diff --git a/cadetrdm/repositories.py b/cadetrdm/repositories.py
index 0eb694f2873065b262b885039c4134ec6334e803..fd71e3f3f11fcc78de3f13dd07129f62d6bed539 100644
--- a/cadetrdm/repositories.py
+++ b/cadetrdm/repositories.py
@@ -600,7 +600,7 @@ class ProjectRepo(BaseRepo):
print("Deprecation Warning. Setting the outputfolder manually during repo instantiation is deprecated"
" and will be removed in a future update.")
- self.output_folder = output_remotes["output_folder_name"]
+ self._output_folder = output_remotes["output_folder_name"]
with open(repository_path / ".cadet-rdm-data.json", "r") as handle:
metadata = json.load(handle)
@@ -609,7 +609,7 @@ class ProjectRepo(BaseRepo):
print(f"Repo version {repo_version} is outdated. Current CADET-RDM version is {cadetrdm_version}\n"
"Updating the repository now.")
- self._output_repo = OutputRepo(self.working_dir / self.output_folder)
+ self._output_repo = OutputRepo(self.working_dir / self._output_folder)
self._on_context_enter_commit_hash = None
self._is_in_context_manager = False
@@ -669,7 +669,7 @@ class ProjectRepo(BaseRepo):
"""
project_repo_hash = str(self.head.commit)
timestamp = datetime.now().strftime("%Y-%m-%d_%H-%M-%S")
- branch_name = "_".join([timestamp, self.output_folder, "from", str(self.active_branch), project_repo_hash[:7]])
+ branch_name = "_".join([timestamp, self._output_folder, "from", str(self.active_branch), project_repo_hash[:7]])
return branch_name
def check_results_master(self):
@@ -694,7 +694,7 @@ class ProjectRepo(BaseRepo):
self.output_repo.checkout("master")
- tsv_filepath = self.working_dir / self.output_folder / "log.tsv"
+ tsv_filepath = self.working_dir / self._output_folder / "log.tsv"
df = pd.read_csv(tsv_filepath, sep="\t", header=0)
# Clean up the headers
@@ -752,11 +752,11 @@ class ProjectRepo(BaseRepo):
:return:
"""
- tsv_filepath = self.working_dir / self.output_folder / "log.tsv"
+ tsv_filepath = self.working_dir / self._output_folder / "log.tsv"
if tsv_filepath.exists():
return
- csv_filepath = self.working_dir / self.output_folder / "log.csv"
+ csv_filepath = self.working_dir / self._output_folder / "log.csv"
if not csv_filepath.exists():
# We have just initialized the repo and neither tsv nor csv exist.
return
@@ -787,7 +787,7 @@ class ProjectRepo(BaseRepo):
self._output_repo._git.checkout("master")
- logs_folderpath = self.working_dir / self.output_folder / "run_history" / output_branch_name
+ logs_folderpath = self.working_dir / self._output_folder / "run_history" / output_branch_name
if not logs_folderpath.exists():
os.makedirs(logs_folderpath)
@@ -876,7 +876,7 @@ class ProjectRepo(BaseRepo):
output_json_filepath = self.working_dir / "output_remotes.json"
with open(output_json_filepath, "w") as file_handle:
remotes_dict = {remote.name: str(remote.url) for remote in self.output_repo.remotes}
- json_dict = {"output_folder_name": self.output_folder, "output_remotes": remotes_dict}
+ json_dict = {"output_folder_name": self._output_folder, "output_remotes": remotes_dict}
json.dump(json_dict, file_handle, indent=2)
def download_file(self, url, file_path):
@@ -927,7 +927,7 @@ class ProjectRepo(BaseRepo):
source_filepath = self.output_repo.working_dir / file_path
- target_folder = self.working_dir / (self.output_folder + "_cached") / branch_name
+ target_folder = self.working_dir / (self._output_folder + "_cached") / branch_name
os.makedirs(target_folder, exist_ok=True)
target_filepath = target_folder / file_path
@@ -957,14 +957,14 @@ class ProjectRepo(BaseRepo):
if sub_path is None:
return self.working_dir / self.output_repo.working_dir
else:
- return self.working_dir / self.output_repo.working_dir, sub_path
+ return self.working_dir / self.output_repo.working_dir / sub_path
def remove_cached_files(self):
"""
Delete all previously cached results.
