From 579502a977bc5b0f1a5708312fa716f875064132 Mon Sep 17 00:00:00 2001
From: Joshua Newton <joshuacwnewton@gmail.com>
Date: Fri, 13 May 2022 09:40:27 -0400
Subject: [PATCH 01/22] `build-ants.yml`: Comment out workflow trigger to save
 resources

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

diff --git a/.github/workflows/build-ants.yml b/.github/workflows/build-ants.yml
index dd81581..c75bbed 100644
--- a/.github/workflows/build-ants.yml
+++ b/.github/workflows/build-ants.yml
@@ -1,8 +1,8 @@
 name: Build ANTs
 
 on:
-  pull_request:
-    branches: [ master ]
+#  pull_request:
+#    branches: [ master ]
   workflow_dispatch:
     inputs:
       git_ref:

From 13e9c2b1cc25d7e2cb3b84a4a85c6d8188e5fad8 Mon Sep 17 00:00:00 2001
From: Joshua Newton <joshuacwnewton@gmail.com>
Date: Fri, 13 May 2022 09:40:43 -0400
Subject: [PATCH 02/22] `build-ants-windows.yml`: Copy Linux build step to
 debug

---
 .github/workflows/build-ants-windows.yml | 114 +++++++++++++++++++++++
 1 file changed, 114 insertions(+)
 create mode 100644 .github/workflows/build-ants-windows.yml

diff --git a/.github/workflows/build-ants-windows.yml b/.github/workflows/build-ants-windows.yml
new file mode 100644
index 0000000..d88d0d6
--- /dev/null
+++ b/.github/workflows/build-ants-windows.yml
@@ -0,0 +1,114 @@
+name: Build ANTs
+
+on:
+  pull_request:
+    branches: [ master ]
+  workflow_dispatch:
+    inputs:
+      git_ref:
+        description: 'Upstream ANTsX/ANTs commit ref to check out when building'
+        required: true
+        default: 'b37e8b56e4e518b0f2947f80d0e3701a5ddfe120'
+
+jobs:
+
+  build:
+    strategy:
+      matrix:
+        os: [ windows-2019 ]
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash
+    steps:
+    # first, rewrite OS names to be safe for github artifacts.
+    - name: names
+      run: |
+        OS="${{ matrix.os }}"
+        OS=$(echo "$OS" | sed s/://)
+        echo "ARTIFACT=$OS" >> $GITHUB_ENV
+    - uses: actions/checkout@v3
+      with:
+        repository: ANTsX/ANTs
+        # NB: This commit mirrors the state of the kousu/ANTs repository
+        #     at the time of https://github.com/kousu/ANTs/pull/5.
+        ref: ${{ github.event.inputs.git_ref || 'b37e8b56e4e518b0f2947f80d0e3701a5ddfe120' }}
+    # The step below sets an option inside the cmake file to use the `https` protocol, which addresses:
+    # https://github.blog/2021-09-01-improving-git-protocol-security-github/#no-more-unauthenticated-git
+    - name: Patch in fix for insecure git:// protocol
+      run: |
+        perl -pi -e 's/http instead." ON\)/http instead." OFF\)/g' SuperBuild.cmake
+    - name: cmake generate
+      run: |
+        mkdir antsbin
+        cd antsbin
+        # TODO: check if cmake picks up CMAKE_CXX_FLAGS without being told about it
+        # NB: `BUILD_TESTING=OFF` fixes https://github.com/ANTsX/ANTs/issues/1236
+        cmake \
+         -DBUILD_TESTING=OFF \
+         -DBUILD_SHARED_LIBS=OFF \
+         -DCMAKE_CXX_FLAGS="$CMAKE_CXX_FLAGS" \
+         ../
+    - name: make
+      working-directory: antsbin
+      run: |
+        make VERBOSE=1 -j 4
+      timeout-minutes: 300
+      # for debugging, don't let a crash/timeout here fail the whole build
+      # (github CI seems glitchy about giving reliable output about what happened on timeouts)
+      continue-on-error: true
+    - name: pre-package
+      run: |
+        mkdir fakeroot/
+        cd antsbin/ANTS-build
+        make VERBOSE=1 -j 4 DESTDIR="../../fakeroot" install
+      continue-on-error: true
+    - name: package
+      run: |
+        # snip out the apps we need for https://github.com/neuropoly/spinalcordtoolbox, since including all of ANTS is too much
+        mkdir sct-apps/
+        cp antsbin/ANTS-build/Examples/{antsRegistration,antsSliceRegularizedRegistration,antsApplyTransforms,ComposeMultiTransform} sct-apps
+        (cd sct-apps; for i in `ls`; do mv $i isct_$i; done)
+        cp COPYING.txt sct-apps
+        tar -zcvf sct-apps_${{ env.ARTIFACT }}.tar.gz sct-apps/
+      continue-on-error: true
+    - name: results (DEBUG)
+      run: find .
+    - name: Upload result
+      uses: actions/upload-artifact@v2-preview
+      with:
+        name: sct-apps_${{ env.ARTIFACT }}
+        #path: fakeroot/ # this is 2.3G large in this build
+        path: sct-apps_${{ env.ARTIFACT }}.tar.gz
+
+  release:
+    needs: [build]
+    runs-on: ubuntu-latest
+    steps:
+      - name: Create Release
+        id: create_release
+        uses: actions/create-release@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          # name the release with the run_id to allow multiple builds on the same branch/tag
+          # https://github.com/actions/create-release/issues/2#issuecomment-613591846
+          tag_name: ${{ github.ref }}-${{github.run_id }}
+          release_name: Release ${{ github.sha }}
+          draft: true
+          prerelease: true
+
+      - uses: actions/download-artifact@v1
+        with:
+          name: sct-apps_windows-2019
+        continue-on-error: true
+      - name: Upload Release Asset
+        uses: actions/upload-release-asset@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          upload_url: ${{ steps.create_release.outputs.upload_url }}
+          asset_path: ./sct-apps_windows-2019/sct-apps_windows-2019.tar.gz
+          asset_name: sct-apps_windows-2019.tar.gz
+          asset_content_type: application/gzip
+        continue-on-error: true

