Merge pull request #16197 from mvdbeek/dev

Merge 23.0 into dev

lib/galaxy/model/store/__init__.py

@@ -2450,7 +2450,7 @@ def _init_crate(self) -> ROCrate:
                     "encodingFormat": encoding_format,
                 }
                 ro_crate.add_file(
-                    file_name,
+                    os.path.join(self.export_directory, file_name),
                     dest_path=file_name,
                     properties=properties,
                 )

lib/galaxy/model/store/ro_crate_utils.py

@@ -6,6 +6,8 @@
     Optional,
 )
 
+from packaging.version import parse
+from rocrate import __version__ as rocrate_version
 from rocrate.model.computationalworkflow import (
     ComputationalWorkflow,
     WorkflowDescription,
@@ -102,13 +104,21 @@ def _add_file(self, dataset: HistoryDatasetAssociation, properties: Dict[Any, An
         if dataset.dataset.id in self.model_store.dataset_id_to_path:
             filename, _ = self.model_store.dataset_id_to_path[dataset.dataset.id]
             if not filename:
+                # dataset was not serialized
                 filename = f"datasets/dataset_{dataset.dataset.uuid}"
+                if parse(rocrate_version) >= parse("0.8.0"):
+                    source = None
+                else:
+                    # Drop in 23.1
+                    source = filename
+            else:
+                source = os.path.join(self.model_store.export_directory, filename)
             name = dataset.name
             encoding_format = dataset.datatype.get_mime()
             properties["name"] = name
             properties["encodingFormat"] = encoding_format
             file_entity = crate.add_file(
-                filename,
+                source,
                 dest_path=filename,
                 properties=properties,
             )
@@ -272,7 +282,7 @@ def _add_attrs_files(self, crate: ROCrate):
                     "encodingFormat": "application/json",
                 }
                 crate.add_file(
-                    attrs,
+                    attrs_path,
                     dest_path=attrs,
                     properties=properties,
                 )

scripts/release.py

@@ -141,8 +141,17 @@ def read_package(package_path: pathlib.Path) -> Package:
     return package
 
 
+def _get_docutils_parser_settings():
+    try:
+        return frontend.get_default_settings(Parser)
+    except AttributeError:
+        # docutils < 0.18. Remove fallback in 23.1
+        components = (Parser,)
+        return frontend.OptionParser(components=components).get_default_values()
+
+
 def parse_changelog(package: Package) -> List[ChangelogItem]:
-    settings = frontend.get_default_settings(Parser)
+    settings = _get_docutils_parser_settings()
     document = utils.new_document(str(package.history_rst), settings)
     Parser().parse(package.history_rst.read_text(), document)
     changelog_items: List[ChangelogItem] = []
@@ -440,6 +449,23 @@ def is_merge_required(base_branch: str, new_branch: str, galaxy_root: pathlib.Pa
     return True
 
 
+def ensure_branches_up_to_date(branches: List[str], base_branch: str, upstream: str, galaxy_root: pathlib.Path):
+    for branch in branches:
+        subprocess.run(["git", "checkout", branch], cwd=galaxy_root).check_returncode()
+        # Check that the head commit matches the commit for the same branch at the specified remote repo url
+        result = subprocess.run(["git", "ls-remote", upstream, f"refs/heads/{branch}"], capture_output=True, text=True)
+        result.check_returncode()
+        remote_commit_hash = result.stdout.split("\t")[0]
+        result = subprocess.run(["git", "rev-parse", "HEAD"], capture_output=True, text=True)
+        result.check_returncode()
+        local_commit_hash = result.stdout.strip()
+        if remote_commit_hash != local_commit_hash:
+            raise Exception(
+                f"Local tip of branch {branch} is {local_commit_hash}, remote tip of branch is {remote_commit_hash}. Make sure that your local branches are up to date and track f{upstream}."
+            )
+    subprocess.run(["git", "checkout", base_branch], cwd=galaxy_root).check_returncode()
+
+
 def push_references(references: List[str], upstream: str = "https://github.com/galaxyproject/galaxy.git"):
     for reference in references:
         subprocess.run(["git", "push", upstream, reference]).check_returncode()
@@ -525,8 +551,11 @@ def create_point_release(
         click.confirm("Does this look correct?", abort=True)
     base_branch = current_branch = get_current_branch(galaxy_root)
     newer_branches = get_branches(galaxy_root, new_version, base_branch)
+    all_branches = newer_branches + [base_branch]
+    click.echo("Making sure that all branches are up to date")
+    ensure_branches_up_to_date(all_branches, base_branch, upstream, galaxy_root)
+
     click.echo("Making sure that merging forward will result in clean merges")
-    merge_required = False
     for new_branch in newer_branches:
         merge_required = is_merge_required(base_branch=current_branch, new_branch=new_branch, galaxy_root=galaxy_root)
         if merge_required:
@@ -537,7 +566,7 @@ def create_point_release(
             if click.confirm("Continue anyway ?", abort=True):
                 current_branch = new_branch
                 break
-    subprocess.run(["git", "checkout", base_branch], cwd=galaxy_root)
+    subprocess.run(["git", "checkout", base_branch], cwd=galaxy_root).check_returncode()
     modified_paths = [set_root_version(galaxy_root, new_version)]
     # read packages and find prs that affect a package
     packages: List[Package] = []
@@ -600,7 +629,7 @@ def create_point_release(
         click.echo(f"Merging {base_branch} into {new_branch}")
         merge_and_resolve_branches(galaxy_root, current_branch, new_branch, packages)
         current_branch = new_branch
-    references = [release_tag, base_branch] + newer_branches
+    references = [release_tag] + all_branches
     if no_confirm or click.confirm(f"Push {','.join(references)} to upstream '{upstream}' ?", abort=True):
         push_references(references=references, upstream=upstream)
 

test/unit/data/model/test_model_store.py

@@ -347,7 +347,6 @@ def validate_has_pl_galaxy(ro_crate: ROCrate):
     assert programming_language.id == "https://w3id.org/workflowhub/workflow-ro-crate#galaxy"
     assert programming_language.name == "Galaxy"
     assert programming_language.url == "https://galaxyproject.org/"
-    assert programming_language.version
 
 
 def validate_organize_action(ro_crate: ROCrate):