fix links and readme icons

README.md

@@ -2,7 +2,7 @@
 
 [![Go Report Card](https://goreportcard.com/badge/github.com/emer/axon)](https://goreportcard.com/report/github.com/emer/axon)
 [![GoDoc](https://godoc.org/github.com/emer/axon?status.svg)](https://godoc.org/github.com/emer/axon)
-[![codecov](https://codecov.io/gh/emer/axon/branch/master/graph/badge.svg)](https://codecov.io/gh/emer/axon)
+[![codecov](https://codecov.io/gh/emer/axon/branch/main/graph/badge.svg)](https://codecov.io/gh/emer/axon)
 ![CI](https://github.com/emer/axon/actions/workflows/build.yml/badge.svg?branch=master)
 
 This is the Go implementation of the Axon algorithm for spiking, biologically based models of cognition, based on the [emergent](https://github.com/emer/emergent) framework.  Development of Axon is supported by the Obelisk project at https://astera.org/ and by collaborations with scientists at the University of California Davis, and other institutions around the world.
@@ -156,7 +156,7 @@ Axon is the spiking version of [Leabra](https://github.com/emer/leabra), which u
 You can copy the markdown source of this README into a file, and run [pandoc](https://pandoc.org/) on it to convert to LaTeX (or other formats) for inclusion in a paper.  As this page is always kept updated, it is best to regenerate from this source -- very easy:
 
 ```bash
-curl "https://raw.githubusercontent.com/emer/axon/master/README.md" -o appendix.md
+curl "https://raw.githubusercontent.com/emer/axon/main/README.md" -o appendix.md
 pandoc appendix.md -f gfm -t latex -o appendix.tex
 ```
 

examples/attn_trn/attn.go

@@ -928,7 +928,7 @@ func (ss *Sim) ConfigGUI() *core.Window {
 	height := 1200
 
 	core.SetAppName("attn")
-	core.SetAppAbout(`attn: This simulation illustrates how object recognition (ventral, what) and spatial (dorsal, where) pathways interact to produce spatial attention effects, and accurately capture the effects of brain damage to the spatial pathway. See <a href="https://github.com/emer/axon/blob/master/examples/attn_trn/README.md">README.md on GitHub</a>.</p>`)
+	core.SetAppAbout(`attn: This simulation illustrates how object recognition (ventral, what) and spatial (dorsal, where) pathways interact to produce spatial attention effects, and accurately capture the effects of brain damage to the spatial pathway. See <a href="https://github.com/emer/axon/blob/main/examples/attn_trn/README.md">README.md on GitHub</a>.</p>`)
 
 	win := core.NewMainWindow("attn", "Attention", width, height)
 	ss.Win = win
@@ -1023,9 +1023,9 @@ func (ss *Sim) ConfigGUI() *core.Window {
 		vp.SetNeedsFullRender()
 	})
 
-	tbar.AddAction(core.ActOpts{Label: "README", Icon: "file-markdown", Tooltip: "Opens your browser on the README file that contains instructions for how to run this model."}, win.This(),
+	tbar.AddAction(core.ActOpts{Label: "README", Icon: icons.FileMarkdown, Tooltip: "Opens your browser on the README file that contains instructions for how to run this model."}, win.This(),
 		func(recv, send tree.Node, sig int64, data interface{}) {
-			core.TheApp.OpenURL("https://github.com/emer/axon/blob/master/examples/attn_trn/README.md")
+			core.TheApp.OpenURL("https://github.com/emer/axon/blob/main/examples/attn_trn/README.md")
 		})
 
 	vp.UpdateEndNoSig(updt)

examples/choose/choose.go

@@ -1398,7 +1398,7 @@ func (ss *Sim) ConfigGUI() {
 			},
 		})
 		ss.GUI.AddToolbarItem(p, egui.ToolbarItem{Label: "README",
-			Icon:    "file-markdown",
+			Icon:    icons.FileMarkdown,
 			Tooltip: "Opens your browser on the README file that contains instructions for how to run this model.",
 			Active:  egui.ActiveAlways,
 			Func: func() {