From 2be97813b72e6773a7929f374f81d34607164b5c Mon Sep 17 00:00:00 2001
From: Joshua Newton <joshuacwnewton@gmail.com>
Date: Fri, 13 May 2022 09:53:00 -0400
Subject: [PATCH 03/22] `build-ants-windows.yml`: Install zlib using MSYS2

---
 .github/workflows/build-ants-windows.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.github/workflows/build-ants-windows.yml b/.github/workflows/build-ants-windows.yml
index d88d0d6..4e3c63b 100644
--- a/.github/workflows/build-ants-windows.yml
+++ b/.github/workflows/build-ants-windows.yml
@@ -27,6 +27,11 @@ jobs:
         OS="${{ matrix.os }}"
         OS=$(echo "$OS" | sed s/://)
         echo "ARTIFACT=$OS" >> $GITHUB_ENV
+    - name: Install zlib
+      uses: msys2/setup-msys2@v2
+      with:
+        update: true
+        install: zlib
     - uses: actions/checkout@v3
       with:
         repository: ANTsX/ANTs

From ba01bf9226dde36b21bc1733281a32c793fa5ea9 Mon Sep 17 00:00:00 2001
From: Joshua Newton <joshuacwnewton@gmail.com>
Date: Fri, 13 May 2022 10:05:20 -0400
Subject: [PATCH 04/22] `build-ants-windows.yml`: Replace zlib install with
 cmake flags

---
 .github/workflows/build-ants-windows.yml | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/build-ants-windows.yml b/.github/workflows/build-ants-windows.yml
index 4e3c63b..5a398c7 100644
--- a/.github/workflows/build-ants-windows.yml
+++ b/.github/workflows/build-ants-windows.yml
@@ -27,11 +27,6 @@ jobs:
         OS="${{ matrix.os }}"
         OS=$(echo "$OS" | sed s/://)
         echo "ARTIFACT=$OS" >> $GITHUB_ENV
-    - name: Install zlib
-      uses: msys2/setup-msys2@v2
-      with:
-        update: true
-        install: zlib
     - uses: actions/checkout@v3
       with:
         repository: ANTsX/ANTs
@@ -53,6 +48,8 @@ jobs:
          -DBUILD_TESTING=OFF \
          -DBUILD_SHARED_LIBS=OFF \
          -DCMAKE_CXX_FLAGS="$CMAKE_CXX_FLAGS" \
+         -DZLIB_INCLUDE_DIR=D:\lib\zlib \
+         -DZLIB_LIBRARY=D:\lib\zlib\libz.dll.a \
          ../
     - name: make
       working-directory: antsbin

From ccc0d42c362eaa400663768afaa48047da2af6c7 Mon Sep 17 00:00:00 2001
From: Joshua Newton <joshuacwnewton@gmail.com>
Date: Fri, 13 May 2022 10:14:35 -0400
Subject: [PATCH 05/22] `build-ants-windows.yml`: DEBUG: Add ls command

---
 .github/workflows/build-ants-windows.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/build-ants-windows.yml b/.github/workflows/build-ants-windows.yml
index 5a398c7..35d2f81 100644
--- a/.github/workflows/build-ants-windows.yml
+++ b/.github/workflows/build-ants-windows.yml
@@ -54,6 +54,7 @@ jobs:
     - name: make
       working-directory: antsbin
       run: |
+        ls
         make VERBOSE=1 -j 4
       timeout-minutes: 300
       # for debugging, don't let a crash/timeout here fail the whole build

From 6f59111bdba9114041c1cafa4f5ca1db994459cc Mon Sep 17 00:00:00 2001
From: Joshua Newton <joshuacwnewton@gmail.com>
Date: Fri, 13 May 2022 10:22:02 -0400
Subject: [PATCH 06/22] `build-ants-windows.yml`: Add '-G "Unix Makefiles"' to
 generate makefile.txt

---
 .github/workflows/build-ants-windows.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/build-ants-windows.yml b/.github/workflows/build-ants-windows.yml
index 35d2f81..51c4d8d 100644
--- a/.github/workflows/build-ants-windows.yml
+++ b/.github/workflows/build-ants-windows.yml
@@ -44,7 +44,9 @@ jobs:
         cd antsbin
         # TODO: check if cmake picks up CMAKE_CXX_FLAGS without being told about it
         # NB: `BUILD_TESTING=OFF` fixes https://github.com/ANTsX/ANTs/issues/1236
+        # NB: `-g "Unix Makefiles"` is needed to generate files for make (https://stackoverflow.com/a/59551107)
         cmake \
+         -G "Unix Makefiles" \
          -DBUILD_TESTING=OFF \
          -DBUILD_SHARED_LIBS=OFF \
          -DCMAKE_CXX_FLAGS="$CMAKE_CXX_FLAGS" \

