import os
import json
from datetime import datetime
import shutil
import contextlib
from tabulate import tabulate
import pandas as pd
try:
import git
except ImportError:
# Adding this hint to save users the confusion of trying $pip install git
raise ImportError("No module named git, please install the gitpython package")
from cadetrdm.utils import ssh_url_to_http_url
class BaseRepo:
def __init__(self, repository_path=None, search_parent_directories=False, *args, **kwargs):
"""
Base class handling most git workflows.
:param repository_path:
Path to the root directory of the repository.
:param search_parent_directories:
if True, all parent directories will be searched for a valid repo as well.
Please note that this was the default behaviour in older versions of GitPython,
which is considered a bug though.
:param args:
Args handed to git.Repo()
:param kwargs:
Kwargs handed to git.Repo()
"""
if repository_path is None or repository_path == ".":
repository_path = os.getcwd()
self._git_repo = git.Repo(repository_path, search_parent_directories=search_parent_directories, *args, **kwargs)
self._git = self._git_repo.git
self._most_recent_branch = self.active_branch.name
self._earliest_commit = None
self.add = self._git.add
@property
def active_branch(self):
return self._git_repo.active_branch
@property
def untracked_files(self):
return self._git_repo.untracked_files
@property
def current_commit_hash(self):
return str(self.head.commit)
@property
def working_dir(self):
return self._git_repo.working_dir
@property
def head(self):
return self._git_repo.head
@property
def remotes(self):
return self._git_repo.remotes
@property
def earliest_commit(self):
if self._earliest_commit is None:
*_, earliest_commit = self._git_repo.iter_commits()
self._earliest_commit = earliest_commit
return self._earliest_commit
def add_remote(self, remote_url, remote_name="origin"):
"""
ToDO add documentation
:param remote_url:
:param remote_name:
:return:
"""
self._git_repo.create_remote(remote_name, url=remote_url)
def checkout(self, *args, **kwargs):
self._most_recent_branch = self.active_branch
self._git.checkout(*args, **kwargs)
def push(self, remote=None, local_branch=None, remote_branch=None):
"""
Push local branch to remote.
:param remote:
Name of the remote to push to.
:param local_branch:
Name of the local branch to push.
:param remote_branch:
Name of the remote branch to push to.
:return:
"""
if local_branch is None:
local_branch = self.active_branch
if remote_branch is None:
remote_branch = local_branch
if remote is None:
remote = list(sorted(self._git_repo.remotes.keys()))[0]
remote_interface = self._git_repo.remotes[remote]
remote_interface.push(refspec=f'{local_branch}:{remote_branch}')
def delete_active_branch_if_branch_is_empty(self):
"""
Delete the currently active branch and checkout the master branch
:return:
"""
previous_branch = self.active_branch.name
if previous_branch == "master":
return
commit_of_current_master = str(self._git.rev_parse("master"))
commit_of_current_branch = str(self.head.commit)
if commit_of_current_branch == commit_of_current_master:
print("Removing empty branch", previous_branch)
self._git.checkout("master")
self._git.branch("-d", previous_branch)
def add_all_files(self, automatically_add_new_files=True):
"""
Stage all changes to git. This includes new, untracked files as well as modified files.
:param automatically_add_new_files:
If this is set to false a user input will be prompted if untracked files are about to be added.
:return:
List of all staged changes.
"""
self.add(".")
def reset_hard_to_head(self):
proceed = input(f'The output directory contains the following uncommitted changes:\n'
f'{self.untracked_files + self.changed_files}\n'
f' These will be lost if you continue\n'
f'Proceed? Y/n \n')
if not (proceed.lower() == "y" or proceed == ""):
raise KeyboardInterrupt
# reset all tracked files to previous commit, -q silences output
self._git.reset("-q", "--hard", "HEAD")
# remove all untracked files and directories, -q silences output
self._git.clean("-q", "-f", "-d")
@property
def changed_files(self):
changed_files = self._git.diff(None, name_only=True).split('\n')
if "" in changed_files:
changed_files.remove("")
return changed_files
@property
def exist_uncomitted_changes(self):
return len(self._git.status("--porcelain")) > 0
def dump_package_list(self, target_folder):
"""
Use "conda env export" and "pip freeze" to create environment.yml and pip_requirements.txt files.
