From 1790c34631488d6260463958c08839f7bbc4f52a Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Thu, 14 Sep 2023 16:58:55 +0200 Subject: [PATCH 1/4] update upper bound for galaxy packages --- requirements.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/requirements.txt b/requirements.txt index b33d9e42d..080f8f932 100644 --- a/requirements.txt +++ b/requirements.txt @@ -3,8 +3,8 @@ bioblend>=1.0.0 click!=8.0.2 cwltool>=1.0.20191225192155 ephemeris>=0.10.3 -galaxy-tool-util>=23.0,<23.1 -galaxy-util[template]>=23.0,<23.1 +galaxy-tool-util>=23.0,<24.0 +galaxy-util[template]>=23.0,<24.0 glob2 gxformat2>=0.14.0 h5py From 6055c7450beaa1366958242ac925dcf04827bf85 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Mon, 13 Nov 2023 10:33:56 +0100 Subject: [PATCH 2/4] conda build: use exit code --- planemo/commands/cmd_conda_build.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/planemo/commands/cmd_conda_build.py b/planemo/commands/cmd_conda_build.py index d0a24a5e6..4b5aab13f 100644 --- a/planemo/commands/cmd_conda_build.py +++ b/planemo/commands/cmd_conda_build.py @@ -24,5 +24,7 @@ def cli(ctx: "PlanemoCliContext", paths: Tuple[str], **kwds) -> None: # Force conda_use_local for building... kwds["conda_use_local"] = True conda_context = build_conda_context(ctx, handle_auto_init=True, **kwds) - if conda_context.exec_command("build", paths) != 0: + exit_code = conda_context.exec_command("build", paths) + if exit_code: error(f"Failed to build [{' '.join(paths)}] with conda.") + ctx.exit(exit_code) From 1f694f590fb1665ac11741d40d65abeb1d3c29e2 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Mon, 13 Nov 2023 11:25:04 +0100 Subject: [PATCH 3/4] conda_search: also use exit code --- planemo/commands/cmd_conda_search.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/planemo/commands/cmd_conda_search.py b/planemo/commands/cmd_conda_search.py index 1faa974f7..fea2e4022 100644 --- a/planemo/commands/cmd_conda_search.py +++ b/planemo/commands/cmd_conda_search.py @@ -30,4 +30,5 @@ def cli(ctx, term, **kwds): if conda_context.conda_version >= VERSION_4_DOT_4: term = "*%s*" % term args = conda_context._override_channels_args + [term] - conda_context.exec_command("search", args) + exit_code = conda_context.exec_command("search", args) + ctx.exit(exit_code) From b6f3b28b96a4cfd856659d9b8d21426c476980f3 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Mon, 13 Nov 2023 16:07:42 +0100 Subject: [PATCH 4/4] conda_install: use exit code --- planemo/commands/cmd_conda_install.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/planemo/commands/cmd_conda_install.py b/planemo/commands/cmd_conda_install.py index 835f7c072..71801be95 100644 --- a/planemo/commands/cmd_conda_install.py +++ b/planemo/commands/cmd_conda_install.py @@ -28,4 +28,5 @@ def cli(ctx, paths, **kwds): conda_target, conda_context=conda_context, skip_environment=kwds.get("global", False) ) return_codes.append(return_code) - return coalesce_return_codes(return_codes, assert_at_least_one=True) + exit_code = coalesce_return_codes(return_codes, assert_at_least_one=True) + ctx.exit(exit_code)