diff --git a/cadetrdm/initialize_repo.py b/cadetrdm/initialize_repo.py
index 8ec8c5daa0bec089cd1b255c4d797af59a7edfb3..7ccda72eb48a4fbf406fb9d3bb5192d38255aeff 100644
--- a/cadetrdm/initialize_repo.py
+++ b/cadetrdm/initialize_repo.py
@@ -98,7 +98,7 @@ def initialize_repo(path_to_repo: str, output_folder_name: (str | bool) = "outpu
write_lines_to_file(path=".gitignore", lines=gitignore, open_type="a")
if output_repo_kwargs is None:
- output_repo_kwargs = {"gitattributes": ["logs/log.csv merge=union"]}
+ output_repo_kwargs = {"gitattributes": ["log.csv merge=union"]}
if output_folder_name:
# This means we are in the project repo and should now initialize the output_repo
@@ -124,6 +124,7 @@ def initialize_repo(path_to_repo: str, output_folder_name: (str | bool) = "outpu
initialize_repo(output_folder_name, output_folder_name=False, **output_repo_kwargs)
# This instance of ProjectRepo is therefore the project repo
repo = ProjectRepo(".", output_folder=output_folder_name)
+ repo.update_output_remotes_json()
else:
# If output_repo_name is False we are in the output_repo and should finish by committing the changes
rdm_data = {
diff --git a/cadetrdm/repositories.py b/cadetrdm/repositories.py
index ab4c0e9daab4a4812735840c6bb2f5e817513cc5..516e187193b23f5ef0070bf86b44573e1651618c 100644
--- a/cadetrdm/repositories.py
+++ b/cadetrdm/repositories.py
@@ -4,6 +4,7 @@ import sys
import traceback
from datetime import datetime
import shutil
+import zipfile
import contextlib
import glob
from stat import S_IREAD, S_IWRITE
@@ -146,11 +147,10 @@ class BaseRepo:
else:
target_repo_location = os.path.join(self.working_dir, target_repo_location)
- multi_options = ["--filter=blob:none", "--branch", source_repo_branch, "--single-branch"]
-
self.add_path_to_gitignore(target_repo_location)
print(f"Cloning from {source_repo_location} into {target_repo_location}")
+ multi_options = ["--filter=blob:none", "--branch", source_repo_branch, "--single-branch"]
repo = git.Repo.clone_from(source_repo_location, target_repo_location, multi_options=multi_options)
repo.git.clear_cache()
@@ -477,8 +477,8 @@ class BaseRepo:
"""
self._git.checkout("master")
self._git.checkout('-b', branch_name) # equivalent to $ git checkout -b %branch_name
- code_backup_path = os.path.join(self.working_dir, "logs", "code_backup")
- logs_path = os.path.join(self.working_dir, "logs")
+ code_backup_path = os.path.join(self.working_dir, "run_history")
+ logs_path = os.path.join(self.working_dir, "log.csv")
if os.path.exists(code_backup_path):
try:
# Remove previous code backup
@@ -617,7 +617,7 @@ class ProjectRepo(BaseRepo):
self.output_repo.checkout("master")
- csv_filepath = os.path.join(self.working_dir, self.output_folder, "logs", "log.csv")
+ csv_filepath = os.path.join(self.working_dir, self.output_folder, "log.csv")
df = pd.read_csv(csv_filepath, sep=",", header=0)
# Clean up the headers
@@ -652,14 +652,14 @@ class ProjectRepo(BaseRepo):
self._output_repo._git.checkout("master")
- logs_folderpath = os.path.join(self.working_dir, self.output_folder, "logs")
+ logs_folderpath = os.path.join(self.working_dir, self.output_folder, "run_history", output_branch_name)
if not os.path.exists(logs_folderpath):
os.makedirs(logs_folderpath)
- json_filepath = os.path.join(logs_folderpath, f"{output_branch_name}.json")
+ json_filepath = os.path.join(logs_folderpath, "metadata.json")
# note: if filename of "log.csv" is changed,
# this also has to be changed in the gitattributes of the init repo func
- csv_filepath = os.path.join(logs_folderpath, "log.csv")
+ csv_filepath = os.path.join(self.output_repo.working_dir, "log.csv")
meta_info_dict = {
"Output repo commit message": output_commit_message,
@@ -693,10 +693,10 @@ class ProjectRepo(BaseRepo):
self.dump_package_list(logs_folderpath)
# Copy all code files from the project git repo to the output repo
- code_copy_folderpath = os.path.join(logs_folderpath, "code_backup")
- if not os.path.exists(code_copy_folderpath):
- os.makedirs(code_copy_folderpath)
- self.copy_code(code_copy_folderpath)
+ # code_copy_folderpath = os.path.join(logs_folderpath, "code_backup")
+ # if not os.path.exists(code_copy_folderpath):
+ # os.makedirs(code_copy_folderpath)
+ self.copy_code(logs_folderpath)
self._output_repo.add(".")
self._output_repo._git.commit("-m", f"log for '{output_commit_message}' \n"
@@ -706,22 +706,21 @@ class ProjectRepo(BaseRepo):
self._most_recent_branch = output_branch_name
def copy_code(self, target_path):
- for file in self._git.ls_files().split("\n"):
- if "\\" in file:
- file = bytes(file, "utf-8").decode("unicode_escape").encode("cp1252").decode("utf-8")
- if "'" in file or '"' in file:
- file = file.replace("'", "").replace('"', '')
- try:
- target_file_path = os.path.join(self.working_dir, target_path, file)
- target_folder = os.path.split(target_file_path)[0]
- if not os.path.exists(target_folder):
- os.makedirs(target_folder)
- shutil.copyfile(
- os.path.join(self.working_dir, file),
- target_file_path
- )
- except:
- traceback.print_exc()
+ """
+ Clone only the current branch of the project repo to the target_path
+ and then compress it into a zip file.
+
+ :param target_path:
+ :return:
+ """
+ code_tmp_folder = os.path.join(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)
+
+ shutil.make_archive(os.path.join(target_path, "code"), "zip", code_tmp_folder)
+
+ delete_path(code_tmp_folder)
def commit(self, message: str, add_all=True):
"""