MaCh3 Validations
-      run: cd /opt/ && git clone https://@github.com/mach3-software/MaCh3Validations.git MaCh3Validations && cd MaCh3Validations && mkdir build && cd build && cmake ../ -DMaCh3_Branch="${{ github.head_ref }}"
+      run: cd /opt/ && git clone https://@github.com/mach3-software/MaCh3Validations.git MaCh3Validations && cd MaCh3Validations && mkdir build && cd build && cmake ../ -DMaCh3_Branch=${{ github.ref }}
 
     - name: Install
       run: make install && source bin/setup.MaCh3.sh && source bin/setup.MaCh3Validations.sh

From 830b4290da1123c29914c3fdd1497ad57dc6d755 Mon Sep 17 00:00:00 2001
From: Kamil Skwarczynski <skwarczynskikamil@gmail.com>
Date: Mon, 2 Sep 2024 13:01:22 +0000
Subject: [PATCH 08/26] arghhh

---
 .github/workflows/CIValidations.yml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.github/workflows/CIValidations.yml b/.github/workflows/CIValidations.yml
index 8bad612f1..8694c3951 100644
--- a/.github/workflows/CIValidations.yml
+++ b/.github/workflows/CIValidations.yml
@@ -29,9 +29,6 @@ jobs:
     steps:
     - uses: actions/checkout@v3
 
-    - name: Debug Branch Name
-      run: echo "Current Branch: ${{ github.ref }}"
-
     - name: Get MaCh3 Validations
       run: cd /opt/ && git clone https://@github.com/mach3-software/MaCh3Validations.git MaCh3Validations && cd MaCh3Validations && mkdir build && cd build && cmake ../ -DMaCh3_Branch=${{ github.ref }}
 

From b72cb8f027b76769d0a8a8e39f70b8e7423e1898 Mon Sep 17 00:00:00 2001
From: Kamil Skwarczynski <skwarczynskikamil@gmail.com>
Date: Mon, 2 Sep 2024 13:04:05 +0000
Subject: [PATCH 09/26] ...

---
 .github/workflows/CIValidations.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/CIValidations.yml b/.github/workflows/CIValidations.yml
index 8694c3951..22d68fe6f 100644
--- a/.github/workflows/CIValidations.yml
+++ b/.github/workflows/CIValidations.yml
@@ -29,8 +29,12 @@ jobs:
     steps:
     - uses: actions/checkout@v3
 
+    - name: Debug Branch Name
+      run: echo "Current Branch: ${{ github.ref }}"
+
     - name: Get MaCh3 Validations
-      run: cd /opt/ && git clone https://@github.com/mach3-software/MaCh3Validations.git MaCh3Validations && cd MaCh3Validations && mkdir build && cd build && cmake ../ -DMaCh3_Branch=${{ github.ref }}
+      run: cd /opt/ && git clone https://@github.com/mach3-software/MaCh3Validations.git MaCh3Validations && cd MaCh3Validations && mkdir build && cd build && cmake ../ -DMaCh3_Branch=feature_CIvalidations
+      #${{ github.head_ref }}
 
     - name: Install
       run: make install && source bin/setup.MaCh3.sh && source bin/setup.MaCh3Validations.sh

From 6c6995474f434e9b1dbcadc3e724c6f5933bfd72 Mon Sep 17 00:00:00 2001
From: Kamil Skwarczynski <skwarczynskikamil@gmail.com>
Date: Mon, 2 Sep 2024 13:05:26 +0000
Subject: [PATCH 10/26] no clue...

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

diff --git a/.github/workflows/CIValidations.yml b/.github/workflows/CIValidations.yml
index 22d68fe6f..f960fc231 100644
--- a/.github/workflows/CIValidations.yml
+++ b/.github/workflows/CIValidations.yml
@@ -33,7 +33,8 @@ jobs:
       run: echo "Current Branch: ${{ github.ref }}"
 
     - name: Get MaCh3 Validations
-      run: cd /opt/ && git clone https://@github.com/mach3-software/MaCh3Validations.git MaCh3Validations && cd MaCh3Validations && mkdir build && cd build && cmake ../ -DMaCh3_Branch=feature_CIvalidations
+      run: cd /opt/ && git clone https://@github.com/mach3-software/MaCh3Validations.git MaCh3Validations && cd MaCh3Validations && mkdir build && cd build && cmake ../ -DMaCh3_Branch=develop
+
       #${{ github.head_ref }}
 
     - name: Install

From df172290c5fbdba5ff69f16ffa005f45f24c69ad Mon Sep 17 00:00:00 2001
From: Kamil Skwarczynski <skwarczynskikamil@gmail.com>
Date: Mon, 2 Sep 2024 13:06:29 +0000
Subject: [PATCH 11/26] why...

