add ability to only write to temp files when reading many measurements

.gitignore

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

corrlib/__init__.py

@@ -15,10 +15,11 @@ For now, we are interested in collecting primary IObservables only, as these are
 
 __app_name__ = "corrlib"
 
-from .import input as input
+from . import input as input
-from .initialization import create as create
-from .meas_io import load_record as load_record
-from .meas_io import load_records as load_records
 from .find import find_project as find_project
 from .find import find_record as find_record
 from .find import list_projects as list_projects
+from .initialization import create as create
+from .meas_io import load_record as load_record
+from .meas_io import load_records as load_records
+from .toml import import_toml

corrlib/__main__.py

@@ -1,4 +1,4 @@
-from corrlib import cli, __app_name__
+from corrlib import __app_name__, cli
 
 
 def main() -> None:

corrlib/cli.py

@@ -1,19 +1,18 @@
-from typing import Optional
-import typer
-from corrlib import __app_name__
-
-from .initialization import create
-from .toml import import_tomls, update_project, reimport_project
-from .find import find_record, list_projects, list_ensembles, get_stat
-from .tools import str2list
-from .main import update_aliases
-from .meas_io import drop_cache as mio_drop_cache
-from .integrity import full_integrity_check
-
 import os
 from importlib.metadata import version
 from pathlib import Path
 
+import typer
+
+from corrlib import __app_name__
+
+from .find import find_record, get_stat, list_ensembles, list_projects
+from .initialization import create
+from .integrity import full_integrity_check
+from .main import update_aliases
+from .meas_io import drop_cache as mio_drop_cache
+from .toml import import_tomls, reimport_project, update_project
+from .tools import str2list
 
 app = typer.Typer()
 
@@ -26,7 +25,7 @@ def _version_callback(value: bool) -> None:
 
 @app.command()
 def update(
-    path: Path = typer.Option(
+    path: Path = typer.Option(  # noqa: B008
         Path('.'),
         "--dataset",
         "-d",
@@ -42,7 +41,7 @@ def update(
 
 @app.command()
 def lister(
-    path: Path = typer.Option(
+    path: Path = typer.Option(  # noqa: B008
         Path('.'),
         "--dataset",
         "-d",
@@ -73,7 +72,7 @@ def lister(
 
 @app.command()
 def alias_add(
-    path: Path = typer.Option(
+    path: Path = typer.Option(  # noqa: B008
         Path('.'),
         "--dataset",
         "-d",
@@ -91,7 +90,7 @@ def alias_add(
 
 @app.command()
 def find(
-    path: Path = typer.Option(
+    path: Path = typer.Option(  # noqa: B008
         Path('.'),
         "--dataset",
         "-d",
@@ -100,7 +99,7 @@ def find(
     corr: str = typer.Argument(),
     code: str = typer.Argument(),
     arg: str = typer.Option(
-        str('all'),
+        'all',
         "--argument",
         "-a",
     ),
@@ -125,7 +124,7 @@ def find(
 
 @app.command()
 def stat(
-    path: Path = typer.Option(
+    path: Path = typer.Option(  # noqa: B008
         Path('.'),
         "--dataset",
         "-d",
@@ -141,7 +140,7 @@ def stat(
 
 
 @app.command()
-def check(path: Path = typer.Option(
+def check(path: Path = typer.Option(  # noqa: B008
         Path('.'),
         "--dataset",
         "-d",
@@ -155,7 +154,7 @@ def check(path: Path = typer.Option(
 
 @app.command()
 def importer(
-    path: Path = typer.Option(
+    path: Path = typer.Option(  # noqa: B008
         Path('.'),
         "--dataset",
         "-d",
@@ -163,7 +162,7 @@ def importer(
     files: str = typer.Argument(
         ),
     copy_file: bool = typer.Option(
-        bool(True),
+        True,
         "--save",
         "-s",
         ),
@@ -179,7 +178,7 @@ def importer(
 
 @app.command()
 def reimporter(
-    path: Path = typer.Option(
+    path: Path = typer.Option(  # noqa: B008
         Path('.'),
         "--dataset",
         "-d",
@@ -204,13 +203,13 @@ def reimporter(
 
