[WIP] Command to generate pipeline container config files

nf_core/components/components_utils.py

@@ -9,6 +9,7 @@
 
 import nf_core.utils
 from nf_core.modules.modules_repo import ModulesRepo
+from nf_core.pipelines.containers_utils import ContainerConfigs
 
 log = logging.getLogger(__name__)
 
@@ -279,3 +280,10 @@ def _iterate_input_output(type) -> DictWithStrAndTuple:
     # If the tool name was not found in the response
     log.warning(f"Could not find an EDAM ontology term for '{tool_name}'")
     return None
+
+
+def try_generate_container_configs(directory: str | Path, path: str):
+    try:
+        ContainerConfigs(directory, path).generate_container_configs()
+    except UserWarning as e:
+        log.warning(f"Could not regenerate container configuration files: {e}")

nf_core/components/install.py

@@ -16,13 +16,13 @@
 from nf_core.components.components_utils import (
     get_components_to_install,
     prompt_component_version_sha,
+    try_generate_container_configs,
 )
 from nf_core.components.constants import (
     NF_CORE_MODULES_NAME,
 )
 from nf_core.modules.modules_json import ModulesJson
 from nf_core.modules.modules_repo import ModulesRepo
-from nf_core.pipelines.containers_utils import ContainerConfigs
 
 log = logging.getLogger(__name__)
 
@@ -170,10 +170,7 @@ def install(self, component: str | dict[str, str], silent: bool = False) -> bool
 
         # Regenerate container configuration files for the pipeline when modules are installed
         if self.component_type == "modules":
-            try:
-                ContainerConfigs(self.directory, self.modules_repo.repo_path).generate_container_configs()
-            except UserWarning as e:
-                log.warning(f"Could not regenerate container configuration files: {e}")
+            try_generate_container_configs(self.directory, self.modules_repo.repo_path)
 
         if not silent:
             modules_json.load()

nf_core/components/remove.py

@@ -8,8 +8,8 @@
 
 import nf_core.utils
 from nf_core.components.components_command import ComponentCommand
+from nf_core.components.components_utils import try_generate_container_configs
 from nf_core.modules.modules_json import ModulesJson
-from nf_core.pipelines.containers_utils import ContainerConfigs
 
 from .install import ComponentInstall
 
@@ -175,10 +175,7 @@ def remove(self, component, repo_url=None, repo_path=None, removed_by=None, remo
                         removed_components.append(component_name.replace("/", "_"))
             # Regenerate container configuration files for the pipeline when modules are removed
             if self.component_type == "modules":
-                try:
-                    ContainerConfigs(self.directory, repo_path).generate_container_configs()
-                except UserWarning as e:
-                    log.warning(f"Could not regenerate container configuration files: {e}")
+                try_generate_container_configs(self.directory, repo_path)
 
             # print removed dependencies
             if removed_components:

nf_core/components/update.py

@@ -13,12 +13,12 @@
 from nf_core.components.components_utils import (
     get_components_to_install,
     prompt_component_version_sha,
+    try_generate_container_configs,
 )
 from nf_core.components.install import ComponentInstall
 from nf_core.components.remove import ComponentRemove
 from nf_core.modules.modules_json import ModulesJson
 from nf_core.modules.modules_repo import ModulesRepo
-from nf_core.pipelines.containers_utils import ContainerConfigs
 from nf_core.utils import plural_es, plural_s, plural_y
 
 log = logging.getLogger(__name__)
@@ -302,10 +302,7 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr
 
                 # Regenerate container configuration files for the pipeline when modules are updated
                 if self.component_type == "modules":
-                    try:
-                        ContainerConfigs(self.directory, modules_repo.repo_path).generate_container_configs()
-                    except UserWarning as e:
-                        log.warning(f"Could not regenerate container configuration files: {e}")
+                    try_generate_container_configs(self.directory, modules_repo.repo_path)
                 recursive_update = True
                 modules_to_update, subworkflows_to_update = self.get_components_to_update(component)
                 if not silent and len(modules_to_update + subworkflows_to_update) > 0:

nf_core/pipelines/containers_utils.py

@@ -106,53 +106,22 @@ def generate_all_container_configs(self, default_config: str) -> None:
                 log.warning(f"Could not find meta.yml for {module_name}")
                 continue
 
-            try:
-                containers["docker_arm64"][module_name] = meta["containers"]["docker"]["linux_arm64"]["name"]
-            except KeyError:
-                log.warning(f"Could not find docker linux_arm64 container for {module_name}")
-                continue
-            try:
-                containers["singularity_oras_amd64"][module_name] = meta["containers"]["singularity"]["linux_amd64"][
-                    "name"
-                ]
-            except KeyError:
-                log.warning(f"Could not find singularity linux_amd64 oras container for {module_name}")
-                continue
-            try:
-                containers["singularity_oras_arm64"][module_name] = meta["containers"]["singularity"]["linux_arm64"][
-                    "name"
-                ]
-            except KeyError:
-                log.warning(f"Could not find singularity linux_arm64 oras container for {module_name}")
-                continue
-            try:
-                containers["singularity_https_amd64"][module_name] = meta["containers"]["singularity"]["linux_amd64"][
-                    "https"
-                ]
-            except KeyError:
-                log.warning(f"Could not find singularity linux_amd64 https URL for {module_name}")
-                continue
-            try:
-                containers["singularity_https_arm64"][module_name] = meta["containers"]["singularity"]["linux_arm64"][
-                    "https"
-                ]
-            except KeyError:
-                log.warning(f"Could not find singularity linux_arm64 https URL for {module_name}")
-                continue
-            try:
-                containers["conda_amd64_lockfile"][module_name] = meta["containers"]["conda"]["linux_amd64"][
-                    "lock_file"
-                ]
-            except KeyError:
-                log.warning(f"Could not find conda linux_amd64 lock file for {module_name}")
-                continue
-            try:
-                containers["conda_arm64_lockfile"][module_name] = meta["containers"]["conda"]["linux_arm64"][
-                    "lock_file"
-                ]
-            except KeyError:
-                log.warning(f"Could not find conda linux_arm64 lock file for {module_name}")
-                continue
+            platforms: dict[str, list[str]] = {
+                "docker_arm64": ["docker", "linux_arm64", "name"],
+                "singularity_oras_amd64": ["singularity", "linux_amd64", "name"],
+                "singularity_oras_arm64": ["singularity", "linux_arm64", "name"],
+                "singularity_https_amd64": ["singularity", "linux_amd64", "https"],
+                "singularity_https_arm64": ["singularity", "linux_arm64", "https"],
+                "conda_amd64_lockfile": ["conda", "linux_amd64", "lock_file"],
+                "conda_arm64_lockfile": ["conda", "linux_arm64", "lock_file"],
+            }
+
+            for p_name, p_keys in platforms.items():
+                try:
+                    containers[p_name][module_name] = meta["containers"][p_keys[0]][p_keys[1]][p_keys[2]]
+                except KeyError:
+                    log.warning(f"Could not find {p_name} container for {module_name}")
+                    continue
 
         # write config files
         for platform in containers.keys():