format etc.

Author: geritwagner

colrev/loader/load_utils.py

@@ -264,9 +264,8 @@ def load_df(
     filename: Path,
 ) -> pd.DataFrame:
     """Load a file and return records as a DataFrame."""
-    assert isinstance(
-        filename, Path
-    ), f"filename must be a Path object, not {type(filename)}"
+    if not isinstance(filename, Path):
+        raise TypeError(f"filename must be a Path object, not {type(filename)}")
     record_dict = load(filename)
     return pd.DataFrame.from_dict(record_dict, orient="index")
 

colrev/ops/checker.py

@@ -208,7 +208,8 @@ def _check_search_history_files(self) -> None:
                 )
 
     def _retrieve_ids_from_bib(self, *, file_path: Path) -> list:
-        assert file_path.suffix == ".bib"
+        if file_path.suffix != ".bib":
+            raise AssertionError(f"Unexpected file suffix: {file_path.suffix}")
         record_ids = []
         with open(file_path, encoding="utf8") as file:
             line = file.readline()

colrev/ops/dedupe.py

@@ -381,7 +381,8 @@ def apply_merges(
         if non_existing_ids:
             print(f"Non-existing IDs: {non_existing_ids}")
             print(f"Records IDs: {records.keys()}")
-        assert not non_existing_ids, "Not all IDs from id_sets are present in records"
+        if non_existing_ids:
+            raise AssertionError("Not all IDs from id_sets are present in records")
 
         # Notify users about items with only one unique ID
         for id_set in id_sets:
@@ -531,7 +532,8 @@ def _revert_merge_for_records(
                     if origins == hist_recs[rid].get(Fields.ORIGIN, []):
                         continue
                     if any(orig in origins for orig in hist_rec.get(Fields.ORIGIN, [])):
-                        assert hist_rec[Fields.ID] not in unmerged_records
+                        if hist_rec[Fields.ID] in unmerged_records:
+                            raise AssertionError("Historical record ID unexpectedly present in unmerged records")
                         hist_rec.update({Fields.STATUS: RecordState.md_processed})
                         self.review_manager.logger.info(
                             f"add historical record: {hist_rec[Fields.ID]}"

colrev/ops/init/readme.md

@@ -2,7 +2,7 @@
 
 This repository is based on the [ColRev](https://github.com/CoLRev-Environment/colrev) standard.
 
-```
+```bash
 # To work on this project, run
 colrev clone URL
 

colrev/ops/load.py

@@ -449,7 +449,8 @@ def load_active_sources(self, *, include_md: bool = False) -> list:
         checker.check_sources()
         sources_settings = []
         for source in self.review_manager.settings.sources:
-            assert isinstance(source, colrev.search_file.ExtendedSearchFile)
+            if not isinstance(source, colrev.search_file.ExtendedSearchFile):
+                raise AssertionError("Expected source to be ExtendedSearchFile")
             source.search_type = SearchType(source.search_type)
             source.search_results_path = Path(source.search_results_path)
             sources_settings.append(source)

colrev/ops/search_api_feed.py

@@ -111,7 +111,8 @@ def __init__(
         self._load_feed()
 
         if prep_mode:
-            assert records is not None
+            if records is None:
+                raise AssertionError("Retrieved records must not be None")
         self.verbose_mode = verbose_mode
         self.prep_mode = prep_mode
         self._retrieved_records_for_saving = False
@@ -504,10 +505,11 @@ def get_records(self) -> dict:
     def save(self, *, skip_print: bool = False) -> None:
         """Save the feed file and records, printing post-run search infos."""
         if self.prep_mode:
-            assert self._retrieved_records_for_saving, (
-                "You must call get_records() before calling save() "
-                "to ensure that the prepared (primary) records are saved."
-            )
+            if not self._retrieved_records_for_saving:
+                raise AssertionError(
+                    "You must call get_records() before calling save() "
+                    "to ensure that the prepared (primary) records are saved."
+                )
 
         if not skip_print and not self.prep_mode:
             self._print_post_run_search_infos()

colrev/ops/upgrade.py

@@ -949,7 +949,8 @@ def __init__(self, version_string: str) -> None:
         """Initialize the instance."""
         if "+" in version_string:
             version_string = version_string[: version_string.find("+")]
-        assert re.match(r"\d+\.\d+\.\d+$", version_string)
+        if not re.match(r"\d+\.\d+\.\d+$", version_string):
+            raise AssertionError(f"Invalid version string: {version_string}")
         self.major = int(version_string[: version_string.find(".")])
         self.minor = int(
             version_string[version_string.find(".") + 1 : version_string.rfind(".")]

colrev/ops/validate.py

@@ -578,7 +578,8 @@ def _get_target_commit(self, *, scope: str, filter_setting: str = "") -> str:
         if scope in ["HEAD", "."]:
             scope = "HEAD~0"
         if scope.startswith("HEAD~"):
-            assert scope.replace("HEAD~", "").isdigit()
+            if not scope.replace("HEAD~", "").isdigit():
+                raise AssertionError(f"Invalid scope value: {scope}")
             back_count = int(scope.replace("HEAD~", ""))
             for commit_item in git_repo.iter_commits():
                 if back_count == 0:

colrev/package_manager/doc_registry_manager.py

@@ -103,9 +103,10 @@ def _initialize_from_colrev_monorepo(self, package_id: str) -> bool:
             ) as file:
                 self.package_metadata = toml.load(file)
 
-            assert str(self.package_dir).endswith(
-                package_id.replace("colrev.", "")
-            ), package_id
+            if not str(self.package_dir).endswith(package_id.replace("colrev.", "")):
+                raise AssertionError(
+                    f"Unexpected package directory for {package_id}: {self.package_dir}"
+                )
 
             return True
         return False

colrev/packages/acm_digital_library/README.md

@@ -4,7 +4,7 @@
 
 ### DB search
 
-```
+```bash
 colrev search --add colrev.acm_digital_library
 ```