update bioimage and molecular cases

eval_cases/molecular_vis/actions/basic_actions.yaml

@@ -1,727 +0,0 @@
-# Basic Actions for Molecular Visualization Benchmark
-# These actions test core functionality of molecular visualization tools
-# https://www.rcsb.org/structure/1CRN
-#
-# Taxonomy Level: Task (small-scale visualization task involving a few operations)
-# Each task is marked with a comment indicating the end of the task and the task name
-
-# ============================================================
-# TASK 1: 1CRN - Load & Basic Representations
-# ============================================================
-
-# Loading a CIF file
-- vars:
-    question: |
-        Remove all molecules from and load the data from "data/1CRN.cif".
-        Take a screenshot to confirm if the dataset has been loaded.
-        Respond with <1> if the cif file has been loaded and the molecule is visible in the viewport, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Basic visualization - Van der Waals representation
-- vars:
-    question: |
-        Change the visualization type to Van-der-Waals.
-        Take a screenshot to validate whether the representation has been changed.
-        Respond with <1> if the molecule in the viewport is in the Van-der-Waals representation, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Licorice representation
-- vars:
-    question: |
-        Change the visualization type to Licorice (stick representation).
-        Take a screenshot to validate whether the representation has been changed.
-        Respond with <1> if the molecule in the viewport is in the Licorice representation showing bonds as sticks, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# END OF TASK 1: 1CRN - Load & Basic Representations
-# Operations: Load CIF file, Van der Waals representation, Licorice representation
-
-# ============================================================
-# TASK 2: 1CRN - Color by Properties
-# ============================================================
-
-# Coloring by element
-- vars:
-    question: |
-        Color the molecule by element (atoms colored according to their chemical element).
-        Take a screenshot to validate whether the coloring has been applied.
-        Respond with <1> if the molecule is colored by element with different colors for different atom types, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Coloring by chain
-- vars:
-    question: |
-        Select chain A and color it red. Color all other chains blue.
-        Take a screenshot to validate whether the selection and coloring has been applied.
-        Respond with <1> if Chain A is colored red and other chains are colored blue, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Coloring by residue type
-- vars:
-    question: |
-        Color the molecule by residue type (amino acids colored according to their type).
-        Take a screenshot to validate whether the coloring has been applied.
-        Respond with <1> if the molecule is colored by residue type with different amino acids having distinct colors, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# END OF TASK 2: 1CRN - Color by Properties
-# Operations: Color by element, color by chain, color by residue type
-
-# ============================================================
-# TASK 3: 1CRN - Region Selection
-# ============================================================
-
-# Selecting and coloring specific residues
-- vars:
-    question: |
-        Select residues 1 to 10 and color them green. Keep the rest of the molecule in its current color.
-        Take a screenshot to validate whether the selection and coloring has been applied.
-        Respond with <1> if residues 1 to 10 are colored green while the rest of the molecule remains in a different color, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Selecting specific atoms
-- vars:
-    question: |
-        Select all carbon atoms and color them cyan.
-        Take a screenshot to validate whether the selection and coloring has been applied.
-        Respond with <1> if all carbon atoms are colored cyan while other atoms have different colors, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# END OF TASK 3: 1CRN - Region Selection
-# Operations: Select and color specific residues, select and color specific atoms
-
-# ============================================================
-# TASK 4: 1CRN - Multi-Representation
-# ============================================================
-
-# Multiple representations
-- vars:
-    question: |
-        Create two representations: show the backbone as Cartoon and all side chains as Licorice.
-        Take a screenshot to validate whether both representations are visible.
-        Respond with <1> if both representations are visible (Cartoon backbone + Licorice side chains), or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Material properties - Opaque
-- vars:
-    question: |
-        Change the material to Opaque (fully opaque, no transparency).
-        Take a screenshot to validate whether the material has been changed.
-        Respond with <1> if the molecule appears fully opaque with no transparency, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Changing representation radius
-- vars:
-    question: |
-        Change the representation to Licorice and set the radius to 0.3.
-        Take a screenshot to validate whether the radius has been changed.
-        Respond with <1> if the Licorice representation shows bonds with a radius of 0.3, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# END OF TASK 4: 1CRN - Multi-Representation
-# Operations: Create multiple representations (cartoon + licorice), adjust material properties (opaque), adjust representation parameters (radius)
-
-# ============================================================
-# TASK 5: 1CRN - Advanced Coloring
-# ============================================================
-
-# Coloring by B-factor (temperature factor)
-- vars:
-    question: |
-        Color the molecule by B-factor (temperature factor, showing flexibility/uncertainty).
-        Take a screenshot to validate whether the coloring has been applied.
-        Respond with <1> if the molecule is colored by B-factor showing a gradient of colors indicating different temperature factors, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Selecting water molecules
-- vars:
-    question: |
-        Select all water molecules (residue name "HOH" or "WAT") and color them cyan.