examples/deep_fsa/deep_fsa.go

@@ -658,11 +658,11 @@ func (ss *Sim) ConfigGUI() {
 			},
 		})
 		ss.GUI.AddToolbarItem(p, egui.ToolbarItem{Label: "README",
-			Icon:    "file-markdown",
+			Icon:    icons.FileMarkdown,
 			Tooltip: "Opens your browser on the README file that contains instructions for how to run this model.",
 			Active:  egui.ActiveAlways,
 			Func: func() {
-				core.TheApp.OpenURL("https://github.com/emer/axon/blob/master/examples/deep_fsa/README.md")
+				core.TheApp.OpenURL("https://github.com/emer/axon/blob/main/examples/deep_fsa/README.md")
 			},
 		})
 	})

examples/deep_move/README.md

@@ -1,6 +1,6 @@
 # deep_move
 
-This example tests the `deep` predictive learning model on predicting the effects of moving within a first-person depth-map view of an agent moving within a simple square-shaped environment.  There are two predictions that are updated: head direction relative to some kind of "north" compass direction, which changes with rotations, and a depth map to the walls, encoded using a population code for each of N angles within an overall field of view (FOV).  This uses a simplified version of the [Flat World](https://github.com/emer/envs/tree/master/fworld) environment, and this project serves as an testing and optimization platform for the larger [Emery Map Nav](https://github.com/ccnlab/map-nav/tree/master/sims/emery2) model.
+This example tests the `deep` predictive learning model on predicting the effects of moving within a first-person depth-map view of an agent moving within a simple square-shaped environment.  There are two predictions that are updated: head direction relative to some kind of "north" compass direction, which changes with rotations, and a depth map to the walls, encoded using a population code for each of N angles within an overall field of view (FOV).  This uses a simplified version of the [Flat World](https://github.com/emer/envs/tree/main/fworld) environment, and this project serves as an testing and optimization platform for the larger [Emery Map Nav](https://github.com/ccnlab/map-nav/tree/main/sims/emery2) model.
 
 The parameters that work well for `deep_music` don't work here at all, for reasons that make sense: https://github.com/emer/axon/discussions/61  This model requires short time scale integration (i.e., Markovian, one-step history) and local, topographic connectivity to process different depth ranges and angle positions independently.  A fully connected hidden layer does not work at all: it tries to process the depth map wholistically, and that just doesn't work.
 

examples/deep_move/deep_move.go

@@ -661,11 +661,11 @@ func (ss *Sim) ConfigGUI() {
 			},
 		})
 		ss.GUI.AddToolbarItem(p, egui.ToolbarItem{Label: "README",
-			Icon:    "file-markdown",
+			Icon:    icons.FileMarkdown,
 			Tooltip: "Opens your browser on the README file that contains instructions for how to run this model.",
 			Active:  egui.ActiveAlways,
 			Func: func() {
-				core.TheApp.OpenURL("https://github.com/emer/axon/blob/master/examples/deep_move/README.md")
+				core.TheApp.OpenURL("https://github.com/emer/axon/blob/main/examples/deep_move/README.md")
 			},
 		})
 	})

examples/deep_music/deep_music.go

@@ -653,11 +653,11 @@ func (ss *Sim) ConfigGUI() {
 			},
 		})
 		ss.GUI.AddToolbarItem(p, egui.ToolbarItem{Label: "README",
-			Icon:    "file-markdown",
+			Icon:    icons.FileMarkdown,
 			Tooltip: "Opens your browser on the README file that contains instructions for how to run this model.",
 			Active:  egui.ActiveAlways,
 			Func: func() {
-				core.TheApp.OpenURL("https://github.com/emer/axon/blob/master/examples/deep_music/README.md")
+				core.TheApp.OpenURL("https://github.com/emer/axon/blob/main/examples/deep_music/README.md")
 			},
 		})
 	})