"""
if target_folder is not None:
dump_path = target_folder
else:
dump_path = self.working_dir
print("Dumping conda environment.yml, this might take a moment.")
os.system(f"conda env export > {dump_path}/conda_environment.yml")
print("Dumping conda independent environment.yml, this might take a moment.")
os.system(f"conda env export --from-history > {dump_path}/conda_independent_environment.yml")
print("Dumping pip requirements.txt.")
os.system(f"pip freeze > {dump_path}/pip_requirements.txt")
print("Dumping pip independent requirements.txt.")
os.system(f"pip list --not-required --format freeze > {dump_path}/pip_independent_requirements.txt")
def commit(self, message: str, add_all=True):
"""
Commit current state of the repository.
:param message:
Commit message
:param add_all:
Option to add all changed and new files to git automatically.
"""
if not self.exist_uncomitted_changes:
print(f"No changes to commit in repo {self.working_dir}")
return
print(f"Commiting changes to repo {self.working_dir}")
if add_all:
self.add(".")
commit_return = self._git.commit("-m", message)
print("\n" + commit_return + "\n")
def git_ammend(self, ):
"""
Call git commit with options --amend --no-edit
"""
self._git.commit("--amend", "--no-edit")
@property
def status(self):
return self._git.status()
@property
def log(self):
return self._git.log()
def log_oneline(self):
return self._git.log("--oneline")
def print_status(self):
"""
prints git status
"""
print(self._git.status())
def print_log(self):
"""
Prints the git log
"""
print(self._git.log())
def stash_all_changes(self):
"""
Adds all untracked files to git and then stashes all changes.
Will raise a RuntimeError if no changes are found.
"""
if not self.exist_uncomitted_changes:
raise RuntimeError("No changes in repo to stash.")
self.add(".")
self._git.stash()
def prepare_new_branch(self, branch_name):
"""
Prepares a new branch to recieve data. This includes:
- checking out the master branch,
- creating a new branch from there
This thereby produces a clear, empty directory for data, while still maintaining
.gitignore and .gitatributes
:param branch_name:
Name of the new branch.
"""
self._git.checkout("master")
self._git.checkout('-b', branch_name) # equivalent to $ git checkout -b %branch_name
def apply_stashed_changes(self):
"""
Apply the last stashed changes.
If a "CONFLICT (modify/delete)" error is encountered, this is ignored.
All other errors are raised.
"""
try:
self._git.stash('pop') # equivalent to $ git stash pop
except git.exc.GitCommandError as e:
# Will raise error because the stash cannot be applied without conflicts. This is expected
if 'CONFLICT (modify/delete)' in e.stdout:
pass
else:
raise e
def test_for_uncommitted_changes(self):
"""
Raise a RuntimeError if uncommitted changes are in the repository.
:return:
"""
if self.exist_uncomitted_changes:
raise RuntimeError(f"Found uncommitted changes in the repository {self.working_dir}.")
def add_list_of_remotes_in_readme_file(self, repo_identifier: str, remotes_url_list: list):
if len(remotes_url_list) > 0:
remotes_url_list_http = [ssh_url_to_http_url(remote)
for remote in remotes_url_list]
output_link_line = " and ".join(f"[{repo_identifier}]({output_repo_remote})"
for output_repo_remote in remotes_url_list_http) + "\n"
readme_filepath = os.path.join(self.working_dir, "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))
if filelines[i].startswith(f"[{repo_identifier}](")]
if len(filelines_giving_output_repo) == 1:
line_to_be_modified = filelines_giving_output_repo[0]
filelines[line_to_be_modified] = output_link_line
elif len(filelines_giving_output_repo) == 0:
filelines.append("The output repo can be found at:\n")
filelines.append(output_link_line)
else:
raise RuntimeError(f"Multiple lines in the README.md at {readme_filepath}"
f" link to the {repo_identifier}. "
"Can't automatically update the link.")
with open(readme_filepath, "w") as file_handle:
file_handle.writelines(filelines)
class ProjectRepo(BaseRepo):
def __init__(self, repository_path=None, output_folder=None,
search_parent_directories=True, *args, **kwargs):
"""
Class for Project-Repositories. Handles interaction between the project repo and
the output (i.e. results) repo.
:param repository_path:
Path to the root of the git repository.
:param output_folder:
Path to the root of the output repository.
:param search_parent_directories:
if True, all parent directories will be searched for a valid repo as well.
Please note that this was the default behaviour in older versions of GitPython,
which is considered a bug though.
:param args:
Additional args to be handed to BaseRepo.
:param kwargs:
Additional kwargs to be handed to BaseRepo.
