From d74d525bdd05e4b8a4bb446af7dd488123dbae9c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20Schm=C3=B6lder?= <j.schmoelder@fz-juelich.de>
Date: Mon, 26 Jan 2026 10:37:26 +0100
Subject: [PATCH 1/6] Separate update_version methods for project and output
 repo

---
 cadetrdm/repositories.py | 136 ++++++++++++++++++++++++++-------------
 1 file changed, 92 insertions(+), 44 deletions(-)

diff --git a/cadetrdm/repositories.py b/cadetrdm/repositories.py
index bb53e8d..7443f91 100644
--- a/cadetrdm/repositories.py
+++ b/cadetrdm/repositories.py
@@ -822,6 +822,8 @@ def __init__(
         self._output_uuid = self._metadata["output_uuid"]
         self._output_folder = self._metadata["output_remotes"]["output_folder_name"]
         self.options = options
+        self._update_version()
+
         if not (self.path / self._output_folder).exists():
             print("Output repository was missing, cloning now.")
             self._clone_output_repo()
@@ -830,9 +832,6 @@ def __init__(
             self,
         )
 
-        if self._metadata["cadet_rdm_version"] != cadetrdm.__version__:
-            self._update_version(self._metadata, cadetrdm.__version__)
-
         self._on_context_enter_commit_hash = None
         self._is_in_context_manager = False
         self.options_hash = None
@@ -864,58 +863,33 @@ def module(self) -> ModuleType:
             sys.path.remove(str(self.path))
             os.chdir(cur_dir)
 
-    def _update_version(self, metadata, cadetrdm_version):
-        current_version = Version.coerce(metadata["cadet_rdm_version"])
+    def _update_version(self) -> None:
+        """Update project repo to latest CADET-RDM specs."""
+        metadata = self._metadata
+        cadetrdm_version = Version(cadetrdm.__version__)
+        current_version = Version(metadata["cadet_rdm_version"])
+
+        # Skip if versions match
+        if cadetrdm_version == current_version:
+            return
 
         changes_were_made = False
 
-        if SimpleSpec("<0.0.9").match(current_version):
+        if current_version < Version("0.0.9"):
             changes_were_made = True
-            self.output_repo._convert_csv_to_tsv_if_necessary()
             self._add_jupytext_file(self.path)
-        if SimpleSpec("<0.0.24").match(current_version):
+        if current_version < Version("0.0.24"):
             changes_were_made = True
-            self.output_repo._expand_tsv_header()
             output_remotes_path = self.path / "output_remotes.json"
             delete_path(output_remotes_path)
             self.add(output_remotes_path)
-        if SimpleSpec("<=0.0.34").match(current_version):
-            changes_were_made = True
-            if self.output_log_file.exists():
-                warnings.warn(
-                    "Repo version has outdated headers."
-                    "Updating log.tsv."
-                )
-                self.output_repo._update_headers()
-        if SimpleSpec("<0.0.34").match(current_version):
-            changes_were_made = True
-            self.output_repo._fix_gitattributes_log_tsv()
-        if SimpleSpec("<1.1.0").match(current_version):
-            # Note, this needs to be performed before upating the hashes, otherwise
-            # instantiating an `OutputLog` will crash when missing the
-            # `project_repo_branch` attribute.
-            changes_were_made = True
-            if self.output_log_file.exists():
-                warnings.warn(
-                    "Repo version has missing project repo branch_name field."
-                    "Updating log.tsv."
-                )
-                self.output_repo._add_branch_name_to_log()
-        if SimpleSpec("<0.1.7").match(current_version):
-            changes_were_made = True
-            if self.output_repo.output_log.n_entries > 0:
-                warnings.warn(
-                    "Repo version has outdated options hashes. "
-                    "Updating option hashes in output log.tsv."
-                )
-                self.output_repo._update_log_hashes()
         if changes_were_made:
             print(
                 f"Repo version {metadata['cadet_rdm_version']} was outdated. "
                 f"Current CADET-RDM version is {cadetrdm.__version__}.\n"
                 "Repo has been updated."
             )
-            metadata["cadet_rdm_version"] = cadetrdm_version
+            metadata["cadet_rdm_version"] = str(cadetrdm_version)
             with open(self.data_json_path, "w", encoding="utf-8") as f:
                 json.dump(metadata, f, indent=2)
             self.add(self.data_json_path)
@@ -1489,6 +1463,8 @@ def __init__(
         self.project_repo = project_repo
         super().__init__(*args, **kwargs)
 
