Merge pull request 'tests/tools' (#22) from tests/tools into develop

Reviewed-on: https://www.kuhl-mann.de/git/git/jkuhl/corrlib/pulls/22

corrlib/cli.py

@@ -11,6 +11,7 @@ from .meas_io import load_record as mio_load_record
 import os
 from pyerrors import Corr
 from importlib.metadata import version
+from pathlib import Path
 
 
 app = typer.Typer()
@@ -24,8 +25,8 @@ def _version_callback(value: bool) -> None:
 
 @app.command()
 def update(
-    path: str = typer.Option(
-        str('./corrlib'),
+    path: Path = typer.Option(
+        Path('./corrlib'),
         "--dataset",
         "-d",
         ),
@@ -40,8 +41,8 @@ def update(
 
 @app.command()
 def lister(
-    path: str = typer.Option(
-        str('./corrlib'),
+    path: Path = typer.Option(
+        Path('./corrlib'),
         "--dataset",
         "-d",
     ),
@@ -52,8 +53,8 @@ def lister(
     """
     if entities in ['ensembles', 'Ensembles','ENSEMBLES']:
         print("Ensembles:")
-        for item in os.listdir(path + "/archive"):
-            if os.path.isdir(os.path.join(path + "/archive", item)):
+        for item in os.listdir(path / "archive"):
+            if os.path.isdir(path / "archive" / item):
                 print(item)
     elif entities == 'projects':
         results = list_projects(path)
@@ -71,8 +72,8 @@ def lister(
 
 @app.command()
 def alias_add(
-    path: str = typer.Option(
-        str('./corrlib'),
+    path: Path = typer.Option(
+        Path('./corrlib'),
         "--dataset",
         "-d",
         ),
@@ -89,8 +90,8 @@ def alias_add(
 
 @app.command()
 def find(
-    path: str = typer.Option(
-        str('./corrlib'),
+    path: Path = typer.Option(
+        Path('./corrlib'),
         "--dataset",
         "-d",
         ),
@@ -116,8 +117,8 @@ def find(
 
 @app.command()
 def stat(
-    path: str = typer.Option(
-        str('./corrlib'),
+    path: Path = typer.Option(
+        Path('./corrlib'),
         "--dataset",
         "-d",
         ),
@@ -136,8 +137,8 @@ def stat(
 
 @app.command()
 def importer(
-    path: str = typer.Option(
-        str('./corrlib'),
+    path: Path = typer.Option(
+        Path('./corrlib'),
         "--dataset",
         "-d",
         ),
@@ -159,8 +160,8 @@ def importer(
 
 @app.command()
 def reimporter(
-    path: str = typer.Option(
-        str('./corrlib'),
+    path: Path = typer.Option(
+        Path('./corrlib'),
         "--dataset",
         "-d",
         ),
@@ -183,8 +184,8 @@ def reimporter(
 
 @app.command()
 def init(
-    path: str = typer.Option(
-        str('./corrlib'),
+    path: Path = typer.Option(
+        Path('./corrlib'),
         "--dataset",
         "-d",
         ),
@@ -203,8 +204,8 @@ def init(
 
 @app.command()
 def drop_cache(
-    path: str = typer.Option(
-        str('./corrlib'),
+    path: Path = typer.Option(
+        Path('./corrlib'),
         "--dataset",
         "-d",
         ),

corrlib/find.py

@@ -7,9 +7,10 @@ from .input.implementations import codes
 from .tools import k2m, get_db_file
 from .tracker import get
 from typing import Any, Optional
+from pathlib import Path
 
 
-def _project_lookup_by_alias(db: str, alias: str) -> str:
+def _project_lookup_by_alias(db: Path, alias: str) -> str:
     """
     Lookup a projects UUID by its (human-readable) alias.
 
@@ -37,7 +38,7 @@ def _project_lookup_by_alias(db: str, alias: str) -> str:
     return str(results[0][0])
 
 
-def _project_lookup_by_id(db: str, uuid: str) -> list[tuple[str, str]]:
+def _project_lookup_by_id(db: Path, uuid: str) -> list[tuple[str, str]]:
     """
     Return the project information available in the database by UUID.
 
@@ -61,7 +62,7 @@ def _project_lookup_by_id(db: str, uuid: str) -> list[tuple[str, str]]:
     return results
 
 
-def _db_lookup(db: str, ensemble: str, correlator_name: str, code: str, project: Optional[str]=None,  parameters: Optional[str]=None,
+def _db_lookup(db: Path, ensemble: str, correlator_name: str, code: str, project: Optional[str]=None,  parameters: Optional[str]=None,
                created_before: Optional[str]=None, created_after: Optional[Any]=None, updated_before: Optional[Any]=None, updated_after: Optional[Any]=None) -> pd.DataFrame:
     """
     Look up a correlator record in the database by the data given to the method.
@@ -228,10 +229,10 @@ def sfcf_filter(results: pd.DataFrame, **kwargs: Any) -> pd.DataFrame:
     return results.drop(drops)
 
 
-def find_record(path: str, ensemble: str, correlator_name: str, code: str, project: Optional[str]=None, parameters: Optional[str]=None,
+def find_record(path: Path, ensemble: str, correlator_name: str, code: str, project: Optional[str]=None, parameters: Optional[str]=None,
                 created_before: Optional[str]=None, created_after: Optional[str]=None, updated_before: Optional[str]=None, updated_after: Optional[str]=None, revision: Optional[str]=None, **kwargs: Any) -> pd.DataFrame:
     db_file = get_db_file(path)
-    db = os.path.join(path, db_file)
+    db = path / db_file
     if code not in codes:
         raise ValueError("Code " + code + "unknown, take one of the following:" + ", ".join(codes))
     get(path, db_file)
@@ -246,7 +247,7 @@ def find_record(path: str, ensemble: str, correlator_name: str, code: str, proje
     return results.reset_index()
 
 
-def find_project(path: str, name: str) -> str:
+def find_project(path: Path, name: str) -> str:
     """
     Find a project by it's human readable name.
 
