Merge branch 'develop' into lint/strict_ruff

.gitignore

@@ -6,3 +6,4 @@ test.ipynb
 .venv
 .pytest_cache
 .coverage
+build

LICENSE

@@ -0,0 +1,9 @@
+MIT License
+
+Copyright (c) 2026 Justus Kuhlmann
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice (including the next paragraph) shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

corrlib/initialization.py

@@ -71,6 +71,7 @@ def _create_config(path: Path, tracker: str, cached: bool) -> ConfigParser:
         'db': 'backlogger.db',
         'projects_path': 'projects',
         'archive_path': 'archive',
+        'plot_path': 'plots',
         'toml_imports_path': 'toml_imports',
         'import_scripts_path': 'import_scripts',
     }
@@ -113,6 +114,7 @@ def create(path: Path, tracker: str = 'datalad', cached: bool = True) -> None:
     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']['plot_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:

corrlib/input/openQCD.py

@@ -4,8 +4,10 @@ import os
 import fnmatch
 from typing import Any, Optional
 from pathlib import Path
+import matplotlib.pyplot as plt
 from ..pars.openQCD import ms1
 from ..pars.openQCD import qcd2
+from ..tools import get_plot_dir
 
 
 
@@ -29,6 +31,8 @@ def load_ms1_infile(path: Path, project: str, file_in_project: str) -> dict[str,
     """
 
     file = os.path.join(path, "projects", project, file_in_project)
+    if not os.path.exists(file):
+        raise IOError(f"File {file} does not exist.")
     ds = os.path.join(path, "projects", project)
     dl.get(file, dataset=ds)
     with open(file, 'r') as fp:
@@ -164,7 +168,7 @@ def read_rwms(path: Path, project: str, dir_in_project: str, param: dict[str, An
     return rw_dict
 
 
-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,
+def extract_t0(path: Path, project: str, dir_in_project: str, ensemble: 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,
                r_start: list[int]=[], r_stop: list[int]=[], r_step:int=1) -> dict[str, Any]:
     """
     Extract t0 measurements from the project.
@@ -224,7 +228,7 @@ def extract_t0(path: Path, project: str, dir_in_project: str, param: dict[str, A
     if not r_stop == []:
         kwargs['r_stop'] = r_stop
     kwargs['r_step'] = r_step
-
+    kwargs['plot_fit'] = True
     t0 = input.extract_t0(directory,
                             prefix,
                             dtr_read,
@@ -234,6 +238,10 @@ def extract_t0(path: Path, project: str, dir_in_project: str, param: dict[str, A
                             c=0.3,
                             **kwargs
                             )
+    plot_dir = path / get_plot_dir(path) / ensemble / project
+    if not os.path.exists(plot_dir):
+        os.makedirs(plot_dir)
+    plt.savefig(plot_dir / "t0.pdf")
     par_list= []
     for k in ["integrator", "eps", "ntot", "dnms"]:
         par_list.append(str(param[k]))
@@ -244,7 +252,7 @@ def extract_t0(path: Path, project: str, dir_in_project: str, param: dict[str, A
     return t0_dict
 
 
-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,
+def extract_t1(path: Path, project: str, dir_in_project: str, ensemble: 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,
                r_start: list[int]=[], r_stop: list[int]=[], r_step:int=1) -> dict[str, Any]:
     """
     Extract t1 measurements from the project.
@@ -302,6 +310,7 @@ def extract_t1(path: Path, project: str, dir_in_project: str, param: dict[str, A
     if not r_stop == []:
         kwargs['r_stop'] = r_stop
     kwargs['r_step'] = r_step
+    kwargs['plot_fit'] = True
     t0 = input.extract_t0(directory,
                             prefix,
                             dtr_read,
@@ -311,6 +320,10 @@ def extract_t1(path: Path, project: str, dir_in_project: str, param: dict[str, A
                             c=2./3,
                             **kwargs
                             )
+    plot_dir = path / get_plot_dir(path) / ensemble / project
+    if not os.path.exists(plot_dir):
+        os.makedirs(plot_dir)
+    plt.savefig(plot_dir / "t1.pdf")
     par_list= []
     for k in ["integrator", "eps", "ntot", "dnms"]:
         par_list.append(str(param[k]))

corrlib/input/sfcf.py

@@ -258,7 +258,7 @@ def get_specs(key: str, parameters: dict[str, Any], sep: str = '/') -> str:
     return s
 
