From f1d963f2ab783af1d8abf8a3e2968f926531e11c Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Fri, 19 Sep 2025 14:37:39 +0100 Subject: [PATCH 1/2] Enable dependabot version updates for GitHub actions --- .github/dependabot.yml | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 .github/dependabot.yml diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 000000000..6a1e6032c --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,12 @@ +# To get started with Dependabot version updates, you'll need to specify which +# package ecosystems to update and where the package manifests are located. +# Please see the documentation for all configuration options: +# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file + +version: 2 +updates: + # Enable version updates for GitHub Actions + - package-ecosystem: "github-actions" + directory: "/" + schedule: + interval: "weekly" From fa45dc6a7dab3d1babf0fb81af0533a62abd7428 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Sat, 20 Sep 2025 18:21:49 +0100 Subject: [PATCH 2/2] Deprecate the redudant ``--postgres`` option Equivalent to `--database_type postgres`. Needed for Click 8.3.0, which reworked the handling of `flag_value` and `default`: https://click.palletsprojects.com/en/stable/changes/#version-8-3-0 Here the default (`None`) of `--postgres` overwrote the default (`auto`) of `--database_type`, causing this error: ``` AssertionError: Planemo command [profile_create profilejobtest] resulted in unexpected exit code [1], expected exit code [0]]. Command output [] Exception [Unknown database type [None].] ``` The alternative solution of adding `default="auto"` to the `--postgres` option would fail the assert at https://github.com/galaxyproject/planemo/blob/ac2191df56b4de32cca239e3f257aa22f80b7ba0/planemo/context.py#L81 --- planemo/options.py | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/planemo/options.py b/planemo/options.py index 5044a7b74..789fb39d9 100644 --- a/planemo/options.py +++ b/planemo/options.py @@ -1706,12 +1706,18 @@ def database_identifier_argument(): ) +def postgres_option_callback(ctx, param, value): + if value: + ctx.fail("The `--postgres` option is deprecated, use `--database_type postgres` instead.") + return value + + def postgres_datatype_type_option(): - return planemo_option( + return click.option( "--postgres", - "database_type", - flag_value="postgres", - help=("Use postgres database type."), + is_flag=True, + hidden=True, + callback=postgres_option_callback, )