Major cleanup

Author: FRidh

.github/workflows/nix.yml

@@ -0,0 +1,21 @@
+name: "Nix tests"
+on:
+  push:
+    branches:
+    - master
+  pull_request:
+    branches:
+    - master
+jobs:
+  tests:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2.3.4
+    - uses: cachix/install-nix-action@v13
+      with:
+        install_url: https://nixos-nix-install-tests.cachix.org/serve/i6laym9jw3wg9mw6ncyrk6gjx4l34vvx/install
+        install_options: '--tarball-url-prefix https://nixos-nix-install-tests.cachix.org/serve'
+        extra_nix_config: |
+          experimental-features = nix-command flakes
+    - run: nix flake check
+    - run: nix build

.github/workflows/tox.yml

@@ -0,0 +1,34 @@
+name: "Tox tests"
+on:
+  push:
+  pull_request:
+  schedule:
+    - cron: "0 8 * * *"
+jobs:
+  test:
+    name: tox test ${{ matrix.py }} - ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        os:
+          - Ubuntu
+          - Windows
+          - MacOs
+        py:
+          - "3.10"
+          - "3.9"
+    steps:
+      - name: Setup python for test ${{ matrix.py }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.py }}
+      - uses: actions/checkout@v2
+      - name: Install tox-gh
+        run: python -m pip install tox-gh
+      - name: Setup test suite
+        run: tox4 r -vv --notest
+      - name: Run test suite
+        run: tox4 r --skip-pkg-install
+        env:
+          PYTEST_ADDOPTS: "-vv --durations=10"

.gitignore

@@ -46,3 +46,5 @@ _build
 *.png
 
 result*
+
+.ipynb_checkpoints

README.md

@@ -1,6 +1,6 @@
 # pstd
 
-A Python implementation of the k-space pseudospectral time-domain method.
+A Python implementation of the $k$-space pseudospectral time-domain method.
 
 This implementation was originally written to quantify the fluctuations in sound pressure due to atmospheric turbulence.
 
@@ -11,19 +11,8 @@ Currently there are no packages available.
 
 The recommended method to install is to clone this repository
 
-`git clone git@github.com:FRidh/pstd.git`
+   pip install git+https://github.com/FRidh/seapy.git
 
-and install this package in development mode
-
-`python setup.py develop`
-
-This way one can easily update to the latest version using
-
-`git pull`
-
-and running again
-
-`python setup.py develop`
 
 ## Examples
 

default.nix

@@ -1,30 +1,60 @@
 { buildPythonPackage
+
+, flit-core
+
 , acoustics
 , h5py
+, numba
 , numpy
 , scipy
 , matplotlib
 , numexpr
 , pyyaml
+
+, black
+, nbconvert
+, pylint
+, pytest
+, pytestCheckHook
 }:
 
 buildPythonPackage rec {
   pname = "pstd";
   version = "dev";
+  format = "pyproject";
 
   src = ./.;
 
+  nativeBuildInputs = [
+    flit-core
+  ];
+
   propagatedBuildInputs = [
     acoustics
     h5py
+    numba
     numpy
     scipy
     matplotlib
     numexpr
     pyyaml
   ];
 
-  # No tests
-  doCheck = false;
+  checkInputs = [
+    black
+    nbconvert
+    pylint
+    pytest
+    pytestCheckHook
+  ];
+
+  preCheck = ''
+    echo "Checking formatting with black..."
+    black --check pstd tests docs/conf.py
+    echo "Static analysis with pylint..."
+    pylint -E pstd
+  '';
+
+  passthru.allInputs = nativeBuildInputs ++ propagatedBuildInputs ++ checkInputs;
 
 }

docs/conf.py

@@ -18,225 +18,221 @@
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-#sys.path.insert(0, os.path.abspath('.'))
+# sys.path.insert(0, os.path.abspath('.'))
 