examples/dls/dls.go

@@ -1029,11 +1029,11 @@ func (ss *Sim) ConfigGUI() {
 			},
 		})
 		ss.GUI.AddToolbarItem(p, egui.ToolbarItem{Label: "README",
-			Icon:    "file-markdown",
+			Icon:    icons.FileMarkdown,
 			Tooltip: "Opens your browser on the README file that contains instructions for how to run this model.",
 			Active:  egui.ActiveAlways,
 			Func: func() {
-				core.TheApp.OpenURL("https://github.com/emer/axon/blob/master/examples/dls/README.md")
+				core.TheApp.OpenURL("https://github.com/emer/axon/blob/main/examples/dls/README.md")
 			},
 		})
 	})

examples/hip/diff/README.md

@@ -1,5 +1,5 @@
 # Net configurations
-And here are the diffs to the standard `hip.go` from `leabra/examples/hip` implementing the different network configuration and `AlphaCyc` code to achieve the above changes.  The full diffs including some changes to logging are here:  https://github.com/emer/leabra/blob/master/examples/hip/best_2-20.diff
+And here are the diffs to the standard `hip.go` from `leabra/examples/hip` implementing the different network configuration and `AlphaCyc` code to achieve the above changes.  The full diffs including some changes to logging are here:  https://github.com/emer/leabra/blob/main/examples/hip/best_2-20.diff
 
 ![](fig_netconfig_diffs.png?raw=true "ConfigNet Diffs")
 

examples/hip/hip.go

@@ -835,11 +835,11 @@ func (ss *Sim) ConfigGUI() {
 			},
 		})
 		ss.GUI.AddToolbarItem(p, egui.ToolbarItem{Label: "README",
-			Icon:    "file-markdown",
+			Icon:    icons.FileMarkdown,
 			Tooltip: "Opens your browser on the README file that contains instructions for how to run this model.",
 			Active:  egui.ActiveAlways,
 			Func: func() {
-				core.TheApp.OpenURL("https://github.com/emer/axon/blob/master/examples/hip/README.md")
+				core.TheApp.OpenURL("https://github.com/emer/axon/blob/main/examples/hip/README.md")
 			},
 		})
 	})

examples/hip/hip.py

@@ -177,7 +177,7 @@ def NewRndSeedCB(recv, send, sig, data):
 
 def ReadmeCB(recv, send, sig, data):
     core.TheApp.OpenURL(
-        "https://github.com/emer/leabra/blob/master/examples/hip/README.md"
+        "https://github.com/emer/leabra/blob/main/examples/hip/README.md"
     )
 
