re-add get_file method

.github/workflows/mypy.yaml

@@ -1,30 +0,0 @@
-name: Mypy
-
-on:
-  push:
-  pull_request:
-  workflow_dispatch:
-
-jobs:
-  mypy:
-    runs-on: ubuntu-latest
-    env:
-      UV_CACHE_DIR: /tmp/.uv-cache
-    steps:
-      - name: Install git-annex
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y git-annex
-      - name: Check out the repository
-        uses: https://github.com/RouxAntoine/checkout@v4.1.8
-        with:
-          show-progress: true
-      - name: Install uv
-        uses: astral-sh/setup-uv@v7
-        with:
-          python-version: ${{ matrix.python-version }}
-          enable-cache: true
-      - name: Install corrlib
-        run: uv sync --locked --all-extras --dev --python "3.12"
-      - name: Run tests
-        run: uv run mypy corrlib

.github/workflows/pytest.yaml

@@ -1,39 +0,0 @@
-name: Pytest
-
-on:
-  push:
-  pull_request:
-  workflow_dispatch:
-  schedule:
-    - cron: '0 4 1 * *'
-
-jobs:
-  pytest:
-    strategy:
-      matrix:
-        python-version:
-          - "3.12"
-          - "3.13"
-          - "3.14"
-
-    runs-on: ubuntu-latest
-    env:
-      UV_CACHE_DIR: /tmp/.uv-cache
-    steps:
-      - name: Install git-annex
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y git-annex
-      - name: Check out the repository
-        uses: https://github.com/RouxAntoine/checkout@v4.1.8
-        with:
-          show-progress: true
-      - name: Install uv
-        uses: astral-sh/setup-uv@v7
-        with:
-          python-version: ${{ matrix.python-version }}
-          enable-cache: true
-      - name: Install corrlib
-        run: uv sync --locked --all-extras --dev --python ${{ matrix.python-version }}
-      - name: Run tests
-        run: uv run pytest --cov=corrlib tests

.github/workflows/ruff.yaml

@@ -1,30 +0,0 @@
-name: Ruff
-
-on:
-  push:
-  pull_request:
-  workflow_dispatch:
-
-jobs:
-  ruff:
-
-    runs-on: ubuntu-latest
-    env:
-      UV_CACHE_DIR: /tmp/.uv-cache
-    steps:
-      - name: Install git-annex
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y git-annex
-      - name: Check out the repository
-        uses: https://github.com/RouxAntoine/checkout@v4.1.8
-        with:
-          show-progress: true
-      - name: Install uv
-        uses: astral-sh/setup-uv@v7
-        with:
-          enable-cache: true
-      - name: Install corrlib
-        run: uv sync --locked --all-extras --dev --python "3.12"
-      - name: Run tests
-        run: uv run ruff check corrlib

.gitignore

@@ -2,7 +2,4 @@ pyerrors_corrlib.egg-info
 __pycache__
 *.egg-info
 test.ipynb
-.vscode
+test_ds
-.venv
-.pytest_cache
-.coverage

.gitmodules

@@ -0,0 +1,5 @@
+[submodule "projects/tmp"]
+	path = projects/tmp
+	url = git@kuhl-mann.de:lattice/charm_SF_data.git
+	datalad-id = 5f402163-77f2-470e-b6f1-64d7bf9f87d4
+	datalad-url = git@kuhl-mann.de:lattice/charm_SF_data.git

README.md

@@ -5,3 +5,12 @@ This is done in a reproducible way using `datalad`.
 In principle, a dataset is created, that is automatically administered by the backlogger, in which data from differnt projects are held together.
 Everything is catalogued by a searchable SQL database, which holds the paths to the respective measurements.
 The original projects can be linked to the dataset and the data may be imported using wrapper functions around the read methonds of pyerrors.
+
+We work with the following nomenclature in this project:
+- Measurement
+    A setis of Observables, including the appropriate metadata.
+- Project
+    A series of measurements that was done by one person as part of their research.
+- Record
+    An entry of a single Correlator in the database of the backlogger.
+- 

TODO.md

@@ -1,14 +1,21 @@
 # TODO
 
 ## Features
-- implement import of non-datalad projects
+- [ ] implement import of non-datalad projects
-- implement a way to use another backlog repo as a project
+- [ ] implement a way to use another backlog repo as a project
-
+- [ ] make cache deadlock resistent (no read while writing)
-- find a way to convey the mathematical structure of what EXACTLY is the form of the correlator in a specific project
+- [ ] find a way to convey the mathematical structure of what EXACTLY is the form of the correlator in a specific project
-    - this could e.g. be done along the lines of mandatory documentation
+    - [ ] this could e.g. be done along the lines of mandatory documentation
-- keep better track of the versions of the code, that was used for a specific measurement.
+- [ ] keep better track of the versions of the code, that was used for a specific measurement.
-    - maybe let this be an input in the project file?
+    - [ ] maybe let this be an input in the project file?
-    - git repo and commit hash/version tag
+    - [ ] git repo and commit hash/version tag
-
+    - [ ] implement a code table?
+- [ ] parallel processing of measurements
+- [ ] extra SQL table for ensembles with UUID and aliases
 ## Bugfixes
 - [ ] revisit the reimport function for single files
+- [ ] drop record needs to look if no records are left in a json file.
+
+## Rough Ideas
+- [ ] multitable could provide a high speed implementation of an HDF5 based format
+- [ ] implement also a way to include compiled binaries in the archives.

corrlib/__init__.py

@@ -15,10 +15,10 @@ For now, we are interested in collecting primary IObservables only, as these are
 
 __app_name__ = "corrlib"
 
+from .main import *
 from .import input as input
-from .initialization import create as create
+from .initialization import *
-from .meas_io import load_record as load_record
+from .meas_io import *
-from .meas_io import load_records as load_records
+from .cache_io import *
-from .find import find_project as find_project
+from .find import *
-from .find import find_record as find_record
+from .version import __version__
-from .find import list_projects as list_projects

corrlib/__main__.py

@@ -1,9 +1,8 @@
 from corrlib import cli, __app_name__
 
 
-def main() -> None:
+def main():
     cli.app(prog_name=__app_name__)
-    return
 
 
 if __name__ == "__main__":

corrlib/cache_io.py

@@ -0,0 +1,58 @@
+from typing import Union, Optional
+import os
+import shutil
+from .tools import record2name_key
+from pyerrors import dump_object
+import datalad.api as dl
+import sqlite3
+
+
+def get_version_hash(path, record):
+    db = os.path.join(path, "backlogger.db")
+    dl.get(db, dataset=path)
+    conn = sqlite3.connect(db)
+    c = conn.cursor()
+    c.execute(f"SELECT current_version FROM 'backlogs' WHERE path = '{record}'")
+    return c.fetchall()[0][0]
+
+
+def drop_cache_files(path: str, fs: Optional[list[str]]=None):
+    cache_dir = os.path.join(path, ".cache")
+    if fs is None:
+        fs = os.listdir(cache_dir)
+    for f in fs:
+        shutil.rmtree(os.path.join(cache_dir, f))
+
+
+def cache_dir(path, file):
+    cache_path_list = [path]
+    cache_path_list.append(".cache")
+    cache_path_list.extend(file.split("/")[1:])
+    cache_path = "/".join(cache_path_list)
+    return cache_path
+
+
+def cache_path(path, file, sha_hash, key):
+    cache_path = os.path.join(cache_dir(path, file), key + "_" +  sha_hash)
+    return cache_path
+
+
+def is_old_version(path, record):
+    version_hash = get_version_hash(path, record)
+    file, key = record2name_key(record)
+    meas_cache_path = os.path.join(cache_dir(path, file))
+    ls = []
+    for p, ds, fs in os.walk(meas_cache_path):
+        ls.extend(fs)
+    for filename in ls:
+        if key == filename.split("_")[0]:
+            if not version_hash == filename.split("_")[1][:-2]:
+                return True
+            else:
+                return False
+
+
+def is_in_cache(path, record):
+    version_hash = get_version_hash(path, record)
+    file, key = record2name_key(record)
+    return os.path.exists(cache_path(path, file, version_hash, key) + ".p")