---
 .github/workflows/CIValidations.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/CIValidations.yml b/.github/workflows/CIValidations.yml
index f960fc231..d9f88be44 100644
--- a/.github/workflows/CIValidations.yml
+++ b/.github/workflows/CIValidations.yml
@@ -33,9 +33,8 @@ jobs:
       run: echo "Current Branch: ${{ github.ref }}"
 
     - name: Get MaCh3 Validations
-      run: cd /opt/ && git clone https://@github.com/mach3-software/MaCh3Validations.git MaCh3Validations && cd MaCh3Validations && mkdir build && cd build && cmake ../ -DMaCh3_Branch=develop
-
-      #${{ github.head_ref }}
+      run: cd /opt/ && git clone https://@github.com/mach3-software/MaCh3Validations.git MaCh3Validations && cd MaCh3Validations && mkdir build && cd build && cmake ../
+      #-DMaCh3_Branch=${{ github.head_ref }}
 
     - name: Install
       run: make install && source bin/setup.MaCh3.sh && source bin/setup.MaCh3Validations.sh

From 45eb499eddccb350c50a647e4bca62ae81a8e111 Mon Sep 17 00:00:00 2001
From: Kamil Skwarczynski <skwarczynskikamil@gmail.com>
Date: Mon, 2 Sep 2024 13:07:12 +0000
Subject: [PATCH 12/26] sry for spam...

---
 .github/workflows/CIValidations.yml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.github/workflows/CIValidations.yml b/.github/workflows/CIValidations.yml
index d9f88be44..e65b8d4de 100644
--- a/.github/workflows/CIValidations.yml
+++ b/.github/workflows/CIValidations.yml
@@ -29,9 +29,6 @@ jobs:
     steps:
     - uses: actions/checkout@v3
 
-    - name: Debug Branch Name
-      run: echo "Current Branch: ${{ github.ref }}"
-
     - name: Get MaCh3 Validations
       run: cd /opt/ && git clone https://@github.com/mach3-software/MaCh3Validations.git MaCh3Validations && cd MaCh3Validations && mkdir build && cd build && cmake ../
       #-DMaCh3_Branch=${{ github.head_ref }}

From a6e23f78e744e6c48264b4ca05729d950ed69dd2 Mon Sep 17 00:00:00 2001
From: Kamil Skwarczynski <skwarczynskikamil@gmail.com>
Date: Mon, 2 Sep 2024 13:11:33 +0000
Subject: [PATCH 13/26] problematic paths...

---
 .github/workflows/CIValidations.yml | 28 ++++++++++++++++++++++------
 1 file changed, 22 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/CIValidations.yml b/.github/workflows/CIValidations.yml
index e65b8d4de..12ce8075c 100644
--- a/.github/workflows/CIValidations.yml
+++ b/.github/workflows/CIValidations.yml
@@ -29,12 +29,28 @@ jobs:
     steps:
     - uses: actions/checkout@v3
 
-    - name: Get MaCh3 Validations
-      run: cd /opt/ && git clone https://@github.com/mach3-software/MaCh3Validations.git MaCh3Validations && cd MaCh3Validations && mkdir build && cd build && cmake ../
-      #-DMaCh3_Branch=${{ github.head_ref }}
 