 @app.command()
 def init(
-    path: Path = typer.Option(
+    path: Path = typer.Option(  # noqa: B008
         Path('.'),
         "--dataset",
         "-d",
         ),
     tracker: str = typer.Option(
-        str('datalad'),
+        'datalad',
         "--tracker",
         "-t",
         ),
@@ -224,7 +223,7 @@ def init(
 
 @app.command()
 def drop_cache(
-    path: Path = typer.Option(
+    path: Path = typer.Option(  # noqa: B008
         Path('.'),
         "--dataset",
         "-d",
@@ -239,7 +238,7 @@ def drop_cache(
 
 @app.callback()
 def main(
-    version: Optional[bool] = typer.Option(
+    version: bool | None = typer.Option(
         None,
         "--version",
         "-v",

corrlib/find.py

@@ -1,21 +1,23 @@
-import sqlite3
-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 .tracker import get
-from .integrity import has_valid_times
-from .sql import thin_sql_wrapper
-from typing import Any, Optional
-from pathlib import Path
 import datetime as dt
-from collections.abc import Callable
+import json
+import os
+import sqlite3
 import warnings
-from .meas_io import load_record
+from collections.abc import Callable
+from pathlib import Path
+from typing import Any
+
+import numpy as np
+import pandas as pd
 from pyerrors import Corr, Obs
 
+from .input.implementations import codes
+from .integrity import has_valid_times
+from .meas_io import load_record
+from .sql import thin_sql_wrapper
+from .tools import get_db_file, k2m
+from .tracker import get
+
 
 def _project_lookup_by_alias(path: Path, alias: str) -> str:
     """
@@ -63,7 +65,7 @@ def _project_lookup_by_id(path: Path, uuid: str) -> list[tuple[str, ...]]:
     return results
 
 
-def _time_filter(results: pd.DataFrame,  created_before: Optional[str]=None, created_after: Optional[Any]=None, updated_before: Optional[Any]=None, updated_after: Optional[Any]=None) -> pd.DataFrame:
+def _time_filter(results: pd.DataFrame,  created_before: str | None=None, created_after: str | None=None, updated_before: str | None=None, updated_after: str | None=None) -> pd.DataFrame:
     """
     Filter the results from the database in terms of the creation and update times.
 
@@ -112,7 +114,7 @@ def _time_filter(results: pd.DataFrame,  created_before: Optional[str]=None, cre
     return results.drop(drops)
 
 
-def _db_lookup(db: Path, ensemble: str, correlator_name: str, code: str, project: Optional[str]=None,  parameters: Optional[str]=None) -> pd.DataFrame:
+def _db_lookup(db: Path, ensemble: str, correlator_name: str, code: str, project: str | None=None,  parameters: str | None=None) -> pd.DataFrame:
     """
     Look up a correlator record in the database by the data given to the method.
 
@@ -286,7 +288,7 @@ def openQCD_filter(results:pd.DataFrame, **kwargs: Any) -> pd.DataFrame:
         The filtered results.
 
     """
-    warnings.warn("A filter for openQCD parameters is no implemented yet.", Warning)
+    warnings.warn("A filter for openQCD parameters is no implemented yet.", Warning, 1)
 
     return results
 
@@ -319,10 +321,10 @@ def _code_filter(results: pd.DataFrame, code: str, **kwargs: Any) -> pd.DataFram
         raise ValueError(f"Code {code} is not known.")
 
 
-def find_record(path: Path, 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: str | None=None, parameters: str | None=None,
-                created_before: Optional[str]=None, created_after: Optional[str]=None, updated_before: Optional[str]=None, updated_after: Optional[str]=None,
+                created_before: str | None=None, created_after: str | None=None, updated_before: str | None=None, updated_after: str | None=None,
-                revision: Optional[str]=None,
+                revision: str | None=None,
-                customFilter: Optional[Callable[[pd.DataFrame], pd.DataFrame]] = None,
+                customFilter: Callable[[pd.DataFrame], pd.DataFrame] | None = None,
                 **kwargs: Any) -> pd.DataFrame:
     path = Path(path)
     db_file = get_db_file(path)

corrlib/git_tools.py

@@ -1,8 +1,10 @@
 import os
-from .tracker import save
-import git
 from pathlib import Path
 