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
-#needs_sphinx = '1.0'
+# needs_sphinx = '1.0'
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ['sphinx.ext.autodoc', 
-              'sphinx.ext.inheritance_diagram', 
-              'sphinx.ext.intersphinx', 
-              'sphinx.ext.pngmath', 
-              'sphinx.ext.viewcode', 
-              'sphinx.ext.autosummary']
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.inheritance_diagram",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.pngmath",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.autosummary",
+]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix of source filenames.
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The encoding of source files.
-#source_encoding = 'utf-8-sig'
+# source_encoding = 'utf-8-sig'
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = u'pstd'
-copyright = u'2014, Frederik Rietdijk'
+project = u"pstd"
+copyright = u"2014, Frederik Rietdijk"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = '0.0'
+version = "0.0"
 # The full version, including alpha/beta/rc tags.
-release = '0.0'
+release = "0.0"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
-#language = None
+# language = None
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
-#today = ''
+# today = ''
 # Else, today_fmt is used as the format for a strftime call.
-#today_fmt = '%B %d, %Y'
+# today_fmt = '%B %d, %Y'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns = ['_build']
+exclude_patterns = ["_build"]
 
 # The reST default role (used for this markup: `text`) to use for all
 # documents.
-#default_role = None
+# default_role = None
 
 # If true, '()' will be appended to :func: etc. cross-reference text.
-#add_function_parentheses = True
+# add_function_parentheses = True
 
 # If true, the current module name will be prepended to all description
 # unit titles (such as .. function::).
-#add_module_names = True
+# add_module_names = True
 
 # If true, sectionauthor and moduleauthor directives will be shown in the
 # output. They are ignored by default.
-#show_authors = False
+# show_authors = False
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # A list of ignored prefixes for module index sorting.
-#modindex_common_prefix = []
+# modindex_common_prefix = []
 
 # If true, keep warnings as "system message" paragraphs in the built documents.
-#keep_warnings = False
+# keep_warnings = False
 
 
 # -- Options for HTML output ----------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'nature'
+html_theme = "nature"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
-#html_theme_options = {}
+# html_theme_options = {}
 
 # Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = []
+# html_theme_path = []
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
-#html_title = None
+# html_title = None
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
-#html_short_title = None
+# html_short_title = None
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-#html_logo = None
+# html_logo = None
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
 # pixels large.
-#html_favicon = None
+# html_favicon = None
 
 # 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"]
 
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied
 # directly to the root of the documentation.
-#html_extra_path = []
+# html_extra_path = []
 
 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.
-#html_last_updated_fmt = '%b %d, %Y'
+# html_last_updated_fmt = '%b %d, %Y'
 
 # If true, SmartyPants will be used to convert quotes and dashes to
 # typographically correct entities.
-#html_use_smartypants = True
+# html_use_smartypants = True
 
 # Custom sidebar templates, maps document names to template names.
-#html_sidebars = {}
+# html_sidebars = {}
 
 # Additional templates that should be rendered to pages, maps page names to
 # template names.
-#html_additional_pages = {}
+# html_additional_pages = {}
 
 # If false, no module index is generated.
-#html_domain_indices = True
+# html_domain_indices = True
 
 # If false, no index is generated.
-#html_use_index = True
+# html_use_index = True
 
 # If true, the index is split into individual pages for each letter.
-#html_split_index = False
+# html_split_index = False
 
 # If true, links to the reST sources are added to the pages.
-#html_show_sourcelink = True
+# html_show_sourcelink = True
 
 # If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
-#html_show_sphinx = True
+# html_show_sphinx = True
 
 # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
-#html_show_copyright = True
+# html_show_copyright = True
 
 # If true, an OpenSearch description file will be output, and all pages will
 # contain a <link> tag referring to it.  The value of this option must be the
 # base URL from which the finished HTML is served.
-#html_use_opensearch = ''
+# html_use_opensearch = ''
 
 # This is the file name suffix for HTML files (e.g. ".xhtml").
-#html_file_suffix = None
+# html_file_suffix = None
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'pstddoc'
+htmlhelp_basename = "pstddoc"
 