"""
super().__init__(repository_path, search_parent_directories=search_parent_directories, *args, **kwargs)
if output_folder is not None:
self.output_folder = output_folder
elif output_folder is None:
self.output_folder = "output"
self._output_repo = ResultsRepo(os.path.join(self.working_dir, self.output_folder))
self._on_context_enter_commit_hash = None
self._is_in_context_manager = False
@property
def output_repo(self):
if self._output_repo is None:
raise ValueError("The output repo has not been set yet.")
return self._output_repo
def get_new_output_branch_name(self):
"""
Construct a name for the new branch in the output repository.
:return: the new branch name
"""
project_repo_hash = str(self.head.commit)
timestamp = datetime.now().strftime("%Y-%m-%d_%H-%M-%S")
branch_name = "_".join([self.output_folder, "from", str(self.active_branch), project_repo_hash[:7], timestamp])
return branch_name
def check_results_master(self):
"""
Checkout the master branch, which contains all the log files.
"""
self._most_recent_branch = self._output_repo.active_branch.name
self._output_repo._git.checkout("master")
def reload_recent_results(self):
"""
Checkout the most recent previous branch.
"""
self._output_repo._git.checkout(self._most_recent_branch)
def print_output_log(self):
def insert_newlines(string, every=30):
lines = []
for i in range(0, len(string), every):
lines.append(string[i:i + every])
return '\n'.join(lines)
self.output_repo.checkout("master")
csv_filepath = os.path.join(self.working_dir, self.output_folder, "logs", "log.csv")
df = pd.read_csv(csv_filepath, sep=",", header=0)
# Clean up the headers
df = df.rename(columns={"Output repo commit message": 'Output commit message',
"Output repo branch": "Output branch",
"Output repo commit hash": "Output hash", "Project repo commit hash": "Project hash"})
# Shorten the commit hashes
df.loc[:, "Output hash"] = df.loc[:, "Output hash"].apply(lambda x: x[:8])
# Shorten commit messages
df.loc[:, "Output commit message"] = df.loc[:, "Output commit message"].apply(lambda x: x[:55])
df.loc[:, "Output commit message"] = df.loc[:, "Output commit message"].apply(insert_newlines)
# Select only columns of interest
df = df.loc[:, ["Output commit message", "Output hash", "Output branch"]]
# Print
print(tabulate(df, headers=df.columns, showindex=False))
self.output_repo.checkout(self.output_repo._most_recent_branch)
def update_output_master_logs(self, ):
"""
Dumps all the metadata information about the project repositories state and
the commit hash and branch name of the ouput repository into the master branch of
the output repository.
"""
output_branch_name = str(self._output_repo.active_branch)
output_repo_hash = str(self._output_repo.head.commit)
output_commit_message = self._output_repo.active_branch.commit.message
output_commit_message = output_commit_message.replace("\n", "; ")
self._output_repo._git.checkout("master")
logs_folderpath = os.path.join(self.working_dir, self.output_folder, "logs")
if not os.path.exists(logs_folderpath):
os.makedirs(logs_folderpath)
json_filepath = os.path.join(logs_folderpath, f"{output_branch_name}.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")
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": os.path.split(self.working_dir)[-1],
"Project repo remotes": [str(remote.url) for remote in self.remotes],
}
csv_header = ",".join(meta_info_dict.keys())
csv_data = ",".join([str(x) for x in meta_info_dict.values()])
with open(json_filepath, "w") as f:
json.dump(meta_info_dict, f, indent=2)
if not os.path.exists(csv_filepath):
with open(csv_filepath, "w") as f:
f.write(csv_header + "\n")
# csv.writer(csv_header + "\n")
with open(csv_filepath, "r") as f:
existing_header = f.readline().replace("\n", "")
if existing_header != csv_header:
raise ValueError("The used structure of the meta_dict doesn't match the header found in log.csv")
with open(csv_filepath, "a") as f:
f.write(csv_data + "\n")
self.dump_package_list(logs_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(code_copy_folderpath)
self._output_repo.add(".")
self._output_repo._git.commit("-m", f"log for '{output_commit_message}' \n"
f"of branch '{output_branch_name}'")
self._output_repo._git.checkout(output_branch_name)
self._most_recent_branch = output_branch_name
def copy_code(self, target_path):
for file in self._git.ls_files().split("\n"):
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
)
def commit(self, message: str, add_all=True):
"""
Commit current state of the repository.
:param message:
Commit message
:param add_all:
Option to add all changed and new files to git automatically.
"""
output_repo_remotes = [str(remote.url) for remote in self.output_repo.remotes]
self.add_list_of_remotes_in_readme_file("output_repo", output_repo_remotes)
output_json_filepath = os.path.join(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.dump(json_dict, file_handle, indent=2)
super().commit(message=message, add_all=add_all)
def load_external_repository(self, url, branch=None, commit=None, name=None, path=None, ):
"""
Load an external git repository as a git submodule into this repository.