+        self._update_version()
+
     @property
     def output_log_file_path(self):
         if not self.active_branch == self.main_branch:
@@ -1561,7 +1537,6 @@ def commit_to_options_map(self) -> dict[str, list[str]]:
             mapping[entry.project_repo_commit_hash].append(entry.options_hash)
         return dict(mapping)
 
-
     def add_filetype_to_lfs(self, file_type):
         """
         Add the filetype given in file_type to the GIT-LFS tracking
@@ -1574,6 +1549,69 @@ def add_filetype_to_lfs(self, file_type):
         self.add_all_files()
         self.commit(f"Add {file_type} to lfs")
 
+    def _update_version(self) -> None:
+        """Update output repo to latest CADET-RDM specs."""
+        metadata = self._metadata
+        cadetrdm_version = Version(cadetrdm.__version__)
+        current_version = Version(metadata["cadet_rdm_version"])
+
+        # Skip if versions match
+        if cadetrdm_version == current_version:
+            return
+
+        changes_were_made = False
+
+        if current_version < Version("0.0.9"):
+            changes_were_made = True
+            self._convert_csv_to_tsv_if_necessary()
+        if current_version < Version("0.0.24"):
+            changes_were_made = True
+            self._expand_tsv_header()
+        if current_version < Version("0.0.34"):
+            changes_were_made = True
+            if self.output_log_file_path.exists():
+                warnings.warn(
+                    "Repo version has outdated headers. "
+                    "Updating log.tsv."
+                )
+                self._update_headers()
+        if current_version < Version("0.0.34"):
+            changes_were_made = True
+            self._fix_gitattributes_log_tsv()
+        if current_version < Version("1.1.0"):
+            # Note, this needs to be performed before upating the hashes, otherwise
+            # instantiating an `OutputLog` will crash when missing the
+            # `project_repo_branch` attribute.
+            changes_were_made = True
+            if self.output_log_file_path.exists():
+                warnings.warn(
+                    "Repo version has missing project repo branch_name field. "
+                    "Updating log.tsv."
+                )
+                self._add_branch_name_to_log()
+        if current_version < Version("0.1.7"):
+            changes_were_made = True
+            if self.output_log.n_entries > 0:
+                warnings.warn(
+                    "Repo version has outdated options hashes. "
+                    "Updating option hashes in output log.tsv."
+                )
+                self._update_log_hashes()
+        if changes_were_made:
+            print(
+                f"Repo version {metadata['cadet_rdm_version']} was outdated. "
+                f"Current CADET-RDM version is {cadetrdm.__version__}.\n"
+                "Repo has been updated."
+            )
+            metadata["cadet_rdm_version"] = str(cadetrdm_version)
+            with open(self.data_json_path, "w", encoding="utf-8") as f:
+                json.dump(metadata, f, indent=2)
+            self.add(self.data_json_path)
+            self.commit(
+                f"Update CADET-RDM version to {cadetrdm_version}",
+                add_all=False
+            )
+
     def _convert_csv_to_tsv_if_necessary(self) -> None:
         """Convert logfile from csv to tsv format."""
         if self.output_log_file_path.exists():
@@ -1596,6 +1634,9 @@ def _convert_csv_to_tsv_if_necessary(self) -> None:
             lines=["rdm-log.tsv merge=union"],
             open_type="a"
         )
+        self.add(self.path / "log.csv")
+        self.add(self.path / "log.tsv")
+        self.commit("Convert csv to tsv", add_all=False)
 
     def _expand_tsv_header(self):
         """Update tsv header."""
@@ -1614,7 +1655,8 @@ def _expand_tsv_header(self):
             "Project repo remotes",
             "Python sys args",
             "Tags",
-            "Options hash", ]
+            "Options hash",
+        ]
         with open(self.output_log_file_path, "w", encoding="utf-8") as f:
             f.writelines(["\t".join(new_header) + "\n"])
             f.writelines(lines[1:])
@@ -1656,6 +1698,7 @@ def _fix_gitattributes_log_tsv(self):
         lines = [line.replace("rdm-log.tsv", "log.tsv") for line in lines]
         with open(file, "w", encoding="utf-8") as handle:
             handle.writelines(lines)
+
         self.add(".gitattributes")
         self.commit("Update .gitattributes", add_all=False)
 