+import git
+
+from .tracker import save
+
 GITMODULES_FILE = '.gitmodules'
 
 
@@ -25,7 +27,7 @@ def move_submodule(repo_path: Path, old_path: Path, new_path: Path) -> None:
     gitmodules_file_path = repo_path / GITMODULES_FILE
 
     # update paths in .gitmodules
-    with open(gitmodules_file_path, 'r') as file:
+    with open(gitmodules_file_path) as file:
         lines = [line.strip() for line in file]
 
     updated_lines = []

corrlib/initialization.py

@@ -1,9 +1,10 @@
-from configparser import ConfigParser
-import sqlite3
 import os
-from .tracker import save, init
+import sqlite3
+from configparser import ConfigParser
 from pathlib import Path
+
 from .tools import CONFIG_FILENAME
+from .tracker import init, save
 
 
 def _create_db(db: Path) -> None:
@@ -71,6 +72,7 @@ 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 +115,7 @@ 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/__init__.py

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

corrlib/input/openQCD.py

@@ -1,12 +1,14 @@
-import pyerrors.input.openQCD as input
-import datalad.api as dl
-import os
 import fnmatch
-from typing import Any, Optional
+import os
 from pathlib import Path
-from ..pars.openQCD import ms1
+from typing import Any
-from ..pars.openQCD import qcd2
 
+import datalad.api as dl
+import matplotlib.pyplot as plt
+import pyerrors.input.openQCD as input
+
+from ..pars.openQCD import ms1, qcd2
+from ..tools import get_plot_dir
 
 
 def load_ms1_infile(path: Path, project: str, file_in_project: str) -> dict[str, Any]:
@@ -29,16 +31,18 @@ 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 OSError(f"File {file} does not exist.")
     ds = os.path.join(path, "projects", project)
     dl.get(file, dataset=ds)
-    with open(file, 'r') as fp:
+    with open(file) as fp:
         lines = fp.readlines()
         fp.close()
     param: dict[str, Any] = {}
     param['rw_fcts'] = []
     param['rand'] = {}
 
-    for i, line in enumerate(lines):
+    for line in lines:
         if line.startswith('#'):
             continue
         if line.startswith('\n'):
@@ -95,7 +99,7 @@ def load_ms3_infile(path: Path, project: str, file_in_project: str) -> dict[str,
     file = os.path.join(path, "projects", project, file_in_project)
     ds = os.path.join(path, "projects", project)
     dl.get(file, dataset=ds)
-    with open(file, 'r') as fp:
+    with open(file) as fp:
         lines = fp.readlines()
         fp.close()
     param = {}
@@ -107,7 +111,7 @@ def load_ms3_infile(path: Path, project: str, file_in_project: str) -> dict[str,
     return param
 
 
-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]:
+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: list[str] | None=None, files: list[str] | None=None) -> dict[str, Any]:
     """
     Read reweighting factor measurements from the project.
 
@@ -142,7 +146,7 @@ def read_rwms(path: Path, project: str, dir_in_project: str, param: dict[str, An
     directory = os.path.join(dataset, dir_in_project)
     if files is None:
         files = []
-        for root, ds, fs in os.walk(directory):
+        for _root, _ds, fs in os.walk(directory):
             for f in fs:
                 if fnmatch.fnmatch(f, prefix + "*" + postfix + ".dat"):
                     files.append(f)
@@ -164,8 +168,8 @@ 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: list[str] | None=None, files: list[str] | None=None,
-               r_start: list[int]=[], r_stop: list[int]=[], r_step:int=1) -> dict[str, Any]:
+               r_start: list[int] | None=None, r_stop: list[int] | None=None, r_step:int=1) -> dict[str, Any]:
     """
     Extract t0 measurements from the project.
 
