Merge branch 'split_from_xclim' of github.com:Ouranosinc/xsdba into s…

…plit_from_xclim

AUTHORS.rst

@@ -5,12 +5,13 @@ Credits
 Development Lead
 ----------------
 
-* Trevor James Smith <smith.trevorj@ouranos.ca> `@Zeitsperre <https://github.com/Zeitsperre>`_
+* Éric Dupuis <dupuis.eric@ouranos.ca> `@coxipi <https://github.com/coxipi>`_
 
 Co-Developers
 -------------
 
-* Éric Dupuis <[email protected]> `@coxipi <https://github.com/coxipi>`_
+* Pascal Bourgault <[email protected]> `@aulemahal <https://github.com/aulemahal>`_
+* Trevor James Smith <[email protected]> `@Zeitsperre <https://github.com/Zeitsperre>`_
 
 Contributors
 ------------

CHANGELOG.rst

@@ -5,7 +5,7 @@ Changelog
 `Unreleased <https://github.com/Ouranosinc/xsdba>`_ (latest)
 ------------------------------------------------------------
 
-Contributors:
+Contributors: Éric Dupuis (:user:`coxipi`), Trevor James Smith (:user:`Zeitsperre`).
 
 Changes
 ^^^^^^^
@@ -20,7 +20,7 @@ Fixes
 `v0.1.0 <https://github.com/Ouranosinc/xsdba/tree/0.1.0>`_
 ----------------------------------------------------------
 
-Contributors: Trevor James Smith (:user:`Ouranosinc`)
+Contributors: Trevor James Smith (:user:`Zeitsperre`)
 
 Changes
 ^^^^^^^

pyproject.toml

@@ -7,9 +7,11 @@ build-backend = "flit_core.buildapi"
 [project]
 name = "xsdba"
 authors = [
+  {name = "Éric Dupuis", email = "[email protected]"},
   {name = "Trevor James Smith", email = "[email protected]"}
 ]
 maintainers = [
+  {name = "Éric Dupuis", email = "[email protected]"},
   {name = "Trevor James Smith", email = "[email protected]"}
 ]
 readme = {file = "README.rst", content-type = "text/x-rst"}
@@ -24,7 +26,6 @@ classifiers = [
   "Operating System :: OS Independent",
   "Programming Language :: Python :: 3",
   "Programming Language :: Python :: 3 :: Only",
-  "Programming Language :: Python :: 3.8",
   "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
@@ -93,7 +94,6 @@ xsdba = "xsdba.cli:app"
 
 [tool.black]
 target-version = [
-  "py38",
   "py39",
   "py310",
   "py311",
@@ -210,7 +210,7 @@ exclude = [
 
 [tool.isort]
 profile = "black"
-py_version = 38
+py_version = 39
 
 [tool.mypy]
 files = "."
@@ -273,7 +273,7 @@ usefixtures = "xdoctest_namespace"
 [tool.ruff]
 src = ["xsdba"]
 line-length = 150
-target-version = "py38"
+target-version = "py39"
 exclude = [
   ".eggs",
   ".git",

src/xsdba/__init__.py

@@ -20,7 +20,7 @@
 
 from __future__ import annotations
 
-from . import base, utils, units, detrending, processing
+from . import base, detrending, processing, units, utils
 
 # , adjustment
 # from . import adjustment, base, detrending, measures, processing, properties, utils

src/xsdba/base.py

@@ -6,26 +6,23 @@
 from __future__ import annotations
 
 import datetime as pydt
+import itertools
 from collections.abc import Sequence
 from inspect import _empty, signature
 from typing import Any, Callable, NewType, TypeVar
-from pint import Quantity
-
-
-import itertools
 
 import cftime
 import dask.array as dsk
 import jsonpickle
 import numpy as np
+import pandas as pd
 import xarray as xr
 from boltons.funcutils import wraps
-import pandas as pd 
+from pint import Quantity
 
 from xsdba.options import OPTIONS, SDBA_ENCODE_CF
 
-
-# XC: 
+# XC:
 #: Type annotation for strings representing full dates (YYYY-MM-DD), may include time.
 DateStr = NewType("DateStr", str)
 
