Merge pull request 'integ/links' (#34) from integ/links into develop

Reviewed-on: https://www.kuhl-mann.de/git/git/jkuhl/corrlib/pulls/34

.github/workflows/mypy.yaml

@@ -8,22 +8,21 @@ on:
 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
+          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
+      - name: Setup python
+        uses: https://github.com/actions/setup-python@v5
         with:
-          python-version: ${{ matrix.python-version }}
-          enable-cache: true
+          python-version: "3.12"
+      - name: Install uv
+        uses: https://github.com/astral-sh/setup-uv@v5
       - name: Install corrlib
         run: uv sync --locked --all-extras --dev --python "3.12"
       - name: Run tests

.github/workflows/pytest.yaml

@@ -17,9 +17,11 @@ jobs:
           - "3.14"
 
     runs-on: ubuntu-latest
-    env:
-      UV_CACHE_DIR: /tmp/.uv-cache
     steps:
+      - name: Setup git
+        run: |
+          git config --global user.email "tester@example.com"
+          git config --global user.name "Tester"
       - name: Install git-annex
         run: |
           sudo apt-get update
@@ -28,11 +30,12 @@ jobs:
         uses: https://github.com/RouxAntoine/checkout@v4.1.8
         with:
           show-progress: true
-      - name: Install uv
-        uses: astral-sh/setup-uv@v7
+      - name: Setup python
+        uses: https://github.com/actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-          enable-cache: true
+      - name: Install uv
+        uses: https://github.com/astral-sh/setup-uv@v5
       - name: Install corrlib
         run: uv sync --locked --all-extras --dev --python ${{ matrix.python-version }}
       - name: Run tests

.github/workflows/ruff.yaml

@@ -9,8 +9,6 @@ jobs:
   ruff:
 
     runs-on: ubuntu-latest
-    env:
-      UV_CACHE_DIR: /tmp/.uv-cache
     steps:
       - name: Install git-annex
         run: |
@@ -20,10 +18,12 @@ jobs:
         uses: https://github.com/RouxAntoine/checkout@v4.1.8
         with:
           show-progress: true
-      - name: Install uv
-        uses: astral-sh/setup-uv@v7
+      - name: Setup python
+        uses: https://github.com/actions/setup-python@v5
         with:
-          enable-cache: true
+          python-version: "3.12"
+      - name: Install uv
+        uses: https://github.com/astral-sh/setup-uv@v5
       - name: Install corrlib
         run: uv sync --locked --all-extras --dev --python "3.12"
       - name: Run tests

corrlib/cli.py

@@ -1,14 +1,20 @@
 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
 from .tools import str2list
 from .main import update_aliases
 from .meas_io import drop_cache as mio_drop_cache
+from .meas_io import load_record as mio_load_record
+from .integrity import full_integrity_check
+
 import os
+from pyerrors import Corr
 from importlib.metadata import version
+from pathlib import Path
 
 
 app = typer.Typer()
@@ -22,8 +28,8 @@ def _version_callback(value: bool) -> None:
 
 @app.command()
 def update(
-    path: str = typer.Option(
-        str('./corrlib'),
+    path: Path = typer.Option(
+        Path('./corrlib'),
         "--dataset",
         "-d",
         ),
@@ -35,10 +41,11 @@ def update(
     update_project(path, uuid)
     return
 
+
 @app.command()
-def list(
-    path: str = typer.Option(
-        str('./corrlib'),
+def lister(
+    path: Path = typer.Option(
+        Path('./corrlib'),
         "--dataset",
         "-d",
     ),
@@ -49,8 +56,8 @@ def list(
     """
     if entities in ['ensembles', 'Ensembles','ENSEMBLES']:
         print("Ensembles:")
-        for item in os.listdir(path + "/archive"):
-            if os.path.isdir(os.path.join(path + "/archive", item)):
+        for item in os.listdir(path / "archive"):
+            if os.path.isdir(path / "archive" / item):
                 print(item)
     elif entities == 'projects':
         results = list_projects(path)
@@ -68,8 +75,8 @@ def list(
 
 @app.command()
 def alias_add(
-    path: str = typer.Option(
-        str('./corrlib'),
+    path: Path = typer.Option(
+        Path('./corrlib'),
         "--dataset",
         "-d",
         ),
@@ -86,26 +93,67 @@ def alias_add(
 
 @app.command()
 def find(
-    path: str = typer.Option(
-        str('./corrlib'),
+    path: Path = typer.Option(
+        Path('./corrlib'),
         "--dataset",
         "-d",
         ),
     ensemble: str = typer.Argument(),
     corr: str = typer.Argument(),
     code: str = typer.Argument(),
+    arg: str = typer.Option(
+        str('all'),
+        "--argument",
+        "-a",
+    ),
     ) -> None:
     """
     Find a record in the backlog at hand. Through specifying it's ensemble and the measured correlator.
     """
     results = find_record(path, ensemble, corr, code)
-    print(results)
+    if results.empty:
+        return
+    if arg == 'all':
+        print(results)
+    else:
+        for r in results[arg].values:
+            print(r)
+
+
+@app.command()
+def stat(
+    path: Path = typer.Option(
+        Path('./corrlib'),
+        "--dataset",
+        "-d",
+        ),
+    record_id: str = typer.Argument(),
+    ) -> None:
+    """
+    Show the statistics of a given record.
+    """
+    record = mio_load_record(path, record_id)
+    if isinstance(record, (list, Corr)):
+        record = record[0]
+    statistics = record.idl
+    print(statistics)
+    return
+
+
+@app.command()
+def check(path: Path = typer.Option(
+        Path('./corrlib'),
+        "--dataset",
+        "-d",
+        ),
+    ) -> None:
+    full_integrity_check(path)
 
 
 @app.command()
 def importer(
-    path: str = typer.Option(
-        str('./corrlib'),
+    path: Path = typer.Option(
+        Path('./corrlib'),
         "--dataset",
         "-d",
         ),
@@ -127,8 +175,8 @@ def importer(
 
 @app.command()
 def reimporter(
-    path: str = typer.Option(
-        str('./corrlib'),
+    path: Path = typer.Option(
+        Path('./corrlib'),
         "--dataset",
         "-d",
         ),
@@ -151,8 +199,8 @@ def reimporter(
 
 @app.command()
 def init(
-    path: str = typer.Option(
-        str('./corrlib'),
+    path: Path = typer.Option(
+        Path('./corrlib'),
         "--dataset",
         "-d",
         ),
@@ -171,8 +219,8 @@ def init(
 
 @app.command()
 def drop_cache(
-    path: str = typer.Option(
-        str('./corrlib'),
+    path: Path = typer.Option(
+        Path('./corrlib'),
         "--dataset",
         "-d",
         ),

corrlib/find.py

@@ -6,10 +6,15 @@ 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 typing import Any, Optional
+from pathlib import Path
+import datetime as dt
+from collections.abc import Callable
+import warnings
 
 
-def _project_lookup_by_alias(db: str, alias: str) -> str:
+def _project_lookup_by_alias(db: Path, alias: str) -> str:
     """
     Lookup a projects UUID by its (human-readable) alias.
 
@@ -27,7 +32,7 @@ def _project_lookup_by_alias(db: str, alias: str) -> str:
     """
     conn = sqlite3.connect(db)
     c = conn.cursor()
-    c.execute(f"SELECT * FROM 'projects' WHERE alias = '{alias}'")
+    c.execute(f"SELECT * FROM 'projects' WHERE aliases = '{alias}'")
     results = c.fetchall()
     conn.close()
     if len(results)>1:
@@ -37,7 +42,7 @@ def _project_lookup_by_alias(db: str, alias: str) -> str:
     return str(results[0][0])
 
 
-def _project_lookup_by_id(db: str, uuid: str) -> list[tuple[str, str]]:
+def _project_lookup_by_id(db: Path, uuid: str) -> list[tuple[str, ...]]:
     """
     Return the project information available in the database by UUID.
 
@@ -61,8 +66,56 @@ 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,
-               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: Optional[str]=None, created_after: Optional[Any]=None, updated_before: Optional[Any]=None, updated_after: Optional[Any]=None) -> pd.DataFrame:
+    """
+    Filter the results from the database in terms of the creation and update times.
+
+    Parameters
+    ----------
+    results: pd.DataFrame
+        The dataframe holding the unfilteres results from the database.
+    created_before: str
+        Contraint on the creation date in datetime.datetime.isoformat. Note that this is exclusive. The creation date has to be truly before the date and time given.
+    created_after: str
+        Contraint on the creation date in datetime.datetime.isoformat. Note that this is exclusive. The creation date has to be truly after the date and time given.
+    updated_before: str
+        Contraint on the creation date in datetime.datetime.isoformat. Note that this is exclusive. The date of the last update has to be truly before the date and time given.
+    updated_after: str
+        Contraint on the creation date in datetime.datetime.isoformat. Note that this is exclusive. The date of the last update has to be truly after the date and time given.
+    """
+    drops = []
+    for ind in range(len(results)):
+        result = results.iloc[ind]
+        created_at = dt.datetime.fromisoformat(result['created_at'])
+        updated_at = dt.datetime.fromisoformat(result['updated_at'])
+        db_times_valid = has_valid_times(result)
+        if not db_times_valid:
+            raise ValueError('Time stamps not valid for result with path', result["path"])
+
+        if created_before is not None:
+            date_created_before = dt.datetime.fromisoformat(created_before)
+            if date_created_before < created_at:
+                drops.append(ind)
+                continue
+        if created_after is not None:
+            date_created_after = dt.datetime.fromisoformat(created_after)
+            if date_created_after > created_at:
+                drops.append(ind)
+                continue
+        if updated_before is not None:
+            date_updated_before = dt.datetime.fromisoformat(updated_before)
+            if date_updated_before < updated_at:
+                drops.append(ind)
+                continue
+        if updated_after is not None:
+            date_updated_after = dt.datetime.fromisoformat(updated_after)
+            if date_updated_after > updated_at:
+                drops.append(ind)
+                continue
+    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:
     """
     Look up a correlator record in the database by the data given to the method.
 