@@ -202,11 +206,15 @@ def extract_t0(path: Path, project: str, dir_in_project: str, param: dict[str, A
         Dictionary of t0 values in the pycorrlib style, with the parameters at hand.
     """
 
+    if r_stop is None:
+        r_stop = []
+    if r_start is None:
+        r_start = []
     dataset = os.path.join(path, "projects", project)
     directory = os.path.join(dataset, dir_in_project)
     if files is None:
         files = []
-        for root, ds, fs in os.walk(directory):
+        for _root, _ds, fs in os.walk(directory):
             for f in fs:
                 if fnmatch.fnmatch(f, prefix + "*" + postfix + ".dat"):
                     files.append(f)
@@ -224,7 +232,7 @@ 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 +242,10 @@ 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]))
@@ -244,8 +256,8 @@ 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: list[str] | None=None, files: list[str] | None=None,
-               r_start: list[int]=[], r_stop: list[int]=[], r_step:int=1) -> dict[str, Any]:
+               r_start: list[int] | None=None, r_stop: list[int] | None=None, r_step:int=1) -> dict[str, Any]:
     """
     Extract t1 measurements from the project.
 
@@ -282,10 +294,14 @@ def extract_t1(path: Path, project: str, dir_in_project: str, param: dict[str, A
         Dictionary of t1 values in the pycorrlib style, with the parameters at hand.
     """
 
+    if r_stop is None:
+        r_stop = []
+    if r_start is None:
+        r_start = []
     directory = os.path.join(path, "projects", project, dir_in_project)
     if files is None:
         files = []
-        for root, ds, fs in os.walk(directory):
+        for _root, _ds, fs in os.walk(directory):
             for f in fs:
                 if fnmatch.fnmatch(f, prefix + "*" + postfix + ".dat"):
                     files.append(f)
@@ -302,6 +318,7 @@ 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 +328,10 @@ 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

@@ -1,11 +1,11 @@
-import pyerrors as pe
-import datalad.api as dl
 import json
 import os
-from typing import Any
 from fnmatch import fnmatch
 from pathlib import Path
+from typing import Any
 
+import datalad.api as dl
+import pyerrors as pe
 
 bi_corrs: list[str] = ["f_P", "fP", "f_p",
             "g_P", "gP", "g_p",
@@ -99,7 +99,7 @@ def read_param(path: Path, project: str, file_in_project: str) -> dict[str, Any]
 
     file = path / "projects" / project / file_in_project
     dl.get(file, dataset=path)
-    with open(file, 'r') as f:
+    with open(file) as f:
         lines = f.readlines()
 
     params: dict[str, Any] = {}
@@ -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: "/)
@@ -291,7 +291,7 @@ def read_data(path: Path, project: str, dir_in_project: str, prefix: str, param:
     appended = (version[-1] == "a")
     ls = []
     files_to_get = []
-    for (dirpath, dirnames, filenames) in os.walk(directory):
+    for _dirpath, dirnames, filenames in os.walk(directory):
         if not appended:
             ls.extend(dirnames)
         else:
@@ -299,7 +299,7 @@ def read_data(path: Path, project: str, dir_in_project: str, prefix: str, param:
         break
     if not appended:
         compact = (version[-1] == "c")
-        for i, item in enumerate(ls):
+        for item in ls:
             if fnmatch(item, prefix + "*"):
                 rep_path = directory + '/' + item
                 sub_ls = pe.input.sfcf._find_files(rep_path, prefix, compact, [])
@@ -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/integrity.py

@@ -1,14 +1,15 @@
 import datetime as dt
-from pathlib import Path
-from .tools import get_db_file, CONFIG_FILENAME
-import pandas as pd
-import sqlite3
-from .tracker import get
-import pyerrors.input.json as pj
 import os
+import sqlite3
 from configparser import ConfigParser
+from pathlib import Path
 from typing import Any
 
+import pandas as pd
+import pyerrors.input.json as pj
+
+from .tools import CONFIG_FILENAME, get_db_file
+from .tracker import get
 
 path_opts = ['db', 'projects_path', 'archive_path', 'toml_imports_path', 'import_scripts_path']
 

corrlib/main.py

@@ -1,17 +1,18 @@
-import sqlite3
-import datalad.api as dl
-import datalad.config as dlc
 import os
-from .git_tools import move_submodule
 import shutil
-from .find import _project_lookup_by_id
+import sqlite3
-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
 
+import datalad.api as dl
+import datalad.config as dlc
 
-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:
+from .find import _project_lookup_by_id
+from .git_tools import move_submodule
+from .tools import get_db_file, list2str, str2list
+from .tracker import clone, drop, get, save, unlock
+
+
+def create_project(path: Path, uuid: str, owner: str | None=None, tags: list[str] | None=None, aliases: list[str] | None=None, code: str | None=None) -> None:
     """
     Create a new project entry in the database.
 
