Fixes for CI (#5)

* ci should work now

* fix a pyright error

* ci uses pre-commit  for checks

* fixed requirements

* fix dependency

* add all the optional packaged to CI

.github/workflows/python-test.yml

@@ -19,11 +19,12 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install pylint pytest pytest-cov hypothesis
-          pip install .
-      - name: Lint with pylint
+          pip install pre-commit pytest pytest-cov hypothesis
+          pre-commit install 
+          pip install .[CI]
+      - name: Run pre-commit checks
         run: |
-          pylint --fail-under=8 prepper
+          pre-commit run --all-files
       - name: Test with pytest
         run: |
           pytest --cov=prepper --cov-report=xml --cov-report=html

.pre-commit-config.yaml

@@ -1,32 +1,37 @@
 repos:
 
-- repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.0.275
+- repo: local
   hooks:
-    - id: ruff
-      args: [ --fix, --exit-non-zero-on-fix ]
-
-- repo: https://github.com/pycqa/isort
-  rev: 5.12.0
-  hooks:
-    - id: isort
-      name: isort (python)
-
--   repo: https://github.com/psf/black.git
-    rev: 23.1.0
-    hooks:
-    - id: black
-      language_version: python3.9
+
+  - id: generate-init
+    name: Generates __init__.py files
+    language: python
+    entry: python hooks/generate_init.py
+    always_run: true
+    require_serial: true 
+    additional_dependencies: ["mkinit", "ruff"]
 
+  - id: fix-line-endings
+    name: Convert CRLF/CR endings to LF
+    language: python
+    require_serial: true 
+    entry: python hooks/fix_line_endings.py
+    types: ["text"]
+
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v4.6.0
   hooks:
-  - id: end-of-file-fixer
-  - id: fix-encoding-pragma
-  - id: trailing-whitespace
-  - id: check-case-conflict
   - id: check-executables-have-shebangs
-  - id: check-merge-conflict
   - id: check-symlinks
-  - id: debug-statements
-  - id: mixed-line-ending
+
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.4.6
+  hooks:
+    #Run the formatter.
+    - id: ruff-format
+      types_or: [ python, pyi, jupyter ]
+    #Run the linter.
+    - id: ruff
+      types_or: [ python, pyi, jupyter ]
+      args: [ --fix, --exit-non-zero-on-fix ]

hooks/fix_line_endings.py

@@ -0,0 +1,56 @@
+#!/usr/bin/env python3
+from __future__ import annotations
+
+import argparse
+from pathlib import Path
+import sys
+
+
+def main(source_path: str) -> bool:
+    """
+    Main entry point of the script.
+
+    Parameters
+    ----------
+    function : Callable
+        Function to execute for the specified validation type.
+    source_path : str
+        Source path representing path to a file/directory.
+    output_format : str
+        Output format of the error message.
+    file_extensions_to_check : str
+        Comma separated values of what file extensions to check.
+    excluded_file_paths : str
+        Comma separated values of what file paths to exclude during the check.
+
+    Returns
+    -------
+    bool
+        True if found any patterns are found related to the given function.
+
+    Raises
+    ------
+    ValueError
+        If the `source_path` is not pointing to existing file/directory.
+    """
+
+    for file_path in source_path:
+        with Path(file_path).open("r", encoding="utf-8") as file_obj:
+            file_text = file_obj.read()
+
+        invalid_ending = "\r" in file_text
+        if invalid_ending:
+            with Path(file_path).open("w", encoding="utf-8") as file_obj:
+                file_obj.write(file_text)
+
+    return invalid_ending
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="CR/CRLF -> LF converter.")
+
+    parser.add_argument("paths", nargs="*", help="Source paths of files to check.")
+
+    args = parser.parse_args()
+
+    sys.exit(main(source_path=args.paths))

hooks/generate_init.py

@@ -0,0 +1,48 @@
+#!/usr/bin/env python3
+from __future__ import annotations
+
+import subprocess
+import sys
+
+from mkinit import static_mkinit
+
+
+def ruff_format(): ...
+def make_init():
+    options = {
+        "with_attrs": True,
+        "with_mods": True,
+        "with_all": True,
+        "relative": True,
+        "lazy_import": False,
+        "lazy_loader": True,
+        "lazy_loader_typed": True,
+        "lazy_boilerplate": None,
+        "use_black": False,
+    }
+
+    static_mkinit.autogen_init(
+        "prepper",
+        respect_all=True,
+        options=options,
+        dry=False,
+        diff=False,
+        recursive=True,
+    )
+    subprocess.run(["ruff", "format"])
+
+
+if __name__ == "__main__":
+    make_init()
+
+    changed_files1 = subprocess.run(
+        ["git", "diff", "--name-only", "--diff-filter=ACM", "--exit-code"]
+    )
+    changed_files2 = subprocess.run(
+        ["git", "ls-files", "--exclude-standard", "--others"], capture_output=True
+    )
+    retcode = changed_files1.returncode + changed_files2.returncode
+    retcode += len(changed_files2.stderr)
+    retcode += len(changed_files2.stdout)
+
+    sys.exit(retcode)

