Update muscle modelling lesson 6 tutorial (#9)

* Update muscle modelling lesson 6 tutorial

* Update installation instructions for AnyPyTools library

* Fix links

* Update link to pixi package manager in contributing.md

* ci: Allowed tagged link check to fail

Author: melund

.github/workflows/build.yaml

@@ -49,25 +49,12 @@ jobs:
           ref: ${{ needs.find-tag.outputs.latest-tag }}
 
       - uses: prefix-dev/setup-pixi@v0.5.1
-        continue-on-error: true
-        id: pixisetup
         with:
           cache: true
           cache-write: ${{ github.event_name == 'push' && github.ref_name == 'master' }}
 
-      - if: steps.pixisetup.outcome == 'success'
-        run: pixi run sphinx-build -M linkcheck . _build -W --keep-going -a -q 
-          
-      - name: Install mamba
-        if: steps.pixisetup.outcome == 'failure'
-        uses: mamba-org/setup-micromamba@v1
-        with:
-          environment-file: environment.yaml
-            
-      - name: build with mamba
-        if: steps.pixisetup.outcome == 'failure'
-        shell: bash -leo pipefail {0} {0}
-        run: sphinx-build -M linkcheck . _build -W --keep-going -a -q 
+      - run: pixi run sphinx-build -M linkcheck . _build -W --keep-going -a -q 
+        continue-on-error: true
 
 
 

Muscle_modeling/Downloads/MuscleDemo.6.any

@@ -73,15 +73,15 @@ Main = {
         AnyRevoluteJoint &Jnt = ..Jnts.Shoulder;
         DriverPos = {-1.7};
         DriverVel = {0.4};
-        Reaction.Type = {0};
+        Reaction.Type = {Off};
       }; // Shoulder driver
 
       //---------------------------------
       AnyKinEqSimpleDriver ElbowMotion = {
         AnyRevoluteJoint &Jnt = ..Jnts.Elbow;
         DriverPos = {1.5};
         DriverVel = {0.7};
-        Reaction.Type = {0};
+        Reaction.Type = {Off};
       }; // Elbow driver
     }; // Driver folder
 

Muscle_modeling/Downloads/MuscleDemo.6.final.any

@@ -0,0 +1,156 @@
+// Demo example for general muscles. 
+
+Main = {
+
+  // The actual body model goes in this folder
+  AnyFolder ArmModel = {
+
+    // Global Reference Frame
+    AnyFixedRefFrame GlobalRef = {
+
+      AnyRefNode Shoulder = { 
+        sRel = {0,0,0}; 
+      };
+    };  // Global reference frame
+
+    // Segments
+    AnyFolder Segs = {
+
+      AnySeg UpperArm = {
+        r0 = {0,-0.15,0};
+        Axes0 = {{0,1,0},{-1,0,0},{0,0,1}};
+        Mass = 2.0;
+        Jii = {0.002,0.005,0.005};
+        AnyDrawSeg DrwSeg = {};
+        AnyRefNode ShoulderNode = {
+          sRel = {-0.2,0,0}; 
+        };
+        AnyRefNode ElbowNode = {
+          sRel = {0.2,0,0}; 
+        };
+      }; // UpperArm
+
+      AnySeg LowerArm = {
+        r0 = {0.25,-0.3,0};
+        Mass = 2.0;
+        Jii = {0.002,0.005,0.005};
+        AnyRefNode ElbowNode = {
+          sRel = {-0.2,0,0};
+        };
+        AnyRefNode HandNode = {
+          sRel = {0.2,0,0};
+        };
+        AnyRefNode PalmNode = {
+          sRel = {0.27,0,0};
+          ARel = {{0,0,1},{0,1,0},{-1,0,0}};
+        };
+        AnyDrawSeg DrwSeg = {};
+     }; // LowerArm
+
+   }; // Segs folder
+
+    AnyFolder Jnts = {
+
+      //---------------------------------
+      AnyRevoluteJoint Shoulder = {
+        Axis = z;
+        AnyRefNode &GroundNode = ..GlobalRef.Shoulder;
+        AnyRefNode &UpperArmNode = ..Segs.UpperArm.ShoulderNode;
+      }; // Shoulder joint
+
+      AnyRevoluteJoint Elbow = {
+        Axis = z;
+        AnyRefNode &UpperArmNode = ..Segs.UpperArm.ElbowNode;
+        AnyRefNode &LowerArmNode = ..Segs.LowerArm.ElbowNode;
+      }; // Elbow joint
+
+    }; // Jnts folder
+    
+    
+    AnyKinLinear HandPos = {
+       AnyRefFrame &ref1 = .GlobalRef.Shoulder;
+       AnyRefFrame &ref2 = .Segs.LowerArm.PalmNode;
+     };
+
+        AnyFolder Drivers = {
+     AnyKinEqSimpleDriver HandDriver = {
+       AnyKinLinear &Measure = ..HandPos;
+       MeasureOrganizer = {0,1};
+       DriverPos = {0.45, -0.6};
+       DriverVel = {0, 0.5};
+       Reaction.Type = {Off, Off};
+     };
+        /*
+      //---------------------------------
+      AnyKinEqSimpleDriver ShoulderMotion = {
+        AnyRevoluteJoint &Jnt = ..Jnts.Shoulder;
+        DriverPos = {-1.7};
+        DriverVel = {0.4};
+        Reaction.Type = {0};
+      }; // Shoulder driver
+
+      //---------------------------------
+      AnyKinEqSimpleDriver ElbowMotion = {
+        AnyRevoluteJoint &Jnt = ..Jnts.Elbow;
+        DriverPos = {1.5};
+        DriverVel = {0.7};
+        Reaction.Type = {0};
+      }; // Elbow driver
+      
+        */ 
+      
+    }; // Driver folder
+  
+  
+   AnyRecruitedActuator WallReaction = {
+      Type = NonNegative;
+      Volume = 1e-6; // Ignore this value. Only used in special volume weighted recruitement
+      Strength = 10000;
+      AnyKinMeasureOrg Org = {
+        AnyKinMeasure &wall = ..HandPos;
+        MeasureOrganizer = {0};
+      };
+    };  
+    
+    AnyMuscleModel MusModel = {
+      F0 = 100.0;
+    };
+   
+    AnyMuscleGeneric ShoulderTorque = 
+    {
+      //viewForce.Visible = Off;
+      Type = NonNegative;
+      AnyMuscleModel &Model = .MusModel;
+      AnyKinMeasure &Angle = .Jnts.Shoulder;
+    };
+    
+    AnyMuscleGeneric ElbowTorque = 
+    {
+      //viewForce.Visible = Off;
+      Type = NonNegative;
+      AnyMuscleModel &Model = .MusModel;
+      AnyKinMeasure &Angle = .Jnts.Elbow;
+    };
+    AnyFolder Loads = {
+
+      //---------------------------------
+      AnyForce3D Dumbbell = {
+        AnyRefNode &PalmNode = ..Segs.LowerArm.PalmNode;
+        F = {0,-100,0}; // Force in Newton
+      };
+    };  // Loads folder
+
+    // Todo. Add the model elements such as
+    //       segments, joints, and muscles here.
+
+  }; // ArmModel
+
+  // The study: Operations to be performed on the model
+  AnyBodyStudy ArmStudy = {
+    AnyFolder &Model = .ArmModel;
+    // InverseDynamics.Criterion.Type = MR_MinMaxStrict;
+    InverseDynamics.Criterion.Type = MR_Quadratic;
+    Gravity = {0.0, -9.81, 0.0};
+  };
+
+};  // Main