update configuration and TODO files

Author: mcobosb

README.md

@@ -8,6 +8,7 @@ It is compound by a list of subpackages that focus on:
 |---------------------------------|----------------------------------------------------------|---------------|
 | environmentaltools.data         | Download environmental data from various sources (CMEMS) | Estable       |
 | environmentaltools.estuaries    | Saint-Venant equations for estuarine dynamics            | En desarrollo |
+| environmentaltools.examples     | Full catalog of examples of each package                 | Estable       |
 | environmentaltools.graphics     | Visualization tools for environmental data               | Estable       |
 | environmentaltools.processes    | Wave modeling and environmental processes (SWAN, COPLA)  | Estable       |
 | environmentaltools.spatial      | Geospatial analysis and topography/bathymetry processing | Estable       |
@@ -16,12 +17,17 @@ It is compound by a list of subpackages that focus on:
 | environmentaltools.temporal     | Time series processing and statistical characterization  | En desarrollo |
 | environmentaltools.utils        | Auxiliary utilities for data handling and processing     | Estable       |
 
+The tool is developed by Manuel Cobos (https://github.es/mcobosb) as part of the **Environmental Fluid Dynamics (GDFA)** team of the University of Granada. The GDFA whishes a good experience in learning process. Enjoy it!
 
 ## Subpackages description
 
 ### **data** subpackage
 The *data* subpackage provides tools for downloading environmental data from various online sources. It includes automated functions to access and retrieve data from the **Marine Copernicus Service (CMEMS)**, allowing users to download oceanographic variables (sea surface temperature, currents, wave data, etc.) for specific spatial domains, depth ranges, and time periods. This module simplifies the process of obtaining high-quality environmental data for analysis and modeling purposes.
 
+### **examples** subpackage
+In the *example** folder can be found a list of Jupyter Notebooks. Each one described how to run the code and how to use the main functions included in *environmentaltools*.
+
+
 ### **estuaries** subpackage
 The *estuaries* subpackage implements numerical solutions for the **Saint-Venant equations** applied to estuarine dynamics. It provides tools to simulate hydrodynamic processes in estuaries, including water level variations, flow velocities, salinity transport, and density computations. The module is designed to study the consequences of natural and anthropogenic actions in estuarine environments, supporting management and decision-making processes for coastal water bodies.
 
@@ -45,10 +51,6 @@ The subpackage *temporal* package aimed at providing users with a friendly, gene
 
 The tools implemented in the package named *temporal* allow to capture the statistical properties of a **non stationary (NS) vector RP** by using **compound or piecewise parametric PMs** to properly describe all the range of values and to **simulate uni- or multivariate time series** with the same random behavior. The statistical parameters of the distributions are assumed to depend on time and are expanded into a Generalized Fourier Series (GFS) [["5"]](#5) in order to reproduce their NS behavior. The applicability of the present approach has been illustrated in several works with different purposes, among others: (i) the observed wave climate variability in the preceding century and expected changes in projections under a climate change scenario [["6"]](#6); (ii) the optimal design and management of an oscillating water column system [["7"]](#7) [["8"]](#8), (iii) the planning of maintenance strategies of coastal structures [["9"]](#9), (iv) the analysis of monthly Wolf sunspot number over a 22 year period [["5"]](#5), and (v) the simulation of estuarine water conditions for the management of the estuary [["10"]](#10).
 
-In the **example folder** can be found a list of Jupyter Notebooks. Each one described how to run the code and how to use the main functions included in *environmentaltools*.
-
-The **Environmental Fluid Dynamics** team of the University of Granada whishes a good experience in learning process. Enjoy it!
-
 ### **utils** subpackage
 The *utils* subpackage contains a collection of **auxiliary utilities** that support the functionality of other modules within the package. It includes functions for data loading and saving in various formats (NetCDF, CSV, pickle), file reading and writing operations, data manipulation and transformation, xarray dataset utilities, and miscellaneous helper functions. The module provides a consistent interface for common operations across the package, improving code reusability and maintainability.
 

TODO.md

@@ -0,0 +1,50 @@
+🧩 General
+- [ ] Define pyproject.toml with modular extras
+- [ ] Add installation instructions for partial environments on README.md
+- [ ] Include module table and usage examples in README.md
+- [ ] Prepare conda-forge recipe for staged-recipes submission
+
+📦 pyproject.toml
+- [ ] Update common dependencies (os, time, pathlib, dotenv, typing, logging, datetime) - Line 34
+
+🧪 Examples
+- [ ] Run examples and check that works fine
+- [ ] Revise examples, input data, results and output graphics
+
+
+## 📂 Module-specific TODOs
+
+### spatiotemporal.raster.analysis
+- [ ] Check that level series files exist - Line 67
+- [ ] Validate that max_level has data for all months and years - Line 67
+- [ ] Implement additional pre-treatment steps as required - Line 227
+
+### temporal
+- [ ] Update initialization message in analysis.py - Line 30
+- [ ] Update docstring for simulation function - Line 62 in simulation.py
+- [ ] Update docstring for _summary_ function - Line 441 in simulation.py
+- [ ] Implement non-normal multivariate analysis (currently only normal distribution) - Line 523 in simulation.py
+- [ ] Review value of 1e-6 subtraction in CDF to avoid 1.0 values - Line 355 in regimes.py
+- [ ] Review peaks selection function for POT analysis - Line 398 in regimes.py
+- [ ] Check groupby count with monthly average weights - Line 221 in analysis.py
+- [ ] Check logic that doesn't make much sense - Line 616 in analysis.py
+- [ ] Verify that True option works correctly - Line 621 in analysis.py
+- [ ] Implement handling for mixed functions - Line 959 in analysis.py
+- [ ] Modify function for storm separation (should not fill gaps) - Line 1025 in analysis.py
+- [ ] Remove temporary fix for calm period indices (waiting for Pedro's fix) - Line 1124 in analysis.py
+- [ ] Modify for more refined and understandable version - Line 1527 in statistical_fit.py
+
+### utils
+- [ ] Implement nearest neighbor function separately - Line 361 in read.py
+- [ ] Change implementation for more than one variable in dataframe conversion - Line 362 in read.py
+- [ ] Enable multi-page reading - Line 707 in read.py
+- [ ] Include morphology options - Line 111 in load.py
+- [ ] Load paths from a file instead of hardcoding - Line 25 in cme.py
+- [ ] Improve parameter extraction for order 1 Fourier series - Line 396 and 1430 in auxiliar.py
+- [ ] Fix discontinuity limitation - Line 481 and 1515 in auxiliar.py
+- [ ] Separate by Fourier order - Line 504 and 1538 in auxiliar.py
+- [ ] Generalize for more than two functions - Line 606 and 1640 in auxiliar.py
+- [ ] Verify calculation - Line 864 in auxiliar.py
+- [ ] Change hardcoded value 51 to a target value - Line 1352 in auxiliar.py
+
+

pyproject.toml

@@ -31,6 +31,13 @@ classifiers = [
 ]
 license = "GPL-3.0-or-later"
 license-files = ["LICENSE"]
+dependencies = ["os", "time", "pathlib", "dotenv", "typing", "logging", "datetime"]  # TODO: update-comunes
+
+[project.optional-dependencies]
+donwload = ["rioxarray", "matplotlib"]
+spatiotemporal-raster = ["scipy"]
+spectral = [""]
+temporal = ["scipy"]
 
 [project.urls]
 Homepage = "https://example.com"