@@ -104,22 +157,86 @@ def _db_lookup(db: str, ensemble: str, correlator_name: str, code: str, project:
         search_expr += f" AND code = '{code}'"
     if parameters:
         search_expr += f" AND parameters = '{parameters}'"
-    if created_before:
-        search_expr += f" AND created_at < '{created_before}'"
-    if created_after:
-        search_expr += f" AND created_at > '{created_after}'"
-    if updated_before:
-        search_expr += f" AND updated_at < '{updated_before}'"
-    if updated_after:
-        search_expr += f" AND updated_at > '{updated_after}'"
     conn = sqlite3.connect(db)
     results = pd.read_sql(search_expr, conn)
     conn.close()
     return results
 
 
+def _sfcf_drop(param: dict[str, Any], **kwargs: Any) -> bool:
+        if 'offset' in kwargs:
+            if kwargs.get('offset') != param['offset']:
+                return True
+        if 'quark_kappas' in kwargs:
+            kappas = kwargs['quark_kappas']
+            if (not np.isclose(kappas[0], param['quarks'][0]['mass']) or not np.isclose(kappas[1], param['quarks'][1]['mass'])):
+                return True
+        if 'quark_masses' in kwargs:
+            masses = kwargs['quark_masses']
+            if (not np.isclose(masses[0], k2m(param['quarks'][0]['mass'])) or not np.isclose(masses[1], k2m(param['quarks'][1]['mass']))):
+                return True
+        if 'qk1' in kwargs:
+            quark_kappa1 = kwargs['qk1']
+            if not isinstance(quark_kappa1, list):
+                if (not np.isclose(quark_kappa1, param['quarks'][0]['mass'])):
+                    return True
+            else:
+                if len(quark_kappa1) == 2:
+                    if (quark_kappa1[0] > param['quarks'][0]['mass']) or (quark_kappa1[1] < param['quarks'][0]['mass']):
+                        return True
+                else:
+                    raise ValueError("quark_kappa1 has to have length 2")
+        if 'qk2' in kwargs:
+            quark_kappa2 = kwargs['qk2']
+            if not isinstance(quark_kappa2, list):
+                if (not np.isclose(quark_kappa2, param['quarks'][1]['mass'])):
+                    return True
+            else:
+                if len(quark_kappa2) == 2:
+                    if (quark_kappa2[0] > param['quarks'][1]['mass']) or (quark_kappa2[1] < param['quarks'][1]['mass']):
+                        return True
+                else:
+                    raise ValueError("quark_kappa2 has to have length 2")
+        if 'qm1' in kwargs:
+            quark_mass1 = kwargs['qm1']
+            if not isinstance(quark_mass1, list):
+                if (not np.isclose(quark_mass1, k2m(param['quarks'][0]['mass']))):
+                    return True
+            else:
+                if len(quark_mass1) == 2:
+                    if (quark_mass1[0] > k2m(param['quarks'][0]['mass'])) or (quark_mass1[1] < k2m(param['quarks'][0]['mass'])):
+                        return True
+                else:
+                    raise ValueError("quark_mass1 has to have length 2")
+        if 'qm2' in kwargs:
+            quark_mass2 = kwargs['qm2']
+            if not isinstance(quark_mass2, list):
+                if (not np.isclose(quark_mass2, k2m(param['quarks'][1]['mass']))):
+                    return True
+            else:
+                if len(quark_mass2) == 2:
+                    if (quark_mass2[0] > k2m(param['quarks'][1]['mass'])) or (quark_mass2[1] < k2m(param['quarks'][1]['mass'])):
+                        return True
+                else:
+                    raise ValueError("quark_mass2 has to have length 2")
+        if 'quark_thetas' in kwargs:
+            quark_thetas = kwargs['quark_thetas']
+            if (quark_thetas[0] != param['quarks'][0]['thetas'] and quark_thetas[1] != param['quarks'][1]['thetas']) or (quark_thetas[0] != param['quarks'][1]['thetas'] and quark_thetas[1] != param['quarks'][0]['thetas']):
+                return True
+        # careful, this is not save, when multiple contributions are present!
+        if 'wf1' in kwargs:
+            wf1 = kwargs['wf1']
+            if not (np.isclose(wf1[0][0], param['wf1'][0][0], 1e-8) and np.isclose(wf1[0][1][0], param['wf1'][0][1][0], 1e-8) and np.isclose(wf1[0][1][1], param['wf1'][0][1][1], 1e-8)):
+                return True
+        if 'wf2' in kwargs:
+            wf2 = kwargs['wf2']
+            if not (np.isclose(wf2[0][0], param['wf2'][0][0], 1e-8) and np.isclose(wf2[0][1][0], param['wf2'][0][1][0], 1e-8) and np.isclose(wf2[0][1][1], param['wf2'][0][1][1], 1e-8)):
+                return True
+        return False
+
+
 def sfcf_filter(results: pd.DataFrame, **kwargs: Any) -> pd.DataFrame:
-    """
+    r"""
     Filter method for the Database entries holding SFCF calculations.
 
     Parameters
@@ -135,9 +252,9 @@ def sfcf_filter(results: pd.DataFrame, **kwargs: Any) -> pd.DataFrame:
     qk2: float, optional
         Mass parameter $\kappa_2$ of the first quark.
     qm1: float, optional
-        Bare quak mass $m_1$ of the first quark.
+        Bare quark mass $m_1$ of the first quark.
     qm2: float, optional
-        Bare quak mass $m_1$ of the first quark.
+        Bare quark mass $m_2$ of the first quark.
     quarks_thetas: list[list[float]], optional
     wf1: optional
     wf2: optional
@@ -147,106 +264,85 @@ def sfcf_filter(results: pd.DataFrame, **kwargs: Any) -> pd.DataFrame:
     results: pd.DataFrame
         The filtered DataFrame, only holding the records that fit to the parameters given.
     """
+
     drops = []
     for ind in range(len(results)):
         result = results.iloc[ind]
         param = json.loads(result['parameters'])
-        if 'offset' in kwargs:
-            if kwargs.get('offset') != param['offset']:
-                drops.append(ind)
-                continue
-        if 'quark_kappas' in kwargs:
-            kappas = kwargs['quark_kappas']
-            if (not np.isclose(kappas[0], param['quarks'][0]['mass']) or not np.isclose(kappas[1], param['quarks'][1]['mass'])):
-                drops.append(ind)
-                continue
-        if 'quark_masses' in kwargs:
-            masses = kwargs['quark_masses']
-            if (not np.isclose(masses[0], k2m(param['quarks'][0]['mass'])) or not np.isclose(masses[1], k2m(param['quarks'][1]['mass']))):
-                drops.append(ind)
-                continue
-        if 'qk1' in kwargs:
-            quark_kappa1 = kwargs['qk1']
-            if not isinstance(quark_kappa1, list):
-                if (not np.isclose(quark_kappa1, param['quarks'][0]['mass'])):
-                    drops.append(ind)
-                    continue
-            else:
-                if len(quark_kappa1) == 2:
-                    if (quark_kappa1[0] > param['quarks'][0]['mass']) or (quark_kappa1[1] < param['quarks'][0]['mass']):
-                        drops.append(ind)
-                        continue
-        if 'qk2' in kwargs:
-            quark_kappa2 = kwargs['qk2']
-            if not isinstance(quark_kappa2, list):
-                if (not np.isclose(quark_kappa2, param['quarks'][1]['mass'])):
-                    drops.append(ind)
-                    continue
-            else:
-                if len(quark_kappa2) == 2:
-                    if (quark_kappa2[0] > param['quarks'][1]['mass']) or (quark_kappa2[1] < param['quarks'][1]['mass']):
-                        drops.append(ind)
-                        continue
-        if 'qm1' in kwargs:
-            quark_mass1 = kwargs['qm1']
-            if not isinstance(quark_mass1, list):
-                if (not np.isclose(quark_mass1, k2m(param['quarks'][0]['mass']))):
-                    drops.append(ind)
-                    continue
-            else:
-                if len(quark_mass1) == 2:
-                    if (quark_mass1[0] > k2m(param['quarks'][0]['mass'])) or (quark_mass1[1] < k2m(param['quarks'][0]['mass'])):
-                        drops.append(ind)
-                        continue
-        if 'qm2' in kwargs:
-            quark_mass2 = kwargs['qm2']
-            if not isinstance(quark_mass2, list):
-                if (not np.isclose(quark_mass2, k2m(param['quarks'][1]['mass']))):
-                    drops.append(ind)
-                    continue
-            else:
-                if len(quark_mass2) == 2:
-                    if (quark_mass2[0] > k2m(param['quarks'][1]['mass'])) or (quark_mass2[1] < k2m(param['quarks'][1]['mass'])):
-                        drops.append(ind)
-                        continue
-        if 'quark_thetas' in kwargs:
-            quark_thetas = kwargs['quark_thetas']
-            if (quark_thetas[0] != param['quarks'][0]['thetas'] and quark_thetas[1] != param['quarks'][1]['thetas']) or (quark_thetas[0] != param['quarks'][1]['thetas'] and quark_thetas[1] != param['quarks'][0]['thetas']):
-                drops.append(ind)
-                continue
-        # careful, this is not save, when multiple contributions are present!
-        if 'wf1' in kwargs:
-            wf1 = kwargs['wf1']
-            if not (np.isclose(wf1[0][0], param['wf1'][0][0], 1e-8) and np.isclose(wf1[0][1][0], param['wf1'][0][1][0], 1e-8) and np.isclose(wf1[0][1][1], param['wf1'][0][1][1], 1e-8)):
-                drops.append(ind)
-                continue
-        if 'wf2' in kwargs:
-            wf2 = kwargs['wf2']
-            if not (np.isclose(wf2[0][0], param['wf2'][0][0], 1e-8) and np.isclose(wf2[0][1][0], param['wf2'][0][1][0], 1e-8) and np.isclose(wf2[0][1][1], param['wf2'][0][1][1], 1e-8)):
-                drops.append(ind)
-                continue
+        if _sfcf_drop(param, **kwargs):
+            drops.append(ind)
     return results.drop(drops)
 
