Encode ordered dicts as regular dicts with ruamel

Older snakemake versions read config files as ordered dicts. Ruamel
would then render these back to yaml with an !!omap type, which would
then in turn be interpreted by pyyaml as lists of tuple pairs.

Fix by handling all OrderedDicts as regular dicts

Additionally, test a template dry run using the current repository state
(where previously we used only the latest pip release)

snakebids/io/yaml.py

@@ -1,4 +1,6 @@
+import collections
 from pathlib import Path, PosixPath, WindowsPath
+from typing import Any, OrderedDict
 
 from ruamel.yaml import YAML, Dumper
 
@@ -12,8 +14,13 @@ def path2str(dumper: Dumper, data: Path):
         return dumper.represent_scalar(
             "tag:yaml.org,2002:str",
             str(data),
-        )
+        )  # type: ignore
+
+    def to_dict(dumper: Dumper, data: OrderedDict[Any, Any]):
+        return dumper.represent_dict(dict(data))
 
     yaml.representer.add_representer(PosixPath, path2str)
     yaml.representer.add_representer(WindowsPath, path2str)
+    yaml.representer.add_representer(collections.OrderedDict, to_dict)
+    yaml.representer.add_representer(OrderedDict, to_dict)
     return yaml

snakebids/tests/helpers.py

@@ -298,7 +298,7 @@ def wrapper(*args: _P.args, **kwargs: _P.kwargs):
                 sp.run(["docker", "image", "inspect", container], check=True)
             except sp.CalledProcessError as err:
                 if not (
-                    match := re.match(r"snakebids/([\w\-])+\:[a-zA-Z0-9\-]+", container)
+                    match := re.match(r"snakebids/([\w\-]+)\:[a-zA-Z0-9\-]+", container)
                 ):
                     pytest.fail(
                         f"Unrecognized docker image: {container}. Should be "
@@ -307,8 +307,8 @@ def wrapper(*args: _P.args, **kwargs: _P.kwargs):
                 container_id = match[1]
                 pytest.fail(
                     f"{container} is not built on this machine. To build container, "
-                    f"run `poetry run poe build-container {container_id}`. To skip "
-                    f"docker tests, use '-m \"not docker\"'. (got error {err})"
+                    f"run:\n\n\t`poetry run poe build-container {container_id}`\n\nTo "
+                    f"skip docker tests, use '-m \"not docker\"'.\n\n(error:) {err}"
                 )
             return func(*args, **kwargs)
 

snakebids/tests/test_template.py

@@ -304,3 +304,36 @@ def test_template_dry_runs_successfully(tmp_path: Path, build: BuildBackend, ven
         print(cmd.stderr, file=sys.stderr)
         raise
     assert "All set" in cmd.stdout.decode()
+
+
+def test_template_dry_runs_with_current_repository(tmp_path: Path):
+    app_name = "snakebids_app"
+    data = get_empty_data(app_name, "setuptools")
+
+    copier.run_copy(
+        str(Path(itx.first(snakebids.__path__), "project_template")),
+        tmp_path / app_name,
+        data=data,
+        unsafe=True,
+    )
+    app_path = tmp_path / app_name
+    cmd = sp.run(
+        [
+            sys.executable,
+            app_path / app_name / "run.py",
+            app_path / "tests/data",
+            app_path / "tests/results",
+            "participant",
+            "-c1",
+            "--skip-bids-validation",
+        ],
+        capture_output=True,
+        check=False,
+    )
+    try:
+        cmd.check_returncode()
+    except Exception:
+        print(cmd.stdout.decode())
+        print(cmd.stderr.decode(), file=sys.stderr)
+        raise
+    assert "All set" in cmd.stdout.decode()

snakebids/tests/test_yaml.py

@@ -1,7 +1,9 @@
 from __future__ import annotations
 
+import io
 from io import StringIO
 from pathlib import Path
+from typing import Any, OrderedDict
 
 import pytest
 from hypothesis import given
@@ -14,8 +16,10 @@
 import snakebids.io.yaml as yamlio
 from snakebids.tests.helpers import allow_function_scoped
 
+YAML_SAFE_CHARS = st.characters(blacklist_characters=["\x85"])
 
-@given(path=st.text(st.characters(blacklist_characters=["\x85"]), min_size=1).map(Path))
+
+@given(path=st.text(YAML_SAFE_CHARS, min_size=1).map(Path))
 def test_paths_formatted_as_str(path: Path):
     string = StringIO()
     yaml = yamlio.get_yaml_io()
@@ -71,3 +75,22 @@ def test_overwrites_file_if_forced(
         mocks = self.io_mocks(mocker)
         configio.write_config(path, {}, force_overwrite=True)
         assert mocks["jsondump"].call_count ^ mocks["yamldump"].call_count
+
+    @given(
+        data=st.recursive(
+            st.text(YAML_SAFE_CHARS),
+            lambda children: st.dictionaries(st.text(YAML_SAFE_CHARS), children),
+        )
+    )
+    def test_ordered_dict_roundtrips_as_dict(self, data: dict[str, Any]):
+        def to_odict(data: dict[str, Any] | str) -> OrderedDict[str, Any] | str:
+            if isinstance(data, str):
+                return data
+            return OrderedDict({key: to_odict(value) for key, value in data.items()})
+
+        stream = io.StringIO()
+        yaml = yamlio.get_yaml_io()
+        odict = to_odict(data)
+        yaml.dump(odict, stream)
+        stream.seek(0)
+        assert yaml.load(stream) == data