-    - name: Install
-      run: make install && source bin/setup.MaCh3.sh && source bin/setup.MaCh3Validations.sh
+    - name: Get MaCh3 Validations
+      run: |
+        cd /opt/
+        git clone https://github.com/mach3-software/MaCh3Validations.git MaCh3Validations
+        cd MaCh3Validations
+        mkdir build
+        cd build
+        cmake ../
+        #-DMaCh3_Branch="${{ github.ref_name }}"
+
+    - name: Build MaCh3 Validations
+      run: |
+        cd /opt/MaCh3Validations/build
+        make install # Build the project
+
+    - name: Source Setup Scripts
+      run: |
+        source /opt/MaCh3Validations/build/bin/setup.MaCh3.sh
+        source /opt/MaCh3Validations/build/bin/setup.MaCh3Validations.sh
 
     - name: Validations
-      run: Apps/${{ matrix.name }}
+      run: |
+        cd /opt/MaCh3Validations/build
+        Apps/${{ matrix.name }}

From a8a4fee4bcac5e17cb83e1c745ec4196aa9b4797 Mon Sep 17 00:00:00 2001
From: Kamil Skwarczynski <skwarczynskikamil@gmail.com>
Date: Mon, 2 Sep 2024 13:30:13 +0000
Subject: [PATCH 14/26] it should work now

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

diff --git a/.github/workflows/CIValidations.yml b/.github/workflows/CIValidations.yml
index 12ce8075c..726b1fe7e 100644
--- a/.github/workflows/CIValidations.yml
+++ b/.github/workflows/CIValidations.yml
@@ -54,3 +54,4 @@ jobs:
       run: |
         cd /opt/MaCh3Validations/build
         Apps/${{ matrix.name }}
+

From cc98a49eca879ed87e9609c7e4fa84f88ec775ae Mon Sep 17 00:00:00 2001
From: Kamil Skwarczynski <skwarczynskikamil@gmail.com>
Date: Mon, 2 Sep 2024 13:41:30 +0000
Subject: [PATCH 15/26] final tidy before PR

---
 .github/workflows/CIValidations.yml | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/.github/workflows/CIValidations.yml b/.github/workflows/CIValidations.yml
index 726b1fe7e..ce2fe5439 100644
--- a/.github/workflows/CIValidations.yml
+++ b/.github/workflows/CIValidations.yml
@@ -4,8 +4,6 @@ name: Validations CI
 on:
   pull_request:
     branches: [ develop ]
-  push:
-    branches: [ feature_CIvalidations ]
 
 permissions:
   contents: read
@@ -37,8 +35,7 @@ jobs:
         cd MaCh3Validations
         mkdir build
         cd build
-        cmake ../
-        #-DMaCh3_Branch="${{ github.ref_name }}"
+        cmake ../ -DMaCh3_Branch="{{ github.ref_name }}
 
     - name: Build MaCh3 Validations
       run: |
@@ -54,4 +51,3 @@ jobs:
       run: |
         cd /opt/MaCh3Validations/build
         Apps/${{ matrix.name }}
-

From f59bb1df2a4c5543f7bdc32ad1d8f3c8d9c57ebd Mon Sep 17 00:00:00 2001
From: Kamil Skwarczynski <skwarczynskikamil@gmail.com>
Date: Mon, 2 Sep 2024 13:45:53 +0000
Subject: [PATCH 16/26] ups...

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

diff --git a/.github/workflows/CIValidations.yml b/.github/workflows/CIValidations.yml
index ce2fe5439..469cb8ecb 100644
--- a/.github/workflows/CIValidations.yml
+++ b/.github/workflows/CIValidations.yml
@@ -35,7 +35,7 @@ jobs:
         cd MaCh3Validations
         mkdir build
         cd build
-        cmake ../ -DMaCh3_Branch="{{ github.ref_name }}
+        cmake ../ -DMaCh3_Branch={{ github.ref_name }}
 
     - name: Build MaCh3 Validations
       run: |

From 63603909e3acbba3f0f0a80e76664782d0f28bef Mon Sep 17 00:00:00 2001
From: Kamil Skwarczynski <skwarczynskikamil@gmail.com>
Date: Mon, 2 Sep 2024 13:49:16 +0000
Subject: [PATCH 17/26] hopefully last one...