@@ -35,6 +32,7 @@
 #: Type annotation for thresholds and other not-exactly-a-variable quantities
 Quantified = TypeVar("Quantified", xr.DataArray, str, Quantity)
 
+
 # ## Base class for the sdba module
 class Parametrizable(dict):
     """Helper base class resembling a dictionary.
@@ -117,7 +115,8 @@ def set_dataset(self, ds: xr.Dataset) -> None:
         self.ds.attrs[self._attribute] = jsonpickle.encode(self)
 
 
-# XC 
+# XC
+
 
 def copy_all_attrs(ds: xr.Dataset | xr.DataArray, ref: xr.Dataset | xr.DataArray):
     """Copy all attributes of ds to ref, including attributes of shared coordinates, and variables in the case of Datasets."""
@@ -128,6 +127,7 @@ def copy_all_attrs(ds: xr.Dataset | xr.DataArray, ref: xr.Dataset | xr.DataArray
         if name in others:
             var.attrs.update(ref[name].attrs)
 
+
 # XC put here to avoid circular import
 def uses_dask(*das: xr.DataArray | xr.Dataset) -> bool:
     r"""Evaluate whether dask is installed and array is loaded as a dask array.
@@ -153,7 +153,8 @@ def uses_dask(*das: xr.DataArray | xr.Dataset) -> bool:
         return True
     return False
 
-# XC 
+
+# XC
 # Maximum day of year in each calendar.
 max_doy = {
     "standard": 366,
@@ -167,7 +168,8 @@ def uses_dask(*das: xr.DataArray | xr.Dataset) -> bool:
     "360_day": 360,
 }
 
-# XC 
+
+# XC
 def parse_offset(freq: str) -> tuple[int, str, bool, str | None]:
     """Parse an offset string.
 
@@ -208,6 +210,7 @@ def parse_offset(freq: str) -> tuple[int, str, bool, str | None]:
         anchor = None
     return mult, base, start, anchor
 
+
 # XC put here to avoid circular import
 def get_calendar(obj: Any, dim: str = "time") -> str:
     """Return the calendar of an object.
@@ -251,7 +254,7 @@ def get_calendar(obj: Any, dim: str = "time") -> str:
     raise ValueError(f"Calendar could not be inferred from object of type {type(obj)}.")
 
 
-# XC 
+# XC
 def gen_call_string(funcname: str, *args, **kwargs) -> str:
     r"""Generate a signature string for use in the history attribute.
 
@@ -294,7 +297,6 @@ def gen_call_string(funcname: str, *args, **kwargs) -> str:
     return f"{funcname}({', '.join(elements)})"
 
 
-
 class Grouper(Parametrizable):
     """Grouper inherited class for parameterizable classes."""
 

src/xsdba/detrending.py

@@ -1,4 +1,4 @@
-"""
+"""# noqa: SS01
 Detrending Objects Utilities
 ============================
 """

src/xsdba/formatting.py

@@ -1,14 +1,17 @@
 """
-Formatting Utilities 
+Formatting Utilities
 ===================================
 """
+
 from __future__ import annotations
 
 import datetime as dt
+import itertools
+from inspect import signature
+
 import xarray as xr
 from boltons.funcutils import wraps
-from inspect import signature
-import itertools
+
 
 # XC
 def merge_attributes(
@@ -63,6 +66,7 @@ def merge_attributes(
         return merged_attr[: -len(new_line)]  # Remove the last added new_line
     return merged_attr
 
+
 # XC
 def update_history(
     hist_str: str,
@@ -115,7 +119,8 @@ def update_history(
     )
     return merged_history
 
-# XC 
+
+# XC
 def update_xsdba_history(func: Callable):
     """Decorator that auto-generates and fills the history attribute.
 