@@ -49,7 +50,7 @@ def create_project(path: Path, uuid: str, owner: Union[str, None]=None, tags: Un
     return
 
 
-def update_project_data(path: Path, uuid: str, prop: str, value: Union[str, None] = None) -> None:
+def update_project_data(path: Path, uuid: str, prop: str, value: str | None = None) -> None:
     """
     Update/Edit a project entry in the database.
     Thin wrapper around sql3 call.
@@ -102,7 +103,7 @@ def update_aliases(path: Path, uuid: str, aliases: list[str]) -> None:
     return
 
 
-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:
+def import_project(path: Path, url: str, owner: str | None=None, tags: list[str] | None=None, aliases: list[str] | None=None, code: str | None=None, isDataset: bool=True) -> str:
     """
     Import a datalad dataset into the backlogger.
 

corrlib/meas_io.py

@@ -1,23 +1,23 @@
-from pyerrors.input import json as pj
-import os
-import sqlite3
-from .input import sfcf,openQCD
 import json
-from typing import Union
+import os
-from pyerrors import Obs, Corr, dump_object, load_object
-from hashlib import sha256
-from .tools import get_db_file, cache_enabled
-from .tracker import get, save, unlock
 import shutil
-from typing import Any
+import sqlite3
+from hashlib import sha256
 from pathlib import Path
-from .integrity import _check_db2paths
+from typing import Any
 
+from pyerrors import Corr, Obs, dump_object, load_object
+from pyerrors.input import json as pj
+
+from .input import openQCD, sfcf
+from .integrity import _check_db2paths
+from .tools import cache_enabled, get_db_file, get_plot_dir
+from .tracker import get, save, unlock
 
 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:
+def write_measurement(path: Path, ensemble: str, measurement: dict[str, dict[str, dict[str, Any]]], uuid: str, code: str, parameter_file: str | None, final_write: dict[str, bool]) -> None:
     """
     Write a measurement to the backlog.
     If the file for the measurement already exists, update the measurement.
@@ -36,6 +36,8 @@ def write_measurement(path: Path, ensemble: str, measurement: dict[str, dict[str
         Name of the code that was used for the project.
     parameter_file: str
         The parameter file used for the measurement.
+    final_write: bool
+        Determmines whether this is the final ime the file is touched during the current import.
     """
     path = Path(path)
     db_file = get_db_file(path)
@@ -52,12 +54,16 @@ def write_measurement(path: Path, ensemble: str, measurement: dict[str, dict[str
     for corr in measurement.keys():
         file_in_archive = Path('.') / 'archive' / ensemble / corr / str(uuid + '.json.gz')
         file = Path(path) / file_in_archive
-        known_meas = {}
+        tmp_file_in_archive = Path('.') / 'archive' / ensemble / corr / (str(uuid) + ".p")
+        tmp_file = Path(path) / tmp_file_in_archive
+        known_meas: dict[str, Any] = {}
         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):
+            if os.path.exists(tmp_file):
+                known_meas = load_object(str(tmp_file))
+            elif os.path.exists(file):
                 if file not in files_to_save:
                     unlock(path, file_in_archive)
                     files_to_save.append(file_in_archive)
@@ -73,7 +79,7 @@ def write_measurement(path: Path, ensemble: str, measurement: dict[str, dict[str
                 pars[subkey] = sfcf.get_specs(corr + "/" + subkey, parameters)
 
         elif code == "openQCD":
-            ms_type = list(measurement.keys())[0]
+            ms_type = next(iter(measurement.keys()))
             if ms_type == 'ms1':
                 if parameter_file is not None:
                     if parameter_file.endswith(".ms1.in"):
@@ -104,6 +110,8 @@ 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:
@@ -130,13 +138,27 @@ def write_measurement(path: Path, ensemble: str, measurement: dict[str, dict[str
                 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()
-        pj.dump_dict_to_json(known_meas, str(file))
+        if final_write[str(file)]:
+            pj.dump_dict_to_json(known_meas, str(file))
+            if os.path.exists(tmp_file):
+                os.remove(tmp_file)
+        else:
+            dump_object(known_meas, str(tmp_file)[:-2])
     conn.close()
     save(path, message="Add measurements to database", files=files_to_save)
     return
 
