updates

conda/meta.yaml

@@ -1,10 +1,10 @@
 package:
   name: sprit
-  version: 0.1.48
+  version: 0.1.49
 
 source:
   git_url: https://github.com/RJbalikian/SPRIT-HVSR
-  git_tag: v0.1.48
+  git_tag: v0.1.49
 
 build:
   number: 0

docs/generate_docs.py

@@ -8,7 +8,9 @@
 #Whether to convert_md using markdown library (True), or let github do it (False)
 convert_md=True
 rtd_theme=False #Not currently working
-release_version= '0.1.48'
+release_version= '0.1.49'
+run_tests=True
+lint_it=True
 
 currentDir = pathlib.Path((__file__)).parent
 docsDir = currentDir
@@ -17,7 +19,7 @@
 spritGUIPath = spritDir.joinpath('sprit_gui.py')
 spritUtilsPath = spritDir.joinpath('sprit_utils.py')
 spritCLIPath = spritDir.joinpath('sprit_cli.py')
-spritPath = spritDir.joinpath('sprit_hvsr.py')
+spritHVSRPath = spritDir.joinpath('sprit_hvsr.py')
 resourcesDir = spritDir.joinpath('resources')
 pyinstallerGUI = currentDir.joinpath('sprit_gui_COPY.py')
 
@@ -173,3 +175,17 @@
 
     with open(cFile.as_posix(), 'w') as f:
         f.write(cFileText)
+
+if lint_it:
+    print('Running linting')
+    fileList = [spritGUIPath, spritCLIPath, spritUtilsPath, spritHVSRPath]
+    for fileP in fileList:
+        print(f'\nLINTING {fileP}')
+        ignoreList = ['E501']
+        strIgnoreList =  "--ignore="+str(str(ignoreList)[1:-1].replace(' ', '').replace("'",""))
+        result = subprocess.run(['flake8', strIgnoreList, fileP.as_posix(),], stdout=subprocess.PIPE)
+        print(result.stdout.decode('utf-8'))
+
+if run_tests:
+    print('Testing sprit.run()')
+    subprocess.run(["pytest", repoDir.as_posix()], shell=True)

docs/main.html

@@ -1272,7 +1272,7 @@ <h2 id="parameters">Parameters</h2>
         dataIN.merge()
 
     params[&#39;batch&#39;] = False #Set False by default, will get corrected later in batch mode        
-    params[&#39;input_stream&#39;] 
+    params[&#39;input_stream&#39;] = dataIN.copy()
     params[&#39;stream&#39;] = dataIN.copy()
     params[&#39;ProcessingStatus&#39;][&#39;FetchDataStatus&#39;] = True
     if verbose and not isinstance(params, HVSRBatch):
@@ -2365,7 +2365,7 @@ <h2 id="returns">Returns</h2>
 </details>
 </dd>
 <dt id="sprit.input_params"><code class="name flex">
-<span>def <span class="ident">input_params</span></span>(<span>datapath, site='HVSR Site', network='AM', station='RAC84', loc='00', channels=['EHZ', 'EHN', 'EHE'], acq_date='2023-10-17', starttime='00:00:00.00', endtime='23:59:59.999999', tzone='UTC', xcoord=-88.2290526, ycoord=40.1012122, elevation=755, input_crs='EPSG:4326', output_crs='EPSG:4326', elev_unit='feet', depth=0, instrument='Raspberry Shake', metapath='', hvsr_band=[0.4, 40], peak_freq_range=[0.4, 40], verbose=False)</span>
+<span>def <span class="ident">input_params</span></span>(<span>datapath, site='HVSR Site', network='AM', station='RAC84', loc='00', channels=['EHZ', 'EHN', 'EHE'], acq_date='2023-10-18', starttime='00:00:00.00', endtime='23:59:59.999999', tzone='UTC', xcoord=-88.2290526, ycoord=40.1012122, elevation=755, input_crs='EPSG:4326', output_crs='EPSG:4326', elev_unit='feet', depth=0, instrument='Raspberry Shake', metapath='', hvsr_band=[0.4, 40], peak_freq_range=[0.4, 40], verbose=False)</span>
 </code></dt>
 <dd>
 <div class="desc"><p>Function for designating input parameters for reading in and processing data</p>

