beautified ipynb outupt, removed stderr cells

bayesian-code.ipynb

@@ -42,11 +42,6 @@
       "Downloading training data (300MB), this can take a few minutes the first time...\n"
      ]
     },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": []
-    },
     {
      "name": "stdout",
      "output_type": "stream",
@@ -405,11 +400,6 @@
     "outputId": "13c2ada4-79bf-42f7-f2f9-4355c0173fb0"
    },
    "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": []
-    },
     {
      "name": "stdout",
      "output_type": "stream",
@@ -1134,4 +1124,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 1
-}
+}

diffphys-code-ns.ipynb

@@ -116,7 +116,7 @@
     {
      "data": {
       "text/plain": [
-       "(inflow_locᵇ=4, xˢ=32, yˢ=40)"
+       "(inflow_loc\u1d47=4, x\u02e2=32, y\u02e2=40)"
       ]
      },
      "execution_count": 2,
@@ -253,7 +253,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Velocity dimensions: (inflow_locᵇ=4, xˢ=32, yˢ=40, vectorᶜ=x,y)\n"
+      "Velocity dimensions: (inflow_loc\u1d47=4, x\u02e2=32, y\u02e2=40, vector\u1d9c=x,y)\n"
      ]
     }
    ],
@@ -295,20 +295,12 @@
     "outputId": "93dae39b-1b31-429a-cf81-f615e23bbf7d"
    },
    "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/Users/thuerey/miniconda3/envs/tf/lib/python3.8/site-packages/IPython/core/interactiveshell.py:3427: SyntaxWarning: Specifying wrt by position is deprecated in phi.math.funcitonal_gradient() and phi.math.jacobian(). Please pass a list or comma-separated string of parameter names.\n",
-      "  exec(code_obj, self.user_global_ns, self.user_ns)\n"
-     ]
-    },
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Some gradient info: StaggeredGrid[(inflow_locᵇ=4, xˢ=32, yˢ=40, vectorᶜ=x,y), size=\u001b[94m(x=32, y=40)\u001b[0m \u001b[93mint64\u001b[0m, extrapolation=\u001b[94m0\u001b[0m]\n",
-      "\u001b[92m(xˢ=31, yˢ=40)\u001b[0m \u001b[94m2.61e-08 ± 8.5e-01\u001b[0m \u001b[37m(-2e+01...1e+01)\u001b[0m\n"
+      "Some gradient info: StaggeredGrid[(inflow_loc\u1d47=4, x\u02e2=32, y\u02e2=40, vector\u1d9c=x,y), size=\u001b[94m(x=32, y=40)\u001b[0m \u001b[93mint64\u001b[0m, extrapolation=\u001b[94m0\u001b[0m]\n",
+      "\u001b[92m(x\u02e2=31, y\u02e2=40)\u001b[0m \u001b[94m2.61e-08 \u00b1 8.5e-01\u001b[0m \u001b[37m(-2e+01...1e+01)\u001b[0m\n"
      ]
     }
    ],
@@ -679,4 +671,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 1
-}
+}

diffphys-code-sol.ipynb

@@ -158,7 +158,7 @@
     "id": "RY1F4kdWPLNG"
    },
    "source": [
-    "Also let's get installing / importing all the necessary libraries out of the way. And while we're at it, we set the random seed - obviously, 42 is the ultimate choice here 🙂"
+    "Also let's get installing / importing all the necessary libraries out of the way. And while we're at it, we set the random seed - obviously, 42 is the ultimate choice here \ud83d\ude42"
    ]
   },
   {
@@ -622,21 +622,6 @@
     "outputId": "9e95aa79-6124-4e30-baf1-28bc37801b0f"
    },
    "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "<ipython-input-10-594cd5e5046a>:10: FutureWarning: Domain (phi.physics._boundaries) is deprecated and will be removed in a future release.\n",
-      "Please create grids directly, replacing the domain with a dict, e.g.\n",
-      "    domain = dict(x=64, y=128, bounds=Box(x=1, y=1))\n",
-      "    grid = CenteredGrid(0, **domain)\n",
-      "  from phi.physics._boundaries import Domain, OPEN, STICKY as CLOSED\n",
-      "<ipython-input-10-594cd5e5046a>:17: DeprecationWarning: Domain is deprecated and will be removed in a future release. Use a dict instead, e.g. CenteredGrid(values, extrapolation, **domain_dict)\n",
-      "  domain = phi.physics._boundaries.Domain(y=source_res[0], x=source_res[1], boundaries=boundary_conditions, bounds=Box(y=2*simulation_length, x=simulation_length))\n",
-      "<ipython-input-10-594cd5e5046a>:17: FutureWarning: Domain is deprecated and will be removed in a future release. Use a dict instead, e.g. CenteredGrid(values, extrapolation, **domain_dict)\n",
-      "  domain = phi.physics._boundaries.Domain(y=source_res[0], x=source_res[1], boundaries=boundary_conditions, bounds=Box(y=2*simulation_length, x=simulation_length))\n"
-     ]
-    },
     {
      "name": "stdout",
      "output_type": "stream",
@@ -864,7 +849,6 @@
       "epoch 003/005, batch 001/002, step 0401/0496: loss=\u001b[94m4.7433133\u001b[0m\n",
       "epoch 004/005, batch 001/002, step 0401/0496: loss=\u001b[94m4.522671\u001b[0m\n",
       "epoch 005/005, batch 001/002, step 0401/0496: loss=\u001b[94m2.0179803\u001b[0m\n",
-      "WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.\n",
       "Training done, saved NN\n"
      ]
     }
@@ -997,7 +981,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Reynolds numbers in test data set: \u001b[94m(120000.000, 480000.000, 1920000.000, 7680000.000)\u001b[0m along \u001b[92mbatchᵇ\u001b[0m\n"
+      "Reynolds numbers in test data set: \u001b[94m(120000.000, 480000.000, 1920000.000, 7680000.000)\u001b[0m along \u001b[92mbatch\u1d47\u001b[0m\n"
      ]
     }
    ],
@@ -1389,4 +1373,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 1
-}
+}

