cerfacs-globc · bzah · Sep 2, 2022 · Jun 17, 2022 · Jun 17, 2022 · Jun 30, 2022
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -2,6 +2,11 @@ default_language_version:
     python: python3
 
 repos:
+-   repo: https://github.com/MarcoGorelli/absolufy-imports
+    rev: v0.3.1
+    hooks:
+    -   id: absolufy-imports
+        name: absolufy-imports
 -   repo: https://github.com/asottile/pyupgrade
     rev: v2.37.3
     hooks:

diff --git a/README.rst b/README.rst
@@ -63,7 +63,7 @@ For a detailed description of each ECA&D index, please visit: https://www.ecad.e
 ..
   Pytest Coverage Comment:Begin
 
-.. |coverage| image:: https://img.shields.io/badge/Coverage-93%25-brightgreen.svg
+.. |coverage| image:: https://img.shields.io/badge/Coverage-92%25-brightgreen.svg
         :target: https://github.com/cerfacs-globc/icclim/blob/master/README.rst#code-coverage
         :alt: Code coverage
 

diff --git a/doc/source/references/custom_indices.rst b/doc/source/references/custom_indices.rst
@@ -33,31 +33,31 @@ In icclim documentation we usually call them custom indices or user indices.
 ~~~~~~~~~~~~~~~~~~~~~~~~~
 ``user_index`` is a dictionary with possible keys:
 
-+--------------------------+-------------------------------------------+--------------------------------------------------------------------------------------+
-|Key                       |Type of value                              |Description                                                                           |
-+==========================+===========================================+======================================================================================+
++------------------------+-------------------------------------------+--------------------------------------------------------------------------------------+
+|Key                     |Type of value                              |Description                                                                           |
++========================+===========================================+======================================================================================+
 |index_name              |*str*                                      |Name of custom index.                                                                 |
-+--------------------------+-------------------------------------------+--------------------------------------------------------------------------------------+
++------------------------+-------------------------------------------+--------------------------------------------------------------------------------------+
 |calc_operation          |*str*                                      |Type of calculation. See below for more details.                                      |
-+--------------------------+-------------------------------------------+--------------------------------------------------------------------------------------+
-|logical_operation       |*str*                                      |gt, lt, get, let or e                                                       |
-+--------------------------+-------------------------------------------+--------------------------------------------------------------------------------------+
++------------------------+-------------------------------------------+--------------------------------------------------------------------------------------+
+|logical_operation       |*str*                                      |gt, lt, get, let or e                                                                 |
++------------------------+-------------------------------------------+--------------------------------------------------------------------------------------+
 |thresh                  |*float* or *str*                           |In case of percentile-based index, must be string which starts with "p" (e.g. "p90"). |
-+--------------------------+-------------------------------------------+--------------------------------------------------------------------------------------+
-|link_logical_operations |*str*                                      |and or or                                                                         |
-+--------------------------+-------------------------------------------+--------------------------------------------------------------------------------------+
-|extreme_mode            |*str*                                      |min or max for computing min or max of running mean/sum.                          |
-+--------------------------+-------------------------------------------+--------------------------------------------------------------------------------------+
++------------------------+-------------------------------------------+--------------------------------------------------------------------------------------+
+|link_logical_operations |*str*                                      |and or or                                                                             |
++------------------------+-------------------------------------------+--------------------------------------------------------------------------------------+
+|extreme_mode            |*str*                                      |min or max for computing min or max of running mean/sum.                              |
++------------------------+-------------------------------------------+--------------------------------------------------------------------------------------+
 |window_width            |*int*                                      |Used for computing running mean/sum.                                                  |
-+--------------------------+-------------------------------------------+--------------------------------------------------------------------------------------+
++------------------------+-------------------------------------------+--------------------------------------------------------------------------------------+
