Merge pull request #72 from legend-exp/dev

Show deprecation warnings in (relevant) docstrings

.pre-commit-config.yaml

@@ -51,7 +51,6 @@ repos:
     rev: "v2.2.6"
     hooks:
       - id: codespell
-        args: ["-L", "nd,unparseable,compiletime"]
 
   - repo: https://github.com/shellcheck-py/shellcheck-py
     rev: "v0.9.0.6"

pyproject.toml

@@ -144,7 +144,6 @@ isort.required-imports = ["from __future__ import annotations"]
 "tests/**" = ["T20"]
 "noxfile.py" = ["T20"]
 
-
 [tool.pylint]
 py-version = "3.8"
 ignore-paths = [".*/_version.py"]
@@ -157,3 +156,14 @@ messages_control.disable = [
   "missing-module-docstring",
   "wrong-import-position",
 ]
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+addopts = ["-ra", "--showlocals", "--strict-markers", "--strict-config"]
+xfail_strict = true
+filterwarnings = ["error", 'ignore:\nPyarrow:DeprecationWarning']
+log_cli_level = "info"
+testpaths = "tests"
+
+[tool.codespell]
+ignore-words-list = "nd, unparseable, compiletime"

src/lgdo/lh5_store.py

@@ -1,3 +1,7 @@
+"""
+.. warning::
+    This subpackage is deprecated, use :mod:`lgdo.lh5`.
+"""
 from __future__ import annotations
 
 import sys
@@ -29,6 +33,11 @@
 
 
 class LH5Iterator(lh5.LH5Iterator):
+    """
+    .. warning::
+        This class is deprecated, use :class:`lgdo.lh5.iterator.LH5Iterator`.
+    """
+
     def __init__(
         self,
         lh5_files: str | list[str],
@@ -70,6 +79,10 @@ def write_object(
         write_start: int = 0,
         **h5py_kwargs,
     ) -> None:
+        """
+        .. warning::
+            This method is deprecated, use :meth:`lgdo.lh5.iterator.LH5Iterator.write`.
+        """
         warn(
             "lgdo.lh5_store has moved to a subfolder lgdo.lh5 containing LH5Iterator. "
             "The object you are calling this function from uses the old LH5Iterator class."
@@ -102,6 +115,10 @@ def read_object(
         obj_buf_start: int = 0,
         decompress: bool = True,
     ) -> tuple[LGDO, int]:
+        """
+        .. warning::
+            This method is deprecated, use :meth:`lgdo.lh5.iterator.LH5Iterator.read`.
+        """
         warn(
             "lgdo.lh5_store has moved to a subfolder lgdo.lh5 containing LH5Iterator. "
             "The object you are calling this function from uses the old LH5Iterator class."
@@ -124,6 +141,11 @@ def read_object(
 
 
 class LH5Store(lh5.LH5Store):
+    """
+    .. warning::
+        This class is deprecated, use :class:`lgdo.lh5.iterator.LH5Store`.
+    """
+
     def __init__(self, base_path: str = "", keep_open: bool = False):
         warn(
             "lgdo.lh5_store has moved to a subfolder lgdo.lh5 containing LH5Store. "
@@ -140,6 +162,10 @@ def read_object(
         lh5_file: str | h5py.File | list[str | h5py.File],
         **kwargs,
     ) -> tuple[LGDO, int]:
+        """
+        .. warning::
+            This method is deprecated, use :meth:`lgdo.lh5.store.LH5Store.read`.
+        """
         warn(
             "LH5Store.read_object() has been renamed to LH5Store.read(), "
             "Please update your code."
@@ -156,6 +182,10 @@ def write_object(
         lh5_file: str | h5py.File,
         **kwargs,
     ) -> tuple[LGDO, int]:
+        """
+        .. warning::
+            This method is deprecated, use :meth:`lgdo.lh5.store.LH5Store.write`.
+        """
         warn(
             "LH5Store.write_object() has been renamed to LH5Store.write(), "
             "Please update your code."
@@ -172,6 +202,11 @@ def load_dfs(
     lh5_group: str = "",
     idx_list: list[np.ndarray | list | tuple] | None = None,
 ) -> pd.DataFrame:
+    """
+    .. warning::
+        This function is deprecated, use :meth:`lgdo.types.lgdo.LGDO.view_as` to
+        view LGDO data as a Pandas data structure.
+    """
     warn(
         "lgdo.lh5_store has moved to a subfolder lgdo.lh5. "
         "Please replace 'from lgdo.lh5_store import load_dfs' with 'from lgdo.lh5 import load_dfs'. "
@@ -188,6 +223,11 @@ def load_nda(
     lh5_group: str = "",
     idx_list: list[np.ndarray | list | tuple] | None = None,
 ) -> dict[str, np.ndarray]:
+    """
+    .. warning::
+        This function is deprecated, use :meth:`lgdo.types.lgdo.LGDO.view_as` to
+        view LGDO data as a NumPy data structure.
+    """
     warn(
         "lgdo.lh5_store has moved to a subfolder lgdo.lh5. "
         "Please replace 'from lgdo.lh5_store import load_nda' with 'from lgdo.lh5 import load_nda'. "
@@ -199,6 +239,10 @@ def load_nda(
 
 
 def ls(lh5_file: str | h5py.Group, lh5_group: str = "") -> list[str]:
+    """
+    .. warning::
+        This function is deprecated, import :func:`lgdo.lh5.tools.ls`.
+    """
     warn(
         "lgdo.lh5_store has moved to a subfolder lgdo.lh5. "
         "Please replace 'from lgdo.lh5_store import ls' with 'from lgdo.lh5 import ls'. "
@@ -216,6 +260,10 @@ def show(
     indent: str = "",
     header: bool = True,
 ) -> None:
+    """
+    .. warning::
+        This function is deprecated, import :func:`lgdo.lh5.tools.show`.
+    """
     warn(
         "lgdo.lh5_store has moved to a subfolder lgdo.lh5. "
         "Please replace 'from lgdo.lh5_store import show' with 'from lgdo.lh5 import show'. "

src/lgdo/types/table.py

@@ -199,6 +199,11 @@ def get_dataframe(
     ) -> pd.DataFrame:
         """Get a :class:`pandas.DataFrame` from the data in the table.
 
+        Warning
+        -------
+        This method is deprecated. Use :meth:`.view_as` to view the table as a
+        Pandas dataframe.
+
         Notes
         -----
         The requested data must be array-like, with the ``nda`` attribute.