docs/sprit_hvsr.html

@@ -1269,7 +1269,7 @@ <h1 class="title">Module <code>sprit.sprit_hvsr</code></h1>
         dataIN.merge()
 
     params[&#39;batch&#39;] = False #Set False by default, will get corrected later in batch mode        
-    params[&#39;input_stream&#39;] 
+    params[&#39;input_stream&#39;] = dataIN.copy()
     params[&#39;stream&#39;] = dataIN.copy()
     params[&#39;ProcessingStatus&#39;][&#39;FetchDataStatus&#39;] = True
     if verbose and not isinstance(params, HVSRBatch):
@@ -6047,6 +6047,7 @@ <h1 class="title">Module <code>sprit.sprit_hvsr</code></h1>
 
     return _peak
 
+
 #Check stability
 def __check_stability(_stdf, _peak, _hvsr_log_std, rank):
     &#34;&#34;&#34;Test peaks for satisfying stability conditions as outlined by SESAME 2004
@@ -6189,6 +6190,7 @@ <h1 class="title">Module <code>sprit.sprit_hvsr</code></h1>
 
     return _peak
 
+
 #Get frequency standard deviation
 def __get_stdf(x_values, indexList, hvsrPeaks):
     &#34;&#34;&#34;Private function to get frequency standard deviation, from multiple time-step HVSR curves&#34;&#34;&#34;
@@ -6201,17 +6203,17 @@ <h1 class="title">Module <code>sprit.sprit_hvsr</code></h1>
                 if p is None:
                     p = hvsrPeaks.iloc[j][k]
                 else:
-                    #Find closest peak in current time to (current) main hvsr peak
+                    # Find closest peak in current time to (current) hvsr peak
                     if abs(index - hvsrPeaks.iloc[j][k]) &lt; abs(index - p):
                         p = hvsrPeaks.iloc[j][k]
-                        #p = hvsrPeaks[j][k]
-                        #print(p=p1, p, p1)
+                        # p = hvsrPeaks[j][k]
+                        # print(p=p1, p, p1)
             if p is not None:
                 point.append(p)
         point.append(index)
         v = list()
-        for l in range(len(point)):
-            v.append(x_values[point[l]])
+        for pl in range(len(point)):
+            v.append(x_values[point[pl]])
         stdf.append(np.std(v))
     return stdf</code></pre>
 </details>
@@ -7096,7 +7098,7 @@ <h2 id="parameters">Parameters</h2>
         dataIN.merge()
 
     params[&#39;batch&#39;] = False #Set False by default, will get corrected later in batch mode        
-    params[&#39;input_stream&#39;] 
+    params[&#39;input_stream&#39;] = dataIN.copy()
     params[&#39;stream&#39;] = dataIN.copy()
     params[&#39;ProcessingStatus&#39;][&#39;FetchDataStatus&#39;] = True
     if verbose and not isinstance(params, HVSRBatch):
@@ -7963,7 +7965,7 @@ <h2 id="returns">Returns</h2>
 </details>
 </dd>
 <dt id="sprit.sprit_hvsr.input_params"><code class="name flex">
-<span>def <span class="ident">input_params</span></span>(<span>datapath, site='HVSR Site', network='AM', station='RAC84', loc='00', channels=['EHZ', 'EHN', 'EHE'], acq_date='2023-10-17', starttime='00:00:00.00', endtime='23:59:59.999999', tzone='UTC', xcoord=-88.2290526, ycoord=40.1012122, elevation=755, input_crs='EPSG:4326', output_crs='EPSG:4326', elev_unit='feet', depth=0, instrument='Raspberry Shake', metapath='', hvsr_band=[0.4, 40], peak_freq_range=[0.4, 40], verbose=False)</span>
+<span>def <span class="ident">input_params</span></span>(<span>datapath, site='HVSR Site', network='AM', station='RAC84', loc='00', channels=['EHZ', 'EHN', 'EHE'], acq_date='2023-10-18', starttime='00:00:00.00', endtime='23:59:59.999999', tzone='UTC', xcoord=-88.2290526, ycoord=40.1012122, elevation=755, input_crs='EPSG:4326', output_crs='EPSG:4326', elev_unit='feet', depth=0, instrument='Raspberry Shake', metapath='', hvsr_band=[0.4, 40], peak_freq_range=[0.4, 40], verbose=False)</span>
 </code></dt>
 <dd>
 <div class="desc"><p>Function for designating input parameters for reading in and processing data</p>

