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Commit d3171c3e authored by r.jaepel's avatar r.jaepel
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Replace .working_dir with .path

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cadetrdm/repositories.py
+ 79
− 41
View file @ d3171c3e
......@@ -77,8 +77,17 @@ class BaseRepo:
def current_commit_hash(self):
return str(self.head.commit)
@property
def path(self):
return Path(self._git_repo.working_dir)
@property
def bare(self):
return self._git_repo.bare
@property
def working_dir(self):
print("Deprecation Warning. .working_dir is getting replaced with .path")
return Path(self._git_repo.working_dir)
@property
......@@ -92,7 +101,7 @@ class BaseRepo:
@property
def remote_urls(self):
if len(self.remotes) == 0:
print(RuntimeWarning(f"No remote for repo at {self.working_dir} set yet. Please add remote ASAP."))
print(RuntimeWarning(f"No remote for repo at {self.path} set yet. Please add remote ASAP."))
return [str(remote.url) for remote in self.remotes]
@property
......@@ -108,11 +117,40 @@ class BaseRepo:
@property
def data_json_path(self):
return self.working_dir / ".cadet-rdm-data.json"
return self.path / ".cadet-rdm-data.json"
@property
def cache_json_path(self):
return self.working_dir / ".cadet-rdm-cache.json"
return self.path / ".cadet-rdm-cache.json"
@property
def has_changes_upstream(self):
try:
remote_hash = str(self.remotes[0].fetch()[0].commit)
if self.current_commit_hash != remote_hash:
return True
else:
return False
except git.GitCommandError as e:
traceback.print_exc()
print(f"Git command error in {self.path}: {e}")
def fetch(self):
self._git.fetch()
def update(self):
try:
self.fetch()
if self.has_changes_upstream:
print(f"New changes detected in {self.remotes[0].origin}, pulling updates...")
self.remotes[0].origin.pull()
except git.GitCommandError as e:
traceback.print_exc()
print(f"Git command error in {self.path}: {e}")
def add_remote(self, remote_url, remote_name=None):
"""
......@@ -129,7 +167,7 @@ class BaseRepo:
rdm_data = json.load(handle)
if rdm_data["is_project_repo"]:
# This folder is a project repo. Use a project repo class to easily access the output repo.
output_repo = ProjectRepo(self.working_dir).output_repo
output_repo = ProjectRepo(self.path).output_repo
if output_repo.active_branch != "main":
if output_repo.exist_uncomitted_changes:
......@@ -140,7 +178,7 @@ class BaseRepo:
output_repo.commit("Add remote for project repo")
if rdm_data["is_output_repo"]:
# This folder is an output repo
project_repo = ProjectRepo(self.working_dir.parent)
project_repo = ProjectRepo(self.path.parent)
project_repo.update_output_remotes_json()
project_repo.add_list_of_remotes_in_readme_file("output_repo", self.remote_urls)
project_repo.commit("Add remote for output repo")
......@@ -153,7 +191,7 @@ class BaseRepo:
Wildcard formatted string. Examples: "*.png" or "*.xlsx"
:return:
"""
init_lfs(lfs_filetypes=[file_type], path=self.working_dir)
init_lfs(lfs_filetypes=[file_type], path=self.path)
self.add_all_files()
self.commit(f"Add {file_type} to lfs")
......@@ -180,9 +218,9 @@ class BaseRepo:
else:
source_repo_name = Path(source_repo_location).name
if target_repo_location is None:
target_repo_location = self.working_dir / "external_cache" / source_repo_name
target_repo_location = self.path / "external_cache" / source_repo_name
else:
target_repo_location = self.working_dir / target_repo_location
target_repo_location = self.path / target_repo_location
self.add_path_to_gitignore(target_repo_location)
......@@ -205,12 +243,12 @@ class BaseRepo:
:return:
"""
path_to_be_ignored = self.ensure_relative_path(path_to_be_ignored)
with open(self.working_dir / ".gitignore", "r") as file_handle:
with open(self.path / ".gitignore", "r") as file_handle:
gitignore = file_handle.readlines()
gitignore[-1] += "\n" # Sometimes there is no trailing newline
if str(path_to_be_ignored) + "\n" not in gitignore:
gitignore.append(str(path_to_be_ignored) + "\n")
with open(self.working_dir / ".gitignore", "w") as file_handle:
with open(self.path / ".gitignore", "w") as file_handle:
file_handle.writelines(gitignore)
def update_cadet_rdm_cache_json(self, source_repo_location, source_repo_branch, target_repo_location):
......@@ -261,7 +299,7 @@ class BaseRepo:
input_path = Path(input_path)
if input_path.is_absolute:
relative_path = input_path.relative_to(self.working_dir)
relative_path = input_path.relative_to(self.path)
else:
relative_path = input_path
return relative_path
......@@ -386,7 +424,7 @@ class BaseRepo:
try:
self._git.clean("-q", "-f", "-d")
except git.exc.GitCommandError:
recursive_chmod(self.working_dir, S_IWRITE)
recursive_chmod(self.path, S_IWRITE)
self._git.clean("-q", "-f", "-d")
@property
......@@ -407,7 +445,7 @@ class BaseRepo:
if target_folder is not None:
dump_path = target_folder
else:
dump_path = self.working_dir
dump_path = self.path
print("Dumping conda environment.yml, this might take a moment.")