 
-def find_record(path: str, ensemble: str, correlator_name: str, code: str, project: Optional[str]=None, parameters: Optional[str]=None,
-                created_before: Optional[str]=None, created_after: Optional[str]=None, updated_before: Optional[str]=None, updated_after: Optional[str]=None, revision: Optional[str]=None, **kwargs: Any) -> pd.DataFrame:
+def openQCD_filter(results:pd.DataFrame, **kwargs: Any) -> pd.DataFrame:
+    """
+    Filter for parameters of openQCD.
+
+    Parameters
+    ----------
+    results: pd.DataFrame
+        The unfiltered list of results from the database.
+
+    Returns
+    -------
+    results: pd.DataFrame
+        The filtered results.
+
+    """
+    warnings.warn("A filter for openQCD parameters is no implemented yet.", Warning)
+
+    return results
+
+
+def _code_filter(results: pd.DataFrame, code: str, **kwargs: Any) -> pd.DataFrame:
+    """
+    Abstraction of the filters for the different codes that are available.
+    At the moment, only openQCD and SFCF are known.
+    The possible key words for the parameters can be seen in the descriptionso f the code-specific filters.
+
+    Parameters
+    ----------
+    results: pd.DataFrame
+        The unfiltered list of results from the database.
+    code: str
+        The name of the code that produced the record at hand.
+    kwargs:
+        The keyworkd args that are handed over to the code-specific filters.
+
+    Returns
+    -------
+    results: pd.DataFrame
+        The filtered results.
+    """
+    if code == "sfcf":
+        return sfcf_filter(results, **kwargs)
+    elif code == "openQCD":
+        return openQCD_filter(results, **kwargs)
+    else:
+        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,
+                created_before: Optional[str]=None, created_after: Optional[str]=None, updated_before: Optional[str]=None, updated_after: Optional[str]=None,
+                revision: Optional[str]=None,
+                customFilter: Optional[Callable[[pd.DataFrame], pd.DataFrame]] = None,
+                **kwargs: Any) -> pd.DataFrame:
     db_file = get_db_file(path)
-    db = os.path.join(path, db_file)
+    db = path / db_file
     if code not in codes:
         raise ValueError("Code " + code + "unknown, take one of the following:" + ", ".join(codes))
     get(path, db_file)
-    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)
-    if code == "sfcf":
-        results = sfcf_filter(results, **kwargs)
-    elif code == "openQCD":
-        pass
-    else:
-        raise Exception
+    results = _db_lookup(db, ensemble, correlator_name,code, project, parameters=parameters)
+    if any([arg is not None for arg in [created_before, created_after, updated_before, updated_after]]):
+        results = _time_filter(results, created_before, created_after, updated_before, updated_after)
+    results = _code_filter(results, code, **kwargs)
+    if customFilter is not None:
+        results =  customFilter(results)
     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: Path, name: str) -> str:
     """
     Find a project by it's human readable name.
 
@@ -264,10 +360,10 @@ def find_project(path: str, name: str) -> str:
     """
     db_file = get_db_file(path)
     get(path, db_file)
-    return _project_lookup_by_alias(os.path.join(path, db_file), name)
+    return _project_lookup_by_alias(path / db_file, name)
 
 
-def list_projects(path: str) -> list[tuple[str, str]]:
+def list_projects(path: Path) -> list[tuple[str, str]]:
     """
     List all projects known to the library.
 

corrlib/git_tools.py

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

corrlib/initialization.py

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

corrlib/input/openQCD.py

@@ -3,9 +3,13 @@ import datalad.api as dl
 import os
 import fnmatch
 from typing import Any, Optional
+from pathlib import Path
+from ..pars.openQCD import ms1
+from ..pars.openQCD import qcd2
 
 
-def read_ms1_param(path: str, project: str, file_in_project: str) -> dict[str, Any]:
+
+def load_ms1_infile(path: Path, project: str, file_in_project: str) -> dict[str, Any]:
     """
     Read the parameters for ms1 measurements from a parameter file in the project.
 
@@ -69,7 +73,7 @@ def read_ms1_param(path: str, project: str, file_in_project: str) -> dict[str, A
     return param
 
 
-def read_ms3_param(path: str, project: str, file_in_project: str) -> dict[str, Any]:
+def load_ms3_infile(path: Path, project: str, file_in_project: str) -> dict[str, Any]:
     """
     Read the parameters for ms3 measurements from a parameter file in the project.
 
@@ -103,7 +107,7 @@ def read_ms3_param(path: str, project: str, file_in_project: str) -> dict[str, A
     return param
 
 
-def read_rwms(path: str, project: str, dir_in_project: str, param: dict[str, Any], prefix: str, postfix: str="ms1", version: str='2.0', names: Optional[list[str]]=None, files: Optional[list[str]]=None) -> dict[str, Any]:
+def read_rwms(path: Path, project: str, dir_in_project: str, param: dict[str, Any], prefix: str, postfix: str="ms1", version: str='2.0', names: Optional[list[str]]=None, files: Optional[list[str]]=None) -> dict[str, Any]:
     """
     Read reweighting factor measurements from the project.
 
@@ -160,7 +164,7 @@ def read_rwms(path: str, project: str, dir_in_project: str, param: dict[str, Any
     return rw_dict
 
 
-def extract_t0(path: str, project: str, dir_in_project: str, param: dict[str, Any], prefix: str, dtr_read: int, xmin: int, spatial_extent: int, fit_range: int = 5, postfix: str="", names: Optional[list[str]]=None, files: Optional[list[str]]=None) -> dict[str, Any]:
+def extract_t0(path: Path, project: str, dir_in_project: str, param: dict[str, Any], prefix: str, dtr_read: int, xmin: int, spatial_extent: int, fit_range: int = 5, postfix: str="", names: Optional[list[str]]=None, files: Optional[list[str]]=None) -> dict[str, Any]:
     """
     Extract t0 measurements from the project.
 
@@ -234,7 +238,7 @@ def extract_t0(path: str, project: str, dir_in_project: str, param: dict[str, An
     return t0_dict
 
 
-def extract_t1(path: str, project: str, dir_in_project: str, param: dict[str, Any], prefix: str, dtr_read: int, xmin: int, spatial_extent: int, fit_range: int = 5, postfix: str = "", names: Optional[list[str]]=None, files: Optional[list[str]]=None) -> dict[str, Any]:
+def extract_t1(path: Path, project: str, dir_in_project: str, param: dict[str, Any], prefix: str, dtr_read: int, xmin: int, spatial_extent: int, fit_range: int = 5, postfix: str = "", names: Optional[list[str]]=None, files: Optional[list[str]]=None) -> dict[str, Any]:
     """
     Extract t1 measurements from the project.
 
@@ -303,3 +307,51 @@ def extract_t1(path: str, project: str, dir_in_project: str, param: dict[str, An
     t1_dict[param["type"]] = {}
     t1_dict[param["type"]][pars] = t0
     return t1_dict
+
+
+def load_qcd2_pars(path: Path, project: str, file_in_project: str)  -> dict[str, Any]:
+    """
+    Thin wrapper around read_qcd2_par_file, getting the file before reading.
+
+    Parameters
+    ----------
+    path: Path
+        Path of the corrlib repository.
+    project: str
+        UUID of the project of the parameter-file.
+    file_in_project: str
+        The loaction of the file in the project directory.
+
+    Returns
+    -------
+    par_dict: dict
+        The dict with the parameters read from the .par-file.
+    """
+    fname = path / "projects" / project / file_in_project
+    ds = os.path.join(path, "projects", project)
+    dl.get(fname, dataset=ds)
+    return qcd2.read_qcd2_par_file(fname)
+
+
+def load_ms1_parfile(path: Path, project: str, file_in_project: str)  -> dict[str, Any]:
+    """
+    Thin wrapper around read_qcd2_ms1_par_file, getting the file before reading.
+
+    Parameters
+    ----------
+    path: Path
+        Path of the corrlib repository.
+    project: str
+        UUID of the project of the parameter-file.
+    file_in_project: str
+        The loaction of the file in the project directory.
+
+    Returns
+    -------
+    par_dict: dict
+        The dict with the parameters read from the .par-file.
+    """
+    fname = path / "projects" / project / file_in_project
+    ds = os.path.join(path, "projects", project)
+    dl.get(fname, dataset=ds)
+    return ms1.read_qcd2_ms1_par_file(fname)

corrlib/input/sfcf.py

@@ -3,6 +3,8 @@ import datalad.api as dl
 import json
 import os
 from typing import Any
+from fnmatch import fnmatch
+from pathlib import Path
 
 
 bi_corrs: list[str] = ["f_P", "fP", "f_p",
@@ -79,7 +81,7 @@ for c in bib_corrs:
     corr_types[c] = 'bib'
 
 
-def read_param(path: str, project: str, file_in_project: str) -> dict[str, Any]:
+def read_param(path: Path, project: str, file_in_project: str) -> dict[str, Any]:
     """
     Read the parameters from the sfcf file.
 
@@ -95,7 +97,7 @@ def read_param(path: str, project: str, file_in_project: str) -> dict[str, Any]:
 
     """
 
-    file = path + "/projects/" + project + '/' + file_in_project
+    file = path / "projects" / project / file_in_project
     dl.get(file, dataset=path)
     with open(file, 'r') as f:
         lines = f.readlines()
@@ -256,7 +258,7 @@ def get_specs(key: str, parameters: dict[str, Any], sep: str = '/') -> str:
     return s
 
 
-def read_data(path: str, project: str, dir_in_project: str, prefix: str, param: dict[str, Any], version: str = '1.0c', cfg_seperator: str = 'n', sep: str = '/', **kwargs: Any) -> dict[str, Any]:
+def read_data(path: Path, project: str, dir_in_project: str, prefix: str, param: dict[str, Any], version: str = '1.0c', cfg_seperator: str = 'n', sep: str = '/', **kwargs: Any) -> dict[str, Any]:
     """
     Extract the data from the sfcf file.
 