 
@@ -326,18 +326,25 @@ def __init__(self):
         self.PoolVocab = patgen.Vocab()
         self.SetTags("PoolVocab", 'display:"no-inline" desc:"pool patterns vocabulary"')
         self.TrainAB = etable.Table()
-        self.SetTags("TrainAB", 'display:"no-inline" desc:"AB training patterns to use"')
+        self.SetTags(
+            "TrainAB", 'display:"no-inline" desc:"AB training patterns to use"'
+        )
         self.TrainAC = etable.Table()
-        self.SetTags("TrainAC", 'display:"no-inline" desc:"AC training patterns to use"')
+        self.SetTags(
+            "TrainAC", 'display:"no-inline" desc:"AC training patterns to use"'
+        )
         self.TestAB = etable.Table()
         self.SetTags("TestAB", 'display:"no-inline" desc:"AB testing patterns to use"')
         self.TestAC = etable.Table()
         self.SetTags("TestAC", 'display:"no-inline" desc:"AC testing patterns to use"')
         self.TestLure = etable.Table()
-        self.SetTags("TestLure", 'display:"no-inline" desc:"Lure testing patterns to use"')
+        self.SetTags(
+            "TestLure", 'display:"no-inline" desc:"Lure testing patterns to use"'
+        )
         self.TrainAll = etable.Table()
         self.SetTags(
-            "TrainAll", 'display:"no-inline" desc:"all training patterns -- for pretrain"'
+            "TrainAll",
+            'display:"no-inline" desc:"all training patterns -- for pretrain"',
         )
         self.TrnTrlLog = etable.Table()
         self.SetTags(
@@ -362,15 +369,19 @@ def __init__(self):
         self.RunLog = etable.Table()
         self.SetTags("RunLog", 'display:"no-inline" desc:"summary log of each run"')
         self.RunStats = etable.Table()
-        self.SetTags("RunStats", 'display:"no-inline" desc:"aggregate stats on all runs"')
+        self.SetTags(
+            "RunStats", 'display:"no-inline" desc:"aggregate stats on all runs"'
+        )
         self.TstStats = etable.Table()
         self.SetTags("TstStats", 'display:"no-inline" desc:"testing stats"')
         self.SimMats = {}
         self.SetTags(
             "SimMats", 'display:"no-inline" desc:"similarity matrix results for layers"'
         )
         self.Params = params.Sets()
-        self.SetTags("Params", 'display:"no-inline" desc:"full collection of param sets"')
+        self.SetTags(
+            "Params", 'display:"no-inline" desc:"full collection of param sets"'
+        )
         self.ParamSet = str()
         self.SetTags(
             "ParamSet",
@@ -1880,7 +1891,9 @@ def ConfigTstTrlPlot(ss, plt, dt):
                 lnm + " ActM.Avg", eplot.Off, eplot.FixMin, 0, eplot.FixMax, 0.5
             )
         for lnm in ss.LayStatNms:
-            plt.SetColumnOptions(lnm + " Act", eplot.Off, eplot.FixMin, 0, eplot.FixMax, 1)
+            plt.SetColumnOptions(
+                lnm + " Act", eplot.Off, eplot.FixMin, 0, eplot.FixMax, 1
+            )
 
         return plt
 
@@ -2036,7 +2049,9 @@ def ConfigTstEpcPlot(ss, plt, dt):
         # order of params: on, fixMin, min, fixMax, max
         plt.SetColumnOptions("Run", eplot.Off, eplot.FixMin, 0, eplot.FloatMax, 0)
         plt.SetColumnOptions("Epoch", eplot.Off, eplot.FixMin, 0, eplot.FloatMax, 0)
-        plt.SetColumnOptions("PerTrlMSec", eplot.Off, eplot.FixMin, 0, eplot.FloatMax, 0)
+        plt.SetColumnOptions(
+            "PerTrlMSec", eplot.Off, eplot.FixMin, 0, eplot.FloatMax, 0
+        )
         plt.SetColumnOptions("SSE", eplot.Off, eplot.FixMin, 0, eplot.FloatMax, 0)
         plt.SetColumnOptions("AvgSSE", eplot.Off, eplot.FixMin, 0, eplot.FloatMax, 0)
         plt.SetColumnOptions("PctErr", eplot.Off, eplot.FixMin, 0, eplot.FixMax, 1)
@@ -2250,9 +2265,13 @@ def ConfigRunStatsPlot(ss, plt, dt):
         plt.Options.Type = eplot.Bar
         plt.Options.XAxisRot = 45
 
-        cp = plt.SetColumnOptions("AB Mem:Mean", eplot.On, eplot.FixMin, 0, eplot.FixMax, 1)
+        cp = plt.SetColumnOptions(
+            "AB Mem:Mean", eplot.On, eplot.FixMin, 0, eplot.FixMax, 1
+        )
         cp.ErrCol = "AB Mem:Sem"
-        cp = plt.SetColumnOptions("AC Mem:Mean", eplot.On, eplot.FixMin, 0, eplot.FixMax, 1)
+        cp = plt.SetColumnOptions(
+            "AC Mem:Mean", eplot.On, eplot.FixMin, 0, eplot.FixMax, 1
+        )
         cp.ErrCol = "AC Mem:Sem"
         cp = plt.SetColumnOptions(
             "FirstZero:Mean", eplot.On, eplot.FixMin, 0, eplot.FixMax, 30
@@ -2465,7 +2484,7 @@ def ConfigGUI(ss):
         tbar.AddAction(
             core.ActOpts(
                 Label="README",
-                Icon="file-markdown",
+                Icon=icons.FileMarkdown,
                 Tooltip="Opens your browser on the README file that contains instructions for how to run this model.",
             ),
             recv,

