Feature/tomlconfig (#9)

* fix: moved 2024 paper to folder

* chore: move build to pyproject

* doc: fixed README

* doc: fixed LICENSE

* chore: fixed pyproject

* chore: move build to pyproject

* doc: fixed README

* chore: fixed pyproject

* chore: fixed version

* chore: fixed pyproject

.coveragerc

@@ -2,5 +2,4 @@
 show_missing = True
 omit =
     src/pyquasoare/__init__.py
-    src/pyquasoare/__version__.py
 

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

@@ -28,12 +28,12 @@ jobs:
       - name: Create conda environment if needed
         run: |
            source $CONDA/etc/profile.d/conda.sh
-           conda env create -f env_mini_v2.yml
+           conda env create -f env_pyquasoare.yml
 
       - name : Install hydrodiy package in conda env 
         run: |
           source $CONDA/etc/profile.d/conda.sh
-          conda activate env_mini_v2
+          conda activate env_pyquasoare
           cd $GITHUB_WORKSPACE
           mkdir -p src
           cd src
@@ -45,7 +45,7 @@ jobs:
       - name : Install pygme package in conda env 
         run: |
           source $CONDA/etc/profile.d/conda.sh
-          conda activate env_mini_v2
+          conda activate env_pyquasoare
           cd $GITHUB_WORKSPACE
           mkdir -p src
           cd src
@@ -57,15 +57,15 @@ jobs:
       - name : Install pyquasoare package in conda env 
         run: |
           source $CONDA/etc/profile.d/conda.sh
-          conda activate env_mini_v2
+          conda activate env_pyquasoare
           cd $GITHUB_WORKSPACE
           echo "--- pyquasoare install : located in $PWD ---"
           pip install -e .
 
       - name: Run tests
         run: |
           source $CONDA/etc/profile.d/conda.sh
-          conda activate env_mini_v2
+          conda activate env_pyquasoare
           cd $GITHUB_WORKSPACE
           echo "--- pyquasoare test : located in $PWD ---"
           pytest --ignore=src/pygme --ignore=src/hydrodiy --doctest-modules src
@@ -98,7 +98,7 @@ jobs:
       - name: Run examples
         run: |
           source $CONDA/etc/profile.d/conda.sh
-          conda activate env_mini_v2
+          conda activate env_pyquasoare
           cd $GITHUB_WORKSPACE
           echo "--- pyquasoare examples : located in $PWD ---"
           python examples/run_all_examples.py

CITATION.cff

@@ -0,0 +1,44 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: pyquasoare
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+authors:
+  - given-names: Julien
+    family-names: Lerat
+    email: [email protected]
+    affiliation: CSIRO
+    orcid: '0000-0003-4521-8874'
+identifiers:
+  - type: doi
+    value: 10.5281/zenodo.13928254
+repository-code: 'https://github.com/csiro-hydroinformatics/pyquasoare'
+url: 'https://github.com/csiro-hydroinformatics/pyquasoare'
+abstract: >-
+  This package implements the Quadratic Solution of the
+  Approximate Reservoir Equation (QuaSoARe) method.
+
+  "Quadratic solution of the approximate reservoir equation
+  (QUASOARE)", HESS, Submitted.
+keywords:
+  - Differential equation
+  - Reservoir
+  - Hydrology
+  - Rainfall-runoff
+license: MIT
+
+references:
+  - type: article
+    title: Technical note: Quadratic solution of the approximate reservoir equation (QuaSoARe)
+    authors:
+      - family-names: "Lerat"
+        given-names: "Julien"
+        orcid: "0000-0003-4521-8874"
+    year: 2024
+    journal: "Hydrology and Earth System Sciences"
+    volume: "in review"
+    url: "https://egusphere.copernicus.org/preprints/2024/egusphere-2024-3184"

README.md

@@ -10,10 +10,10 @@ piecewise quadratic interpolation following the QuaSoARe method.
 This package implements the Quadratic Solution of the Approximate Reservoir 
 Equation (QuaSoARe) method described in the following paper:
 Lerat, J. (2024),  
-"Quadratic solution of the approximate reservoir equation (QUASOARE)", HESS, Submitted.
+"Technical note: Quadratic solution of the approximate reservoir equation (QuaASOARE)", HESS, Submitted.
 
 # Installation
-- Create a suitable python environment. We recommend using [miniconda](https://docs.conda.io/projects/miniconda/en/latest/) combined with the environment specification provided in the [env\_mini2.yml] (env_mini2.yml) file in this repository.
+- Create a suitable python environment. We recommend using [miniconda](https://docs.conda.io/projects/miniconda/en/latest/) combined with the environment specification provided in the [env_pyquasoare.yml] (env_pyquasoare.yml) file in this repository.
 - Git clone this repository and run `pip install .`
 