@@ -298,9 +300,10 @@ def read_data(path: str, project: str, dir_in_project: str, prefix: str, param:
     if not appended:
         compact = (version[-1] == "c")
         for i, item in enumerate(ls):
-            rep_path = directory + '/' + item
-            sub_ls = pe.input.sfcf._find_files(rep_path, prefix, compact, [])
-            files_to_get.extend([rep_path + "/" + filename for filename in sub_ls])
+            if fnmatch(item, prefix + "*"):
+                rep_path = directory + '/' + item
+                sub_ls = pe.input.sfcf._find_files(rep_path, prefix, compact, [])
+                files_to_get.extend([rep_path + "/" + filename for filename in sub_ls])
 
 
     print("Getting data, this might take a while...")
@@ -318,10 +321,10 @@ def read_data(path: str, 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, names=names)
+                                                     range(len(param['wf_basis'])), range(len(param['wf_basis'])), version, cfg_seperator, 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)
+                                                     range(len(param['wf_basis'])), range(len(param['wf_basis'])), version, cfg_seperator, keyed_out=True, silent=True)
         for key in data_crr.keys():
             data[key] = data_crr[key]
 

corrlib/integrity.py

@@ -0,0 +1,87 @@
+import datetime as dt
+from pathlib import Path
+from .tools import get_db_file
+import pandas as pd
+import sqlite3
+from .tracker import get
+import pyerrors.input.json as pj
+
+from typing import Any
+
+
+def has_valid_times(result: pd.Series) -> bool:
+    # we expect created_at <= updated_at <= now
+    created_at = dt.datetime.fromisoformat(result['created_at'])
+    updated_at = dt.datetime.fromisoformat(result['updated_at'])
+    if created_at > updated_at:
+        return False
+    if updated_at > dt.datetime.now():
+        return False
+    return True
+
+def are_keys_unique(db: Path, table: str, col: str) -> bool:
+    conn = sqlite3.connect(db)
+    c = conn.cursor()
+    c.execute(f"SELECT COUNT( DISTINCT CAST(path AS nvarchar(4000))), COUNT({col}) FROM {table};")
+    results = c.fetchall()[0]
+    conn.close()
+    return bool(results[0] == results[1])
+
+
+def check_db_integrity(path: Path) -> None:
+    db = get_db_file(path)
+
+    if not are_keys_unique(path / db, 'backlogs', 'path'):
+        raise Exception("The paths the backlog table of the database links are not unique.")
+
+    search_expr = "SELECT * FROM 'backlogs'"
+    conn = sqlite3.connect(path / db)
+    results = pd.read_sql(search_expr, conn)
+
+    for _, result in results.iterrows():
+        if not has_valid_times(result):
+            raise ValueError(f"Result with id {result[id]} has wrong time signatures.")
+    print("DB:\t✅")
+    return
+
+
+def _check_db2paths(path: Path, meas_paths: list[str]) -> None:
+    needed_data: dict[str, list[str]] = {}
+    for mpath in meas_paths:
+        file = mpath.split("::")[0]
+        if file not in needed_data.keys():
+            needed_data[file] = []
+        key = mpath.split("::")[1]
+        needed_data[file].append(key)
+
+    totf = len(needed_data.keys())
+    for i, file in enumerate(needed_data.keys()):
+        print(f"Check against file {i}/{totf}: {file}")
+        get(path, Path(file))
+        filedict: dict[str, Any] = pj.load_json_dict(str(path / file))
+        if not set(filedict.keys()).issubset(needed_data[file]):
+            for key in filedict.keys():
+                if key not in needed_data[file]:
+                    raise ValueError(f"Found unintended key {key} in file {file}.")
+        if not set(needed_data[file]).issubset(filedict.keys()):
+            for key in needed_data[file]:
+                if key not in filedict.keys():
+                    raise ValueError(f"Did not find data for key {key} that should be in file {file}.")
+    print("Links:\t✅")
+    return
+
+
+def check_db_file_links(path: Path) -> None:
+    db = get_db_file(path)
+    search_expr = "SELECT path FROM 'backlogs'"
+    conn = sqlite3.connect(path / db)
+    results = pd.read_sql(search_expr, conn)['path'].values
+    _check_db2paths(path, list(results))
+
+
+def full_integrity_check(path: Path) -> None:
+    check_db_integrity(path)
+    check_db_file_links(path)
+    print("Full:\t✅")
+
+

corrlib/main.py

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

corrlib/meas_io.py

@@ -10,9 +10,14 @@ from .tools import get_db_file, cache_enabled
 from .tracker import get, save, unlock
 import shutil
 from typing import Any
+from pathlib import Path
+from .integrity import _check_db2paths
 
 
-def write_measurement(path: str, ensemble: str, measurement: dict[str, dict[str, dict[str, Any]]], uuid: str, code: str, parameter_file: str) -> None:
+CACHE_DIR = ".cache"
+
+
+def write_measurement(path: Path, ensemble: str, measurement: dict[str, dict[str, dict[str, Any]]], uuid: str, code: str, parameter_file: Union[str, None]) -> None:
     """
     Write a measurement to the backlog.
     If the file for the measurement already exists, update the measurement.
@@ -33,25 +38,34 @@ def write_measurement(path: str, ensemble: str, measurement: dict[str, dict[str,
         The parameter file used for the measurement.
     """
     db_file = get_db_file(path)
-    db = os.path.join(path, db_file)
+    db = path / db_file
+
+    files_to_save = []
+
     get(path, db_file)
     unlock(path, db_file)
+    files_to_save.append(db_file)
+
     conn = sqlite3.connect(db)
     c = conn.cursor()
-    files = []
     for corr in measurement.keys():
-        file_in_archive = os.path.join('.', 'archive', ensemble, corr,  uuid + '.json.gz')
-        file = os.path.join(path, file_in_archive)
-        files.append(file)
+        file_in_archive = Path('.') / 'archive' / ensemble / corr / str(uuid + '.json.gz')
+        file = path / file_in_archive
         known_meas = {}
-        if not os.path.exists(os.path.join(path, '.', 'archive', ensemble, corr)):
-            os.makedirs(os.path.join(path, '.', 'archive', ensemble, corr))
+        if not os.path.exists(path / 'archive' / ensemble / corr):
+            os.makedirs(path / 'archive' / ensemble / corr)
+            files_to_save.append(file_in_archive)
         else:
             if os.path.exists(file):
-                unlock(path, file_in_archive)
-                known_meas = pj.load_json_dict(file)
+                if file not in files_to_save:
+                    unlock(path, file_in_archive)
+                    files_to_save.append(file_in_archive)
+                known_meas = pj.load_json_dict(str(file), verbose=False)
         if code == "sfcf":
-            parameters = sfcf.read_param(path, uuid, parameter_file)
+            if parameter_file is not None:
+                parameters = sfcf.read_param(path, uuid, parameter_file)
+            else:
+                raise Exception("Need parameter file for this code!")
             pars = {}
             subkeys = list(measurement[corr].keys())
             for subkey in subkeys:
@@ -60,7 +74,25 @@ def write_measurement(path: str, ensemble: str, measurement: dict[str, dict[str,
         elif code == "openQCD":
             ms_type = list(measurement.keys())[0]
             if ms_type == 'ms1':
-                parameters = openQCD.read_ms1_param(path, uuid, parameter_file)
+                if parameter_file is not None:
+                    if parameter_file.endswith(".ms1.in"):
+                        parameters = openQCD.load_ms1_infile(path, uuid, parameter_file)
+                    elif parameter_file.endswith(".ms1.par"):
+                        parameters = openQCD.load_ms1_parfile(path, uuid, parameter_file)
+                else:
+                    # Temporary solution
+                    parameters = {}
+                    parameters["rand"] = {}
+                    parameters["rw_fcts"] = [{}]
+                    for nrw in range(1):
+                        if "nsrc" not in parameters["rw_fcts"][nrw]:
+                            parameters["rw_fcts"][nrw]["nsrc"] = 1
+                        if "mu" not in parameters["rw_fcts"][nrw]:
+                            parameters["rw_fcts"][nrw]["mu"] = "None"
+                        if "np" not in parameters["rw_fcts"][nrw]:
+                            parameters["rw_fcts"][nrw]["np"] = "None"
+                        if "irp" not in parameters["rw_fcts"][nrw]:
+                            parameters["rw_fcts"][nrw]["irp"] = "None"
                 pars = {}
                 subkeys = []
                 for i in range(len(parameters["rw_fcts"])):
@@ -72,7 +104,7 @@ def write_measurement(path: str, ensemble: str, measurement: dict[str, dict[str,
                     pars[subkey] = json.dumps(parameters["rw_fcts"][i])
             elif ms_type in ['t0', 't1']:
                 if parameter_file is not None:
-                    parameters = openQCD.read_ms3_param(path, uuid, parameter_file)
+                    parameters = openQCD.load_ms3_infile(path, uuid, parameter_file)
                 else:
                     parameters = {}
                     for rwp in ["integrator", "eps", "ntot", "dnms"]:
@@ -87,7 +119,7 @@ def write_measurement(path: str, ensemble: str, measurement: dict[str, dict[str,
                 pars[subkey] = json.dumps(parameters)
         for subkey in subkeys:
             parHash = sha256(str(pars[subkey]).encode('UTF-8')).hexdigest()
-            meas_path = file_in_archive + "::" + parHash
+            meas_path = str(file_in_archive) + "::" + parHash
 
             known_meas[parHash] = measurement[corr][subkey]
 
@@ -97,14 +129,13 @@ def write_measurement(path: str, 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, file)
-    files.append(os.path.join(path, db_file))
+        pj.dump_dict_to_json(known_meas, str(file))
     conn.close()
-    save(path, message="Add measurements to database", files=files)
+    save(path, message="Add measurements to database", files=files_to_save)
     return
 
 
-def load_record(path: str, meas_path: str) -> Union[Corr, Obs]:
+def load_record(path: Path, meas_path: str) -> Union[Corr, Obs]:
     """
     Load a list of records by their paths.
 
@@ -123,7 +154,7 @@ def load_record(path: str, meas_path: str) -> Union[Corr, Obs]:
     return load_records(path, [meas_path])[0]
 
 
-def load_records(path: str, meas_paths: list[str], preloaded: dict[str, Any] = {}) -> list[Union[Corr, Obs]]:
+def load_records(path: Path, meas_paths: list[str], preloaded: dict[str, Any] = {}, dry_run: bool = False) -> list[Union[Corr, Obs]]:
     """
     Load a list of records by their paths.
 
@@ -133,14 +164,19 @@ def load_records(path: str, meas_paths: list[str], preloaded: dict[str, Any] = {
         Path of the correlator library.
     meas_paths: list[str]
         A list of the paths to the correlator in the backlog system.
-    perloaded: dict[str, Any]
-        The data that is already prelaoded. Of interest if data has alread been loaded in the same script.
+    preloaded: dict[str, Any]
+        The data that is already preloaded. Of interest if data has alread been loaded in the same script.
+    dry_run: bool
+        Do not load datda, just check whether we can reach the data we are interested in.
 
