.github/workflows/pytest.yaml

@@ -20,10 +20,6 @@ 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:
@@ -36,4 +32,4 @@ jobs:
       - name: Install corrlib
         run: uv sync --locked --all-extras --dev --python ${{ matrix.python-version }}
       - name: Run tests
-        run: uv run pytest --cov=corrlib tests
+        run: uv run pytest tests

.gitignore

@@ -5,4 +5,3 @@ test.ipynb
 .vscode
 .venv
 .pytest_cache
-.coverage

corrlib/__init__.py

@@ -15,10 +15,8 @@ For now, we are interested in collecting primary IObservables only, as these are
 
 __app_name__ = "corrlib"
 
+from .main import *
 from .import input as input
-from .initialization import create as create
+from .initialization import *
-from .meas_io import load_record as load_record
+from .meas_io import *
-from .meas_io import load_records as load_records
+from .find import *
-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
+from importlib.metadata import version, PackageNotFoundError
 
 
 app = typer.Typer()

corrlib/find.py

@@ -1,4 +1,5 @@
 import sqlite3
+import datalad.api as dl
 import os
 import json
 import pandas as pd

corrlib/input/__init__.py

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

corrlib/tools.py

@@ -26,3 +26,4 @@ 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

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

pyproject.toml

@@ -27,19 +27,10 @@ include = ["corrlib", "corrlib.*"]
 write_to = "corrlib/version.py"
 
 [tool.ruff.lint]
-ignore = ["E501"]
+ignore = ["F403"]
-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

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

tests/test_initialization.py

@@ -1,68 +0,0 @@
-import corrlib.initialization as init
-import os
-import sqlite3 as sql
-
-def test_init_folders(tmp_path):
-    dataset_path = tmp_path / "test_dataset"
-    init.create(str(dataset_path))
-    assert os.path.exists(str(dataset_path))
-    assert os.path.exists(str(dataset_path / "backlogger.db"))
-
-
-def test_init_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

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