From 68af81b6448ecb12b123cdb733071c93f6042ea0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Miguel=20=C3=81lvarez=20Herrera?= Date: Mon, 9 Feb 2026 13:35:08 +0100 Subject: [PATCH 1/5] fix: pin setuptools to avoid deprecation error in Snakemake 7 --- .test/environment_v7.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.test/environment_v7.yaml b/.test/environment_v7.yaml index 8e2b008..db4f147 100644 --- a/.test/environment_v7.yaml +++ b/.test/environment_v7.yaml @@ -7,3 +7,4 @@ dependencies: - python==3.11.6 - snakemake==7.32.4 - pulp<2.8 + - setuptools<81 From d81e9ff2cc1265cf0a983fad8da9af861e792413 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Miguel=20=C3=81lvarez=20Herrera?= Date: Mon, 9 Feb 2026 13:35:27 +0100 Subject: [PATCH 2/5] refactor: update deprecated setup-miniconda option --- .github/workflows/install.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/install.yml b/.github/workflows/install.yml index a74cc81..9a4daa3 100644 --- a/.github/workflows/install.yml +++ b/.github/workflows/install.yml @@ -14,7 +14,6 @@ jobs: with: channel-priority: strict activate-environment: snakemake - auto-activate-base: false environment-file: .test/environment_v7.yaml - name: Create environments shell: bash -el {0} @@ -30,7 +29,6 @@ jobs: with: channel-priority: strict activate-environment: snakemake - auto-activate-base: false environment-file: .test/environment_v7.yaml - name: Dry run shell: bash -el {0} From 86f27e4d107b0e38f86376fa68fdf064d96597ef Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Miguel=20=C3=81lvarez=20Herrera?= Date: Mon, 9 Feb 2026 13:36:17 +0100 Subject: [PATCH 3/5] chore: update test version string --- .test/Snakefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.test/Snakefile b/.test/Snakefile index a8dd4aa..7c3d4f8 100644 --- a/.test/Snakefile +++ b/.test/Snakefile @@ -8,7 +8,7 @@ import subprocess min_version("7.19") # Workflow version -__version__ = "1.3.0" +__version__ = "test" # Rules include: "../workflow/core.smk" From d1b2d1256f2e028cbd259cd0a98af00aaf0d20b8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Miguel=20=C3=81lvarez=20Herrera?= Date: Mon, 9 Feb 2026 16:47:38 +0100 Subject: [PATCH 4/5] build: update pangolin environment Bumps version and adds nodefaults channel. Bounding setuptools avoids ModuleNotFoundError when pangolin tries to import pkg_resources (deprecated, see https://setuptools.pypa.io/en/latest/pkg_resources.html and cov-lineages/pangolin#570). --- workflow/envs/pangolin.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/workflow/envs/pangolin.yaml b/workflow/envs/pangolin.yaml index 63bc184..a409b27 100644 --- a/workflow/envs/pangolin.yaml +++ b/workflow/envs/pangolin.yaml @@ -1,5 +1,7 @@ channels: - conda-forge - bioconda + - nodefaults dependencies: - - pangolin==4.3.1 + - pangolin==4.3.4 + - setuptools<81 From 5cabedcb86e993cf286afd2fc8de661360d9bb54 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Miguel=20=C3=81lvarez=20Herrera?= Date: Mon, 9 Feb 2026 16:49:18 +0100 Subject: [PATCH 5/5] build: update pangolin environment in Dockerfile --- Dockerfile | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/Dockerfile b/Dockerfile index 2bb0e5a..6c2556e 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,6 +1,6 @@ FROM condaforge/miniforge3:latest LABEL io.github.snakemake.containerized="true" -LABEL io.github.snakemake.conda_env_hash="a74592ad8bd4ec05cb4d3f2bde91dd12ba674df1828dc48cc7e2c39b95aed05c" +LABEL io.github.snakemake.conda_env_hash="ed26b44bdff1bc9f7a99d3830ae812bf262f78427b95a45fa1ac1ce255c5f054" # Step 2: Retrieve conda environments @@ -89,14 +89,16 @@ COPY workflow/envs/nextalign.yaml /conda-envs/04a3347f94ddf7e21c34bc49e5246076/e # Conda environment: # source: workflow/envs/pangolin.yaml -# prefix: /conda-envs/fd645c541ee7a3d43fb9167441b77888 +# prefix: /conda-envs/fb978640cd765c8a63bbcdc01f3a206b # channels: # - conda-forge # - bioconda +# - nodefaults # dependencies: -# - pangolin==4.3.1 -RUN mkdir -p /conda-envs/fd645c541ee7a3d43fb9167441b77888 -COPY workflow/envs/pangolin.yaml /conda-envs/fd645c541ee7a3d43fb9167441b77888/environment.yaml +# - pangolin==4.3.4 +# - setuptools<81 +RUN mkdir -p /conda-envs/fb978640cd765c8a63bbcdc01f3a206b +COPY workflow/envs/pangolin.yaml /conda-envs/fb978640cd765c8a63bbcdc01f3a206b/environment.yaml # Conda environment: # source: workflow/envs/quarto_render.yaml @@ -169,7 +171,7 @@ RUN conda env create --prefix /conda-envs/9c24a867826615972cc288081976e7fc --fil conda env create --prefix /conda-envs/3fad3c9cdfa40bee9404f6a2e8fda69f --file /conda-envs/3fad3c9cdfa40bee9404f6a2e8fda69f/environment.yaml && \ conda env create --prefix /conda-envs/0a608afb24723cb6fa8aef748f5efbc8 --file /conda-envs/0a608afb24723cb6fa8aef748f5efbc8/environment.yaml && \ conda env create --prefix /conda-envs/04a3347f94ddf7e21c34bc49e5246076 --file /conda-envs/04a3347f94ddf7e21c34bc49e5246076/environment.yaml && \ - conda env create --prefix /conda-envs/fd645c541ee7a3d43fb9167441b77888 --file /conda-envs/fd645c541ee7a3d43fb9167441b77888/environment.yaml && \ + conda env create --prefix /conda-envs/fb978640cd765c8a63bbcdc01f3a206b --file /conda-envs/fb978640cd765c8a63bbcdc01f3a206b/environment.yaml && \ conda env create --prefix /conda-envs/96f3c1cec4b3ce5d72f708992272e9c1 --file /conda-envs/96f3c1cec4b3ce5d72f708992272e9c1/environment.yaml && \ conda env create --prefix /conda-envs/8ad6cdcf265d30289788da99d5bf9fff --file /conda-envs/8ad6cdcf265d30289788da99d5bf9fff/environment.yaml && \ conda env create --prefix /conda-envs/0adafb79cb1bec58ef4c77bf4cca4f95 --file /conda-envs/0adafb79cb1bec58ef4c77bf4cca4f95/environment.yaml && \