@@ -1680,7 +1723,9 @@ def _update_log_hashes(self):
         self.checkout(self.main_branch)
         if self.output_log.n_entries > 0:
             log.write()
-        self.commit(message="Updated log hashes", add_all=True)
+
+        self.add(self.output_log_file_path)
+        self.commit(message="Updated log hashes", add_all=False)
 
     def _add_branch_name_to_log(self) -> None:
         """
@@ -1713,7 +1758,10 @@ def _add_branch_name_to_log(self) -> None:
             writer.writerows(rows)
 
         self.add("log.tsv")
-        self.commit(message="Add project_repo_branch_name to log.tsv")
+        self.commit(
+            message="Add project_repo_branch_name to log.tsv",
+            add_all=False,
+        )
 
 
 class JupyterInterfaceRepo(ProjectRepo):

From bc979d5e35bfb614bd8547ed4d75716d43e8244c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20Schm=C3=B6lder?= <j.schmoelder@fz-juelich.de>
Date: Mon, 26 Jan 2026 11:44:24 +0100
Subject: [PATCH 2/6] Pass all args to super().commit

---
 cadetrdm/repositories.py | 32 ++++++++++++++++----------------
 1 file changed, 16 insertions(+), 16 deletions(-)

diff --git a/cadetrdm/repositories.py b/cadetrdm/repositories.py
index 7443f91..f94628d 100644
--- a/cadetrdm/repositories.py
+++ b/cadetrdm/repositories.py
@@ -1,5 +1,6 @@
 import contextlib
 import csv
+from functools import wraps
 import glob
 import importlib
 import json
@@ -285,7 +286,12 @@ def remote_set_url(self, name: str, url: str):
         """
         self._git_repo.remotes[name].set_url(url)
 
-    def commit(self, message: str | None = None, add_all=True, verbosity=1):
+    def commit(
+        self,
+        message: str | None = None,
+        add_all=True,
+        verbosity=1,
+    ) -> None:
         """
         Commit current state of the repository.
 
@@ -1079,8 +1085,7 @@ def update_output_main_logs(self, output_dict: dict = None):
         self.output_repo.add(".")
         self.output_repo._git.commit(
             "-m",
-            f"log for '{output_commit_message}' \n"
-            f"of branch '{output_branch_name}'"
+            f"log for '{output_commit_message}' of branch '{output_branch_name}'",
         )
 
         self.output_repo._git.checkout(output_branch_name)
@@ -1103,20 +1108,15 @@ def _copy_code(self, target_path):
             self.active_branch, output=code_tmp_folder
         )
 
-    def commit(self, message: str | None = None, add_all=True, verbosity=1):
-        """
-        Commit current state of the repository.
-
-        :param message:
-            Commit message
-        :param add_all:
-            Option to add all changed and new files to git automatically.
-        :param verbosity:
-            Option to choose degree of printed feedback.
-        """
+    @wraps(BaseRepo.commit)
+    def commit(
+        self,
+        *args,
+        **kwargs,
+    ):
+        """Update output remotes before committing."""
         self.update_output_remotes_json()
-
-        super().commit(message=message, add_all=add_all, verbosity=verbosity)
+        super().commit(*args, **kwargs)
 
     def check(self, commit=True):
         """

From 6fe2a7e892176f9b493da5200d2cc03402c32536 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20Schm=C3=B6lder?= <j.schmoelder@fz-juelich.de>
Date: Mon, 26 Jan 2026 10:47:44 +0100
Subject: [PATCH 3/6] Remove options from project repo