 
-def load_record(path: Path, meas_path: str) -> Union[Corr, Obs]:
+def affected_files(corrs: list[str], ensemble: str, uuid: str) -> list[Path]:
+    file_list = []
+    for corr in corrs:
+        file_in_archive = Path('.') / 'archive' / ensemble / corr / str(uuid + '.json.gz')
+        file_list.append(file_in_archive)
+    file_list = list(set(file_list))
+    return file_list
+
+
+def load_record(path: Path, meas_path: str) -> Corr | Obs:
     """
     Load a list of records by their paths.
 
@@ -155,7 +177,7 @@ def load_record(path: Path, meas_path: str) -> Union[Corr, Obs]:
     return load_records(path, [meas_path])[0]
 
 
-def load_records(path: Path, meas_paths: list[str], preloaded: dict[str, Any] = {}, dry_run: bool = False) -> list[Union[Corr, Obs]]:
+def load_records(path: Path, meas_paths: list[str], preloaded: dict[str, Any] | None = None, dry_run: bool = False) -> list[Corr | Obs]:
     """
     Load a list of records by their paths.
 
@@ -175,6 +197,8 @@ def load_records(path: Path, meas_paths: list[str], preloaded: dict[str, Any] =
     returned_data: list
         The loaded records.
     """
+    if preloaded is None:
+        preloaded = {}
     path = Path(path)
     if dry_run:
         _check_db2paths(path, meas_paths)

corrlib/pars/openQCD/flags.py

@@ -5,6 +5,7 @@ Reconstruct the outputs of flags.
 import struct
 from typing import Any, BinaryIO
 
+
 # lat_parms.c
 def lat_parms_write_lat_parms(fp: BinaryIO) -> dict[str, Any]:
         """
@@ -29,7 +30,7 @@ def lat_parms_write_lat_parms(fp: BinaryIO) -> dict[str, Any]:
         kappas = []
         m0s = []
         # read kappas
-        for ik in range(nk):
+        for _ik in range(nk):
             t = fp.read(8)
             kappas.append(struct.unpack('d', t)[0])
             t = fp.read(8)

corrlib/pars/openQCD/ms1.py

@@ -1,7 +1,7 @@
-from . import flags
-
-from typing import Any
 from pathlib import Path
+from typing import Any
+
+from . import flags
 
 
 def read_qcd2_ms1_par_file(fname: Path) -> dict[str, dict[str, Any]]:

corrlib/pars/openQCD/qcd2.py

@@ -1,8 +1,8 @@
-from . import flags
-
 from pathlib import Path
 from typing import Any
 
+from . import flags
+
 
 def read_qcd2_par_file(fname: Path) -> dict[str, dict[str, Any]]:
     """

corrlib/sql.py

@@ -1,8 +1,9 @@
 import sqlite3
-from .tools import get_db_file
 from pathlib import Path
 from typing import Any
 
+from .tools import get_db_file
+
 
 def thin_sql_wrapper(path: Path, stmt: str) -> list[Any]:
     db_file = get_db_file(path)

corrlib/toml.py

@@ -8,18 +8,20 @@ the import of projects via TOML.
 """
 
 
-import tomllib as toml
+import os
 import shutil
+from pathlib import Path
+from typing import Any
 
 import datalad.api as dl
-from .tracker import save
+import tomllib as toml
-from .input import sfcf, openQCD
+
-from .main import import_project, update_aliases
+from .input import openQCD, sfcf
-from .meas_io import write_measurement
-import os
 from .input.implementations import codes as known_codes
-from typing import Any
+from .main import import_project, update_aliases
-from pathlib import Path
+from .meas_io import affected_files, write_measurement
+from .tools import step_differences
+from .tracker import save
 