corrlib/cli.py

@@ -1,14 +1,13 @@
 from typing import Optional
 import typer
-from corrlib import __app_name__
+from corrlib import __app_name__, __version__
 from .initialization import create
 from .toml import import_tomls, update_project, reimport_project
 from .find import find_record, list_projects
 from .tools import str2list
 from .main import update_aliases
-from .meas_io import drop_cache as mio_drop_cache
+from .cache_io import drop_cache_files as cio_drop_cache_files
 import os
-from importlib.metadata import version
 
 
 app = typer.Typer()
@@ -16,7 +15,7 @@ app = typer.Typer()
 
 def _version_callback(value: bool) -> None:
     if value:
-        print(__app_name__, version(__app_name__))
+        typer.echo(f"{__app_name__} v{__version__}")
         raise typer.Exit()
 
 
@@ -26,9 +25,9 @@ def update(
         str('./corrlib'),
         "--dataset",
         "-d",
-        ),
+    ),
     uuid: str = typer.Argument(),
-    ) -> None:
+) -> None:
     """
     Update a project by it's UUID.
     """
@@ -43,7 +42,7 @@ def list(
         "-d",
     ),
     entities: str = typer.Argument('ensembles'),
-    ) -> None:
+) -> None:
     """
     List entities. (ensembles, projects)
     """
@@ -72,10 +71,10 @@ def alias_add(
         str('./corrlib'),
         "--dataset",
         "-d",
-        ),
+    ),
     uuid: str = typer.Argument(),
     alias: str = typer.Argument(),
-    ) -> None:
+) -> None:
     """
     Add an alias to a project UUID.
     """
@@ -90,11 +89,11 @@ def find(
         str('./corrlib'),
         "--dataset",
         "-d",
-        ),
+    ),
     ensemble: str = typer.Argument(),
     corr: str = typer.Argument(),
     code: str = typer.Argument(),
-    ) -> None:
+) -> None:
     """
     Find a record in the backlog at hand. Through specifying it's ensemble and the measured correlator.
     """
@@ -108,15 +107,15 @@ def importer(
         str('./corrlib'),
         "--dataset",
         "-d",
-        ),
+    ),
     files: str = typer.Argument(
-        ),
+    ),
     copy_file: bool = typer.Option(
         bool(True),
         "--save",
         "-s",
-        ),
+    ),
-    ) -> None:
+) -> None:
     """
     Import a project from a .toml-file via CLI.
     """
@@ -152,17 +151,12 @@ def init(
         str('./corrlib'),
         "--dataset",
         "-d",
-        ),
+    ),
-    tracker: str = typer.Option(
+) -> None:
-        str('datalad'),
-        "--tracker",
-        "-t",
-        ),
-    ) -> None:
     """
     Initialize a new backlog-database.
     """
-    create(path, tracker)
+    create(path)
     return
 
 
@@ -172,12 +166,12 @@ def drop_cache(
         str('./corrlib'),
         "--dataset",
         "-d",
-        ),
+    ),
-    ) -> None:
+) -> None:
     """
     Drop the currect cache directory of the dataset.
     """
-    mio_drop_cache(path)
+    cio_drop_cache_files(path)
     return
 
 
@@ -190,6 +184,6 @@ def main(
         help="Show the application's version and exit.",
         callback=_version_callback,
         is_eager=True,
-        )
+    )
-    ) -> None:
+) -> None:
     return

corrlib/find.py

@@ -1,31 +1,29 @@
 import sqlite3
+import datalad.api as dl
 import os
 import json
 import pandas as pd
 import numpy as np
 from .input.implementations import codes
-from .tools import k2m, get_db_file
+from .tools import k2m, get_file
-from .tracker import get
-from typing import Any, Optional
-
 # this will implement the search functionality
 
 
-def _project_lookup_by_alias(db: str, alias: str) -> str:
+def _project_lookup_by_alias(db, alias):
     # this will lookup the project name based on the alias
     conn = sqlite3.connect(db)
     c = conn.cursor()
     c.execute(f"SELECT * FROM 'projects' WHERE alias = '{alias}'")
     results = c.fetchall()
     conn.close()
-    if len(results)>1:
+    if len(results) > 1:
         print("Error: multiple projects found with alias " + alias)
     elif len(results) == 0:
         raise Exception("Error: no project found with alias " + alias)
-    return str(results[0][0])
+    return results[0][0]
 
 
-def _project_lookup_by_id(db: str, uuid: str) -> list[tuple[str, str]]:
+def _project_lookup_by_id(db, uuid):
     conn = sqlite3.connect(db)
     c = conn.cursor()
     c.execute(f"SELECT * FROM 'projects' WHERE id = '{uuid}'")
@@ -34,8 +32,7 @@ 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, ensemble, correlator_name,code, project=None,  parameters=None, created_before=None, created_after=None, updated_before=None, updated_after=None, revision=None):
-               created_before: Optional[str]=None, created_after: Optional[Any]=None, updated_before: Optional[Any]=None, updated_after: Optional[Any]=None) -> pd.DataFrame:
     project_str = project
 
     search_expr = f"SELECT * FROM 'backlogs' WHERE name = '{correlator_name}' AND ensemble = '{ensemble}'"
@@ -59,7 +56,7 @@ def _db_lookup(db: str, ensemble: str, correlator_name: str, code: str, project:
     return results
 
 
-def sfcf_filter(results: pd.DataFrame, **kwargs: Any) -> pd.DataFrame:
+def sfcf_filter(results, **kwargs):
     drops = []
     for ind in range(len(results)):
         result = results.iloc[ind]
@@ -142,30 +139,27 @@ 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, ensemble, correlator_name, code, project=None, parameters=None, created_before=None, created_after=None, updated_before=None, updated_after=None, revision=None, **kwargs):
-                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 = path + '/backlogger.db'
-    db_file = get_db_file(path)
-    db = os.path.join(path, db_file)
     if code not in codes:
         raise ValueError("Code " + code + "unknown, take one of the following:" + ", ".join(codes))
-    get(path, db_file)
+    get_file(path, "backlogger.db")
-    results = _db_lookup(db, ensemble, correlator_name,code, project, parameters=parameters, created_before=created_before, created_after=created_after, updated_before=updated_before, updated_after=updated_after)
+    results = _db_lookup(db, ensemble, correlator_name,code, project, parameters=parameters, created_before=created_before, created_after=created_after, updated_before=updated_before, updated_after=updated_after, revision=revision)
     if code == "sfcf":
         results = sfcf_filter(results, **kwargs)
     print("Found " + str(len(results)) + " result" + ("s" if len(results)>1 else ""))
     return results.reset_index()
 
 
-def find_project(path: str, name: str) -> str:
+def find_project(path, name):
-    db_file = get_db_file(path)
+    get_file(path, "backlogger.db")
-    get(path, db_file)
+    return _project_lookup_by_alias(os.path.join(path, "backlogger.db"), name)
-    return _project_lookup_by_alias(os.path.join(path, db_file), name)
 
 
-def list_projects(path: str) -> list[tuple[str, str]]:
+def list_projects(path):
-    db_file = get_db_file(path)
+    db = path + '/backlogger.db'
-    get(path, db_file)
+    get_file(path, "backlogger.db")
-    conn = sqlite3.connect(os.path.join(path, db_file))
+    conn = sqlite3.connect(db)
     c = conn.cursor()
     c.execute("SELECT id,aliases FROM projects")
     results = c.fetchall()

corrlib/git_tools.py

@@ -1,11 +1,11 @@
 import os
-from .tracker import save
+import datalad.api as dl
 import git
 
 GITMODULES_FILE = '.gitmodules'
 
 
-def move_submodule(repo_path: str, old_path: str, new_path: str) -> None:
+def move_submodule(repo_path, old_path, new_path):
     """
     Move a submodule to a new location.
 
