Add linting via flake to github actions

.github/workflows/testing.yml

@@ -0,0 +1,47 @@
+name: Storm surge examples testing
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.10"
+    - name: Checkout clawpack
+      uses: actions/checkout@v4.1.5
+      with:
+        repository: clawpack/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: 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
+        # 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

World_Simulation/setplot.py

@@ -181,14 +181,7 @@ def gauge_afteraxes(cd):
         axes.set_xticks([0, 1, 2, 3, 4, 5, 6, 7, 8])
         axes.set_xticklabels([r"$0$",r"$1$",r"$2$", r"$3$", r"$4$", r"$5$", r"$6$", r"$7$", r"$8$"])
         axes.grid(True)
-
-
-    try:
-        gauge_data=gauges[cd.gaugeno-1]
-        axes.plot(gauge_data[:,0], gauge_data[:,1], label=data_names[cd.gaugeno-1])
-        axes.legend()
-    except:
-            print('Gauge Data Unavailable')
+
     plotaxes.afteraxes = gauge_afteraxes
 
 

delta_2020/setrun.py

@@ -443,7 +443,7 @@ def setgeo(rundata):
 
     # Convert ATCF data to GeoClaw format
     clawutil.data.get_remote_file("http://ftp.nhc.noaa.gov/atcf/archive/2020/bal262020.dat.gz")
-    atcf_path = os.path.join(data_dir, "bal262020.dat")
+    atcf_path = os.path.join(scratch_dir, "bal262020.dat")
     # Note that the get_remote_file function does not support gzip files which
     # are not also tar files.  The following code handles this
     with gzip.open(".".join((atcf_path, 'gz')), 'rb') as atcf_file,    \

dennis_2005/setrun.py

@@ -399,7 +399,7 @@ def setgeo(rundata):
     topo_path = os.path.join(scratch_dir, 'gulf_caribbean.tt3')
     topo_data.topofiles.append([3, topo_path])
 
-clawutil.data.get_remote_file(
+    clawutil.data.get_remote_file(
            "https://www.jumbomail.me/l/en/gallery/6C697261515A333163756E464B3342347436653838673D3D/715049578")
     topo_path = os.path.join(scratch_dir, 'gulf_caribbean.tt3')
     topo_data.topofiles.append([3, topo_path])

florence_2018/setplot.py

@@ -6,6 +6,8 @@
     
 """
 import os
+import io
+import urllib.request
 
 import numpy as np
 import matplotlib
@@ -43,7 +45,7 @@ def setplot(plotdata):
 
     # Load data from output
     clawdata = clawpack.clawutil.data.ClawInputData(2)
-    clawdata.read('claw.data')
+    clawdata.read(os.path.join(plotdata.outdir,'claw.data'))
     physics = clawpack.geoclaw.data.GeoClawData()
     physics.read(os.path.join(plotdata.outdir,'geoclaw.data'))
     surge_data = clawpack.geoclaw.data.SurgeData()
@@ -388,8 +390,8 @@ def fetch(product, expected_header, col_idx, col_types):
             if verbose:
                 print('Fetching {} data from NOAA for station {}'.format(
                     product, station))
-            full_url = '{}?{}'.format(NOAA_API_URL, urlencode(noaa_params))
-            with urlopen(full_url) as response:
+            full_url = '{}?{}'.format(NOAA_API_URL, urllib.request.urlencode(noaa_params))
+            with urllib.request.urlopen(full_url) as response:
                 text = response.read().decode('utf-8')
                 with io.StringIO(text) as data:
                     # ensure that received header is correct
@@ -633,7 +635,7 @@ def gauge_afteraxes(cd):
     # Set up for axes in this figure:
     plotaxes = plotfigure.new_plotaxes()
     try:
-        plotaxes.xlimits = [amrdata.t0,amrdata.tfinal]
+        plotaxes.xlimits = [clawdata.t0, clawdata.tfinal]
     except:
         pass
     plotaxes.ylimits = surface_limits

ike_2008/setplot.py

@@ -71,7 +71,7 @@ def read_tide_gauge_data(base_path, skiprows=5, verbose=False):
     station_info_file = open(os.path.join(base_path,'Ike_Gauges_web.txt'),'r')
 