:param url:
URL of the git repository.
:param branch:
Branch of the external repository to check out.
:param commit:
Commit of the external repository to check out.
:param name:
Optional custom name for the repository.
:param path:
Optional custom relative path where the repository should be placed.
:return:
"""
if path is None or name is None:
if "/" in url:
sep = "/"
elif "\\" in url:
sep = "\\"
else:
raise RuntimeError("Could not automatically extract name from URL"
" because the URL is not of a known format")
if path is None:
repo_name = url.split(sep)[-1]
path = os.path.join("external_repos", repo_name)
if name is None:
name = url.split(sep)[-1]
self._git_repo.create_submodule(name=name, url=url, branch=branch, path=path)
if commit is not None:
submodule = BaseRepo(path)
submodule._git.checkout(commit)
full_path = os.path.join(self.working_dir, path)
return full_path
def load_previous_output(self, branch_name, file_path):
"""
Load previously generated results to iterate upon.
:param branch_name:
Name of the branch of the output repository in which the results are stored
:param file_path:
Relative path within the output repository to the file you wish to load.
:return:
Absolute path to the newly copied file.
"""
if self.output_repo.exist_uncomitted_changes:
self.output_repo.stash_all_changes()
has_stashed_changes = True
else:
has_stashed_changes = False
previous_branch = self.output_repo.active_branch.name
self.output_repo._git.checkout(branch_name)
source_filepath = os.path.join(self.output_repo.working_dir, file_path)
# target_folder = os.path.join(self._output_folder + "_cached", branch_name)
target_folder = os.path.join(self.output_repo.working_dir, "cached", branch_name)
os.makedirs(target_folder, exist_ok=True)
target_filepath = os.path.join(target_folder, file_path)
shutil.copyfile(source_filepath, target_filepath)
self.output_repo._git.checkout(previous_branch)
if has_stashed_changes:
self.output_repo.apply_stashed_changes()
return target_filepath
def remove_cached_files(self):
"""
Delete all previously cached results.
"""
if os.path.exists(self.output_folder + "_cached"):
shutil.rmtree(self.output_folder + "_cached")
def enter_context(self, ):
"""
Enter the tracking context. This includes:
- Ensure no uncommitted changes in the project repository
- Remove all uncommitted changes in the output repository
- Clean up empty branches in the output repository
- Create a new empty output branch in the output repository
:return:
The name of the newly created output branch.
"""
self.test_for_uncommitted_changes()
self._on_context_enter_commit_hash = self.current_commit_hash
self._is_in_context_manager = True
output_repo = self.output_repo
if output_repo.exist_uncomitted_changes:
output_repo.reset_hard_to_head()
output_repo.delete_active_branch_if_branch_is_empty()
new_branch_name = self.get_new_output_branch_name()
# update urls in master branch of output_repo
output_repo._git.checkout("master")
project_repo_remotes = [str(remote.url) for remote in self.remotes]
output_repo.add_list_of_remotes_in_readme_file("project_repo", project_repo_remotes)
output_repo.commit("Update urls")
output_repo.prepare_new_branch(new_branch_name)
return new_branch_name
def exit_context(self, message):
"""
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
- Stage all changes in the output repository
- Commit all changes in the output repository with the given commit message.
- Update the log files in the master branch of the output repository.
:param message:
Commit message for the output repository commit.
"""
self.test_for_uncommitted_changes()
if self._on_context_enter_commit_hash != self.current_commit_hash:
raise RuntimeError("Code has changed since starting the context. Don't do that.")
print("Completed computations, commiting results")
self.output_repo.add(".")
try:
# This has to be from ._git.commit because this way it raises an error if no results have been written.
commit_return = self.output_repo._git.commit("-m", message)
self.update_output_master_logs()
print("\n" + commit_return + "\n")
except git.exc.GitCommandError as e:
raise e
finally:
self.remove_cached_files()
self._is_in_context_manager = False
self._on_context_enter_commit_hash = None
@contextlib.contextmanager
def track_results(self, results_commit_message: str, debug=False):
"""
Context manager to be used when running project code that produces output that should
be tracked in the output repository.
:param results_commit_message:
Commit message for the commit of the output repository.
"""
if debug:
yield "debug"
return
new_branch_name = self.enter_context()
try:
yield new_branch_name
except Exception as e:
raise e
else:
self.exit_context(message=results_commit_message)
class ResultsRepo(BaseRepo):
pass