 
 # -- Options for LaTeX output ---------------------------------------------
 
 latex_elements = {
-# The paper size ('letterpaper' or 'a4paper').
-#'papersize': 'letterpaper',
-
-# The font size ('10pt', '11pt' or '12pt').
-#'pointsize': '10pt',
-
-# Additional stuff for the LaTeX preamble.
-#'preamble': '',
+    # The paper size ('letterpaper' or 'a4paper').
+    #'papersize': 'letterpaper',
+    # The font size ('10pt', '11pt' or '12pt').
+    #'pointsize': '10pt',
+    # Additional stuff for the LaTeX preamble.
+    #'preamble': '',
 }
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-  ('index', 'pstd.tex', u'pstd Documentation',
-   u'Frederik Rietdijk', 'manual'),
+    ("index", "pstd.tex", u"pstd Documentation", u"Frederik Rietdijk", "manual"),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
 # the title page.
-#latex_logo = None
+# latex_logo = None
 
 # For "manual" documents, if this is true, then toplevel headings are parts,
 # not chapters.
-#latex_use_parts = False
+# latex_use_parts = False
 
 # If true, show page references after internal links.
-#latex_show_pagerefs = False
+# latex_show_pagerefs = False
 
 # If true, show URL addresses after external links.
-#latex_show_urls = False
+# latex_show_urls = False
 
 # Documents to append as an appendix to all manuals.
-#latex_appendices = []
+# latex_appendices = []
 
 # If false, no module index is generated.
-#latex_domain_indices = True
+# latex_domain_indices = True
 
 
 # -- Options for manual page output ---------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    ('index', 'pstd', u'pstd Documentation',
-     [u'Frederik Rietdijk'], 1)
-]
+man_pages = [("index", "pstd", u"pstd Documentation", [u"Frederik Rietdijk"], 1)]
 
 # If true, show URL addresses after external links.
-#man_show_urls = False
+# man_show_urls = False
 
 
 # -- Options for Texinfo output -------------------------------------------
@@ -245,47 +241,58 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-  ('index', 'pstd', u'pstd Documentation',
-   u'Frederik Rietdijk', 'pstd', 'One line description of project.',
-   'Miscellaneous'),
+    (
+        "index",
+        "pstd",
+        u"pstd Documentation",
+        u"Frederik Rietdijk",
+        "pstd",
+        "One line description of project.",
+        "Miscellaneous",
+    ),
 ]
 
 # Documents to append as an appendix to all manuals.
-#texinfo_appendices = []
+# texinfo_appendices = []
 
 # If false, no module index is generated.
-#texinfo_domain_indices = True
+# texinfo_domain_indices = True
 
 # How to display URL addresses: 'footnote', 'no', or 'inline'.
-#texinfo_show_urls = 'footnote'
+# texinfo_show_urls = 'footnote'
 
 # If true, do not generate a @detailmenu in the "Top" node's menu.
-#texinfo_no_detailmenu = False
+# texinfo_no_detailmenu = False
 
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'http://docs.python.org/': None}
+intersphinx_mapping = {"http://docs.python.org/": None}
+
+intersphinx_mapping = {
+    "python": ("http://docs.python.org/3", None),
+    "numpy": ("http://docs.scipy.org/doc/numpy/", None),
+    "np": ("http://docs.scipy.org/doc/numpy/", None),
+    "scipy": ("http://docs.scipy.org/doc/scipy/reference/", None),
+    "matplotlib": ("http://matplotlib.sourceforge.net/", None),
+}
 
-intersphinx_mapping = {'python': ('http://docs.python.org/3', None),
-                       'numpy': ('http://docs.scipy.org/doc/numpy/', None),
-                       'np': ('http://docs.scipy.org/doc/numpy/', None),
-                       'scipy': ('http://docs.scipy.org/doc/scipy/reference/', None),
-                       'matplotlib': ('http://matplotlib.sourceforge.net/', None)}
+autodoc_default_flags = ["members", "show-inheritance"]
 
-autodoc_default_flags = ['members', 'show-inheritance']
 
 def skip(app, what, name, obj, skip, options):
     if name == "__init__":
         return False
     return skip
 