@@ -264,10 +265,10 @@ def find_project(path: str, name: str) -> str:
     """
     db_file = get_db_file(path)
     get(path, db_file)
-    return _project_lookup_by_alias(os.path.join(path, db_file), name)
+    return _project_lookup_by_alias(path / db_file, name)
 
 
-def list_projects(path: str) -> list[tuple[str, str]]:
+def list_projects(path: Path) -> list[tuple[str, str]]:
     """
     List all projects known to the library.
 

corrlib/git_tools.py

@@ -1,27 +1,28 @@
 import os
 from .tracker import save
 import git
+from pathlib import Path
 
 GITMODULES_FILE = '.gitmodules'
 
 
-def move_submodule(repo_path: str, old_path: str, new_path: str) -> None:
+def move_submodule(repo_path: Path, old_path: Path, new_path: Path) -> None:
     """
     Move a submodule to a new location.
 
     Parameters
     ----------
-    repo_path: str
+    repo_path: Path
     Path to the repository.
-    old_path: str
+    old_path: Path
         The old path of the module.
-    new_path: str
+    new_path: Path
         The new path of the module.
     """
 
-    os.rename(os.path.join(repo_path, old_path), os.path.join(repo_path, new_path))
+    os.rename(repo_path / old_path, repo_path / new_path)
 
-    gitmodules_file_path = os.path.join(repo_path, GITMODULES_FILE)
+    gitmodules_file_path = repo_path / GITMODULES_FILE
 
     # update paths in .gitmodules
     with open(gitmodules_file_path, 'r') as file:
@@ -29,8 +30,8 @@ def move_submodule(repo_path: str, old_path: str, new_path: str) -> None:
 
     updated_lines = []
     for line in lines:
-        if old_path in line:
-            line = line.replace(old_path, new_path)
+        if str(old_path) in line:
+            line = line.replace(str(old_path), str(new_path))
         updated_lines.append(line)
 
     with open(gitmodules_file_path, 'w') as file:
@@ -40,6 +41,6 @@ def move_submodule(repo_path: str, old_path: str, new_path: str) -> None:
     repo = git.Repo(repo_path)
     repo.git.add('.gitmodules')
     # save new state of the dataset
-    save(repo_path, message=f"Move module from {old_path} to {new_path}", files=['.gitmodules', repo_path])
+    save(repo_path, message=f"Move module from {old_path} to {new_path}", files=[Path('.gitmodules'), repo_path])
 
     return

corrlib/initialization.py

@@ -2,9 +2,10 @@ from configparser import ConfigParser
 import sqlite3
 import os
 from .tracker import save, init
+from pathlib import Path
 
 
-def _create_db(db: str) -> None:
+def _create_db(db: Path) -> None:
     """
     Create the database file and the table.
 
@@ -40,7 +41,7 @@ def _create_db(db: str) -> None:
     return
 
 
-def _create_config(path: str, tracker: str, cached: bool) -> ConfigParser:
+def _create_config(path: Path, tracker: str, cached: bool) -> ConfigParser:
     """
     Create the config file construction for backlogger.
 
@@ -75,7 +76,7 @@ def _create_config(path: str, tracker: str, cached: bool) -> ConfigParser:
     return config
 
 
-def _write_config(path: str, config: ConfigParser) -> None:
+def _write_config(path: Path, config: ConfigParser) -> None:
     """
     Write the config file to disk.
 
@@ -91,7 +92,7 @@ def _write_config(path: str, config: ConfigParser) -> None:
     return
 
 
-def create(path: str, tracker: str = 'datalad', cached: bool = True) -> None:
+def create(path: Path, tracker: str = 'datalad', cached: bool = True) -> None:
     """
     Create folder of backlogs.
 
@@ -107,13 +108,13 @@ def create(path: str, tracker: str = 'datalad', cached: bool = True) -> None:
     config = _create_config(path, tracker, cached)
     init(path, tracker)
     _write_config(path, config)
-    _create_db(os.path.join(path, config['paths']['db']))
-    os.chmod(os.path.join(path, config['paths']['db']), 0o666)
-    os.makedirs(os.path.join(path, config['paths']['projects_path']))
-    os.makedirs(os.path.join(path, config['paths']['archive_path']))
-    os.makedirs(os.path.join(path, config['paths']['toml_imports_path']))
-    os.makedirs(os.path.join(path, config['paths']['import_scripts_path'], 'template.py'))
-    with open(os.path.join(path, ".gitignore"), "w") as fp:
+    _create_db(path / config['paths']['db'])
+    os.chmod(path / config['paths']['db'], 0o666)
+    os.makedirs(path / config['paths']['projects_path'])
+    os.makedirs(path / config['paths']['archive_path'])
+    os.makedirs(path / config['paths']['toml_imports_path'])
+    os.makedirs(path / config['paths']['import_scripts_path'] / 'template.py')
+    with open(path / ".gitignore", "w") as fp:
         fp.write(".cache")
         fp.close()
     save(path, message="Initialized correlator library")

corrlib/input/openQCD.py

@@ -3,9 +3,10 @@ import datalad.api as dl
 import os
 import fnmatch
 from typing import Any, Optional
+from pathlib import Path
 
 
-def read_ms1_param(path: str, project: str, file_in_project: str) -> dict[str, Any]:
+def read_ms1_param(path: Path, project: str, file_in_project: str) -> dict[str, Any]:
     """
     Read the parameters for ms1 measurements from a parameter file in the project.
 
