Merge branch 'master' of github.com:devitocodes/devito_book into jakubbober-advec

Author: jakubbober

.github/workflows/deploy-jupyter-book.yml

@@ -1,3 +1,4 @@
+# Workflow for deploying fdm-jupyter-book to GitHub Pages (https://www.devitoproject.org/devito_book/)
 name: Deploy Jupyter Book
 
 # Only run this when the master branch changes

.github/workflows/jupyter-notebooks.yml

@@ -1,3 +1,4 @@
+# Workflow for checking notebooks in fdm-devito-notebooks are compiling using nbval
 name: Jupyter Notebooks
 
 on:
@@ -69,9 +70,18 @@ jobs:
         pip install -e .
         pip install matplotlib
         pip install --user git+https://github.com/devitocodes/devito.git
+    - name: Vibration ODE notebooks (1.1 to 1.8)
+      run: |
+        $RUN_CMD python -m pytest -W ignore::DeprecationWarning --nbval --cov . --cov-config=.coveragerc --cov-report=xml:vib_coverage.xml $SKIP fdm-devito-notebooks/01_vib/vib_undamped.ipynb  
     - name: Waves notebooks (2.1 and 2.2)
       run: |
         $RUN_CMD python -m pytest -W ignore::DeprecationWarning --nbval --cov . --cov-config=.coveragerc --cov-report=xml:waves_coverage.xml $SKIP fdm-devito-notebooks/02_wave/wave1D_fd1.ipynb
+    - name: Waves notebooks (2.3 to 2.5)
+      run: |
+        $RUN_CMD python -m pytest -W ignore::DeprecationWarning --nbval --cov . --cov-config=.coveragerc --cov-report=xml:waves_coverage.xml $SKIP fdm-devito-notebooks/02_wave/wave1D_prog.ipynb
+    - name: Diffusion notebooks (3.7)
+      run: |
+        $RUN_CMD python -m pytest -W ignore::DeprecationWarning --nbval --cov . --cov-config=.coveragerc --cov-report=xml:diffu_coverage.xml $SKIP fdm-devito-notebooks/03_diffu/diffu_rw.ipynb
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v1.0.6
       with:

.github/workflows/verification.yml

@@ -1,3 +1,4 @@
+# Workflow for running verification tests from original textbook on Devito functions
 name: Verification
 
 on:
@@ -71,10 +72,16 @@ jobs:
         pip install -e .
         pip install matplotlib
         pip install --user git+https://github.com/devitocodes/devito.git
-#     - name: Waves (2.1 to 2.4)
-#       run: |
-#         cd fdm-devito-notebooks/wave/src-wave/wave1D/devito
-#         $RUN_CMD py.test -s -v $SKIP wave1D_u0.py::test_quadratic wave1D_u0.py::test_constant
+    - name: Waves (2.1 to 2.5)
+      run: |
+        cd fdm-devito-notebooks/02_wave/src-wave/wave1D
+        $RUN_CMD python -m pytest -W ignore::DeprecationWarning -s -v --cov . --cov-config=.coveragerc --cov-report=xml:waves_coverage.xml $SKIP wave1D_u0.py::test_constant
+    - name: Diffusion (3.7)
+      run: |
+        cd fdm-devito-notebooks/03_diffu/src-diffu
+        $RUN_CMD python -m pytest -W ignore::DeprecationWarning -s -v --cov . --cov-config=.coveragerc --cov-report=xml:diffu_coverage.xml $SKIP random_walk.py
+     
+    
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v1.0.6
       with:

README.md

@@ -7,7 +7,7 @@
 ![Jupyter Notebooks](https://github.com/devitocodes/devito_book/workflows/Jupyter%20Notebooks/badge.svg)
 ![Verification](https://github.com/devitocodes/devito_book/workflows/Verification/badge.svg)
 ![Deploy Jupyter Book](https://github.com/devitocodes/devito_book/workflows/Deploy%20Jupyter%20Book/badge.svg)
-[![Slack Status](https://img.shields.io/badge/chat-on%20slack-%2336C5F0)](https://opesci-slackin.now.sh)
+[![Slack Status](https://img.shields.io/badge/chat-on%20slack-%2336C5F0)](https://devitocodes.slack.com/join/shared_invite/zt-gtd2yxj9-Y31YKk_7lr9AwfXeL2iMFg#/)
 
 
 ## The Devito Book
@@ -21,11 +21,10 @@ This work is licensed under a
 
 ### Directory structure
 
-A summary of the most important subdirectories of this repository is as follows:
+The most important subdirectories in this repository are:
 
-* `doc` and `src` contain the documents and source code for the [original book](https://github.com/hplgit/fdm-book)
-* `fdm-devito-notebooks` contains Jupyter notebooks of the original book with Devito implementations (WIP)
-* `fdm-jupyter-book` contains the completed Jupyter notebooks from `fdm-devito-notebooks`, deployed using GitHub pages [here](https://devitoproject.org/devito_book)
+* `fdm-devito-notebooks`, which contains the Jupyter notebooks from the original book with Devito implementations (WIP)
+* `fdm-jupyter-book`, which contains the **completed** Jupyter notebooks from `fdm-devito-notebooks`, deployed using GitHub pages [here](https://devitoproject.org/devito_book)
 
 ### How to use the Devito Book