fix: adjust all lints to reflect new outputs: structure

.github/workflows/changevisibility.yml

@@ -10,7 +10,7 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - name: Check Containers and Set Public
         run: |
@@ -20,8 +20,9 @@ jobs:
           QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_BIOCONTAINERS_TOKEN }}
 
       - name: Upload logs
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v6
         with:
           name: logs
           path: biocontainers-*.txt
           retention-days: 7
+

.github/workflows/release-please.yml

@@ -2,6 +2,7 @@ on:
   push:
     branches:
       - master
+  workflow_dispatch:
 
 name: release-please
 
@@ -12,7 +13,7 @@ jobs:
       release_created: ${{ steps.release.outputs.release_created }}
       tag_name: ${{ steps.release.outputs.tag_name }}
     steps:
-      - uses: GoogleCloudPlatform/release-please-action@v4
+      - uses: googleapis/release-please-action@v4
         id: release
         with:
           release-type: python
@@ -23,7 +24,7 @@ jobs:
     needs: release_please
     if: needs.release_please.outputs.release_created
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
 

CHANGELOG.md

@@ -1,5 +1,31 @@
 # Changelog
 
+## [4.1.0](https://github.com/bioconda/bioconda-utils/compare/v4.0.0...v4.1.0) (2026-03-04)
+
+
+### Features
+
+* eliminate redundant host-side solver run for Docker builds ([#1081](https://github.com/bioconda/bioconda-utils/issues/1081)) ([3d4c9e1](https://github.com/bioconda/bioconda-utils/commit/3d4c9e1110ce0f9d7915685f1a43752bdda3e085))
+* pre-solved environments for mulled tests ([#1082](https://github.com/bioconda/bioconda-utils/issues/1082)) ([af1ac9c](https://github.com/bioconda/bioconda-utils/commit/af1ac9c8ddfa17f4055aab065aa61b93973f8c30))
+
+
+### Bug Fixes
+
+* add raise_for_status to CircleCI workflow API call ([#1083](https://github.com/bioconda/bioconda-utils/issues/1083)) ([2f558ee](https://github.com/bioconda/bioconda-utils/commit/2f558ee0664af9fbd4a2435ca8d7001c6c28cb19))
+
+## [4.0.0](https://github.com/bioconda/bioconda-utils/compare/v3.9.2...v4.0.0) (2026-02-11)
+
+
+### ⚠ BREAKING CHANGES
+
+* also find tests under outputs, ensure all outputs have tests, ensure outputs names are different from package name ([#1057](https://github.com/bioconda/bioconda-utils/issues/1057))
+
+### Bug Fixes
+
+* also find tests under outputs, ensure all outputs have tests, ensure outputs names are different from package name ([#1057](https://github.com/bioconda/bioconda-utils/issues/1057)) ([dd17aa7](https://github.com/bioconda/bioconda-utils/commit/dd17aa76b2410901649fb33c14e876452d26be1b))
+* update actions ([#1076](https://github.com/bioconda/bioconda-utils/issues/1076)) ([e301b5c](https://github.com/bioconda/bioconda-utils/commit/e301b5c6d8139ce80fddb7262c9355cf3284320b))
+* Update anaconda-client version to 1.14.* ([#1075](https://github.com/bioconda/bioconda-utils/issues/1075)) ([0bdd2a9](https://github.com/bioconda/bioconda-utils/commit/0bdd2a9202ec84e00c0ec923a24fafe68e9ee3a0)), closes [#1074](https://github.com/bioconda/bioconda-utils/issues/1074)
+
 ## [3.9.2](https://github.com/bioconda/bioconda-utils/compare/v3.9.1...v3.9.2) (2026-01-09)
 