@@ -69,7 +70,7 @@ def read_ms1_param(path: str, project: str, file_in_project: str) -> dict[str, A
     return param
 
 
-def read_ms3_param(path: str, project: str, file_in_project: str) -> dict[str, Any]:
+def read_ms3_param(path: Path, project: str, file_in_project: str) -> dict[str, Any]:
     """
     Read the parameters for ms3 measurements from a parameter file in the project.
 
@@ -103,7 +104,7 @@ def read_ms3_param(path: str, project: str, file_in_project: str) -> dict[str, A
     return param
 
 
-def read_rwms(path: str, project: str, dir_in_project: str, param: dict[str, Any], prefix: str, postfix: str="ms1", version: str='2.0', names: Optional[list[str]]=None, files: Optional[list[str]]=None) -> dict[str, Any]:
+def read_rwms(path: Path, project: str, dir_in_project: str, param: dict[str, Any], prefix: str, postfix: str="ms1", version: str='2.0', names: Optional[list[str]]=None, files: Optional[list[str]]=None) -> dict[str, Any]:
     """
     Read reweighting factor measurements from the project.
 
@@ -160,7 +161,7 @@ def read_rwms(path: str, project: str, dir_in_project: str, param: dict[str, Any
     return rw_dict
 
 
-def extract_t0(path: str, project: str, dir_in_project: str, param: dict[str, Any], prefix: str, dtr_read: int, xmin: int, spatial_extent: int, fit_range: int = 5, postfix: str="", names: Optional[list[str]]=None, files: Optional[list[str]]=None) -> dict[str, Any]:
+def extract_t0(path: Path, project: str, dir_in_project: str, param: dict[str, Any], prefix: str, dtr_read: int, xmin: int, spatial_extent: int, fit_range: int = 5, postfix: str="", names: Optional[list[str]]=None, files: Optional[list[str]]=None) -> dict[str, Any]:
     """
     Extract t0 measurements from the project.
 
@@ -234,7 +235,7 @@ def extract_t0(path: str, project: str, dir_in_project: str, param: dict[str, An
     return t0_dict
 
 
-def extract_t1(path: str, project: str, dir_in_project: str, param: dict[str, Any], prefix: str, dtr_read: int, xmin: int, spatial_extent: int, fit_range: int = 5, postfix: str = "", names: Optional[list[str]]=None, files: Optional[list[str]]=None) -> dict[str, Any]:
+def extract_t1(path: Path, project: str, dir_in_project: str, param: dict[str, Any], prefix: str, dtr_read: int, xmin: int, spatial_extent: int, fit_range: int = 5, postfix: str = "", names: Optional[list[str]]=None, files: Optional[list[str]]=None) -> dict[str, Any]:
     """
     Extract t1 measurements from the project.
 

corrlib/input/sfcf.py

@@ -4,6 +4,7 @@ import json
 import os
 from typing import Any
 from fnmatch import fnmatch
+from pathlib import Path
 
 
 bi_corrs: list[str] = ["f_P", "fP", "f_p",
@@ -80,7 +81,7 @@ for c in bib_corrs:
     corr_types[c] = 'bib'
 
 
-def read_param(path: str, project: str, file_in_project: str) -> dict[str, Any]:
+def read_param(path: Path, project: str, file_in_project: str) -> dict[str, Any]:
     """
     Read the parameters from the sfcf file.
 
@@ -96,7 +97,7 @@ def read_param(path: str, project: str, file_in_project: str) -> dict[str, Any]:
 
     """
 
-    file = path + "/projects/" + project + '/' + file_in_project
+    file = path / "projects" / project / file_in_project
     dl.get(file, dataset=path)
     with open(file, 'r') as f:
         lines = f.readlines()
@@ -257,7 +258,7 @@ def get_specs(key: str, parameters: dict[str, Any], sep: str = '/') -> str:
     return s
 
 
-def read_data(path: str, project: str, dir_in_project: str, prefix: str, param: dict[str, Any], version: str = '1.0c', cfg_seperator: str = 'n', sep: str = '/', **kwargs: Any) -> dict[str, Any]:
+def read_data(path: Path, project: str, dir_in_project: str, prefix: str, param: dict[str, Any], version: str = '1.0c', cfg_seperator: str = 'n', sep: str = '/', **kwargs: Any) -> dict[str, Any]:
     """
     Extract the data from the sfcf file.
 

corrlib/main.py

@@ -8,9 +8,10 @@ from .find import _project_lookup_by_id
 from .tools import list2str, str2list, get_db_file
 from .tracker import get, save, unlock, clone, drop
 from typing import Union, Optional
+from pathlib import Path
 
 
-def create_project(path: str, uuid: str, owner: Union[str, None]=None, tags: Union[list[str], None]=None, aliases: Union[list[str], None]=None, code: Union[str, None]=None) -> None:
+def create_project(path: Path, uuid: str, owner: Union[str, None]=None, tags: Union[list[str], None]=None, aliases: Union[list[str], None]=None, code: Union[str, None]=None) -> None:
     """
     Create a new project entry in the database.
 
@@ -48,7 +49,7 @@ def create_project(path: str, uuid: str, owner: Union[str, None]=None, tags: Uni
     return
 
 
-def update_project_data(path: str, uuid: str, prop: str, value: Union[str, None] = None) -> None:
+def update_project_data(path: Path, uuid: str, prop: str, value: Union[str, None] = None) -> None:
     """
     Update/Edit a project entry in the database.
     Thin wrapper around sql3 call.
@@ -74,9 +75,9 @@ def update_project_data(path: str, uuid: str, prop: str, value: Union[str, None]
     return
 
 
-def update_aliases(path: str, uuid: str, aliases: list[str]) -> None:
+def update_aliases(path: Path, uuid: str, aliases: list[str]) -> None:
     db_file = get_db_file(path)
-    db = os.path.join(path, db_file)
+    db = path / db_file
     get(path, db_file)
     known_data = _project_lookup_by_id(db, uuid)[0]
     known_aliases = known_data[1]
@@ -102,7 +103,7 @@ def update_aliases(path: str, uuid: str, aliases: list[str]) -> None:
     return
 
 
-def import_project(path: str, url: str, owner: Union[str, None]=None, tags: Optional[list[str]]=None, aliases: Optional[list[str]]=None, code: Optional[str]=None, isDataset: bool=True) -> str:
+def import_project(path: Path, url: str, owner: Union[str, None]=None, tags: Optional[list[str]]=None, aliases: Optional[list[str]]=None, code: Optional[str]=None, isDataset: bool=True) -> str:
     """
     Import a datalad dataset into the backlogger.
 
@@ -134,14 +135,14 @@ def import_project(path: str, url: str, owner: Union[str, None]=None, tags: Opti
     uuid = str(conf.get("datalad.dataset.id"))
     if not uuid:
         raise ValueError("The dataset does not have a uuid!")
-    if not os.path.exists(path + "/projects/" + uuid):
+    if not os.path.exists(path / "projects" / uuid):
         db_file = get_db_file(path)
         get(path, db_file)
         unlock(path, db_file)
         create_project(path, uuid, owner, tags, aliases, code)
-        move_submodule(path, 'projects/tmp', 'projects/' + uuid)
-        os.mkdir(path + '/import_scripts/' + uuid)
-        save(path, message="Import project from " + url, files=['projects/' + uuid, db_file])
+        move_submodule(path, Path('projects/tmp'), Path('projects') / uuid)
+        os.mkdir(path / 'import_scripts' / uuid)
+        save(path, message="Import project from " + url, files=[Path(f'projects/{uuid}'), db_file])
     else:
         dl.drop(tmp_path, reckless='kill')
         shutil.rmtree(tmp_path)
@@ -156,7 +157,7 @@ def import_project(path: str, url: str, owner: Union[str, None]=None, tags: Opti
     return uuid
 
 
-def drop_project_data(path: str, uuid: str, path_in_project: str = "") -> None:
+def drop_project_data(path: Path, uuid: str, path_in_project: str = "") -> None:
     """
     Drop (parts of) a project to free up diskspace
 
@@ -169,6 +170,5 @@ def drop_project_data(path: str, uuid: str, path_in_project: str = "") -> None:
     path_pn_project: str, optional
         If set, only the given path within the project is dropped.
     """
-    drop(path + "/projects/" + uuid + "/" + path_in_project)
+    drop(path / "projects" / uuid / path_in_project)
     return
-

corrlib/meas_io.py

@@ -10,9 +10,13 @@ from .tools import get_db_file, cache_enabled
 from .tracker import get, save, unlock
 import shutil
 from typing import Any
+from pathlib import Path
 
 
-def write_measurement(path: str, ensemble: str, measurement: dict[str, dict[str, dict[str, Any]]], uuid: str, code: str, parameter_file: Union[str, None]) -> None:
+CACHE_DIR = ".cache"
+
+
+def write_measurement(path: Path, ensemble: str, measurement: dict[str, dict[str, dict[str, Any]]], uuid: str, code: str, parameter_file: Union[str, None]) -> None:
     """
     Write a measurement to the backlog.
     If the file for the measurement already exists, update the measurement.
@@ -33,7 +37,7 @@ def write_measurement(path: str, ensemble: str, measurement: dict[str, dict[str,
         The parameter file used for the measurement.
     """
     db_file = get_db_file(path)
-    db = os.path.join(path, db_file)
+    db = path / db_file
 
     files_to_save = []
 
@@ -44,11 +48,11 @@ def write_measurement(path: str, ensemble: str, measurement: dict[str, dict[str,
     conn = sqlite3.connect(db)
     c = conn.cursor()
     for corr in measurement.keys():
-        file_in_archive = os.path.join('.', 'archive', ensemble, corr,  uuid + '.json.gz')
-        file = os.path.join(path, file_in_archive)
+        file_in_archive = Path('.') / 'archive' / ensemble / corr / str(uuid + '.json.gz')
+        file = path / file_in_archive
         known_meas = {}
-        if not os.path.exists(os.path.join(path, '.', 'archive', ensemble, corr)):
-            os.makedirs(os.path.join(path, '.', 'archive', ensemble, corr))
+        if not os.path.exists(path / 'archive' / ensemble / corr):
+            os.makedirs(path / 'archive' / ensemble / corr)
             files_to_save.append(file_in_archive)
         else:
             if os.path.exists(file):
@@ -99,7 +103,7 @@ def write_measurement(path: str, ensemble: str, measurement: dict[str, dict[str,
                 pars[subkey] = json.dumps(parameters)
         for subkey in subkeys:
             parHash = sha256(str(pars[subkey]).encode('UTF-8')).hexdigest()
-            meas_path = file_in_archive + "::" + parHash
+            meas_path = str(file_in_archive) + "::" + parHash
 
             known_meas[parHash] = measurement[corr][subkey]
 
@@ -115,7 +119,7 @@ def write_measurement(path: str, ensemble: str, measurement: dict[str, dict[str,
     return
 
 
-def load_record(path: str, meas_path: str) -> Union[Corr, Obs]:
+def load_record(path: Path, meas_path: str) -> Union[Corr, Obs]:
     """
     Load a list of records by their paths.
 
@@ -134,7 +138,7 @@ def load_record(path: str, meas_path: str) -> Union[Corr, Obs]:
     return load_records(path, [meas_path])[0]
 
 
-def load_records(path: str, meas_paths: list[str], preloaded: dict[str, Any] = {}) -> list[Union[Corr, Obs]]:
+def load_records(path: Path, meas_paths: list[str], preloaded: dict[str, Any] = {}) -> list[Union[Corr, Obs]]:
     """
     Load a list of records by their paths.
 
@@ -162,11 +166,11 @@ def load_records(path: str, meas_paths: list[str], preloaded: dict[str, Any] = {
     returned_data: list[Any] = []
     for file in needed_data.keys():
         for key in list(needed_data[file]):
-            if os.path.exists(cache_path(path, file, key) + ".p"):
-                returned_data.append(load_object(cache_path(path, file, key) + ".p"))
+            if os.path.exists(str(cache_path(path, file, key)) + ".p"):
+                returned_data.append(load_object(str(cache_path(path, file, key)) + ".p"))
             else:
                 if file not in preloaded:
-                    preloaded[file] = preload(path, file)
+                    preloaded[file] = preload(path, Path(file))
                 returned_data.append(preloaded[file][key])
                 if cache_enabled(path):
                     if not os.path.exists(cache_dir(path, file)):
@@ -175,7 +179,7 @@ def load_records(path: str, meas_paths: list[str], preloaded: dict[str, Any] = {
     return returned_data
 
 
-def cache_dir(path: str, file: str) -> str:
+def cache_dir(path: Path, file: str) -> Path:
     """
     Returns the directory corresponding to the cache for the given file.
 
@@ -190,14 +194,14 @@ def cache_dir(path: str, file: str) -> str:
     cache_path: str
         The path holding the cached data for the given file.
     """
-    cache_path_list = [path]
-    cache_path_list.append(".cache")
-    cache_path_list.extend(file.split("/")[1:])
-    cache_path = "/".join(cache_path_list)
+    cache_path_list = file.split("/")[1:]
+    cache_path = path / CACHE_DIR
+    for directory in cache_path_list:
+        cache_path /= directory
     return cache_path
 
 
-def cache_path(path: str, file: str, key: str) -> str:
+def cache_path(path: Path, file: str, key: str) -> Path:
     """
     Parameters
     ----------
@@ -213,11 +217,11 @@ def cache_path(path: str, file: str, key: str) -> str:
     cache_path: str
         The path at which the measurement of the given file and key is cached.
     """
-    cache_path = os.path.join(cache_dir(path, file), key)
+    cache_path = cache_dir(path, file) / key
     return cache_path
 
 
-def preload(path: str, file: str) -> dict[str, Any]:
+def preload(path: Path, file: Path) -> dict[str, Any]:
     """
     Read the contents of a file into a json dictionary with the pyerrors.json.load_json_dict method.
 
@@ -234,12 +238,12 @@ def preload(path: str, file: str) -> dict[str, Any]:
         The data read from the file.
     """
     get(path, file)
-    filedict: dict[str, Any] = pj.load_json_dict(os.path.join(path, file))
+    filedict: dict[str, Any] = pj.load_json_dict(path / file)
     print("> read file")
     return filedict
 
 
-def drop_record(path: str, meas_path: str) -> None:
+def drop_record(path: Path, meas_path: str) -> None:
     """
     Drop a record by it's path.
 
@@ -251,9 +255,9 @@ def drop_record(path: str, meas_path: str) -> None:
         The measurement path as noted in the database.
     """
     file_in_archive = meas_path.split("::")[0]
-    file = os.path.join(path, file_in_archive)
+    file = path / file_in_archive
     db_file = get_db_file(path)
-    db = os.path.join(path, db_file)
+    db = path / db_file
     get(path, db_file)
     sub_key = meas_path.split("::")[1]
     unlock(path, db_file)
@@ -268,7 +272,7 @@ def drop_record(path: str, meas_path: str) -> None:
     known_meas = pj.load_json_dict(file)
     if sub_key in known_meas:
         del known_meas[sub_key]
-        unlock(path, file_in_archive)
+        unlock(path, Path(file_in_archive))
         pj.dump_dict_to_json(known_meas, file)
         save(path, message="Drop measurements to database", files=[db, file])
         return
@@ -276,7 +280,7 @@ def drop_record(path: str, meas_path: str) -> None:
         raise ValueError("This measurement does not exist as a file!")
 