pyproject.toml

@@ -7,7 +7,7 @@ name = "sprit"
 authors = [{name="Riley Balikian"}, {name="Hongyu Xaio"}]
 dynamic = ["readme"]
 license = {file = "LICENSE"}
-version="0.1.48"
+version="0.1.49"
 description = "A package for processing and analyzing HVSR (Horizontal to Vertical Spectral Ratio) data"
 keywords = ["HVSR", "seismic", "horizontal to vertical spectral ratio", "obspy", 'geology', 'geophysics', 'geotechnical']
 requires-python = ">=3.9"

run_test.py

@@ -0,0 +1,10 @@
+import sprit
+
+def test_run():
+    try:
+        sprit.run("sample")
+        test_passed = True
+    except:
+        test_passed = False
+
+    assert test_passed

setup.py

@@ -7,7 +7,7 @@
     name="sprit",
     author= "Riley Balikian",
     author_email = "[email protected]",
-    version="0.1.48",
+    version="0.1.49",
     package_data={'sprit': ['resources/*', 'resources/icon/*', 'resources/themes/*', 'resources/themes/forest-dark/*', 'resources/themes/forest-light/*', 'resources/sample_data/*',]},
     long_description_content_type="text/markdown",
     long_description=long_description,

sprit/sprit_hvsr.py

@@ -1238,7 +1238,7 @@ def fetch_data(params, source='file', trim_dir=None, export_format='mseed', detr
         dataIN.merge()
 
     params['batch'] = False #Set False by default, will get corrected later in batch mode        
-    params['input_stream'] 
+    params['input_stream'] = dataIN.copy()
     params['stream'] = dataIN.copy()
     params['ProcessingStatus']['FetchDataStatus'] = True
     if verbose and not isinstance(params, HVSRBatch):
@@ -5720,8 +5720,8 @@ def _plot_specgram_stream(stream, params=None, component='Z', stack_type='linear
 
     return
 
-##Helper functions for checking peaks
-#Initialize peaks
+# HELPER functions for checking peaks
+# Initialize peaks
 def __init_peaks(_x, _y, _index_list, _hvsr_band, peak_freq_range=[0.4, 40], _min_peak_amp=1):
     """ Initialize peaks.
         
@@ -5759,7 +5759,7 @@ def __init_peaks(_x, _y, _index_list, _hvsr_band, peak_freq_range=[0.4, 40], _mi
                           'PeakPasses':False})
     return _peak
 
-#Check reliability of HVSR of curve
+# Check reliability of HVSR of curve
 def __check_curve_reliability(hvsr_data, _peak):
     """Tests to check for reliable H/V curve
 
@@ -5938,7 +5938,7 @@ def __check_clarity(_x, _y, _peak, do_rank=True):
 
     return _peak
 
-#Check the stability of the frequency peak
+# Check the stability of the frequency peak
 def __check_freq_stability(_peak, _peakm, _peakp):
     """Test peaks for satisfying stability conditions 
 
@@ -5962,12 +5962,10 @@ def __check_freq_stability(_peak, _peakm, _peakp):
     """
     global max_rank
 