---
 cadetrdm/repositories.py | 88 ++++++++++++++++++++++++++++------------
 cadetrdm/wrapper.py      |  7 ++--
 2 files changed, 66 insertions(+), 29 deletions(-)

diff --git a/cadetrdm/repositories.py b/cadetrdm/repositories.py
index f94628d..ad2c164 100644
--- a/cadetrdm/repositories.py
+++ b/cadetrdm/repositories.py
@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import contextlib
 import csv
 from functools import wraps
@@ -773,7 +775,6 @@ def __init__(
         suppress_lfs_warning: bool = False,
         url: str = None,
         branch: str = None,
-        options: Options | None = None,
         package_dir: str | None = None,
          *args: Any,
          **kwargs: Any,
@@ -798,8 +799,6 @@ def __init__(
             Optional branch to check out upon initialization
         :param package_dir:
             Name of the directory containing the main package.
-        :param options:
-            Options dictionary containing ...
         :param args:
             Additional args to be handed to BaseRepo.
         :param kwargs:
@@ -827,7 +826,7 @@ def __init__(
         self._project_uuid = self._metadata["project_uuid"]
         self._output_uuid = self._metadata["output_uuid"]
         self._output_folder = self._metadata["output_remotes"]["output_folder_name"]
-        self.options = options
+
         self._update_version()
 
         if not (self.path / self._output_folder).exists():
@@ -840,7 +839,6 @@ def __init__(
 
         self._on_context_enter_commit_hash = None
         self._is_in_context_manager = False
-        self.options_hash = None
 
         if branch is not None:
             self.checkout(branch)
@@ -959,9 +957,10 @@ def create_remotes(self, name, namespace, url=None, username=None, push=True):
         if errors_encountered == 0 and push:
             self.push(push_all=True)
 
-    def get_new_output_branch_name(self):
+    def get_new_output_branch_name(self, branch_prefix: str | None = None) -> str:
         """
         Construct a name for the new branch in the output repository.
+        :param branch_prefix: Optional branch name prefix.
         :return: the new branch name
         """
         project_repo_hash = str(self.head.commit)
@@ -969,8 +968,8 @@ def get_new_output_branch_name(self):
 
         branch_name = f"{timestamp}_{self.active_branch}_{project_repo_hash[:7]}"
 
-        if self.options and "branch_prefix" in self.options:
-            branch_name = f"{self.options['branch_prefix']}_{branch_name}"
+        if branch_prefix:
+            branch_name = f"{branch_prefix}_{branch_name}"
 
         return branch_name
 
@@ -1030,7 +1029,11 @@ def output_log_file(self):
     def output_log(self):
         return self.output_repo.output_log
 
-    def update_output_main_logs(self, output_dict: dict = None):
+    def update_output_main_logs(
+        self,
+        output_dict: dict = None,
+        options: Options | None = None,
+    ):
         """
         Dumps all the metadata information about the project repositories state and
         the commit hash and branch name of the ouput repository into the main branch of
@@ -1063,7 +1066,7 @@ def update_output_main_logs(self, output_dict: dict = None):
             project_repo_remotes=self.remote_urls,
             python_sys_args=str(sys.argv),
             tags=", ".join(self.tags),
-            options_hash=self.options_hash,
+            options_hash=options.get_hash() if options else None,
             filepath=None,
             **output_dict
         )
@@ -1071,8 +1074,8 @@ def update_output_main_logs(self, output_dict: dict = None):
         with open(logs_dir / "metadata.json", "w", encoding="utf-8") as f:
             json.dump(entry.to_dict(), f, indent=2)
 
-        if self.options is not None:
-            self.options.dump_json_file(logs_dir / "options.json", indent=2)
+        if options:
+            options.dump_json_file(logs_dir / "options.json", indent=2)
 
         log = OutputLog(self.output_log_file)
         log.entries[output_branch_name] = entry
@@ -1217,7 +1220,12 @@ def import_static_data(self, source_path: Path | str, commit_message):
         self._commit_output_data(commit_message, output_dict={})
         return new_branch_name
 
-    def enter_context(self, force=False, debug=False):
+    def enter_context(
+        self,
+        force=False,
+        debug=False,
+        branch_prefix: str | None = None,
+    ) -> str | None:
         """
         Enter the tracking context. This includes:
          - Ensure no uncommitted changes in the project repository
@@ -1225,11 +1233,12 @@ def enter_context(self, force=False, debug=False):
          - Clean up empty branches in the output repository
          - Create a new empty output branch in the output repository
 
