First release to PyPI

Climdyn · Jun 18, 2023 · 269c5b3 · 269c5b3
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diff --git a/.gitignore b/.gitignore
@@ -9,3 +9,5 @@ documentation/source/files/examples/.ipynb_checkpoints/
 documentation/source/files/examples/*_files/
 documentation/source/files/examples/*.rst
 documentation/source/_build/
+dist
+*egg-info
diff --git a/LICENSE.txt b/LICENSE.txt
@@ -1,7 +1,7 @@
 
 The MIT License (MIT)
 
-Copyright (c) 2020 qgs Developers and Contributors
+Copyright (c) 2020-2023 qgs Developers and Contributors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/README.md b/README.md
@@ -2,6 +2,10 @@
 Quasi-Geostrophic Spectral model (qgs)
 ======================================
 
+
+[![PyPI version](https://badge.fury.io/py/qgs.svg)](https://badge.fury.io/py/qgs)
+[![PyPI pyversions](https://img.shields.io/pypi/pyversions/qgs.svg)](https://pypi.org/project/qgs/)
+[![PyPI Package download count (per month)](https://img.shields.io/pypi/dm/qgs)](https://pypi.org/project/qgs/)
 [![DOI](https://zenodo.org/badge/246609584.svg)](https://zenodo.org/badge/latestdoi/246609584)
 [![DOI](https://joss.theoj.org/papers/10.21105/joss.02597/status.svg)](https://doi.org/10.21105/joss.02597)
 [![Documentation Status](https://readthedocs.org/projects/qgs/badge/?version=latest)](https://qgs.readthedocs.io/en/latest/?badge=latest)
@@ -16,7 +20,7 @@ a 2-layer [quasi-geostrophic](https://en.wikipedia.org/wiki/Quasi-geostrophic_eq
 atmosphere on a [beta-plane](https://en.wikipedia.org/wiki/Beta_plane), coupled to a simple land or
 [shallow-water](https://en.wikipedia.org/wiki/Shallow_water_equations) ocean component. 
 
-![](./misc/figs/readme.gif)
+![](https://github.com/Climdyn/qgs/blob/master/misc/figs/readme.gif?raw=true)
 
 About
 -----
@@ -25,7 +29,7 @@ About
 
 Part of the code originates from the Python [MAOOAM](https://github.com/Climdyn/MAOOAM) implementation by Maxime Tondeur and Jonathan Demaeyer.
 
-See [LICENSE.txt](./LICENSE.txt) for license information.
+See [LICENSE.txt](https://raw.githubusercontent.com/Climdyn/qgs/master/LICENSE.txt) for license information.
 
 **Please cite the code description article if you use (a part of) this software for a publication:**
 
@@ -38,7 +42,31 @@ Please consult the qgs [code repository](http://www.github.com/Climdyn/qgs) for
 Installation
 ------------
 
-The easiest way to run qgs is to use an appropriate environment created through [Anaconda](https://www.anaconda.com/).
+#### With pip
+
+The easiest way to install and run qgs is to use [pip](https://pypi.org/)
+
+    pip install qgs
+
+and you are set!
+
+Additionally, you can clone the repository
+
+    git clone https://github.com/Climdyn/qgs.git
+
+and perform a test by running the script
+
+    python qgs/qgs_rp.py
+
+to see if everything runs smoothly (this should take less than a minute).
+
+> **Note:** 
+> With the pip installation, in order to be able to generate the movies with the diagnostics, 
+> you need to install separately [ffmpeg](https://ffmpeg.org/).
+
+#### With Anaconda
+
+The second easiest way to install and run qgs is to use an appropriate environment created through [Anaconda](https://www.anaconda.com/).
 
 First install Anaconda and clone the repository:
 
@@ -139,7 +167,7 @@ qgs needs mainly:
    * [Numba](https://numba.pydata.org/) for code acceleration
    * [Sympy](https://www.sympy.org/) for symbolic manipulation of inner products
 
-Check the yaml file [environment.yml](./environment.yml) for the dependencies.
+Check the yaml file [environment.yml](https://raw.githubusercontent.com/Climdyn/qgs/master/environment.yml) for the dependencies.
 