 

bioconda_utils/artifacts.py

@@ -216,6 +216,7 @@ def get_circleci_artifacts(check_run, platform):
     # Use API v2 because v1.1 does not have a workflow endpoint
     url_wf = f"https://circleci.com/api/v2/workflow/{circleci_workflow_id}/job"
     res_wf = requests.get(url_wf, headers=headers)
+    res_wf.raise_for_status()
     json_wf = json.loads(res_wf.text)
 
     if len(json_wf["items"]) == 0:

bioconda_utils/bioconda_utils-requirements.txt

@@ -27,7 +27,7 @@ boltons=25.0.*                #
 jsonschema=4.25.*             # JSON schema verification
 jinja2=3.1.*                  #
 
-anaconda-client=1.13.*        # anaconda_upload
+anaconda-client=1.14.*        # anaconda_upload
 galaxy-tool-util=25.*         # mulled test and container build
 involucro=1.1.*               # mulled test and container build
 skopeo=1.15.*                 # docker upload

bioconda_utils/build.py

@@ -62,6 +62,8 @@ def build(
     dag: Optional[nx.DiGraph] = None,
     skiplist_leafs: bool = False,
     live_logs: bool = True,
+    presolved_mulled_test: bool = True,
+    mulled_upload_target=None,
 ) -> BuildResult:
     """
     Build a single recipe for a single env
@@ -198,6 +200,8 @@ def build(
     if mulled_test:
         logger.info("TEST START via mulled-build %s", recipe)
         mulled_images = []
+        # Use pre-solved test env unless we need the mulled-build image for upload
+        use_presolved = presolved_mulled_test and not mulled_upload_target
         for pkg_path in pkg_paths:
             try:
                 report_resources(f"Starting mulled build for {pkg_path}")
@@ -206,6 +210,7 @@ def build(
                     base_image=base_image,
                     conda_image=mulled_conda_image,
                     live_logs=live_logs,
+                    presolved=use_presolved,
                 )
             except sp.CalledProcessError:
                 logger.error("TEST FAILED: %s", recipe)
@@ -366,6 +371,8 @@ def build_recipes(
     live_logs: bool = True,
     exclude: List[str] = None,
     subdag_depth: int = None,
+    presolved_mulled_test: bool = True,
+    fast_resolve: bool = True,
 ):
     """
     Build one or many bioconda packages.
@@ -482,7 +489,17 @@ def build_recipes(
 
         logger.info("Determining expected packages for %s", recipe)
         try:
-            pkg_paths = utils.get_package_paths(recipe, check_channels, force=force)
+            # When building with Docker, skip the expensive finalized render
+            # on the host since Docker's conda-build will re-solve anyway.
+            # Non-finalized metas use bypass_env_check which avoids costly
+            # dependency resolution. The --no-fast-resolve flag can override this.
+            finalize = (docker_builder is None) if fast_resolve else True
+            pkg_paths = utils.get_package_paths(
+                recipe,
+                check_channels,
+                force=force,
+                finalize=finalize,
+            )
         except utils.DivergentBuildsError as exc:
             logger.error(
                 "BUILD ERROR: packages with divergent build strings in repository "
@@ -521,6 +538,8 @@ def build_recipes(
             record_build_failure=record_build_failures,
             skiplist_leafs=skiplist_leafs,
             live_logs=live_logs,
+            presolved_mulled_test=presolved_mulled_test,
+            mulled_upload_target=mulled_upload_target,
         )
 
         if not res.success:

bioconda_utils/cli.py

@@ -619,6 +619,18 @@ def do_lint(
     action="store_true",
     help="Disable live logging during the build process",
 )
+@arg(
+    "--no-presolved-mulled-test",
+    action="store_true",
+    help="Disable pre-solved mulled tests: always use mulled-build to solve and install "
+    "the test environment from scratch.",
+)
+@arg(
+    "--no-fast-resolve",
+    action="store_true",
+    help="Disable fast resolve: always run the full finalized conda solver on the host, "
+    "even when building with Docker. Useful for debugging build string mismatches.",
+)
 @arg("--exclude", nargs="+", help="Packages to exclude during this run")
 @arg(
     "--subdag-depth",
@@ -652,6 +664,8 @@ def build(
     record_build_failures=False,
     skiplist_leafs=False,
     disable_live_logs=False,
+    no_presolved_mulled_test=False,
+    no_fast_resolve=False,
     exclude=None,
     subdag_depth=None,
 ):
@@ -726,6 +740,8 @@ def build(
         live_logs=(not disable_live_logs),
         exclude=exclude,
         subdag_depth=subdag_depth,
+        presolved_mulled_test=not no_presolved_mulled_test,
+        fast_resolve=not no_fast_resolve,
     )
     exit(0 if success else 1)
 