 # Basic use
@@ -84,7 +84,9 @@ for iax, ax in enumerate(axs):
 plt.show()
 ```
 
-# License
-The source code and documentation of the pyquasoare package is licensed under the
-[MIT license](LICENSE.txt).
+## Attribution
+This project is licensed under the [MIT License](LICENSE), which allows for free use, modification, and distribution of the code under the terms of the license.
+
+For proper citation of this project, please refer to the [CITATION.cff](CITATION.cff) file, which provides guidance on 
+how to cite the software and relevant publications.
 

env_mini_v2.yml → env_pyquasoare.yml

@@ -1,4 +1,4 @@
-name: env_mini_v2
+name: env_pyquasoare
 channels:
   - conda-forge
   - defaults

pyproject.toml

@@ -0,0 +1,46 @@
+[build-system]
+requires = [
+    "setuptools >= 64",
+    "cython >= 3.0.10",
+    "numpy >= 1.20.0"
+]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "pyquasoare"
+authors = [{name = "Julien Lerat, CSIRO Environment", email="[email protected]"}]
+description = "Solve the approximate reservoir equation using the QuaSoARe method"
+readme = "README.md"
+license = {file = "LICENSE"}
+keywords = ["differential equation", "reservoir", "dynamic system", "store", "routing", "rainfall-runoff", "hydrology"]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python 3",
+    "Programming Language :: C",
+    "Topic :: Scientific/Engineering :: Mathematics",
+    "Topic :: Scientific/Engineering :: Hydrology"
+]    
+requires-python = ">= 3.8"
+dependencies = [
+    "hydrodiy",
+    "numpy >= 1.20.0",
+    "scipy >= 1.0.0",
+    "pandas >= 2.0.0"
+]
+dynamic = ["version"]
+
+[project.urls]
+Homepage = "https://github.com/csiro-hydroinformatics/pyquasoare"
+Repository = "https://github.com/csiro-hydroinformatics/pyquasoare"
+
+[tool.pytest.ini_options]
+testpaths = [
+    "tests"
+]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.dynamic]
+version = {attr = "pyquasoare.__version__"}

setup.py

@@ -1,71 +1,26 @@
 #!/usr/bin/env python
 
-import os
 import numpy
-from pathlib import Path
 
-from setuptools import setup, Extension, find_packages
+from setuptools import setup, Extension
+from Cython.Build import cythonize
 
-from Cython.Distutils import build_ext
-
-import versioneer
-
-def read(fname):
-    thisfolder = Path(__file__).resolve().parent
-    with (thisfolder / fname).open() as fo:
-        return fo.read()
-
-# C extensions
-ext_quasoare=Extension(name="c_pyquasoare",
-    sources=[
+extensions = [
+    Extension(name="c_pyquasoare",
+        sources=[
         "src/pyquasoare/c_pyquasoare.pyx",
         "src/pyquasoare/c_quasoare_utils.c",
         "src/pyquasoare/c_quasoare_core.c",
         "src/pyquasoare/c_nonlinrouting.c",
         "src/pyquasoare/c_gr4jprod.c"
-    ],
-    extra_cflags=["-O3"],
-    include_dirs=[numpy.get_include()])
-
-cmdclass = versioneer.get_cmdclass()
-cmdclass["build_ext"] = build_ext
+        ],
+        include_dirs=[numpy.get_include()])
+]
 
-# Package config
 setup(
     name="pyquasoare",
-    author= "Julien Lerat",
-    author_email= "[email protected]",
-    url= "https://github.com/csiro-hydroinformatics/pyquasoare",
-    download_url= "hhttps://github.com/csiro-hydroinformatics/pyquasoare/tags",
-    version=versioneer.get_version(),
-    description= "Solve the approximate reservoir equation using the QuaSoARe method",
-    long_description= read("README.md"),
-    packages=find_packages(),
-    package_dir={"": "src"},
-    package_data={
-        "pyquasoare": [
-            "data/*.csv",
-            "data/daily/*.zip",
-            "data/hourly/*.zip"
-        ],
-    },
-    install_requires= [
-        "cython",
-        "hydrodiy",
-        "numpy >= 1.8.0",
-        "scipy (>=0.14.0)",
-        "pandas >= 0.16"
-    ],
-    cmdclass=cmdclass,
-    ext_modules=[ext_quasoare],
-    classifiers=[
-        "Operating System :: OS Independent",
-        "Intended Audience :: Developers",
-        "Intended Audience :: Science/Research",
-        "Development Status :: 3 - Alpha",
-        "Programming Language :: Python :: 3",
-        "License :: OSI Approved :: BSD License"
-    ]
+    ext_modules=cythonize(extensions, \
+            compiler_directives={"language_level": 3, "profile": False})
 )
 
 

src/pyquasoare/__init__.py

@@ -1,5 +1,7 @@
 import importlib
 
+__version__ = "1.2"
+
 def has_c_module(raise_error=True):
     name = f"c_pyquasoare"
     out = importlib.util.find_spec(name)
@@ -13,9 +15,4 @@ def has_c_module(raise_error=True):
         else:
             return False
 
-#from ._version import get_versions
-#__version__ = get_versions()['version']
-#del get_versions
 
-from . import _version
-__version__ = _version.get_versions()['version']