feat: Add --mulled-conda-image (#867)

This patch try to add `--mulled-conda-image` to bioconda-utils, after
this patch, users can specify customized mulled test image. Such as
multi-arch case, users can sepcified multi-arch image.

Related: #706

Signed-off-by: Yikun Jiang <yikunkero@gmail.com>
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>

bioconda_utils/build.py

@@ -50,7 +50,8 @@ def build(recipe: str, pkg_paths: List[str] = None,
           channels: List[str] = None,
           docker_builder: docker_utils.RecipeBuilder = None,
           raise_error: bool = False,
-          linter=None) -> BuildResult:
+          linter=None,
+          mulled_conda_image: str = pkg_test.MULLED_CONDA_IMAGE) -> BuildResult:
     """
     Build a single recipe for a single env
 
@@ -149,7 +150,8 @@ def build(recipe: str, pkg_paths: List[str] = None,
         mulled_images = []
         for pkg_path in pkg_paths:
             try:
-                pkg_test.test_package(pkg_path, base_image=base_image)
+                pkg_test.test_package(pkg_path, base_image=base_image,
+                                      conda_image=mulled_conda_image)
             except sp.CalledProcessError:
                 logger.error('TEST FAILED: %s', recipe)
                 return BuildResult(False, None)
@@ -225,7 +227,8 @@ def build_recipes(recipe_folder: str, config_path: str, recipes: List[str],
                   lint_exclude: List[str] = None,
                   n_workers: int = 1,
                   worker_offset: int = 0,
-                  keep_old_work: bool = False):
+                  keep_old_work: bool = False,
+                  mulled_conda_image: str = pkg_test.MULLED_CONDA_IMAGE):
     """
     Build one or many bioconda packages.
 
@@ -343,7 +346,8 @@ def build_recipes(recipe_folder: str, config_path: str, recipes: List[str],
                     mulled_test=mulled_test,
                     channels=config['channels'],
                     docker_builder=docker_builder,
-                    linter=linter)
+                    linter=linter,
+                    mulled_conda_image=mulled_conda_image)
 
         if not res.success:
             failed.append(recipe)

bioconda_utils/cli.py

@@ -35,6 +35,7 @@
 from . import cran_skeleton
 from . import update_pinnings
 from . import graph
+from . import pkg_test
 from .githandler import BiocondaRepo, install_gpg_key
 
 logger = logging.getLogger(__name__)
@@ -379,6 +380,8 @@ def do_lint(recipe_folder, config, packages="*", cache=None, list_checks=False,
      help='Build packages in docker container.')
 @arg('--mulled-test', action='store_true', help="Run a mulled-build test on the built package")
 @arg('--mulled-upload-target', help="Provide a quay.io target to push mulled docker images to.")
+@arg('--mulled-conda-image', help='''Conda Docker image to install the package with during
+     the mulled based tests.''')
 @arg('--build_script_template', help='''Filename to optionally replace build
      script template used by the Docker container. By default use
      docker_utils.BUILD_SCRIPT_TEMPLATE. Only used if --docker is True.''')
@@ -428,7 +431,8 @@ def build(recipe_folder, config, packages="*", git_range=None, testonly=False,
           force=False, docker=None, mulled_test=False, build_script_template=None,
           pkg_dir=None, anaconda_upload=False, mulled_upload_target=None,
           build_image=False, keep_image=False, lint=False, lint_exclude=None,
-          check_channels=None, n_workers=1, worker_offset=0, keep_old_work=False):
+          check_channels=None, n_workers=1, worker_offset=0, keep_old_work=False,
+          mulled_conda_image=pkg_test.MULLED_CONDA_IMAGE):
     cfg = utils.load_config(config)
     setup = cfg.get('setup', None)
     if setup:
@@ -476,7 +480,8 @@ def build(recipe_folder, config, packages="*", git_range=None, testonly=False,
                             label=label,
                             n_workers=n_workers,
                             worker_offset=worker_offset,
-                            keep_old_work=keep_old_work)
+                            keep_old_work=keep_old_work,
+                            mulled_conda_image=mulled_conda_image)
     exit(0 if success else 1)
 
 

bioconda_utils/pkg_test.py

@@ -17,7 +17,6 @@
 
 logger = logging.getLogger(__name__)
 
-# TODO: Make this configurable in bioconda_utils.build and bioconda_utils.cli.
 MULLED_CONDA_IMAGE = "quay.io/bioconda/create-env:latest"