 
-def drop_cache(path: str) -> None:
+def drop_cache(path: Path) -> None:
     """
     Drop the cache directory of the library.
 
@@ -285,7 +289,7 @@ def drop_cache(path: str) -> None:
     path: str
         The path of the library.
     """
-    cache_dir = os.path.join(path, ".cache")
+    cache_dir = path / ".cache"
     for f in os.listdir(cache_dir):
-        shutil.rmtree(os.path.join(cache_dir, f))
+        shutil.rmtree(cache_dir / f)
     return

corrlib/toml.py

@@ -19,6 +19,7 @@ from .meas_io import write_measurement
 import os
 from .input.implementations import codes as known_codes
 from typing import Any
+from pathlib import Path
 
 
 def replace_string(string: str, name: str, val: str) -> str:
@@ -126,7 +127,7 @@ def check_measurement_data(measurements: dict[str, dict[str, str]], code: str) -
     return
 
 
-def import_tomls(path: str, files: list[str], copy_files: bool=True) -> None:
+def import_tomls(path: Path, files: list[str], copy_files: bool=True) -> None:
     """
     Import multiple toml files.
 
@@ -144,7 +145,7 @@ def import_tomls(path: str, files: list[str], copy_files: bool=True) -> None:
     return
 
 
-def import_toml(path: str, file: str, copy_file: bool=True) -> None:
+def import_toml(path: Path, file: str, copy_file: bool=True) -> None:
     """
     Import a project decribed by a .toml file.
 
@@ -171,7 +172,7 @@ def import_toml(path: str, file: str, copy_file: bool=True) -> None:
     aliases = project.get('aliases', [])
     uuid = project.get('uuid', None)
     if uuid is not None:
-        if not os.path.exists(path + "/projects/" + uuid):
+        if not os.path.exists(path / "projects" / uuid):
             uuid = import_project(path, project['url'], aliases=aliases)
         else:
             update_aliases(path, uuid, aliases)
@@ -213,18 +214,18 @@ def import_toml(path: str, file: str, copy_file: bool=True) -> None:
         write_measurement(path, ensemble, measurement, uuid, project['code'], (md['param_file'] if 'param_file' in md else None))
         print(mname + " imported.")
 
-    if not os.path.exists(os.path.join(path, "toml_imports", uuid)):
-        os.makedirs(os.path.join(path, "toml_imports", uuid))
+    if not os.path.exists(path / "toml_imports" / uuid):
+        os.makedirs(path / "toml_imports" / uuid)
     if copy_file:
-        import_file = os.path.join(path, "toml_imports", uuid, file.split("/")[-1])
+        import_file = path / "toml_imports" / uuid / file.split("/")[-1]
         shutil.copy(file, import_file)
-        save(path, files=[import_file], message="Import using " + import_file)
-        print("File copied to " + import_file)
+        save(path, files=[import_file], message=f"Import using {import_file}")
+        print(f"File copied to {import_file}")
     print("Imported project.")
     return
 
 
-def reimport_project(path: str, uuid: str) -> None:
+def reimport_project(path: Path, uuid: str) -> None:
     """
     Reimport an existing project using the files that are already available for this project.
 
@@ -235,14 +236,14 @@ def reimport_project(path: str, uuid: str) -> None:
     uuid: str
     uuid of the project that is to be reimported.
     """
-    config_path = "/".join([path, "import_scripts", uuid])
+    config_path = path / "import_scripts" / uuid
     for p, filenames, dirnames in os.walk(config_path):
         for fname in filenames:
             import_toml(path, os.path.join(config_path, fname), copy_file=False)
     return
 
 
-def update_project(path: str, uuid: str) -> None:
+def update_project(path: Path, uuid: str) -> None:
     """
     Update all entries associated with a given project.
 

corrlib/tools.py

@@ -1,6 +1,7 @@
 import os
 from configparser import ConfigParser
 from typing import Any
+from pathlib import Path
 
 CONFIG_FILENAME = ".corrlib"
 cached: bool = True
@@ -73,7 +74,7 @@ def k2m(k: float) -> float:
     return (1/(2*k))-4
 
 
-def set_config(path: str, section: str, option: str, value: Any) -> None:
+def set_config(path: Path, section: str, option: str, value: Any) -> None:
     """
     Set configuration parameters for the library.
 
@@ -88,7 +89,7 @@ def set_config(path: str, section: str, option: str, value: Any) -> None:
     value: Any
         The value we set the option to.
     """
-    config_path = os.path.join(path, '.corrlib')
+    config_path = os.path.join(path, CONFIG_FILENAME)
     config = ConfigParser()
     if os.path.exists(config_path):
         config.read(config_path)
@@ -100,7 +101,7 @@ def set_config(path: str, section: str, option: str, value: Any) -> None:
     return
 
 
-def get_db_file(path: str) -> str:
+def get_db_file(path: Path) -> Path:
     """
     Get the database file associated with the library at the given path.
 