     # Skip past header
-    for i in xrange(skiprows):
+    for i in range(skiprows):
         station_info_file.readline()
 
     # Read in each station
@@ -88,7 +88,7 @@ def read_tide_gauge_data(base_path, skiprows=5, verbose=False):
             else:
                 stations[data_line[0]]['gauge_no'] = int(data_line[1])
             if verbose:
-                print "Station %s: %s" % (data_line[0],stations[data_line[0]])
+                print("Station %s: %s" % (data_line[0],stations[data_line[0]]))
 
             # Load and extract real station data
             data = scipy.io.loadmat(os.path.join(base_path,'result_%s.mat' % data_line[0]))
@@ -116,7 +116,7 @@ def read_adcirc_gauge_data(only_gauges=None, base_path="", verbose=False):
         data = numpy.loadtxt(gauge_file)
         stations[i+1] = data
         if verbose:
-            print "Read in ADCIRC gauge file %s" % gauge_file
+            print("Read in ADCIRC gauge file %s" % gauge_file)
 
     return stations
 
@@ -144,7 +144,7 @@ def read_adcirc_gauge_data(only_gauges=None, base_path="", verbose=False):
     adcirc_path = "./gauge_data"
     ADCIRC_gauges = read_adcirc_gauge_data(base_path=os.path.join(adcirc_path,'new_data'))
 except:
-    print "Could not load external gauge files, ignoring."
+    print("Could not load external gauge files, ignoring.")
     pass
 
 

ike_2008/setrun.py

@@ -7,13 +7,14 @@
 
 """
 
-from __future__ import print_function
-
 import os
 import datetime
 
 import numpy as np
 
+import clawpack.clawutil.data
+import clawpack.geoclaw.topotools as topotools
+
 # Need to adjust the date a bit due to weirdness with leap year (I think)
 ike_landfall = datetime.datetime(2008,9,13 - 1,7) - datetime.datetime(2008,1,1,0)
 
@@ -579,7 +580,7 @@ def get_topo(plot=False):
             os.path.join(base_url, "NOAA_Galveston_Houston.tt3.tar.bz2"),
             os.path.join(base_url, "galveston_tx.asc.tar.bz2")]
     for url in urls:
-        data.get_remote_file(url, verbose=True)
+        clawpack.clawutil.data.get_remote_file(url, verbose=True)
 
     # Plot if requested
     if plot:

irene_2011/setplot.py

@@ -215,12 +215,12 @@ def gauge_afteraxes(cd):
         axes.grid(True)
 
 
-    try:
-        gauge_data=gauges[cd.gaugeno-1]
-        axes.plot(gauge_data[:,0], gauge_data[:,1], label=data_names[cd.gaugeno-1])
-        axes.legend()
-    except:
-            print('Gauge Data Unavailable')
+    # try:
+    #     gauge_data=gauges[cd.gaugeno-1]
+    #     axes.plot(gauge_data[:,0], gauge_data[:,1], label=data_names[cd.gaugeno-1])
+    #     axes.legend()
+    # except:
+    #         print('Gauge Data Unavailable')
     plotaxes.afteraxes = gauge_afteraxes
 
 

karen_2013/setrun.py

@@ -431,7 +431,7 @@ def setgeo(rundata):
     try:
         geo_data = rundata.geo_data
     except:
-        print "*** Error, this rundata has no geo_data attribute"
+        print("*** Error, this rundata has no geo_data attribute")
         raise AttributeError("Missing geo_data attribute")
 
     # == Physics ==

maria_2017/setplot.py

@@ -203,12 +203,12 @@ def gauge_afteraxes(cd):
 