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

diff --git a/.github/workflows/CIValidations.yml b/.github/workflows/CIValidations.yml
index 469cb8ecb..224acd4dd 100644
--- a/.github/workflows/CIValidations.yml
+++ b/.github/workflows/CIValidations.yml
@@ -35,7 +35,7 @@ jobs:
         cd MaCh3Validations
         mkdir build
         cd build
-        cmake ../ -DMaCh3_Branch={{ github.ref_name }}
+        cmake ../ -DMaCh3_Branch=${{ github.ref_name }}
 
     - name: Build MaCh3 Validations
       run: |

From bfc2354bbb998102c94d44f18260e61e64d77449 Mon Sep 17 00:00:00 2001
From: Kamil Skwarczynski <skwarczynskikamil@gmail.com>
Date: Mon, 2 Sep 2024 13:53:18 +0000
Subject: [PATCH 18/26] sumimasen

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

diff --git a/.github/workflows/CIValidations.yml b/.github/workflows/CIValidations.yml
index 224acd4dd..d8cd4a828 100644
--- a/.github/workflows/CIValidations.yml
+++ b/.github/workflows/CIValidations.yml
@@ -35,7 +35,7 @@ jobs:
         cd MaCh3Validations
         mkdir build
         cd build
-        cmake ../ -DMaCh3_Branch=${{ github.ref_name }}
+        cmake ../ -DMaCh3_Branch=${{ github.head_ref }}
 
     - name: Build MaCh3 Validations
       run: |

From d4d492e0dde966e017804f7ebdc567855bb252bb Mon Sep 17 00:00:00 2001
From: Kamil Skwarczynski <skwarczynskikamil@gmail.com>
Date: Mon, 2 Sep 2024 16:28:41 +0000
Subject: [PATCH 19/26] Minor fixes to cmake related to python binding and now
 Python interface is being used for containers and CI

---
 CMakeLists.txt                              | 3 +--
 Doc/MaCh3DockerFiles/Alma9/Dockerfile       | 2 +-
 Doc/MaCh3DockerFiles/Fedora32/Dockerfile    | 2 +-
 Doc/MaCh3DockerFiles/Ubuntu22.04/Dockerfile | 2 +-
 README.md                                   | 2 +-
 cmake/Templates/MaCh3Config.cmake.in        | 1 +
 plotting/plottingUtils/CMakeLists.txt       | 4 +---
 plotting/plottingUtils/inputManager.cpp     | 4 ++--
 8 files changed, 9 insertions(+), 11 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index fef31ca38..c3b5cdd14 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -188,6 +188,7 @@ LIST(APPEND ALL_FEATURES
   DEBUG
   MULTITHREAD
   GPU
+  PYTHON
   LOW_MEMORY_STRUCTS
   Oscillator
   Fitter
@@ -232,8 +233,6 @@ if( MaCh3_PYTHON_ENABLED )
 endif()
 
 
-
-
 #This is to export the target properties of MaCh3
 #Anything that links to "MaCh3" will get all of these target properties
 add_library(MaCh3 INTERFACE)
diff --git a/Doc/MaCh3DockerFiles/Alma9/Dockerfile b/Doc/MaCh3DockerFiles/Alma9/Dockerfile
index 1509d59e6..fd9eec0d1 100644
--- a/Doc/MaCh3DockerFiles/Alma9/Dockerfile
+++ b/Doc/MaCh3DockerFiles/Alma9/Dockerfile
@@ -18,7 +18,7 @@ RUN git checkout ${MACH3_VERSION}
 
 RUN mkdir -p ${MACH3_INSTALL_DIR}
 WORKDIR ${MACH3_INSTALL_DIR}
-RUN cmake ${MACH3_WORK_DIR}
+RUN cmake -DMaCh3_PYTHON_ENABLED=ON ${MACH3_WORK_DIR}
 RUN make VERBOSE=1 && make install
 
 # KS: Need to set them here, otherwise container using this container will not be able to find MaCh3
diff --git a/Doc/MaCh3DockerFiles/Fedora32/Dockerfile b/Doc/MaCh3DockerFiles/Fedora32/Dockerfile
index 0586ccf94..cc5f457a4 100644
--- a/Doc/MaCh3DockerFiles/Fedora32/Dockerfile
+++ b/Doc/MaCh3DockerFiles/Fedora32/Dockerfile
@@ -18,7 +18,7 @@ RUN git checkout ${MACH3_VERSION}
 
