Merge pull request #3238 from nf-core/revert-2680-add-rocreate

Revert "Add new command `nf-core rocrate` to create a Research Object (RO) crate for a pipeline"

.github/actions/create-lint-wf/action.yml

@@ -65,12 +65,6 @@ runs:
       run: find nf-core-testpipeline -type f -exec sed -i 's/zenodo.XXXXXX/zenodo.123456/g' {} \;
       working-directory: create-lint-wf
 
-    # Add empty ro-crate file
-    - name: add empty ro-crate file
-      shell: bash
-      run: touch nf-core-testpipeline/ro-crate-metadata.json
-      working-directory: create-lint-wf
-
     # Run nf-core pipelines linting
     - name: nf-core pipelines lint
       shell: bash

.github/workflows/create-test-lint-wf-template.yml

@@ -112,9 +112,6 @@ jobs:
         run: |
           cd create-test-lint-wf
           nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --template-yaml template_skip_${{ matrix.TEMPLATE }}.yml
-          # fake ro-crate
-          touch my-prefix-testpipeline/ro-crate-metadata.json
-          git commit -am "add ro-crate"
 
       - name: run the pipeline
         run: |
@@ -150,11 +147,6 @@ jobs:
         run: find my-prefix-testpipeline -type f -exec sed -i 's/zenodo.XXXXXX/zenodo.123456/g' {} \;
         working-directory: create-test-lint-wf
 
-      # Add empty ro-crate file
-      - name: add empty ro-crate file
-        run: touch my-prefix-testpipeline/ro-crate-metadata.json
-        working-directory: create-test-lint-wf
-
       # Run nf-core linting
       - name: nf-core pipelines lint
         run: nf-core --log-file log.txt --hide-progress pipelines lint --dir my-prefix-testpipeline --fail-warned

nf_core/__main__.py

@@ -4,7 +4,6 @@
 import logging
 import os
 import sys
-from pathlib import Path
 
 import rich
 import rich.console
@@ -36,7 +35,6 @@
     pipelines_launch,
     pipelines_lint,
     pipelines_list,
-    pipelines_rocrate,
     pipelines_schema_build,
     pipelines_schema_docs,
     pipelines_schema_lint,
@@ -87,7 +85,7 @@
         },
         {
             "name": "For developers",
-            "commands": ["create", "lint", "bump-version", "sync", "schema", "rocrate", "create-logo"],
+            "commands": ["create", "lint", "bump-version", "sync", "schema", "create-logo"],
         },
     ],
     "nf-core modules": [
@@ -571,44 +569,6 @@ def command_pipelines_list(ctx, keywords, sort, json, show_archived):
     pipelines_list(ctx, keywords, sort, json, show_archived)
 
 
-# nf-core pipelines rocrate
-@pipelines.command("rocrate")
-@click.argument(
-    "pipeline_dir",
-    type=click.Path(exists=True),
-    default=Path.cwd(),
-    required=True,
-    metavar="<pipeline directory>",
-)
-@click.option(
-    "-j",
-    "--json_path",
-    default=Path.cwd(),
-    type=str,
-    help="Path to save RO Crate metadata json file to",
-)
-@click.option("-z", "--zip_path", type=str, help="Path to save RO Crate zip file to")
-@click.option(
-    "-pv",
-    "--pipeline_version",
-    type=str,
-    help="Version of pipeline to use for RO Crate",
-    default="",
-)
-@click.pass_context
-def rocrate(
-    ctx,
-    pipeline_dir: str,
-    json_path: str,
-    zip_path: str,
-    pipeline_version: str,
-):
-    """
-    Make an Research Object Crate
-    """
-    pipelines_rocrate(ctx, pipeline_dir, json_path, zip_path, pipeline_version)
-
-
 # nf-core pipelines sync
 @pipelines.command("sync")
 @click.pass_context
@@ -1732,7 +1692,7 @@ def command_schema_validate(pipeline, params):
 @click.option(
     "--url",
     type=str,
-    default="https://oldsite.nf-co.re/pipeline_schema_builder",
+    default="https://nf-co.re/pipeline_schema_builder",
     help="Customise the builder URL (for development work)",
 )
 def command_schema_build(directory, no_prompts, web_only, url):

nf_core/commands_pipelines.py

@@ -2,7 +2,6 @@
 import os
 import sys
 from pathlib import Path
-from typing import Optional, Union
 
 import rich
 
@@ -278,33 +277,6 @@ def pipelines_list(ctx, keywords, sort, json, show_archived):
     stdout.print(list_workflows(keywords, sort, json, show_archived))
 