@@ -40,6 +40,4 @@ 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])
+    dl.save(repo_path, message=f"Move module from {old_path} to {new_path}", dataset=repo_path)
-
-    return

corrlib/initialization.py

@@ -1,10 +1,9 @@
-from configparser import ConfigParser
 import sqlite3
+import datalad.api as dl
 import os
-from .tracker import save, init
 
 
-def _create_db(db: str) -> None:
+def _create_db(db):
     """
     Create the database file and the table.
 
@@ -22,7 +21,8 @@ def _create_db(db: str) -> None:
                   parameters TEXT,
                   parameter_file TEXT,
                   created_at TEXT,
-                  updated_at TEXT)''')
+                  updated_at TEXT,
+                  current_version TEXT)''')
     c.execute('''CREATE TABLE IF NOT EXISTS projects
                  (id TEXT PRIMARY KEY,
                   aliases TEXT,
@@ -33,55 +33,21 @@ def _create_db(db: str) -> None:
                   updated_at TEXT)''')
     conn.commit()
     conn.close()
-    return
 
 
-def _create_config(path: str, tracker: str, cached: bool) -> ConfigParser:
+def create(path):
-    """
-    Create the config file for backlogger.
-
-    """
-    config = ConfigParser()
-    config['core'] = {
-        'version': '1.0',
-        'tracker': tracker,
-        'cached': str(cached),
-    }
-    config['paths'] = {
-        'db': 'backlogger.db',
-        'projects_path': 'projects',
-        'archive_path': 'archive',
-        'toml_imports_path': 'toml_imports',
-        'import_scripts_path': 'import_scripts',
-    }
-    return config
-
-
-def _write_config(path: str, config: ConfigParser) -> None:
-    """
-    Write the config file to disk.
-    """
-    with open(os.path.join(path, '.corrlib'), 'w') as configfile:
-        config.write(configfile)
-    return
-
-
-def create(path: str, tracker: str = 'datalad', cached: bool = True) -> None:
     """
     Create folder of backlogs.
 
     """
-    config = _create_config(path, tracker, cached)
+    dl.create(path)
-    init(path, tracker)
+    _create_db(path + '/backlogger.db')
-    _write_config(path, config)
+    os.chmod(path + '/backlogger.db', 0o666)  # why does this not work?
-    _create_db(os.path.join(path, config['paths']['db']))
+    os.makedirs(path + '/projects')
-    os.chmod(os.path.join(path, config['paths']['db']), 0o666)
+    os.makedirs(path + '/archive')
-    os.makedirs(os.path.join(path, config['paths']['projects_path']))
+    os.makedirs(path + '/toml_imports')
-    os.makedirs(os.path.join(path, config['paths']['archive_path']))
+    os.makedirs(path + '/import_scripts/template.py')
-    os.makedirs(os.path.join(path, config['paths']['toml_imports_path']))
+    with open(path + "/.gitignore", "w") as fp:
-    os.makedirs(os.path.join(path, config['paths']['import_scripts_path'], 'template.py'))
-    with open(os.path.join(path, ".gitignore"), "w") as fp:
         fp.write(".cache")
         fp.close()
-    save(path, message="Initialized correlator library")
+    dl.save(path, dataset=path, message="Initialize backlogger directory.")
-    return

corrlib/input/__init__.py

@@ -2,6 +2,6 @@
 Import functions for different codes.
 """
 
-from . import sfcf as sfcf
+from . import sfcf
-from . import openQCD as openQCD
+from . import openQCD
-from . import implementations as implementations
+from . import implementations

corrlib/input/openQCD.py

@@ -2,7 +2,7 @@ import pyerrors.input.openQCD as input
 import datalad.api as dl
 import os
 import fnmatch
-from typing import Any, Optional
+from typing import Any
 
 
 def read_ms1_param(path: str, project: str, file_in_project: str) -> dict[str, Any]:
@@ -67,7 +67,7 @@ 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: str, project: str, dir_in_project: str, param: dict[str, Any], prefix: str, postfix: str="ms1", version: str='2.0', names: list[str]=None, files: list[str]=None) -> dict[str, Any]:
     dataset = os.path.join(path, "projects", project)
     directory = os.path.join(dataset, dir_in_project)
     if files is None:
@@ -94,7 +94,7 @@ 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: 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=None, names: list[str]=None, files: list[str]=None) -> dict[str, Any]:
     dataset = os.path.join(path, "projects", project)
     directory = os.path.join(dataset, dir_in_project)
     if files is None:
@@ -132,7 +132,7 @@ 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: 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 = None, names: list[str]=None, files: list[str]=None) -> dict[str, Any]:
     directory = os.path.join(path, "projects", project, dir_in_project)
     if files is None:
         files = []

corrlib/input/sfcf.py

@@ -5,7 +5,7 @@ import os
 from typing import Any
 
 
-bi_corrs: list[str] = ["f_P", "fP", "f_p",
+bi_corrs: list = ["f_P", "fP", "f_p",
             "g_P", "gP", "g_p",
             "fA0", "f_A", "f_a",
             "gA0", "g_A", "g_a",
@@ -43,7 +43,7 @@ bi_corrs: list[str] = ["f_P", "fP", "f_p",
             "l3A2", "l3_A2", "g_av23",
             ]
 
-bb_corrs: list[str] = [
+bb_corrs: list = [
             'F1',
             'F_1',
             'f_1',
@@ -64,7 +64,7 @@ bb_corrs: list[str] = [
             'F_sPdP_d',
             ]
 
-bib_corrs: list[str] = [
+bib_corrs: list = [
             'F_V0',
             'K_V0',
             ]
@@ -184,7 +184,7 @@ def read_param(path: str, project: str, file_in_project: str) -> dict[str, Any]:
     return params
 
 
-def _map_params(params: dict[str, Any], spec_list: list[str]) -> dict[str, Any]:
+def _map_params(params: dict, spec_list: list) -> dict[str, Any]:
     """
     Map the extracted parameters to the extracted data.
 
@@ -228,7 +228,7 @@ def _map_params(params: dict[str, Any], spec_list: list[str]) -> dict[str, Any]:
     return new_specs
 
 
-def get_specs(key: str, parameters: dict[str, Any], sep: str = '/') -> str:
+def get_specs(key, parameters, sep='/') -> str:
     key_parts = key.split(sep)
     if corr_types[key_parts[0]] == 'bi':
         param = _map_params(parameters, key_parts[1:-1])
@@ -238,7 +238,7 @@ 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, project, dir_in_project, prefix, param, version='1.0c', cfg_seperator='n', sep='/', **kwargs) -> dict:
     """
     Extract the data from the sfcf file.
 

corrlib/main.py

@@ -5,12 +5,11 @@ import os
 from .git_tools import move_submodule
 import shutil
 from .find import _project_lookup_by_id
-from .tools import list2str, str2list, get_db_file
+from .tools import list2str, str2list, get_file
-from .tracker import get, save, unlock, clone, drop
+from typing import Union
-from typing import Union, Optional
 
 
-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: str, uuid: str, owner: Union[str, None]=None, tags: Union[str, None]=None, aliases: Union[str, None]=None, code: Union[str, None]=None):
     """
     Create a new project entry in the database.
 
