Merge branch 'develop' of github.com:shom-fr/xoa into develop

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,22 @@
+### Description
+
+<!-- Explain the problem, what you did, what went wrong and what you expected to happen -->
+
+
+### Code to reproduce
+
+<!-- Include a maximum of details -->
+
+```python
+
+```
+
+### Versions
+
+<!-- Paste below the output of the commandline script `xoa info versions` -->
+
+```
+
+
+```
+

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,10 @@
+# Description
+
+
+
+# Check list
+
+- [ ] Closes #xxxx
+- [ ] Tests added
+- [ ] User visible changes (including notable bug fixes) are documented in `CHANGES.rst`
+- [ ] New modules are listed in `api.rst`

.github/dependabot.yml

@@ -0,0 +1,12 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"
+    open-pull-requests-limit: 10

.github/workflows/python-package-conda.yml

@@ -1,4 +1,4 @@
-name: Python Package using Conda
+name: CI
 
 on: [push]
 
@@ -9,9 +9,9 @@ jobs:
       max-parallel: 5
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python 3.8
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: 3.8
     - name: Add conda to system path

.github/workflows/python-publish.yml

@@ -13,9 +13,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: '3.x'
     - name: Install dependencies

.readthedocs.yml

@@ -5,17 +5,17 @@ version: 2
 sphinx:
   fail_on_warning: false
 
-# Optionally set the version of Python and requirements required to build your docs
+# Install current library
 python:
-  version: 3.7
-  system_packages: true
   install:
     - method: pip
       path: .
 
 # Build
 build:
-  image: stable
+  os: "ubuntu-22.04"
+  tools:
+      python: "mambaforge-4.10"
 
 # Conda
 conda:

CHANGES.rst

@@ -1,72 +1,83 @@
 What's new
 ##########
 
-Ongoing developments
-====================
+
+0.7.1 (2023-07-21)
+==================
 
 New features
 ------------
+- Add support for not creating multi-indexes in :func:`xoa.coords.geo_stack`.
+
+Bug fixes
+---------
+- Fix :func:`xoa.geo.get_distances` that was not able to handle multi-indexes from :func:`xoa.coords.geo_stack`.
+- Fix doc generation [:pull:`83`].
+- Fix :func:`xoa.sigma.get_cs` to keep it compatible with pure numpy arrays
+
+
+Documentation
+-------------
+- Add a link to the github repository.
+
+
+0.7.0 (2023-07-17)
+==================
+
+New features
+------------
+- Add issue and pull request templates.
+- Add the :func:`xoa.filter.smooth` function [:pull:`76`].
+- Improved the default `sig` and `std` parameter values for filter windows that accept them [:pull:`76`].
+- Add the :func:`xoa.plot.plot_minimap` and :func:`xoa.plot.plot_double_minimap` functions to display the geographic situation of a set of coordinates [:pull:`73`].
+- Add support for the `min_extent` keyword to :func:`xoa.geo.get_extent` [:pull:`73`]
+- Add dask support to :mod:`xoa.sigma` sigma to depth converters [:pull:`72`].
 - Add the :mod:`xoa.num` module that contains low level numeric utilities.
-- Add the :func:`xoa.thermdyn.mixed_layer_depth` fonction to compute
-  the mixed layer depth with three different methods [:pull:`67`].
-- Add the :func:`xoa.thermdyn.is_temp` and :func:`xoa.thermdyn.is_dens` functions
-  to if an array of temperature or density type [:pull:`67`].
-- Add `kernel_kwargs` keyword to :func:`xoa.filter.convolve` to better control
-  the kernel generation by :func:`xoa.filter.generate_kernel` [:pull:`64`].
-- Add inference of parameters for some window functions, like the gaussian
-  shape, in :func:`xoa.filter.get_window_func` [:pull:`64`].
-- Add :func:`xoa.regrid.isoslice` based on :func:`xoa.interp.isoslice` core function
-  [:pull:`63`].
+- Add the :func:`xoa.thermdyn.mixed_layer_depth` function to compute the mixed layer depth with three different methods [:pull:`67`, :pull:`75`].
+- Add the :func:`xoa.thermdyn.is_temp`, :func:`xoa.thermdyn.is_sal` and :func:`xoa.thermdyn.is_dens` functions to infer if an array of temperature, salinity or density type, and added the related :func:`xoa.thermdyn.get_temp`, :func:`xoa.thermdyn.get_sal` and :func:`xoa.thermdyn.get_dens` function to search in datasets[:pull:`67`, :pull:`79`].
+- Add `kernel_kwargs` keyword to :func:`xoa.filter.convolve` to better control the kernel generation by :func:`xoa.filter.generate_kernel` [:pull:`64`].
+- Add inference of parameters for some window functions, like the gaussian shape, in :func:`xoa.filter.get_window_func` [:pull:`64`].
+- Add :func:`xoa.regrid.isoslice` based on :func:`xoa.interp.isoslice` core function [:pull:`63`].
 
