Flow

.flake8

@@ -0,0 +1,5 @@
+[flake8]
+ignore = E203, E266, E501, W503, F403, F401
+max-line-length = 79
+max-complexity = 18
+select = B,C,E,F,W,T4,B9

.github/workflows/ci.yml

@@ -1,24 +1,27 @@
 name: CI
 on:
-    push:
-        branches:
-        - master
-    pull_request:
+  push:
+    branches:
+      - master
+  pull_request:
 
 jobs:
-    test:
-        name: QBMMTest
-        runs-on: ubuntu-latest
-
-        steps:
-        -   uses: actions/checkout@v2
-        - name: Set up Python 3.8
-          uses: actions/setup-python@v2
-          with:
-            python-version: 3.8
-        -   name: Install dependencis
-            run: |
-            python -m pip install --upgrade pip
-            pip install -r requirements.txt
-        -   name: "Test QBMM"
-            run: pytest test/test_qbmm.py
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - uses: actions/setup-python@v2
+      with:
+        python-version: '3.8'
+    - name: Install pip
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install pipreqs
+        pipreqs --force
+    - name: Install requirements
+      run: python -m pip install -r requirements.txt
+    - name: Test QBMM
+      run: cd test && pytest test_qbmm.py
+
+
+

.gitignore

@@ -4,6 +4,8 @@ tags
 *.ipynb_checkpoints
 
 D
+src/output
 _build
 __pycache__
-mmatica_qbmmlib
+
+profile*

README.md

@@ -1,5 +1,6 @@
 # PyQBMMlib
 
+![CI](https://github.com/sbryngelson/PyQBMMlib/workflows/CI/badge.svg)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 [![Documentation Status](https://readthedocs.org/projects/pyqbmmlib/badge/?version=latest)](https://pyqbmmlib.readthedocs.io/en/latest/?badge=latest)
 [![DOI](https://zenodo.org/badge/doi/10.1016/j.softx.2020.100615.svg)](http://dx.doi.org/10.1016/j.softx.2020.100615)

docs/conf.py

@@ -14,21 +14,22 @@
 #
 import os
 import sys
-sys.path.insert(0, os.path.abspath('../src/'))
-sys.path.insert(0, os.path.abspath('../utils/'))
-sys.path.insert(0, os.path.abspath('../test/'))
+
+sys.path.insert(0, os.path.abspath("../src/"))
+sys.path.insert(0, os.path.abspath("../utils/"))
+sys.path.insert(0, os.path.abspath("../test/"))
 
 
 # -- Project information -----------------------------------------------------
 
-project = u'PyQBMMlib'
-copyright = u'2020, Spencer Bryngelson'
-author = u'Spencer H. Bryngelson and Esteban Cisneros'
+project = u"PyQBMMlib"
+copyright = u"2020, Spencer Bryngelson"
+author = u"Spencer H. Bryngelson and Esteban Cisneros"
 
 # The short X.Y version
-version = u''
+version = u""
 # The full version, including alpha/beta/rc tags
-release = u''
+release = u""
 
 
 # -- General configuration ---------------------------------------------------
@@ -41,25 +42,25 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.doctest',
-    'sphinx.ext.coverage',
-    'sphinx.ext.mathjax',
-    'sphinx.ext.inheritance_diagram',
-    'sphinx.ext.napoleon'
+    "sphinx.ext.autodoc",
+    "sphinx.ext.doctest",
+    "sphinx.ext.coverage",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.inheritance_diagram",
+    "sphinx.ext.napoleon",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -71,7 +72,7 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = [u'_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = [u"_build", "Thumbs.db", ".DS_Store"]
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = None
@@ -82,7 +83,7 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'classic'
+html_theme = "classic"
 # html_theme = 'alabaster'
 
 # Theme options are theme-specific and customize the look and feel of a theme
@@ -94,7 +95,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.
@@ -110,7 +111,7 @@
 # -- Options for HTMLHelp output ---------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'PyQBMMlibdoc'
+htmlhelp_basename = "PyQBMMlibdoc"
 
 
 # -- Options for LaTeX output ------------------------------------------------
@@ -119,15 +120,12 @@
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     #
     # 'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     #
     # 'preamble': '',
-
     # Latex figure (float) alignment
     #
     # 'figure_align': 'htbp',
@@ -137,19 +135,15 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'PyQBMMlib.tex', u'PyQBMMlib Documentation',
-     u'SHB', 'manual'),
+    (master_doc, "PyQBMMlib.tex", u"PyQBMMlib Documentation", u"SHB", "manual"),
 ]
 
 
 # -- Options for manual page output ------------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'pyqbmmlib', u'PyQBMMlib Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "pyqbmmlib", u"PyQBMMlib Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output ----------------------------------------------
@@ -158,9 +152,15 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'PyQBMMlib', u'PyQBMMlib Documentation',
-     author, 'PyQBMMlib', 'One line description of project.',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "PyQBMMlib",
+        u"PyQBMMlib Documentation",
+        author,
+        "PyQBMMlib",
+        "One line description of project.",
+        "Miscellaneous",
+    ),
 ]
 
 
@@ -179,15 +179,15 @@
 # epub_uid = ''
 
 # A list of files that should not be packed into the epub file.
-epub_exclude_files = ['search.html']
+epub_exclude_files = ["search.html"]
 
 
 # -- Extension configuration -------------------------------------------------
 
 # -- Options for intersphinx extension ---------------------------------------
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'https://docs.python.org/': None}
+intersphinx_mapping = {"https://docs.python.org/": None}
 
 # -- Options for todo extension ----------------------------------------------
 

inputs/example_2d.yaml

@@ -6,17 +6,17 @@ qbmm:
     flow: no
     governing_dynamics:   " - x - xdot"
     num_internal_coords:  2
-    num_quadrature_nodes: 9
+    num_quadrature_nodes: 4
     method:               "chyqmom"
     adaptive:             no
     max_skewness:         30
     checks:               no
 
 advancer:
-    method:          "RK23"
+    method:          "RK3"
     time_step:       1.0e-5
     final_time:      15.0
-    error_tol:       1.0e-7
+    error_tol:       1.0e-6
     num_steps:       10000
     num_steps_print: 100
     num_steps_write: 100

notebooks/Untitled.ipynb

@@ -0,0 +1,92 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "some_string\n",
+      "y is empty\n"
+     ]
+    }
+   ],
+   "source": [
+    "x = \"some_string\"\n",
+    "y = \"\"\n",
+    "\n",
+    "if x:\n",
+    "    print(x)\n",
+    "else:\n",
+    "    print(\"x is empty\")\n",
+    "    \n",
+    "if y:\n",
+    "    print(y)\n",
+    "else:\n",
+    "    print(\"y is empty\")\n",
+    "    "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "['CavityFlame.aux', 'CavityFlame.blg']"
+      ]
+     },
+     "execution_count": 2,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "project_name = \"CavityFlame\"\n",
+    "[project_name+ext for ext in [\".aux\",\".blg\"]]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 2",
+   "language": "python",
+   "name": "python2"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}