From c242012b1e1e9c27289a238acc6226b1977d0589 Mon Sep 17 00:00:00 2001
From: Joshua Newton <joshuacwnewton@gmail.com>
Date: Fri, 13 May 2022 10:31:31 -0400
Subject: [PATCH 07/22] Revert "`build-ants-windows.yml`: DEBUG: Add ls
 command"

This reverts commit ccc0d42c362eaa400663768afaa48047da2af6c7.
---
 .github/workflows/build-ants-windows.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/build-ants-windows.yml b/.github/workflows/build-ants-windows.yml
index 51c4d8d..076e5c4 100644
--- a/.github/workflows/build-ants-windows.yml
+++ b/.github/workflows/build-ants-windows.yml
@@ -56,7 +56,6 @@ jobs:
     - name: make
       working-directory: antsbin
       run: |
-        ls
         make VERBOSE=1 -j 4
       timeout-minutes: 300
       # for debugging, don't let a crash/timeout here fail the whole build

From cc3bd751c81a60b672525b434db8a8ced28ae6c0 Mon Sep 17 00:00:00 2001
From: Joshua Newton <joshuacwnewton@gmail.com>
Date: Fri, 13 May 2022 10:52:18 -0400
Subject: [PATCH 08/22] `build-ants-windows.yml`: DEBUG: Add `-d` to make

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

diff --git a/.github/workflows/build-ants-windows.yml b/.github/workflows/build-ants-windows.yml
index 076e5c4..63297f4 100644
--- a/.github/workflows/build-ants-windows.yml
+++ b/.github/workflows/build-ants-windows.yml
@@ -56,7 +56,7 @@ jobs:
     - name: make
       working-directory: antsbin
       run: |
-        make VERBOSE=1 -j 4
+        make VERBOSE=1 -j 4 -d
       timeout-minutes: 300
       # for debugging, don't let a crash/timeout here fail the whole build
       # (github CI seems glitchy about giving reliable output about what happened on timeouts)

From b8d3ac2c92e1cd93013d95e72c8fe7f68b1f2dc3 Mon Sep 17 00:00:00 2001
From: Joshua Newton <joshuacwnewton@gmail.com>
Date: Fri, 13 May 2022 10:52:34 -0400
Subject: [PATCH 09/22] `build-ants-windows.yml`: DEBUG: Add `-k` to make

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

diff --git a/.github/workflows/build-ants-windows.yml b/.github/workflows/build-ants-windows.yml
index 63297f4..7abd274 100644
--- a/.github/workflows/build-ants-windows.yml
+++ b/.github/workflows/build-ants-windows.yml
@@ -56,7 +56,7 @@ jobs:
     - name: make
       working-directory: antsbin
       run: |
-        make VERBOSE=1 -j 4 -d
+        make VERBOSE=1 -j 4 -d -k
       timeout-minutes: 300
       # for debugging, don't let a crash/timeout here fail the whole build
       # (github CI seems glitchy about giving reliable output about what happened on timeouts)

From 8d367332c67dff452723f44d1c1a55d342080b80 Mon Sep 17 00:00:00 2001
From: Joshua Newton <joshuacwnewton@gmail.com>
Date: Fri, 13 May 2022 11:19:07 -0400
Subject: [PATCH 10/22] `build-ants-windows.yml`: DEBUG: Remove `-d` from make

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

diff --git a/.github/workflows/build-ants-windows.yml b/.github/workflows/build-ants-windows.yml
index 7abd274..9be7b28 100644
--- a/.github/workflows/build-ants-windows.yml
+++ b/.github/workflows/build-ants-windows.yml
@@ -56,7 +56,7 @@ jobs:
     - name: make
       working-directory: antsbin
       run: |
-        make VERBOSE=1 -j 4 -d -k
+        make VERBOSE=1 -j 4 -k
       timeout-minutes: 300
       # for debugging, don't let a crash/timeout here fail the whole build
       # (github CI seems glitchy about giving reliable output about what happened on timeouts)

From ed5617ace96ab2c24869c52a9dcb5e4ad27307da Mon Sep 17 00:00:00 2001
From: Joshua Newton <joshuacwnewton@gmail.com>
Date: Fri, 13 May 2022 11:19:24 -0400
Subject: [PATCH 11/22] `build-ants-windows.yml`: Build 'Release' version

---
 .github/workflows/build-ants-windows.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/build-ants-windows.yml b/.github/workflows/build-ants-windows.yml
index 9be7b28..6fddec2 100644
--- a/.github/workflows/build-ants-windows.yml
+++ b/.github/workflows/build-ants-windows.yml
@@ -45,6 +45,7 @@ jobs:
         # TODO: check if cmake picks up CMAKE_CXX_FLAGS without being told about it
         # NB: `BUILD_TESTING=OFF` fixes https://github.com/ANTsX/ANTs/issues/1236
         # NB: `-g "Unix Makefiles"` is needed to generate files for make (https://stackoverflow.com/a/59551107)
+        # NB: `CMAKE_CONFIGURATION_TYPES=Release` is needed on Windows to build the Release version (https://stackoverflow.com/a/20423820)
         cmake \
          -G "Unix Makefiles" \
          -DBUILD_TESTING=OFF \
@@ -52,6 +53,8 @@ jobs:
          -DCMAKE_CXX_FLAGS="$CMAKE_CXX_FLAGS" \
          -DZLIB_INCLUDE_DIR=D:\lib\zlib \
          -DZLIB_LIBRARY=D:\lib\zlib\libz.dll.a \
+         -DCMAKE_BUILD_TYPE=Release \
+         -DCMAKE_CONFIGURATION_TYPES=Release \
          ../
     - name: make
       working-directory: antsbin

