Merge branch 'develop'

Author: hulecom

CHANGELOG.md

@@ -2,6 +2,11 @@
 
 All notable changes to **LENAPY** will be documented in this file.
 
+## [1.1] - 2025-12-03
+- Performance improvement for climato functions
+- Typo correction in documentation, versions and README
+- Publication describing lenapy functionalities and applications to Journal of Open Source Software (JOSS)
+
 ## [1.0] - 2025-07-15
 Introduction of the first official release of lenapy
 

CITATION.cff

@@ -0,0 +1,21 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+preferred-citation:
+  type: article
+  authors:
+  - family-names: "Lecomte"
+    given-names: "Hugo"
+    orcid: "https://orcid.org/0000-0002-7007-4748"
+  - family-names: "Fourest"
+    given-names: "Sebastien"
+    orcid: "https://orcid.org/0009-0001-3123-1026"
+  - family-names: "Blazquez"
+    given-names: "Alejandro"
+    orcid: "https://orcid.org/0000-0002-7719-7468"
+  title: "Lenapy: Enhancing xarray for multidimensional geophysical data analysis"
+  journal: "Journal of Open Source Software"
+  doi: "(submitted)"
+  volume: xx
+  issue: xx
+  start: xxxx
+  year: 2025

README.md

@@ -1,8 +1,18 @@
 # Getting started with LENAPY
 
+[![Docs](https://img.shields.io/badge/documentation-darkgreen.svg)](https://lenapy.readthedocs.io/en/latest/)
+[![conda-forge](https://img.shields.io/conda/vn/conda-forge/lenapy)](
+https://anaconda.org/conda-forge/lenapy)
+[![status](https://joss.theoj.org/papers/bee28b7acdd65939a408b1c8ce921111/status.svg)](https://joss.theoj.org/papers/bee28b7acdd65939a408b1c8ce921111)
+
+`Lenapy` is a Python library designed to facilitate the processing and analysis of geophysical and climate datasets, such as those used in oceanography, geodesy, and Earth observation in general.
+Built on top of `xarray` and compatible with `dask`, it enables scalable workflows on multidimensional datasets using community standards for data formats (NetCDF) and metadata conventions (CF).
+
+A key feature of `lenapy` is its ability to produce consistent computations of the Global Mean Sea Level components from various data sources, including satellite altimetry, GRACE/GRACE-FO, thermo-steric datasets, and climate model outputs.
+
 ## Documentation
 
-Documentation can be found [here](https://lenapy.readthedocs.io/en/latest/)
+Documentation can be found at [https://lenapy.readthedocs.io/en/latest/](https://lenapy.readthedocs.io/en/latest/).
 
 ## Installation
 
@@ -27,7 +37,7 @@ conda --version
 
 ### Step 2: Install lenapy Using Conda
 
-Once Conda is installed, you can install lenapy by following these steps:
+Once Conda is installed, you can install `lenapy` by following these steps:
 
 #### 1. Create a new Conda environment (recommended):
 ```bash
@@ -44,7 +54,7 @@ conda activate lenapy_env
 conda install -c conda-forge lenapy
 ```
 
-This installs lenapy and its dependencies from the conda-forge channel.
+This installs `lenapy` and its dependencies from the conda-forge channel.
 
