Unverified Commit 0c09d02d authored by José Manuel Domínguez's avatar José Manuel Domínguez Committed by Nicola Soranzo
Browse files

Fix `test_mulled_build.py::test_mulled_build_files_cli` with `use_mamba=True` 

Test `tests/tool_util/mulled/test_mulled_build.py::test_mulled_build_files_cli[True]`, where `[True]` refers to the parameter `use_mamba`, fails because if `conda install --quiet --yes 'mamba='` (the preinstall command) runs before `mamba install -p /usr/local`, then the latter expects either `/usr/local` not to exist or to be an existing environment.

To work this around, create an environment in `/usr/local/env`, but still put it on the expected location `/usr/local` later.
parent 18312cfc

lib/galaxy/tool_util/deps/mulled/invfile.lua

+3 −2
Original line number Diff line number Diff line
@@ -88,13 +88,14 @@ inv.task('build') 
    .using(conda_image)

        .withHostConfig({binds = bind_args})

        .run('/bin/sh', '-c', preinstall

            .. conda_bin .. ' create --quiet --yes -p /usr/local/env --copy  && '

            .. conda_bin .. ' install '

            .. channel_args .. ' '

            .. target_args

            .. ' --strict-channel-priority -p /usr/local --copy --yes '

            .. ' --strict-channel-priority -p /usr/local/env --copy --yes '

            .. verbose

            .. postinstall)

    .wrap('build/dist')

    .wrap('build/dist/env')

        .at('/usr/local')

        .inImage(destination_base_image)

        .as(repo)

lib/galaxy/tool_util/deps/mulled/mulled_search.py

+2 −1
Original line number Diff line number Diff line
@@ -148,7 +148,8 @@ class CondaSearch: 
            elif header_found:

                lines_fields.append(line.split())

        return [

            {"package": line_fields[0], "version": line_fields[1], "build": line_fields[2]} for line_fields in lines_fields

            {"package": line_fields[0], "version": line_fields[1], "build": line_fields[2]}

            for line_fields in lines_fields

        ]