     Returns
     -------
-    retruned_data: list
+    returned_data: list
         The loaded records.
     """
+    if dry_run:
+        _check_db2paths(path, meas_paths)
+        return []
     needed_data: dict[str, list[str]] = {}
     for mpath in meas_paths:
         file = mpath.split("::")[0]
@@ -151,20 +187,20 @@ def load_records(path: str, meas_paths: list[str], preloaded: dict[str, Any] = {
     returned_data: list[Any] = []
     for file in needed_data.keys():
         for key in list(needed_data[file]):
-            if os.path.exists(cache_path(path, file, key) + ".p"):
-                returned_data.append(load_object(cache_path(path, file, key) + ".p"))
+            if os.path.exists(str(cache_path(path, file, key)) + ".p"):
+                returned_data.append(load_object(str(cache_path(path, file, key)) + ".p"))
             else:
                 if file not in preloaded:
-                    preloaded[file] = preload(path, file)
+                    preloaded[file] = preload(path, Path(file))
                 returned_data.append(preloaded[file][key])
                 if cache_enabled(path):
                     if not os.path.exists(cache_dir(path, file)):
                         os.makedirs(cache_dir(path, file))
-                    dump_object(preloaded[file][key], cache_path(path, file, key))
+                    dump_object(preloaded[file][key], str(cache_path(path, file, key)))
     return returned_data
 
 
-def cache_dir(path: str, file: str) -> str:
+def cache_dir(path: Path, file: str) -> Path:
     """
     Returns the directory corresponding to the cache for the given file.
 
@@ -179,14 +215,14 @@ def cache_dir(path: str, file: str) -> str:
     cache_path: str
         The path holding the cached data for the given file.
     """
-    cache_path_list = [path]
-    cache_path_list.append(".cache")
-    cache_path_list.extend(file.split("/")[1:])
-    cache_path = "/".join(cache_path_list)
+    cache_path_list = file.split("/")[1:]
+    cache_path = Path(path) / CACHE_DIR
+    for directory in cache_path_list:
+        cache_path /= directory
     return cache_path
 
 
-def cache_path(path: str, file: str, key: str) -> str:
+def cache_path(path: Path, file: str, key: str) -> Path:
     """
     Parameters
     ----------
@@ -202,11 +238,11 @@ def cache_path(path: str, file: str, key: str) -> str:
     cache_path: str
         The path at which the measurement of the given file and key is cached.
     """
-    cache_path = os.path.join(cache_dir(path, file), key)
+    cache_path = cache_dir(path, file) / key
     return cache_path
 
 
-def preload(path: str, file: str) -> dict[str, Any]:
+def preload(path: Path, file: Path) -> dict[str, Any]:
     """
     Read the contents of a file into a json dictionary with the pyerrors.json.load_json_dict method.
 
@@ -223,12 +259,12 @@ def preload(path: str, file: str) -> dict[str, Any]:
         The data read from the file.
     """
     get(path, file)
-    filedict: dict[str, Any] = pj.load_json_dict(os.path.join(path, file))
+    filedict: dict[str, Any] = pj.load_json_dict(str(path / file))
     print("> read file")
     return filedict
 
 
-def drop_record(path: str, meas_path: str) -> None:
+def drop_record(path: Path, meas_path: str) -> None:
     """
     Drop a record by it's path.
 
@@ -240,9 +276,9 @@ def drop_record(path: str, meas_path: str) -> None:
         The measurement path as noted in the database.
     """
     file_in_archive = meas_path.split("::")[0]
-    file = os.path.join(path, file_in_archive)
+    file = path / file_in_archive
     db_file = get_db_file(path)
-    db = os.path.join(path, db_file)
+    db = path / db_file
     get(path, db_file)
     sub_key = meas_path.split("::")[1]
     unlock(path, db_file)
@@ -254,18 +290,18 @@ def drop_record(path: str, meas_path: str) -> None:
         raise ValueError("This measurement does not exist as an entry!")
 
     conn.commit()
-    known_meas = pj.load_json_dict(file)
+    known_meas = pj.load_json_dict(str(file))
     if sub_key in known_meas:
         del known_meas[sub_key]
-        unlock(path, file_in_archive)
-        pj.dump_dict_to_json(known_meas, file)
+        unlock(path, Path(file_in_archive))
+        pj.dump_dict_to_json(known_meas, str(file))
         save(path, message="Drop measurements to database", files=[db, file])
         return
     else:
         raise ValueError("This measurement does not exist as a file!")
 
 
-def drop_cache(path: str) -> None:
+def drop_cache(path: Path) -> None:
     """
     Drop the cache directory of the library.
 
@@ -274,7 +310,7 @@ def drop_cache(path: str) -> None:
     path: str
         The path of the library.
     """
-    cache_dir = os.path.join(path, ".cache")
+    cache_dir = path / ".cache"
     for f in os.listdir(cache_dir):
-        shutil.rmtree(os.path.join(cache_dir, f))
+        shutil.rmtree(cache_dir / f)
     return

corrlib/pars/openQCD/__init__.py

@@ -0,0 +1,3 @@
+
+from . import ms1 as ms1
+from . import qcd2 as qcd2

corrlib/pars/openQCD/flags.py

@@ -0,0 +1,59 @@
+"""
+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]:
+        """
+        NOTE: This is a duplcation from qcd2.
+        Unpack the lattice parameters written by write_lat_parms.
+        """
+        lat_pars = {}
+        t = fp.read(16)
+        lat_pars["N"] = list(struct.unpack('iiii', t)) # lattice extends
+        t = fp.read(8)
+        nk, isw = struct.unpack('ii', t) # number of kappas and isw parameter
+        lat_pars["nk"] = nk
+        lat_pars["isw"] = isw
+        t = fp.read(8)
+        lat_pars["beta"] = struct.unpack('d', t)[0] # beta
+        t = fp.read(8)
+        lat_pars["c0"] = struct.unpack('d', t)[0]
+        t = fp.read(8)
+        lat_pars["c1"] = struct.unpack('d', t)[0]
+        t = fp.read(8)
+        lat_pars["csw"] = struct.unpack('d', t)[0] # csw factor
+        kappas = []
+        m0s = []
+        # read kappas
+        for ik in range(nk):
+            t = fp.read(8)
+            kappas.append(struct.unpack('d', t)[0])
+            t = fp.read(8)
+            m0s.append(struct.unpack('d', t)[0])
+        lat_pars["kappas"] = kappas
+        lat_pars["m0s"] = m0s
+        return lat_pars
+
+
+def lat_parms_write_bc_parms(fp: BinaryIO) -> dict[str, Any]:
+        """
+        NOTE: This is a duplcation from qcd2.
+        Unpack the boundary parameters written by write_bc_parms.
+        """
+        bc_pars: dict[str, Any] = {}
+        t = fp.read(4)
+        bc_pars["type"] = struct.unpack('i', t)[0] # type of hte boundaries
+        t = fp.read(104)
+        bc_parms = struct.unpack('d'*13, t)
+        bc_pars["cG"] = list(bc_parms[:2]) # boundary gauge field improvement
+        bc_pars["cF"] = list(bc_parms[2:4]) # boundary fermion field improvement
+        phi: list[list[float]] = [[], []]
+        phi[0] = list(bc_parms[4:7])
+        phi[1] = list(bc_parms[7:10])
+        bc_pars["phi"] = phi
+        bc_pars["theta"] = list(bc_parms[10:])
+        return bc_pars

corrlib/pars/openQCD/ms1.py

@@ -0,0 +1,30 @@
+from . import flags
+
+from typing import Any
+from pathlib import Path
+
+
+def read_qcd2_ms1_par_file(fname: Path) -> dict[str, dict[str, Any]]:
+    """
+    The subroutines written here have names according to the openQCD programs and functions that write out the data.
+    Parameters
+    ----------
+    fname: Path
+        Location of the parameter file.
+
+    Returns
+    -------
+    par_dict: dict
+        Dictionary holding the parameters specified in the given file.
+    """
+
+    with open(fname, "rb") as fp:
+        lat_par_dict = flags.lat_parms_write_lat_parms(fp)
+        bc_par_dict = flags.lat_parms_write_bc_parms(fp)
+        fp.close()
+    par_dict = {}
+    par_dict["lat"] = lat_par_dict
+    par_dict["bc"] = bc_par_dict
+    return par_dict
+
+

corrlib/pars/openQCD/qcd2.py

@@ -0,0 +1,29 @@
+from . import flags
+
+from pathlib import Path
+from typing import Any
+
+
+def read_qcd2_par_file(fname: Path) -> dict[str, dict[str, Any]]:
+    """
+    The subroutines written here have names according to the openQCD programs and functions that write out the data.
+
+    Parameters
+    ----------
+    fname: Path
+        Location of the parameter file.
+
+    Returns
+    -------
+    par_dict: dict
+        Dictionary holding the parameters specified in the given file.
+    """
+
+    with open(fname, "rb") as fp:
+        lat_par_dict = flags.lat_parms_write_lat_parms(fp)
+        bc_par_dict = flags.lat_parms_write_bc_parms(fp)
+        fp.close()
+    par_dict = {}
+    par_dict["lat"] = lat_par_dict
+    par_dict["bc"] = bc_par_dict
+    return par_dict

corrlib/toml.py

@@ -19,6 +19,7 @@ from .meas_io import write_measurement
 import os
 from .input.implementations import codes as known_codes
 from typing import Any
+from pathlib import Path
 
 
 def replace_string(string: str, name: str, val: str) -> str:
@@ -126,7 +127,7 @@ def check_measurement_data(measurements: dict[str, dict[str, str]], code: str) -
     return
 
 
-def import_tomls(path: str, files: list[str], copy_files: bool=True) -> None:
+def import_tomls(path: Path, files: list[str], copy_files: bool=True) -> None:
     """
     Import multiple toml files.
 
@@ -144,7 +145,7 @@ def import_tomls(path: str, files: list[str], copy_files: bool=True) -> None:
     return
 
 
-def import_toml(path: str, file: str, copy_file: bool=True) -> None:
+def import_toml(path: Path, file: str, copy_file: bool=True) -> None:
     """
     Import a project decribed by a .toml file.
 