examples/inhib/inhib.go

@@ -561,11 +561,11 @@ func (ss *Sim) ConfigGUI() {
 			},
 		})
 		ss.GUI.AddToolbarItem(p, egui.ToolbarItem{Label: "README",
-			Icon:    "file-markdown",
+			Icon:    icons.FileMarkdown,
 			Tooltip: "Opens your browser on the README file that contains instructions for how to run this model.",
 			Active:  egui.ActiveAlways,
 			Func: func() {
-				core.TheApp.OpenURL("https://github.com/emer/axon/blob/master/examples/inhib/README.md")
+				core.TheApp.OpenURL("https://github.com/emer/axon/blob/main/examples/inhib/README.md")
 			},
 		})
 	})

examples/kinaseq/sim.go

@@ -140,7 +140,7 @@ func (ss *Sim) ResetTstCycPlot() {
 // ConfigGUI configures the Cogent Core GUI interface for this simulation.
 func (ss *Sim) ConfigGUI() {
 	title := "Kinase Eq"
-	ss.GUI.MakeBody(ss, "kinaseq", title, `kinaseq: Explores calcium-based synaptic learning rules, specifically at the synaptic level. See <a href="https://github.com/emer/axon/blob/master/examples/kinaseq/README.md">README.md on GitHub</a>.</p>`)
+	ss.GUI.MakeBody(ss, "kinaseq", title, `kinaseq: Explores calcium-based synaptic learning rules, specifically at the synaptic level. See <a href="https://github.com/emer/axon/blob/main/examples/kinaseq/README.md">README.md on GitHub</a>.</p>`)
 	ss.GUI.CycleUpdateInterval = 10
 
 	ss.GUI.AddPlots(title, &ss.Logs)
@@ -229,11 +229,11 @@ func (ss *Sim) ConfigGUI() {
 			},
 		})
 		ss.GUI.AddToolbarItem(p, egui.ToolbarItem{Label: "README",
-			Icon:    "file-markdown",
+			Icon:    icons.FileMarkdown,
 			Tooltip: "Opens your browser on the README file that contains instructions for how to run this model.",
 			Active:  egui.ActiveAlways,
 			Func: func() {
-				core.TheApp.OpenURL("https://github.com/emer/axon/blob/master/examples/neuron/README.md")
+				core.TheApp.OpenURL("https://github.com/emer/axon/blob/main/examples/neuron/README.md")
 			},
 		})
 	})

examples/mpi/ra25.go

@@ -745,11 +745,11 @@ func (ss *Sim) ConfigGUI() {
 			},
 		})
 		ss.GUI.AddToolbarItem(p, egui.ToolbarItem{Label: "README",
-			Icon:    "file-markdown",
+			Icon:    icons.FileMarkdown,
 			Tooltip: "Opens your browser on the README file that contains instructions for how to run this model.",
 			Active:  egui.ActiveAlways,
 			Func: func() {
-				core.TheApp.OpenURL("https://github.com/emer/axon/blob/master/examples/mpi/README.md")
+				core.TheApp.OpenURL("https://github.com/emer/axon/blob/main/examples/mpi/README.md")
 			},
 		})
 	})

examples/neuron/neuron.go

@@ -380,7 +380,7 @@ func (ss *Sim) ConfigNetView(nv *netview.NetView) {
 // ConfigGUI configures the Cogent Core GUI interface for this simulation.
 func (ss *Sim) ConfigGUI() {
 	title := "Neuron"
-	ss.GUI.MakeBody(ss, "neuron", title, `This simulation illustrates the basic properties of neural spiking and rate-code activation, reflecting a balance of excitatory and inhibitory influences (including leak and synaptic inhibition). See <a href="https://github.com/emer/axon/blob/master/examples/neuron/README.md">README.md on GitHub</a>.</p>`)
+	ss.GUI.MakeBody(ss, "neuron", title, `This simulation illustrates the basic properties of neural spiking and rate-code activation, reflecting a balance of excitatory and inhibitory influences (including leak and synaptic inhibition). See <a href="https://github.com/emer/axon/blob/main/examples/neuron/README.md">README.md on GitHub</a>.</p>`)
 	ss.GUI.CycleUpdateInterval = 10
 
