From 06de0375a284fa303ff79e3c6e63f36e4fe76104 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 17 Feb 2025 09:08:56 +0100 Subject: [PATCH 01/23] ci: use junifer-data for docs-preview.yml --- .github/workflows/docs-preview.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/docs-preview.yml b/.github/workflows/docs-preview.yml index c255faec4..1c67b5e05 100644 --- a/.github/workflows/docs-preview.yml +++ b/.github/workflows/docs-preview.yml @@ -33,9 +33,9 @@ jobs: git-annex \ make \ jq - # Copy xfms directory - mkdir -p $HOME/junifer/data/xfms && \ - cp -ar /root/junifer/data/xfms/. $HOME/junifer/data/xfms/ + # Copy junifer-data directory + mkdir -p $HOME/junifer_data/v1 && \ + cp -ar /root/junifer_data/v1/. $HOME/junifer_data/v1/ - name: Checkout source uses: actions/checkout@v4 with: -- 2.52.0 From 1f6ec5dbdf95178af9b287b1edb25a4badcc8566 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 17 Feb 2025 09:12:58 +0100 Subject: [PATCH 02/23] ci: add gcc to docs-preview.yml --- .github/workflows/docs-preview.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/docs-preview.yml b/.github/workflows/docs-preview.yml index 1c67b5e05..2c2644a82 100644 --- a/.github/workflows/docs-preview.yml +++ b/.github/workflows/docs-preview.yml @@ -32,7 +32,8 @@ jobs: git \ git-annex \ make \ - jq + jq \ + gcc # Copy junifer-data directory mkdir -p $HOME/junifer_data/v1 && \ cp -ar /root/junifer_data/v1/. $HOME/junifer_data/v1/ -- 2.52.0 From ea9b19381288b05ae0b6f8b5fc889fa08ae729ad Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 17 Feb 2025 09:16:41 +0100 Subject: [PATCH 03/23] ci: add g++ to docs-preview.yml --- .github/workflows/docs-preview.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/docs-preview.yml b/.github/workflows/docs-preview.yml index 2c2644a82..3410269b8 100644 --- a/.github/workflows/docs-preview.yml +++ b/.github/workflows/docs-preview.yml @@ -33,7 +33,8 @@ jobs: git-annex \ make \ jq \ - gcc + gcc \ + g++ # Copy junifer-data directory mkdir -p $HOME/junifer_data/v1 && \ cp -ar /root/junifer_data/v1/. $HOME/junifer_data/v1/ -- 2.52.0 From c7f9211a3082eb3bf08ae375b30c039a2bbaf1de Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 17 Feb 2025 09:27:25 +0100 Subject: [PATCH 04/23] ci: add pkg-config to docs-preview.yml --- .github/workflows/docs-preview.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/docs-preview.yml b/.github/workflows/docs-preview.yml index 3410269b8..c46242da7 100644 --- a/.github/workflows/docs-preview.yml +++ b/.github/workflows/docs-preview.yml @@ -34,7 +34,8 @@ jobs: make \ jq \ gcc \ - g++ + g++ \ + pkg-config # Copy junifer-data directory mkdir -p $HOME/junifer_data/v1 && \ cp -ar /root/junifer_data/v1/. $HOME/junifer_data/v1/ -- 2.52.0 From ffaf3e8db7d547bd0abce3f5997697f0730e5a84 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 17 Feb 2025 09:31:33 +0100 Subject: [PATCH 05/23] ci: use ubuntu-24.04 for docs-preview.yml --- .github/workflows/docs-preview.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docs-preview.yml b/.github/workflows/docs-preview.yml index c46242da7..5a492bc8e 100644 --- a/.github/workflows/docs-preview.yml +++ b/.github/workflows/docs-preview.yml @@ -17,7 +17,7 @@ concurrency: preview-${{ github.ref }} jobs: build-docs: - runs-on: ubuntu-22.04 + runs-on: ubuntu-24.04 # Use custom docs CI image container: ghcr.io/juaml/junifer-docs:main steps: -- 2.52.0 From 9c338452fa11dc59b83ad63234a43cde8633788c Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 17 Feb 2025 09:40:26 +0100 Subject: [PATCH 06/23] ci: use python 3.12 for docs-preview.yml --- .github/workflows/docs-preview.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docs-preview.yml b/.github/workflows/docs-preview.yml index 5a492bc8e..ec617a588 100644 --- a/.github/workflows/docs-preview.yml +++ b/.github/workflows/docs-preview.yml @@ -47,7 +47,7 @@ jobs: - name: Set up Python uses: actions/setup-python@v5 with: - python-version: "3.x" + python-version: "3.12" - name: Install Python dependencies run: | python -m pip install --upgrade pip setuptools wheel -- 2.52.0 From ba87a5a344ef50ffc3d43caf710fa865152eeb33 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 17 Feb 2025 09:44:21 +0100 Subject: [PATCH 07/23] Revert "ci: use python 3.12 for docs-preview.yml" This reverts commit 9c338452fa11dc59b83ad63234a43cde8633788c. --- .github/workflows/docs-preview.