@@ -25,32 +24,30 @@ def create_project(path: str, uuid: str, owner: Union[str, None]=None, tags: Uni
     code: str (optional)
         The code that was used to create the measurements.
     """
-    db_file = get_db_file(path)
+    db = path + "/backlogger.db"
-    db = os.path.join(path, db_file)
+    get_file(path, "backlogger.db")
-    get(path, db_file)
     conn = sqlite3.connect(db)
     c = conn.cursor()
     known_projects = c.execute("SELECT * FROM projects WHERE id=?", (uuid,))
     if known_projects.fetchone():
         raise ValueError("Project already imported, use update_project() instead.")
 
-    unlock(path, db_file)
+    dl.unlock(db, dataset=path)
-    alias_str = ""
+    alias_str = None
     if aliases is not None:
         alias_str = list2str(aliases)
-    tag_str = ""
+    tag_str = None
     if tags is not None:
         tag_str = list2str(tags)
     c.execute("INSERT INTO projects (id, aliases, customTags, owner, code, created_at, updated_at) VALUES (?, ?, ?, ?, ?, datetime('now'), datetime('now'))", (uuid, alias_str, tag_str, owner, code))
     conn.commit()
     conn.close()
-    save(path, message="Added entry for project " + uuid + " to database", files=[db_file])
+    dl.save(db, message="Added entry for project " + uuid + " to database", dataset=path)
 
 
-def update_project_data(path: str, uuid: str, prop: str, value: Union[str, None] = None) -> None:
+def update_project_data(path, uuid, prop, value = None):
-    db_file = get_db_file(path)
+    get_file(path, "backlogger.db")
-    get(path, db_file)
+    conn = sqlite3.connect(os.path.join(path, "backlogger.db"))
-    conn = sqlite3.connect(os.path.join(path, db_file))
     c = conn.cursor()
     c.execute(f"UPDATE projects SET '{prop}' = '{value}' WHERE id == '{uuid}'")
     conn.commit()
@@ -58,10 +55,9 @@ 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: str, uuid: str, aliases: list[str]):
-    db_file = get_db_file(path)
+    db = os.path.join(path, "backlogger.db")
-    db = os.path.join(path, db_file)
+    get_file(path, "backlogger.db")
-    get(path, db_file)
     known_data = _project_lookup_by_id(db, uuid)[0]
     known_aliases = known_data[1]
 
@@ -80,13 +76,13 @@ def update_aliases(path: str, uuid: str, aliases: list[str]) -> None:
 
     if not len(new_alias_list) == len(known_alias_list):
         alias_str = list2str(new_alias_list)
-        unlock(path, db_file)
+        dl.unlock(db, dataset=path)
         update_project_data(path, uuid, "aliases", alias_str)
-        save(path, message="Updated aliases for project " + uuid, files=[db_file])
+        dl.save(db, dataset=path)
     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: str, url: str, owner: Union[str, None]=None, tags: Union[str, None]=None, aliases: Union[str, None]=None, code: Union[str, None]=None, isDataset: bool=True):
     """
     Parameters
     ----------
@@ -112,21 +108,26 @@ def import_project(path: str, url: str, owner: Union[str, None]=None, tags: Opti
         in order to receive a uuid and have a consistent interface.
 
     """
-    tmp_path = os.path.join(path, 'projects/tmp')
+    tmp_path = path + '/projects/tmp'
-    clone(path, source=url, target=tmp_path)
+    if not isDataset:
+        dl.create(tmp_path, dataset=path)
+        shutil.copytree(url + "/*", path + '/projects/tmp/')
+        dl.save(tmp_path, dataset=path)
+    else:
+        dl.install(path=tmp_path, source=url, dataset=path)
     tmp_ds = dl.Dataset(tmp_path)
     conf = dlc.ConfigManager(tmp_ds)
-    uuid = str(conf.get("datalad.dataset.id"))
+    uuid = 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):
-        db_file = get_db_file(path)
+        db = path + "/backlogger.db"
-        get(path, db_file)
+        get_file(path, "backlogger.db")
-        unlock(path, db_file)
+        dl.unlock(db, dataset=path)
         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])
+        dl.save([db, path + '/projects/' + uuid], message="Import project from " + url, dataset=path)
     else:
         dl.drop(tmp_path, reckless='kill')
         shutil.rmtree(tmp_path)    
@@ -141,10 +142,9 @@ 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: str, uuid: str, path_in_project: str = ""):
     """
-    Drop (parts of) a project to free up diskspace
+    Drop (parts of) a prject to free up diskspace
     """
-    drop(path + "/projects/" + uuid + "/" + path_in_project)
+    dl.drop(path + "/projects/" + uuid + "/" + path_in_project)
-    return
 

corrlib/meas_io.py

@@ -1,18 +1,17 @@
 from pyerrors.input import json as pj
 import os
+import datalad.api as dl
 import sqlite3
 from .input import sfcf,openQCD
 import json
-from typing import Union
+from typing import Union, Optional
-from pyerrors import Obs, Corr, dump_object, load_object
+from pyerrors import Obs, Corr, load_object, dump_object
-from hashlib import sha256
+from hashlib import sha256, sha1
-from .tools import get_db_file, cache_enabled
+from .tools import cached, get_file, record2name_key, name_key2record, make_version_hash
-from .tracker import get, save, unlock
+from .cache_io import is_in_cache, cache_path, cache_dir, get_version_hash
-import shutil
-from typing import Any
 
