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PussInDasBootPussInDasBoot
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Pv 2362 increase test coverage (#266)
* Add coveragerc Only include test, seismic and util directories for testing. Exclude legacy etc * Show coverage for develop branch * Add build status * Fix coveragerc * Stream processing zerophase resampling tests * Run tests * Just test stream processing * Change test directory * Remove main * Add files * Add coveralls * Check root directory * Verbose coveralls * Debug coveralls * Run coverage * Add parenthesis * ./ * Add other parenthesis * Revert to --cov * Fix syntax errors * run coverage * xml coverage report * Run all tests in codecov * Test zerophase resampling when resample_hz < sampling rate * Test trace ordering when trace channel not in ordering array * Run all tests * Exclude import statements from coverage * Simplify invalid type zerophase resampling test * Exclude from * Exclude lines from report * Remove files from codecov * Remove old coverage.xml * List files * Verbose codecov * list files twice * Cat xml files * Grep coverage.xml * Specify coveragerc file * Absolute path to coveragerc * Don't cache home/runner * Remove commands for missing coverage.xml file when cache not used * Run all tests * Add PhasePApy to cache * Remove test changes * Cache hiperseis directory * Check cache working
1 parent f395124 commit a22a2cf

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+58
-52
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‎.coveragerc‎

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@@ -0,0 +1,10 @@
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[run]
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source =
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seismic
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utils
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tests
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branch = True
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[report]
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exclude_lines =
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import
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from

‎.github/workflows/hiperseis_main_ci.yml‎

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@@ -21,7 +21,7 @@ jobs:
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uses: actions/cache@main
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with:
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path: |
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/home/runner
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/home/runner/work/hiperseis
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/usr/share/miniconda/envs/hiperseis
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key: anaconda
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- name: Setting up environment
@@ -42,7 +42,8 @@ jobs:
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eval "$(conda shell.bash hook)"
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conda init
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conda activate hiperseis
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pytest --cov --cov-report=xml ./tests
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coverage run -m pytest tests
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coverage xml
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- name: Upload coverage reports to Codecov
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uses: codecov/codecov-action@main
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with:

‎README.rst‎

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@@ -1,7 +1,17 @@
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HiPerSeis: High Performance Software Package for Seismology Data/Metadata Processing and Analysis
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=================================================================================================
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|Build Status| |Coverage Status| |Documentation Status|
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.. image:: https://github.com/GeoscienceAustralia/hiperseis/actions/workflows/hiperseis_main_ci.yml/badge.svg
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:target: https://github.com/GeoscienceAustralia/hiperseis/actions/workflows/hiperseis_main_ci.yml
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:alt: Github Actions
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.. image:: https://codecov.io/gh/GeoscienceAustralia/hiperseis/branch/develop/graph/badge.svg
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:target: https://codecov.io/gh/GeoscienceAustralia/hiperseis
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:alt: codecov
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.. image:: https://readthedocs.org/projects/hiperseis/badge/?version=develop
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:target: http://hiperseis.readthedocs.io/en/develop/
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:alt: readthedocs
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How to Cite
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===========
@@ -62,10 +72,3 @@ License
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HiPerSeis is licensed under the GPL version 3
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.. |Coverage Status| image:: https://coveralls.io/repos/github/GeoscienceAustralia/hiperseis/badge.svg
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:target: https://coveralls.io/github/GeoscienceAustralia/hiperseis
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.. |Documentation Status| image:: https://readthedocs.org/projects/hiperseis/badge/?version=develop
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:target: http://hiperseis.readthedocs.io/en/develop/
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‎seismic/ml_classifier/data_harvester/cataloguing-ISC-noise.py‎

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@@ -44,7 +44,7 @@
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dist=float(pick[-1].strip())
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#get all S picks
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if ph=='S' and dist > 10:
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print ph
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print(ph)
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Sctr+=1
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ch=pick[1].strip()
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@@ -103,12 +103,12 @@
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wf.write(saveDir+str(wfctr)+'_N.pkl',format="PICKLE")
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np.save(saveDir+str(wfctr)+'_N.npy',wf.data)
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succ=True
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print "Got a rotated horizontal waveform"
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print("Got a rotated horizontal waveform")
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except Exception as e:
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#handle data missing
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print >> sys.stderr, e
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print(sys.stderr, e)
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stream=None
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else:
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wf=getWave(irisclient,st,ch,starttime,endtime,saveDir=saveDir)