+
 def setup(app):
     app.connect("autodoc-skip-member", skip)
-    
-    
+
+
 # -----------------------------------------------------------------------------
 # Autosummary
 # -----------------------------------------------------------------------------
 
 import glob
+
 autosummary_generate = glob.glob("reference/*.rst")

examples/basic_example.ipynb

@@ -327,7 +327,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -341,7 +341,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.5"
+   "version": "3.9.9"
   }
  },
  "nbformat": 4,

examples/turbulence_example.ipynb

@@ -1,34 +1,45 @@
 {
-  description = "PSTD";
+  description = "K-space PSTD for Python.";
 
-  inputs.nixpkgs.url = "github:nixos/nixpkgs?ref=nixpkgs-unstable";
-  inputs.flake-utils.url = "github:numtide/flake-utils";
+  inputs.nixpkgs.url = "nixpkgs/nixpkgs-unstable";
+  inputs.utils.url = "github:numtide/flake-utils";
 
-  outputs = { self, nixpkgs, flake-utils }: flake-utils.lib.eachDefaultSystem (system: let
-      pkgs = nixpkgs.legacyPackages.${system};
-  in rec {
-
-    packages = rec {
+  outputs = { self, nixpkgs, utils }: {
+    overlay = final: prev: {
+      pythonPackagesOverrides = (prev.pythonPackagesOverrides or []) ++ [
+        (self: super: {
+          pstd = self.callPackage ./. {};
+        })
+      ];
+      # Remove when https://github.com/NixOS/nixpkgs/pull/91850 is fixed.
       python3 = let
-        python = pkgs.python3;
-      in python.override {
-        packageOverrides = final: prev: {
-          pstd = final.callPackage ./default.nix {};
+        composeOverlays = nixpkgs.lib.foldl' nixpkgs.lib.composeExtensions (self: super: {});
+        self = prev.python3.override {
+          inherit self;
+          packageOverrides = composeOverlays final.pythonPackagesOverrides;
         };
-        self = python;
-      };
-
-      pstd = python3.pkgs.pstd;
+      in self;
     };
+  } // (utils.lib.eachSystem [ "x86_64-linux" ] (system: let
+    pkgs = (import nixpkgs {
+      inherit system;
+      overlays = [ self.overlay ];
+    });
+    python = pkgs.python3;
+    pstd = python.pkgs.pstd;
+    devEnv = python.withPackages(ps: with ps.pstd; nativeBuildInputs ++ propagatedBuildInputs);
+  in {
+    # Our own overlay does not get applied to nixpkgs because that would lead to
+    # an infinite recursion. Therefore, we need to import nixpkgs and apply it ourselves.
+    defaultPackage = pstd;
 
-    defaultPackage = packages.pstd;
-
-    # devShell = (pkgs.mkShell {
-    #   nativeBuildInputs = with packages.python3.pkgs; [ notebook ] ++ pstd.propagatedBuildInputs;
-
-    # });
-    devShell = (packages.python3.withPackages(ps: with ps; [
-      notebook
-    ] ++ pstd.propagatedBuildInputs)).env;
-  });
-}
+    devShell = pkgs.mkShell {
+      nativeBuildInputs = [
+        devEnv
+      ];
+      shellHook = ''
+        export PYTHONPATH=$(readlink -f $(find . -maxdepth 1  -type d ) | tr '\n' ':'):$PYTHONPATH
+      '';
+    };
+  }));
+}

flake.lock

@@ -1,19 +1,21 @@
+"""
+k-space
+=======
+"""
+
+__version__ = "0.0.0"
 
 from .model import *
 
-#try:
-    #from .pstd_using_numba import PSTD
-#except ImportError:
-    #from .pstd import PSTD
+# try:
+# from .pstd_using_numba import PSTD
+# except ImportError:
+# from .pstd import PSTD
 
 from .pstd import PSTD
 
-#try:
-    #from .pstd_using_numba import PSTD_using_numba
-#except ImportError:
-    #raise ImportWarning("Cannot import numba. pstd_using_numba is not available")
-#from pstd_using_cuda import PSTD_using_cuda
-
-
-
-
+# try:
+# from .pstd_using_numba import PSTD_using_numba
+# except ImportError:
+# raise ImportWarning("Cannot import numba. pstd_using_numba is not available")
+# from pstd_using_cuda import PSTD_using_cuda