 
-def write_measurement(path: str, ensemble: str, measurement: dict[str, dict[str, dict[str, Any]]], uuid: str, code: str, parameter_file: str) -> None:
+def write_measurement(path, ensemble, measurement, uuid, code, parameter_file: Optional[str]=None):
     """
     Write a measurement to the backlog.
     If the file for the measurement already exists, update the measurement.
@@ -28,10 +27,9 @@ def write_measurement(path: str, ensemble: str, measurement: dict[str, dict[str,
     uuid: str
         The uuid of the project.
     """
-    db_file = get_db_file(path)
+    db = os.path.join(path, 'backlogger.db')
-    db = os.path.join(path, db_file)
+    get_file(path, "backlogger.db")
-    get(path, db_file)
+    dl.unlock(db, dataset=path)
-    unlock(path, db_file)
     conn = sqlite3.connect(db)
     c = conn.cursor()
     files = []
@@ -44,7 +42,7 @@ def write_measurement(path: str, ensemble: str, measurement: dict[str, dict[str,
             os.makedirs(os.path.join(path, '.', 'archive', ensemble, corr))
         else:
             if os.path.exists(file):
-                unlock(path, file_in_archive)
+                dl.unlock(file, dataset=path)
                 known_meas = pj.load_json_dict(file)
         if code == "sfcf":
             parameters = sfcf.read_param(path, uuid, parameter_file)
@@ -81,25 +79,26 @@ def write_measurement(path: str, ensemble: str, measurement: dict[str, dict[str,
                 subkey = "/".join(par_list)
                 subkeys = [subkey]
                 pars[subkey] = json.dumps(parameters)
+
+        meas_paths = []
         for subkey in subkeys:                
-            parHash = sha256(str(pars[subkey]).encode('UTF-8')).hexdigest()
+            par_hash = sha256(str(pars[subkey]).encode('UTF-8')).hexdigest()
-            meas_path = file_in_archive + "::" + parHash
+            meas_path = name_key2record(file_in_archive, par_hash)
-
+            meas_paths.append(meas_path)
-            known_meas[parHash] = measurement[corr][subkey]
+            known_meas[par_hash] = measurement[corr][subkey]
-
+            data_hash = make_version_hash(path, meas_path)
-            if c.execute("SELECT * FROM backlogs WHERE path = ?", (meas_path,)).fetchone() is not None:
+            if c.execute("SELECT * FROM backlogs WHERE path = ?", (meas_path,)).fetchone() is None:
-                c.execute("UPDATE backlogs SET updated_at = datetime('now') WHERE path = ?", (meas_path, ))
+                c.execute("INSERT INTO backlogs (name, ensemble, code, path, project, parameters, parameter_file, created_at) VALUES (?, ?, ?, ?, ?, ?, ?, datetime('now'))",
-            else:
-                c.execute("INSERT INTO backlogs (name, ensemble, code, path, project, parameters, parameter_file, created_at, updated_at) VALUES (?, ?, ?, ?, ?, ?, ?, datetime('now'), datetime('now'))",
                                                 (corr, ensemble, code, meas_path, uuid, pars[subkey], parameter_file))
-        conn.commit()
+            c.execute("UPDATE backlogs SET current_version = ?, updated_at = datetime('now') WHERE path = ?", (data_hash, meas_path))
         pj.dump_dict_to_json(known_meas, file)
-    files.append(os.path.join(path, db_file))
+        conn.commit()
+    files.append(db)
     conn.close()
-    save(path, message="Add measurements to database", files=files)
+    dl.save(files, message="Add measurements to database", dataset=path)
 
 
-def load_record(path: str, meas_path: str) -> Union[Corr, Obs]:
+def load_record(path: str, meas_path: str):
     """
     Load a list of records by their paths.
 
@@ -118,7 +117,7 @@ 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: str, record_paths: list[str], preloaded = {}) -> list[Union[Corr, Obs]]:
     """
     Load a list of records by their paths.
 
@@ -134,56 +133,45 @@ def load_records(path: str, meas_paths: list[str], preloaded: dict[str, Any] = {
     List
     """
     needed_data: dict[str, list[str]] = {}
-    for mpath in meas_paths:
+    for rpath in record_paths:
-        file = mpath.split("::")[0]
+        file, key = record2name_key(rpath)
         if file not in needed_data.keys():
             needed_data[file] = []
-        key = mpath.split("::")[1]
         needed_data[file].append(key)
-    returned_data: list[Any] = []
+    returned_data: list = []
     for file in needed_data.keys():
         for key in list(needed_data[file]):
-            if os.path.exists(cache_path(path, file, key) + ".p"):
+            record = name_key2record(file, key)
-                returned_data.append(load_object(cache_path(path, file, key) + ".p"))
+            current_version = get_version_hash(path, record)
+            if is_in_cache(path, record):
+                returned_data.append(load_object(cache_path(path, file, current_version, key) + ".p"))
             else:
                 if file not in preloaded:
                     preloaded[file] = preload(path, file)
                 returned_data.append(preloaded[file][key])
-                if cache_enabled(path):
+                if cached:
-                    if not os.path.exists(cache_dir(path, file)):
+                    if not is_in_cache(path, record):
-                        os.makedirs(cache_dir(path, file))
+                        file, key = record2name_key(record)
-                    dump_object(preloaded[file][key], cache_path(path, file, key))
+                        if not os.path.exists(cache_dir(path, file)):
+                            os.makedirs(cache_dir(path, file))
+                        current_version = get_version_hash(path, record)
+                        dump_object(preloaded[file][key], cache_path(path, file, current_version, key))
     return returned_data
 
 
-def cache_dir(path: str, file: str) -> str:
+def preload(path: str, file: str):
-    cache_path_list = [path]
+    get_file(path, file)
-    cache_path_list.append(".cache")
+    filedict = pj.load_json_dict(os.path.join(path, file))
-    cache_path_list.extend(file.split("/")[1:])
-    cache_path = "/".join(cache_path_list)
-    return cache_path
-
-
-def cache_path(path: str, file: str, key: str) -> str:
-    cache_path = os.path.join(cache_dir(path, file), key)
-    return cache_path
-
-
-def preload(path: str, file: str) -> dict[str, Any]:
-    get(path, file)
-    filedict: dict[str, Any] = pj.load_json_dict(os.path.join(path, file))
     print("> read file")
     return filedict
 
 
-def drop_record(path: str, meas_path: str) -> None:
+def drop_record(path: str, meas_path: str):
-    file_in_archive = meas_path.split("::")[0]
+    file_in_archive, sub_key = record2name_key(meas_path)
     file = os.path.join(path, file_in_archive)
-    db_file = get_db_file(path)
+    db = os.path.join(path, 'backlogger.db')
-    db = os.path.join(path, db_file)
+    get_file(path, 'backlogger.db')
-    get(path, db_file)
+    dl.unlock(db, dataset=path)
-    sub_key = meas_path.split("::")[1]
-    unlock(path, db_file)
     conn = sqlite3.connect(db)
     c = conn.cursor()
     if c.execute("SELECT * FROM backlogs WHERE path = ?", (meas_path, )).fetchone() is not None:
@@ -195,16 +183,10 @@ 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)
+        dl.unlock(file, dataset=path)
         pj.dump_dict_to_json(known_meas, file)
-        save(path, message="Drop measurements to database", files=[db, file])
+        dl.save([db, file], message="Drop measurements to database", dataset=path)
         return
     else:
         raise ValueError("This measurement does not exist as a file!")
 
-
-def drop_cache(path: str) -> None:
-    cache_dir = os.path.join(path, ".cache")
-    for f in os.listdir(cache_dir):
-        shutil.rmtree(os.path.join(cache_dir, f))
-    return

corrlib/toml.py

@@ -10,26 +10,21 @@ the import of projects via TOML.
 
 import tomllib as toml
 import shutil
-
-import datalad.api as dl
-from .tracker import save
 from .input import sfcf, openQCD
 from .main import import_project, update_aliases
 from .meas_io import write_measurement
+import datalad.api as dl
 import os
 from .input.implementations import codes as known_codes
-from typing import Any
 
-
+def replace_string(string: str, name: str, val: str):
-def replace_string(string: str, name: str, val: str) -> str:
     if '{' + name + '}' in string:
         n = string.replace('{' + name + '}', val)
         return n
     else:
         return string
 
-
+def replace_in_meas(measurements: dict, vars: dict[str, str]):
-def replace_in_meas(measurements: dict[str, dict[str, Any]], vars: dict[str, str]) -> dict[str, dict[str, Any]]:
     # replace global variables
     for name, value in vars.items():
         for m in measurements.keys():
@@ -41,8 +36,7 @@ def replace_in_meas(measurements: dict[str, dict[str, Any]], vars: dict[str, str
                         measurements[m][key][i] = replace_string(measurements[m][key][i], name, value)
     return measurements
 
-
+def fill_cons(measurements, constants):
-def fill_cons(measurements: dict[str, dict[str, Any]], constants: dict[str, str]) -> dict[str, dict[str, Any]]:
     for m in measurements.keys():
         for name, val in constants.items():
             if name not in measurements[m].keys():
@@ -50,7 +44,7 @@ def fill_cons(measurements: dict[str, dict[str, Any]], constants: dict[str, str]
     return measurements
 