bioconda_utils/lint/__init__.py

@@ -246,8 +246,20 @@ def run(self, recipe: _recipe.Recipe, fix: bool = False) -> List[LintMessage]:
             for num, src in enumerate(source):
                 self.check_source(src, f"source/{num}")
 
-        # Run depends checks
-        self.check_deps(recipe.get_deps_dict())
+        # Run depends checks, per outputs: package if necessary
+        outputs = recipe.get("outputs", dict())
+        deps = recipe.get_deps_dict()
+        if outputs:
+            for i in range(len(outputs)):
+                output_location = f"outputs/{i}/"
+                # filter down to dependencies for this outputs: package
+                output_deps = dict()
+                for dep in deps:
+                    if any(output_location in d for d in deps[dep]):
+                        output_deps[dep] = deps[dep]
+                self.check_deps(output_deps, output_location)
+        else:
+            self.check_deps(deps, "")
 
         return self.messages
 
@@ -270,7 +282,7 @@ def check_source(self, source: Dict, section: str) -> None:
                    ``source/0`` (1,2,3...).
         """
 
-    def check_deps(self, deps: Dict[str, List[str]]) -> None:
+    def check_deps(self, deps: Dict[str, List[str]], package_location: str) -> None:
         """Execute check on recipe dependencies
 
         Example format for **deps**::
@@ -287,6 +299,12 @@ def check_deps(self, deps: Dict[str, List[str]]) -> None:
         Args:
           deps: Dictionary mapping requirements occurring in the recipe
                 to their locations within the recipe.
+          package_location: Path to the main location for the build and
+                            requirements sections. Empty string for the top
+                            level in single-package recipes, something like
+                            ``outputs/0/`` for recipes with packages specified
+                            in an outputs section.
+
         """
 
     def fix(self, message, data) -> LintMessage:
@@ -438,6 +456,17 @@ class jinja_render_failure(LintCheck):
     """
 
 
+class skipping_recipe(LintCheck):
+    """skipping linting of this recipe as requested
+
+    As specified via ``extra: skip-recipes:``, this recipe is being
+    skipped during linting. This is meant for the linter test
+    suite.
+    """
+
+    severity: Severity = INFO
+
+
 class unknown_check(LintCheck):
     """Something went wrong inside the linter
 
@@ -499,13 +528,11 @@ def __init__(
         )
         self.checks_dag = dag
 
+    def order_and_load_checks(self):
         try:
-            self.checks_ordered = reversed(list(nx.topological_sort(dag)))
+            self.checks_ordered = reversed(list(nx.topological_sort(self.checks_dag)))
         except nx.NetworkXUnfeasible:
             raise RuntimeError("Cycle in LintCheck requirements!")
-        self.reload_checks()
-
-    def reload_checks(self):
         self.check_instances = {str(check): check(self) for check in get_checks()}
 
     def get_skiplist(self) -> Set[str]:
@@ -568,6 +595,7 @@ def lint(self, recipe_names: List[str], fix: bool = False) -> bool:
 
         """
         for recipe_name in utils.tqdm(sorted(recipe_names)):
+            self.order_and_load_checks()
             try:
                 msgs = self.lint_one(recipe_name, fix=fix)
             except Exception:
@@ -597,6 +625,17 @@ def lint_one(self, recipe_name: str, fix: bool = False) -> List[LintMessage]:
             check_cls = recipe_error_to_lint_check.get(exc.__class__, linter_failure)
             return [check_cls.make_message(recipe=recipe, line=getattr(exc, "line"))]
 