"""
- if (self.working_dir / (self.output_folder + "_cached")).exists():
- delete_path(self.working_dir / (self.output_folder + "_cached"))
+ if (self.working_dir / (self._output_folder + "_cached")).exists():
+ delete_path(self.working_dir / (self._output_folder + "_cached"))
def test_for_correct_repo_setup(self):
"""
@@ -1024,7 +1024,7 @@ class ProjectRepo(BaseRepo):
previous_branch = self.output_repo.active_branch.name
self.output_repo.checkout(branch_name)
- target_folder = self.working_dir / (self.output_folder + "_cached") / branch_name
+ target_folder = self.working_dir / (self._output_folder + "_cached") / branch_name
shutil.copytree(source_filepath, target_folder)
diff --git a/docs/source/user_guide/getting-started.md b/docs/source/user_guide/getting-started.md
index 5a525a08ec938bca1fd41615343ff7d605944414..fff79444b70c07f8bedbbc01255b0c8d95929734 100644
--- a/docs/source/user_guide/getting-started.md
+++ b/docs/source/user_guide/getting-started.md
@@ -56,6 +56,7 @@ You can add datatypes you require by running:
repo.output_repo.add_filetype_to_lfs("*.npy")
````
+
or from within the output folder:
```bash
diff --git a/tests/test_git_adapter.py b/tests/test_git_adapter.py
index f0679c4ac15aa7acfc085680aaf07deca22d427d..b917a52c561864f4b5a6b76e588c01cba74bada1 100644
--- a/tests/test_git_adapter.py
+++ b/tests/test_git_adapter.py
@@ -77,12 +77,20 @@ def try_commit_results_data(path_to_repo):
repo = ProjectRepo(path_to_repo)
current_commit_number = count_commit_number(repo.output_repo)
with repo.track_results(results_commit_message="Add array"):
- example_generate_results_array(path_to_repo, output_folder=repo.output_folder)
+ example_generate_results_array(path_to_repo, output_folder=repo.output_path)
updated_commit_number = count_commit_number(repo.output_repo)
assert current_commit_number <= updated_commit_number
return str(repo.output_repo.active_branch)
+def try_output_function(path_to_repo):
+ repo = ProjectRepo(path_to_repo)
+ filepath = repo.output_path / "foo" / "bar"
+ assert isinstance(filepath, Path)
+ filepath = repo.output_data("foo/bar")
+ assert isinstance(filepath, Path)
+
+
def try_print_log(path_to_repo):
repo = ProjectRepo(path_to_repo)
repo.print_output_log()
@@ -93,7 +101,7 @@ def try_commit_results_with_uncommitted_code_changes(path_to_repo):
modify_code(path_to_repo)
with pytest.raises(Exception):
with repo.track_results(results_commit_message="Add array"):
- example_generate_results_array(path_to_repo, output_folder=repo.output_folder)
+ example_generate_results_array(path_to_repo, output_folder=repo.output_path)
repo.commit("add code to print random number", add_all=True)
@@ -104,7 +112,7 @@ def try_load_previous_output(path_to_repo, branch_name):
file_path="result.csv")
previous_array = np.loadtxt(cached_array_path, delimiter=",")
extended_array = np.concatenate([previous_array, previous_array])
- extended_array_file_path = path_to_repo / repo.output_folder / "extended_result.csv"
+ extended_array_file_path = path_to_repo / repo.output_path / "extended_result.csv"
np.savetxt(extended_array_file_path,
extended_array,
delimiter=",")
@@ -201,8 +209,8 @@ def test_cadet_rdm(path_to_repo):
try_commit_code(path_to_repo)
try_commit_code_without_code_changes(path_to_repo)
try_commit_results_with_uncommitted_code_changes(path_to_repo)
+ try_output_function(path_to_repo)
- results_branch_name = try_commit_results_data(path_to_repo)
results_branch_name = try_commit_results_data(path_to_repo)
try_print_log(path_to_repo)