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docs-preview.yml b/.github/workflows/docs-preview.yml index ec617a588..5a492bc8e 100644 --- a/.github/workflows/docs-preview.yml +++ b/.github/workflows/docs-preview.yml @@ -47,7 +47,7 @@ jobs: - name: Set up Python uses: actions/setup-python@v5 with: - python-version: "3.12" + python-version: "3.x" - name: Install Python dependencies run: | python -m pip install --upgrade pip setuptools wheel -- 2.52.0 From 0daf5d3fd72b41fbe110852520f1a5c636b428e7 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 17 Feb 2025 09:44:34 +0100 Subject: [PATCH 08/23] Revert "ci: use ubuntu-24.04 for docs-preview.yml" This reverts commit ffaf3e8db7d547bd0abce3f5997697f0730e5a84. --- .github/workflows/docs-preview.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docs-preview.yml b/.github/workflows/docs-preview.yml index 5a492bc8e..c46242da7 100644 --- a/.github/workflows/docs-preview.yml +++ b/.github/workflows/docs-preview.yml @@ -17,7 +17,7 @@ concurrency: preview-${{ github.ref }} jobs: build-docs: - runs-on: ubuntu-24.04 + runs-on: ubuntu-22.04 # Use custom docs CI image container: ghcr.io/juaml/junifer-docs:main steps: -- 2.52.0 From 301368fe40c0e5d3723e60cac82f0037979f888b Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 17 Feb 2025 09:44:57 +0100 Subject: [PATCH 09/23] ci: add comment for using ubuntu-22.04 in docs-preview.yml --- .github/workflows/docs-preview.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/docs-preview.yml b/.github/workflows/docs-preview.yml index c46242da7..e86a77456 100644 --- a/.github/workflows/docs-preview.yml +++ b/.github/workflows/docs-preview.yml @@ -17,6 +17,7 @@ concurrency: preview-${{ github.ref }} jobs: build-docs: + # https://github.com/actions/setup-python/issues/1013#issuecomment-2642078401 runs-on: ubuntu-22.04 # Use custom docs CI image container: ghcr.io/juaml/junifer-docs:main -- 2.52.0 From 45588179602d718512eb0b8348587ea3771b7a34 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 17 Feb 2025 09:45:56 +0100 Subject: [PATCH 10/23] Revert "Revert "ci: use python 3.12 for docs-preview.yml"" This reverts commit ba87a5a344ef50ffc3d43caf710fa865152eeb33. --- .github/workflows/docs-preview.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docs-preview.yml b/.github/workflows/docs-preview.yml index e86a77456..d9f313efc 100644 --- a/.github/workflows/docs-preview.yml +++ b/.github/workflows/docs-preview.yml @@ -48,7 +48,7 @@ jobs: - name: Set up Python uses: actions/setup-python@v5 with: - python-version: "3.x" + python-version: "3.12" - name: Install Python dependencies run: | python -m pip install --upgrade pip setuptools wheel -- 2.52.0 From 935403ec1c7e41ed5c5ddd16f44f8897b884ff1e Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 17 Feb 2025 10:39:10 +0100 Subject: [PATCH 11/23] ci: use junifer-data for ci.yml --- .github/workflows/ci.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 65dd1c1ae..8053469f3 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -43,10 +43,10 @@ jobs: git-annex \ make \ jq - - name: Copy xfms directory + - name: Copy junifer-data directory run: | - mkdir -p $HOME/junifer/data/xfms - cp -ar /root/junifer/data/xfms/. $HOME/junifer/data/xfms/ + mkdir -p $HOME/junifer_data/v1 + cp -ar /root/junifer_data/v1/. $HOME/junifer_data/v1/ - name: Checkout repository uses: actions/checkout@v4 with: -- 2.52.0 From df686de207a5ade40f2ab8842e958ccb71754b4a Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 17 Feb 2025 10:39:22 +0100 Subject: [PATCH 12/23] ci: update commentary for ci.yml --- .github/workflows/ci.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 8053469f3..2716b1c15 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -16,8 +16,9 @@ on: jobs: run-tests: + # https://github.com/actions/setup-python/issues/1013#issuecomment-2642078401 runs-on: ubuntu-22.04 - # Use custom docs CI image + # Use custom CI image container: ghcr.io/juaml/junifer-ci:main strategy: fail-fast: false -- 2.52.0 From 1ae3cd04dccdd2c2786d66b67d079848ca43d2ba Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 17 Feb 2025 10:39:47 +0100 Subject: [PATCH 13/23] ci: make junifer-data copying separate step in docs-preview.yml --- .github/workflows/docs-preview.