.github/workflows/pytest.yaml

@@ -20,6 +20,10 @@ jobs:
     env:
       UV_CACHE_DIR: /tmp/.uv-cache
     steps:
+      - name: Install git-annex
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y git-annex
       - name: Check out the repository
         uses: https://github.com/RouxAntoine/checkout@v4.1.8
         with:
@@ -32,4 +36,4 @@ jobs:
       - name: Install corrlib
         run: uv sync --locked --all-extras --dev --python ${{ matrix.python-version }}
       - name: Run tests
-        run: uv run pytest tests
+        run: uv run pytest --cov=corrlib tests

.gitignore

@@ -4,4 +4,5 @@ __pycache__
 test.ipynb
 .vscode
 .venv
-.pytest_cache
+.pytest_cache
+.coverage

corrlib/__init__.py

@@ -1,5 +1,5 @@
 """
-The aim of this project is to extend pyerrors to be able to collect measurements from different projects and make them easily accessable to 
+The aim of this project is to extend pyerrors to be able to collect measurements from different projects and make them easily accessable to
 the research group. The idea is to build a database, in which the researcher can easily search for measurements on a correlator basis,
 which may be reusable.
 As a standard to store the measurements, we will use the .json.gz format from pyerrors.
@@ -15,8 +15,10 @@ For now, we are interested in collecting primary IObservables only, as these are
 
 __app_name__ = "corrlib"
 
-from .main import *
 from .import input as input
-from .initialization import *
-from .meas_io import *
-from .find import *
+from .initialization import create as create
+from .meas_io import load_record as load_record
+from .meas_io import load_records as load_records
+from .find import find_project as find_project
+from .find import find_record as find_record
+from .find import list_projects as list_projects

corrlib/cli.py

@@ -8,7 +8,7 @@ from .tools import str2list
 from .main import update_aliases
 from .meas_io import drop_cache as mio_drop_cache
 import os
-from importlib.metadata import version, PackageNotFoundError
+from importlib.metadata import version
 
 
 app = typer.Typer()

corrlib/find.py

@@ -1,5 +1,4 @@
 import sqlite3
-import datalad.api as dl
 import os
 import json
 import pandas as pd
@@ -16,7 +15,7 @@ def _project_lookup_by_alias(db, alias):
     c.execute(f"SELECT * FROM 'projects' WHERE alias = '{alias}'")
     results = c.fetchall()
     conn.close()
-    if len(results) > 1:
+    if len(results)>1:
         print("Error: multiple projects found with alias " + alias)
     elif len(results) == 0:
         raise Exception("Error: no project found with alias " + alias)

corrlib/input/__init__.py

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

corrlib/main.py

@@ -130,14 +130,14 @@ def import_project(path: str, url: str, owner: Union[str, None]=None, tags: Unio
         dl.save([db, path + '/projects/' + uuid], message="Import project from " + url, dataset=path)
     else:
         dl.drop(tmp_path, reckless='kill')
-        shutil.rmtree(tmp_path)    
+        shutil.rmtree(tmp_path)
         if aliases is not None:
             if isinstance(aliases, str):
                 alias_list = [aliases]
             else:
                 alias_list = aliases
             update_aliases(path, uuid, alias_list)
-            
+
     # make this more concrete
     return uuid
 

corrlib/meas_io.py

@@ -58,7 +58,7 @@ def write_measurement(path, ensemble, measurement, uuid, code, parameter_file=No
                 pars = {}
                 subkeys = []
                 for i in range(len(parameters["rw_fcts"])):
-                    par_list = []                
+                    par_list = []
                     for k in parameters["rw_fcts"][i].keys():
                         par_list.append(str(parameters["rw_fcts"][i][k]))
                     subkey = "/".join(par_list)
@@ -79,12 +79,12 @@ def write_measurement(path, ensemble, measurement, uuid, code, parameter_file=No
                 subkey = "/".join(par_list)
                 subkeys = [subkey]
                 pars[subkey] = json.dumps(parameters)
-        for subkey in subkeys:                
+        for subkey in subkeys:
             parHash = sha256(str(pars[subkey]).encode('UTF-8')).hexdigest()
             meas_path = file_in_archive + "::" + parHash
 
             known_meas[parHash] = measurement[corr][subkey]
-            
+
             if c.execute("SELECT * FROM backlogs WHERE path = ?", (meas_path,)).fetchone() is not None:
                 c.execute("UPDATE backlogs SET updated_at = datetime('now') WHERE path = ?", (meas_path, ))
             else:
@@ -107,7 +107,7 @@ def load_record(path: str, meas_path: str):
         Path of the correlator library.
     meas_path: str
         The path to the correlator in the backlog system.
-    
+
     Returns
     -------
     co : Corr or Obs
@@ -126,7 +126,7 @@ def load_records(path: str, meas_paths: list[str], preloaded = {}) -> list[Union
         Path of the correlator library.
     meas_paths: list[str]
         A list of the paths to the correlator in the backlog system.
-    
+
     Returns
     -------
     List