-        Take a screenshot to validate whether the water molecules have been selected and colored.
-        Respond with <1> if all water molecules are colored cyan and visible in the viewport, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Coloring by charge
-- vars:
-    question: |
-        Color the molecule by charge (positive charges one color, negative charges another, neutral a third color).
-        Take a screenshot to validate whether the coloring has been applied.
-        Respond with <1> if the molecule is colored by charge with distinct colors for positive, negative, and neutral regions, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Coloring by hydrophobicity
-- vars:
-    question: |
-        Color the molecule by hydrophobicity (hydrophobic residues one color, hydrophilic another).
-        Take a screenshot to validate whether the coloring has been applied.
-        Respond with <1> if the molecule is colored by hydrophobicity with distinct colors for hydrophobic and hydrophilic regions, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# END OF TASK 5: 1CRN - Advanced Coloring
-# Operations: Color by B-factor, select and color water molecules, color by charge, color by hydrophobicity
-
-# ============================================================
-# TASK 6: 1CRN - Active Site Selection
-# ============================================================
-
-# Selecting and highlighting active site
-- vars:
-    question: |
-        Select residues within 5 Angstroms of residue 25 and color them yellow. Color the rest of the molecule gray.
-        Take a screenshot to validate whether the selection and coloring has been applied.
-        Respond with <1> if residues within 5 Angstroms of residue 25 are colored yellow and the rest of the molecule is colored gray, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Selecting protein vs non-protein
-- vars:
-    question: |
-        Color all protein atoms green and all non-protein atoms (water, ions, ligands) red.
-        Take a screenshot to validate whether the coloring has been applied.
-        Respond with <1> if protein atoms are colored green and non-protein atoms (water, ions, ligands) are colored red, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Changing background color
-- vars:
-    question: |
-        Change the background color to white.
-        Take a screenshot to validate whether the background color has been changed.
-        Respond with <1> if the background of the viewport is white, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# END OF TASK 6: 1CRN - Active Site Selection
-# Operations: Distance-based selection (5Å around residue), distinguish protein vs non-protein components, adjust view settings (background color)
-
-# ============================================================
-# TASK 7: 1CRN - Spatial Queries
-# ============================================================
-
-# Selecting specific atom types in a range
-- vars:
-    question: |
-        Select all oxygen atoms in residues 1 to 20 and color them red.
-        Take a screenshot to validate whether the selection and coloring has been applied.
-        Respond with <1> if all oxygen atoms in residues 1 to 20 are colored red, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Selecting atoms within distance
-- vars:
-    question: |
-        Select all atoms within 3 Angstroms of any atom in residue 15 and color them magenta.
-        Take a screenshot to validate whether the selection and coloring has been applied.
-        Respond with <1> if all atoms within 3 Angstroms of residue 15 are colored magenta, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# END OF TASK 7: 1CRN - Spatial Queries
-# Operations: Select specific atom types in residue ranges, distance-based atom selection
-
-# ============================================================
-# TASK 8: 1CRN - Visibility Control
-# ============================================================
-
-# Selecting and hiding specific residues
-- vars:
-    question: |
-        Select residues 20 to 30 and hide them (make them invisible).
-        Take a screenshot to validate whether the residues have been hidden.
-        Respond with <1> if residues 20 to 30 are not visible in the viewport while the rest of the molecule remains visible, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Selecting and showing only specific atoms
-- vars:
-    question: |
-        Show only atoms with element type "N" (nitrogen) and hide all other atoms.
-        Take a screenshot to validate whether only nitrogen atoms are visible.
-        Respond with <1> if only nitrogen atoms are visible in the viewport and all other atoms are hidden, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Selecting and showing only backbone
-- vars:
-    question: |
-        Show only the backbone atoms (N, CA, C, O) as Licorice representation.
-        Take a screenshot to validate whether only backbone atoms are visible.
-        Respond with <1> if only backbone atoms (N, CA, C, O) are visible in Licorice representation and side chains are hidden, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Selecting and showing only side chains
-- vars:
-    question: |
-        Show only side chain atoms (excluding backbone atoms N, CA, C, O) as Van-der-Waals representation.
-        Take a screenshot to validate whether only side chain atoms are visible.
-        Respond with <1> if only side chain atoms are visible in Van-der-Waals representation and backbone atoms are hidden, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# END OF TASK 8: 1CRN - Visibility Control
-# Operations: Hide specific residues, show only specific element types, show only backbone, show only side chains
-
-# ============================================================
-# TASK 9: 1CRN - Residue Selection
-# ============================================================
-
-# Selecting aromatic residues
-- vars:
-    question: |
-        Select all aromatic residues (PHE, TYR, TRP) and color them purple.
-        Take a screenshot to validate whether the aromatic residues have been selected and colored.
-        Respond with <1> if all aromatic residues (PHE, TYR, TRP) are colored purple, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Selecting charged residues
-- vars:
-    question: |
-        Select all charged residues (ARG, LYS, ASP, GLU) and color them red for positive charges and blue for negative charges.