-
         :param force:
             If False, wait for user prompts before deleting data during clean up. If True, don't wait, just delete.
         :param debug:
             If True, just return None.
+        :param branch_prefix:
+            Optional branch name prefix.
         :return:
             The name of the newly created output branch.
         """
@@ -1244,10 +1253,14 @@ def enter_context(self, force=False, debug=False):
         self._on_context_enter_commit_hash = self.current_commit_hash
         self._is_in_context_manager = True
 
-        new_branch_name = self._get_new_output_branch(force)
+        new_branch_name = self._get_new_output_branch(force, branch_prefix)
         return new_branch_name
 
-    def _get_new_output_branch(self, force=False):
+    def _get_new_output_branch(
+        self,
+        force: bool = False,
+        branch_prefix: str | None = None
+    ):
         """
         Prepares a new branch to receive data. This includes:
          - checking out the output main branch,
@@ -1257,8 +1270,9 @@ def _get_new_output_branch(self, force=False):
 
         :param force:
             If False, wait for user prompts before deleting data during clean up. If True, don't wait, just delete.
+        :param branch_prefix:
+            Optional branch name prefix.
         """
-
         output_repo = self.output_repo
 
         # ensure that LFS is properly initialized
@@ -1268,7 +1282,7 @@ def _get_new_output_branch(self, force=False):
         if output_repo.has_uncomitted_changes:
             output_repo._reset_hard_to_head(force_entry=force)
         output_repo.delete_active_branch_if_branch_is_empty()
-        new_branch_name = self.get_new_output_branch_name()
+        new_branch_name = self.get_new_output_branch_name(branch_prefix)
 
         # update urls in main branch of output_repo
         output_repo._git.checkout(output_repo.main_branch)
@@ -1367,7 +1381,12 @@ def copy_data_to_cache(self, branch_name=None, target_folder=None):
 
         return target_folder
 
-    def exit_context(self, message, output_dict: dict = None):
+    def exit_context(
+        self,
+        message,
+        output_dict: dict = None,
+        options: Options | None = None,
+    ):
         """
         After running all project code, this prepares the commit of the results to the output repository. This includes
          - Ensure no uncommitted changes in the project repository
@@ -1386,9 +1405,14 @@ def exit_context(self, message, output_dict: dict = None):
         if self._on_context_enter_commit_hash != self.current_commit_hash:
             raise RuntimeError("Code has changed since starting the context. Don't do that.")
 
-        self._commit_output_data(message, output_dict)
+        self._commit_output_data(message, output_dict, options)
 
-    def _commit_output_data(self, message, output_dict):
+    def _commit_output_data(
+        self,
+        message: str,
+        output_dict: dict,
+        options: Options | None = None
+    ):
         """
         Commit the data in the output repository.
          - Stage all changes in the output repository
@@ -1398,6 +1422,8 @@ def _commit_output_data(self, message, output_dict):
             Commit message for the output repository commit.
         :param output_dict:
             Dictionary containing optional output tracking parameters
+        :param options:
+            Optional case options.
         """
         print("Completed computations, commiting results")
         self.output_repo.add(".")
@@ -1405,7 +1431,7 @@ def _commit_output_data(self, message, output_dict):
             # This has to be using ._git.commit to raise an error if no results have been written.
             commit_return = self.output_repo._git.commit("-m", message)
             self.copy_data_to_cache()
-            self.update_output_main_logs(output_dict)
+            self.update_output_main_logs(output_dict, options)
             main_cach_path = self.path / (self._output_folder + "_cached") / self.output_repo.main_branch
             if main_cach_path.exists():
                 delete_path(main_cach_path)
@@ -1419,7 +1445,13 @@ def _commit_output_data(self, message, output_dict):
             self._on_context_enter_commit_hash = None
 
     @contextlib.contextmanager
-    def track_results(self, results_commit_message: str, debug=False, force=False):
+    def track_results(
+        self,
+        results_commit_message: str,
+        debug=False,
+        force=False,
+        options: Options | None = None,
+    ) -> str | None:
         """
         Context manager to be used when running project code that produces output that should
         be tracked in the output repository.
@@ -1429,6 +1461,8 @@ def track_results(self, results_commit_message: str, debug=False, force=False):
             Perform calculations without tracking output.
         :param force:
             Skip confirmation and force tracking of results.
+        :param options:
+            Optional case options.
         """
         if debug:
             yield "debug"
@@ -1439,14 +1473,18 @@ def track_results(self, results_commit_message: str, debug=False, force=False):
             yield "detached_head"
             return
 