@@ -171,14 +172,16 @@ def import_toml(path: str, file: str, copy_file: bool=True) -> None:
     aliases = project.get('aliases', [])
     uuid = project.get('uuid', None)
     if uuid is not None:
-        if not os.path.exists(path + "/projects/" + uuid):
+        if not os.path.exists(path / "projects" / uuid):
             uuid = import_project(path, project['url'], aliases=aliases)
         else:
             update_aliases(path, uuid, aliases)
     else:
         uuid = import_project(path, project['url'], aliases=aliases)
+    imeas = 1
+    nmeas = len(measurements.keys())
     for mname, md in measurements.items():
-        print("Import measurement: " + mname)
+        print(f"Import measurement {imeas}/{nmeas}: {mname}")
         ensemble = md['ensemble']
         if project['code'] == 'sfcf':
             param = sfcf.read_param(path, uuid, md['param_file'])
@@ -189,15 +192,34 @@ def import_toml(path: str, file: str, copy_file: bool=True) -> None:
                 measurement = sfcf.read_data(path, uuid, md['path'], md['prefix'], param,
                                             version=md['version'], cfg_seperator=md['cfg_seperator'], sep='/')
 
-            print(mname + " imported.")
         elif project['code'] == 'openQCD':
             if md['measurement'] == 'ms1':
-                param = openQCD.read_ms1_param(path, uuid, md['param_file'])
+                if 'param_file' in md.keys():
+                    parameter_file = md['param_file']
+                    if parameter_file.endswith(".ms1.in"):
+                        param = openQCD.load_ms1_infile(path, uuid, parameter_file)
+                    elif parameter_file.endswith(".ms1.par"):
+                        param = openQCD.load_ms1_parfile(path, uuid, parameter_file)
+                else:
+                    # Temporary solution
+                    parameters: dict[str, Any] = {}
+                    parameters["rand"] = {}
+                    parameters["rw_fcts"] = [{}]
+                    for nrw in range(1):
+                        if "nsrc" not in parameters["rw_fcts"][nrw]:
+                            parameters["rw_fcts"][nrw]["nsrc"] = 1
+                        if "mu" not in parameters["rw_fcts"][nrw]:
+                            parameters["rw_fcts"][nrw]["mu"] = "None"
+                        if "np" not in parameters["rw_fcts"][nrw]:
+                            parameters["rw_fcts"][nrw]["np"] = "None"
+                        if "irp" not in parameters["rw_fcts"][nrw]:
+                            parameters["rw_fcts"][nrw]["irp"] = "None"
+                    param = parameters
                 param['type'] = 'ms1'
                 measurement = openQCD.read_rwms(path, uuid, md['path'], param, md["prefix"], version=md["version"], names=md['names'], files=md['files'])
             elif md['measurement'] == 't0':
                 if 'param_file' in md:
-                    param = openQCD.read_ms3_param(path, uuid, md['param_file'])
+                    param = openQCD.load_ms3_infile(path, uuid, md['param_file'])
                 else:
                     param = {}
                     for rwp in ["integrator", "eps", "ntot", "dnms"]:
@@ -207,25 +229,26 @@ def import_toml(path: str, file: str, copy_file: bool=True) -> None:
                                                  fit_range=int(md.get('fit_range', 5)), postfix=str(md.get('postfix', '')), names=md.get('names', []), files=md.get('files', []))
             elif md['measurement'] == 't1':
                 if 'param_file' in md:
-                    param = openQCD.read_ms3_param(path, uuid, md['param_file'])
+                    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"]),
                                                  fit_range=int(md.get('fit_range', 5)), postfix=str(md.get('postfix', '')), names=md.get('names', []), files=md.get('files', []))
+        write_measurement(path, ensemble, measurement, uuid, project['code'], (md['param_file'] if 'param_file' in md else None))
+        imeas += 1
+        print(mname + " imported.")
 
-        write_measurement(path, ensemble, measurement, uuid, project['code'], (md['param_file'] if 'param_file' in md else ''))
-
-    if not os.path.exists(os.path.join(path, "toml_imports", uuid)):
-        os.makedirs(os.path.join(path, "toml_imports", uuid))
+    if not os.path.exists(path / "toml_imports" / uuid):
+        os.makedirs(path / "toml_imports" / uuid)
     if copy_file:
-        import_file = os.path.join(path, "toml_imports", uuid, file.split("/")[-1])
+        import_file = path / "toml_imports" / uuid / file.split("/")[-1]
         shutil.copy(file, import_file)
-        save(path, files=[import_file], message="Import using " + import_file)
-        print("File copied to " + import_file)
+        save(path, files=[import_file], message=f"Import using {import_file}")
+        print(f"File copied to {import_file}")
     print("Imported project.")
     return
 
 
-def reimport_project(path: str, uuid: str) -> None:
+def reimport_project(path: Path, uuid: str) -> None:
     """
     Reimport an existing project using the files that are already available for this project.
 
@@ -236,14 +259,14 @@ def reimport_project(path: str, uuid: str) -> None:
     uuid: str
     uuid of the project that is to be reimported.
     """
-    config_path = "/".join([path, "import_scripts", uuid])
+    config_path = path / "import_scripts" / uuid
     for p, filenames, dirnames in os.walk(config_path):
         for fname in filenames:
             import_toml(path, os.path.join(config_path, fname), copy_file=False)
     return
 
 
-def update_project(path: str, uuid: str) -> None:
+def update_project(path: Path, uuid: str) -> None:
     """
     Update all entries associated with a given project.
 

corrlib/tools.py

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

corrlib/tracker.py

@@ -4,9 +4,10 @@ import datalad.api as dl
 from typing import Optional
 import shutil
 from .tools import get_db_file
+from pathlib import Path
 
 
-def get_tracker(path: str) -> str:
+def get_tracker(path: Path) -> str:
     """
     Get the tracker used in the dataset located at path.
 
@@ -30,7 +31,7 @@ def get_tracker(path: str) -> str:
     return tracker
 
 
-def get(path: str, file: str) -> None:
+def get(path: Path, file: Path) -> None:
     """
     Wrapper function to get a file from the dataset located at path with the specified tracker.
 
@@ -56,7 +57,7 @@ def get(path: str, file: str) -> None:
     return
 
 
-def save(path: str, message: str, files: Optional[list[str]]=None) -> None:
+def save(path: Path, message: str, files: Optional[list[Path]]=None) -> None:
     """
     Wrapper function to save a file to the dataset located at path with the specified tracker.
 
@@ -72,7 +73,7 @@ def save(path: str, message: str, files: Optional[list[str]]=None) -> None:
     tracker = get_tracker(path)
     if tracker == 'datalad':
         if files is not None:
-            files = [os.path.join(path, f) for f in files]
+            files = [path / f for f in files]
         dl.save(files, message=message, dataset=path)
     elif tracker == 'None':
         Warning("Tracker 'None' does not implement save.")
@@ -81,7 +82,7 @@ def save(path: str, message: str, files: Optional[list[str]]=None) -> None:
         raise ValueError(f"Tracker {tracker} is not supported.")
 
 
-def init(path: str, tracker: str='datalad') -> None:
+def init(path: Path, tracker: str='datalad') -> None:
     """
     Initialize a dataset at the specified path with the specified tracker.
 
@@ -101,7 +102,7 @@ def init(path: str, tracker: str='datalad') -> None:
     return
 
 
-def unlock(path: str, file: str) -> None:
+def unlock(path: Path, file: Path) -> None:
     """
     Wrapper function to unlock a file in the dataset located at path with the specified tracker.
 
@@ -114,7 +115,7 @@ def unlock(path: str, file: str) -> None:
     """
     tracker = get_tracker(path)
     if tracker == 'datalad':
-        dl.unlock(file, dataset=path)
+        dl.unlock(os.path.join(path, file), dataset=path)
     elif tracker == 'None':
         Warning("Tracker 'None' does not implement unlock.")
         pass
@@ -123,7 +124,7 @@ def unlock(path: str, file: str) -> None:
     return
 
 
-def clone(path: str, source: str, target: str) -> None:
+def clone(path: Path, source: str, target: str) -> None:
     """
     Wrapper function to clone a dataset from source to target with the specified tracker.
     Parameters
@@ -147,7 +148,7 @@ def clone(path: str, source: str, target: str) -> None:
     return
 
 
-def drop(path: str, reckless: Optional[str]=None) -> None:
+def drop(path: Path, reckless: Optional[str]=None) -> None:
     """
     Wrapper function to drop data from a dataset located at path with the specified tracker.
 

tests/cli_test.py

@@ -2,18 +2,19 @@ from typer.testing import CliRunner
 from corrlib.cli import app
 import os
 import sqlite3 as sql
+from pathlib import Path
 
 
 runner = CliRunner()
 
 
-def test_version():
+def test_version() -> None:
     result = runner.invoke(app, ["--version"])
     assert result.exit_code == 0
     assert "corrlib" in result.output
 
 
-def test_init_folders(tmp_path):
+def test_init_folders(tmp_path: Path) -> None:
     dataset_path = tmp_path / "test_dataset"
     result = runner.invoke(app, ["init", "--dataset", str(dataset_path)])
     assert result.exit_code == 0
@@ -21,7 +22,7 @@ def test_init_folders(tmp_path):
     assert os.path.exists(str(dataset_path / "backlogger.db"))
 
 
-def test_init_db(tmp_path):
+def test_init_db(tmp_path: Path) -> None:
     dataset_path = tmp_path / "test_dataset"
     result = runner.invoke(app, ["init", "--dataset", str(dataset_path)])
     assert result.exit_code == 0
@@ -37,7 +38,7 @@ def test_init_db(tmp_path):
     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
@@ -60,7 +61,7 @@ def test_init_db(tmp_path):
     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 = [
@@ -81,11 +82,11 @@ def test_init_db(tmp_path):
         assert expected_col in backlog_column_names
 