 Breaking changes
 ----------------
-- func:`~xoa.filter.get_window_func` accepts now only one positional argument
-  and all other arguments must be named.
+- :func:`~xoa.filter.get_window_func` now accepts only one positional argument and all other arguments must be named.
 
 Bug fixes
 ---------
+- Fix :func:`xoa.cfgm.is_boolstr` which now supports the new :mod:`configobj`.
 - Fix broadcasting :mod:`xoa.interp` 1d interpolation routines [:issue:`69`].
 - Fix :func:`xoa.sigma.get_sigma_terms` so that it works in case of multiple levels coordinates [:pull:`60`].
 - Fix :func:`xoa.grid.to_rect` that now infers coordinates and can emit a warning or raise an error.
 
 Documentation
 -------------
-- Add an example of `xoa.thermdyn.mixed_layer_depth` to
-  :ref:`sphx_glr_examples_plot_croco_section.py` example [:pull:`67`].
+- Add an example of `xoa.plot.plot_double_minimap` to :ref:`sphx_glr_examples_plot_mercator_argo.py` and :ref:`sphx_glr_examples_plot_hycom_gdp.py` examples [:pull:`73`].
+- Add an example of `xoa.thermdyn.mixed_layer_depth` to :ref:`sphx_glr_examples_plot_croco_section.py` example [:pull:`67`].
 
 
 0.6.1 (2022-02-24)
 ==================
 
 New features
 ------------
-- Add a warning to :func:`xoa.open_data_sample` that is emitted when the request edfile
-  is not an internal data sample [:pull:`47`].
-- Add the :func:`xoa.plot.add_shadow`, :func:`xoa.plot.add_glow` and
-  :func:`xoa.plot.add_lightshading` function to add path effects to plots [:pull:`44`].
+- Add a warning to :func:`xoa.open_data_sample` that is emitted when the requested file is not an internal data sample [:pull:`47`].
+- Add the :func:`xoa.plot.add_shadow`, :func:`xoa.plot.add_glow` and :func:`xoa.plot.add_lightshading` function to add path effects to plots [:pull:`44`].
 - Add the :func:`xoa.plot.plot_ts` function to make T-S diagrams [:pull:`43`].
-- Add the :func:`xoa.filter.demerliac` function to apply a Dermerliac filter
-  to time serie [:pull:`41`].
-- Add support for fine tuning masking in :func:`xoa.filter.convolve` through the `na_thres`
-  parameter [:pull:`41`].
-- Add the :func:`xoa.geo.cdist` and :func:`xoa.geo.pdist` functions to compute
-  haversine distances respectively between two dataset and with a dataset  [:pull:`40`].
-- Add the :func:`xoa.coords.geo_stack` function to stack longitudes and latitudes
-  into another dimension, in a dataset or data array  [:pull:`40`].
-- Add the :func:`xoa.filter.decimate` function to crudely undersample a geographic
-  dataset or data array with a radius of proximity [:pull:`40`].
-- Add the :func:`xoa.geo.get_distances` to compute the Haversine distances between
-  locations inside a single dataset or between txo datasets [:pull:`40`].
+- Add the :func:`xoa.filter.demerliac` function to apply a Dermerliac filter to time serie [:pull:`41`].
+- Add support for fine tuning masking in :func:`xoa.filter.convolve` through the `na_thres` parameter [:pull:`41`].
+- Add the :func:`xoa.geo.cdist` and :func:`xoa.geo.pdist` functions to compute haversine distances respectively between two dataset and with a dataset  [:pull:`40`].
+- Add the :func:`xoa.coords.geo_stack` function to stack longitudes and latitudes into another dimension, in a dataset or data array  [:pull:`40`].
+- Add the :func:`xoa.filter.decimate` function to crudely undersample a geographic dataset or data array with a radius of proximity [:pull:`40`].
+- Add the :func:`xoa.geo.get_distances` to compute the Haversine distances between locations inside a single dataset or between txo datasets [:pull:`40`].
 - Add the :func:`xoa.krig.empirical_variogram` function to estimate variogram parameters.
 - Add the :class:`xoa.krig.VariogramModel` to manage a variogram model [:pull:`40`].
 - Add the :class:`xoa.krig.Kriger` and :func:`xoa.krig.krig` to perform kriging [:pull:`40`].
-- Add the `exclude` option to data var and coordinate specifications of
-  :class:`xoa.cf.CFSpecs` instances [:pull:`38`].
+- Add the `exclude` option to data var and coordinate specifications of :class:`xoa.cf.CFSpecs` instances [:pull:`38`].
 