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/docs-preview.yml b/.github/workflows/docs-preview.yml index d9f313efc..5f4bfb6c6 100644 --- a/.github/workflows/docs-preview.yml +++ b/.github/workflows/docs-preview.yml @@ -37,8 +37,9 @@ jobs: gcc \ g++ \ pkg-config - # Copy junifer-data directory - mkdir -p $HOME/junifer_data/v1 && \ + - name: Copy junifer-data directory + run: | + mkdir -p $HOME/junifer_data/v1 cp -ar /root/junifer_data/v1/. $HOME/junifer_data/v1/ - name: Checkout source uses: actions/checkout@v4 -- 2.52.0 From f55027103722d5714dec1370402b12f81da3b203 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 17 Feb 2025 10:40:21 +0100 Subject: [PATCH 14/23] ci: update commentary for docs-preview.yml --- .github/workflows/docs-preview.yml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/.github/workflows/docs-preview.yml b/.github/workflows/docs-preview.yml index 5f4bfb6c6..98a104501 100644 --- a/.github/workflows/docs-preview.yml +++ b/.github/workflows/docs-preview.yml @@ -26,9 +26,8 @@ jobs: run: | echo "Using ANTs : $(antsRegistration --version)" - name: Install system dependencies + # actions/checkout fails to identify Git as it's not in the CI image run: | - # actions/checkout fails to identify Git as it's not in the CI image - apt-get -qq update && \ apt-get -qq install -y \ git \ git-annex \ @@ -41,7 +40,7 @@ jobs: run: | mkdir -p $HOME/junifer_data/v1 cp -ar /root/junifer_data/v1/. $HOME/junifer_data/v1/ - - name: Checkout source + - name: Checkout repository uses: actions/checkout@v4 with: fetch-depth: 0 -- 2.52.0 From c4bdfeb43653487fe38d8a76fc2fa8b5c472bca9 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 17 Feb 2025 10:41:10 +0100 Subject: [PATCH 15/23] ci: update run in docs-preview.yml --- .github/workflows/docs-preview.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/docs-preview.yml b/.github/workflows/docs-preview.yml index 98a104501..32eef5dab 100644 --- a/.github/workflows/docs-preview.yml +++ b/.github/workflows/docs-preview.yml @@ -28,6 +28,7 @@ jobs: - name: Install system dependencies # actions/checkout fails to identify Git as it's not in the CI image run: | + apt-get -qq update apt-get -qq install -y \ git \ git-annex \ -- 2.52.0 From 6b352b456de07a678219b4b1818e0123bd7ed32e Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 17 Feb 2025 11:19:27 +0100 Subject: [PATCH 16/23] Revert "ci: add pkg-config to docs-preview.yml" This reverts commit c7f9211a3082eb3bf08ae375b30c039a2bbaf1de. --- .github/workflows/docs-preview.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/docs-preview.yml b/.github/workflows/docs-preview.yml index 32eef5dab..c1939e6eb 100644 --- a/.github/workflows/docs-preview.yml +++ b/.github/workflows/docs-preview.yml @@ -35,8 +35,7 @@ jobs: make \ jq \ gcc \ - g++ \ - pkg-config + g++ - name: Copy junifer-data directory run: | mkdir -p $HOME/junifer_data/v1 -- 2.52.0 From a9ab0f4a560b22c1631fc15e67e31f73c8cbd0c9 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 17 Feb 2025 11:20:20 +0100 Subject: [PATCH 17/23] Revert "ci: add g++ to docs-preview.yml" This reverts commit ea9b19381288b05ae0b6f8b5fc889fa08ae729ad. --- .github/workflows/docs-preview.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/docs-preview.yml b/.github/workflows/docs-preview.yml index c1939e6eb..012cf1118 100644 --- a/.github/workflows/docs-preview.yml +++ b/.github/workflows/docs-preview.yml @@ -34,8 +34,7 @@ jobs: git-annex \ make \ jq \ - gcc \ - g++ + gcc - name: Copy junifer-data directory run: | mkdir -p $HOME/junifer_data/v1 -- 2.52.0 From 33c540c3e6cc1bf69379bbc3a72f688d7d49a1c0 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 17 Feb 2025 11:21:01 +0100 Subject: [PATCH 18/23] Revert "ci: add gcc to docs-preview.yml" This reverts commit 1f6ec5dbdf95178af9b287b1edb25a4badcc8566. --- .github/workflows/docs-preview.