-        new_branch_name = self.enter_context(force=force)
+        new_branch_name = self.enter_context(
+            force=force,
+            debug=debug,
+            branch_prefix=options.get("branch_prefix"),
+        )
         try:
             yield new_branch_name
         except Exception as e:
             self.capture_error(e)
             raise e
         else:
-            self.exit_context(message=results_commit_message)
+            self.exit_context(message=results_commit_message, options=options)
 
     def capture_error(self, error):
         print(traceback.format_exc())
diff --git a/cadetrdm/wrapper.py b/cadetrdm/wrapper.py
index 69248e0..486bb20 100644
--- a/cadetrdm/wrapper.py
+++ b/cadetrdm/wrapper.py
@@ -29,14 +29,13 @@ def wrapper(options, repo_path='.'):
         if options.get_hash() != Options.load_json_str(options.dump_json_str()).get_hash():
             raise ValueError("Options are not serializable. Please only use python natives and numpy ndarrays.")
 
-        project_repo = ProjectRepo(repo_path, options=options)
-
-        project_repo.options_hash = options.get_hash()
+        project_repo = ProjectRepo(repo_path)
 
         with project_repo.track_results(
                 options.commit_message,
                 debug=options.debug,
-                force=True
+                force=True,
+                options=options,
         ) as new_branch_name:
             options.dump_json_file(project_repo.output_path / "options.json")
             results = func(project_repo, options)

From 3846e53216e8fa1d38ee9c5f3f21e9c9869475a1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20Schm=C3=B6lder?= <j.schmoelder@fz-juelich.de>
Date: Mon, 26 Jan 2026 13:13:08 +0100
Subject: [PATCH 4/6] fixup! Remove options from project repo

---
 cadetrdm/repositories.py  | 2 +-
 tests/test_git_adapter.py | 4 ++++
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/cadetrdm/repositories.py b/cadetrdm/repositories.py
index ad2c164..37ae17f 100644
--- a/cadetrdm/repositories.py
+++ b/cadetrdm/repositories.py
@@ -1476,7 +1476,7 @@ def track_results(
         new_branch_name = self.enter_context(
             force=force,
             debug=debug,
-            branch_prefix=options.get("branch_prefix"),
+            branch_prefix=options.get("branch_prefix") if options else None,
         )
         try:
             yield new_branch_name
diff --git a/tests/test_git_adapter.py b/tests/test_git_adapter.py
index f53f343..d407e95 100644
--- a/tests/test_git_adapter.py
+++ b/tests/test_git_adapter.py
@@ -430,3 +430,7 @@ def test_with_detached_head():
 #         repo.verify_unchanged_cache()
 #
 #     os.chdir("..")
+
+
+if __name__ == "__main__":
+    pytest.main(["-v", __file__])

From 78e409410ee6e4ffa8f00784ced26bb83ca08a3f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20Schm=C3=B6lder?= <j.schmoelder@fz-juelich.de>
Date: Mon, 26 Jan 2026 14:05:17 +0100
Subject: [PATCH 5/6] fixup! Remove options from project repo

---
 tests/test_options.py | 20 +++++++++++++-------
 1 file changed, 13 insertions(+), 7 deletions(-)

diff --git a/tests/test_options.py b/tests/test_options.py
index b8108cf..c11e8b5 100644
--- a/tests/test_options.py
+++ b/tests/test_options.py
@@ -1,11 +1,13 @@
-import numpy as np
+from pathlib import Path
 import re
 
+import numpy as np
+import pytest
+
 from cadetrdm import Options
 from cadetrdm.options import remove_invalid_keys
-from cadetrdm import process_example
 from cadetrdm import ProjectRepo
-from pathlib import Path
+
 
 def test_options_hash():
     opt = Options()
@@ -115,7 +117,7 @@ def test_branch_name():
     options.push = False
     options.source_directory = "src"
 