 
-def check_project_data(d: dict[str, dict[str, str]]) -> None:
+def check_project_data(d: dict) -> None:
     if 'project' not in d.keys() or 'measurements' not in d.keys() or len(list(d.keys())) > 4:
         raise ValueError('There should only be maximally be four keys on the top level, "project" and "measurements" are mandatory, "contants" is optional!')
     project_data = d['project']
@@ -63,7 +57,7 @@ def check_project_data(d: dict[str, dict[str, str]]) -> None:
     return
 
 
-def check_measurement_data(measurements: dict[str, dict[str, str]], code: str) -> None:
+def check_measurement_data(measurements: dict, code: str) -> None:
     var_names: list[str] = []
     if code == "sfcf":
         var_names = ["path", "ensemble", "param_file", "version", "prefix", "cfg_seperator", "names"]
@@ -97,14 +91,14 @@ def import_toml(path: str, file: str, copy_file: bool=True) -> None:
     with open(file, 'rb') as fp:
         toml_dict = toml.load(fp)
     check_project_data(toml_dict)
-    project: dict[str, Any] = toml_dict['project']
+    project: dict = toml_dict['project']
     if project['code'] not in known_codes:
         raise ValueError('Code' + project['code'] + 'has no import implementation!')
-    measurements: dict[str, dict[str, Any]] = toml_dict['measurements']
+    measurements: dict = toml_dict['measurements']
     measurements = fill_cons(measurements, toml_dict['constants'] if 'constants' in toml_dict else {})
     measurements = replace_in_meas(measurements, toml_dict['replace'] if 'replace' in toml_dict else {})
     check_measurement_data(measurements, project['code'])
-    aliases = project.get('aliases', [])
+    aliases = project.get('aliases', None)
     uuid = project.get('uuid', None)
     if uuid is not None:
         if not os.path.exists(path + "/projects/" + uuid):
@@ -139,29 +133,29 @@ def import_toml(path: str, file: str, copy_file: bool=True) -> None:
                     for rwp in ["integrator", "eps", "ntot", "dnms"]:
                         param[rwp] = "Unknown"
                 param['type'] = 't0'
-                measurement = openQCD.extract_t0(path, uuid, md['path'], param, str(md["prefix"]), int(md["dtr_read"]), int(md["xmin"]), int(md["spatial_extent"]),
+                measurement = openQCD.extract_t0(path, uuid, md['path'], param, md["prefix"], md["dtr_read"], md["xmin"], md["spatial_extent"],
-                                                 fit_range=int(md.get('fit_range', 5)), postfix=str(md.get('postfix', '')), names=md.get('names', []), files=md.get('files', []))
+                                                 fit_range=md.get('fit_range', 5), postfix=md.get('postfix', None), names=md.get('names', None), files=md.get('files', None))
             elif md['measurement'] == 't1':
                 if 'param_file' in md:
                     param = openQCD.read_ms3_param(path, uuid, md['param_file'])
                 param['type'] = 't1'
-                measurement = openQCD.extract_t1(path, uuid, md['path'], param, str(md["prefix"]), int(md["dtr_read"]), int(md["xmin"]), int(md["spatial_extent"]),
+                measurement = openQCD.extract_t1(path, uuid, md['path'], param, md["prefix"], md["dtr_read"], md["xmin"], md["spatial_extent"],
-                                                 fit_range=int(md.get('fit_range', 5)), postfix=str(md.get('postfix', '')), names=md.get('names', []), files=md.get('files', []))
+                                                 fit_range=md.get('fit_range', 5), postfix=md.get('postfix', None), names=md.get('names', None), files=md.get('files', None))
 
-        write_measurement(path, ensemble, measurement, uuid, project['code'], (md['param_file'] if 'param_file' in md else ''))
+        write_measurement(path, ensemble, measurement, uuid, project['code'], (md['param_file'] if 'param_file' in md else None))
 
     if not os.path.exists(os.path.join(path, "toml_imports", uuid)):
         os.makedirs(os.path.join(path, "toml_imports", uuid))
     if copy_file:
         import_file = os.path.join(path, "toml_imports", uuid, file.split("/")[-1])
         shutil.copy(file, import_file)
-        save(path, files=[import_file], message="Import using " + import_file)
+        dl.save(import_file, message="Import using " + import_file, dataset=path)
         print("File copied to " + import_file)
     print("Imported project.")
     return
 
 
-def reimport_project(path: str, uuid: str) -> None:
+def reimport_project(path, uuid):
     """
     Reimport an existing project using the files that are already available for this project.
 
@@ -179,7 +173,6 @@ def reimport_project(path: str, uuid: str) -> None:
     return
 
 
-def update_project(path: str, uuid: str) -> None:
+def update_project(path, uuid):
     dl.update(how='merge', follow='sibling', dataset=os.path.join(path, "projects", uuid))
     # reimport_project(path, uuid)
-    return

corrlib/tools.py

@@ -1,54 +1,45 @@
 import os
-from configparser import ConfigParser
+import datalad.api as dl
-from typing import Any
+import hashlib
 
-CONFIG_FILENAME = ".corrlib"
+def str2list(string):
-
-
-def str2list(string: str) -> list[str]:
     return string.split(",")
 
-def list2str(mylist: list[str]) -> str:
+def list2str(mylist):
     s = ",".join(mylist)
     return s
 
-cached: bool = True
+cached = True
 
-def m2k(m: float) -> float:
+def m2k(m):
     return 1/(2*m+8)
 
 
-def k2m(k: float) -> float:
+def k2m(k):
     return (1/(2*k))-4
 
 
-def set_config(path: str, section: str, option: str, value: Any) -> None:
+def get_file(path, file):
-    config_path = os.path.join(path, '.corrlib')
+    if file == "backlogger.db":
-    config = ConfigParser()
+        print("Downloading database...")
-    if os.path.exists(config_path):
+    else:
-        config.read(config_path)
+        print("Downloading data...")
-    if not config.has_section(section):
+    dl.get(os.path.join(path, file), dataset=path)
-        config.add_section(section)
+    print("> downloaded file")
-    config.set(section, option, value)
-    with open(config_path, 'w') as configfile:
-        config.write(configfile)
-    return
 
 
-def get_db_file(path: str) -> str:
+def record2name_key(record_path: str):
-    config_path = os.path.join(path, CONFIG_FILENAME)
+    file = record_path.split("::")[0]
-    config = ConfigParser()
+    key = record_path.split("::")[1]
-    if os.path.exists(config_path):
+    return file, key
-        config.read(config_path)
-    db_file = config.get('paths', 'db', fallback='backlogger.db')
-    return db_file
 
