more cleaning

.qt-research-project

-71d17c7f9d876d48567b31cc350694db2eeb2cc8
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analysis/codes

-../codes/
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analysis/data

-../data
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publication/README.md

-Put your publication latex here

setup

-#! /usr/bin/env python3
-# -*- coding: utf-8 -*-
-
-import os
-import shutil
-from pathlib import Path
-from getpass import getpass
-from tempfile import mkdtemp
-from contextlib import contextmanager
-
-from git import Repo
-import gitlab
-from gitlab import Gitlab, GitlabGetError
-
-
-# Configuration variables
-
-GITLAB = "https://gitlab.kwant-project.org"
-API_VERSION = 4
-
-# API token for use in CI is stored in a snippet that is
-# only accessible to the appropriate users.
-CI_API_TOKEN_SNIPPET = ("qt/skeleton", "gitlab-api-token")
-CI_API_TOKEN_VARIABLE = "GITLAB_API_TOKEN"
-
-PARENT_GROUP = "qt"
-MARKER_FILE = ".qt-research-project"
-TEMPLATE_DIR = ".templates"
-
-BRANCH_PROTECTION_LEVEL = gitlab.const.DEVELOPER_ACCESS
-
-PRE_COMMIT_HOOK_TARGET = ".git/hooks/pre-commit"
-PRE_COMMIT_HOOK_SOURCE = ".hooks/pre-commit"
-
-FILTERS = {
-    'diff "notebook"': {
-        "command": (
-            "git-nbdiffdriver diff "
-            "--ignore-details "
-            "--ignore-outputs "
-            "--ignore-metadata"
-        )
-    },
-    'merge "notebook"': {
-        "driver": "git-nbmergedriver merge %O %A %B %L %P",
-        "name": "jupyter notebook merge driver",
-    },
-    'filter "whitespace"': {
-        "clean": r'sed -e "s/\\s\\+$//"',
-    },
-}
-
-
-@contextmanager
-def status(message):
-    print(message, "...", sep="", end="", flush=True)
-    try:
-        yield
-    except Exception:
-        print("failed")
-        raise
-    except:
-        print("aborting")
-        raise
-    else:
-        print("done")
-
-
-def is_new_project():
-    return not os.path.isfile(MARKER_FILE)
-
-
-def project_name():
-    return Path(".").absolute().name
-
-
-def project_data_name():
-    return project_name() + "-data"
-
-
-def create_gitlab_project(client, name, tags):
-    full_name = "/".join((PARENT_GROUP, name))
-    group = client.groups.get(PARENT_GROUP)
-    with status("creating project {} on {}".format(full_name, GITLAB)):
-        project = client.projects.create(
-            dict(name=name, namespace_id=group.id, visibility="private", tag_list=tags)
-        )
-    return project
-
-
-def get_snippet(client, project_name, snippet_name):
-    try:
-        project = client.projects.get(project_name)
-        snippets = project.snippets.list(as_list=False)
-        return next(s for s in snippets if s.title == snippet_name)
-    except GitlabGetError:
-        raise KeyError("project {} does not exist".format(project_name))
-    except StopIteration:
-        raise KeyError("{} has no snippet named {}".format(project_name, snippet_name))
-
-
-def init_project(api_token):
-    assert is_new_project()
-
-    with status("logging in to {}".format(GITLAB)):
-        gl = Gitlab(GITLAB, api_token, api_version=API_VERSION)
-        gl.auth()
-    gitlab_repo = create_gitlab_project(gl, project_name(), tags=["research"])
-    gitlab_data_repo = create_gitlab_project(
-        gl, project_data_name(), tags=["research", "data"]
-    )
-
-    try:
-        with status("setting API access token for CI"):
-            token = get_snippet(gl, *CI_API_TOKEN_SNIPPET).content()
-            gitlab_repo.variables.create(
-                dict(
-                    key=CI_API_TOKEN_VARIABLE,
-                    value=token.decode(),
-                )
-            )
-    except Exception:
-        print("CI jobs will not be able to access the Gitlab API")
-
-    data_dir = mkdtemp()
-    # Initialize data repository with empty commit and push to Gitlab