From a376189a7ace105f6c80451f579b1ea3aeab242b Mon Sep 17 00:00:00 2001
From: Joshua Newton <joshuacwnewton@gmail.com>
Date: Fri, 13 May 2022 12:07:10 -0400
Subject: [PATCH 12/22] `build-ants-windows.yml`: Replace `make` with `MSBuild`

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

diff --git a/.github/workflows/build-ants-windows.yml b/.github/workflows/build-ants-windows.yml
index 6fddec2..9eabe83 100644
--- a/.github/workflows/build-ants-windows.yml
+++ b/.github/workflows/build-ants-windows.yml
@@ -59,7 +59,7 @@ jobs:
     - name: make
       working-directory: antsbin
       run: |
-        make VERBOSE=1 -j 4 -k
+        MSBuild SuperBuild_ANTS.sln
       timeout-minutes: 300
       # for debugging, don't let a crash/timeout here fail the whole build
       # (github CI seems glitchy about giving reliable output about what happened on timeouts)

From e91cb65e5de4f75e5b3a750662bdc037deea4f51 Mon Sep 17 00:00:00 2001
From: Joshua Newton <joshuacwnewton@gmail.com>
Date: Fri, 13 May 2022 12:22:24 -0400
Subject: [PATCH 13/22] `build-ants-windows.yml`: Try `setup-msbuild`

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

diff --git a/.github/workflows/build-ants-windows.yml b/.github/workflows/build-ants-windows.yml
index 9eabe83..b2f7b99 100644
--- a/.github/workflows/build-ants-windows.yml
+++ b/.github/workflows/build-ants-windows.yml
@@ -56,10 +56,14 @@ jobs:
          -DCMAKE_BUILD_TYPE=Release \
          -DCMAKE_CONFIGURATION_TYPES=Release \
          ../
+    - name: Add msbuild to PATH
+      uses: microsoft/setup-msbuild@v1.1
+      with:
+        msbuild-architecture: x64
     - name: make
       working-directory: antsbin
       run: |
-        MSBuild SuperBuild_ANTS.sln
+        msbuild ALL_BUILD.vcxproj -t:rebuild -verbosity:diag -property:Configuration=Release
       timeout-minutes: 300
       # for debugging, don't let a crash/timeout here fail the whole build
       # (github CI seems glitchy about giving reliable output about what happened on timeouts)

From 4b59c556d50aacc19dec433d50266a18434aafdd Mon Sep 17 00:00:00 2001
From: Joshua Newton <joshuacwnewton@gmail.com>
Date: Fri, 13 May 2022 12:26:36 -0400
Subject: [PATCH 14/22] `build-ants-windows.yml`: Try `cmd` in build step

---
 .github/workflows/build-ants-windows.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/build-ants-windows.yml b/.github/workflows/build-ants-windows.yml
index b2f7b99..57e8213 100644
--- a/.github/workflows/build-ants-windows.yml
+++ b/.github/workflows/build-ants-windows.yml
@@ -62,6 +62,7 @@ jobs:
         msbuild-architecture: x64
     - name: make
       working-directory: antsbin
+      shell: cmd
       run: |
         msbuild ALL_BUILD.vcxproj -t:rebuild -verbosity:diag -property:Configuration=Release
       timeout-minutes: 300

From 13f3da402430f93d864ad7de05e8fa76220c16f6 Mon Sep 17 00:00:00 2001
From: Joshua Newton <joshuacwnewton@gmail.com>
Date: Fri, 13 May 2022 12:34:18 -0400
Subject: [PATCH 15/22] `build-ants-windows.yml`: Debug

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

diff --git a/.github/workflows/build-ants-windows.yml b/.github/workflows/build-ants-windows.yml
index 57e8213..00d1f0e 100644
--- a/.github/workflows/build-ants-windows.yml
+++ b/.github/workflows/build-ants-windows.yml
@@ -56,14 +56,14 @@ jobs:
          -DCMAKE_BUILD_TYPE=Release \
          -DCMAKE_CONFIGURATION_TYPES=Release \
          ../
+        ls
     - name: Add msbuild to PATH
       uses: microsoft/setup-msbuild@v1.1
-      with:
-        msbuild-architecture: x64
     - name: make
       working-directory: antsbin
       shell: cmd
       run: |
+        dir
         msbuild ALL_BUILD.vcxproj -t:rebuild -verbosity:diag -property:Configuration=Release
       timeout-minutes: 300
       # for debugging, don't let a crash/timeout here fail the whole build