 |coef                    |*float*                                    |Constant for multiplying input data array.                                            |
-+--------------------------+-------------------------------------------+--------------------------------------------------------------------------------------+
++------------------------+-------------------------------------------+--------------------------------------------------------------------------------------+
 |date_event              |*bool*                                     |To keep or not the date of event. See below for more details.                         |
-+--------------------------+-------------------------------------------+--------------------------------------------------------------------------------------+
++------------------------+-------------------------------------------+--------------------------------------------------------------------------------------+
 |var_type                |*str*                                      |"t" or "p". See below for more details.                                               |
-+--------------------------+-------------------------------------------+--------------------------------------------------------------------------------------+
++------------------------+-------------------------------------------+--------------------------------------------------------------------------------------+
 |ref_time_range          |[*datetime.datetime*, *datetime.datetime*] |Time range of reference (baseline) period for computing anomalies.                    |
-+--------------------------+-------------------------------------------+--------------------------------------------------------------------------------------+
++------------------------+-------------------------------------------+--------------------------------------------------------------------------------------+
 
 Additional information about ``user_index`` keys are given below.
 
@@ -66,7 +66,7 @@ calc_operation key
 ++++++++++++++++++
 
 =======================================	===========================================================================
-value									description
+Value									   Description
 =======================================	===========================================================================
 ``max``								    	maximum
 ``min``								    	minimum

diff --git a/doc/source/references/icclim_index_api.rst b/doc/source/references/icclim_index_api.rst
@@ -351,6 +351,8 @@ in *icclim* as ``hyndman_fan`` interpolation, also known as type 8.
 Percentile-based indices (TX10p, TX90p, TN10p, TN90p, TG10p, TG90p, R75p, R95p and R99p) could be returned as number of days (default)
 or as percentage of days (``out_unit`` = "%").
 
+.. _custom_indices_old:
+
 Custom indices
 --------------
 

diff --git a/doc/source/references/release_notes.rst b/doc/source/references/release_notes.rst
@@ -1,6 +1,25 @@
 Release history
 ===============
 
+6.0 (unreleased)
+----------------
+* [enh] Add generic indices
+* [enh] Make in_files.var.threshold and threshold parameters work with string values (a value with a unit or a percentile stamp)
+* [maint] **BREAKING CHANGE:** ECAD indices are no longer configurable! Use a generic index instead.
+* [fix] **BREAKING CHANGE:** ECAD indices CW, CD, WW, WD were computing the precipitation percentiles on day of year values where it should have been percentiles of the whole period (excluding dry days). This has been fixed.
+* [maint] icclim no longer carries a version of the clix-meta yml file. Previously it was used to generate the doc string and a few metadata of ECAD indices. It's no longer needed as we have put these metadata within StandardIndex declaration.
+* [maint] **BREAKING CHANGE:** Removed the `clipped_season` option from `slice_mode`. With generic indices, `season` should work with every indices.
+In particular, spell based indices (e.g. wsdi) are mapped to `max_consecutive_occurrence` generic indicator, which computes the spell length before doing the resampling operation.
+So a spell that start and end outside the output frequency interval is properly accounted for its whole duration.
+That's for example the case of `slice_mode="month"`, but with a spell that start in january and end in March, the whole spell length would be available in january results.
+* [maint] **BREAKING CHANGE:** User index `max_nb_consecutive_events` is also mapped to `max_consecutive_occurrence`, consequently spells are also counted for their whole duration.
+* [enh] Make it possible to pass a simple dictionary in `in_files`, merging together basic `in_files` and `var_name` features.
+It looks like `in_files={"tasmax": "tasmax.nc", "tasmin": "tasmin.zarr"}`
+* [enh] Add `min_spell_length` parameter to index API in order to control the minimum duration of spells in `sum_of_spell_lengths`.
+* [enh] Add `rolling_window_width` parameter to index API in order to control the width of the rolling window in `max|min_of_rolling_sum|average`.
+* [enh] Add `doy_window_width` parameter to index API in order to control the width of aggregation windows when computing doy percentiles.
+* [maint] Deprecate `window_width` parameter. When filled, it is mapped to It is still mapped `doy_window_width`.
+
 5.4.0
 -----
 * [fix] When giving input as a list of netcdf files, the coordinate values are now merged using the `override` strategy, thus the first file with a given dimension define this dimension for all the files.

diff --git a/icclim/__init__.py b/icclim/__init__.py
@@ -1,8 +1,7 @@
 # keep imports below to expose api in `icclim` namespace
+from icclim._generated_api import *  # noqa
+from icclim.main import index, indice, indices  # noqa
 from icclim.models.constants import ICCLIM_VERSION
-
-from ._generated_api import *  # noqa
-from .main import index, indice, indices  # noqa
-from .pre_processing.rechunk import create_optimized_zarr_store  # noqa
+from icclim.pre_processing.rechunk import create_optimized_zarr_store  # noqa
 
 __version__ = ICCLIM_VERSION