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make sed cross-platform #48

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Jul 31, 2022
Merged

make sed cross-platform #48

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42 changes: 15 additions & 27 deletions modeldb/modeldb-run.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -465,10 +465,7 @@
- load_file("sample.hoc")
- verify_graph_()
script:
- sed 's,tstop *=,tstop = 100//,
- /whichAP/,$d
- ''' sample.hoc > temp.tmp'
- mv temp.tmp sample.hoc
- sed -i'.bak' -e 's/tstop *=/tstop = 100\/\//g;/whichAP/,$d' sample.hoc
76879:
run:
- tstop=20
Expand Down Expand Up @@ -503,10 +500,7 @@
83590:
run: []
script:
- sed 's/mustart = -0.400/mustart = 0.800/
- ' s/sigmastart = 0.064/sigmastart = 0.128/'
- ''' mylibs/TFparams.hoc > temp.tmp'
- mv temp.tmp mylibs/TFparams.hoc
- sed -i'.bak' -e 's/mustart = -0.400/mustart = 0.800/g;s/sigmastart = 0.064/sigmastart = 0.128/g' mylibs/TFparams.hoc
84589:
run:
- //ignore sim in subdirectory
Expand Down Expand Up @@ -673,9 +667,7 @@
- load_file("batch_.hoc")
- verify_graph_()
script:
- sed 's/batch_flag=0/batch_flag=1/
- s/tstop = 1e3/tstop = 20/' batch_.hoc > temp.tmp
- mv temp.tmp batch_.hoc
- sed -i'.bak' -e 's/batch_flag=0/batch_flag=1/g;s/tstop = 1e3/tstop = 20/g' batch_.hoc
106551:
run:
- use_mcell_ran4(1)
Expand Down Expand Up @@ -823,8 +815,7 @@
- //load_file("init.hoc")
- //verify_graph_()
script:
- sed 's/tstop = 100/tstop = 20/' init.hoc > temp.tmp
- mv temp.tmp init.hoc
- sed -i'.bak' -e 's/tstop = 100/tstop = 20/g' init.hoc
116835:
run:
- tstop=10
Expand All @@ -836,8 +827,7 @@
- run()
- verify_graph_()
script:
- sed 's/^showdemo=1/showdemo=0/' mosinit.hoc > temp.tmp
- mv temp.tmp mosinit.hoc
- sed -i'.bak' -e 's/^showdemo=1/showdemo=0/g' mosinit.hoc
116956:
run:
- run()
Expand Down Expand Up @@ -962,16 +952,14 @@
- run()
- verify_graph_()
script:
- sed 's/tstop = 6500/tstop = 100/' session.ses > temp.tmp
- mv temp.tmp session.ses
- sed -i'.bak' -e 's/tstop = 6500/tstop = 100/g' session.ses
124291:
run:
- stim.amp = 0.1
- runa()
- verify_graph_()
script: # todo -> fix model for NEURON 8.0.0 and remove this script
- sed 's/return 0;//' MOPP_Fig_1B_left/ichan2.mod > temp.tmp
- mv temp.tmp MOPP_Fig_1B_left/ichan2.mod
- sed -i'.bak' -e 's/return 0;//g' MOPP_Fig_1B_left/ichan2.mod
138321:
run:
- run()
Expand Down Expand Up @@ -1076,21 +1064,21 @@
- run()
- verify_graph_()
script:
- sed -i 's/tstop = /tstop = 50\/\//' Fig8_tuft_NMDA_spike.hoc
- sed -i 's/simul_iter=/simul_iter=2 \/\//' Fig8_tuft_NMDA_spike.hoc
- sed -i'.bak' -e 's/tstop = /tstop = 50\/\//' Fig8_tuft_NMDA_spike.hoc
- sed -i'.bak' -e 's/simul_iter=/simul_iter=2 \/\//' Fig8_tuft_NMDA_spike.hoc
comment: usual simulation time is ~ 10 minutes (tstop = 120 and simul_iter=10)
206267:
run:
- run()
- verify_graph_()
script:
- sed -i 's/tstop=/tstop=100 \/\//' Start.hoc
- sed -i'.bak' -e 's/tstop=/tstop=100 \/\//' Start.hoc
157157:
run:
- run()
- verify_graph_()
script:
- sed -i 's/tstop = 5000/tstop = 250 \/\//g' PC.ses
- sed -i'.bak' -e 's/tstop = 5000/tstop = 250 \/\//g' PC.ses
244848:
run: null
comment: not straightforward to cut down simulation time, takes too long
Expand All @@ -1105,22 +1093,22 @@
- run()
- verify_graph_()
script:
- sed -i 's/500/5/g' BPF.hoc
- sed -i 's/2\([0|1]\)000/2\1/g' BPF.hoc
- sed -i'.bak' -e 's/500/5/g' BPF.hoc
- sed -i'.bak' -e 's/2\([0|1]\)000/2\1/g' BPF.hoc
comment: diving some numbers with 100 halvened the sim time
151126:
run:
- run()
- verify_graph_()
script:
- sed -i 's/tstop = 550/tstop = 100/' HAM_SR1.ses
- sed -i'.bak' -e 's/tstop = 550/tstop = 100/' HAM_SR1.ses
# python models
189922:
python: true
run:
- import os; os.system("python mosinit.py"); quit();
script:
- 2to3 -w .
- sed -i 's/plt.show()/plt.show(block=False);plt.pause(1);plt.close();quit()/' clay_mohit.py
- sed -i'.bak' -e 's/plt.show()/plt.show(block=False);plt.pause(1);plt.close();quit()/' clay_mohit.py