 
-def test_list(tmp_path):
+def test_list(tmp_path: Path) -> None:
     dataset_path = tmp_path / "test_dataset"
     result = runner.invoke(app, ["init", "--dataset", str(dataset_path)])
     assert result.exit_code == 0
-    result = runner.invoke(app, ["list", "--dataset", str(dataset_path), "ensembles"])
+    result = runner.invoke(app, ["lister", "--dataset", str(dataset_path), "ensembles"])
     assert result.exit_code == 0
-    result = runner.invoke(app, ["list", "--dataset", str(dataset_path), "projects"])
+    result = runner.invoke(app, ["lister", "--dataset", str(dataset_path), "projects"])
     assert result.exit_code == 0

tests/find_test.py

@@ -0,0 +1,432 @@
+import corrlib.find as find
+import sqlite3
+from pathlib import Path
+import corrlib.initialization as cinit
+import pytest
+import pandas as pd
+import datalad.api as dl
+import datetime as dt
+
+
+def make_sql(path: Path) -> Path:
+    db = path / "test.db"
+    cinit._create_db(db)
+    return db
+
+
+def test_find_lookup_by_one_alias(tmp_path: Path) -> None:
+    db = make_sql(tmp_path)
+    conn = sqlite3.connect(db)
+    c = conn.cursor()
+    uuid = "test_uuid"
+    alias_str = "fun_project"
+    tag_str = "tt"
+    owner = "tester"
+    code = "test_code"
+    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()
+    assert uuid == find._project_lookup_by_alias(db, "fun_project")
+    uuid = "test_uuid2"
+    alias_str = "fun_project"
+    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()
+    with pytest.raises(Exception):
+        assert uuid == find._project_lookup_by_alias(db, "fun_project")
+    conn.close()
+
+def test_find_lookup_by_id(tmp_path: Path) -> None:
+    db = make_sql(tmp_path)
+    conn = sqlite3.connect(db)
+    c = conn.cursor()
+    uuid = "test_uuid"
+    alias_str = "fun_project"
+    tag_str = "tt"
+    owner = "tester"
+    code = "test_code"
+    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()
+    result = find._project_lookup_by_id(db, uuid)[0]
+    assert uuid == result[0]
+    assert alias_str == result[1]
+    assert tag_str == result[2]
+    assert owner == result[3]
+    assert code == result[4]
+
+
+def test_time_filter() -> None:
+    record_A = ["f_A", "ensA", "sfcf", "archive/SF_A/f_A/Project_A.json.gz::asdfasdfasdf0", "SF_A", '{"par_A": 5.0, "par_B": 5.0}', "projects/SF_A/input.in",
+            '2025-03-26 12:55:18.229966', '2025-03-26 12:55:18.229966'] # only created
+    record_B = ["f_A", "ensA", "sfcf", "archive/SF_A/f_A/Project_A.json.gz::asdfasdfasdf1", "SF_A", '{"par_A": 5.0, "par_B": 5.0}', "projects/SF_A/input.in",
+                '2025-03-26 12:55:18.229966', '2025-04-26 12:55:18.229966'] # created and updated
+    record_C = ["f_A", "ensA", "sfcf", "archive/SF_A/f_A/Project_A.json.gz::asdfasdfasdf2", "SF_A", '{"par_A": 5.0, "par_B": 5.0}', "projects/SF_A/input.in",
+                '2026-03-26 12:55:18.229966', '2026-04-14 12:55:18.229966'] # created and updated later
+    record_D = ["f_A", "ensA", "sfcf", "archive/SF_A/f_A/Project_A.json.gz::asdfasdfasdf3", "SF_A", '{"par_A": 5.0, "par_B": 5.0}', "projects/SF_A/input.in",
+                '2026-03-26 12:55:18.229966', '2026-03-27 12:55:18.229966']
+    record_E = ["f_A", "ensA", "sfcf", "archive/SF_A/f_A/Project_A.json.gz::asdfasdfasdf4", "SF_A", '{"par_A": 5.0, "par_B": 5.0}', "projects/SF_A/input.in",
+                '2024-03-26 12:55:18.229966', '2024-03-26 12:55:18.229966'] # only created, earlier
+    record_F = ["f_A", "ensA", "sfcf", "archive/SF_A/f_A/Project_A.json.gz::asdfasdfasdf5", "SF_A", '{"par_A": 5.0, "par_B": 5.0}', "projects/SF_A/input.in",
+                '2026-03-26 12:55:18.229966', '2024-03-26 12:55:18.229966'] # this is invalid...
+    record_G = ["f_A", "ensA", "sfcf", "archive/SF_A/f_A/Project_A.json.gz::asdfasdfasdf2", "SF_A", '{"par_A": 5.0, "par_B": 5.0}', "projects/SF_A/input.in",
+                '2026-03-26 12:55:18.229966', str(dt.datetime.now() + dt.timedelta(days=2, hours=3, minutes=5, seconds=30))] # created and updated later
+
+    data = [record_A, record_B, record_C, record_D, record_E]
+    cols = ["name",
+            "ensemble",
+            "code",
+            "path",
+            "project",
+            "parameters",
+            "parameter_file",
+            "created_at",
+            "updated_at"]
+    df = pd.DataFrame(data,columns=cols)
+
+    results = find._time_filter(df, created_before='2023-03-26 12:55:18.229966')
+    assert results.empty
+    results = find._time_filter(df, created_before='2027-03-26 12:55:18.229966')
+    assert len(results) == 5
+    results = find._time_filter(df, created_before='2026-03-25 12:55:18.229966')
+    assert len(results) == 3
+    results = find._time_filter(df, created_before='2026-03-26 12:55:18.229965')
+    assert len(results) == 3
+    results = find._time_filter(df, created_before='2025-03-04 12:55:18.229965')
+    assert len(results) == 1
+
+    results = find._time_filter(df, created_after='2023-03-26 12:55:18.229966')
+    assert len(results) == 5
+    results = find._time_filter(df, created_after='2027-03-26 12:55:18.229966')
+    assert results.empty
+    results = find._time_filter(df, created_after='2026-03-25 12:55:18.229966')
+    assert len(results) == 2
+    results = find._time_filter(df, created_after='2026-03-26 12:55:18.229965')
+    assert len(results) == 2
+    results = find._time_filter(df, created_after='2025-03-04 12:55:18.229965')
+    assert len(results) == 4
+
+    results = find._time_filter(df, updated_before='2023-03-26 12:55:18.229966')
+    assert results.empty
+    results = find._time_filter(df, updated_before='2027-03-26 12:55:18.229966')
+    assert len(results) == 5
+    results = find._time_filter(df, updated_before='2026-03-25 12:55:18.229966')
+    assert len(results) == 3
+    results = find._time_filter(df, updated_before='2026-03-26 12:55:18.229965')
+    assert len(results) == 3
+    results = find._time_filter(df, updated_before='2025-03-04 12:55:18.229965')
+    assert len(results) == 1
+
+    results = find._time_filter(df, updated_after='2023-03-26 12:55:18.229966')
+    assert len(results) == 5
+    results = find._time_filter(df, updated_after='2027-03-26 12:55:18.229966')
+    assert results.empty
+    results = find._time_filter(df, updated_after='2026-03-25 12:55:18.229966')
+    assert len(results) == 2
+    results = find._time_filter(df, updated_after='2026-03-26 12:55:18.229965')
+    assert len(results) == 2
+    results = find._time_filter(df, updated_after='2025-03-04 12:55:18.229965')
+    assert len(results) == 4
+
+    data = [record_A, record_B, record_C, record_D, record_F]
+    cols = ["name",
+            "ensemble",
+            "code",
+            "path",
+            "project",
+            "parameters",
+            "parameter_file",
+            "created_at",
+            "updated_at"]
+    df = pd.DataFrame(data,columns=cols)
+
+    with pytest.raises(ValueError):
+        results = find._time_filter(df, created_before='2023-03-26 12:55:18.229966')
+
+    data = [record_A, record_B, record_C, record_D, record_G]
+    cols = ["name",
+            "ensemble",
+            "code",
+            "path",
+            "project",
+            "parameters",
+            "parameter_file",
+            "created_at",
+            "updated_at"]
+    df = pd.DataFrame(data,columns=cols)
+
+    with pytest.raises(ValueError):
+        results = find._time_filter(df, created_before='2023-03-26 12:55:18.229966')
+
+
+def test_db_lookup(tmp_path: Path) -> None:
+    db = make_sql(tmp_path)
+    conn = sqlite3.connect(db)
+    c = conn.cursor()
+
+    corr = "f_A"
+    ensemble = "SF_A"
+    code = "openQCD"
+    meas_path = "archive/SF_A/f_A/Project_A.json.gz::asdfasdfasdf"
+    uuid = "Project_A"
+    pars = "{par_A: 3.0, par_B: 5.0}"
+    parameter_file = "projects/Project_A/myinput.in"
+    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, parameter_file))
+    conn.commit()
+
+    results = find._db_lookup(db, ensemble, corr, code)
+    assert len(results) == 1
+    results = find._db_lookup(db, "SF_B", corr, code)
+    assert results.empty
+    results = find._db_lookup(db, ensemble, "g_A", code)
+    assert results.empty
+    results = find._db_lookup(db, ensemble, corr, "sfcf")
+    assert results.empty
+    results = find._db_lookup(db, ensemble, corr, code, project = "Project_A")
+    assert len(results) == 1
+    results = find._db_lookup(db, ensemble, corr, code, project = "Project_B")
+    assert results.empty
+    results = find._db_lookup(db, ensemble, corr, code, parameters = pars)
+    assert len(results) == 1
+    results = find._db_lookup(db, ensemble, corr, code, parameters = '{"par_A": 3.0, "par_B": 4.0}')
+    assert results.empty
+
+    corr = "g_A"
+    ensemble = "SF_A"
+    code = "openQCD"
+    meas_path = "archive/SF_A/f_A/Project_A.json.gz::asdfasdfasdf"
+    uuid = "Project_A"
+    pars = '{"par_A": 3.0, "par_B": 4.0}'
+    parameter_file = "projects/Project_A/myinput.in"
+    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, parameter_file))
+    conn.commit()
+
+    corr = "f_A"
+    results = find._db_lookup(db, ensemble, corr, code)
+    assert len(results) == 1
+    results = find._db_lookup(db, "SF_B", corr, code)
+    assert results.empty