 
-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]:
+def read_data(path: Path, project: str, dir_in_project: str, prefix: str, param: dict[str, Any], version: str = '1.0c', cfg_separator: str = 'n', sep: str = '/', **kwargs: Any) -> dict[str, Any]:
     """
     Extract the data from the sfcf file.
 
@@ -274,7 +274,7 @@ def read_data(path: Path, project: str, dir_in_project: str, prefix: str, param:
         The parameter dictionary, as given by read_param.
     version: str
         Version of sfcf.
-    cfg_seperator: str
+    cfg_separator: str
         Separator of the configuration number. Needed for reading. default: "n"
     sep: str
         Seperator for the key in return dict. (default: "/)
@@ -321,10 +321,10 @@ def read_data(path: Path, project: str, dir_in_project: str, prefix: str, param:
     if not param['crr'] == []:
         if names is not None:
             data_crr = pe.input.sfcf.read_sfcf_multi(directory, prefix, param['crr'], param['mrr'], corr_type_list, range(len(param['wf_offsets'])),
-                                                     range(len(param['wf_basis'])), range(len(param['wf_basis'])), version, cfg_seperator, keyed_out=True, silent=True, names=names)
+                                                     range(len(param['wf_basis'])), range(len(param['wf_basis'])), version, cfg_separator, keyed_out=True, silent=True, names=names)
         else:
             data_crr = pe.input.sfcf.read_sfcf_multi(directory, prefix, param['crr'], param['mrr'], corr_type_list, range(len(param['wf_offsets'])),
-                                                     range(len(param['wf_basis'])), range(len(param['wf_basis'])), version, cfg_seperator, keyed_out=True, silent=True)
+                                                     range(len(param['wf_basis'])), range(len(param['wf_basis'])), version, cfg_separator, keyed_out=True, silent=True)
         for key in data_crr.keys():
             data[key] = data_crr[key]
 

corrlib/meas_io.py

@@ -6,7 +6,7 @@ import json
 from typing import Union
 from pyerrors import Obs, Corr, dump_object, load_object
 from hashlib import sha256
-from .tools import get_db_file, cache_enabled
+from .tools import get_db_file, cache_enabled, get_plot_dir
 from .tracker import get, save, unlock
 import shutil
 from typing import Any
@@ -104,6 +104,8 @@ def write_measurement(path: Path, ensemble: str, measurement: dict[str, dict[str
                     subkeys.append(subkey)
                     pars[subkey] = json.dumps(parameters["rw_fcts"][i])
             elif ms_type in ['t0', 't1']:
+                plot_file = path / get_plot_dir(path) / ensemble / uuid / (ms_type + ".pdf")
+                files_to_save.append(plot_file)
                 if parameter_file is not None:
                     parameters = openQCD.load_ms3_infile(path, uuid, parameter_file)
                 else:

corrlib/toml.py

@@ -116,7 +116,7 @@ def check_measurement_data(measurements: dict[str, dict[str, str]], code: str) -
     """
     var_names: list[str] = []
     if code == "sfcf":
-        var_names = ["path", "ensemble", "param_file", "version", "prefix", "cfg_seperator", "names"]
+        var_names = ["path", "ensemble", "param_file", "version", "prefix", "cfg_separator", "names"]
     elif code == "openQCD":
         var_names = ["path", "ensemble", "measurement", "prefix"] # , "param_file"
     for mname, md in measurements.items():
@@ -191,10 +191,10 @@ def import_toml(path: Path, file: str, copy_file: bool=True) -> None:
             param = sfcf.read_param(path, uuid, md['param_file'])
             if 'names' in md.keys():
                 measurement = sfcf.read_data(path, uuid, md['path'], md['prefix'], param,
-                                            version=md['version'], cfg_seperator=md['cfg_seperator'], sep='/', names=md['names'])
+                                            version=md['version'], cfg_separator=md['cfg_separator'], sep='/', names=md['names'])
             else:
                 measurement = sfcf.read_data(path, uuid, md['path'], md['prefix'], param,
-                                            version=md['version'], cfg_seperator=md['cfg_seperator'], sep='/')
+                                            version=md['version'], cfg_separator=md['cfg_separator'], sep='/')
 
