containers obj

nf-core · JulianFlesch · Dec 2, 2025 · Dec 2, 2025 · Dec 2, 2025 · Dec 2, 2025
commit 8328f6fdb7980156945438a10d3e722a7d025ffb
diff --git a/nf_core/modules/containers.py b/nf_core/modules/containers.py
@@ -1 +1,108 @@
-import logging
+import logging
+from pathlib import Path
+
+import yaml
+
+log = logging.getLogger(__name__)
+
+
+class ModuleContainers:
+    """
+    Helpers for building, linting and listing module containers.
+    """
+
+    def __init__( # not sure how accurate this is...
+        self,
+        directory: str | Path = ".",
+        remote_url: str | None = None,
+        branch: str | None = None,
+        no_pull: bool = False,
+        hide_progress: bool | None = None,
+    ):
+        self.directory = Path(directory)
+        self.remote_url = remote_url
+        self.branch = branch
+        self.no_pull = no_pull
+        self.hide_progress = hide_progress
+
+    def create(self, module: str, await_: bool = False) -> list[list[str]]:
+        """
+        Build docker and singularity containers for linux/amd64 and linux/arm64 using wave.
+        """
+        # module_dir = self._resolve_module_dir(module)
+        # env_path = self._environment_path(module_dir)
+
+        commands: list[list[str]] = []
+        for profile in ["docker", "singularity"]:
+            for platform in ["linux/amd64", "linux/arm64"]:
+                cmd = ["wave", "--conda-file", str(env_path), "--freeze", "--platform", platform]
+                # here "--tower-token" ${{ secrets.TOWER_ACCESS_TOKEN }} --tower-workspace-id ${{ secrets.TOWER_WORKSPACE_ID }}]
+                if profile == "singularity":
+                    cmd.append("--singularity")
+                if await_:
+                    cmd.append("--await")
+                commands.append(cmd)
+        return commands
+
+    # def conda_lock(self, module: str) -> list[str]:
+    #     """
+    #     Build a Docker linux/arm64 container and fetch the conda lock file using wave.
+    #     """
+    #     module_dir = self._resolve_module_dir(module)
+    #     env_path = self._environment_path(module_dir)
+    #     return ["wave", "--conda-file", str(env_path), "--freeze", "--platform", "linux/arm64", "--await"]
+
+    # def lint(self, module: str) -> list[str]:
+    #     """
+    #     Confirm containers are defined for the module.
+    #     """
+    #     return self._containers_from_meta(self._resolve_module_dir(module))
+
+    # def list_containers(self, module: str) -> list[str]:
+    #     """
+    #     Return containers defined in the module meta.yml.
+    #     """
+    #     return self._containers_from_meta(self._resolve_module_dir(module))
+
+    def _resolve_module_dir(self, module: str) -> Path:
+        if module is None:
+            raise UserWarning("Please specify a module name.")
+
+        module_path = Path(module)
+        if module_path.parts and module_path.parts[0] == "nf-core":
+            module_path = Path(*module_path.parts[1:])
+
+        module_dir = self.directory / "modules" / "nf-core" / module_path
+        if not module_dir.exists():
+            raise LookupError(f"Module '{module}' not found at {module_dir}")
+        return module_dir
+
+    @staticmethod
+    def _environment_path(module_dir: Path) -> Path:
+        env_path = module_dir / "environment.yml"
+        if not env_path.exists():
+            raise FileNotFoundError(f"environment.yml not found for module at {module_dir}")
+        return env_path
+
+    # @staticmethod
+    # def _containers_from_meta(module_dir: Path) -> list[str]:
+    #     meta_path = module_dir / "meta.yml"
+    #     if not meta_path.exists():
+    #         raise FileNotFoundError(f"meta.yml not found for module at {module_dir}")
+
+    #     with open(meta_path) as fh:
+    #         meta = yaml.safe_load(fh) or {}
+
+    #     containers = meta.get("containers")
+    #     if containers is None:
+    #         raise UserWarning("No containers defined in meta.yml")
+    #     if not isinstance(containers, list):
+    #         raise ValueError("Expected 'containers' to be a list in meta.yml")
+
+    #     cleaned = [c for c in containers if c is not None and str(c).strip()]
+    #     if len(cleaned) != len(containers):
+    #         raise UserWarning("Empty container entries found in meta.yml")
+    #     if len(cleaned) == 0:
+    #         raise UserWarning("No containers defined in meta.yml")
+
+    #     return cleaned