 Breaking changes
 ----------------
-- A single Nan now contaminates the data over the kernel emprise in :func:`xoa.filter.convolve`
-  since `na_thres` is set to zero by default  [:pull:`40`].
+- A single Nan now contaminates the data over the kernel emprise in :func:`xoa.filter.convolve` since `na_thres` is set to zero by default  [:pull:`40`].
 - xoa now requires the :mod:`gsw` package.
 
 Bug fixes
@@ -104,33 +115,23 @@ Bug fixes
 
 New features
 ------------
-- Add the `hlocs` argument to :func:`xoa.sigma.get_sigma_terms`
-  and :func:`xoa.sigma.decode_cf_sigma` to decode at several horizontal
-  staggered grid locations  [:pull:`34`].
-- Add the `edges` argument to :func:`xoa.regrid.regrid1d` to manually specify
-  the edges that are used by the "cellave" regridding method  [:pull:`34`].
-- Add back the `loc` argument to the formatting methods of :mod:`xoa.cf`
-   [:pull:`34`].
-- Add dimension checking and support for dask arrays in :mod:`xoa.sigma`
-   [:pull:`34`].
-- Expose a few options of :meth:`xoa.cfgm.ConfigManager` to the
-  :func:`xoa.cfgm.cfgargparse` function.
-- Add the :confval:`cfgm_cfg_file` sphinx configuration option
-  to save the default configuration of a :meth:`xoa.cfgm.ConfigManager`.
+- Add the `hlocs` argument to :func:`xoa.sigma.get_sigma_terms` and :func:`xoa.sigma.decode_cf_sigma` to decode at several horizontal staggered grid locations  [:pull:`34`].
+- Add the `edges` argument to :func:`xoa.regrid.regrid1d` to manually specify the edges that are used by the "cellave" regridding method  [:pull:`34`].
+- Add back the `loc` argument to the formatting methods of :mod:`xoa.cf` [:pull:`34`].
+- Add dimension checking and support for dask arrays in :mod:`xoa.sigma` [:pull:`34`].
+- Expose a few options of :meth:`xoa.cfgm.ConfigManager` to the :func:`xoa.cfgm.cfgargparse` function.
+- Add the :confval:`cfgm_cfg_file` sphinx configuration option to save the default configuration of a :meth:`xoa.cfgm.ConfigManager`.
 
 Bug fixes
 ---------
 - Fix :func:`xoa.regrid.regrid1d` with "cellave" method  [:pull:`34`].
-- Fix :meth:`xoa.cf.CFSpecs.get_location_mapping` for coordinates that have
-  no axis attribute specifications  [:pull:`34`].
-- Fix :func:`xoa.grid.dz2depth` that was not working properly with 4D+ arrays
-  [:pull:`34`].
+- Fix :meth:`xoa.cf.CFSpecs.get_location_mapping` for coordinates that have no axis attribute specifications  [:pull:`34`].
+- Fix :func:`xoa.grid.dz2depth` that was not working properly with 4D+ arrays [:pull:`34`].
 
 
 Breaking changes
 ----------------
-- The `loc` argument of :func:`xoa.sigma.get_sigma_terms` is renamed `vloc`
-   [:pull:`34`].
+- The `loc` argument of :func:`xoa.sigma.get_sigma_terms` is renamed `vloc` [:pull:`34`].
 
 
 0.4.0 (2021-09-02)
@@ -139,63 +140,47 @@ Breaking changes
 New features
 ------------
 - :meth:`xoa.cf.CFSpecs.decode` better supports staggered grids.
-- :meth:`xoa.cf.CFSpecs.search_dim` supports generic names in addition
-  to dimension types as second argument.
-- Add the :meth:`xoa.cf.CFSpecs.match_dim` method to check if a given
-  dimension name is known.
-- Add the :meth:`~xoa.cf.CFSpecs.reloc` and :meth:`~xoa.cf.CFSpecs.to_loc` methods
-  to :class:`xoa.cf.CFSpecs` for quickly changing the staggered grid indicators
-  in names.
-- Add the :meth:`xoa.cf.SGLocator.add_loc` method to quickly change the location
-  markers in a data array.
+- :meth:`xoa.cf.CFSpecs.search_dim` supports generic names in addition to dimension types as second argument.
+- Add the :meth:`xoa.cf.CFSpecs.match_dim` method to check if a given dimension name is known.
+- Add the :meth:`~xoa.cf.CFSpecs.reloc` and :meth:`~xoa.cf.CFSpecs.to_loc` methods to :class:`xoa.cf.CFSpecs` for quickly changing the staggered grid indicators in names.
+- Add the :meth:`xoa.cf.SGLocator.add_loc` method to quickly change the location markers in a data array.
 