 
-def cache_enabled(path: str) -> bool:
+def name_key2record(name: str, key: str):
-    config_path = os.path.join(path, CONFIG_FILENAME)
+    return name + "::" + key
-    config = ConfigParser()
+
-    if os.path.exists(config_path):
+
-        config.read(config_path)
+def make_version_hash(path, record):
-    cached_str = config.get('core', 'cached', fallback='True')
+    file, key = record2name_key(record)
-    cached_bool = cached_str == ('True')
+    with open(os.path.join(path, file), 'rb') as fp:
-    return cached_bool
+        file_hash = hashlib.file_digest(fp, 'sha1').hexdigest()
+    return file_hash

corrlib/tracker.py

@@ -1,169 +0,0 @@
-import os
-from configparser import ConfigParser
-import datalad.api as dl
-from typing import Optional
-import shutil
-from .tools import get_db_file
-
-
-def get_tracker(path: str) -> str:
-    """
-    Get the tracker used in the dataset located at path.
-
-    Parameters
-    ----------
-    path: str
-        The path to the backlogger folder.
-
-    Returns
-    -------
-    tracker: str
-        The tracker used in the dataset.
-    """
-    config_path = os.path.join(path, '.corrlib')
-    config = ConfigParser()
-    if os.path.exists(config_path):
-        config.read(config_path)
-    else:
-        raise FileNotFoundError(f"No config file found in {path}.")
-    tracker = config.get('core', 'tracker', fallback='datalad')
-    return tracker
-
-
-def get(path: str, file: str) -> None:
-    """
-    Wrapper function to get a file from the dataset located at path with the specified tracker.
-
-    Parameters
-    ----------
-    path: str
-        The path to the backlogger folder.
-    file: str
-        The file to get.
-    """
-    tracker = get_tracker(path)
-    if tracker == 'datalad':
-        if file == get_db_file(path):
-            print("Downloading database...")
-        else:
-            print("Downloading data...")
-        dl.get(os.path.join(path, file), dataset=path)
-        print("> downloaded file")
-    elif tracker == 'None':
-        pass
-    else:
-        raise ValueError(f"Tracker {tracker} is not supported.")
-    return
-
-
-def save(path: str, message: str, files: Optional[list[str]]=None) -> None:
-    """
-    Wrapper function to save a file to the dataset located at path with the specified tracker.
-
-    Parameters
-    ----------
-    path: str
-        The path to the backlogger folder.
-    message: str
-        The commit message.
-    files: list[str], optional
-        The files to save. If None, all changes are saved.
-    """
-    tracker = get_tracker(path)
-    if tracker == 'datalad':
-        if files is not None:
-            files = [os.path.join(path, f) for f in files]
-        dl.save(files, message=message, dataset=path)
-    elif tracker == 'None':
-        Warning("Tracker 'None' does not implement save.")
-        pass
-    else:
-        raise ValueError(f"Tracker {tracker} is not supported.")
-
-
-def init(path: str, tracker: str='datalad') -> None:
-    """
-    Initialize a dataset at the specified path with the specified tracker.
-
-    Parameters
-    ----------
-    path: str
-        The path to initialize the dataset.
-    tracker: str
-        The tracker to use. Currently only 'datalad' and 'None' are supported.
-    """
-    if tracker == 'datalad':
-        dl.create(path)
-    elif tracker == 'None':
-        os.makedirs(path, exist_ok=True)
-    else:
-        raise ValueError(f"Tracker {tracker} is not supported.")
-    return
-
-
-def unlock(path: str, file: str) -> None:
-    """
-    Wrapper function to unlock a file in the dataset located at path with the specified tracker.
-
-    Parameters
-    ----------
-    path    : str
-        The path to the backlogger folder.
-    file    : str
-        The file to unlock.
-    """
-    tracker = get_tracker(path)
-    if tracker == 'datalad':
-        dl.unlock(file, dataset=path)
-    elif tracker == 'None':
-        Warning("Tracker 'None' does not implement unlock.")
-        pass
-    else:
-        raise ValueError(f"Tracker {tracker} is not supported.")
-    return
-
-
-def clone(path: str, source: str, target: str) -> None:
-    """
-    Wrapper function to clone a dataset from source to target with the specified tracker.
-    Parameters
-    ----------
-    path: str
-        The path to the backlogger folder.
-    source: str
-        The source dataset to clone.
-    target: str
-        The target path to clone the dataset to.
-    """
-    tracker = get_tracker(path)
-    if tracker == 'datalad':
-        dl.clone(target=target, source=source, dataset=path)
-    elif tracker == 'None':
-        os.makedirs(path, exist_ok=True)
-        # Implement a simple clone by copying files
-        shutil.copytree(source, target, dirs_exist_ok=False)
-    else:
-        raise ValueError(f"Tracker {tracker} is not supported.")
-    return
-
-
-def drop(path: str, reckless: Optional[str]=None) -> None:
-    """
-    Wrapper function to drop data from a dataset located at path with the specified tracker.
-
-    Parameters
-    ----------
-    path: str
-        The path to the backlogger folder.
-    reckless: Optional[str]
-        The datalad's reckless option for dropping data.
-    """
-    tracker = get_tracker(path)
-    if tracker == 'datalad':
-        dl.drop(path, reckless=reckless)
-    elif tracker == 'None':
-        Warning("Tracker 'None' does not implement drop.")
-        pass
-    else:
-        raise ValueError(f"Tracker {tracker} is not supported.")
-    return

corrlib/version.py

@@ -1,34 +1 @@
-# file generated by setuptools-scm
+__version__ = "0.2.3"
-# don't change, don't track in version control
-
-__all__ = [
-    "__version__",
-    "__version_tuple__",
-    "version",
-    "version_tuple",
-    "__commit_id__",
-    "commit_id",
-]
-
-TYPE_CHECKING = False
-if TYPE_CHECKING:
-    from typing import Tuple
-    from typing import Union
-
-    VERSION_TUPLE = Tuple[Union[int, str], ...]
-    COMMIT_ID = Union[str, None]
-else:
-    VERSION_TUPLE = object
-    COMMIT_ID = object
-
-version: str
-__version__: str
-__version_tuple__: VERSION_TUPLE
-version_tuple: VERSION_TUPLE
-commit_id: COMMIT_ID
-__commit_id__: COMMIT_ID
-
-__version__ = version = '0.2.4.dev14+g602324f84.d20251202'
-__version_tuple__ = version_tuple = (0, 2, 4, 'dev14', 'g602324f84.d20251202')
-
-__commit_id__ = commit_id = 'g602324f84'

pyproject.toml

@@ -1,52 +1,6 @@
 [build-system]
-requires = ["setuptools >= 63.0.0", "wheel", "setuptools-scm"]
+requires = ["setuptools >= 63.0.0", "wheel"]
 build-backend = "setuptools.build_meta"
 
-[project]
-requires-python = ">=3.10"
-name = "corrlib"
-dynamic = ["version"]
-dependencies = [
-    "gitpython>=3.1.45",
-    'pyerrors>=2.11.1',
-    "datalad>=1.1.0",
-    'typer>=0.12.5',
-]
-description = "Python correlation library"
-authors = [
-  { name = 'Justus Kuhlmann', email = 'j_kuhl19@uni-muenster.de'}
-]
-
-[project.scripts]
-pcl = "corrlib.cli:app"
-
-[tool.setuptools.packages.find]
-include = ["corrlib", "corrlib.*"]
-
-[tool.setuptools_scm]
-write_to = "corrlib/version.py"
-
 [tool.ruff.lint]
-ignore = ["E501"]
+ignore = ["F403"]
-extend-select = [
-  "YTT",
-  "E",
-  "W",
-  "F",
-]
-
-[tool.mypy]
-strict = true
-implicit_reexport = false
-follow_untyped_imports = false
-ignore_missing_imports = true
-
-[dependency-groups]
-dev = [
-    "mypy>=1.19.0",
-    "pandas-stubs>=2.3.3.251201",
-    "pytest>=9.0.1",
-    "pytest-cov>=7.0.0",
-    "pytest-pretty>=1.3.0",
-    "ruff>=0.14.7",
-]