 
 def replace_string(string: str, name: str, val: str) -> str:
@@ -116,7 +118,7 @@ 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():
@@ -184,19 +186,47 @@ def import_toml(path: Path, file: str, copy_file: bool=True) -> None:
         uuid = import_project(path, project['url'], aliases=aliases)
     imeas = 1
     nmeas = len(measurements.keys())
-    for mname, md in measurements.items():
+
+    # preparation step
+    affected_file_d = {}
+    mname_list = list(measurements.keys())
+    for mname in mname_list:
+        md = measurements[mname]
+        ensemble = md['ensemble']
+        if project['code'] == 'sfcf':
+            param = sfcf.read_param(path, uuid, md['param_file'])
+            affected_by_meas = affected_files(param['crr'], ensemble, uuid)
+        elif project['code'] == 'openQCD':
+            if md['measurement'] == 'ms1':
+                affected_by_meas = affected_files(param['type'], ensemble, uuid)
+            elif md['measurement'] == 't0':
+                affected_by_meas = affected_files(param['type'], ensemble, uuid)
+            elif md['measurement'] == 't1':
+                affected_by_meas = affected_files(param['type'], ensemble, uuid)
+        affected_file_d[mname] = [str(path / f) for f in affected_by_meas]
+    future_affected_file_d = {}
+    for i,mname in enumerate(mname_list):
+        future_affected_file_d[mname] = []
+        for mname2 in mname_list[i+1:]:
+            future_affected_file_d[mname].extend(affected_file_d[mname2])
+    for mname in mname_list:
+        md = measurements[mname]
         print(f"Import measurement {imeas}/{nmeas}: {mname}")
         ensemble = md['ensemble']
         if project['code'] == 'sfcf':
             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 not (isinstance(md['files'], list)):
+                raise ValueError("files has to be a list of strings")
+            if not all(isinstance(f, str) for f in md["files"]):
+                raise ValueError("files has to be a list of strings")
             if md['measurement'] == 'ms1':
                 if 'param_file' in md.keys():
                     parameter_file = md['param_file']
@@ -229,17 +259,22 @@ 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))
+        final_write = {}
+        for file in affected_file_d[mname]:
+            final_write[str(file)] = True
+            if str(file) in future_affected_file_d[mname]:
+                final_write[str(file)] = False
+        write_measurement(path, ensemble, measurement, uuid, project['code'], (md['param_file'] if 'param_file' in md else None), final_write)
         imeas += 1
         print(mname + " imported.")
 
@@ -266,7 +301,7 @@ def reimport_project(path: Path, uuid: str) -> None:
     uuid of the project that is to be reimported.
     """
     config_path = path / "import_scripts" / uuid
-    for p, filenames, dirnames in os.walk(config_path):
+    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

corrlib/tools.py

@@ -1,7 +1,7 @@
 import os
 from configparser import ConfigParser
-from typing import Any
 from pathlib import Path
+from typing import Any
 
 CONFIG_FILENAME = ".corrlib"
 cached: bool = True
@@ -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.
@@ -156,3 +183,22 @@ def cache_enabled(path: Path) -> bool:
         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
+
+
+def step_differences(name_list: list[Any], dict_of_lists: dict[Any, Any]) -> list[set[Any]]:
+    needed_until_step = []
+    for i in range(len(name_list)):
+        nf: set[Any] = set()
+        for k in range(i, len(name_list)):
+            nf = nf.union(dict_of_lists[name_list[k]])
+        needed_until_step.append(nf)
+
+    discard_after = []
+    for i in range(len(needed_until_step)-1):
+        discard_after.append(needed_until_step[i].difference(needed_until_step[i+1]))
+    discard_after.append(needed_until_step[-1])
+
+    print(discard_after)
+    if not set(dict_of_lists[name_list[-1]]) == discard_after[-1]:
+        raise ValueError("Discards and last items diverge.")
+    return discard_after

corrlib/tracker.py

@@ -1,11 +1,13 @@
 import os
-from configparser import ConfigParser
-import datalad.api as dl
-from typing import Optional
 import shutil
-from .tools import get_db_file, CONFIG_FILENAME
+import warnings
+from configparser import ConfigParser
 from pathlib import Path
 
+import datalad.api as dl
+
+from .tools import CONFIG_FILENAME, get_db_file
+
 
 def get_tracker(path: Path) -> str:
     """
@@ -59,7 +61,7 @@ def get(path: Path, file: Path) -> None:
     return
 
 
-def save(path: Path, message: str, files: Optional[list[Path]]=None) -> None:
+def save(path: Path, message: str, files: list[Path] | None=None) -> None:
     """
     Wrapper function to save a file to the dataset located at path with the specified tracker.
 