From 8f20e618e7b1af6f26d1afb5c8fc1f1b0c56a31c Mon Sep 17 00:00:00 2001
From: Joshua Newton <joshuacwnewton@gmail.com>
Date: Fri, 13 May 2022 12:40:38 -0400
Subject: [PATCH 16/22] `build-ants-windows.yml`: Remove unix makefiles

---
 .github/workflows/build-ants-windows.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/build-ants-windows.yml b/.github/workflows/build-ants-windows.yml
index 00d1f0e..6b870ac 100644
--- a/.github/workflows/build-ants-windows.yml
+++ b/.github/workflows/build-ants-windows.yml
@@ -47,7 +47,6 @@ jobs:
         # NB: `-g "Unix Makefiles"` is needed to generate files for make (https://stackoverflow.com/a/59551107)
         # NB: `CMAKE_CONFIGURATION_TYPES=Release` is needed on Windows to build the Release version (https://stackoverflow.com/a/20423820)
         cmake \
-         -G "Unix Makefiles" \
          -DBUILD_TESTING=OFF \
          -DBUILD_SHARED_LIBS=OFF \
          -DCMAKE_CXX_FLAGS="$CMAKE_CXX_FLAGS" \

From 9f599a0ee2da131b403a41397687cfc914fe519d Mon Sep 17 00:00:00 2001
From: Joshua Newton <joshuacwnewton@gmail.com>
Date: Fri, 13 May 2022 13:25:51 -0400
Subject: [PATCH 17/22] `build-ants-windows.yml`: Testing different msbuild
 options

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

diff --git a/.github/workflows/build-ants-windows.yml b/.github/workflows/build-ants-windows.yml
index 6b870ac..ba52b17 100644
--- a/.github/workflows/build-ants-windows.yml
+++ b/.github/workflows/build-ants-windows.yml
@@ -58,12 +58,14 @@ jobs:
         ls
     - name: Add msbuild to PATH
       uses: microsoft/setup-msbuild@v1.1
+      with:
+        msbuild-architecture: x64
     - name: make
       working-directory: antsbin
       shell: cmd
       run: |
         dir
-        msbuild ALL_BUILD.vcxproj -t:rebuild -verbosity:diag -property:Configuration=Release
+        msbuild ALL_BUILD.vcxproj -t:all -property:Configuration=Release
       timeout-minutes: 300
       # for debugging, don't let a crash/timeout here fail the whole build
       # (github CI seems glitchy about giving reliable output about what happened on timeouts)

From 4fa9b28b5786c4d39f38759ec5ddea5f7cea9e4c Mon Sep 17 00:00:00 2001
From: Joshua Newton <joshuacwnewton@gmail.com>
Date: Fri, 13 May 2022 13:30:09 -0400
Subject: [PATCH 18/22] `build-ants-windows.yml`: Testing different msbuild
 options

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

diff --git a/.github/workflows/build-ants-windows.yml b/.github/workflows/build-ants-windows.yml
index ba52b17..294ebf2 100644
--- a/.github/workflows/build-ants-windows.yml
+++ b/.github/workflows/build-ants-windows.yml
@@ -65,7 +65,7 @@ jobs:
       shell: cmd
       run: |
         dir
-        msbuild ALL_BUILD.vcxproj -t:all -property:Configuration=Release
+        msbuild ALL_BUILD.vcxproj -property:Configuration=Release
       timeout-minutes: 300
       # for debugging, don't let a crash/timeout here fail the whole build
       # (github CI seems glitchy about giving reliable output about what happened on timeouts)

From 07a466dc083c61199df19c67ae32d59e9ac08508 Mon Sep 17 00:00:00 2001
From: Joshua Newton <joshuacwnewton@gmail.com>
Date: Fri, 13 May 2022 14:37:57 -0400
Subject: [PATCH 19/22] Use ANTs version that fetches ITK v5.2.0

This is an attempt to fix https://github.com/spinalcordtoolbox/build_ANTs/pull/3/files#r872663217, but may have unintended consequences for SCT.

I'm just trying this out to see how the build goes across our platforms.
---
 .github/workflows/build-ants-windows.yml | 4 ++--
 .github/workflows/build-ants.yml         | 6 +++---
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/build-ants-windows.yml b/.github/workflows/build-ants-windows.yml
index 294ebf2..63c251e 100644
--- a/.github/workflows/build-ants-windows.yml
+++ b/.github/workflows/build-ants-windows.yml
@@ -8,7 +8,7 @@ on:
       git_ref:
         description: 'Upstream ANTsX/ANTs commit ref to check out when building'
         required: true
-        default: 'b37e8b56e4e518b0f2947f80d0e3701a5ddfe120'
+        default: 'bca6205c685784336c0bd17057cd99d8114e3a62'
 
 jobs:
 
@@ -32,7 +32,7 @@ jobs:
         repository: ANTsX/ANTs
         # NB: This commit mirrors the state of the kousu/ANTs repository
         #     at the time of https://github.com/kousu/ANTs/pull/5.
-        ref: ${{ github.event.inputs.git_ref || 'b37e8b56e4e518b0f2947f80d0e3701a5ddfe120' }}
+        ref: ${{ github.event.inputs.git_ref || 'bca6205c685784336c0bd17057cd99d8114e3a62' }}
     # The step below sets an option inside the cmake file to use the `https` protocol, which addresses:
     # https://github.blog/2021-09-01-improving-git-protocol-security-github/#no-more-unauthenticated-git
     - name: Patch in fix for insecure git:// protocol
diff --git a/.github/workflows/build-ants.yml b/.github/workflows/build-ants.yml
index c75bbed..2fd4226 100644
--- a/.github/workflows/build-ants.yml
+++ b/.github/workflows/build-ants.yml
@@ -8,7 +8,7 @@ on:
       git_ref:
         description: 'Upstream ANTsX/ANTs commit ref to check out when building'
         required: true
-        default: 'b37e8b56e4e518b0f2947f80d0e3701a5ddfe120'
+        default: 'bca6205c685784336c0bd17057cd99d8114e3a62'
 
 jobs:
 