try:
os.system(f"conda env export > {dump_path}/conda_environment.yml")
......@@ -432,10 +470,10 @@ class BaseRepo:
"""
if not self.exist_uncomitted_changes:
print(f"No changes to commit in repo {self.working_dir}")
print(f"No changes to commit in repo {self.path}")
return
print(f"Commiting changes to repo {self.working_dir}")
print(f"Commiting changes to repo {self.path}")
if add_all:
self.add(".")
......@@ -496,8 +534,8 @@ class BaseRepo:
"""
self._git.checkout("main")
self._git.checkout('-b', branch_name) # equivalent to $ git checkout -b %branch_name
code_backup_path = self.working_dir / "run_history"
logs_path = self.working_dir / "log.tsv"
code_backup_path = self.path / "run_history"
logs_path = self.path / "log.tsv"
if code_backup_path.exists():
try:
# Remove previous code backup
......@@ -533,7 +571,7 @@ class BaseRepo:
:return:
"""
if self.exist_uncomitted_changes:
raise RuntimeError(f"Found uncommitted changes in the repository {self.working_dir}.")
raise RuntimeError(f"Found uncommitted changes in the repository {self.path}.")
def add_list_of_remotes_in_readme_file(self, repo_identifier: str, remotes_url_list: list):
if len(remotes_url_list) > 0:
......@@ -542,7 +580,7 @@ class BaseRepo:
output_link_line = " and ".join(f"[{repo_identifier}]({output_repo_remote})"
for output_repo_remote in remotes_url_list_http) + "\n"
readme_filepath = self.working_dir / "README.md"
readme_filepath = self.path / "README.md"
with open(readme_filepath, "r") as file_handle:
filelines = file_handle.readlines()
filelines_giving_output_repo = [i for i in range(len(filelines))
......@@ -585,11 +623,11 @@ class ProjectRepo(BaseRepo):
"""
super().__init__(repository_path, search_parent_directories=search_parent_directories, *args, **kwargs)
with open(self.working_dir / "output_remotes.json", "r") as handle:
with open(self.path / "output_remotes.json", "r") as handle:
try:
output_remotes = json.load(handle)
except FileNotFoundError:
raise RuntimeError(f"Folder {self.working_dir} does not appear to be a CADET-RDM repository.")
raise RuntimeError(f"Folder {self.path} does not appear to be a CADET-RDM repository.")
if output_folder is not None:
print("Deprecation Warning. Setting the outputfolder manually during repo instantiation is deprecated"
......@@ -609,7 +647,7 @@ class ProjectRepo(BaseRepo):
with open(".cadet-rdm-data.json", "w") as f:
json.dump(metadata, f, indent=2)
self._output_repo = OutputRepo(self.working_dir / self._output_folder)
self._output_repo = OutputRepo(self.path / self._output_folder)
self._on_context_enter_commit_hash = None
self._is_in_context_manager = False
......@@ -624,7 +662,7 @@ class ProjectRepo(BaseRepo):
version_sum = major * 1000 * 1000 + minor * 1000 + patch
if version_sum < 9:
self.convert_csv_to_tsv_if_necessary()
self.add_jupytext_file(self.working_dir)
self.add_jupytext_file(self.path)
@staticmethod
def add_jupytext_file(path_root: str | Path = "."):
......@@ -714,11 +752,11 @@ class ProjectRepo(BaseRepo):
:return:
"""
tsv_filepath = self.working_dir / self._output_folder / "log.tsv"
tsv_filepath = self.path / self._output_folder / "log.tsv"
if tsv_filepath.exists():
return
csv_filepath = self.working_dir / self._output_folder / "log.csv"
csv_filepath = self.path / self._output_folder / "log.csv"
if not csv_filepath.exists():
