From 6a1f8b4512d63972a77b71a6daf0bfb56c956e5a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Tue, 9 Jun 2026 15:25:22 +0200 Subject: [PATCH 1/4] Limit regular tests to Ubuntu version --- .github/workflows/build.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 43454a56..0971c843 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -97,6 +97,7 @@ jobs: run: tar -xvf source/source_bin.tar -C source && source/trimal && ./scripts/generate_trimmed_msas.sh && ./scripts/compare_trimmed_msas.sh build_macos: + if: endsWith(github.head_ref, 'release') strategy: matrix: version: [macos-14, macos-15-intel] @@ -115,6 +116,7 @@ jobs: if-no-files-found: error test_macos: + if: endsWith(github.head_ref, 'release') strategy: matrix: version: [macos-14, macos-15-intel] @@ -133,6 +135,7 @@ jobs: ./scripts/generate_trimmed_msas.sh && ./scripts/compare_trimmed_msas.sh build_windows: + if: endsWith(github.head_ref, 'release') runs-on: windows-2022 steps: - uses: actions/checkout@v4 @@ -164,6 +167,7 @@ jobs: if-no-files-found: error test_windows: + if: endsWith(github.head_ref, 'release') runs-on: windows-2022 needs: build_windows steps: From b887c110fca9fd09fc11d259aea087ed7a7b1c97 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Tue, 9 Jun 2026 15:26:21 +0200 Subject: [PATCH 2/4] Update tests to use Ubuntu 24.04 --- .github/workflows/build.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 0971c843..33c528b8 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -21,7 +21,7 @@ name: Build jobs: build_ubuntu_x86_64: - runs-on: ubuntu-22.04 + runs-on: ubuntu-24.04 steps: - uses: actions/checkout@v4 - name: Build trimAl for Linux x86_64 @@ -37,7 +37,7 @@ jobs: build_ubuntu_aarch64: if: endsWith(github.head_ref, 'release') - runs-on: ubuntu-22.04 + runs-on: ubuntu-24.04 steps: - uses: actions/checkout@v4 - name: Build trimAl for Linux aarch64 @@ -63,7 +63,7 @@ jobs: if-no-files-found: error test_ubuntu_x86_64: - runs-on: ubuntu-22.04 + runs-on: ubuntu-24.04 needs: build_ubuntu_x86_64 steps: - uses: actions/checkout@v4 @@ -77,7 +77,7 @@ jobs: test_ubuntu_aarch64: if: endsWith(github.head_ref, 'release') - runs-on: ubuntu-22.04 + runs-on: ubuntu-24.04 needs: build_ubuntu_aarch64 steps: - uses: actions/checkout@v4 From 3d6cdd27164af20f0b606d18b67e0cfac958f746 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Tue, 9 Jun 2026 15:29:31 +0200 Subject: [PATCH 3/4] Update deprecated actions --- .github/workflows/build.yml | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 33c528b8..12680b1c 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -23,11 +23,11 @@ jobs: build_ubuntu_x86_64: runs-on: ubuntu-24.04 steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 - name: Build trimAl for Linux x86_64 run: cd source && make all && file trimal && file readal && file statal && cd .. && tar -cvf source_bin.tar -C source trimal readal statal - name: Upload build binaries for Linux x86_64 - uses: actions/upload-artifact@v4 + uses: actions/upload-artifact@v7 with: name: trimal_linux_x86_64 path: source_bin.tar @@ -39,7 +39,7 @@ jobs: if: endsWith(github.head_ref, 'release') runs-on: ubuntu-24.04 steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 - name: Build trimAl for Linux aarch64 uses: uraimo/run-on-arch-action@v3 with: @@ -54,7 +54,7 @@ jobs: run: | cd /trimal/source && make all && file trimal && file readal && file statal && cd .. && tar -cvf source_bin.tar -C source trimal readal statal - name: Upload build binaries for Linux aarch64 - uses: actions/upload-artifact@v4 + uses: actions/upload-artifact@v7 with: name: trimal_linux_aarch64 path: source_bin.tar @@ -66,7 +66,7 @@ jobs: runs-on: ubuntu-24.04 needs: build_ubuntu_x86_64 steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 - name: Download build binaries for Linux x86_64 uses: actions/download-artifact@v4 with: @@ -80,7 +80,7 @@ jobs: runs-on: ubuntu-24.04 needs: build_ubuntu_aarch64 steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 - name: Download build binaries for Linux aarch64 uses: actions/download-artifact@v4 with: @@ -103,7 +103,7 @@ jobs: version: [macos-14, macos-15-intel] runs-on: ${{ matrix.version }} steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 - name: Build trimAl for ${{ matrix.version }} run: cd source && make all && file trimal && file readal && file statal && cd .. && tar -cvf source_bin.tar -C source trimal readal statal - name: Upload build binaries for ${{ matrix.version }} @@ -123,7 +123,7 @@ jobs: runs-on: ${{ matrix.version }} needs: build_macos steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 - name: Download build binaries for ${{ matrix.version }} uses: actions/download-artifact@v4 with: @@ -138,7 +138,7 @@ jobs: if: endsWith(github.head_ref, 'release') runs-on: windows-2022 steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 - name: Set up MSYS2 uses: msys2/setup-msys2@v2 with: @@ -171,7 +171,7 @@ jobs: runs-on: windows-2022 needs: build_windows steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 - name: Download build binaries for Windows uses: actions/download-artifact@v4 with: From 6614f9038555e28a87138b0256dbc9a8f659ff65 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= Date: Wed, 10 Jun 2026 10:27:46 +0200 Subject: [PATCH 4/4] Update release version to v1.5.2 --- docs/source/conf.py | 4 ++-- docs/source/installation.rst | 8 ++++---- source/alignment.cpp | 6 +++--- source/alignment.h | 4 ++-- source/autAlignment.cpp | 2 +- source/compareFiles.cpp | 2 +- source/compareFiles.h | 2 +- source/defines.h | 6 +++--- source/main.cpp | 2 +- source/readAl.cpp | 2 +- source/rwAlignment.cpp | 8 ++++---- source/sequencesMatrix.cpp | 2 +- source/sequencesMatrix.h | 2 +- source/similarityMatrix.cpp | 2 +- source/similarityMatrix.h | 2 +- source/statAl.cpp | 2 +- source/statisticsConservation.cpp | 2 +- source/statisticsConservation.h | 2 +- source/statisticsFiles.cpp | 2 +- source/statisticsFiles.h | 2 +- source/statisticsGaps.cpp | 2 +- source/statisticsGaps.h | 2 +- source/utils.cpp | 4 ++-- source/utils.h | 4 ++-- source/values.h | 2 +- 25 files changed, 39 insertions(+), 39 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index 6e0012fe..f0f8b2b3 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -7,9 +7,9 @@ # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information project = 'trimAl' -copyright = '2025, trimAl team' +copyright = '2026, trimAl team' author = 'trimAl team' -release = '1.5.1' +release = '1.5.2' version = release # -- General configuration --------------------------------------------------- diff --git a/docs/source/installation.rst b/docs/source/installation.rst index ca7ffa5e..57bdf1c3 100644 --- a/docs/source/installation.rst +++ b/docs/source/installation.rst @@ -2,11 +2,11 @@ Installation ************* -Version 1.5.1 +Version 1.5.2 ======================== -The binaries can be downloaded for `Linux `_, -`MacOS `_ and `Windows `_. You may also download -the source code from `Github repository `_ and then compile it yourself. +The binaries can be downloaded for `Linux `_, +`MacOS `_ and `Windows `_. You may also download +the source code from `Github repository `_ and then compile it yourself. The simplest way to compile this package is: 1. Go to the directory containing the package's source code ('source'). diff --git a/source/alignment.cpp b/source/alignment.cpp index 71b8e08a..1f686220 100644 --- a/source/alignment.cpp +++ b/source/alignment.cpp @@ -1,13 +1,13 @@ /* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** - trimAl v1.5.1: a tool for automated alignment trimming in large-scale + trimAl v1.5.2: a tool for automated alignment trimming in large-scale phylogenetics analyses. - readAl v1.5.1: a tool for automated alignment conversion among different + readAl v1.5.2: a tool for automated alignment conversion among different formats. - statAl v1.5.1: a tool for getting stats about multiple sequence alignments. + statAl v1.5.2: a tool for getting stats about multiple sequence alignments. 2009-2020 diff --git a/source/alignment.h b/source/alignment.h index 517a2d59..1ba372c1 100644 --- a/source/alignment.h +++ b/source/alignment.h @@ -1,10 +1,10 @@ /* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** - trimAl v1.5.1: a tool for automated alignment trimming in large-scale + trimAl v1.5.2: a tool for automated alignment trimming in large-scale phylogenetics analyses. - readAl v1.5.1: a tool for automated alignment conversion among different + readAl v1.5.2: a tool for automated alignment conversion among different formats. 2009-2020 diff --git a/source/autAlignment.cpp b/source/autAlignment.cpp index 39a3d694..d3923439 100644 --- a/source/autAlignment.cpp +++ b/source/autAlignment.cpp @@ -1,7 +1,7 @@ /* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** - trimAl v1.5.1: a tool for automated alignment trimming in large-scale + trimAl v1.5.2: a tool for automated alignment trimming in large-scale phylogenetics analyses. 2009-2020 diff --git a/source/compareFiles.cpp b/source/compareFiles.cpp index 44aea372..684359cc 100644 --- a/source/compareFiles.cpp +++ b/source/compareFiles.cpp @@ -1,7 +1,7 @@ /* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** - trimAl v1.5.1: a tool for automated alignment trimming in large-scale + trimAl v1.5.2: a tool for automated alignment trimming in large-scale phylogenetics analyses. 2009-2020 diff --git a/source/compareFiles.h b/source/compareFiles.h index a315b88c..fb3adf34 100644 --- a/source/compareFiles.h +++ b/source/compareFiles.h @@ -1,7 +1,7 @@ /* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** - trimAl v1.5.1: a tool for automated alignment trimming in large-scale + trimAl v1.5.2: a tool for automated alignment trimming in large-scale phylogenetics analyses. 2009-2020 diff --git a/source/defines.h b/source/defines.h index 8596f865..bca53b8f 100644 --- a/source/defines.h +++ b/source/defines.h @@ -1,13 +1,13 @@ /* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** - trimAl v1.5.1: a tool for automated alignment trimming in large-scale + trimAl v1.5.2: a tool for automated alignment trimming in large-scale phylogenetics analyses. - readAl v1.5.1: a tool for automated alignment conversion among different + readAl v1.5.2: a tool for automated alignment conversion among different formats. - statAl v1.5.1: a tool for getting descriptive alignment features/scores. + statAl v1.5.2: a tool for getting descriptive alignment features/scores. 2009-2020 Fernandez-Rodriguez V. (victor.fernandez@bsc.es) diff --git a/source/main.cpp b/source/main.cpp index b86f8301..7b51c492 100644 --- a/source/main.cpp +++ b/source/main.cpp @@ -1,7 +1,7 @@ /* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** - trimAl v1.5.1: a tool for automated alignment trimming in large-scale + trimAl v1.5.2: a tool for automated alignment trimming in large-scale phylogenetics analyses. 2009-2020 diff --git a/source/readAl.cpp b/source/readAl.cpp index 48d18e37..6f0335cb 100644 --- a/source/readAl.cpp +++ b/source/readAl.cpp @@ -1,7 +1,7 @@ /* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** - readAl v1.5.1: a tool for automated alignment conversion among different + readAl v1.5.2: a tool for automated alignment conversion among different formats. 2009-2020 diff --git a/source/rwAlignment.cpp b/source/rwAlignment.cpp index cf8e9bd2..54de89c6 100644 --- a/source/rwAlignment.cpp +++ b/source/rwAlignment.cpp @@ -1,10 +1,10 @@ /* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** - trimAl v1.5.1: a tool for automated alignment trimming in large-scale + trimAl v1.5.2: a tool for automated alignment trimming in large-scale phylogenetics analyses. - readAl v1.5.1: a tool for automated alignment conversion among different + readAl v1.5.2: a tool for automated alignment conversion among different formats. 2009-2020 @@ -1922,7 +1922,7 @@ bool alignment::alignmentSummaryHTML(char *destFile, int residues, int seqs, \ /* Print HTML header into output file */ file << "" << endl << "" << endl << " " - << endl << " trimAl v1.5.1 Summary" << endl + << endl << " trimAl v1.5.2 Summary" << endl << "