Clean up

Author: rly

Diff for: README.md

@@ -5,9 +5,7 @@ Support for N-dimensional arrays in LinkML.
 # Quick reference for common commands
 
 ```bash
-cd linkml-model
-poetry run gen-json-schema tests/input/examples/schema_definition-array-2.yaml
-poetry run gen-pydantic tests/input/examples/schema_definition-array-2.yaml
+poetry run gen-pydantic tests/input/temperature_schema.yaml > tests/array_classes_lol.py
 ```
 
 # Acknowledgements

Diff for: src/linkml_arrays/dumpers/yaml_array_file_dumper.py

@@ -1,4 +1,4 @@
-"""Base class for dumping a LinkML model to a YAML file with paths to files containing individual arrays."""
+"""Base class for dumping a LinkML model to YAML with paths to files containing arrays."""
 
 import os
 from abc import ABCMeta, abstractmethod

Diff for: src/linkml_arrays/dumpers/yaml_dumper.py

@@ -1,4 +1,4 @@
-"""Class for dumping a LinkML model to a YAML file."""
+"""Class for dumping a LinkML model to YAML."""
 
 from typing import Union
 

Diff for: src/linkml_arrays/dumpers/yaml_hdf5_dumper.py

@@ -1,4 +1,4 @@
-"""Class for dumping a LinkML model to a YAML file with paths to HDF5 files."""
+"""Class for dumping a LinkML model to YAML with paths to HDF5 files."""
 
 from pathlib import Path
 from typing import List, Union
@@ -10,7 +10,7 @@
 
 
 class YamlHdf5Dumper(YamlArrayFileDumper):
-    """Dumper class for LinkML models to YAML files with paths to HDF5 files, one for each array.
+    """Dumper class for LinkML models to YAML with paths to HDF5 files, one per array.
 
     Each array is written to an HDF5 dataset at path "/data" in a new HDF5 file.
     """

Diff for: src/linkml_arrays/dumpers/yaml_numpy_dumper.py

@@ -1,4 +1,4 @@
-"""Class for dumping a LinkML model to a YAML file with paths to NumPy files."""
+"""Class for dumping a LinkML model to YAML with paths to NumPy files."""
 
 from pathlib import Path
 from typing import List, Union
@@ -9,7 +9,7 @@
 
 
 class YamlNumpyDumper(YamlArrayFileDumper):
-    """Dumper class for LinkML models to YAML files with paths to NumPy .npy files, one for each array.
+    """Dumper class for LinkML models to YAML with paths to .npy files, one per array.
 
     Each array is written to an HDF5 dataset at path "/data" in a new HDF5 file.
     """

Diff for: src/linkml_arrays/loaders/yaml_loader.py

@@ -2,7 +2,6 @@
 
 from typing import Type, Union
 
-import numpy as np
 import yaml
 from linkml_runtime import SchemaView
 from linkml_runtime.linkml_model import ClassDefinition

Diff for: tests/test_dumpers/test_dumpers.py

@@ -1,7 +1,6 @@
 """Test dumping LinkML pydantic models with arrays as lists-of-lists to various file formats."""
 
 import os
-import unittest
 from pathlib import Path
 
 import h5py
@@ -30,7 +29,7 @@
 INPUT_DIR = Path(__file__).parent.parent / "input"
 
 
-def create_container() -> Container:
+def _create_container() -> Container:
     latitude_in_deg = LatitudeInDegSeries(name="my_latitude", values=[[1, 2], [3, 4]])
     longitude_in_deg = LongitudeInDegSeries(name="my_longitude", values=[[5, 6], [7, 8]])
     date = DateSeries(values=["2020-01-01", "2020-01-02"])
@@ -39,9 +38,10 @@ def create_container() -> Container:
         conversion_factor=1000.0,
         values=[[[0, 1], [2, 3]], [[4, 5], [6, 7]]],
     )
+    # NOTE: currently no way to pass in the actual LatitudeInDegSeries object
     temperature_dataset = TemperatureDataset(
         name="my_temperature",
-        latitude_in_deg="my_latitude",  # currently no way to pass in the actual LatitudeInDegSeries object
+        latitude_in_deg="my_latitude",
         longitude_in_deg="my_longitude",
         date=date,
         day_in_d=days_in_d_since,
@@ -59,7 +59,7 @@ def create_container() -> Container:
 
 def test_yaml_dumper():
     """Test YamlDumper dumping to a YAML file."""
-    container = create_container()
+    container = _create_container()
 
     schemaview = SchemaView(INPUT_DIR / "temperature_schema.yaml")
     ret = YamlDumper().dumps(container, schemaview=schemaview)
@@ -75,7 +75,7 @@ def test_yaml_dumper():
 
 def test_yaml_numpy_dumper():
     """Test YamlNumpyDumper dumping to a YAML file and NumPy .npy files in a directory."""
-    container = create_container()
+    container = _create_container()
 
     schemaview = SchemaView(INPUT_DIR / "temperature_schema.yaml")
     ret = YamlNumpyDumper().dumps(container, schemaview=schemaview, output_dir="./out")
@@ -91,7 +91,7 @@ def test_yaml_numpy_dumper():
 
 def test_yaml_hdf5_dumper():
     """Test YamlNumpyDumper dumping to a YAML file and HDF5 datasets in a directory."""
-    container = create_container()
+    container = _create_container()
 
     schemaview = SchemaView(INPUT_DIR / "temperature_schema.yaml")
     ret = YamlHdf5Dumper().dumps(container, schemaview=schemaview, output_dir="./out")
@@ -107,7 +107,7 @@ def test_yaml_hdf5_dumper():
 
 def test_hdf5_dumper(tmp_path):
     """Test Hdf5Dumper dumping to an HDF5 file."""
-    container = create_container()
+    container = _create_container()
 
     schemaview = SchemaView(INPUT_DIR / "temperature_schema.yaml")
     output_file_path = tmp_path / "my_container.h5"
@@ -137,7 +137,7 @@ def test_hdf5_dumper(tmp_path):
 
 def test_zarr_directory_store_dumper(tmp_path):
     """Test ZarrDumper dumping to an HDF5 file."""
-    container = create_container()
+    container = _create_container()
 
     schemaview = SchemaView(INPUT_DIR / "temperature_schema.yaml")
     output_file_path = tmp_path / "my_container.zarr"