 	nv := ss.GUI.AddNetView("NetView")
@@ -448,11 +448,11 @@ func (ss *Sim) ConfigGUI() {
 			},
 		})
 		ss.GUI.AddToolbarItem(p, egui.ToolbarItem{Label: "README",
-			Icon:    "file-markdown",
+			Icon:    icons.FileMarkdown,
 			Tooltip: "Opens your browser on the README file that contains instructions for how to run this model.",
 			Active:  egui.ActiveAlways,
 			Func: func() {
-				core.TheApp.OpenURL("https://github.com/emer/axon/blob/master/examples/neuron/README.md")
+				core.TheApp.OpenURL("https://github.com/emer/axon/blob/main/examples/neuron/README.md")
 			},
 		})
 	})

examples/objrec/README.md

@@ -12,4 +12,4 @@ Changes:
 
 TODOs:
 - [ ] Delete lots of the unnecessary code (like everything in logging, except the most basic stats e.g. `CorSim`)
-- [ ] Instead of being `package main`, turn the `main()` into a `BenchmarkObjrec(b *testing.B)` to make it easier to run & profile. Currently, this prohibits the use of a GUI (the window never gets created, just blocks [here](https://github.com/go-gl/glfw/blob/master/v3.3/glfw/window.go#L348) forever).
+- [ ] Instead of being `package main`, turn the `main()` into a `BenchmarkObjrec(b *testing.B)` to make it easier to run & profile. Currently, this prohibits the use of a GUI (the window never gets created, just blocks [here](https://github.com/go-gl/glfw/blob/main/v3.3/glfw/window.go#L348) forever).

examples/objrec/objrec.go

@@ -658,7 +658,7 @@ func (ss *Sim) ConfigActRFs() {
 // ConfigGUI configures the Cogent Core GUI interface for this simulation.
 func (ss *Sim) ConfigGUI() {
 	title := "Object Recognition"
-	ss.GUI.MakeBody(ss, "objrec", title, `This simulation explores how a hierarchy of areas in the ventral stream of visual processing (up to inferotemporal (IT) cortex) can produce robust object recognition that is invariant to changes in position, size, etc of retinal input images. See <a href="https://github.com/CompCogNeuro/sims/blob/master/ch6/objrec/README.md">README.md on GitHub</a>.</p>`)
+	ss.GUI.MakeBody(ss, "objrec", title, `This simulation explores how a hierarchy of areas in the ventral stream of visual processing (up to inferotemporal (IT) cortex) can produce robust object recognition that is invariant to changes in position, size, etc of retinal input images. See <a href="https://github.com/CompCogNeuro/sims/blob/main/ch6/objrec/README.md">README.md on GitHub</a>.</p>`)
 	ss.GUI.CycleUpdateInterval = 10
 
 	nv := ss.GUI.AddNetView("NetView")
@@ -728,11 +728,11 @@ func (ss *Sim) ConfigGUI() {
 			},
 		})
 		ss.GUI.AddToolbarItem(p, egui.ToolbarItem{Label: "README",
-			Icon:    "file-markdown",
+			Icon:    icons.FileMarkdown,
 			Tooltip: "Opens your browser on the README file that contains instructions for how to run this model.",
 			Active:  egui.ActiveAlways,
 			Func: func() {
-				core.TheApp.OpenURL("https://github.com/emer/axon/blob/master/examples/bench_objrec/README.md")
+				core.TheApp.OpenURL("https://github.com/emer/axon/blob/main/examples/bench_objrec/README.md")
 			},
 		})
 	})