 RUN mkdir -p ${MACH3_INSTALL_DIR}
 WORKDIR ${MACH3_INSTALL_DIR}
-RUN cmake ${MACH3_WORK_DIR}
+RUN cmake -DMaCh3_PYTHON_ENABLED=ON ${MACH3_WORK_DIR}
 RUN make VERBOSE=1
 RUN make install
 
diff --git a/Doc/MaCh3DockerFiles/Ubuntu22.04/Dockerfile b/Doc/MaCh3DockerFiles/Ubuntu22.04/Dockerfile
index bc8423eca..8670c54f8 100644
--- a/Doc/MaCh3DockerFiles/Ubuntu22.04/Dockerfile
+++ b/Doc/MaCh3DockerFiles/Ubuntu22.04/Dockerfile
@@ -24,7 +24,7 @@ RUN git checkout ${MACH3_VERSION}
 
 RUN mkdir -p ${MACH3_INSTALL_DIR}
 WORKDIR ${MACH3_INSTALL_DIR}
-RUN cmake ${MACH3_WORK_DIR}
+RUN cmake -DMaCh3_PYTHON_ENABLED=ON ${MACH3_WORK_DIR}
 RUN make VERBOSE=1
 RUN make install
 
diff --git a/README.md b/README.md
index da36cd2f5..153ab0978 100644
--- a/README.md
+++ b/README.md
@@ -55,7 +55,7 @@ Some functionalities rely on setting `Env{MACH3}` which should point to path exp
 
 MaCh3 can be compiled with a python interface by specifying the cmake option
 ```
-cmake ../ MaCh3_PYTHON_ENABLED=ON
+cmake ../ -DMaCh3_PYTHON_ENABLED=ON
 make && make install
 ```
 and then adding the path to the installed module to your `PYTHONPATH` environment variable:
diff --git a/cmake/Templates/MaCh3Config.cmake.in b/cmake/Templates/MaCh3Config.cmake.in
index 20cabb4a5..37344f915 100644
--- a/cmake/Templates/MaCh3Config.cmake.in
+++ b/cmake/Templates/MaCh3Config.cmake.in
@@ -10,6 +10,7 @@ set(DEBUG_LEVEL @DEBUG_LEVEL@)
 set(MaCh3_DEBUG_ENABLED @MaCh3_DEBUG_ENABLED@)
 set(MaCh3_MULTITHREAD_ENABLED @MaCh3_MULTITHREAD_ENABLED@)
 set(MaCh3_GPU_ENABLED @MaCh3_GPU_ENABLED@)
+set(MaCh3_PYTHON_ENABLED @MaCh3_PYTHON_ENABLED@)
 set(MaCh3_MINUIT2_ENABLED @MaCh3_MINUIT2_ENABLED@)
 
 get_filename_component(MaCh3_CMAKE_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH)
diff --git a/plotting/plottingUtils/CMakeLists.txt b/plotting/plottingUtils/CMakeLists.txt
index 58bb07fcd..004c03378 100644
--- a/plotting/plottingUtils/CMakeLists.txt
+++ b/plotting/plottingUtils/CMakeLists.txt
@@ -21,9 +21,7 @@ target_link_libraries( Plotting ${ROOT_LIBRARIES} MaCh3::Manager )
 
 ## to be compiled into python module needs to be compiled as position independent library
 if( MaCh3_PYTHON_ENABLED )
-
     set_property( TARGET Plotting PROPERTY POSITION_INDEPENDENT_CODE ON )
-
 endif()
 
 install(TARGETS Plotting
@@ -32,4 +30,4 @@ install(TARGETS Plotting
     PUBLIC_HEADER DESTINATION include/plotting
 )
 
-add_library(MaCh3::Plotting ALIAS Plotting)
\ No newline at end of file
+add_library(MaCh3::Plotting ALIAS Plotting)
diff --git a/plotting/plottingUtils/inputManager.cpp b/plotting/plottingUtils/inputManager.cpp
index 47a33a950..8e9e69811 100644
--- a/plotting/plottingUtils/inputManager.cpp
+++ b/plotting/plottingUtils/inputManager.cpp
@@ -205,7 +205,7 @@ std::vector<std::string> InputManager::getTaggedValues(const std::vector<std::st
     if (valTags.size() == 0) continue;
 