@@ -118,11 +119,13 @@ def get_db_file(path: str) -> str:
     config = ConfigParser()
     if os.path.exists(config_path):
         config.read(config_path)
-    db_file = config.get('paths', 'db', fallback='backlogger.db')
+    else:
+        raise FileNotFoundError("Configuration file not found.")
+    db_file = Path(config.get('paths', 'db', fallback='backlogger.db'))
     return db_file
 
 
-def cache_enabled(path: str) -> bool:
+def cache_enabled(path: Path) -> bool:
     """
     Check, whether the library is cached.
     Fallback is true.
@@ -141,6 +144,10 @@ def cache_enabled(path: str) -> bool:
     config = ConfigParser()
     if os.path.exists(config_path):
         config.read(config_path)
+    else:
+        raise FileNotFoundError("Configuration file not found.")
     cached_str = config.get('core', 'cached', fallback='True')
+    if cached_str not in ['True', 'False']:
+        raise ValueError(f"String {cached_str} is not a valid option, only True and False are allowed!")
     cached_bool = cached_str == ('True')
     return cached_bool

corrlib/tracker.py

@@ -4,9 +4,10 @@ import datalad.api as dl
 from typing import Optional
 import shutil
 from .tools import get_db_file
+from pathlib import Path
 
 
-def get_tracker(path: str) -> str:
+def get_tracker(path: Path) -> str:
     """
     Get the tracker used in the dataset located at path.
 
@@ -30,7 +31,7 @@ def get_tracker(path: str) -> str:
     return tracker
 
 
-def get(path: str, file: str) -> None:
+def get(path: Path, file: Path) -> None:
     """
     Wrapper function to get a file from the dataset located at path with the specified tracker.
 
@@ -56,7 +57,7 @@ def get(path: str, file: str) -> None:
     return
 
 
-def save(path: str, message: str, files: Optional[list[str]]=None) -> None:
+def save(path: Path, message: str, files: Optional[list[Path]]=None) -> None:
     """
     Wrapper function to save a file to the dataset located at path with the specified tracker.
 
@@ -72,7 +73,7 @@ def save(path: str, message: str, files: Optional[list[str]]=None) -> None:
     tracker = get_tracker(path)
     if tracker == 'datalad':
         if files is not None:
-            files = [os.path.join(path, f) for f in files]
+            files = [path / f for f in files]
         dl.save(files, message=message, dataset=path)
     elif tracker == 'None':
         Warning("Tracker 'None' does not implement save.")
@@ -81,7 +82,7 @@ def save(path: str, message: str, files: Optional[list[str]]=None) -> None:
         raise ValueError(f"Tracker {tracker} is not supported.")
 
 
-def init(path: str, tracker: str='datalad') -> None:
+def init(path: Path, tracker: str='datalad') -> None:
     """
     Initialize a dataset at the specified path with the specified tracker.
 
@@ -101,7 +102,7 @@ def init(path: str, tracker: str='datalad') -> None:
     return
 
 
-def unlock(path: str, file: str) -> None:
+def unlock(path: Path, file: Path) -> None:
     """
     Wrapper function to unlock a file in the dataset located at path with the specified tracker.
 
@@ -123,7 +124,7 @@ def unlock(path: str, file: str) -> None:
     return
 
 
-def clone(path: str, source: str, target: str) -> None:
+def clone(path: Path, source: str, target: str) -> None:
     """
     Wrapper function to clone a dataset from source to target with the specified tracker.
     Parameters
@@ -147,7 +148,7 @@ def clone(path: str, source: str, target: str) -> None:
     return
 
 
-def drop(path: str, reckless: Optional[str]=None) -> None:
+def drop(path: Path, reckless: Optional[str]=None) -> None:
     """
     Wrapper function to drop data from a dataset located at path with the specified tracker.
 

tests/cli_test.py

@@ -2,18 +2,19 @@ from typer.testing import CliRunner
 from corrlib.cli import app
 import os
 import sqlite3 as sql
+from pathlib import Path
 
 
 runner = CliRunner()
 
 
-def test_version():
+def test_version() -> None:
     result = runner.invoke(app, ["--version"])
     assert result.exit_code == 0
     assert "corrlib" in result.output
 
 
-def test_init_folders(tmp_path):
+def test_init_folders(tmp_path: Path) -> None:
     dataset_path = tmp_path / "test_dataset"
     result = runner.invoke(app, ["init", "--dataset", str(dataset_path)])
     assert result.exit_code == 0
@@ -21,7 +22,7 @@ def test_init_folders(tmp_path):
     assert os.path.exists(str(dataset_path / "backlogger.db"))
 
 
-def test_init_db(tmp_path):
+def test_init_db(tmp_path: Path) -> None:
     dataset_path = tmp_path / "test_dataset"
     result = runner.invoke(app, ["init", "--dataset", str(dataset_path)])
     assert result.exit_code == 0
@@ -81,7 +82,7 @@ def test_init_db(tmp_path):
         assert expected_col in backlog_column_names
 
 
-def test_list(tmp_path):
+def test_list(tmp_path: Path) -> None:
     dataset_path = tmp_path / "test_dataset"
     result = runner.invoke(app, ["init", "--dataset", str(dataset_path)])
     assert result.exit_code == 0

tests/import_project_test.py

@@ -1,7 +1,7 @@
 import corrlib.toml as t
 
 
-def test_toml_check_measurement_data():
+def test_toml_check_measurement_data() -> None:
     measurements = {
                     "a":
                         {

tests/sfcf_in_test.py

@@ -1,7 +1,7 @@
 import corrlib.input.sfcf as input
 import json
 
-def test_get_specs():
+def test_get_specs() -> None:
     parameters = {
         'crr': [
             'f_P', 'f_A'
@@ -26,4 +26,4 @@ def test_get_specs():
     key = "f_P/q1 q2/1/0/0"
     specs = json.loads(input.get_specs(key, parameters))
     assert specs['quarks'] == ['a', 'b']
-    assert specs['wf1'][0] == [1, [0, 0]]
+    assert specs['wf1'][0] == [1, [0, 0]]

tests/test_initialization.py

@@ -1,24 +1,25 @@
 import corrlib.initialization as init
 import os
 import sqlite3 as sql
+from pathlib import Path
 