flake.nix

@@ -5,32 +5,31 @@
 import numba
 from . import pstd
 
-kappa = numba.autojit(pstd.kappa)
-#abs_exp = numba.autojit(pstd.abs_exp)
-pressure_abs_exp = numba.autojit(pstd.pressure_abs_exp)
-velocity_abs_exp = numba.autojit(pstd.velocity_abs_exp)
-pressure_with_pml = numba.autojit(pstd.pressure_with_pml)
-velocity_with_pml = numba.autojit(pstd.pressure_with_pml)
-to_pressure_gradient = numba.autojit(pstd.to_pressure_gradient)
-to_velocity_gradient = numba.autojit(pstd.to_velocity_gradient)
-update = numba.autojit(pstd.update)
+kappa = numba.jit(pstd.kappa)
+# abs_exp = numba.jit(pstd.abs_exp)
+pressure_abs_exp = numba.jit(pstd.pressure_abs_exp)
+velocity_abs_exp = numba.jit(pstd.velocity_abs_exp)
+pressure_with_pml = numba.jit(pstd.pressure_with_pml)
+velocity_with_pml = numba.jit(pstd.pressure_with_pml)
+to_pressure_gradient = numba.jit(pstd.to_pressure_gradient)
+to_velocity_gradient = numba.jit(pstd.to_velocity_gradient)
+update = numba.jit(pstd.update)
+
 
 class PSTD(pstd.PSTD):
-    
+
     _update = staticmethod(update)
-    
-    #_record = numba.autojit(pstd.PSTD._record)
-    
-    #kappa = staticmethod(numba.autojit(PSTD.kappa))
-    #abs_exp = staticmethod(numba.autojit(PSTD.abs_exp))
-    #pressure_with_pml = staticmethod(numba.autojit(PSTD.pressure_with_pml))
-    #velocity_with_pml = staticmethod(numba.autojit(PSTD.velocity_with_pml))
-    #pressure_gradient = staticmethod(numba.autojit(PSTD.to_pressure_gradient))
-    #velocity_gradient = staticmethod(numba.autojit(PSTD.to_velocity_gradient))
-    #update = classmethod(numba.autojit(PSTD.update))
-    
-    #pre_run = numba.autojit(PSTD.pre_run)
-    
-    #run = numba.autojit(Model.run)
-
-      
+
+    # _record = numba.jit(pstd.PSTD._record)
+
+    # kappa = staticmethod(numba.jit(PSTD.kappa))
+    # abs_exp = staticmethod(numba.jit(PSTD.abs_exp))
+    # pressure_with_pml = staticmethod(numba.jit(PSTD.pressure_with_pml))
+    # velocity_with_pml = staticmethod(numba.jit(PSTD.velocity_with_pml))
+    # pressure_gradient = staticmethod(numba.jit(PSTD.to_pressure_gradient))
+    # velocity_gradient = staticmethod(numba.jit(PSTD.to_velocity_gradient))
+    # update = classmethod(numba.jit(PSTD.update))
+
+    # pre_run = numba.jit(PSTD.pre_run)
+
+    # run = numba.jit(Model.run)

pstd/__init__.py

@@ -0,0 +1,31 @@
+[build-system]
+requires = ["flit_core >=2,<4"]
+build-backend = "flit_core.buildapi"
+
+[tool.flit.metadata]
+module = "pstd"
+author = "Frederik Rietdijk"
+requires = [
+    "acoustics",
+    "numpy",
+    "scipy",
+    "matplotlib",
+    "numexpr",
+    "pyyaml",
+]
+[tool.tox]
+legacy_tox_ini = """
+[tox]
+envlist = py39, py310
+
+[gh-actions]
+python =
+    3.9: py39
+    3.10: py310
+
+[testenv]
+deps =
+    nbconvert
+    pytest    
+commands = pytest -k "not test_notebook" {posargs}
+"""

pstd/model.py

@@ -2,36 +2,35 @@
 import numpy as np
 from pstd import Model, PSTD, Medium
 
-class TestModel():
+
+class TestModel:
     """
     Test Model.
     """
-    
-    
+
     def test_init_abstract_class(self):
         """
         __init__
         """
         f_max = 100.0
-        with pytest.raises(TypeError):
+        with pytest.raises(RuntimeError):
             model = Model(f_max)
-            
 
-class TestMedium():
-    """Test Medium.
-    """
-    
+
+class TestMedium:
+    """Test Medium."""
+
     def test_init_default(self):
         medium = Medium()
-            
+
     def test_soundspeed_for_calculation(self):
         """Test when not used in a model."""
-        
+
         # Single value. Can return
         medium = Medium()
         medium.soundspeed_for_calculation
-        
+
         # Grid. Needs to know Model grid/pml.
-        medium = Medium(np.ones((10,10)))
+        medium = Medium(np.ones((10, 10)))
         with pytest.raises(ValueError):
             medium.soundspeed_for_calculation

pstd/pstd.py

@@ -0,0 +1,18 @@
+import pathlib
+import pytest
+
+import nbformat
+import nbconvert.preprocessors
+
+
+NOTEBOOKS = list((pathlib.Path(__file__).parent.parent / "examples").glob("*.ipynb"))
+
+
+@pytest.mark.parametrize("notebook", NOTEBOOKS)
+def test_notebook(notebook):
+
+    executor = nbconvert.preprocessors.ExecutePreprocessor(timeout=60)
+
+    with open(notebook) as fin:
+        contents = nbformat.read(fin, as_version=4)
+        executor.preprocess(contents)

pstd/pstd_using_cuda.py

@@ -4,49 +4,46 @@
 
 model_parameters = [
     {
-        'maximum_frequency' :   1000.0,
-        'cfl'               :   0.05,
-        'size'              :   (15, 15),
-        },
+        "maximum_frequency": 1000.0,
+        "cfl": 0.05,
+        "size": (15, 15),
+    },
     {
-        'maximum_frequency' :   1000.0,
-        'cfl'               :   0.10,
-        'size'              :   (20, 20),
-        },
-    ]
+        "maximum_frequency": 1000.0,
+        "cfl": 0.10,
+        "size": (20, 20),
+    },
+]
 
 
-
-class TestPSTD():
+class TestPSTD:
     """
     Test Model.
     """
-    
-    #@pytest.fixture(params=[0.05, 0.10])
-    #def cfl(self, request):
-        #return request.param
-    
-    
+
+    # @pytest.fixture(params=[0.05, 0.10])
+    # def cfl(self, request):
+    # return request.param
+
     @pytest.fixture(params=model_parameters)
     def model(self, request):
         kwargs = request.param
-        kwargs['pml'] = PML(depth=10.0)
+        kwargs["pml"] = PML(depth=10.0)
         model = PSTD(**kwargs)
         return model
-    
-    
-    @pytest.fixture(params=[0, 10])
+
+    @pytest.fixture(params=[10])
     def steps(self, request):
         return request.param
-    
-    @pytest.fixture(params=[0.0, 0.001])
+
+    @pytest.fixture(params=[0.001])
     def seconds(self, request):
         return request.param
-    
+
     def test_init(self, model):
         """Initialization of model.
-        
-        If this passes, then the models returned by the fixture 
+
+        If this passes, then the models returned by the fixture
         were initialized successfully.
         """
         pass
@@ -59,88 +56,77 @@ def test_init_no_size(self):
         with pytest.raises(RuntimeError):
             model = PSTD(maximum_frequency=f_max)
 
-   
     def test_overview(self, model):
         model.overview()
 
     def test_properties(self, model):
-        
-        properties = ['cfl', 'constant_field', 'ndim', 
-                      'timestep', 'sample_frequency'
-                      ]
+
+        properties = ["cfl", "constant_field", "timestep"]
 
         for prop in properties:
             getattr(model, prop)
 
-
     def test_run_steps(self, model, steps):
         model.run(steps=steps)
 
     def test_run_seconds(self, model, seconds):
         model.run(seconds=seconds)
-      
-class TestPML():
+
+
+class TestPML:
     """Test PML.
-    
+
     Should use Mock!
     """
-    
+
     def setup_method(self, method):
         time = 1.0
         f_max = 100.0
         size = (100.0, 50.0)
         self.model = PSTD(maximum_frequency=f_max, size=size)
-        
-    
+
     def test_init_default(self):
         pass
-        
-    
+
     def test_init_custom(self):
-        absorption_coefficient = (100.0,100.0)
+        absorption_coefficient = (100.0, 100.0)
         depth = 5.0
         pml = PML(absorption_coefficient, depth)
-    
+
     def test_depth(self):
-        
-        assert(self.model.pml.depth == 0.0)
-        
+
+        assert self.model.pml.depth == 0.0
+
         self.model.pml.depth_target = 1.0
-        assert(self.model.pml.depth != 0.0)
-    
+        assert self.model.pml.depth != 0.0
+
     def test_nodes(self):
-        
-        assert(self.model.pml.nodes == 0)
-        
+
+        assert self.model.pml.nodes == 0
+
         self.model.pml.depth_target = 1.0
-        assert(self.model.pml.nodes != 0.0)
-    
+        assert self.model.pml.nodes != 0.0
+
     def is_used(self):
-        
-        assert(self.model.is_used)
-        
-        self.model.settings['pml']['use'] = False
-        assert(not self.model.is_used)
-    
+
+        assert self.model.is_used
+
+        self.model.settings["pml"]["use"] = False
+        assert not self.model.is_used
+
     def generate_grid(self):
-        
-        with pytest.raises(ValueError): # Zero size, cannot generate a PML.
+
+        with pytest.raises(ValueError):  # Zero size, cannot generate a PML.
             self.model.pml.generate_grid()
-            
+
         self.model.pml.depth_target = 1.0
         pml = self.model.pml.generate_grid()
-        
-        assert(isinstance(pml, collections.MutableMapping))
-        assert(isinstance(pml, dict))
-        
-        
-        
-        
-#class TestCalculation():
-    
-    
-    #def test_
-    
-    
-    
-        
+
+        assert isinstance(pml, collections.MutableMapping)
+        assert isinstance(pml, dict)
+
+
+# class TestCalculation():
+
+
+# def test_

pstd/pstd_using_numba.py

@@ -5,73 +5,63 @@
 
 from numpy.testing import assert_array_almost_equal
 
-#import acoustics.td.pstd
-#import acoustics.td.pstd_using_cuda
+# import acoustics.td.pstd
+# import acoustics.td.pstd_using_cuda
 
-#class PSTD(unittest.TestCase):
-    
-    #def test_pressure_with_pml(self):
-        #pass
-    
-    #def test_velocity_with_pml(self):
-        #pass
+# class PSTD(unittest.TestCase):
 
+# def test_pressure_with_pml(self):
+# pass
 
+# def test_velocity_with_pml(self):
+# pass
 
 
+##class Validate_PSTD(unittest.TestCase):
+##"""
+##PSTD related tests.
+##"""
 
+##def test_amplitude_and_phase(self):
+##"""
+##Validate the response in the frequency domain.
+##"""
 