     #may or may not keep this? see irene example
     #credit for below code to author of Irene example
-    try:
-        gauge_data=gaugea[cd.gaugeno-1]
-        axes.plot(gauge_data[:,0], gauge_data[:,1], label=data_names[cd.gaugeno-1])
-        axes.legend()
-    except:
-            print('Gauge Data Unavailable')
+    # try:
+    #     gauge_data=gaugea[cd.gaugeno-1]
+    #     axes.plot(gauge_data[:,0], gauge_data[:,1], label=data_names[cd.gaugeno-1])
+    #     axes.legend()
+    # except:
+    #         print('Gauge Data Unavailable')
     #irene code ends here
     plotaxes.afteraxes = gauge_afteraxes #originally line 209 - KEEP!!
 

mumbai/extract_track_data.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-from __future__ import print_function
+
 
 import sys
 import os
@@ -50,7 +50,7 @@ def create_storm_file(storm, output_path="mumbai.storm"):
         # "(8x      i4  i2i2i26x    a4  2x,i3,1x,i4,a1,2x,i4,a1,2x,i3,2x,i4,47x,i3,2x,i3)"
         # "(8x      i4  i2i2i26x    a4  2xi3 xi4  a i4   a i3 2x,i4,47x,i3,2x,i3)"
         # "(        YYYYMMDDHH      BEST  FOR lat_D long_D max  cpre                                               rrp  rad"
-        for n in xrange(len(storm['track'][0])):
+        for n in range(len(storm['track'][0])):
             # AL, 00, HHHHMMDDHH,   , BEST,  0, LATN, LONW, XX, CPRE, TS,  , 0, 0, 0, 0,
             date = "%s%s%s%s" % (    storm['time'][n].year, 
                                  str(storm['time'][n].month).zfill(2),
@@ -94,7 +94,7 @@ def plot_tracks(storms, plot_cat=True):
         # print(storm['track'])
         # print(longitude, latitude)
         # import pdb; pdb.set_trace()
-        for i in xrange(len(longitude)):
+        for i in range(len(longitude)):
             if plot_cat:
                 color = category_color[storm['category'][i]]
             else:
@@ -146,7 +146,7 @@ def extract_data(path, mask_dist=numpy.infty, mask_category=0):
 
     # Convert into storms and truncate zeros
     storms = []
-    for n in xrange(lon.shape[0]):
+    for n in range(lon.shape[0]):
         m = len(lon[n].nonzero()[0])
 
         distance = numpy.sqrt(  (lon[n, :m] - mumbai[0])**2
@@ -156,7 +156,7 @@ def extract_data(path, mask_dist=numpy.infty, mask_category=0):
                  'time': [datetime.datetime(year[0, n],
                                             month[n, i],
                                             day[n, i],
-                                            hour[n, i]) for i in xrange(m)],
+                                            hour[n, i]) for i in range(m)],
                  'max_winds': max_winds[n, :m],
                  'radius_max_winds': radius_max_winds[n, :m],
                  'central_pressure': central_pressure[n, :m],

mumbai/setplot.py

@@ -64,7 +64,7 @@
 
 # Gauge name translation
 gauge_landfall = []
-for i in xrange(3):
+for i in range(3):
     if storm_num == 1:
         # Storm 1
         gauge_landfall.append(datetime.datetime(1997, 11, 15, 3) - datetime.datetime(1997, 1, 1, 0))
@@ -163,7 +163,7 @@ def add_custom_colorbar_ticks_to_axes(axes, item_name, ticks, tick_labels=None):
     full_xlimits = regions['Full Domain (Grids)'][0]
     full_ylimits = regions['Full Domain (Grids)'][1]
 
-    for (name, region_data) in regions.iteritems():
+    for (name, region_data) in regions.items():
 
         #
         #  Surface
@@ -251,7 +251,7 @@ def friction_after_axes(cd):
     # ==========================
     grids = [[0, 0, 0, 0, 0, 0, 0], [1, 1, 1, 1, 1, 1, 1]]
     label = ["(No Grids)", "(Grids)"]
-    for i in xrange(2):
+    for i in range(2):
         # Pressure field
         plotfigure = plotdata.new_plotfigure(name='Pressure %s' % label[i],  
                                              figno=fig_num_counter.get_counter())

mumbai/setrun.py

@@ -381,7 +381,7 @@ def setgeo(rundata):
     try:
         geo_data = rundata.geo_data
     except:
-        print "*** Error, this rundata has no geo_data attribute"
+        print("*** Error, this rundata has no geo_data attribute")
         raise AttributeError("Missing geo_data attribute")
 
