use upstream changes that move to pytest (#36)

* change nodata_value to -99999 in topotools

Previous value -9999 did not have enough digits since new etopo 2022
data has this as an actual topography value in the Mariana Trench
(when written with `Z_format='%.0f'`).

* Fix bug related to tracking pressure at gauges

* simplify make_fgout_animation.py use of update_artists

These do not need to be passed into update, unpacked, and repacked,
since the objects created in the script will be used into update.
If blit==False then they are not needed at all.

* use image backend Agg in make_fgout_animation.py so animation size agrees with specified figure size

* set blit=False and auto-detect number of fgout frames

* clean up make_fgout_animation.py

* added new chile2010_fgmax-fgout/make_fgout_animation_with_transect.py

* Add dZ_format parameter to DTopography.write function

The default is now '%.3f', millimeter resolution, making smaller dtopo
files than previously.

* handle 0 radius

* fix type on set_pressure

* fix duplicate r

* make comparison fp-safe

* handle underflow

* avoid underflow in wind setting too

* Initial CI GitHub action script

* Update testing.yml

* Add checking out of clawpack and geoclaw

* Add lint and testing to CI

* Disable linting for the time being

* Re-enable linting but only for geoclaw

* Exclude old_topotools.py

Do not want to touch the old topotools file for reference.

* update testing for our branch names

* fix checkout in CI

---------

Co-authored-by: Randy LeVeque <rjl@uw.edu>
Co-authored-by: Kyle Mandli <kyle.Mandli@gmail.com>

.github/workflows/testing.yml

@@ -0,0 +1,59 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python application
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.12"
+    - name: Checkout clawpack
+      uses: actions/checkout@v4.1.5
+      with:
+        repository: climateimpactlab/clawpack
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install gfortran liblapack-pic liblapack-dev libnetcdf-dev libnetcdff-dev
+        python -m pip install --upgrade pip
+        pip install flake8 pytest
+    - name: Setup clawpack super repository
+      run: |
+        git submodule init
+        git submodule update
+        pip install --user -e .
+    - name: Setup geoclaw
+      run: |
+        cd geoclaw
+        if [[ "${{ github.event_name }}" == "pull_request" ]]; then
+          git fetch origin pull/${{ github.event.pull_request.number }}/merge:PR
+          git checkout PR
+        else
+          git checkout ${{ github.ref_name }}
+        fi
+    - name: Lint with flake8
+      run: |
+        cd geoclaw
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --exclude old_dtopotools.py
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        cd geoclaw
+        pytest