     // count how many of the specified tags match the tags of the current value 
-    int tagCount = 0;
+    unsigned int tagCount = 0;
     for ( const std::string &tag: tags )
     {
       if ( std::find( valTags.begin(), valTags.end(), tag ) != valTags.end() ) 
@@ -734,4 +734,4 @@ void InputManager::fillFileData(InputFile &inputFileDef, bool printThoughts) {
   }
 }
 
-} // namespace MaCh3Plotting
\ No newline at end of file
+} // namespace MaCh3Plotting

From f74e393636494aca25b7429fd2bc342a8ac62cbb Mon Sep 17 00:00:00 2001
From: Kamil Skwarczynski <skwarczynskikamil@gmail.com>
Date: Mon, 2 Sep 2024 17:54:44 +0000
Subject: [PATCH 20/26] Now also covaraince valdiations

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

diff --git a/.github/workflows/CIValidations.yml b/.github/workflows/CIValidations.yml
index d8cd4a828..b0cb8e5f2 100644
--- a/.github/workflows/CIValidations.yml
+++ b/.github/workflows/CIValidations.yml
@@ -20,7 +20,7 @@ jobs:
       matrix:
         include:
           - name: SplineValidations
-
+          - name: CovarianceValidations
     container:
       image: ghcr.io/mach3-software/mach3:alma9latest
 

From d0528c88290490f3217e5367e354fa3669effc09 Mon Sep 17 00:00:00 2001
From: Kamil Skwarczynski <skwarczynskikamil@gmail.com>
Date: Tue, 3 Sep 2024 09:56:22 +0000
Subject: [PATCH 21/26] bump

---
 .github/workflows/CDImage.yml | 1 -
 README.md                     | 4 ++--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/CDImage.yml b/.github/workflows/CDImage.yml
index 9747d5080..b04efc135 100644
--- a/.github/workflows/CDImage.yml
+++ b/.github/workflows/CDImage.yml
@@ -40,7 +40,6 @@ jobs:
     - name: Build Docker image
       run: |
         if [ "${{ github.event_name }}" == 'release' ]; then
-          docker build . --file ${{ matrix.file }} --tag ghcr.io/${{ github.repository_owner }}/mach3:${{ matrix.tag_release }} --build-arg MACH3_VERSION=develop
           docker build . --file ${{ matrix.file }} --tag ghcr.io/${{ github.repository_owner }}/mach3:${{ matrix.os }}v${{ github.event.release.tag_name }} --build-arg MACH3_VERSION=develop
         else
           docker build . --file ${{ matrix.file }} --tag ghcr.io/${{ github.repository_owner }}/mach3:${{ matrix.tag_latest }} --build-arg MACH3_VERSION=develop
diff --git a/README.md b/README.md
index da36cd2f5..6f3f06083 100644
--- a/README.md
+++ b/README.md
@@ -4,7 +4,7 @@ The Markov Chain 3 flavour is a framework born in 2013 as a Bayesian MCMC fitter
 The framework has also evolved to allow non MCMC modules to interrogate the likelihoods implemented.
 
 [![License](https://img.shields.io/badge/License-BSD_3--Clause-blue.svg)](https://github.com/mach3-software/MaCh3/blob/develop/LICENSE.txt)
-[![Release - v1.0.0](https://img.shields.io/badge/Release-v1.0.0-2ea44f)](https://github.com/mach3-software/MaCh3/releases)
+[![Release - v1.1.0](https://img.shields.io/badge/Release-v1.1.0-2ea44f)](https://github.com/mach3-software/MaCh3/releases)
 [![Container Image](https://img.shields.io/badge/Container-Image-brightgreen)](https://github.com/mach3-software/MaCh3/pkgs/container/mach3)
 [![Code - Documented](https://img.shields.io/badge/Code-Documented-2ea44f)](https://github.com/mach3-software/MaCh3/wiki)
 [![Code - Doxygen](https://img.shields.io/badge/Code-Doxygen-2ea44f)](https://mach3-software.github.io/MaCh3/index.html)
@@ -15,7 +15,7 @@ Example of plots made using MaCh3 apparent in scientific publications, for more
 <img src="Doc/Plots/Jarlskog.png" alt="MaCh3" align="center" width="200"/>
 
 ## Cite
-When citing MaCh3, please use [on Zenodo](https://zenodo.org/records/10949376) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10949376.svg)](https://doi.org/10.5281/zenodo.10949376).
+When citing MaCh3, please use [on Zenodo](https://zenodo.org/records/7608367) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13642670.svg)](https://doi.org/10.5281/zenodo.13642670).
 