setup.py

@@ -0,0 +1,18 @@
+from setuptools import setup
+from distutils.util import convert_path
+
+
+version = {}
+with open(convert_path('corrlib/version.py')) as ver_file:
+    exec(ver_file.read(), version)
+
+setup(name='pycorrlib',
+      version=version['__version__'],
+      author='Justus Kuhlmann',
+      author_email='j_kuhl19@uni-muenster.de',
+      install_requires=['pyerrors>=2.11.1', 'datalad>=1.1.0', 'typer>=0.12.5', 'gitpython>=3.1.45'],
+      entry_points = {
+        'console_scripts': ['pcl=corrlib.cli:app'],
+        },
+      packages=['corrlib', 'corrlib.input']
+      )

tests/cli_test.py

@@ -1,91 +0,0 @@
-from typer.testing import CliRunner
-from corrlib.cli import app
-import os
-import sqlite3 as sql
-
-
-runner = CliRunner()
-
-
-def test_version():
-    result = runner.invoke(app, ["--version"])
-    assert result.exit_code == 0
-    assert "corrlib" in result.output
-
-
-def test_init_folders(tmp_path):
-    dataset_path = tmp_path / "test_dataset"
-    result = runner.invoke(app, ["init", "--dataset", str(dataset_path)])
-    assert result.exit_code == 0
-    assert os.path.exists(str(dataset_path))
-    assert os.path.exists(str(dataset_path / "backlogger.db"))
-
-
-def test_init_db(tmp_path):
-    dataset_path = tmp_path / "test_dataset"
-    result = runner.invoke(app, ["init", "--dataset", str(dataset_path)])
-    assert result.exit_code == 0
-    assert os.path.exists(str(dataset_path / "backlogger.db"))
-    conn = sql.connect(str(dataset_path / "backlogger.db"))
-    cursor = conn.cursor()
-    cursor.execute("SELECT name FROM sqlite_master WHERE type='table';")
-    tables = cursor.fetchall()
-    expected_tables = [
-        'projects',
-        'backlogs',
-        ]
-    table_names = [table[0] for table in tables]
-    for expected_table in expected_tables:
-        assert expected_table in table_names
-    
-    cursor.execute("SELECT * FROM projects;")
-    projects = cursor.fetchall()
-    assert len(projects) == 0
-
-    cursor.execute("SELECT * FROM backlogs;")
-    backlogs = cursor.fetchall()
-    assert len(backlogs) == 0
-
-    cursor.execute("PRAGMA table_info('projects');")
-    project_columns = cursor.fetchall()
-    expected_project_columns = [
-        "id",
-        "aliases",
-        "customTags",
-        "owner",
-        "code",
-        "created_at",
-        "updated_at"
-        ]
-    project_column_names = [col[1] for col in project_columns]
-    for expected_col in expected_project_columns:
-        assert expected_col in project_column_names
-    
-    cursor.execute("PRAGMA table_info('backlogs');")
-    backlog_columns = cursor.fetchall()
-    expected_backlog_columns = [
-        "id",
-        "name",
-        "ensemble",
-        "code",
-        "path",
-        "project",
-        "customTags",
-        "parameters",
-        "parameter_file",
-        "created_at",
-        "updated_at"
-        ]
-    backlog_column_names = [col[1] for col in backlog_columns]
-    for expected_col in expected_backlog_columns:
-        assert expected_col in backlog_column_names
-
-
-def test_list(tmp_path):
-    dataset_path = tmp_path / "test_dataset"
-    result = runner.invoke(app, ["init", "--dataset", str(dataset_path)])
-    assert result.exit_code == 0
-    result = runner.invoke(app, ["list", "--dataset", str(dataset_path), "ensembles"])
-    assert result.exit_code == 0
-    result = runner.invoke(app, ["list", "--dataset", str(dataset_path), "projects"])
-    assert result.exit_code == 0

tests/import_project_test.py

@@ -14,4 +14,4 @@ def test_toml_check_measurement_data():
                             "names": ['list', 'of', 'names']
                         }
                     }
-    t.check_measurement_data(measurements, "sfcf")
+    t.check_measurement_data(measurements)

tests/test_initialization.py

@@ -1,93 +0,0 @@
-import corrlib.initialization as init
-import os
-import sqlite3 as sql
-
-def test_init_folders(tmp_path):
-    dataset_path = tmp_path / "test_dataset"
-    init.create(str(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):
-    dataset_path = tmp_path / "test_dataset"
-    init.create(str(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):
-    dataset_path = tmp_path / "test_dataset"
-    init.create(str(dataset_path), tracker="None")
-    config_path = dataset_path / ".corrlib"
-    assert os.path.exists(str(config_path))
-    from configparser import ConfigParser
-    config = ConfigParser()
-    config.read(str(config_path))
-    assert config.get("core", "tracker") == "None"
-    assert config.get("core", "version") == "1.0"
-    assert config.get("core", "cached") == "True"
-    assert config.get("paths", "db") == "backlogger.db"
-    assert config.get("paths", "projects_path") == "projects"
-    assert config.get("paths", "archive_path") == "archive"
-    assert config.get("paths", "toml_imports_path") == "toml_imports"
-    assert config.get("paths", "import_scripts_path") == "import_scripts"
-
-
-def test_init_db(tmp_path):
-    dataset_path = tmp_path / "test_dataset"
-    init.create(str(dataset_path))
-    assert os.path.exists(str(dataset_path / "backlogger.db"))
-    conn = sql.connect(str(dataset_path / "backlogger.db"))
-    cursor = conn.cursor()
-    cursor.execute("SELECT name FROM sqlite_master WHERE type='table';")
-    tables = cursor.fetchall()
-    expected_tables = [
-        'projects',
-        'backlogs',
-        ]
-    table_names = [table[0] for table in tables]
-    for expected_table in expected_tables:
-        assert expected_table in table_names
-
-    cursor.execute("SELECT * FROM projects;")
-    projects = cursor.fetchall()
-    assert len(projects) == 0
-
-    cursor.execute("SELECT * FROM backlogs;")
-    backlogs = cursor.fetchall()
-    assert len(backlogs) == 0
-
-    cursor.execute("PRAGMA table_info('projects');")
-    project_columns = cursor.fetchall()
-    expected_project_columns = [
-        "id",
-        "aliases",
-        "customTags",
-        "owner",
-        "code",
-        "created_at",
-        "updated_at"
-        ]
-    project_column_names = [col[1] for col in project_columns]
-    for expected_col in expected_project_columns:
-        assert expected_col in project_column_names
-
-    cursor.execute("PRAGMA table_info('backlogs');")
-    backlog_columns = cursor.fetchall()
-    expected_backlog_columns = [
-        "id",
-        "name",
-        "ensemble",
-        "code",
-        "path",
-        "project",
-        "customTags",
-        "parameters",
-        "parameter_file",
-        "created_at",
-        "updated_at"
-        ]
-    backlog_column_names = [col[1] for col in backlog_columns]
-    for expected_col in expected_backlog_columns:
-        assert expected_col in backlog_column_names

tests/tools_test.py

@@ -1,31 +0,0 @@
-
-
-from corrlib import tools as tl
-
-
-def test_m2k():
-    for m in [0.1, 0.5, 1.0]:
-        expected_k = 1 / (2 * m + 8)
-        assert tl.m2k(m) == expected_k
-
-
-def test_k2m():
-    for m in [0.1, 0.5, 1.0]:
-        assert tl.k2m(m) == (1/(2*m))-4
-
-
-def test_k2m_m2k():
-    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():
-    assert tl.str2list("a,b,c") == ["a", "b", "c"]
-    assert tl.str2list("1,2,3") == ["1", "2", "3"]
-
-
-def test_list2str():
-    assert tl.list2str(["a", "b", "c"]) == "a,b,c"
-    assert tl.list2str(["1", "2", "3"]) == "1,2,3"