-def test_init_folders(tmp_path):
+def test_init_folders(tmp_path: Path) -> None:
     dataset_path = tmp_path / "test_dataset"
-    init.create(str(dataset_path))
+    init.create(dataset_path)
     assert os.path.exists(str(dataset_path))
     assert os.path.exists(str(dataset_path / "backlogger.db"))
 
 
-def test_init_folders_no_tracker(tmp_path):
+def test_init_folders_no_tracker(tmp_path: Path) -> None:
     dataset_path = tmp_path / "test_dataset"
-    init.create(str(dataset_path), tracker="None")
+    init.create(dataset_path, tracker="None")
     assert os.path.exists(str(dataset_path))
     assert os.path.exists(str(dataset_path / "backlogger.db"))
 
 
-def test_init_config(tmp_path):
+def test_init_config(tmp_path: Path) -> None:
     dataset_path = tmp_path / "test_dataset"
-    init.create(str(dataset_path), tracker="None")
+    init.create(dataset_path, tracker="None")
     config_path = dataset_path / ".corrlib"
     assert os.path.exists(str(config_path))
     from configparser import ConfigParser
@@ -34,9 +35,9 @@ def test_init_config(tmp_path):
     assert config.get("paths", "import_scripts_path") == "import_scripts"
 
 
-def test_init_db(tmp_path):
+def test_init_db(tmp_path: Path) -> None:
     dataset_path = tmp_path / "test_dataset"
-    init.create(str(dataset_path))
+    init.create(dataset_path)
     assert os.path.exists(str(dataset_path / "backlogger.db"))
     conn = sql.connect(str(dataset_path / "backlogger.db"))
     cursor = conn.cursor()

tests/tools_test.py

@@ -1,31 +1,84 @@
-
-
 from corrlib import tools as tl
+from configparser import ConfigParser
+from pathlib import Path
+import pytest
 
 
-def test_m2k():
+def test_m2k() -> None:
     for m in [0.1, 0.5, 1.0]:
         expected_k = 1 / (2 * m + 8)
         assert tl.m2k(m) == expected_k
 
 
-def test_k2m():
+def test_k2m() -> None:
     for m in [0.1, 0.5, 1.0]:
         assert tl.k2m(m) == (1/(2*m))-4
 
 
-def test_k2m_m2k():
+def test_k2m_m2k() -> None:
     for m in [0.1, 0.5, 1.0]:
         k = tl.m2k(m)
         m_converted = tl.k2m(k)
         assert abs(m - m_converted) < 1e-9
 
 
-def test_str2list():
+def test_str2list() -> None:
     assert tl.str2list("a,b,c") == ["a", "b", "c"]
     assert tl.str2list("1,2,3") == ["1", "2", "3"]
 
 
-def test_list2str():
+def test_list2str() -> None:
     assert tl.list2str(["a", "b", "c"]) == "a,b,c"
     assert tl.list2str(["1", "2", "3"]) == "1,2,3"
+
+
+def test_set_config(tmp_path: Path) -> None:
+    section = "core"
+    option = "test_option"
+    value = "test_value"
+    # config is not yet available
+    tl.set_config(tmp_path, section, option, value)
+    config_path = tmp_path / '.corrlib'
+    config = ConfigParser()
+    config.read(config_path)
+    assert config.get('core', 'test_option', fallback="not the value") == "test_value"
+    # now, a config file is already present
+    section = "core"
+    option = "test_option2"
+    value = "test_value2"
+    tl.set_config(tmp_path, section, option, value)
+    config_path = tmp_path / '.corrlib'
+    config = ConfigParser()
+    config.read(config_path)
+    assert config.get('core', 'test_option2', fallback="not the value") == "test_value2"
+    # update option 2
+    section = "core"
+    option = "test_option2"
+    value = "test_value3"
+    tl.set_config(tmp_path, section, option, value)
+    config_path = tmp_path / '.corrlib'
+    config = ConfigParser()
+    config.read(config_path)
+    assert config.get('core', 'test_option2', fallback="not the value") == "test_value3"
+
+
+def test_get_db_file(tmp_path: Path) -> None:
+    section = "paths"
+    option = "db"
+    value = "test_value"
+    # config is not yet available
+    tl.set_config(tmp_path, section, option, value)
+    assert tl.get_db_file(tmp_path) == Path("test_value")
+
+
+def test_cache_enabled(tmp_path: Path) -> None:
+    section = "core"
+    option = "cached"
+    # config is not yet available
+    tl.set_config(tmp_path, section, option, "True")
+    assert tl.cache_enabled(tmp_path)
+    tl.set_config(tmp_path, section, option, "False")
+    assert not tl.cache_enabled(tmp_path)
+    tl.set_config(tmp_path, section, option, "lalala")
+    with pytest.raises(ValueError):
+        tl.cache_enabled(tmp_path)