merge back to dev

.github/workflows/draft-pdf.yml

@@ -0,0 +1,23 @@
+on: [push]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v1
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: paper.pdf

0mq/cpymax.py

@@ -0,0 +1,29 @@
+import concore
+import time
+concore.delay = 0.01
+#Nsim = 100
+init_simtime_u = "[0.0, 0.0, 0.0]"
+init_simtime_ym = "[0.0, 0.0, 0.0]"
+minElasped = 10000000
+maxElasped = 0
+sumElasped  = 0
+u = concore.initval(init_simtime_u)
+wallclock1 = time.perf_counter()
+while(concore.simtime<concore.maxtime):
+    while concore.unchanged():
+        ym = concore.read(1,"ym",init_simtime_ym)
+    u[0]  = ym[0]+1
+    print("ym="+str(ym[0])+" u="+str(u[0]));
+    concore.write(1,"u",u);
+    wallclock2 = time.perf_counter()
+    elasped = wallclock2-wallclock1
+    sumElasped += elasped
+    wallclock1 = wallclock2
+    minElasped = min(minElasped, elasped)
+    maxElasped = max(maxElasped, elasped)
+
+#concore.write(1,"u",init_simtime_u)
+print("retry="+str(concore.retrycount))
+print("min="+str(minElasped))
+print("avg="+str(sumElasped/concore.maxtime))
+print("max="+str(maxElasped))

0mq/funbody.dir/concore2.py

@@ -0,0 +1,113 @@
+import time
+import os
+from ast import literal_eval
+import sys
+import re
+
+#if windows, create script to kill this process 
+# because batch files don't provide easy way to know pid of last command
+# ignored for posix!=windows, because "concorepid" is handled by script
+# ignored for docker (linux!=windows), because handled by docker stop
+if hasattr(sys, 'getwindowsversion'):
+    with open("concorekill.bat","w") as fpid:
+        fpid.write("taskkill /F /PID "+str(os.getpid())+"\n")
+
+try:
+    iport = literal_eval(open("concore.iport").read())
+except:
+    iport = dict()
+try:
+    oport = literal_eval(open("concore.oport").read())
+except:
+    oport = dict()
+
+
+s = ''
+olds = ''
+delay = 1
+retrycount = 0
+inpath = "./in" #must be rel path for local
+outpath = "./out"
+
+#9/21/22
+try:
+    sparams = open(inpath+"1/concore.params").read()
+    if sparams[0] == '"':  #windows keeps "" need to remove
+        sparams = sparams[1:]
+        sparams = sparams[0:sparams.find('"')]
+    if sparams != '{':
+        print("converting sparams: "+sparams)
+        sparams = "{'"+re.sub(';',",'",re.sub('=',"':",re.sub(' ','',sparams)))+"}"
+        print("converted sparams: " + sparams)
+    try:
+        params = literal_eval(sparams)
+    except:
+        print("bad params: "+sparams)
+except:
+    params = dict()
+#9/30/22
+def tryparam(n,i):
+    try:
+       return params[n]
+    except:
+       return i
+
+
+#9/12/21
+def default_maxtime(default):
+    global maxtime
+    try:
+        maxtime = literal_eval(open(inpath+"1/concore.maxtime").read())
+    except:
+        maxtime = default 
+default_maxtime(100)
+
+def unchanged():
+    global olds,s
+    if olds==s:
+        s = ''
+        return True
+    else:       
+        olds = s       
+        return False
+
+def read(port, name, initstr):
+    global s,simtime,retrycount
+    time.sleep(delay)
+    try:
+        infile = open(inpath+str(port)+"/"+name);
+        ins = infile.read()
+    except:
+        ins = initstr
+    while len(ins)==0:
+        time.sleep(delay)
+        ins = infile.read()
+        retrycount += 1
+    s += ins
+    inval = literal_eval(ins)
+    simtime = max(simtime,inval[0])
+    return inval[1:]
+
+def write(port, name, val, delta=0):
+    global outpath,simtime
+    if isinstance(val,str):
+        time.sleep(2*delay)
+    elif isinstance(val,list)==False:
+        print("mywrite must have list or str")
+        quit() 
+    try:
+        with open(outpath+str(port)+"/"+name,"w") as outfile:     
+            if isinstance(val,list):
+                outfile.write(str([simtime+delta]+val))
+                simtime += delta
+            else:
+                outfile.write(val)
+    except:
+        print("skipping"+outpath+str(port)+"/"+name);
+
+def initval(simtime_val):
+    global simtime
+    val = literal_eval(simtime_val)
+    simtime = val[0]
+    return val[1:]
+