 Forthcoming developments
 ------------------------

diff --git a/documentation/source/conf.py b/documentation/source/conf.py
@@ -22,7 +22,7 @@
 author = 'Jonathan Demaeyer, Lesley De Cruz and Oisín Hamilton'
 
 # The full version, including alpha/beta/rc tags
-release = 'v0.2.7'  # temporary
+release = 'v0.2.8'  # temporary
 version = release
 
 

diff --git a/documentation/source/files/examples/DDV2016.ipynb b/documentation/source/files/examples/DDV2016.ipynb
@@ -223,7 +223,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Qgs v0.2.7 parameters summary\n",
+      "Qgs v0.2.8 parameters summary\n",
       "=============================\n",
       "\n",
       "General Parameters:\n",

diff --git a/documentation/source/files/examples/Hamiltonetal2023.ipynb b/documentation/source/files/examples/Hamiltonetal2023.ipynb
@@ -228,7 +228,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Qgs v0.2.7 parameters summary\n",
+      "Qgs v0.2.8 parameters summary\n",
       "=============================\n",
       "\n",
       "General Parameters:\n",

diff --git a/documentation/source/files/examples/Lietal2017.ipynb b/documentation/source/files/examples/Lietal2017.ipynb
@@ -184,7 +184,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Qgs v0.2.7 parameters summary\n",
+      "Qgs v0.2.8 parameters summary\n",
       "=============================\n",
       "\n",
       "General Parameters:\n",

diff --git a/documentation/source/files/examples/RP1982.ipynb b/documentation/source/files/examples/RP1982.ipynb
@@ -185,7 +185,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Qgs v0.2.7 parameters summary\n",
+      "Qgs v0.2.8 parameters summary\n",
       "=============================\n",
       "\n",
       "General Parameters:\n",

diff --git a/documentation/source/files/examples/VSPD2019.ipynb b/documentation/source/files/examples/VSPD2019.ipynb
@@ -206,7 +206,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Qgs v0.2.7 parameters summary\n",
+      "Qgs v0.2.8 parameters summary\n",
       "=============================\n",
       "\n",
       "General Parameters:\n",

diff --git a/documentation/source/files/examples/diffeq_example.ipynb b/documentation/source/files/examples/diffeq_example.ipynb
@@ -223,7 +223,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Qgs v0.2.7 parameters summary\n",
+      "Qgs v0.2.8 parameters summary\n",
       "=============================\n",
       "\n",
       "General Parameters:\n",

diff --git a/documentation/source/files/examples/manual_basis.ipynb b/documentation/source/files/examples/manual_basis.ipynb
@@ -372,7 +372,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Qgs v0.2.7 parameters summary\n",
+      "Qgs v0.2.8 parameters summary\n",
       "=============================\n",
       "\n",
       "General Parameters:\n",

diff --git a/documentation/source/files/examples/tgls_example.ipynb b/documentation/source/files/examples/tgls_example.ipynb
@@ -189,7 +189,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Qgs v0.2.7 parameters summary\n",
+      "Qgs v0.2.8 parameters summary\n",
       "=============================\n",
       "\n",
       "General Parameters:\n",

diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,58 @@
+
+# pyproject.toml
+
+[build-system]
+requires = ["setuptools", "wheel"]
+
+[project]
+requires-python = ">=3.8"
+name = "qgs"
+version = "0.2.8"
+description = "A 2-layer quasi-geostrophic atmospheric model. Can be coupled to a simple land or shallow-water ocean component."
+readme = "README.md"
+authors = [
+    { name = "qgs Developers and Contributors", email = "jodemaey@meteo.be" },
+]
+license = { file = "LICENSE.txt" }
+classifiers = [
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Operating System :: OS Independent",
+    "Development Status :: 5 - Production/Stable",
+    "Framework :: Jupyter",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Atmospheric Science",
+]
+keywords = ["meteorology", "climate", "climate-variability", "atmospheric-models", "ocean-atmosphere-model"]
+dependencies = [
+    "ipython",
+    "jupyter",
+    "matplotlib>=3.4",
+    "numba",
+    "numpy",
+    "scipy",
+    "sympy",
+    "sparse",
+    "pebble",
+]
+
+[project.urls]
+homepage = "https://github.com/Climdyn/qgs"
+documentation = "https://qgs.readthedocs.io"
+
+[tool.setuptools]
+packages = ["qgs",
+            "qgs.basis",
+            "qgs.diagnostics",
+            "qgs.functions",
+            "qgs.inner_products",
+            "qgs.integrators",
+            "qgs.params",
+            "qgs.plotting",
+            "qgs.tensors",
+            "qgs.toolbox",
+            ]
diff --git a/qgs/__init__.py b/qgs/__init__.py
@@ -0,0 +1,2 @@
+
+__version__ = '0.2.8'
diff --git a/qgs/basis/__init__.py b/qgs/basis/__init__.py
diff --git a/qgs/diagnostics/__init__.py b/qgs/diagnostics/__init__.py
diff --git a/qgs/functions/__init__.py b/qgs/functions/__init__.py
diff --git a/qgs/inner_products/__init__.py b/qgs/inner_products/__init__.py
diff --git a/qgs/integrators/__init__.py b/qgs/integrators/__init__.py
diff --git a/qgs/params/__init__.py b/qgs/params/__init__.py
diff --git a/qgs/params/params.py b/qgs/params/params.py
@@ -1195,7 +1195,7 @@ def print_params(self):
             if self.gotemperature_params is not None:
                 s += self.gotemperature_params._list_params() + "\n"
 
-        print("Qgs v0.2.7 parameters summary")
+        print("Qgs v0.2.8 parameters summary")
         print("=============================\n")
         print(s)
 

diff --git a/qgs/plotting/__init__.py b/qgs/plotting/__init__.py
diff --git a/qgs/tensors/__init__.py b/qgs/tensors/__init__.py
diff --git a/qgs/toolbox/__init__.py b/qgs/toolbox/__init__.py
diff --git a/qgs_maooam.py b/qgs_maooam.py
@@ -54,7 +54,7 @@ class Bcolors:
         UNDERLINE = '\033[4m'
 
 
-    print("\n" + Bcolors.HEADER + Bcolors.BOLD + "Model qgs v0.2.7 (Atmosphere + ocean (MAOOAM) configuration)" + Bcolors.ENDC)
+    print("\n" + Bcolors.HEADER + Bcolors.BOLD + "Model qgs v0.2.8 (Atmosphere + ocean (MAOOAM) configuration)" + Bcolors.ENDC)
     print(Bcolors.HEADER + "============================================================" + Bcolors.ENDC + "\n")
     print(Bcolors.OKBLUE + "Initialization ..." + Bcolors.ENDC)
     # ## Systems definition

diff --git a/qgs_rp.py b/qgs_rp.py
@@ -53,7 +53,7 @@ class Bcolors:
         UNDERLINE = '\033[4m'
 
 
-    print("\n" + Bcolors.HEADER + Bcolors.BOLD + "Model qgs v0.2.7 (Atmosphere + orography configuration)" + Bcolors.ENDC)
+    print("\n" + Bcolors.HEADER + Bcolors.BOLD + "Model qgs v0.2.8 (Atmosphere + orography configuration)" + Bcolors.ENDC)
     print(Bcolors.HEADER + "=======================================================" + Bcolors.ENDC + "\n")
     print(Bcolors.OKBLUE + "Initialization ..." + Bcolors.ENDC)
     # ## Systems definition

diff --git a/requirements.txt b/requirements.txt
@@ -7,7 +7,7 @@ python>=3.8
 scipy
 sympy
 sphinx
-sphinx_rtd_theme
+sphinx_rtd_theme>0.5.1
 sparse
 julia
 diffeqpy