From 814fc265903816d046505ea8b44c6fdb3001415c Mon Sep 17 00:00:00 2001 From: Tim Van Rillaer Date: Wed, 18 Feb 2026 16:49:08 +0100 Subject: [PATCH 1/7] Update BATS setup action version in CI workflow --- .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 6d07b79..724107f 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -42,7 +42,7 @@ jobs: environment-file: ${{ matrix.env-file }} auto-activate: true - name: Setup BATS - uses: mig4/setup-bats@v4 + uses: mig4/setup-bats@v1 with: bats-version: 1.2.1 - uses: brokenpip3/setup-bats-libs@1.5.2 From c61355cc5dee54a8655b9bf09ecc8595c8cf4ae4 Mon Sep 17 00:00:00 2001 From: Tim Van Rillaer Date: Wed, 18 Feb 2026 16:54:45 +0100 Subject: [PATCH 2/7] Simplify Python version specification in CI Updated Python versions in CI workflow to use shorter format. --- .github/workflows/ci.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 724107f..fb54883 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -17,10 +17,10 @@ jobs: strategy: matrix: include: - - python-version: "3.7.17" + - python-version: "3.7" os: ubuntu-22.04 env-file: "test/environment_min.yml" - - python-version: "3.12.11" + - python-version: "3.12" os: ubuntu-24.04 env-file: "test/environment_max.yml" From cf8d10a4ea63080aa686df99f6544cccf2fb9bd6 Mon Sep 17 00:00:00 2001 From: Tim Van Rillaer Date: Wed, 18 Feb 2026 16:59:53 +0100 Subject: [PATCH 3/7] Downgrade bats-libs version --- .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 fb54883..fb361ab 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -45,7 +45,7 @@ jobs: uses: mig4/setup-bats@v1 with: bats-version: 1.2.1 - - uses: brokenpip3/setup-bats-libs@1.5.2 + - uses: brokenpip3/setup-bats-libs@0.0.2 with: support-path: ${{ github.workspace }}/test/test_helper/bats-support assert-path: ${{ github.workspace }}/test/test_helper/bats-assert From 752897c13e004db815aa73785f433c529b019426 Mon Sep 17 00:00:00 2001 From: Tim Van Rillaer Date: Wed, 18 Feb 2026 17:04:49 +0100 Subject: [PATCH 4/7] Change activate-environment to an empty string Updated the activate-environment parameter to an empty string. --- .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 fb361ab..e470e0c 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -38,7 +38,7 @@ jobs: uses: conda-incubator/setup-miniconda@v3 with: python-version: ${{ matrix.python-version }} - activate-environment: anaconda-client-env + activate-environment: "" environment-file: ${{ matrix.env-file }} auto-activate: true - name: Setup BATS From 89aee75267a933253b426fe0b5084149602fc389 Mon Sep 17 00:00:00 2001 From: Tim Van Rillaer Date: Wed, 18 Feb 2026 17:11:00 +0100 Subject: [PATCH 5/7] Configure default shell and conda environment Added default shell configuration for the build step and specified the test environment for conda activation. --- .github/workflows/ci.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index e470e0c..89b9ac6 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -26,6 +26,9 @@ jobs: name: build-linux runs-on: ${{ matrix.os }} + defaults: + run: + shell: bash -el {0} steps: - uses: actions/checkout@v6 - name: Checkout test data @@ -38,7 +41,7 @@ jobs: uses: conda-incubator/setup-miniconda@v3 with: python-version: ${{ matrix.python-version }} - activate-environment: "" + activate-environment: "test-env" environment-file: ${{ matrix.env-file }} auto-activate: true - name: Setup BATS From fe2cb2778eb0826d5b952de31ee9762ff3867397 Mon Sep 17 00:00:00 2001 From: Tim Van Rillaer Date: Wed, 18 Feb 2026 17:19:33 +0100 Subject: [PATCH 6/7] Update minimum Python version to 3.8 --- .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 89b9ac6..329e4a7 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -17,7 +17,7 @@ jobs: strategy: matrix: include: - - python-version: "3.7" + - python-version: "3.8" os: ubuntu-22.04 env-file: "test/environment_min.yml" - python-version: "3.12" From e7430bcaa53c2c8466ca8cc6ee25b5c5fcf14927 Mon Sep 17 00:00:00 2001 From: Tim Van Rillaer Date: Wed, 18 Feb 2026 17:22:08 +0100 Subject: [PATCH 7/7] Set higher max python version --- test/environment_min.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/environment_min.yml b/test/environment_min.yml index 5511755..53bc9c8 100644 --- a/test/environment_min.yml +++ b/test/environment_min.yml @@ -8,7 +8,7 @@ channels: dependencies: - bioconda::mafft=7.407 - bioconda::mmseqs2=11.e1a1c - - python=3.7 # 3.6 needs pip v21 which gives issues + - python=3.8 # 3.7 lacks importlib.metadata - biopython=1.79 - ete3=3.1.2 - numpy=1.18.5