         elif project['code'] == 'openQCD':
             if md['measurement'] == 'ms1':
@@ -229,14 +229,14 @@ def import_toml(path: Path, 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'], ensemble, param, str(md["prefix"]), int(md["dtr_read"]), int(md["xmin"]), int(md["spatial_extent"]),
                                                  fit_range=int(md.get('fit_range', 5)), postfix=str(md.get('postfix', '')), names=md.get('names', []), files=md.get('files', []),
                                                  r_start=md.get('r_start', []), r_stop=md.get('r_stop', []), r_step=md.get('r_step', 1))
             elif md['measurement'] == 't1':
                 if 'param_file' in md:
                     param = openQCD.load_ms3_infile(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'], ensemble, param, str(md["prefix"]), int(md["dtr_read"]), int(md["xmin"]), int(md["spatial_extent"]),
                                                  fit_range=int(md.get('fit_range', 5)), postfix=str(md.get('postfix', '')), names=md.get('names', []), files=md.get('files', []),
                                                  r_start=md.get('r_start', []), r_stop=md.get('r_stop', []), r_step=md.get('r_step', 1))
         write_measurement(path, ensemble, measurement, uuid, project['code'], (md['param_file'] if 'param_file' in md else None))

corrlib/tools.py

@@ -129,6 +129,33 @@ def get_db_file(path: Path) -> Path:
     return db_file
 
 
+def get_plot_dir(path: Path) -> Path:
+    """
+    Get the plots directory associated with the library at the given path.
+
+    Parameters
+    ----------
+    path: str
+        The path of the library.
+
+    Returns
+    -------
+    db_file: str
+        The file holding the database.
+    """
+    path = Path(path)
+    if not os.path.exists(path):
+        raise FileNotFoundError(f"Corrlib path {path} does not exist.")
+    config_path = path / CONFIG_FILENAME
+    config = ConfigParser()
+    if os.path.exists(config_path):
+        config.read(config_path)
+    else:
+        raise FileNotFoundError("Configuration file not found.")
+    plot_dir = Path(config.get('paths', 'plot_dir', fallback='plots'))
+    return plot_dir
+
+
 def cache_enabled(path: Path) -> bool:
     """
     Check, whether the library is cached.

corrlib/tracker.py

@@ -144,7 +144,7 @@ def clone(path: Path, source: str, target: str) -> None:
     path = Path(path)
     tracker = get_tracker(path)
     if tracker == 'datalad':
-        dl.clone(target=target, source=source, dataset=path)
+        dl.clone(path=target, source=source, dataset=path)
     elif tracker == 'None':
         os.makedirs(path, exist_ok=True)
         # Implement a simple clone by copying files

pyproject.toml

@@ -11,6 +11,7 @@ dependencies = [
     'pyerrors>=2.11.1',
     "datalad>=1.1.0",
     'typer>=0.12.5',
+    "matplotlib>=3.10.7",
 ]
 description = "Python correlation library"
 authors = [

uv.lock

@@ -409,6 +409,7 @@ source = { editable = "." }
 dependencies = [
     { name = "datalad" },
     { name = "gitpython" },
+    { name = "matplotlib" },
     { name = "pyerrors" },
     { name = "typer" },
 ]
@@ -427,6 +428,7 @@ dev = [
 requires-dist = [
     { name = "datalad", specifier = ">=1.1.0" },
     { name = "gitpython", specifier = ">=3.1.45" },
+    { name = "matplotlib", specifier = ">=3.10.7" },
     { name = "pyerrors", specifier = ">=2.11.1" },
     { name = "typer", specifier = ">=0.12.5" },
 ]