-    push_url = gitlab_data_repo.http_url_to_repo.replace(
-        "https://", f"https://oauth2:{api_token}@"
-    )
-    try:
-        with status("initializing data repository"):
-            data_repo = Repo.init(data_dir)
-            data_repo.index.commit("init")
-            data_repo.create_head("main")
-            data_repo.create_remote("origin", push_url)
-        with status("syncing data repository"):
-            data_repo.remotes.origin.push(refspec="main:main")
-    finally:
-        shutil.rmtree(data_dir, ignore_errors=True)
-
-    # Initialize project repository.
-    # Squash all commits from skeleton down into one and add the data
-    # repo as a submodule.
-    repo = Repo(".")
-    with status("linking data submodule"):
-        # Use the remote URL to create the data submodule (so we can remove
-        # the local data repo, then set the URL to a relative one so that
-        # CI etc. works.
-        sub = repo.create_submodule("data", "data", push_url)
-        sub.config_writer().set_value("url", "../" + project_data_name())
-
-    with status("initializing repository"):
-        # Write the skeleton "version: into the marker file
-        with open(MARKER_FILE, "w") as f:
-            f.write(repo.head.commit.hexsha)
-        repo.index.add([MARKER_FILE, ".gitmodules"])
-        # Remove main branch so that everything is squashed into one commit
-        repo.git.update_ref("-d", "refs/heads/main")
-        # Move the templates into the project
-        templates = os.listdir(TEMPLATE_DIR)
-        for file in templates:
-            shutil.copy(os.path.join(TEMPLATE_DIR, file), ".")
-        repo.index.remove([TEMPLATE_DIR], working_tree=True, r=True, f=True)
-        repo.index.add(templates)
-
-        repo.index.commit("init")
-
-    # Push repo
-    with status("syncing repository"):
-        repo.remotes.origin.set_url(
-            gitlab_repo.http_url_to_repo.replace(
-                "https://", f"https://oauth2:{api_token}@"
-            )
-        )
-        repo.remotes.origin.push(refspec="main:main")
-
-    return gitlab_repo, gitlab_data_repo
-
-
-def setup_config():
-    repo = Repo(".")
-    with repo.config_writer() as cfg:
-        with status("setting up core config"):
-            cfg.set("core", "attributesfile", ".gitattrbutes")
-
-        with status("setting up filters"):
-            for section, filters in FILTERS.items():
-                for filter, driver in filters.items():
-                    if section not in cfg.sections():
-                        cfg.add_section(section)
-                    cfg.set(section, filter, driver)
-
-    if os.path.exists(PRE_COMMIT_HOOK_TARGET):
-        print(
-            "pre-commit hook already exists: "
-            'if you want to reinstall "skeleton" version run:\n\t'
-            "rm {} && ./setup".format(PRE_COMMIT_HOOK_TARGET)
-        )
-    else:
-        shutil.copy(PRE_COMMIT_HOOK_SOURCE, PRE_COMMIT_HOOK_TARGET)
-        os.chmod(PRE_COMMIT_HOOK_TARGET, 0o775)
-        print("pre-commit hook have been installed")
-
-    with status("retrieving data submodule"):
-        repo.git.submodule("update", "--init", "--recursive")
-
-
-def main():
-    if is_new_project():
-        print("configuring new project", project_name())
-        try:
-            api_token = os.getenv("GITLAB_API_TOKEN")
-        except KeyError:
-            api_token = getpass(
-                "enter a Gitlab personal access token "
-                "(generate here {}/profile/personal_access_tokens): ".format(GITLAB)
-            )
-        gitlab_repo, gitlab_data_repo = init_project(api_token)
-        setup_config()
-        print(10 * "-")
-        print("project:", gitlab_repo.web_url)
-        print("data:", gitlab_data_repo.web_url)
-    else:
-        setup_config()
-
-
-if __name__ == "__main__":
-    main()