@@ -33,7 +33,7 @@ jobs:
         repository: ANTsX/ANTs
         # NB: This commit mirrors the state of the kousu/ANTs repository
         #     at the time of https://github.com/kousu/ANTs/pull/5.
-        ref: ${{ github.event.inputs.git_ref || 'b37e8b56e4e518b0f2947f80d0e3701a5ddfe120' }}
+        ref: ${{ github.event.inputs.git_ref || 'bca6205c685784336c0bd17057cd99d8114e3a62' }}
     # The step below sets an option inside the cmake file to use the `https` protocol, which addresses:
     # https://github.blog/2021-09-01-improving-git-protocol-security-github/#no-more-unauthenticated-git
     - name: Patch in fix for insecure git:// protocol
@@ -121,7 +121,7 @@ jobs:
         repository: ANTsX/ANTs
         # NB: This commit mirrors the state of the kousu/ANTs repository
         #     at the time of https://github.com/kousu/ANTs/pull/5.
-        ref: ${{ github.event.inputs.git_ref || 'b37e8b56e4e518b0f2947f80d0e3701a5ddfe120' }}
+        ref: ${{ github.event.inputs.git_ref || 'bca6205c685784336c0bd17057cd99d8114e3a62' }}
     # The step below sets an option inside the cmake file to use the `https` protocol, which addresses:
     # https://github.blog/2021-09-01-improving-git-protocol-security-github/#no-more-unauthenticated-git
     - name: Patch in fix for insecure git:// protocol

From a37d141889b649bc1a5e4bad5ae94e4156e6e55e Mon Sep 17 00:00:00 2001
From: Joshua Newton <joshuacwnewton@gmail.com>
Date: Fri, 13 May 2022 15:59:58 -0400
Subject: [PATCH 20/22] `build-ants-windows.yml`: Trim `make install` step

I don't think this is strictly necessary for our purposes.
---
 .github/workflows/build-ants-windows.yml | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/.github/workflows/build-ants-windows.yml b/.github/workflows/build-ants-windows.yml
index 63c251e..08b166f 100644
--- a/.github/workflows/build-ants-windows.yml
+++ b/.github/workflows/build-ants-windows.yml
@@ -70,17 +70,11 @@ jobs:
       # for debugging, don't let a crash/timeout here fail the whole build
       # (github CI seems glitchy about giving reliable output about what happened on timeouts)
       continue-on-error: true
-    - name: pre-package
-      run: |
-        mkdir fakeroot/
-        cd antsbin/ANTS-build
-        make VERBOSE=1 -j 4 DESTDIR="../../fakeroot" install
-      continue-on-error: true
     - name: package
       run: |
         # snip out the apps we need for https://github.com/neuropoly/spinalcordtoolbox, since including all of ANTS is too much
         mkdir sct-apps/
-        cp antsbin/ANTS-build/Examples/{antsRegistration,antsSliceRegularizedRegistration,antsApplyTransforms,ComposeMultiTransform} sct-apps
+        cp antsbin/ANTS-build/Examples/Release/{antsRegistration,antsSliceRegularizedRegistration,antsApplyTransforms,ComposeMultiTransform}.exe sct-apps
         (cd sct-apps; for i in `ls`; do mv $i isct_$i; done)
         cp COPYING.txt sct-apps
         tar -zcvf sct-apps_${{ env.ARTIFACT }}.tar.gz sct-apps/

From 7567172e212bdc48d03689e437b973a3c51f908e Mon Sep 17 00:00:00 2001
From: Joshua Newton <joshuacwnewton@gmail.com>
Date: Fri, 13 May 2022 16:03:09 -0400
Subject: [PATCH 21/22] `build-ants-windows.yml`: Fold Windows install into
 `built-ants.yml`

---
 .github/workflows/build-ants-windows.yml | 121 -----------------------
 .github/workflows/build-ants.yml         |  90 ++++++++++++++++-
 2 files changed, 89 insertions(+), 122 deletions(-)
 delete mode 100644 .github/workflows/build-ants-windows.yml

