display_complex_field (#193)

* deprecation warning for plot_complex_field in favor of display_complex_field
* updated save_video and notebooks
* made actions more granular

.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 +1,23 @@
+# 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'
+
+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 +4,14 @@ 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)
 
 ## [0.1.3] - 2023-06-28
 ### Added
@@ -69,4 +77,3 @@ 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/notebooks/others/save_video.ipynb

@@ -7,69 +7,44 @@
    "source": [
     "# Save video\n",
     "\n",
-    "Note that the `save_video` funcion requires [`imageio`](https://imageio.readthedocs.io/en/stable/) and [`tqdm`](https://tqdm.github.io/), which are not installed by default. \n",
-    "\n",
-    ":warning: Note that his function also **deletes** and uses the temporary folder `/tmp/jwave_video`."
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "51cb654b-3517-434e-ad67-1a459c08854e",
-   "metadata": {},
-   "source": [
-    "⚠️ Run the next cell only if you don't have `imageio-ffmpeg` installed, otherwise it will be reinstalled"
+    "⚠️ The `save_video` funcion requires [`opencv`](https://pypi.org/project/opencv-python/) and (optionally) [`tqdm`](https://tqdm.github.io/), which are not installed by default. "
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 1,
-   "id": "7bb6d056-f7f7-4372-97fe-29ec292ead0b",
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Collecting imageio-ffmpeg\n",
-      "  Using cached imageio_ffmpeg-0.4.7-py3-none-manylinux2010_x86_64.whl (26.9 MB)\n",
-      "Installing collected packages: imageio-ffmpeg\n",
-      "Successfully installed imageio-ffmpeg-0.4.7\n"
-     ]
-    }
-   ],
-   "source": [
-    "!pip install imageio-ffmpeg"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 2,
    "id": "52df5536-f518-4b65-aaa7-6f99327bce93",
    "metadata": {},
    "outputs": [],
    "source": [
     "import numpy as np\n",
     "from jax import jit\n",
     "from jax import numpy as jnp\n",
-    "from jaxdf import FourierSeries\n",
-    "from matplotlib import pyplot as plt\n",
     "\n",
     "from jwave import FourierSeries\n",
+    "from jwave.geometry import Domain, Medium, TimeAxis\n",
     "from jwave.acoustics import simulate_wave_propagation\n",
-    "from jwave.geometry import *\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))"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 2,
    "id": "8bbe4e23-f7d6-4c50-97df-44a437069445",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "No GPU/TPU found, falling back to CPU. (Set TF_CPP_MIN_LOG_LEVEL=0 and rerun for more info.)\n"
+     ]
+    }
+   ],
    "source": [
+    "# Defining an heterogeneous density map\n",
     "density = np.ones(domain.N) * 1000\n",
     "density[50:90, 65:100] = 2300\n",
     "density = FourierSeries(np.expand_dims(density, -1), domain)\n",
@@ -86,7 +61,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 3,
    "id": "e5386fc6-cbe7-43c8-a5ec-e6a150c6fed9",
    "metadata": {},
    "outputs": [],
@@ -97,31 +72,39 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 4,
    "id": "513ae3ad-8ae0-4d7f-8e65-71b89eff7abf",
    "metadata": {},
    "outputs": [
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "100%|█████████████████████████████████████████████████████████████████████████████████████| 600/600 [01:02<00:00,  9.62it/s]\n"
+      "100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 599/599 [00:01<00:00, 347.57it/s]\n"
      ]
     }
    ],
    "source": [
     "from jwave.extras.export import save_video\n",
     "\n",
-    "save_video(pressure, './sample_video.mp4', vmax=0.1, vmin=-0.1, fps=50)"
+    "save_video(pressure, './sample_video.mp4', vmax=0.05, vmin=-0.05, fps=50)"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "de9580f7-3460-49bc-9fea-aef4af8bfc33",
+   "id": "1230bbf5-48f3-4039-902e-d0532f1164c4",
    "metadata": {},
    "source": [
-    "<video src=\"./sample_video.mp4\" controls=\"controls\"></video>"
+    "You can now find a video in the same folder as this notebook"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "18f77b37-eff6-4b40-9486-1b7c4a856e5f",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
@@ -140,7 +123,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.5"
+   "version": "3.11.4"
   }
  },
  "nbformat": 4,