def lint_requirements_in_conda(tool_source, lint_ctx):
"""Check requirements of tool source against best practice Conda channels."""
conda_targets = tool_source_conda_targets(tool_source)
if not conda_targets:
lint_ctx.warn(
"No valid package requirement tags found to check against Conda.")
return
for conda_target in conda_targets:
(best_hit, exact) = best_practice_search(conda_target)
conda_target_str = conda_target.package
if conda_target.version:
conda_target_str += "@%s" % (conda_target.version)
if best_hit and exact:
template = "Requirement [%s] matches target in best practice Conda channel [%s]."
message = template % (conda_target_str, best_hit.get("channel"))
lint_ctx.info(message)
elif best_hit:
template = "Requirement [%s] doesn't exactly match available version [%s] in best practice Conda channel [%s]."
message = template % (conda_target_str, best_hit['version'],
best_hit.get("channel"))
lint_ctx.warn(message)
else:
template = "Requirement [%s] doesn't match any recipe in a best practice conda channel [%s]."
message = template % (conda_target_str, BEST_PRACTICE_CHANNELS)
lint_ctx.warn(message)
def cli(ctx, paths, **kwds):
"""Register multi-requirement containers as needed.
BioContainers publishes all Bioconda packages automatically as individual
container images. These however are not enough for tools with multiple
best-practice requirements. Such requirements should be recorded and published
so that a container can be created and registered for these tools.
"""
registry_target = RegistryTarget(ctx, **kwds)
conda_context = build_conda_context(ctx, **kwds)
combinations_added = 0
conda_targets_list, tool_paths_list = collect_conda_target_lists_and_tool_paths(ctx, paths, recursive=kwds["recursive"])
for conda_targets, tool_paths in zip(conda_targets_list, tool_paths_list):
ctx.vlog("Handling conda_targets [%s]" % conda_targets)
mulled_targets = conda_to_mulled_targets(conda_targets)
mulled_targets_str = "- " + "\n- ".join(map(conda_build_target_str, mulled_targets))
if len(mulled_targets) < 2:
ctx.vlog("Skipping registeration, fewer than 2 targets discovered.")
# Skip these for now, we will want to revisit this for conda-forge dependencies and such.
continue
best_practice_requirements = True
for conda_target in conda_targets:
best_hit, exact = best_practice_search(conda_target, conda_context=conda_context)
if not best_hit or not exact:
ctx.vlog("Target [%s] is not available in best practice channels - skipping" % conda_target)
best_practice_requirements = False
if not best_practice_requirements:
continue
name = v2_image_name(mulled_targets)
tag = "0"
name_and_tag = "%s-%s" % (name, tag)
target_filename = os.path.join(registry_target.output_directory, "%s.tsv" % name_and_tag)
ctx.vlog("Target filename for registeration is [%s]" % target_filename)
if os.path.exists(target_filename):
ctx.vlog("Target file already exists, skipping")
continue
namespace = kwds["mulled_namespace"]
repo_data = quay_repository(namespace, name)
if "tags" in repo_data:
ctx.vlog("quay repository already exists, skipping")
continue
if registry_target.has_pull_request_for(name):
ctx.vlog("Found matching open pull request for [%s], skipping" % name)
continue
registry_target.write_targets(ctx, target_filename, mulled_targets)
tools_str = "\n".join(map(lambda p: "- " + os.path.basename(p), tool_paths))
registry_target.handle_pull_request(ctx, name, target_filename, mulled_targets_str, tools_str, **kwds)
combinations_added += 1
def lint_requirements_in_conda(tool_source, lint_ctx):
"""Check requirements of tool source against best practice Conda channels."""
conda_targets = tool_source_conda_targets(tool_source)
if not conda_targets:
lint_ctx.warn("No valid package requirement tags found to check against Conda.")
return
for conda_target in conda_targets:
(best_hit, exact) = best_practice_search(conda_target)
conda_target_str = conda_target.package
if conda_target.version:
conda_target_str += "@%s" % (conda_target.version)
if best_hit and exact:
template = "Requirement [%s] matches target in best practice Conda channel [%s]."
message = template % (conda_target_str, best_hit.get("channel"))
lint_ctx.info(message)
elif best_hit:
template = "Requirement [%s] doesn't exactly match available version [%s] in best practice Conda channel [%s]."
message = template % (conda_target_str, best_hit['version'], best_hit.get("channel"))
lint_ctx.warn(message)
else:
template = "Requirement [%s] doesn't match any recipe in a best practice conda channel [%s]."
message = template % (conda_target_str, BEST_PRACTICE_CHANNELS)
lint_ctx.warn(message)
def cli(ctx, paths, **kwds):
"""Register multi-requirement containers as needed.
BioContainers publishes all Bioconda packages automatically as individual
container images. These however are not enough for tools with multiple
best-practice requirements. Such requirements should be recorded and published
so that a container can be created and registered for these tools.
"""
registry_target = RegistryTarget(ctx, **kwds)
conda_context = build_conda_context(ctx, **kwds)
combinations_added = 0
conda_targets_list, tool_paths_list = collect_conda_target_lists_and_tool_paths(
ctx, paths, recursive=kwds["recursive"])
for conda_targets, tool_paths in zip(conda_targets_list, tool_paths_list):
ctx.vlog("Handling conda_targets [%s]" % conda_targets)
mulled_targets = conda_to_mulled_targets(conda_targets)
mulled_targets_str = "- " + "\n- ".join(
map(conda_build_target_str, mulled_targets))
best_practice_requirements = True
for conda_target in conda_targets:
best_hit, exact = best_practice_search(
conda_target,
conda_context=conda_context,
platform=BIOCONTAINERS_PLATFORM)
if not best_hit:
ctx.log(
"Target [%s] is not available in best practice channels - skipping"
% conda_target)
best_practice_requirements = False
if not exact:
ctx.log(
"Target version [%s] for package [%s] is not available in best practice channels - please specify the full version",
conda_target.version, conda_target.package)
if not best_practice_requirements:
continue
base_image = DEFAULT_BASE_IMAGE
for conda_target in conda_targets:
base_image = base_image_for_targets([conda_target],
conda_context=conda_context)
if base_image != DEFAULT_BASE_IMAGE:
ctx.log("%s requires '%s' as base image" %
(conda_target, base_image))
break
if len(mulled_targets) < 1:
ctx.log("Skipping registration, no targets discovered.")
continue
name = v2_image_name(mulled_targets)
tag = "0"
name_and_tag = "%s-%s" % (name, tag)
target_filename = os.path.join(registry_target.output_directory,
"%s.tsv" % name_and_tag)
if os.path.exists(target_filename):
ctx.log("Target file '%s' already exists, skipping" %
target_filename)
continue
if targets_to_mulled_name(mulled_targets,
hash_func='v2',
namespace=kwds["mulled_namespace"]):
ctx.vlog("quay repository already exists, skipping")
continue
if registry_target.has_pull_request_for(name):
ctx.vlog("Found matching open pull request for [%s], skipping" %
name)
continue
registry_target.write_targets(ctx, target_filename, mulled_targets,
tag, base_image)
tools_str = "\n".join(
map(lambda p: "- " + os.path.basename(p), tool_paths))
registry_target.handle_pull_request(ctx, name, target_filename,
mulled_targets_str, tools_str,
base_image, **kwds)
combinations_added += 1