-    repo = ProjectRepo(Path("./test_repo_cli"), options=options)
+    repo = ProjectRepo(Path("./test_repo_cli"))
 
     hash = str(repo.head.commit)[:7]
     active_branch = str(repo.active_branch)
@@ -136,14 +138,18 @@ def test_branch_name_with_prefix():
     options.source_directory = "src"
     options.branch_prefix = "Test_Prefix"
 
-    repo = ProjectRepo(Path("./test_repo_cli"), options=options)
+    repo = ProjectRepo(Path("./test_repo_cli"))
 
     hash = str(repo.head.commit)[:7]
     active_branch = str(repo.active_branch)
-    new_branch = repo.get_new_output_branch_name()
+    new_branch = repo.get_new_output_branch_name(options.branch_prefix)
 
     escaped_branch = re.escape(active_branch)
 
     pattern = rf"^Test_Prefix_\d{{4}}-\d{{2}}-\d{{2}}_\d{{2}}-\d{{2}}-\d{{2}}_{escaped_branch}_{hash}$"
 
-    assert re.match(pattern, new_branch), f"Branch name '{new_branch}' does not match expected format"
\ No newline at end of file
+    assert re.match(pattern, new_branch), f"Branch name '{new_branch}' does not match expected format"
+
+
+if __name__ == "__main__":
+    pytest.main(["-v", __file__])

From cd813507fe5f4ede5ce2b79876fed442be02da27 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20Schm=C3=B6lder?= <j.schmoelder@fz-juelich.de>
Date: Mon, 26 Jan 2026 14:06:11 +0100
Subject: [PATCH 6/6] Refactor test_options

---
 tests/test_options.py | 144 +++++++++++++++---------------------------
 1 file changed, 52 insertions(+), 92 deletions(-)

diff --git a/tests/test_options.py b/tests/test_options.py
index c11e8b5..5f305b6 100644
--- a/tests/test_options.py
+++ b/tests/test_options.py
@@ -1,14 +1,23 @@
-from pathlib import Path
 import re
 
 import numpy as np
 import pytest
 
+from cadetrdm import initialize_repo
 from cadetrdm import Options
 from cadetrdm.options import remove_invalid_keys
 from cadetrdm import ProjectRepo
 
 
+@pytest.fixture
+def clean_repo(tmp_path):
+    """Fixture to initialize and clean up a test repository."""
+    repo_path = tmp_path / "test_repo_cli"
+    initialize_repo(repo_path)
+    repo = ProjectRepo(repo_path)
+    yield repo
+
+
 def test_options_hash():
     opt = Options()
     opt["array"] = np.linspace(2, 200)
@@ -21,116 +30,71 @@ def test_options_hash():
     assert opt == opt_recovered
 
 
-def test_options_file_io():
+def test_options_file_io(tmp_path):
     opt = Options()
     opt["array"] = np.linspace(0, 2, 200)
     opt["nested_dict"] = {"ba": "foo", "bb": "bar"}
     initial_hash = opt.get_hash()
-    opt.dump_json_file("options.json")
-    opt_recovered = Options.load_json_file("options.json")
+    opt.dump_json_file(tmp_path / "options.json")
+    opt_recovered = Options.load_json_file(tmp_path / "options.json")
     post_serialization_hash = opt_recovered.get_hash()
     assert initial_hash == post_serialization_hash
     assert opt == opt_recovered
 