-    #
     # check σf and σA
-    #
     max_rank += 1
 
-    #First check below
+    # First check below
     _found_m = list()
     for _i in range(len(_peak)):
         _dx = 1000000.
@@ -5986,12 +5984,12 @@ def __check_freq_stability(_peak, _peakm, _peakp):
             _peak[_i]['Report']['P-'] = '%0.3f within ±5%s of %0.3f %1s' % (_peakm[_j]['f0'], '%', ##changed i to j
                                                                              _peak[_i]['f0'], '✘')
 
-    #Then Check above
+    # Then Check above
     _found_p = list()
     for _i in range(len(_peak)):
         _dx = 1000000.
         _found_p.append(False)
-        _peak[_i]['Report']['P+'] = '✘'
+        _peak[_i]['Report']['P+'] = sprit_utils.x_mark()
         for _j in range(len(_peakp)):
             if abs(_peakp[_j]['f0'] - _peak[_i]['f0']) < _dx:
                 _index = _j
@@ -6010,13 +6008,14 @@ def __check_freq_stability(_peak, _peakm, _peakp):
             else:
                 _peak[_i]['Report']['P+'] = '%0.3f within ±5%s of %0.3f %1s' % (_peakp[_j]['f0'], '%', _peak[_i]['f0'], '✘')
                 _peak[_i]['PassList']['FreqStability'] = False                
-        if _peak[_i]['Report']['P+'] == '✘' and len(_peakp) > 0:
+        if _peak[_i]['Report']['P+'] == sprit_utils.x_mark() and len(_peakp) > 0:
             _peak[_i]['Report']['P+'] = '%0.3f within ±5%s of %0.3f %1s' % (
-                _peakp[_j]['f0'], '%', _peak[_i]['f0'], '✘')###changed i to j
+                _peakp[_j]['f0'], '%', _peak[_i]['f0'], sprit_utils.x_mark())  #changed i to j
 
     return _peak
 
-#Check stability
+
+# Check stability
 def __check_stability(_stdf, _peak, _hvsr_log_std, rank):
     """Test peaks for satisfying stability conditions as outlined by SESAME 2004
     This includes:
@@ -6033,12 +6032,12 @@ def __check_stability(_stdf, _peak, _hvsr_log_std, rank):
     _hvsr_log_std : list
         List of dictionaries containing log standard deviation along curve
     rank : int
-        Integer value, higher value is "higher-ranked" peak, helps determine which peak is actual hvsr peak  
+        Integer value, higher value is "higher-ranked" peak, helps determine which peak is actual hvsr peak
 
     Returns
     -------
     _peak : list
-        List of dictionaries containing output information about peak test  
+        List of dictionaries containing output information about peak test
     """
 
     global max_rank
@@ -6158,7 +6157,8 @@ def __check_stability(_stdf, _peak, _hvsr_log_std, rank):
 
     return _peak
 
-#Get frequency standard deviation
+
+# Get frequency standard deviation
 def __get_stdf(x_values, indexList, hvsrPeaks):
     """Private function to get frequency standard deviation, from multiple time-step HVSR curves"""
     stdf = list()
@@ -6170,16 +6170,16 @@ def __get_stdf(x_values, indexList, hvsrPeaks):
                 if p is None:
                     p = hvsrPeaks.iloc[j][k]
                 else:
-                    #Find closest peak in current time to (current) main hvsr peak
+                    # Find closest peak in current time to (current) hvsr peak
                     if abs(index - hvsrPeaks.iloc[j][k]) < abs(index - p):
                         p = hvsrPeaks.iloc[j][k]
-                        #p = hvsrPeaks[j][k]
-                        #print(p=p1, p, p1)
+                        # p = hvsrPeaks[j][k]
+                        # print(p=p1, p, p1)
             if p is not None:
                 point.append(p)
         point.append(index)
         v = list()
-        for l in range(len(point)):
-            v.append(x_values[point[l]])
+        for pl in range(len(point)):
+            v.append(x_values[point[pl]])
         stdf.append(np.std(v))
-    return stdf
+    return stdf