corrlib/tools.py

@@ -26,4 +26,3 @@ def get_file(path: str, file: str):
         print("Downloading data...")
     dl.get(os.path.join(path, file), dataset=path)
     print("> downloaded file")
-    

corrlib/version.py

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

pyproject.toml

@@ -27,10 +27,19 @@ include = ["corrlib", "corrlib.*"]
 write_to = "corrlib/version.py"
 
 [tool.ruff.lint]
-ignore = ["F403"]
+ignore = ["E501"]
+extend-select = [
+  "YTT",
+  "E",
+  "W",
+  "F",
+]
 
 [dependency-groups]
 dev = [
+    "mypy>=1.19.0",
     "pytest>=9.0.1",
+    "pytest-cov>=7.0.0",
     "pytest-pretty>=1.3.0",
+    "ruff>=0.14.7",
 ]

tests/cli_test.py

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

tests/test_initialization.py

@@ -0,0 +1,68 @@
+import corrlib.initialization as init
+import os
+import sqlite3 as sql
+
+def test_init_folders(tmp_path):
+    dataset_path = tmp_path / "test_dataset"
+    init.create(str(dataset_path))
+    assert os.path.exists(str(dataset_path))
+    assert os.path.exists(str(dataset_path / "backlogger.db"))
+
+
+def test_init_db(tmp_path):
+    dataset_path = tmp_path / "test_dataset"
+    init.create(str(dataset_path))
+    assert os.path.exists(str(dataset_path / "backlogger.db"))
+    conn = sql.connect(str(dataset_path / "backlogger.db"))
+    cursor = conn.cursor()
+    cursor.execute("SELECT name FROM sqlite_master WHERE type='table';")
+    tables = cursor.fetchall()
+    expected_tables = [
+        'projects',
+        'backlogs',
+        ]
+    table_names = [table[0] for table in tables]
+    for expected_table in expected_tables:
+        assert expected_table in table_names
+    
+    cursor.execute("SELECT * FROM projects;")
+    projects = cursor.fetchall()
+    assert len(projects) == 0
+
+    cursor.execute("SELECT * FROM backlogs;")
+    backlogs = cursor.fetchall()
+    assert len(backlogs) == 0
+
+    cursor.execute("PRAGMA table_info('projects');")
+    project_columns = cursor.fetchall()
+    expected_project_columns = [
+        "id",
+        "aliases",
+        "customTags",
+        "owner",
+        "code",
+        "created_at",
+        "updated_at"
+        ]
+    project_column_names = [col[1] for col in project_columns]
+    for expected_col in expected_project_columns:
+        assert expected_col in project_column_names
+    
+    cursor.execute("PRAGMA table_info('backlogs');")
+    backlog_columns = cursor.fetchall()
+    expected_backlog_columns = [
+        "id",
+        "name",
+        "ensemble",
+        "code",
+        "path",
+        "project",
+        "customTags",
+        "parameters",
+        "parameter_file",
+        "created_at",
+        "updated_at"
+        ]
+    backlog_column_names = [col[1] for col in backlog_columns]
+    for expected_col in expected_backlog_columns:
+        assert expected_col in backlog_column_names

tests/tools_test.py

@@ -4,15 +4,21 @@ from corrlib import tools as tl
 
 
 def test_m2k():
-    assert tl.m2k(0.1) == 1/(2*0.1+8)
-    assert tl.m2k(0.5) == 1/(2*0.5+8)
-    assert tl.m2k(1.0) == 1/(2*1.0+8)
+    for m in [0.1, 0.5, 1.0]:
+        expected_k = 1 / (2 * m + 8)
+        assert tl.m2k(m) == expected_k
 
 
 def test_k2m():
-    assert tl.k2m(0.1) == (1/(2*0.1))-4
-    assert tl.k2m(0.5) == (1/(2*0.5))-4
-    assert tl.k2m(1.0) == (1/(2*1.0))-4
+    for m in [0.1, 0.5, 1.0]:
+        assert tl.k2m(m) == (1/(2*m))-4
+
+
+def test_k2m_m2k():
+    for m in [0.1, 0.5, 1.0]:
+        k = tl.m2k(m)
+        m_converted = tl.k2m(k)
+        assert abs(m - m_converted) < 1e-9
 
 
 def test_str2list():