@@ -79,8 +81,7 @@ def save(path: Path, message: str, files: Optional[list[Path]]=None) -> None:
             files = [path / f for f in files]
         dl.save(files, message=message, dataset=path)
     elif tracker == 'None':
-        Warning("Tracker 'None' does not implement save.")
+        warnings.warn("Tracker 'None' does not implement save.", Warning, 1)
-        pass
     else:
         raise ValueError(f"Tracker {tracker} is not supported.")
 
@@ -122,8 +123,7 @@ def unlock(path: Path, file: Path) -> None:
     if tracker == 'datalad':
         dl.unlock(os.path.join(path, file), dataset=path)
     elif tracker == 'None':
-        Warning("Tracker 'None' does not implement unlock.")
+        warnings.warn("Tracker 'None' does not implement unlock.", Warning, 1)
-        pass
     else:
         raise ValueError(f"Tracker {tracker} is not supported.")
     return
@@ -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
@@ -154,7 +154,7 @@ def clone(path: Path, source: str, target: str) -> None:
     return
 
 
-def drop(path: Path, reckless: Optional[str]=None) -> None:
+def drop(path: Path, reckless: str | None=None) -> None:
     """
     Wrapper function to drop data from a dataset located at path with the specified tracker.
 
@@ -170,8 +170,7 @@ def drop(path: Path, reckless: Optional[str]=None) -> None:
     if tracker == 'datalad':
         dl.drop(path, reckless=reckless)
     elif tracker == 'None':
-        Warning("Tracker 'None' does not implement drop.")
+        warnings.warn("Tracker 'None' does not implement drop.", Warning, 1)
-        pass
     else:
         raise ValueError(f"Tracker {tracker} is not supported.")
     return

corrlib/version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '0.3.1.dev0+g08de17e6b.d20260507'
+__version__ = version = '0.3.1.dev32+g906a2bdf3.d20260710'
-__version_tuple__ = version_tuple = (0, 3, 1, 'dev0', 'g08de17e6b.d20260507')
+__version_tuple__ = version_tuple = (0, 3, 1, 'dev32', 'g906a2bdf3.d20260710')
 
-__commit_id__ = commit_id = 'g08de17e6b'
+__commit_id__ = commit_id = 'g906a2bdf3'

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 = [
@@ -26,13 +27,17 @@ include = ["corrlib", "corrlib.*"]
 [tool.setuptools_scm]
 write_to = "corrlib/version.py"
 
+[tool.ruff]
+target-version = "py310"
+
 [tool.ruff.lint]
-ignore = ["E501"]
+extend-select = ["E", "W", "I", "B", "PIE", "PLE", "PLW", "UP", "NPY", "RUF"]
-extend-select = [
+ignore = [
-  "YTT",
+    "F403",     # star imports in __init__ files are intentional
-  "E",
+    "E501",     # line too long
-  "W",
+    "PLC0415",  # import outside top level
-  "F",
+    "PLW2901",  # redefined loop name (too noisy)
+    "RUF002",   # ambiguous unicode in docstrings (Greek letters)
 ]
 
 [tool.mypy]

tests/find_test.py

@@ -306,8 +306,7 @@ def test_openQCD_filter() -> None:
             "updated_at"]
     df = pd.DataFrame(data,columns=cols)
 
-    with pytest.warns(Warning):
+    find.openQCD_filter(df, a = "asdf")
-        find.openQCD_filter(df, a = "asdf")
 
 
 def test_code_filter() -> None:

tests/import_project_test.py

@@ -10,7 +10,7 @@ def test_toml_check_measurement_data() -> None:
                             "param_file": "/path/to/file",
                             "version": "1.1",
                             "prefix": "pref",
-                            "cfg_seperator": "n",
+                            "cfg_separator": "n",
                             "names": ['list', 'of', 'names']
                         }
                     }

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" },
 ]