 # How to Compile
 MaCh3 follows standard cmake pattern. By default you should get most optimal build setting although below we list many configurable options:

From b5efe9728d50b46a7209cf9a1296c112edfcb344 Mon Sep 17 00:00:00 2001
From: Kamil Skwarczynski <skwarczynskikamil@gmail.com>
Date: Tue, 3 Sep 2024 10:04:10 +0000
Subject: [PATCH 22/26] Expand CI

---
 .github/workflows/CIValidations.yml | 3 ++-
 mcmc/FitterBase.cpp                 | 4 ++--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/CIValidations.yml b/.github/workflows/CIValidations.yml
index b0cb8e5f2..c2d0d4408 100644
--- a/.github/workflows/CIValidations.yml
+++ b/.github/workflows/CIValidations.yml
@@ -13,7 +13,7 @@ jobs:
   build:
     runs-on: ubuntu-latest
 
-    name: Validations CI ${{ matrix.name }}
+    name: ${{ matrix.name }}
 
     strategy:
       fail-fast: false  # Prevents cancellation of remaining jobs if one fails
@@ -21,6 +21,7 @@ jobs:
         include:
           - name: SplineValidations
           - name: CovarianceValidations
+          - name: FitterValidations
     container:
       image: ghcr.io/mach3-software/mach3:alma9latest
 
diff --git a/mcmc/FitterBase.cpp b/mcmc/FitterBase.cpp
index 4d66d21df..dddb38457 100644
--- a/mcmc/FitterBase.cpp
+++ b/mcmc/FitterBase.cpp
@@ -175,8 +175,8 @@ void FitterBase::PrepareOutput() {
   {
     // Check that we have added samples
     if (!samples.size()) {
-      MACH3LOG_CRITICAL("No samples Found! If this is what you want find me here");
-      throw MaCh3Exception(__FILE__ , __LINE__ );
+      MACH3LOG_CRITICAL("No samples Found! Is this really what you wanted?");
+      //throw MaCh3Exception(__FILE__ , __LINE__ );
     }
 
     // Prepare the output trees

From 39612ff14c241ac94363f7a42b147b284e7c7d9d Mon Sep 17 00:00:00 2001
From: Kamil Skwarczynski <skwarczynskikamil@gmail.com>
Date: Tue, 3 Sep 2024 10:16:50 +0000
Subject: [PATCH 23/26] minor

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

diff --git a/.github/workflows/CIValidations.yml b/.github/workflows/CIValidations.yml
index c2d0d4408..391de9a62 100644
--- a/.github/workflows/CIValidations.yml
+++ b/.github/workflows/CIValidations.yml
@@ -43,12 +43,9 @@ jobs:
         cd /opt/MaCh3Validations/build
         make install # Build the project
 
-    - name: Source Setup Scripts
+    - name: Validations
       run: |
         source /opt/MaCh3Validations/build/bin/setup.MaCh3.sh
         source /opt/MaCh3Validations/build/bin/setup.MaCh3Validations.sh
-
-    - name: Validations
-      run: |
         cd /opt/MaCh3Validations/build
         Apps/${{ matrix.name }}

From 63590b46e1f07bbbed97b52533db7917e4c7c7cb Mon Sep 17 00:00:00 2001
From: Kamil <45295406+KSkwarczynski@users.noreply.github.com>
Date: Tue, 3 Sep 2024 11:33:29 +0100
Subject: [PATCH 24/26] Update readme after discussion on general meeting