diff --git a/.github/workflows/build-ants-windows.yml b/.github/workflows/build-ants-windows.yml
deleted file mode 100644
index 08b166f..0000000
--- a/.github/workflows/build-ants-windows.yml
+++ /dev/null
@@ -1,121 +0,0 @@
-name: Build ANTs
-
-on:
-  pull_request:
-    branches: [ master ]
-  workflow_dispatch:
-    inputs:
-      git_ref:
-        description: 'Upstream ANTsX/ANTs commit ref to check out when building'
-        required: true
-        default: 'bca6205c685784336c0bd17057cd99d8114e3a62'
-
-jobs:
-
-  build:
-    strategy:
-      matrix:
-        os: [ windows-2019 ]
-    runs-on: ${{ matrix.os }}
-    defaults:
-      run:
-        shell: bash
-    steps:
-    # first, rewrite OS names to be safe for github artifacts.
-    - name: names
-      run: |
-        OS="${{ matrix.os }}"
-        OS=$(echo "$OS" | sed s/://)
-        echo "ARTIFACT=$OS" >> $GITHUB_ENV
-    - uses: actions/checkout@v3
-      with:
-        repository: ANTsX/ANTs
-        # NB: This commit mirrors the state of the kousu/ANTs repository
-        #     at the time of https://github.com/kousu/ANTs/pull/5.
-        ref: ${{ github.event.inputs.git_ref || 'bca6205c685784336c0bd17057cd99d8114e3a62' }}
-    # The step below sets an option inside the cmake file to use the `https` protocol, which addresses:
-    # https://github.blog/2021-09-01-improving-git-protocol-security-github/#no-more-unauthenticated-git
-    - name: Patch in fix for insecure git:// protocol
-      run: |
-        perl -pi -e 's/http instead." ON\)/http instead." OFF\)/g' SuperBuild.cmake
-    - name: cmake generate
-      run: |
-        mkdir antsbin
-        cd antsbin
-        # TODO: check if cmake picks up CMAKE_CXX_FLAGS without being told about it
-        # NB: `BUILD_TESTING=OFF` fixes https://github.com/ANTsX/ANTs/issues/1236
-        # NB: `-g "Unix Makefiles"` is needed to generate files for make (https://stackoverflow.com/a/59551107)
-        # NB: `CMAKE_CONFIGURATION_TYPES=Release` is needed on Windows to build the Release version (https://stackoverflow.com/a/20423820)
-        cmake \
-         -DBUILD_TESTING=OFF \
-         -DBUILD_SHARED_LIBS=OFF \
-         -DCMAKE_CXX_FLAGS="$CMAKE_CXX_FLAGS" \
-         -DZLIB_INCLUDE_DIR=D:\lib\zlib \
-         -DZLIB_LIBRARY=D:\lib\zlib\libz.dll.a \
-         -DCMAKE_BUILD_TYPE=Release \
-         -DCMAKE_CONFIGURATION_TYPES=Release \
-         ../
-        ls
-    - name: Add msbuild to PATH
-      uses: microsoft/setup-msbuild@v1.1
-      with:
-        msbuild-architecture: x64
-    - name: make
-      working-directory: antsbin
-      shell: cmd
-      run: |
-        dir
-        msbuild ALL_BUILD.vcxproj -property:Configuration=Release
-      timeout-minutes: 300
-      # for debugging, don't let a crash/timeout here fail the whole build
-      # (github CI seems glitchy about giving reliable output about what happened on timeouts)
-      continue-on-error: true
-    - name: package
-      run: |
-        # snip out the apps we need for https://github.com/neuropoly/spinalcordtoolbox, since including all of ANTS is too much
-        mkdir sct-apps/
-        cp antsbin/ANTS-build/Examples/Release/{antsRegistration,antsSliceRegularizedRegistration,antsApplyTransforms,ComposeMultiTransform}.exe sct-apps
-        (cd sct-apps; for i in `ls`; do mv $i isct_$i; done)
-        cp COPYING.txt sct-apps
-        tar -zcvf sct-apps_${{ env.ARTIFACT }}.tar.gz sct-apps/
-      continue-on-error: true
-    - name: results (DEBUG)
-      run: find .
-    - name: Upload result
-      uses: actions/upload-artifact@v2-preview
-      with:
-        name: sct-apps_${{ env.ARTIFACT }}
-        #path: fakeroot/ # this is 2.3G large in this build
-        path: sct-apps_${{ env.ARTIFACT }}.tar.gz
-
-  release:
-    needs: [build]
-    runs-on: ubuntu-latest
-    steps:
-      - name: Create Release
-        id: create_release
-        uses: actions/create-release@v1
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        with:
-          # name the release with the run_id to allow multiple builds on the same branch/tag
-          # https://github.com/actions/create-release/issues/2#issuecomment-613591846
-          tag_name: ${{ github.ref }}-${{github.run_id }}
-          release_name: Release ${{ github.sha }}
-          draft: true
-          prerelease: true
-
-      - uses: actions/download-artifact@v1
-        with:
-          name: sct-apps_windows-2019
-        continue-on-error: true
-      - name: Upload Release Asset
-        uses: actions/upload-release-asset@v1
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        with:
-          upload_url: ${{ steps.create_release.outputs.upload_url }}
-          asset_path: ./sct-apps_windows-2019/sct-apps_windows-2019.tar.gz
-          asset_name: sct-apps_windows-2019.tar.gz
-          asset_content_type: application/gzip
-        continue-on-error: true
diff --git a/.github/workflows/build-ants.yml b/.github/workflows/build-ants.yml
index 2fd4226..bdeb37f 100644
--- a/.github/workflows/build-ants.yml
+++ b/.github/workflows/build-ants.yml
@@ -182,8 +182,81 @@ jobs:
         #path: fakeroot/ # this is 2.3G large in this build
         path: sct-apps_${{ env.ARTIFACT }}.tar.gz
 