0mq/funbody.py

@@ -0,0 +1,69 @@
+import concore
+import concore2
+import time
+from osparc_control import CommandManifest
+from osparc_control import CommandParameter
+from osparc_control import CommandType
+from osparc_control import PairedTransmitter
+# declare some commands to which a reply can be provided
+CONCORE_MANIFEST = CommandManifest(
+    action="fun",
+    description="function call",
+    params=[
+        CommandParameter(name="u", description="control move"),
+    ],
+    command_type=CommandType.WITH_IMMEDIATE_REPLY,
+)
+
+
+print("funbody 0mq")
+# initialization of 0mq/osparc-control "paired_transmitter"
+paired_transmitter = PairedTransmitter(
+    remote_host="localhost",
+    exposed_commands=[CONCORE_MANIFEST],
+    remote_port=2346,
+    listen_port=2345,)
+
+paired_transmitter.start_background_sync()
+
+concore.delay = 0.07
+concore2.delay = 0.07
+concore2.inpath = concore.inpath
+concore2.outpath = concore.outpath
+concore2.simtime = 0
+concore.default_maxtime(100)
+init_simtime_u = "[0.0, 0.0, 0.0]"
+init_simtime_ym = "[0.0, 0.0, 0.0]"
+
+u = concore.initval(init_simtime_u)
+ym = concore2.initval(init_simtime_ym)
+while(concore2.simtime<concore.maxtime):
+    #while concore.unchanged():
+    #    u = concore.read(concore.iport['U1'],"u",init_simtime_u)
+    command_list = paired_transmitter.get_incoming_requests()
+    while len(command_list)==0:
+        time.sleep(.01)
+        command_list = paired_transmitter.get_incoming_requests()
+    if len(command_list)>1:
+        print("too many commands at once!")
+    command = command_list[0]
+    if command.action == CONCORE_MANIFEST.action:
+        u = command.params["u"]
+        concore.simtime = u[0]
+        u = u[1:] 
+        concore.write(concore.oport['U2'],"u",u)
+        print(u)
+        old2 = concore2.simtime
+        while concore2.unchanged() or concore2.simtime <= old2:
+            ym = concore2.read(concore.iport['Y2'],"ym",init_simtime_ym)
+        ym = [concore2.simtime]+ym
+        print(f"Replying to {command.action} with {ym}")
+        paired_transmitter.reply_to_command(
+           request_id=command.request_id, payload=ym)
+    else:
+        print("undefined action"+str(command.action)) 
+        quit()
+    #concore2.write(concore.oport['Y1'],"ym",ym)
+    print("funbody u="+str(u)+" ym="+str(ym)+" time="+str(concore2.simtime))
+paired_transmitter.stop_background_sync()
+print("retry="+str(concore.retrycount))

0mq/funbody2.dir/concore2.py

@@ -0,0 +1,113 @@
+import time
+import os
+from ast import literal_eval
+import sys
+import re
+
+#if windows, create script to kill this process 
+# because batch files don't provide easy way to know pid of last command
+# ignored for posix!=windows, because "concorepid" is handled by script
+# ignored for docker (linux!=windows), because handled by docker stop
+if hasattr(sys, 'getwindowsversion'):
+    with open("concorekill.bat","w") as fpid:
+        fpid.write("taskkill /F /PID "+str(os.getpid())+"\n")
+
+try:
+    iport = literal_eval(open("concore.iport").read())
+except:
+    iport = dict()
+try:
+    oport = literal_eval(open("concore.oport").read())
+except:
+    oport = dict()
+
+
+s = ''
+olds = ''
+delay = 1
+retrycount = 0
+inpath = "./in" #must be rel path for local
+outpath = "./out"
+
+#9/21/22
+try:
+    sparams = open(inpath+"1/concore.params").read()
+    if sparams[0] == '"':  #windows keeps "" need to remove
+        sparams = sparams[1:]
+        sparams = sparams[0:sparams.find('"')]
+    if sparams != '{':
+        print("converting sparams: "+sparams)
+        sparams = "{'"+re.sub(';',",'",re.sub('=',"':",re.sub(' ','',sparams)))+"}"
+        print("converted sparams: " + sparams)
+    try:
+        params = literal_eval(sparams)
+    except:
+        print("bad params: "+sparams)
+except:
+    params = dict()
+#9/30/22
+def tryparam(n,i):
+    try:
+       return params[n]
+    except:
+       return i
+
+
+#9/12/21
+def default_maxtime(default):
+    global maxtime
+    try:
+        maxtime = literal_eval(open(inpath+"1/concore.maxtime").read())
+    except:
+        maxtime = default 
+default_maxtime(100)
+
+def unchanged():
+    global olds,s
+    if olds==s:
+        s = ''
+        return True
+    else:       
+        olds = s       
+        return False
+
+def read(port, name, initstr):
+    global s,simtime,retrycount
+    time.sleep(delay)
+    try:
+        infile = open(inpath+str(port)+"/"+name);
+        ins = infile.read()
+    except:
+        ins = initstr
+    while len(ins)==0:
+        time.sleep(delay)
+        ins = infile.read()
+        retrycount += 1
+    s += ins
+    inval = literal_eval(ins)
+    simtime = max(simtime,inval[0])
+    return inval[1:]
+
+def write(port, name, val, delta=0):
+    global outpath,simtime
+    if isinstance(val,str):
+        time.sleep(2*delay)
+    elif isinstance(val,list)==False:
+        print("mywrite must have list or str")
+        quit() 
+    try:
+        with open(outpath+str(port)+"/"+name,"w") as outfile:     
+            if isinstance(val,list):
+                outfile.write(str([simtime+delta]+val))
+                simtime += delta
+            else:
+                outfile.write(val)
+    except:
+        print("skipping"+outpath+str(port)+"/"+name);
+
+def initval(simtime_val):
+    global simtime
+    val = literal_eval(simtime_val)
+    simtime = val[0]
+    return val[1:]
+