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/docs-preview.yml b/.github/workflows/docs-preview.yml index 012cf1118..70a4d7250 100644 --- a/.github/workflows/docs-preview.yml +++ b/.github/workflows/docs-preview.yml @@ -33,8 +33,7 @@ jobs: git \ git-annex \ make \ - jq \ - gcc + jq - name: Copy junifer-data directory run: | mkdir -p $HOME/junifer_data/v1 -- 2.52.0 From b543d91e0a56b1feb4edeb44773da4f22ab9fabb Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 17 Feb 2025 11:22:05 +0100 Subject: [PATCH 19/23] ci: update docs.yml --- .github/workflows/docs.yml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index d16c90133..3a721e5dc 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -12,6 +12,7 @@ on: jobs: build-docs: + # https://github.com/actions/setup-python/issues/1013#issuecomment-2642078401 runs-on: ubuntu-22.04 # Use custom docs CI image container: ghcr.io/juaml/junifer-docs:main @@ -28,10 +29,10 @@ jobs: git-annex \ make \ jq - - name: Copy xfms directory + - name: Copy junifer-data directory run: | - mkdir -p $HOME/junifer/data/xfms - cp -ar /root/junifer/data/xfms/. $HOME/junifer/data/xfms/ + mkdir -p $HOME/junifer_data/v1 + cp -ar /root/junifer_data/v1/. $HOME/junifer_data/v1/ - name: Checkout repository uses: actions/checkout@v4 with: @@ -41,7 +42,7 @@ jobs: - name: Set up Python uses: actions/setup-python@v5 with: - python-version: "3.x" + python-version: "3.12" - name: Install Python dependencies run: | python -m pip install --upgrade pip setuptools wheel -- 2.52.0 From e0aa2523f74fea18fa0311674edc0cd778005cfd Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 17 Feb 2025 11:23:12 +0100 Subject: [PATCH 20/23] ci: add extra system deps on python 3.13 for ci.yml --- .github/workflows/ci.yml | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 2716b1c15..1519fc34e 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -44,6 +44,14 @@ jobs: git-annex \ make \ jq + - name: Install extra system dependencies + run: | + apt-get -qq install -y \ + gcc \ + g++ \ + pkg-config \ + python-dev + if: matrix.python-version == 3.13 - name: Copy junifer-data directory run: | mkdir -p $HOME/junifer_data/v1 -- 2.52.0 From 3e08590cc74738b3a8e9342e7f2c01133e1e2aee Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 17 Feb 2025 11:24:52 +0100 Subject: [PATCH 21/23] chore: add changelog 428.misc --- docs/changes/newsfragments/428.misc | 1 + 1 file changed, 1 insertion(+) create mode 100644 docs/changes/newsfragments/428.misc diff --git a/docs/changes/newsfragments/428.misc b/docs/changes/newsfragments/428.misc new file mode 100644 index 000000000..83fb0431e --- /dev/null +++ b/docs/changes/newsfragments/428.misc @@ -0,0 +1 @@ +Improve GitHub Actions workflows by `Synchon Mandal`_ -- 2.52.0 From 57ee5e42ba717e2ae51923b2e7f3037c953f5d30 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 17 Feb 2025 11:31:25 +0100 Subject: [PATCH 22/23] ci: explicit python3.13-dev for ci.yml --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 1519fc34e..9fca4a0c2 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -50,7 +50,7 @@ jobs: gcc \ g++ \ pkg-config \ - python-dev + python3.13-dev if: matrix.python-version == 3.13 - name: Copy junifer-data directory run: | -- 2.52.0 From da414c8b20ea8caeaa000bea94b594fdb7e0f0c9 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 17 Feb 2025 12:07:05 +0100 Subject: [PATCH 23/23] ci: remove python 3.13 as it's incompatible with the current setup; consider in future --- .github/workflows/ci.yml | 10 +--------- 1 file changed, 1 insertion(+), 9 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 9fca4a0c2..ba9e2a7de 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -23,7 +23,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ['3.9', '3.10', '3.11', '3.12', '3.13'] + python-version: ['3.9', '3.10', '3.11', '3.12'] steps: - name: Check ANTs @@ -44,14 +44,6 @@ jobs: git-annex \ make \ jq - - name: Install extra system dependencies - run: | - apt-get -qq install -y \ - gcc \ - g++ \ - pkg-config \ - python3.13-dev - if: matrix.python-version == 3.13 - name: Copy junifer-data directory run: | mkdir -p $HOME/junifer_data/v1 -- 2.52.0