 
-# nf-core pipelines rocrate
-def pipelines_rocrate(
-    ctx,
-    pipeline_dir: Union[str, Path],
-    json_path: Optional[Union[str, Path]],
-    zip_path: Optional[Union[str, Path]],
-    pipeline_version: str,
-) -> None:
-    from nf_core.pipelines.rocrate import ROCrate
-
-    if json_path is None and zip_path is None:
-        log.error("Either `--json_path` or `--zip_path` must be specified.")
-        sys.exit(1)
-    else:
-        pipeline_dir = Path(pipeline_dir)
-        if json_path is not None:
-            json_path = Path(json_path)
-        if zip_path is not None:
-            zip_path = Path(zip_path)
-        try:
-            rocrate_obj = ROCrate(pipeline_dir, pipeline_version)
-            rocrate_obj.create_rocrate(pipeline_dir, json_path=json_path, zip_path=zip_path)
-        except (UserWarning, LookupError, FileNotFoundError) as e:
-            log.error(e)
-            sys.exit(1)
-
-
 # nf-core pipelines sync
 def pipelines_sync(ctx, directory, from_branch, pull_request, github_repository, username, template_yaml, force_pr):
     """

nf_core/components/info.py

@@ -211,9 +211,9 @@ def get_local_yaml(self) -> Optional[Dict]:
                         return yaml.safe_load(fh)
             log.debug(f"{self.component_type[:-1].title()} '{self.component}' meta.yml not found locally")
 
-        return {}
+        return None
 
-    def get_remote_yaml(self) -> Optional[Dict]:
+    def get_remote_yaml(self) -> Optional[dict]:
         """Attempt to get the meta.yml file from a remote repo.
 
         Returns:

nf_core/modules/modules_json.py

@@ -1119,10 +1119,8 @@ def dump(self, run_prettier: bool = False) -> None:
         """
         Sort the modules.json, and write it to file
         """
-        # Sort the modules.json
-        if self.modules_json is None:
-            self.load()
         if self.modules_json is not None:
+            # Sort the modules.json
             self.modules_json["repos"] = nf_core.utils.sort_dictionary(self.modules_json["repos"])
             if run_prettier:
                 dump_json_with_prettier(self.modules_json_path, self.modules_json)

nf_core/pipelines/lint/files_exist.py

@@ -66,7 +66,6 @@ def files_exist(self) -> Dict[str, List[str]]:
         conf/igenomes.config
         .github/workflows/awstest.yml
         .github/workflows/awsfulltest.yml
-        ro-crate-metadata.json
 
     Files that *must not* be present, due to being renamed or removed in the template:
 
@@ -172,7 +171,6 @@ def files_exist(self) -> Dict[str, List[str]]:
         [Path(".github", "workflows", "awstest.yml")],
         [Path(".github", "workflows", "awsfulltest.yml")],
         [Path("modules.json")],
-        [Path("ro-crate-metadata.json")],
     ]
 
     # List of strings. Fails / warns if any of the strings exist.
@@ -200,12 +198,6 @@ def files_exist(self) -> Dict[str, List[str]]:
     ]
     files_warn_ifexists = [Path(".travis.yml")]
 
-    files_hint = [
-        [
-            ["ro-crate-metadata.json"],
-            ". Run `nf-core rocrate` to generate this file. Read more about RO-Crates in the [nf-core/tools docs](https://nf-co.re/tools#create-a-ro-crate-metadata-file).",
-        ],
-    ]
     # Remove files that should be ignored according to the linting config
     ignore_files = self.lint_config.get("files_exist", []) if self.lint_config is not None else []
 
@@ -233,11 +225,7 @@ def pf(file_path: Union[str, Path]) -> Path:
         if any([pf(f).is_file() for f in files]):
             passed.append(f"File found: {self._wrap_quotes(files)}")
         else:
-            hint = ""
-            for file_hint in files_hint:
-                if file_hint[0] == files:
-                    hint = str(file_hint[1])
-            warned.append(f"File not found: {self._wrap_quotes(files)}{hint}")
+            warned.append(f"File not found: {self._wrap_quotes(files)}")
 
     # Files that cause an error if they exist
     for file in files_fail_ifexists: