Towards 0.2.0 (#194)

* display_complex_field (#193)
* deprecation warning for plot_complex_field in favor of display_complex_field
* updated save_video and notebooks
* points_on_circle, unit_fibonacci_sphere, circ_mask, bli_function are not private anymore
* added css and js files to paths for build_docs action
* removed __about__
* removed transformations module
* added more tests for signal_processing
* update docs and example with display_complex_field

.github/actions/python-poetry-env/action.yml

@@ -19,3 +19,6 @@ runs:
     - name: Create virtual environment
       run: poetry install --with=dev
       shell: bash
+    - name: Install jaxlib
+      run: poetry run pip install jax[cpu]
+      shell: bash

.github/workflows/build_docs.yml

@@ -0,0 +1,25 @@
+# This is a workflow that runs whenever a pull request
+# changes some documentation files or the mkdocs.yml file. It
+# checks that the documentation builds correctly.
+
+name: Build Docs
+
+on:
+  pull_request:
+    paths:
+      - 'docs/**'
+      - 'mkdocs.yml'
+      - '**.md'
+      - '**.ipynb'
+      - '**.sh'
+      - '**.css'
+      - '**.js'
+
+jobs:
+  build-and-publish:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: ./.github/actions/python-poetry-env
+      - name: Build docs
+        run: poetry run mkdocs build

.github/workflows/ci_tests.yml

@@ -0,0 +1,34 @@
+# This workflow runs both the regression tests and the unit/integration tests.
+# It is triggered on push to the main branch.
+
+name: CI
+
+on:
+  push:
+    branches: [ main ]
+
+jobs:
+  full_tests:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: ./.github/actions/python-poetry-env
+      - name: Downloading test data
+        run: |
+          make get_test_data
+      - name: Running Regression Tests
+        run: |
+          poetry run coverage run --source=jwave -m pytest -xvs ./tests/regression_tests
+      - name: Remove coverage data from regression tests
+        run: |
+          rm ./.coverage
+      - name: Running Unit and Integration tests
+        run: |
+          poetry run coverage run --source=jwave -m pytest -xvs --ignore=tests/regression_tests
+          poetry run coverage xml
+      - name: "Upload coverage to Codecov"
+        uses: codecov/codecov-action@v3
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml
+          name: codecov-umbrella

.github/workflows/regression_tests.yml

@@ -0,0 +1,20 @@
+# This is a workflow for Regression Tests.
+# It is triggered by a pull request to the main branch.
+
+name: Regression Tests
+
+on:
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  regression_tests:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: ./.github/actions/python-poetry-env
+      - name: Downloading test data
+        run: |
+          make get_test_data
+      - name: Running tests
+        run: poetry run coverage run --source=jwave -m pytest -xvs ./tests/regression_tests

.github/workflows/unit_integration_tests.yml

@@ -0,0 +1,33 @@
+# This is a workflow for Unit, Integration, and Regression Tests
+# It is used to test the code on every pull request, whenever a
+# python, matlab, yaml, makefile, or markdown file is changed.
+
+name: Unit and Integration Tests
+
+on:
+  pull_request:
+    paths:
+      - '**.py'
+      - '**.m'
+      - '**.yaml'
+      - '**Makefile'
+
+jobs:
+  unit_and_integration_tests:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: ./.github/actions/python-poetry-env
+      - name: Downloading test data
+        run: |
+          make get_test_data
+      - name: Running tests
+        run: |
+          poetry run coverage run --source=jwave -m pytest -xvs --ignore=tests/regression_tests
+          poetry run coverage xml
+      - name: "Upload coverage to Codecov"
+        uses: codecov/codecov-action@v3
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml
+          name: codecov-umbrella

CHANGELOG.md

@@ -4,6 +4,22 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
+### Changed
+- Refactored `save_video` to use opencv.
+
+### Deprecated
+- `plot_complex_field` has been deprecated in favor of `display_complex_field`
+
+### Removed
+- Removed the uncertainty propagation notebook example. For a more in depth example of using linear uncertainty propagation see [this repository](https://github.com/ucl-bug/linear-uncertainty)
+
+### Added
+- Exposed `points_on_circle` function to generate points on a circle
+- Exposed `unit_fibonacci_sphere` function
+- Exposed `fibonacci_sphere` function
+- Exposed `sphere_mask` function for creating spherical binary masks
+- Exposed `circ_mask` function for creating circular binary masks
+- Exposed bli_function that is used to compute the band limited interpolant
 
 ## [0.1.3] - 2023-06-28
 ### Added
@@ -69,4 +85,3 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 [0.0.3]: https://github.com/ucl-bug/jwave/compare/0.0.2...0.0.3
 [0.0.2]: https://github.com/ucl-bug/jwave/compare/0.0.1...0.0.2
 [0.0.1]: https://github.com/ucl-bug/jwave/releases/tag/0.0.1
-

README.md

@@ -6,7 +6,7 @@
 
 [![Support](https://dcbadge.vercel.app/api/server/VtUb4fFznt?style=flat)](https://discord.gg/VtUb4fFznt)
 [![License: LGPL v3](https://img.shields.io/badge/License-LGPL_v3-blue.svg)](LICENSE)
-[![Continous Integration](https://github.com/ucl-bug/jwave/actions/workflows/tests.yml/badge.svg)](https://github.com/ucl-bug/jwave/actions/workflows/tests.yml)
+[![Continous Integration](https://github.com/ucl-bug/jwave/actions/workflows/ci_tests.yml/badge.svg)](https://github.com/ucl-bug/jwave/actions/workflows/ci_tests.yml)
 [![codecov](https://codecov.io/gh/ucl-bug/jwave/branch/main/graph/badge.svg?token=6J03OMVJS1)](https://codecov.io/gh/ucl-bug/jwave)
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ucl-bug/jwave/main?labpath=docs%2Fnotebooks%2Fivp%2Fhomogeneous_medium.ipynb)
 [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1xAHAognF1v9un6GNvaGPSfdVeCDK8l9z?usp=sharing)

docs/api_utils.md

@@ -4,6 +4,6 @@
     handler: python
     members:
         - is_numeric
-        - plot_complex_field
+        - display_complex_field
     show_root_heading: true
     show_source: false

docs/notebooks/harmonic/helmholtz_problem.ipynb

@@ -46,8 +46,8 @@
     "from matplotlib import pyplot as plt\n",
     "\n",
     "from jwave import FiniteDifferences, FourierSeries\n",
-    "from jwave.geometry import Domain, Medium, _circ_mask\n",
-    "from jwave.utils import plot_complex_field, show_positive_field\n",
+    "from jwave.geometry import Domain, Medium, circ_mask\n",
+    "from jwave.utils import display_complex_field, show_positive_field\n",
     "\n",
     "key = random.PRNGKey(42)  # Random seed"
    ]
@@ -104,7 +104,7 @@
     "src = FourierSeries(jnp.expand_dims(src_field, -1), domain) * omega\n",
     "\n",
     "# Plotting\n",
-    "_ = plot_complex_field(src)"
+    "_ = display_complex_field(src)"
    ]
   },
   {
@@ -119,8 +119,8 @@
     "sound_speed = sound_speed.at[20:105, 20:200].set(1.0)\n",
     "sound_speed = (\n",
     "    sound_speed\n",
-    "    * (1 - _circ_mask(N, 90, [64, 180]))\n",
-    "    * (1 - _circ_mask(N, 50, [64, 22]))\n",
+    "    * (1 - circ_mask(N, 90, [64, 180]))\n",
+    "    * (1 - circ_mask(N, 50, [64, 22]))\n",
     "    * 0.5\n",
     "    + 1\n",
     ")\n",
@@ -170,7 +170,7 @@
     }
    ],
    "source": [
-    "_ = plot_complex_field(field, max_intensity=2e5)"
+    "_ = display_complex_field(field, max_intensity=2e5)"
    ]
   },
   {
@@ -272,7 +272,7 @@
    "source": [
     "# Solve new problem\n",
     "field = solve_helmholtz(medium, params)\n",
-    "_ = plot_complex_field(field, max_intensity=2e5)"
+    "_ = display_complex_field(field, max_intensity=2e5)"
    ]
   },
   {
@@ -316,7 +316,7 @@
     "\n",
     "# Solve new problem\n",
     "field = solve_helmholtz(medium, params)\n",
-    "_ = plot_complex_field(field, max_intensity=2e5)"
+    "_ = display_complex_field(field, max_intensity=2e5)"
    ]
   },
   {

docs/notebooks/ivp/custom_sensors.ipynb

@@ -30,7 +30,7 @@
     "from jwave import FourierSeries\n",
     "from jwave.acoustics import simulate_wave_propagation\n",
     "from jwave.geometry import *\n",
-    "from jwave.geometry import _circ_mask\n",
+    "from jwave.geometry import circ_mask\n",
     "from jwave.utils import show_field\n",
     "\n",
     "domain = Domain((128, 128), (0.1e-3, 0.1e-3))\n",
@@ -48,10 +48,10 @@
     "# Defining the initial pressure\n",
     "\n",
     "N = domain.N\n",
-    "mask1 = _circ_mask(N, 8, (50, 50))\n",
-    "mask2 = _circ_mask(N, 5, (80, 60))\n",
-    "mask3 = _circ_mask(N, 10, (64, 64))\n",
-    "mask4 = _circ_mask(N, 30, (64, 64))\n",
+    "mask1 = circ_mask(N, 8, (50, 50))\n",
+    "mask2 = circ_mask(N, 5, (80, 60))\n",
+    "mask3 = circ_mask(N, 10, (64, 64))\n",
+    "mask4 = circ_mask(N, 30, (64, 64))\n",
     "p0 = 5.0 * mask1 + 3.0 * mask2 + 4.0 * mask3 + 0.5 * mask4\n",
     "\n",
     "p0 = 1.0 * jnp.expand_dims(p0, -1)\n",

docs/notebooks/ivp/different_discretizations.ipynb

@@ -20,7 +20,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from jwave.geometry import Domain, Medium, TimeAxis, _circ_mask\n",
+    "from jwave.geometry import Domain, Medium, TimeAxis, circ_mask\n",
     "from jwave.acoustics.time_varying import simulate_wave_propagation\n",
     "from jwave import FiniteDifferences, FourierSeries\n",
     "from jwave.signal_processing import smooth\n",
@@ -50,7 +50,7 @@
     "\n",
     "# Smoothed initial pressure distribution\n",
     "Nx = domain.N\n",
-    "p0 = 5.0 * _circ_mask(Nx, 5, (128, 40))\n",
+    "p0 = 5.0 * circ_mask(Nx, 5, (128, 40))\n",
     "p0 = smooth(p0)\n",
     "\n",
     "# Getting time axis\n",

docs/notebooks/ivp/heterogeneous_medium.ipynb

@@ -25,7 +25,7 @@
     "from jwave import FourierSeries\n",
     "from jwave.acoustics import simulate_wave_propagation\n",
     "from jwave.geometry import *\n",
-    "from jwave.geometry import _circ_mask\n",
+    "from jwave.geometry import circ_mask\n",
     "from jwave.utils import show_field, show_positive_field\n",
     "\n",
     "domain = Domain((128, 128), (0.1e-3, 0.1e-3))"
@@ -87,7 +87,7 @@
     "# Defining the initial pressure\n",
     "\n",
     "N = domain.N\n",
-    "p0 = _circ_mask(N, 3, (64, 30))\n",
+    "p0 = circ_mask(N, 3, (64, 30))\n",
     "\n",
     "p0 = 1.0 * jnp.expand_dims(p0, -1)\n",
     "p0 = FourierSeries(p0, domain)"
@@ -244,7 +244,7 @@
     "density = FiniteDifferences(np.expand_dims(density, -1), domain, accuracy=8)\n",
     "\n",
     "N = domain.N\n",
-    "p0 = _circ_mask(N, 3, (64, 30))\n",
+    "p0 = circ_mask(N, 3, (64, 30))\n",
     "\n",
     "p0 = 1.0 * jnp.expand_dims(p0, -1)\n",
     "p0 = FiniteDifferences(p0, domain, accuracy=8)"

docs/notebooks/ivp/homogeneous_medium.ipynb

@@ -147,9 +147,9 @@
     "from jax import numpy as jnp\n",
     "\n",
     "from jwave import FourierSeries\n",
-    "from jwave.geometry import _circ_mask\n",
+    "from jwave.geometry import circ_mask\n",
     "\n",
-    "p0 = 1.0 * jnp.expand_dims(_circ_mask(N, 4, (80, 60)), -1)\n",
+    "p0 = 1.0 * jnp.expand_dims(circ_mask(N, 4, (80, 60)), -1)\n",
     "p0 = FourierSeries(p0, domain)"
    ]
   },