-##class Validate_PSTD(unittest.TestCase):
-    ##"""
-    ##PSTD related tests.
-    ##"""
-    
-    ##def test_amplitude_and_phase(self):
-        ##"""
-        ##Validate the response in the frequency domain.
-        ##"""
-        
-        ##x, y = 40.0, 40.0
-        
-        ##c = 343.2
-        
-        ##source = Source(Position2D(x/2.0, 5.0), pressure=0.1)
-        ##receiver = Receiver(Position2D(x/2.0, 35.0), quantities=['p'])
-        ##medium = Medium(soundspeed=c, density=1.296)
-        
-        ##time = y / c
-        
-        ##pml = PML((10.0, 10.0), depth=5.0)
-        
-        ##model = PSTD(time=time, f_max=200.0, pml=pml, medium=medium, cfl=0.3, size=[x, y])
-        
-        ##model.sources.append(source)
-        ##model.receivers.append(receiver)
-        
-        ##print model.timesteps
-        
-        ##import logging
-        ##logger = logging.getLogger('acoustics.td')    # Module name
-        ##logger.setLevel(logging.INFO)                   # Logging level
-
-        
-        ##model.run()
-        
-        
-        ##p_pstd = np.fft.fft(receiver.data['p'])
-        
-        ##print p_pstd
-        
-        ##r = receiver.position[1] - source.position[1]
-        
-        ##p_freq = A / r * np.exp(1j*k*r)
-        
-        
-        
-    
-    
-
-    
-        
-if __name__ == '__main__':
+##x, y = 40.0, 40.0
+
+##c = 343.2
+
+##source = Source(Position2D(x/2.0, 5.0), pressure=0.1)
+##receiver = Receiver(Position2D(x/2.0, 35.0), quantities=['p'])
+##medium = Medium(soundspeed=c, density=1.296)
+
+##time = y / c
+
+##pml = PML((10.0, 10.0), depth=5.0)
+
+##model = PSTD(time=time, f_max=200.0, pml=pml, medium=medium, cfl=0.3, size=[x, y])
+
+##model.sources.append(source)
+##model.receivers.append(receiver)
+
+##print model.timesteps
+
+##import logging
+##logger = logging.getLogger('acoustics.td')    # Module name
+##logger.setLevel(logging.INFO)                   # Logging level
+
+
+##model.run()
+
+
+##p_pstd = np.fft.fft(receiver.data['p'])
+
+##print p_pstd
+
+##r = receiver.position[1] - source.position[1]
+
+##p_freq = A / r * np.exp(1j*k*r)
+
+
+if __name__ == "__main__":
     unittest.main()

pstd/pstd_using_numexpr.py

@@ -1,32 +1,36 @@
-try:
-    import numbapro
-except ImportError:
-    ImportWarning("numbapro not available. Cannot run tests.")
+import sys
+import pytest
 
 try:
-    from acoustics.td.pstd_using_cuda import exp, add
-except numbapro.cudadrv.error.CudaSupportError:
+    from pstd.pstd_using_cuda import exp, add
+except ImportError:
     pass
 
-class Cuda(unittest.TestCase):
+
+@pytest.mark.skipif("cupy" not in sys.modules, reason="requires cuda")
+class TestCuda:
     """
     Cuda related tests.
     """
-    
+
     def test_add(self):
-        
-        a = np.random.randn(100).astype('complex64') + 1j*np.random.randn(100).astype('complex64')
-        b = np.random.randn(100).astype('complex64') + 1j*np.random.randn(100).astype('complex64')
-    
-        assert_array_almost_equal(a+b, add(a,b))
-    
+
+        a = np.random.randn(100).astype("complex64") + 1j * np.random.randn(100).astype(
+            "complex64"
+        )
+        b = np.random.randn(100).astype("complex64") + 1j * np.random.randn(100).astype(
+            "complex64"
+        )
+
+        assert_array_almost_equal(a + b, add(a, b))
+
     def test_exp(self):
-        
-        theta = np.linspace(0.0, 2.0*np.pi, 100).astype('complex64')
-        assert_array_almost_equal(np.exp(1j*theta), exp(1j*theta))
-        
-        a = (np.random.randn(100) + 1j * np.random.randn(100)).astype('complex64')
+
+        theta = np.linspace(0.0, 2.0 * np.pi, 100).astype("complex64")
+        assert_array_almost_equal(np.exp(1j * theta), exp(1j * theta))
+
+        a = (np.random.randn(100) + 1j * np.random.randn(100)).astype("complex64")
         assert_array_almost_equal(np.log(np.exp(a)), np.log(exp(a)))
-        
-        x = np.arange(50).astype('complex64')
+
+        x = np.arange(50).astype("complex64")
         assert_array_almost_equal(np.log(np.exp(x)), np.log(exp(x)))