     # == Physics ==

sandy_2012/setplot.py

@@ -14,6 +14,7 @@
 import clawpack.amrclaw.data as amrclaw
 import clawpack.geoclaw.data as geodata
 import clawpack.geoclaw.surge.plot as surgeplot
+import clawpack.geoclaw.topotools as topotools
 import csv
 from clawpack.geoclaw.util import fetch_noaa_tide_data
 

scripts/gauge_comparison.py

@@ -49,7 +49,7 @@ def read_tide_gauge_data(base_path, skiprows=5, verbose=True):
     station_info_file = open(os.path.join(base_path,'Ike_Gauges_web.txt'),'r')
 
     # Skip past header
-    for i in xrange(skiprows):
+    for i in range(skiprows):
         station_info_file.readline()
 
     # Read in each station
@@ -66,7 +66,7 @@ def read_tide_gauge_data(base_path, skiprows=5, verbose=True):
             else:
                 stations[data_line[0]]['gauge_no'] = int(data_line[1])
             if verbose:
-                print "Station %s: %s" % (data_line[0],stations[data_line[0]])
+                print("Station %s: %s" % (data_line[0],stations[data_line[0]]))
 
             # Load and extract real station data
             data = scipy.io.loadmat(os.path.join(base_path,'result_%s.mat' % data_line[0]))
@@ -94,7 +94,7 @@ def read_adcirc_gauge_data(only_gauges=None, base_path="", verbose=True):
         data = np.loadtxt(gauge_file)
         stations[i+1] = data
         if verbose:
-            print "Read in ADCIRC gauge file %s" % gauge_file
+            print("Read in ADCIRC gauge file %s" % gauge_file)
 
     return stations
 
@@ -129,10 +129,10 @@ def load_geoclaw_gauge_data(only_gauges=None, base_path="_output", verbose=True)
     try:
         file_path = os.path.join(base_path,'fort.gauge')
         if not os.path.exists(file_path):
-            print '*** Warning: cannot find gauge data file %s'%file_path
+            print('*** Warning: cannot find gauge data file %s'%file_path)
             pass
         else:
-            print "Reading gauge data from %s" % file_path
+            print("Reading gauge data from %s" % file_path)
             raw_data = np.loadtxt(file_path)
 
             gauge_read_string = ""
@@ -151,11 +151,11 @@ def load_geoclaw_gauge_data(only_gauges=None, base_path="_output", verbose=True)
                 gauges[n] = gauge
 
             if verbose:
-                print "Read in GeoClaw gauge [%s]" % gauge_read_string[1:]
+                print("Read in GeoClaw gauge [%s]" % gauge_read_string[1:])
 
     except Exception as e:
-        print '*** Error reading gauges in ClawPlotData.getgauge'
-        print '*** outdir = ', base_path
+        print('*** Error reading gauges in ClawPlotData.getgauge')
+        print('*** outdir = ', base_path)
         raise e
 
     # for (i,gauge_no) in enumerate(gauge_list):
@@ -165,7 +165,7 @@ def load_geoclaw_gauge_data(only_gauges=None, base_path="_output", verbose=True)
 
 
     elapsed = (time.clock() - start)
-    print "Single gauge reading elapsed time = %s" % elapsed
+    print("Single gauge reading elapsed time = %s" % elapsed)
 
     start = time.clock()
     raw_data = np.loadtxt(os.path.join(base_path,'fort.gauge'))
@@ -183,7 +183,7 @@ def load_geoclaw_gauge_data(only_gauges=None, base_path="_output", verbose=True)
         # self.gaugesoln_dict[(n, outdir)] = gauge
 
     elapsed = (time.clock() - start)
-    print "All gauges reading elapsed time = %s" % elapsed
+    print("All gauges reading elapsed time = %s" % elapsed)
     return gauges