Diff for: tests/test_loaders/test_loaders.py

@@ -1,9 +1,7 @@
-"""Test loading data from various file formats into LinkML pydantic models with arrays as lists-of-lists."""
+"""Test loading data from various file formats into pydantic models with arrays as LoLs."""
 
-import unittest
 from pathlib import Path
 
-import numpy as np
 from hbreader import hbread
 from linkml_runtime import SchemaView
 
@@ -25,7 +23,7 @@
 )
 
 
-def check_container(container: Container):
+def _check_container(container: Container):
     assert isinstance(container, Container)
     assert container.name == "my_container"
 
@@ -40,8 +38,9 @@ def check_container(container: Container):
     assert isinstance(container.temperature_dataset, TemperatureDataset)
     assert container.temperature_dataset.name == "my_temperature"
     assert container.temperature_dataset.latitude_in_deg == "my_latitude"
-    # currently no way to get the actual LatitudeInDegSeries object from the TemperatureDataset object
-    # because the TemperatureDataset Pydantic object expects a string for the latitude_in_deg field
+    # currently no way to get the actual LatitudeInDegSeries object from the
+    # TemperatureDataset object because the TemperatureDataset Pydantic object
+    # expects a string for the latitude_in_deg field
     # to be isomorphic with the json schema / yaml representation
 
     assert container.temperature_dataset.longitude_in_deg == "my_longitude"
@@ -65,31 +64,31 @@ def test_yaml_loader():
     data_yaml = hbread("container_yaml.yaml", base_path=str(Path(__file__) / "../../input"))
     schemaview = SchemaView(Path(__file__) / "../../input/temperature_schema.yaml")
     container = YamlLoader().loads(data_yaml, target_class=Container, schemaview=schemaview)
-    check_container(container)
+    _check_container(container)
 
 
 def test_yaml_numpy_loader():
     """Test loading of pydantic-style classes from YAML + Numpy arrays."""
     read_yaml = hbread("container_yaml_numpy.yaml", base_path=str(Path(__file__) / "../../input"))
     schemaview = SchemaView(Path(__file__) / "../../input/temperature_schema.yaml")
     container = YamlNumpyLoader().loads(read_yaml, target_class=Container, schemaview=schemaview)
-    check_container(container)
+    _check_container(container)
 
 
 def test_yaml_hdf5_loader():
     """Test loading of pydantic-style classes from YAML + Numpy arrays."""
     read_yaml = hbread("container_yaml_hdf5.yaml", base_path=str(Path(__file__) / "../../input"))
     schemaview = SchemaView(Path(__file__) / "../../input/temperature_schema.yaml")
     container = YamlHdf5Loader().loads(read_yaml, target_class=Container, schemaview=schemaview)
-    check_container(container)
+    _check_container(container)
 
 
 def test_hdf5_loader():
     """Test loading of pydantic-style classes from HDF5 datasets."""
     file_path = str(Path(__file__).parent.parent / "input" / "my_container.h5")
     schemaview = SchemaView(Path(__file__) / "../../input/temperature_schema.yaml")
     container = Hdf5Loader().loads(file_path, target_class=Container, schemaview=schemaview)
-    check_container(container)
+    _check_container(container)
 
 
 def test_zarr_directory_store_loader():
@@ -99,5 +98,4 @@ def test_zarr_directory_store_loader():
     container = ZarrDirectoryStoreLoader().loads(
         file_path, target_class=Container, schemaview=schemaview
     )
-    check_container(container)
-
+    _check_container(container)

Diff for: tox.ini

@@ -53,7 +53,7 @@ description = Run documentation linters.
 skip_install = true
 deps =
     darglint
-    flake8<5.0.0
+    flake8
     flake8-black
     flake8-bandit
     flake8-bugbear
@@ -73,14 +73,20 @@ description = Run the flake8 tool with several plugins (bandit, docstrings, impo
 [flake8]
 max-line-length = 100
 ignore =
-    DAR101 # Missing parameter(s) in Docstring: - with_git_hash
-    DAR201 # Missing "Returns" in Docstring: - return
-    DAR301 # Missing "Yields" in Docstring: - yield
-    E111 # indentation is not a multiple of 4
-    T201 # print found.
-    S101 # Use of assert detected.
+    DAR101
+    DAR201
+    DAR301
+    E111
+    T201
+    S101
+    ; DAR101 # Missing parameter(s) in Docstring: - with_git_hash
+    ; DAR201 # Missing "Returns" in Docstring: - return
+    ; DAR301 # Missing "Yields" in Docstring: - yield
+    ; E111 # indentation is not a multiple of 4
+    ; T201 # print found.
+    ; S101 # Use of assert detected.
 exclude =
-    tests/test_dumpers/array_classes.py
+    tests/array_classes_lol.py
 
 [testenv:mypy]
 deps = mypy