‎seismic/ml_classifier/data_harvester/cataloguing-ISC.py‎

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@@ -44,7 +44,7 @@
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dist=float(pick[-1].strip())
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#get all S picks
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if ph=='S' and dist > 10:
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print ph
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print(ph)
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Sctr+=1
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ch=pick[1].strip()
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wf.write(saveDir+str(wfctr)+'_S.pkl',format="PICKLE")
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np.save(saveDir+str(wfctr)+'_S.npy',wf.data)
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succ=True
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print "Got a rotated horizontal waveform"
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print("Got a rotated horizontal waveform")
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except Exception as e:
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#handle data missing
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print >> sys.stderr, e
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print(sys.stderr, e)
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stream=None
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else:
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wf=getWave(irisclient,st,ch,starttime,endtime,saveDir=saveDir)

‎seismic/ml_classifier/data_harvester/events.py‎

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@@ -4,4 +4,4 @@
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GA=loadmat("GA.mat")['GA']
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print GA['picks'].keys()
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print(GA['picks'].keys())

‎seismic/ml_classifier/data_harvester/getwave.py‎

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@@ -25,7 +25,7 @@ def _genTS(fdsnclient,st,ch,starttime,endtime,loc=None,net=None):
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loc=statinfo[2]
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waveforms=fdsnclient.get_waveforms(net,st,loc,ch,starttime,endtime)
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if len(waveforms)>0:
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print "Got an IRIS waveform!"
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print("Got an IRIS waveform!")
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ret=waveforms[0]
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else:
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ret=None
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if not ret:
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print "No waveform found."
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print("No waveform found.")
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return ret
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def getWave(webclient,st,chloc,starttime,endtime,saveDir="/g/data/ha3/rlt118/neural-datasets/categoriser-teleseismic/",phase='S',ISC=True,network=None):
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global wfctr
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print starttime
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print(starttime)
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st=st.strip()
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if '?' in chloc:
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return False

‎seismic/ml_classifier/data_harvester/process-traces.py‎

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@@ -105,24 +105,19 @@ def genTS(net,st,ch,loc,ptime,stime):
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stime=UTCDateTime(*(stimeint+[smsec]))
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#get a waveform to train against
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wf=genTS(net,st,chan,loc,ptime,stime)
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if not(wf is None) and len(wf)>100:#discard bad or short waveforms extracted from the database
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if not(wf is None) and len(wf)>100:#discard bad or short waveforms extracted from the database
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wfctr+=1
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#resample the waveforms to 1000 points, detrend and normalise. The extra 0.01 ensures that the resulting trace
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#does in fact have 1000 points
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wf.resample(1000.01/wf.stats.npts*wf.stats.sampling_rate)
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wf.detrend()
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wf.normalize()
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#generate the pick distributions and normalise them
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pdist=np.exp(-np.power(wf.times()-(ptime-wf.times("utcdatetime")[0]),2)/(0.02))#sigma is 0.1
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sdist=np.exp(-np.power(wf.times()-(stime-wf.times("utcdatetime")[0]),2)/(0.02))
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pdist=pdist/np.sum(pdist)
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sdist=sdist/np.sum(sdist)
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#plot the resulting final waveform to a file
121-
outfname='wftestplot/'+'_'.join((net,st,chan,loc,ptime.ctime(),stime.ctime()))+'.png'
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wf.plot(outfile=outfname)
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#pickle the data and save it to a file
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#generate the pick distributions and normalise them
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pdist=np.exp(-np.power(wf.times()-(ptime-wf.times("utcdatetime")[0]),2)/(0.02))#sigma is 0.1
117+
sdist=np.exp(-np.power(wf.times()-(stime-wf.times("utcdatetime")[0]),2)/(0.02))
118+
pdist=pdist/np.sum(pdist)
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sdist=sdist/np.sum(sdist)
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#plot the resulting final waveform to a file
121+
outfname='wftestplot/'+'_'.join((net,st,chan,loc,ptime.ctime(),stime.ctime()))+'.png'
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wf.plot(outfile=outfname)
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#pickle the data and save it to a file

‎seismic/ml_classifier/data_harvester/save-noise.py‎

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@@ -70,11 +70,11 @@ def genTS(net,st,ch,loc,starttime,endtime):
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wf.normalize()
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Sctr+=1
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os.system('clear')
73-
print len(wf)
73+
print(len(wf))
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wf.write(saveDir+str(Sctr)+'_N.pkl',format="PICKLE")
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np.save(saveDir+str(Sctr)+'_N.npy',wf.data)
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77-
print str(Sctr)+'/'+str(pSctr)
77+
print(str(Sctr)+'/'+str(pSctr))
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80-
print str(Sctr)+'/'+str(pSctr),"waveforms harvested"
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print(str(Sctr)+'/'+str(pSctr),"waveforms harvested")

‎seismic/ml_classifier/data_harvester/save-traces-3D.py‎

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@@ -61,7 +61,7 @@ def stripChannel(channel):
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break
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print simulctr
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print(simulctr)
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6666
"""
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