# We have just initialized the repo and neither tsv nor csv exist.
return
......@@ -731,7 +769,7 @@ class ProjectRepo(BaseRepo):
with open(tsv_filepath, "w") as f:
f.writelines(tsv_lines)
write_lines_to_file(path=self.working_dir / ".gitattributes",
write_lines_to_file(path=self.path / ".gitattributes",
lines=["rdm-log.tsv merge=union"],
open_type="a")
......@@ -749,21 +787,21 @@ class ProjectRepo(BaseRepo):
self._output_repo._git.checkout("main")
logs_folderpath = self.working_dir / self._output_folder / "run_history" / output_branch_name
logs_folderpath = self.path / self._output_folder / "run_history" / output_branch_name
if not logs_folderpath.exists():
os.makedirs(logs_folderpath)
json_filepath = logs_folderpath / "metadata.json"
# note: if filename of "log.tsv" is changed,
# this also has to be changed in the gitattributes of the init repo func
tsv_filepath = self.output_repo.working_dir / "log.tsv"
tsv_filepath = self.output_repo.path / "log.tsv"
meta_info_dict = {
"Output repo commit message": output_commit_message,
"Output repo branch": output_branch_name,
"Output repo commit hash": output_repo_hash,
"Project repo commit hash": str(self.head.commit),
"Project repo folder name": self.working_dir.name,
"Project repo folder name": self.path.name,
"Project repo remotes": self.remote_urls,
"Python sys args": str(sys.argv),
"Tags": ", ".join(self.tags),
......@@ -812,7 +850,7 @@ class ProjectRepo(BaseRepo):
code_tmp_folder = target_path / "git_repo"
multi_options = ["--filter=blob:none", "--single-branch"]
git.Repo.clone_from(self.working_dir, code_tmp_folder, multi_options=multi_options)
git.Repo.clone_from(self.path, code_tmp_folder, multi_options=multi_options)
shutil.make_archive(target_path / "code", "zip", code_tmp_folder)
......@@ -835,7 +873,7 @@ class ProjectRepo(BaseRepo):
def update_output_remotes_json(self):
output_repo_remotes = self.output_repo.remote_urls
self.add_list_of_remotes_in_readme_file("output_repo", output_repo_remotes)
output_json_filepath = self.working_dir / "output_remotes.json"
output_json_filepath = self.path / "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}
......@@ -887,9 +925,9 @@ class ProjectRepo(BaseRepo):
previous_branch = self.output_repo.active_branch.name
self.output_repo._git.checkout(branch_name)
source_filepath = self.output_repo.working_dir / file_path
source_filepath = self.output_repo.path / file_path
target_folder = self.working_dir / (self._output_folder + "_cached") / branch_name
target_folder = self.path / (self._output_folder + "_cached") / branch_name
os.makedirs(target_folder, exist_ok=True)
target_filepath = target_folder / file_path
......@@ -917,16 +955,16 @@ class ProjectRepo(BaseRepo):
:return:
"""
if sub_path is None:
return self.working_dir / self.output_repo.working_dir
return self.path / self.output_repo.path
else:
return self.working_dir / self.output_repo.working_dir / sub_path
return self.path / self.output_repo.path / 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.path / (self._output_folder + "_cached")).exists():
delete_path(self.path / (self._output_folder + "_cached"))
def test_for_correct_repo_setup(self):
"""
......@@ -977,7 +1015,7 @@ class ProjectRepo(BaseRepo):
:return:
"""
try:
source_filepath = self.output_repo.working_dir
source_filepath = self.output_repo.path
if branch_name is None:
branch_name = self.output_repo.active_branch.name
......@@ -986,7 +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.path / (self._output_folder + "_cached") / branch_name
shutil.copytree(source_filepath, target_folder)
......@@ -1068,7 +1106,7 @@ class OutputRepo(BaseRepo):
def print_data_log(self):
self.checkout("main")
tsv_filepath = self.working_dir / "log.tsv"
tsv_filepath = self.path / "log.tsv"
with open(tsv_filepath, "r") as filehandle:
lines = filehandle.readlines()
......@@ -1097,7 +1135,7 @@ class JupyterInterfaceRepo(ProjectRepo):
return
# This is reached in the first call of this function
if not Path(notebook_path).is_absolute():
notebook_path = self.working_dir / notebook_path
notebook_path = self.path / notebook_path
notebook = Notebook(notebook_path)
......
tests/test_gitlab_api.py
+ 2
− 0
View file @ d3171c3e
......@@ -88,3 +88,5 @@ def test_repo_gitlab_integration():
repo = ProjectRepo(repo_name)
repo.create_remotes(url=url, namespace=namespace, name=name, username="r.jaepel")
assert repo.has_changes_upstream is False
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