+        # collect recipes to skip
+        if isinstance(recipe.get("extra/skip-recipes", []), list):
+            if any(
+                recipe_name.endswith(name) for name in recipe.get("extra/skip-recipes")
+            ):
+                return [
+                    skipping_recipe.make_message(
+                        recipe=recipe,
+                    )
+                ]
+
         # collect checks to skip
         checks_to_skip = set(self.skip[recipe_name])
         checks_to_skip.update(self.exclude)

bioconda_utils/lint/check_build_help.py

@@ -41,7 +41,7 @@ class should_use_compilers(LintCheck):
         "rust",
     )
 
-    def check_deps(self, deps):
+    def check_deps(self, deps, _package_location):
         for compiler in self.compilers:
             for location in deps.get(compiler, []):
                 self.message(section=location)
@@ -55,7 +55,7 @@ class compilers_must_be_in_build(LintCheck):
 
     """
 
-    def check_deps(self, deps):
+    def check_deps(self, deps, _package_location):
         for dep in deps:
             if dep.startswith("compiler_"):
                 for location in deps[dep]:
@@ -101,7 +101,7 @@ def _check_line(line: str) -> bool:
             return True
         return False
 
-    def check_deps(self, deps):
+    def check_deps(self, deps, _package_location):
         if "setuptools" not in deps:
             return  # no setuptools, no problem
 
@@ -127,7 +127,7 @@ class cython_must_be_in_host(LintCheck):
           - cython
     """
 
-    def check_deps(self, deps):
+    def check_deps(self, deps, _package_location):
         if "cython" in deps:
             if any("host" not in location for location in deps["cython"]):
                 self.message()
@@ -146,13 +146,13 @@ class cython_needs_compiler(LintCheck):
 
     severity = WARNING
 
-    def check_deps(self, deps):
+    def check_deps(self, deps, _package_location):
         if "cython" in deps and "compiler_c" not in deps and "compiler_cxx" not in deps:
             self.message()
 
 
 class missing_run_exports(LintCheck):
-    """Recipe should have a run_exports statement that ensures correct pinning in downstream packages
+    """Recipe should have a run_exports statement for each package, ensuring correct pinning in downstream packages
 
     This ensures that the package is automatically pinned to a compatible version if
     it is used as a dependency in another recipe.
@@ -163,6 +163,15 @@ class missing_run_exports(LintCheck):
     libraries) but also for e.g. Python packages, as those might also
     introduce breaking changes in their APIs or command line interfaces.
 
+    A ``run_exports:`` specification should be specified in the relevant
+    ``build:`` section for all packages that are built. This means either:
+    (i) in the main ``build`` section, if only one package is built from this
+        recipe, or:
+    (ii) in each outputs' ``build:`` section, if multiple ``outputs:`` are
+        specified. In this case, the main recipe ``build:`` section does not
+        refer to a package that is being built, but only to the recipe, so a
+        ``run_exports:`` section for it does not make sense.
+
     We distinguish between four cases.
 
     **Case 1:** If the software follows semantic versioning (or it has at least a normal version string (like 1.2.3) and the actual strategy of the devs is unknown), add run_exports to the recipe like this::
@@ -210,6 +219,11 @@ class missing_run_exports(LintCheck):
     """
 
     def check_recipe(self, recipe):
-        build = recipe.meta.get("build", dict())
-        if "run_exports" not in build:
-            self.message()
+        outputs = recipe.get("outputs", dict())
+        if outputs:
+            build_sections = [o.get("build", dict()) for o in outputs]
+        else:
+            build_sections = [recipe.meta.get("build", dict())]
+        for build in build_sections:
+            if "run_exports" not in build:
+                self.message()