---
 README.md | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/README.md b/README.md
index 6f3f06083..6a1e6303b 100644
--- a/README.md
+++ b/README.md
@@ -32,11 +32,7 @@ Don't forget to:
 source bin/setup.MaCh3.sh
 ```
 ## Building against MaCh3
-If you compiled MaCh3 and sourced it you can simply call
-```
-find_package(MaCh3)
-```
-and cmake will find it. Alternatively, you can use CPM, for example:
+To include MaCh3 in your cmake project you can use following syntax
 ```
 CPMFindPackage(
   NAME MaCh3
@@ -44,6 +40,12 @@ CPMFindPackage(
   GITHUB_REPOSITORY mach3-software/MaCh3
 )
 ```
+Where "blarb" is the MaCh3 version. You can find a list of releases [here](https://github.com/mach3-software/MaCh3/wiki/0.1.-History)  
+If you compiled MaCh3 and sourced it you can simply call
+```
+find_package(MaCh3)
+```
+
 Once you found MaCh3 you might want to link your library against MaCh3. You can do this as follows:
 ```
 target_link_libraries(blarb MaCh3::All)

From f095a025e932026da9e6c41c57919f74ce79d845 Mon Sep 17 00:00:00 2001
From: Kamil Skwarczynski <skwarczynskikamil@gmail.com>
Date: Tue, 3 Sep 2024 19:45:55 +0000
Subject: [PATCH 25/26] let's test more robust CI

---
 covariance/covarianceBase.cpp | 6 ------
 mcmc/MinuitFit.cpp            | 2 +-
 2 files changed, 1 insertion(+), 7 deletions(-)

diff --git a/covariance/covarianceBase.cpp b/covariance/covarianceBase.cpp
index 16628db7f..ed43b8f42 100644
--- a/covariance/covarianceBase.cpp
+++ b/covariance/covarianceBase.cpp
@@ -1005,12 +1005,6 @@ void covarianceBase::setParameters(const std::vector<double>& pars) {
     }
   }
 
-  MACH3LOG_DEBUG("Set parameters to:");
-  std::cout << "Set parameters to: " << std::endl;
-  for(int par_i = 0 ; par_i < pars.size() ; ++par_i){
-	MACH3LOG_DEBUG("{} : {}", par_i, _fPropVal[par_i]);
-  }
-
   // And if pca make the transfer
   if (pca) {
     TransferToPCA();
diff --git a/mcmc/MinuitFit.cpp b/mcmc/MinuitFit.cpp
index a9cb8417a..db350e970 100644
--- a/mcmc/MinuitFit.cpp
+++ b/mcmc/MinuitFit.cpp
@@ -37,7 +37,7 @@ void MinuitFit::runMCMC() {
   //KS: add config or something
   minuit->SetPrintLevel(2);
   minuit->SetTolerance(0.01);
-  minuit->SetMaxFunctionCalls(fitMan->raw()["General.NSteps"].as<double>());
+  minuit->SetMaxFunctionCalls(fitMan->raw()["General"]["Minuit2"]["NSteps"].as<double>(););
   minuit->SetMaxIterations(10000);
 
   MACH3LOG_INFO("Preparing Minuit");

From d123f1ac13c2ed0e0069692a7644cc278a6ddffa Mon Sep 17 00:00:00 2001
From: Kamil Skwarczynski <skwarczynskikamil@gmail.com>
Date: Tue, 3 Sep 2024 19:53:00 +0000
Subject: [PATCH 26/26] ups...

---
 mcmc/MinuitFit.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mcmc/MinuitFit.cpp b/mcmc/MinuitFit.cpp
index db350e970..e54feb94a 100644
--- a/mcmc/MinuitFit.cpp
+++ b/mcmc/MinuitFit.cpp
@@ -37,7 +37,7 @@ void MinuitFit::runMCMC() {
   //KS: add config or something
   minuit->SetPrintLevel(2);
   minuit->SetTolerance(0.01);
-  minuit->SetMaxFunctionCalls(fitMan->raw()["General"]["Minuit2"]["NSteps"].as<double>(););
+  minuit->SetMaxFunctionCalls(fitMan->raw()["General"]["Minuit2"]["NSteps"].as<double>());
   minuit->SetMaxIterations(10000);
 
   MACH3LOG_INFO("Preparing Minuit");