+    results = find._db_lookup(db, ensemble, "g_A", code)
+    assert len(results) == 1
+    results = find._db_lookup(db, ensemble, corr, "sfcf")
+    assert results.empty
+    results = find._db_lookup(db, ensemble, corr, code, project = "Project_A")
+    assert len(results) == 1
+    results = find._db_lookup(db, ensemble, "g_A", code, project = "Project_A")
+    assert len(results) == 1
+    results = find._db_lookup(db, ensemble, corr, code, project = "Project_B")
+    assert results.empty
+    results = find._db_lookup(db, ensemble, "g_A", code, project = "Project_B")
+    assert results.empty
+    results = find._db_lookup(db, ensemble, corr, code, parameters = pars)
+    assert results.empty
+    results = find._db_lookup(db, ensemble, "g_A", code, parameters = '{"par_A": 3.0, "par_B": 4.0}')
+    assert len(results) == 1
+
+    conn.close()
+
+
+def test_sfcf_drop() -> None:
+    parameters0 = {
+                    'offset': [0,0,0],
+                    'quarks': [{'mass': 1, 'thetas': [0,0,0]}, {'mass': 2, 'thetas': [0,0,1]}], # m0s = -3.5, -3.75
+                    'wf1': [[1, [0, 0]], [0.5, [1, 0]], [.75, [.5, .5]]],
+                    'wf2': [[1, [2, 1]], [2, [0.5, -0.5]], [.5, [.75, .72]]],
+                   }
+
+    assert not find._sfcf_drop(parameters0, offset=[0,0,0])
+    assert find._sfcf_drop(parameters0, offset=[1,0,0])
+
+    assert not find._sfcf_drop(parameters0, quark_kappas = [1, 2])
+    assert find._sfcf_drop(parameters0, quark_kappas = [-3.1, -3.72])
+
+    assert not find._sfcf_drop(parameters0, quark_masses = [-3.5, -3.75])
+    assert find._sfcf_drop(parameters0, quark_masses = [-3.1, -3.72])
+
+    assert not find._sfcf_drop(parameters0, qk1 = 1)
+    assert not find._sfcf_drop(parameters0, qk2 = 2)
+    assert find._sfcf_drop(parameters0, qk1 = 2)
+    assert find._sfcf_drop(parameters0, qk2 = 1)
+
+    assert not find._sfcf_drop(parameters0, qk1 = [0.5,1.5])
+    assert not find._sfcf_drop(parameters0, qk2 = [1.5,2.5])
+    assert find._sfcf_drop(parameters0, qk1 = 2)
+    assert find._sfcf_drop(parameters0, qk2 = 1)
+    with pytest.raises(ValueError):
+        assert not find._sfcf_drop(parameters0, qk1 = [0.5,1,5])
+    with pytest.raises(ValueError):
+        assert not find._sfcf_drop(parameters0, qk2 = [1,5,2.5])
+
+    assert find._sfcf_drop(parameters0, qm1 = 1.2)
+    assert find._sfcf_drop(parameters0, qm2 = 2.2)
+    assert not find._sfcf_drop(parameters0, qm1 = -3.5)
+    assert not find._sfcf_drop(parameters0, qm2 = -3.75)
+
+    assert find._sfcf_drop(parameters0, qm2 = 1.2)
+    assert find._sfcf_drop(parameters0, qm1 = 2.2)
+    with pytest.raises(ValueError):
+        assert not find._sfcf_drop(parameters0, qm1 = [0.5,1,5])
+    with pytest.raises(ValueError):
+        assert not find._sfcf_drop(parameters0, qm2 = [1,5,2.5])
+
+
+def test_openQCD_filter() -> None:
+    record_0 = ["f_A", "ensA", "sfcf", "archive/SF_A/f_A/Project_A.json.gz::asdfasdfasdf", "SF_A", '{"par_A": 5.0, "par_B": 5.0}', "projects/SF_A/input.in",
+            '2025-03-26 12:55:18.229966', '2025-03-26 12:55:18.229966']
+    record_1 = ["f_A", "ensA", "sfcf", "archive/SF_A/f_A/Project_A.json.gz::asdfasdfasdf", "SF_A", '{"par_A": 5.0, "par_B": 5.0}', "projects/SF_A/input.in",
+            '2025-03-26 12:55:18.229966', '2025-03-26 12:55:18.229966']
+    record_2 = ["f_P", "ensA", "sfcf", "archive/SF_A/f_A/Project_A.json.gz::asdfasdfasdf", "SF_A", '{"par_A": 5.0, "par_B": 5.0}', "projects/SF_A/input.in",
+            '2025-03-26 12:55:18.229966', '2025-03-26 12:55:18.229966']
+    record_3 = ["f_P", "ensA", "sfcf", "archive/SF_A/f_A/Project_A.json.gz::asdfasdfasdf", "SF_A", '{"par_A": 5.0, "par_B": 5.0}', "projects/SF_A/input.in",
+            '2025-03-26 12:55:18.229966', '2025-03-26 12:55:18.229966']
+    data = [
+        record_0,
+        record_1,
+        record_2,
+        record_3,
+    ]
+    cols = ["name",
+            "ensemble",
+            "code",
+            "path",
+            "project",
+            "parameters",
+            "parameter_file",
+            "created_at",
+            "updated_at"]
+    df = pd.DataFrame(data,columns=cols)
+
+    with pytest.warns(Warning):
+        find.openQCD_filter(df, a = "asdf")
+
+
+def test_code_filter() -> None:
+    record_0 = ["f_A", "ensA", "sfcf", "archive/SF_A/f_A/Project_A.json.gz::asdfasdfasdf", "SF_A", '{"par_A": 5.0, "par_B": 5.0}', "projects/SF_A/input.in",
+            '2025-03-26 12:55:18.229966', '2025-03-26 12:55:18.229966']
+    record_1 = ["f_A", "ensA", "sfcf", "archive/SF_A/f_A/Project_A.json.gz::asdfasdfasdf", "SF_A", '{"par_A": 5.0, "par_B": 5.0}', "projects/SF_A/input.in",
+            '2025-03-26 12:55:18.229966', '2025-03-26 12:55:18.229966']
+    record_2 = ["f_P", "ensA", "sfcf", "archive/SF_A/f_A/Project_A.json.gz::asdfasdfasdf", "SF_A", '{"par_A": 5.0, "par_B": 5.0}', "projects/SF_A/input.in",
+            '2025-03-26 12:55:18.229966', '2025-03-26 12:55:18.229966']
+    record_3 = ["f_P", "ensA", "sfcf", "archive/SF_A/f_A/Project_A.json.gz::asdfasdfasdf", "SF_A", '{"par_A": 5.0, "par_B": 5.0}', "projects/SF_A/input.in",
+            '2025-03-26 12:55:18.229966', '2025-03-26 12:55:18.229966']
+    record_4 = ["f_A", "ensA", "openQCD", "archive/SF_A/f_A/Project_A.json.gz::asdfasdfasdf", "SF_A", '{"par_A": 5.0, "par_B": 5.0}', "projects/SF_A/input.in",
+            '2025-03-26 12:55:18.229966', '2025-03-26 12:55:18.229966']
+    record_5 = ["f_A", "ensA", "openQCD", "archive/SF_A/f_A/Project_A.json.gz::asdfasdfasdf", "SF_A", '{"par_A": 5.0, "par_B": 5.0}', "projects/SF_A/input.in",
+            '2025-03-26 12:55:18.229966', '2025-03-26 12:55:18.229966']
+    record_6 = ["f_P", "ensA", "openQCD", "archive/SF_A/f_A/Project_A.json.gz::asdfasdfasdf", "SF_A", '{"par_A": 5.0, "par_B": 5.0}', "projects/SF_A/input.in",
+            '2025-03-26 12:55:18.229966', '2025-03-26 12:55:18.229966']
+    record_7 = ["f_P", "ensA", "openQCD", "archive/SF_A/f_A/Project_A.json.gz::asdfasdfasdf", "SF_A", '{"par_A": 5.0, "par_B": 5.0}', "projects/SF_A/input.in",
+            '2025-03-26 12:55:18.229966', '2025-03-26 12:55:18.229966']
+    record_8 = ["f_P", "ensA", "openQCD", "archive/SF_A/f_A/Project_A.json.gz::asdfasdfasdf", "SF_A", '{"par_A": 5.0, "par_B": 5.0}', "projects/SF_A/input.in",
+            '2025-03-26 12:55:18.229966', '2025-03-26 12:55:18.229966']
+    data = [
+        record_0,
+        record_1,
+        record_2,
+        record_3,
+    ]
+    cols = ["name",
+            "ensemble",
+            "code",
+            "path",
+            "project",
+            "parameters",
+            "parameter_file",
+            "created_at",
+            "updated_at"]
+    df = pd.DataFrame(data,columns=cols)
+
+    res = find._code_filter(df, "sfcf")
+    assert len(res) == 4
+
+    data = [
+        record_4,
+        record_5,
+        record_6,
+        record_7,
+        record_8,
+    ]
+    cols = ["name",
+            "ensemble",
+            "code",
+            "path",
+            "project",
+            "parameters",
+            "parameter_file",
+            "created_at",
+            "updated_at"]
+    df = pd.DataFrame(data,columns=cols)
+
+    res = find._code_filter(df, "openQCD")
+    assert len(res) == 5
+    with pytest.raises(ValueError):
+        res = find._code_filter(df, "asdf")
+
+
+def test_find_record() -> None:
+    assert True
+
+
+def test_find_project(tmp_path: Path) -> None:
+    cinit.create(tmp_path)
+    db = tmp_path / "backlogger.db"
+    dl.unlock(str(db), dataset=str(tmp_path))
+    conn = sqlite3.connect(db)
+    c = conn.cursor()
+    uuid = "test_uuid"
+    alias_str = "fun_project"
+    tag_str = "tt"
+    owner = "tester"
+    code = "test_code"
+    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()
+
+    assert uuid == find.find_project(tmp_path, "fun_project")
+
+    uuid = "test_uuid2"
+    alias_str = "fun_project"
+    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()
+
+    with pytest.raises(Exception):
+        assert uuid == find._project_lookup_by_alias(tmp_path, "fun_project")
+    conn.close()
+
+
+def test_list_projects(tmp_path: Path) -> None:
+    cinit.create(tmp_path)
+    db = tmp_path / "backlogger.db"
+    dl.unlock(str(db), dataset=str(tmp_path))
+    conn = sqlite3.connect(db)
+    c = conn.cursor()
+    uuid = "test_uuid"
+    alias_str = "fun_project"
+    tag_str = "tt"
+    owner = "tester"
+    code = "test_code"
+
+    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))
+    uuid = "test_uuid2"
+    alias_str = "fun_project2"
+    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))
+    uuid = "test_uuid3"
+    alias_str = "fun_project3"
+    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))
+    uuid = "test_uuid4"
+    alias_str = "fun_project4"
+    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()
+    results = find.list_projects(tmp_path)
+    assert len(results) == 4
+    for i in range(4):
+        assert len(results[i]) == 2

tests/import_project_test.py

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

tests/initialization_test.py

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

tests/sfcf_in_test.py

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

tests/tools_test.py

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