 Breaking changes
 ----------------
 - :func:`xoa.coords.get_dims` is renamed to :func:`xoa.coords.get_cf_dims`.
-- The `name` argument of :class:`xoa.cf.CFSpecs` methods is renamed to `cf_name`,
-  and the `dim_type(s)` argument is renamed to `cf_arg(s)`.
-- :meth:`xoa.cf.SGLocator.get_location` is renamed to
-  :meth:`~xoa.cf.SGLocator.get_loc_from_da` and the :meth:`~xoa.cf.SGLocator.get_loc` is added.
+- The `name` argument of :class:`xoa.cf.CFSpecs` methods is renamed to `cf_name`, and the `dim_type(s)` argument is renamed to `cf_arg(s)`.
+- :meth:`xoa.cf.SGLocator.get_location` is renamed to :meth:`~xoa.cf.SGLocator.get_loc_from_da` and the :meth:`~xoa.cf.SGLocator.get_loc` is added.
 
 Bug fixes
 ---------
 - Fix the output formatting of :func:`xoa.grid.dz2depth`.
 
 Documentation
 -------------
-- The :ref:`uses.cf` section and :ref:`sphx_glr_examples_plot_hycom_gdp.py` example
-  are adapted to reflect changes.
+- The :ref:`uses.cf` section and :ref:`sphx_glr_examples_plot_hycom_gdp.py` example are adapted to reflect changes.
 
 
 v0.3.1 (2021-05-21)
 ===================
 
 New features
 ------------
-
-- Add an `autolim` keyword to :func:`xoa.plot.plot_flow` to speedup
-  the processing with cartopy maps.
+- Add an `autolim` keyword to :func:`xoa.plot.plot_flow` to speedup the processing with cartopy maps.
 
 Breaking changes
 ----------------
-
-- Rename the `cf` and `sigma` keyword of :func:`xoa.register_accessors`
-  respectively to `xcf` and `decode_sigma` to match the default
-  name of accessors.
+- Rename the `cf` and `sigma` keyword of :func:`xoa.register_accessors` respectively to `xcf` and `decode_sigma` to match the default name of accessors.
 - Rename the `sigma` accessor to `decode_sigma`.
 
 Bug fixes
 ---------
-
 - Fix the access to the xoa executable on windows.
 - Fix the minimal version for xarray [:pull:`23`].
 
 Documentation
 -------------
-
 - Add a "How to start" section.
-- Accessors are now documented separately with `sphinx-autosummary-accessors`
-  [:pull:`20`].
+- Accessors are now documented separately with `sphinx-autosummary-accessors` [:pull:`20`].
 - The Hycom-GDP example now uses :func:`xoa.plot.plot_flow`.
 
 
@@ -204,21 +189,15 @@ v0.3.0 (2021-05-12)
 
 New features
 ------------
-
 - Add the :func:`xoa.plot.plot_flow` function [:pull:`9`].
-- Improve :func:`xoa.coords.get_depth` so that it can compute
-  depth from sigma coordinates or layer thinknesses [:pull:`8`].
+- Improve :func:`xoa.coords.get_depth` so that it can compute depth from sigma coordinates or layer thinknesses [:pull:`8`].
 - Add the :func:`xoa.dyn.flow2d` function [:pull:`7`].
 - Add the :func:`xoa.regrid.extrap1d` function.
-- Add the :func:`xoa.filter.erode_coast` function which is specialized version
-  of the :func:`xoa.filter.erode_mask` for horizontal data.
-- Add the :func:`xoa.coords.get_xdim`, :func:`~xoa.coords.get_ydim`,
-  :func:`~xoa.coords.get_zdim`, :func:`~xoa.coords.get_tdim` and
-  :func:`~xoa.coords.get_fdim` for quickly finding standard dimensions.
+- Add the :func:`xoa.filter.erode_coast` function which is specialized version of the :func:`xoa.filter.erode_mask` for horizontal data.
+- Add the :func:`xoa.coords.get_xdim`, :func:`~xoa.coords.get_ydim`, :func:`~xoa.coords.get_zdim`, :func:`~xoa.coords.get_tdim` and :func:`~xoa.coords.get_fdim` for quickly finding standard dimensions.
 
 Bug fixes
 ---------
-
 - Fix u and v CF config [:pull:`6`]