Merge pull request 'test/more' (#9) from test/more into develop

Reviewed-on: https://www.kuhl-mann.de/git/git/jkuhl/corrlib/pulls/9

.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

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

corrlib/__init__.py

@@ -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

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/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():