 
-def test_remove_keys_starting_with_underscore():
-    input_dict = {
-        "_private": 1,
-        "valid": 2,
-        "__magic__": 3
-    }
-    expected = {"valid": 2}
-    assert remove_invalid_keys(input_dict) == expected
-
-
-def test_remove_keys_containing_double_underscore():
-    input_dict = {
-        "normal": 1,
-        "with__double": 2,
-        "another": 3
-    }
-    expected = {"normal": 1, "another": 3}
-    assert remove_invalid_keys(input_dict) == expected
-
-
-def test_nested_dict_removal():
-    input_dict = {
-        "level1": {
-            "_invalid": 1,
-            "valid": {
-                "__still_invalid__": 2,
-                "ok": 3
-            }
-        },
-        "__should_be_removed__": "nope"
-    }
-    expected = {
-        "level1": {
-            "valid": {
-                "ok": 3
-            }
-        }
-    }
+@pytest.mark.parametrize(
+    "input_dict, expected",
+    [
+        ({"_private": 1, "valid": 2, "__magic__": 3}, {"valid": 2}),
+        (
+            {
+                "level1": {
+                    "_invalid": 1,
+                    "valid": {"__still_invalid__": 2, "ok": 3},
+                },
+                "__should_be_removed__": "nope",
+            },
+            {"level1": {"valid": {"ok": 3}}},
+        ),
+        ({}, {}),
+        ({"_one": 1, "__two__": 2, "with__double": 3}, {}),
+        ({"a": 1, "b": {"c": 2}}, {"a": 1, "b": {"c": 2}}),
+    ],
+    ids=[
+        "keys_starting_with_underscore",
+        "nested_dict_removal",
+        "empty_dict",
+        "all_invalid_keys",
+        "no_invalid_keys",
+    ],
+)
+def test_remove_invalid_keys(input_dict, expected):
     assert remove_invalid_keys(input_dict) == expected
 
 
-def test_empty_dict():
-    assert remove_invalid_keys({}) == {}
-
-
-def test_all_invalid_keys():
-    input_dict = {
-        "_one": 1,
-        "__two__": 2,
-        "with__double": 3
-    }
-    assert remove_invalid_keys(input_dict) == {}
-
-
-def test_no_invalid_keys():
-    input_dict = {
-        "a": 1,
-        "b": {
-            "c": 2
-        }
-    }
-    assert remove_invalid_keys(input_dict) == input_dict
-
-def test_explicit_invalid_keys():
-    input_dict = {
-        "a": 1,
-        "b": {
-            "c": 2
-        }
-    }
-    expected = {
-        "b": {
-            "c": 2
-        }
-    }
+def test_remove_explicit_invalid_keys():
+    input_dict = {"a": 1, "b": {"c": 2}}
+    expected = {"b": {"c": 2}}
     assert remove_invalid_keys(input_dict, excluded_keys=["a"]) == expected
 
-def test_branch_name():
+
+def test_branch_name(clean_repo):
     options = Options()
     options.commit_message = "Commit Message Test"
     options.debug = True
     options.push = False
     options.source_directory = "src"
 
-    repo = ProjectRepo(Path("./test_repo_cli"))
-
-    hash = str(repo.head.commit)[:7]
-    active_branch = str(repo.active_branch)
-    new_branch = repo.get_new_output_branch_name()
+    hash = str(clean_repo.head.commit)[:7]
+    active_branch = str(clean_repo.active_branch)
+    new_branch = clean_repo.get_new_output_branch_name()
 
     escaped_branch = re.escape(active_branch)
-
     pattern = rf"^\d{{4}}-\d{{2}}-\d{{2}}_\d{{2}}-\d{{2}}-\d{{2}}_{escaped_branch}_{hash}$"
-
     assert re.match(pattern, new_branch), f"Branch name '{new_branch}' does not match expected format"
 
-def test_branch_name_with_prefix():
 
+def test_branch_name_with_prefix(clean_repo):
     options = Options()
     options.commit_message = "Commit Message Test"
     options.debug = True
@@ -138,16 +102,12 @@ def test_branch_name_with_prefix():
     options.source_directory = "src"
     options.branch_prefix = "Test_Prefix"
 
-    repo = ProjectRepo(Path("./test_repo_cli"))
-
-    hash = str(repo.head.commit)[:7]
-    active_branch = str(repo.active_branch)
-    new_branch = repo.get_new_output_branch_name(options.branch_prefix)
+    hash = str(clean_repo.head.commit)[:7]
+    active_branch = str(clean_repo.active_branch)
+    new_branch = clean_repo.get_new_output_branch_name(options.branch_prefix)
 
     escaped_branch = re.escape(active_branch)
-
     pattern = rf"^Test_Prefix_\d{{4}}-\d{{2}}-\d{{2}}_\d{{2}}-\d{{2}}-\d{{2}}_{escaped_branch}_{hash}$"
-
     assert re.match(pattern, new_branch), f"Branch name '{new_branch}' does not match expected format"