@@ -199,4 +204,4 @@ def gen_call_string(funcname: str, *args, **kwargs) -> str:
 
         elements.append(rep)
 
-    return f"{funcname}({', '.join(elements)})"
+    return f"{funcname}({', '.join(elements)})"

src/xsdba/processing.py

@@ -13,15 +13,17 @@
 import numpy as np
 import xarray as xr
 from xarray.core.utils import get_temp_dimname
+
 from xsdba.base import get_calendar, max_doy, parse_offset, uses_dask
 from xsdba.formatting import update_xsdba_history
-# from xclim.core.units import convert_units_to, infer_context, units
 
 from ._processing import _adapt_freq, _normalize, _reordering
 from .base import Grouper
 from .nbutils import _escore
+from .units import check_units, convert_units_to, harmonize_units
 from .utils import ADDITIVE, copy_all_attrs
-from .units import check_units, harmonize_units, convert_units_to
+
+# from xclim.core.units import convert_units_to, infer_context, units
 
 
 __all__ = [
@@ -227,9 +229,7 @@ def jitter(
             jitter_dist = np.random.uniform(
                 low=jitter_min, high=jitter_lower, size=x.shape
             )
-        out = out.where(
-            ~((x < jitter_lower) & notnull), jitter_dist.astype(x.dtype)
-        )
+        out = out.where(~((x < jitter_lower) & notnull), jitter_dist.astype(x.dtype))
     if upper is not None:
         if maximum is None:
             raise ValueError("If 'upper' is given, so must 'maximum'.")
@@ -243,16 +243,14 @@ def jitter(
             jitter_dist = np.random.uniform(
                 low=jitter_upper, high=jitter_max, size=x.shape
             )
-        out = out.where(
-            ~((x >= jitter_upper) & notnull), jitter_dist.astype(x.dtype)
-        )
+        out = out.where(~((x >= jitter_upper) & notnull), jitter_dist.astype(x.dtype))
 
     copy_all_attrs(out, x)  # copy attrs and same units
     return out
 
 
 @update_xsdba_history
-@harmonize_units(["data","norm"])
+@harmonize_units(["data", "norm"])
 def normalize(
     data: xr.DataArray,
     norm: xr.DataArray | None = None,
@@ -577,9 +575,7 @@ def to_additive_space(
     # with units.context(infer_context(data.attrs.get("standard_name"))):
     lower_bound_array = np.array(lower_bound).astype(float)
     if upper_bound is not None:
-        upper_bound_array = np.array(upper_bound).astype(
-            float
-        )
+        upper_bound_array = np.array(upper_bound).astype(float)
 
     with xr.set_options(keep_attrs=True), np.errstate(divide="ignore"):
         if trans == "log":
@@ -698,9 +694,7 @@ def from_additive_space(
         # FIXME: convert_units_to is causing issues since it can't handle all variations of Quantified here
         lower_bound_array = np.array(lower_bound).astype(float)
         if trans == "logit":
-            upper_bound_array = np.array(upper_bound).astype(
-                float
-            )
+            upper_bound_array = np.array(upper_bound).astype(float)
     else:
         raise ValueError(
             "Parameters missing. Either all parameters are given as attributes of data, "

src/xsdba/units.py

@@ -1,4 +1,4 @@
-"""
+"""# noqa: SS01
 Units Handling Submodule
 ========================
 """
@@ -115,6 +115,7 @@ def str2pint(val: str) -> pint.Quantity:
 
 
 def extract_units(arg):
+    """Extract units from a string, DataArray, or scalar."""
     if not (isinstance(arg, (str, xr.DataArray)) or np.isscalar(arg)):
         print(arg)
         raise TypeError(f"Argument must be a str, DataArray, or scalar. Got {type(arg)}")
@@ -129,7 +130,7 @@ def extract_units(arg):
 
 
 def check_units(args_to_check):
-    """Check that units are compatible with dimensions, otherwise raise a `ValidationError`."""
+    """Decorator to check that all arguments have the same units (or no units)."""
     # if no units are present (DataArray without units attribute or float), then no check is performed
     # if units are present, then check is performed
     # in mixed cases, an error is raised

tests/conftest.py

@@ -19,8 +19,9 @@
 from filelock import FileLock
 from packaging.version import Version
 
-from xsdba.testing import TESTDATA_BRANCH, test_timelonlatseries, test_timeseries
+from xsdba.testing import TESTDATA_BRANCH
 from xsdba.testing import open_dataset as _open_dataset
+from xsdba.testing import test_timelonlatseries, test_timeseries
 
 # import xclim
 # from xclim import __version__ as __xclim_version__