json-cleanup-for-pdf.py

@@ -21,11 +21,15 @@ fileList = [
 	]
 
 #fileList = [ "physgrad-code.ipynb"] # debug, only 1 file
+#fileList = [ "t1.ipynb" ] # debug
 
 
 # main
 
 for fnOut in fileList:
+	if not os.path.isfile(fnOut):
+		print("Error: "+fnOut+" not found!"); exit(1)
+
 	# create backups
 	fn0 = fnOut[:-5] + "bak"
 	fn = fn0 + "0"; cnt = 0
@@ -47,6 +51,7 @@ for fnOut in fileList:
 	#print(d.keys()) #print(d["cells"][0].keys())
 
 	# remove TF / pytorch warnings, build list of regular expressions to search for
+	# double check, redundant with removing stderr cells (cf delE)
 	res = []
 	res.append( re.compile(r"WARNING:tensorflow:") )
 	res.append( re.compile(r"UserWarning:") )
@@ -90,16 +95,26 @@ for fnOut in fileList:
 					deletes = deletes+1
 					#print( d[t][i]["source"][j] +"\n >>> \n" +d2 )
 
+			delE = [] # collect whole entries (sections) to delete
+
 			#print(len( d[t][i]["outputs"] ))
 			for j in range(len( d[t][i]["outputs"] )):
 				#print(type( d[t][i]["outputs"][j] ))
 				#print( d[t][i]["outputs"][j].keys() )
 
+				# search for error stderr cells
+				if d[t][i]["outputs"][j]["output_type"]=="stream":
+					#print("output j name: "+ format( d[t][i]["outputs"][j]["name"] ) )
+					#print("output j: "+ format( d[t][i]["outputs"][j] ) )
+					if d[t][i]["outputs"][j]["name"]=="stderr":
+						print("stderr found! len text "+ format(len( d[t][i]["outputs"][j]["text"]) ) +", removing entry "+format(j) )
+						delE.append(j) # remove the whole stderr entry
+
 				# images
 				if d[t][i]["outputs"][j]["output_type"]=="stream":
-					#print("len "+  len( d[t][i]["outputs"][j]["text"] ) )
+					#print("len "+  format(len( d[t][i]["outputs"][j]["text"] )) )
 
-					dell = [] # collect entries to delete
+					dell = [] # collect lines to delete
 					for k in range(  len( d[t][i]["outputs"][j]["text"] )  ):
 						#print(" tout "+   d[t][i]["outputs"][j]["text"][k] ) # debug , print all lines
 						nums = []; all_good = True
@@ -117,8 +132,17 @@ for fnOut in fileList:
 
 					for dl in dell:
 						d[t][i]["outputs"][j]["text"].remove(dl)
+				#print("len after "+format( len( d[t][i]["outputs"][j]["text"] )) + " A") # debug
 
-					#print("len after "+format( len( d[t][i]["outputs"][j]["text"] )) + " A") # debug
+			# afterwards (potentially remove whole entries)
+			# if len(delE)>0:
+			# 	print("len bef "+format( len( d[t][i]["outputs"] )) + " A " + format(delE)) # debug
+			for de in delE:
+				#print(type(d[t][i]["outputs"])); print(de)
+				d[t][i]["outputs"].pop(de) # remove array element
+				deletes+=1
+			# if len(delE)>0:
+			# 	print("len after "+format( len( d[t][i]["outputs"] )) + " A") # debug
 
 	if deletes==0:
 		print("Warning: Nothing found in "+fn+"!")

physgrad-code.ipynb

@@ -363,11 +363,6 @@
     "outputId": "4d938ed4-484b-46df-d0ca-d2268cb97dd0"
    },
    "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": []
-    },
     {
      "name": "stdout",
      "output_type": "stream",
@@ -413,11 +408,6 @@
     }
    },
    "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": []
-    },
     {
      "name": "stdout",
      "output_type": "stream",
@@ -615,4 +605,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 0
-}
+}