From b4d00467a7e5734d9092eb8f582f3f17fa457474 Mon Sep 17 00:00:00 2001 From: Kris Thielemans Date: Mon, 9 Dec 2024 22:48:30 +0000 Subject: [PATCH 1/8] fix GHA workflow --- .github/workflows/build-test.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/build-test.yml b/.github/workflows/build-test.yml index 8bb89f6..e377f96 100644 --- a/.github/workflows/build-test.yml +++ b/.github/workflows/build-test.yml @@ -107,6 +107,7 @@ jobs: fi # other dependencies sudo apt install libinsighttoolkit5-dev + ;; (macOS*) brew install itk ;; @@ -173,4 +174,4 @@ jobs: set -vx cd ${GITHUB_WORKSPACE}/build cpack - \ No newline at end of file + # outputs PETPVC-1.*.*.sh, .tar.gz and .tar.Z \ No newline at end of file From 3ac1b66dc05091cdd0bbbf03565319460b8c18a0 Mon Sep 17 00:00:00 2001 From: Kris Thielemans Date: Mon, 9 Dec 2024 22:54:22 +0000 Subject: [PATCH 2/8] [GHA] use ITK 4.* --- .github/workflows/build-test.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/build-test.yml b/.github/workflows/build-test.yml index e377f96..bd8928b 100644 --- a/.github/workflows/build-test.yml +++ b/.github/workflows/build-test.yml @@ -106,7 +106,8 @@ jobs: sudo apt install $CXX fi # other dependencies - sudo apt install libinsighttoolkit5-dev + # note: v5 is distributed without the REVIEW module + sudo apt install libinsighttoolkit4-dev ;; (macOS*) brew install itk From fc238f4f8cf9a27baea924b9e91c1962fb01d4db Mon Sep 17 00:00:00 2001 From: Kris Thielemans Date: Mon, 9 Dec 2024 22:55:32 +0000 Subject: [PATCH 3/8] [GHA] test g++-12 --- .github/workflows/build-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build-test.yml b/.github/workflows/build-test.yml index bd8928b..8db4763 100644 --- a/.github/workflows/build-test.yml +++ b/.github/workflows/build-test.yml @@ -40,7 +40,7 @@ jobs: BUILD_TYPE: "Debug" - os: ubuntu-latest compiler: gcc - compiler_version: 13 + compiler_version: 12 BUILD_TYPE: "Release" - os: ubuntu-latest compiler: clang From 43e89a7fa347a246e9e460b30374fdefa2ba2a44 Mon Sep 17 00:00:00 2001 From: Kris Thielemans Date: Mon, 9 Dec 2024 23:03:34 +0000 Subject: [PATCH 4/8] [CI] don't run certain CI when irrelevant files change --- .github/workflows/build-test.yml | 6 ++++-- appveyor.yml | 10 ++++++++++ 2 files changed, 14 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build-test.yml b/.github/workflows/build-test.yml index 8db4763..235f7be 100644 --- a/.github/workflows/build-test.yml +++ b/.github/workflows/build-test.yml @@ -5,7 +5,8 @@ on: branches: - master paths-ignore: - - '.appveyor.yml' + - 'appveyor.yml' + - 'azure-pipelines.yml' - 'CITATION.cff' - '**/*.md' - '**/*.html' @@ -16,7 +17,8 @@ on: branches: - master paths-ignore: - - '.appveyor.yml' + - 'appveyor.yml' + - 'azure-pipelines.yml' - 'CITATION.cff' - '**/*.md' - '**/*.html' diff --git a/appveyor.yml b/appveyor.yml index 74cb670..d68c686 100644 --- a/appveyor.yml +++ b/appveyor.yml @@ -1,3 +1,13 @@ +skip_commits: + files: + - .github/**/* + - 'azure-pipelines.yml' + - 'CITATION.cff' + - '**/*.md' + - '**/*.html' + - '**/*.htm' + - '**/*.tex' + # version format version: "{build}" From 29836af373664e1f93f4955f460e0ad18d622100 Mon Sep 17 00:00:00 2001 From: Kris Thielemans Date: Mon, 9 Dec 2024 23:04:14 +0000 Subject: [PATCH 5/8] add CITATION.cff --- CITATION.cff | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 CITATION.cff diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..5802889 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,26 @@ +cff-version: 1.2.0 +title: PETPVC PET Partial Volume Correction +message: >- + If you use this software, please cite it using the + metadata from this file. +type: software +authors: + - family-names: Thomas + given-names: Benjamin + orcid: 'https://orcid.org/0000-0002-9784-1177' + affiliation: University College London + - family-names: Thielemans + given-names: Kris + orcid: 'https://orcid.org/0000-0002-5514-199X' + affiliation: University College London +identifiers: + - type: doi + value: 10.1088/0031-9155/61/22/7975 +repository-code: 'https://github.com/UCL/PETPVC' +keywords: + - pet + - spect + - medical imaging + - partial volume correction + - open-source software +license: Apache-2.0 From bf0638dcbb615aa1716c6edcccb03f841760226f Mon Sep 17 00:00:00 2001 From: Kris Thielemans Date: Mon, 9 Dec 2024 23:06:24 +0000 Subject: [PATCH 6/8] [GHA] fix title of workflow [ci skip] --- .github/workflows/build-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build-test.yml b/.github/workflows/build-test.yml index 235f7be..dfe8142 100644 --- a/.github/workflows/build-test.yml +++ b/.github/workflows/build-test.yml @@ -1,4 +1,4 @@ -name: Build and ctest and recon_test_pack CI +name: Build and ctest CI on: push: From f7e3bc2c92c1e965ab8419c8032735bc8891e644 Mon Sep 17 00:00:00 2001 From: Kris Thielemans Date: Mon, 9 Dec 2024 23:06:57 +0000 Subject: [PATCH 7/8] add GitHub Actions badge [ci skip] --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 82abf4b..84f1257 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@ # PETPVC -[![Build Status](https://dev.azure.com/petpvc/petpvc/_apis/build/status/UCL.PETPVC?branchName=master)](https://dev.azure.com/petpvc/petpvc/_build/latest?definitionId=1&branchName=master) [![Build status](https://ci.appveyor.com/api/projects/status/7kk9ua9r0lybinwa/branch/master?svg=true)](https://ci.appveyor.com/project/bathomas/petpvc/branch/master) [![Codacy Badge](https://api.codacy.com/project/badge/Grade/ab83c41f20194c2c82fbc74e8788f928)](https://www.codacy.com/app/bathomas/PETPVC?utm_source=github.com&utm_medium=referral&utm_content=UCL/PETPVC&utm_campaign=badger) [![DOI](https://zenodo.org/badge/17082200.svg)](https://zenodo.org/badge/latestdoi/17082200) +[![Build and ctest and recon_test_pack CI](https://github.com/UCL/PETPVC/actions/workflows/build-test.yml/badge.svg)](https://github.com/UCL/PETPVC/actions/workflows/build-test.yml)[![Build Status](https://dev.azure.com/petpvc/petpvc/_apis/build/status/UCL.PETPVC?branchName=master)](https://dev.azure.com/petpvc/petpvc/_build/latest?definitionId=1&branchName=master) [![Build status](https://ci.appveyor.com/api/projects/status/7kk9ua9r0lybinwa/branch/master?svg=true)](https://ci.appveyor.com/project/bathomas/petpvc/branch/master) [![Codacy Badge](https://api.codacy.com/project/badge/Grade/ab83c41f20194c2c82fbc74e8788f928)](https://www.codacy.com/app/bathomas/PETPVC?utm_source=github.com&utm_medium=referral&utm_content=UCL/PETPVC&utm_campaign=badger) [![DOI](https://zenodo.org/badge/17082200.svg)](https://zenodo.org/badge/latestdoi/17082200) PETPVC: toolbox for partial volume correction (PVC) in positron emission tomography (PET) From 6fb02360569d49d9e4614a83bdb65e1ab469ae91 Mon Sep 17 00:00:00 2001 From: Kris Thielemans Date: Mon, 9 Dec 2024 23:19:11 +0000 Subject: [PATCH 8/8] [GHA] upload cpack files as artefact --- .github/workflows/build-test.yml | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/.github/workflows/build-test.yml b/.github/workflows/build-test.yml index dfe8142..e4540d0 100644 --- a/.github/workflows/build-test.yml +++ b/.github/workflows/build-test.yml @@ -177,4 +177,12 @@ jobs: set -vx cd ${GITHUB_WORKSPACE}/build cpack - # outputs PETPVC-1.*.*.sh, .tar.gz and .tar.Z \ No newline at end of file + # outputs PETPVC-1.*.*.sh, .tar.gz and .tar.Z + + - name: Upload cpack output + uses: actions/upload-artifact@v4 + with: + name: cpack_files-${{ matrix.os }}-${{ matrix.compiler }}${{ matrix.compiler_version }}-${{ matrix.BUILD_TYPE }} + path: | + ${{ github.workspace }}/build/PETPVC-*.*.*.* + retention-days: 10