prepper/__init__.py

@@ -1,23 +1,53 @@
-# -*- coding: utf-8 -*-
 from __future__ import annotations
 
-import h5py
+__protected__ = ["utils", "io_handlers", "enums", "utils"]
+
+
+# <AUTOGEN_INIT>
+import lazy_loader
+
+
+__getattr__, __dir__, __all__ = lazy_loader.attach_stub(__name__, __file__)
 
 __all__ = [
+    "ExportableClassMixin",
+    "H5StoreException",
+    "NATIVE_DTYPES",
+    "NotASaveableClass",
+    "SimpleSaveableClass",
+    "SimpleSaveableClass2",
+    "break_key",
     "cached_property",
+    "caching",
+    "ensure_required_attributes",
+    "enums",
+    "exceptions",
+    "exportable",
+    "io_handlers",
     "local_cache",
-    "ExportableClassMixin",
+    "make_cache_name",
+    "req_class_attrs",
+    "req_dataset_attrs",
+    "req_none_attrs",
+    "roundtrip",
     "saveable_class",
+    "test_IO",
+    "test_cached_property",
+    "test_decorators",
+    "test_local_cache",
+    "test_saveable_class",
+    "test_with_float_list",
+    "test_with_floats",
+    "test_with_heterogenous_list",
+    "test_with_int_list",
+    "test_with_ints",
+    "test_with_str_list",
+    "tests",
+    "utils",
 ]
+# </AUTOGEN_INIT>
 
+import h5py
 
 # Make h5py write groups in order
 h5py.get_config().track_order = True
-
-
-class H5StoreException(Exception):
-    "An exception for when the HDF5 store does not meet spec"
-
-
-from .caching import cached_property, local_cache  # noqa E402
-from .exportable import ExportableClassMixin, saveable_class  # noqa E402

prepper/__init__.pyi

@@ -0,0 +1,80 @@
+from . import caching
+from . import enums
+from . import exceptions
+from . import exportable
+from . import io_handlers
+from . import tests
+from . import utils
+
+from .caching import (
+    break_key,
+    cached_property,
+    local_cache,
+    make_cache_name,
+)
+from .exceptions import (
+    H5StoreException,
+)
+from .exportable import (
+    ExportableClassMixin,
+    saveable_class,
+)
+from .tests import (
+    NATIVE_DTYPES,
+    NotASaveableClass,
+    SimpleSaveableClass,
+    SimpleSaveableClass2,
+    ensure_required_attributes,
+    req_class_attrs,
+    req_dataset_attrs,
+    req_none_attrs,
+    roundtrip,
+    test_IO,
+    test_cached_property,
+    test_decorators,
+    test_local_cache,
+    test_saveable_class,
+    test_with_float_list,
+    test_with_floats,
+    test_with_heterogenous_list,
+    test_with_int_list,
+    test_with_ints,
+    test_with_str_list,
+)
+
+__all__ = [
+    "ExportableClassMixin",
+    "H5StoreException",
+    "NATIVE_DTYPES",
+    "NotASaveableClass",
+    "SimpleSaveableClass",
+    "SimpleSaveableClass2",
+    "break_key",
+    "cached_property",
+    "caching",
+    "ensure_required_attributes",
+    "enums",
+    "exceptions",
+    "exportable",
+    "io_handlers",
+    "local_cache",
+    "make_cache_name",
+    "req_class_attrs",
+    "req_dataset_attrs",
+    "req_none_attrs",
+    "roundtrip",
+    "saveable_class",
+    "test_IO",
+    "test_cached_property",
+    "test_decorators",
+    "test_local_cache",
+    "test_saveable_class",
+    "test_with_float_list",
+    "test_with_floats",
+    "test_with_heterogenous_list",
+    "test_with_int_list",
+    "test_with_ints",
+    "test_with_str_list",
+    "tests",
+    "utils",
+]