+  build-windows:
+    strategy:
+      matrix:
+        os: [ windows-2019 ]
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash
+    steps:
+    # first, rewrite OS names to be safe for github artifacts.
+    - name: names
+      run: |
+        OS="${{ matrix.os }}"
+        OS=$(echo "$OS" | sed s/://)
+        echo "ARTIFACT=$OS" >> $GITHUB_ENV
+    - uses: actions/checkout@v3
+      with:
+        repository: ANTsX/ANTs
+        # NB: This commit mirrors the state of the kousu/ANTs repository
+        #     at the time of https://github.com/kousu/ANTs/pull/5.
+        ref: ${{ github.event.inputs.git_ref || 'bca6205c685784336c0bd17057cd99d8114e3a62' }}
+    # The step below sets an option inside the cmake file to use the `https` protocol, which addresses:
+    # https://github.blog/2021-09-01-improving-git-protocol-security-github/#no-more-unauthenticated-git
+    - name: Patch in fix for insecure git:// protocol
+      run: |
+        perl -pi -e 's/http instead." ON\)/http instead." OFF\)/g' SuperBuild.cmake
+    - name: cmake generate
+      run: |
+        mkdir antsbin
+        cd antsbin
+        # TODO: check if cmake picks up CMAKE_CXX_FLAGS without being told about it
+        # NB: `BUILD_TESTING=OFF` fixes https://github.com/ANTsX/ANTs/issues/1236
+        # NB: `-g "Unix Makefiles"` is needed to generate files for make (https://stackoverflow.com/a/59551107)
+        # NB: `CMAKE_CONFIGURATION_TYPES=Release` is needed on Windows to build the Release version (https://stackoverflow.com/a/20423820)
+        cmake \
+         -DBUILD_TESTING=OFF \
+         -DBUILD_SHARED_LIBS=OFF \
+         -DCMAKE_CXX_FLAGS="$CMAKE_CXX_FLAGS" \
+         -DZLIB_INCLUDE_DIR=D:\lib\zlib \
+         -DZLIB_LIBRARY=D:\lib\zlib\libz.dll.a \
+         -DCMAKE_BUILD_TYPE=Release \
+         -DCMAKE_CONFIGURATION_TYPES=Release \
+         ../
+    - name: Add msbuild to PATH
+      uses: microsoft/setup-msbuild@v1.1
+      with:
+        msbuild-architecture: x64
+    - name: make
+      working-directory: antsbin
+      shell: cmd
+      run: |
+        msbuild ALL_BUILD.vcxproj -property:Configuration=Release
+      timeout-minutes: 300
+      # for debugging, don't let a crash/timeout here fail the whole build
+      # (github CI seems glitchy about giving reliable output about what happened on timeouts)
+      continue-on-error: true
+    - name: package
+      run: |
+        # snip out the apps we need for https://github.com/neuropoly/spinalcordtoolbox, since including all of ANTS is too much
+        mkdir sct-apps/
+        cp antsbin/ANTS-build/Examples/Release/{antsRegistration,antsSliceRegularizedRegistration,antsApplyTransforms,ComposeMultiTransform}.exe sct-apps
+        (cd sct-apps; for i in `ls`; do mv $i isct_$i; done)
+        cp COPYING.txt sct-apps
+        tar -zcvf sct-apps_${{ env.ARTIFACT }}.tar.gz sct-apps/
+      continue-on-error: true
+    - name: results (DEBUG)
+      run: find .
+    - name: Upload result
+      uses: actions/upload-artifact@v2-preview
+      with:
+        name: sct-apps_${{ env.ARTIFACT }}
+        path: sct-apps_${{ env.ARTIFACT }}.tar.gz
+
   release:
-    needs: [build, build-manylinuxes]
+    needs: [build, build-manylinuxes, build-windows]
     runs-on: ubuntu-latest
     steps:
       - name: Create Release
@@ -293,3 +366,18 @@ jobs:
           asset_name: sct-apps_macos-10.15.tar.gz
           asset_content_type: application/gzip
         continue-on-error: true
+
+      - uses: actions/download-artifact@v1
+        with:
+          name: sct-apps_windows-2019
+        continue-on-error: true
+      - name: Upload Release Asset
+        uses: actions/upload-release-asset@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          upload_url: ${{ steps.create_release.outputs.upload_url }}
+          asset_path: ./sct-apps_windows-2019/sct-apps_windows-2019.tar.gz
+          asset_name: sct-apps_windows-2019.tar.gz
+          asset_content_type: application/gzip
+        continue-on-error: true

From 04a4a586a7c02fb8f3711c78a31203a9dca71cea Mon Sep 17 00:00:00 2001
From: Joshua Newton <joshuacwnewton@gmail.com>
Date: Fri, 13 May 2022 16:03:15 -0400
Subject: [PATCH 22/22] Revert "`build-ants.yml`: Comment out workflow trigger
 to save resources"

This reverts commit 579502a977bc5b0f1a5708312fa716f875064132.
---
 .github/workflows/build-ants.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build-ants.yml b/.github/workflows/build-ants.yml
index bdeb37f..9cb7183 100644
--- a/.github/workflows/build-ants.yml
+++ b/.github/workflows/build-ants.yml
@@ -1,8 +1,8 @@
 name: Build ANTs
 
 on:
-#  pull_request:
-#    branches: [ master ]
+  pull_request:
+    branches: [ master ]
   workflow_dispatch:
     inputs:
       git_ref: