From 883c4c4533cc04e65abb70f2b529d73c79bc5cd6 Mon Sep 17 00:00:00 2001 From: Radovan Bast Date: Sat, 5 Apr 2025 13:24:11 +0200 Subject: [PATCH 1/2] update software environment --- environment.yml | 34 ++++++++++++++++------------------ 1 file changed, 16 insertions(+), 18 deletions(-) diff --git a/environment.yml b/environment.yml index bc3498b..18c96a0 100644 --- a/environment.yml +++ b/environment.yml @@ -1,25 +1,23 @@ name: coderefinery channels: - conda-forge - - defaults - bioconda dependencies: - - python>=3.10 + - python>=3.10,<3.14 - click=8.1.7 - - ipywidgets=8.1.2 - - jupyterlab=4.1.2 - - jupyterlab-git=0.50.0 - - matplotlib=3.8.3 - - myst-parser=2.0.0 - - nbdime=4.0.1 - - numpy=1.26.4 - - pandas=2.2.1 - - pytest=8.0.2 - - pytest-cov=4.1.0 + - ipywidgets=8.1.5 + - jupyterlab=4.4.0 + - jupyterlab-git=0.51.1 + - matplotlib=3.10.1 + - myst-parser=4.0.1 + - nbdime=4.0.2 + - numpy=2.2.4 + - pandas=2.2.3 + - pytest=8.3.5 + - pytest-cov=6.0.0 - seaborn=0.13.2 - - snakemake-minimal=8.5.3 - - pulp<2.8.0 - - sphinx=7.2.6 - - sphinx-autobuild=2024.2.4 - - sphinx_rtd_theme=2.0.0 - - sphinx-autodoc2 + - snakemake-minimal=9.1.7 + - sphinx=8.2.3 + - sphinx-autobuild=2024.10.3 + - sphinx_rtd_theme=3.0.1 + - sphinx-autodoc2=0.5.0 From c6d31aff0f6010d0561ccf771d063b7ad935402a Mon Sep 17 00:00:00 2001 From: Radovan Bast Date: Sat, 5 Apr 2025 13:37:17 +0200 Subject: [PATCH 2/2] make the requirements.txt versions match environment.yml --- requirements.txt | 30 +++++++++++++++--------------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/requirements.txt b/requirements.txt index 4f6159f..0ef24ec 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,17 +1,17 @@ click==8.1.7 -ipywidgets==8.1.2 -jupyterlab==4.1.2 -jupyterlab-git==0.50.0 -matplotlib==3.8.3 -myst-parser==2.0.0 -nbdime==4.0.1 -numpy==1.26.4 -pandas==2.2.1 -pytest==8.0.2 -pytest-cov==4.1.0 +ipywidgets==8.1.5 +jupyterlab==4.4.0 +jupyterlab-git==0.51.1 +matplotlib==3.10.1 +myst-parser==4.0.1 +nbdime==4.0.2 +numpy==2.2.4 +pandas==2.2.3 +pytest==8.3.5 +pytest-cov==6.0.0 seaborn==0.13.2 -snakemake==8.5.3 -pulp<2.8.0 -sphinx==7.2.6 -sphinx-autobuild==2024.2.4 -sphinx_rtd_theme==2.0.0 +snakemake==9.1.7 +sphinx==8.2.3 +sphinx-autobuild==2024.10.3 +sphinx_rtd_theme==3.0.1 +sphinx-autodoc2==0.5.0