 ## Use
 
@@ -54,12 +64,20 @@ In your python code, simply import the library with ::
   import lenapy
   ```
 
-You can now use all the functionnalities of lenapy by adding the right suffixe after your Dataset or DataArray ::
+You can now use all the functionalities of `lenapy` by adding the right suffix after your Dataset or DataArray ::
   ```
   import xarray as xr
   import lenapy
   ds = lenapy.utils.geo.rename_data(xr.tutorial.open_dataset('air_temperature'))
   ds.air.lngeo.mean(['latitude','longitude'],weights=['latitude']).lntime.climato().plot()
   ```
-  
-  
+More complete notebooks tutorials and functions descriptions can be found in the documentation.
+
+[Notebooks tutorials](https://lenapy.readthedocs.io/en/latest/tutorials.html)
+
+[Functions reference](https://lenapy.readthedocs.io/en/latest/api/index.html)
+
+## Contributing
+We welcome contributions to `lenapy`!
+
+Guidelines: [https://lenapy.readthedocs.io/en/latest/contributing.html](https://lenapy.readthedocs.io/en/latest/contributing.html)

doc/conf.py

@@ -8,6 +8,8 @@
 import os
 import sys
 
+import lenapy
+
 __location__ = os.path.join(
     os.getcwd(), os.path.dirname(inspect.getfile(inspect.currentframe()))
 )
@@ -25,7 +27,7 @@
 copyright = f"2023 - {curr_year}, Sebastien Fourest"
 author = "Sebastien Fourest"
 # The short X.Y version.
-version = "0.9"
+version = lenapy.__version__
 # The full version, including alpha/beta/rc tags.
 release = "First beta version on github"
 

doc/index.rst

@@ -13,7 +13,7 @@ Welcome to lenapy's documentation!
 * lenapy_time: common operations on time series (filtering, climatology, regressions, etc.)
 * lenapy_harmo: operations related to spherical harmonics decomposition and their projections on latitude/longitude grids
 
-This library is based on the principle of class extension, i.e. functions can be applied directly to Datasets or DataArrays, by adding the extension of the module concerned and the name of the method. Ex: ds.lntime.filter(...), ds.lngeo.mean(...), de.lnocean.gohc, etc.
+This library is based on the principle of class extension, i.e. functions can be applied directly to Datasets or DataArrays, by adding the extension of the module concerned and the name of the method. Each module extension is an abbreviation of the module name with the logic **lenapy_xxx** abbreviate by **ds.lnxxx**. e.g.: ds.lntime.filter(...), ds.lngeo.mean(...), de.lnocean.gohc
 
 Reading interfaces are implemented, enabling netcdf files to be opened with a compatible formalism from the **lenapy** library.
 

doc/tutorials/Tutorial_lnharmo.ipynb

@@ -1,10 +1,18 @@
 import warnings
+from importlib.metadata import version as _version
 
 from lenapy import constants, lenapy_geo, lenapy_harmo, lenapy_time
 
+try:
+    __version__ = _version("lenapy")
+except Exception:
+    # Local copy or not installed with setuptools.
+    # Disable minimum version checks on downstream libraries.
+    __version__ = "9999"
+
 try:
     from lenapy import lenapy_ocean
-except:
+except Exception:
     warnings.warn("To use lenapy_ocean, please install gsw : pip install gsw>=3.6.16")
 import cf_xarray as cfxr
 

lenapy/__init__.py

@@ -949,7 +949,7 @@ def open_dataset(
 
         # Read file with pandas, delim_whitespace for variable space delimiters
         data = pd.read_csv(
-            file, delim_whitespace=True, header=None, names=col_names, engine="python"
+            file, sep="\s+", header=None, names=col_names, engine="python"
         )
 
         # test if gfct key then have to deal with time

lenapy/readers/gravi_reader.py

@@ -20,7 +20,7 @@ def rename_data(data, **kwargs):
     """
     Standardization of coordinates names of a product.
     Looks for different possible names for latitude, longitude, and time, and turn them into a standardized name.
-    Definitions are specified in setup.py and are based on standard cf attributes and units : https://cfconventions.org
+    Definitions are based on standard cf attributes and units : https://cfconventions.org
     Custom names changes can also be performed with kwargs parameter.
 
     Parameters

lenapy/utils/geo.py

@@ -4,14 +4,14 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "lenapy"
-version = "0.9"
-description = "Second beta release of lenapy on github"
+version = "1.1"
+description = "Geophysical analysis in Python with xarray"
 readme = "README.md"
 authors = [
-    { name = "Sebastien Fourest & EMC2 team", email = "sebastien.fourest@cnes.fr" }
+    { name = "Sebastien Fourest & Hugo Lecomte & EMC2 team", email = "sebastien.fourest@cnes.fr" }
 ]
 license = { text = "GPL-3.0" }
-requires-python = ">=3.7"
+requires-python = ">=3.11"
 dependencies = [
     "matplotlib>=3.6",
     "xesmf>=0.8.2",