From d6859567d1d9bf032c097aa26bc2b21347dbeb88 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Fri, 17 Jan 2025 15:09:59 +0100 Subject: [PATCH 1/4] remove defaults channel --- planemo/conda.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/planemo/conda.py b/planemo/conda.py index f21e8210b..9346ab5c6 100644 --- a/planemo/conda.py +++ b/planemo/conda.py @@ -40,7 +40,7 @@ if TYPE_CHECKING: from planemo.cli import PlanemoCliContext -BEST_PRACTICE_CHANNELS = ["conda-forge", "bioconda", "defaults"] +BEST_PRACTICE_CHANNELS = ["conda-forge", "bioconda"] def build_conda_context(ctx: "PlanemoCliContext", **kwds) -> CondaContext: From 462c75c54bd22e1fdfc4452f735af2e59e321a09 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Fri, 17 Jan 2025 15:11:26 +0100 Subject: [PATCH 2/4] remove from option's default --- planemo/options.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/planemo/options.py b/planemo/options.py index 867d637c2..462eb5d91 100644 --- a/planemo/options.py +++ b/planemo/options.py @@ -617,7 +617,7 @@ def conda_ensure_channels_option(): use_global_config=True, use_env_var=True, help=("Ensure conda is configured with specified comma separated " "list of channels."), - default="conda-forge,bioconda,defaults", + default="conda-forge,bioconda", ) From 0f619df52ba8dbf714d17918ee2eb0e69846a9f2 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Fri, 17 Jan 2025 15:14:26 +0100 Subject: [PATCH 3/4] eliminate more traces to miniconda --- planemo/options.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/planemo/options.py b/planemo/options.py index 462eb5d91..4198f16c4 100644 --- a/planemo/options.py +++ b/planemo/options.py @@ -637,7 +637,7 @@ def conda_auto_init_option(): default=True, help=( "Conda dependency resolution for Galaxy will auto install " - "conda itself using miniconda if not availabe on conda_prefix." + "conda itself using miniforge if not availabe on conda_prefix." ), ) @@ -2061,7 +2061,7 @@ def mulled_conda_option(): default=None, help=( "Install a specific version of Conda before running the command, by " - "default the version that comes with the continuumio miniconda3 image " + "default the version that comes with the continuumio miniforge image " "will be used under Linux and under Mac OS X Conda will be upgraded to " "to work around a bug in 4.2." ), From b005ce7b1e0faad61b354707bce1519dda5d831e Mon Sep 17 00:00:00 2001 From: M Bernt Date: Fri, 17 Jan 2025 15:52:16 +0100 Subject: [PATCH 4/4] Update planemo/options.py Co-authored-by: Nicola Soranzo --- planemo/options.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/planemo/options.py b/planemo/options.py index 4198f16c4..dee63b1fb 100644 --- a/planemo/options.py +++ b/planemo/options.py @@ -2061,7 +2061,7 @@ def mulled_conda_option(): default=None, help=( "Install a specific version of Conda before running the command, by " - "default the version that comes with the continuumio miniforge image " + "default the version that comes with the miniforge image " "will be used under Linux and under Mac OS X Conda will be upgraded to " "to work around a bug in 4.2." ),