-        Take a screenshot to validate whether the charged residues have been selected and colored correctly.
-        Respond with <1> if charged residues are colored correctly (ARG/LYS red, ASP/GLU blue), or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# END OF TASK 9: 1CRN - Residue Selection
-# Operations: Select aromatic residues, select charged residues with differential coloring
-
-# ============================================================
-# TASK 10: 1CRN - Combined Representations
-# ============================================================
-
-# Multiple selections with different representations
-- vars:
-    question: |
-        Show the backbone as Cartoon colored by chain, and show all side chain atoms as Van-der-Waals colored by element.
-        Take a screenshot to validate whether both representations are visible with their respective colorings.
-        Respond with <1> if the backbone is shown as Cartoon colored by chain and side chain atoms are shown as Van-der-Waals colored by element, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Selecting and coloring by atom selection - backbone with sidechain by element
-- vars:
-    question: |
-        Show backbone atoms (N, CA, C, O) as Licorice colored blue, and show side chain atoms as Van-der-Waals colored by element.
-        Take a screenshot to validate whether both representations are visible with their respective colorings.
-        Respond with <1> if backbone atoms are shown as Licorice colored blue and side chain atoms are shown as Van-der-Waals colored by element, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# END OF TASK 10: 1CRN - Combined Representations
-# Operations: Multiple representations with different color schemes (cartoon by chain + VdW by element), multiple representations with structural segmentation (backbone vs side chains)
-
-# ============================================================
-# TASK 11: 1CRN - Distance-based Selection
-# ============================================================
-
-# Selecting and coloring by distance from specific atom
-- vars:
-    question: |
-        Select all atoms within 4 Angstroms of the CA atom of residue 10 and color them green. Color all other atoms gray.
-        Take a screenshot to validate whether the selection and coloring has been applied.
-        Respond with <1> if all atoms within 4 Angstroms of the CA atom of residue 10 are colored green and all other atoms are colored gray, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Coloring by atom selection with multiple criteria
-- vars:
-    question: |
-        Select all atoms that are either oxygen or nitrogen atoms in residues 1 to 20, and color them red. Color all other atoms gray.
-        Take a screenshot to validate whether the selection and coloring has been applied.
-        Respond with <1> if all oxygen and nitrogen atoms in residues 1 to 20 are colored red and all other atoms are colored gray, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Selecting and coloring by atom property
-- vars:
-    question: |
-        Select all atoms with element type "S" (sulfur) and color them yellow. Keep all other atoms in their default color.
-        Take a screenshot to validate whether the selection and coloring has been applied.
-        Respond with <1> if all sulfur atoms are colored yellow while other atoms remain in their default color, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# END OF TASK 11: 1CRN - Distance-based Selection
-# Operations: Distance from specific atom (CA of residue), combined criteria (element type AND residue range), element-specific coloring (sulfur atoms)
-
-# ============================================================
-# TASK 12: 1CRN - Gradient Coloring
-# ============================================================
-
-# Coloring by residue number
-- vars:
-    question: |
-        Color the molecule by residue number (gradient from N-terminus to C-terminus).
-        Take a screenshot to validate whether the coloring has been applied.
-        Respond with <1> if the molecule is colored by residue number showing a gradient from the beginning to the end of the sequence, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Selecting and coloring by atom type in specific region
-- vars:
-    question: |
-        Select all nitrogen atoms in residues 5 to 15 and color them blue. Color all other atoms gray.
-        Take a screenshot to validate whether the selection and coloring has been applied.
-        Respond with <1> if all nitrogen atoms in residues 5 to 15 are colored blue and all other atoms are colored gray, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Selecting and coloring by atom selection - element and residue combination
-- vars:
-    question: |
-        Select all oxygen atoms in polar residues (SER, THR, ASN, GLN, TYR, CYS) and color them cyan. Color all other atoms gray.
-        Take a screenshot to validate whether the selection and coloring has been applied.
-        Respond with <1> if all oxygen atoms in polar residues are colored cyan and all other atoms are colored gray, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Selecting and coloring by atom selection - distance-based with element filter
-- vars:
-    question: |
-        Select all oxygen atoms within 5 Angstroms of residue 15 and color them red. Color all other atoms gray.
-        Take a screenshot to validate whether the selection and coloring has been applied.
-        Respond with <1> if all oxygen atoms within 5 Angstroms of residue 15 are colored red and all other atoms are colored gray, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# END OF TASK 12: 1CRN - Gradient Coloring
-# Operations: Color by residue number (gradient), element selection in residue ranges, element + residue type combination (oxygen in polar residues), distance-based with element filter
-
-# ============================================================
-# TASK 13: 1CRN - Multi-Criteria Selection
-# ============================================================
-
-# Selecting and coloring by atom selection - backbone with sidechain by element
-- vars:
-    question: |
-        Show the backbone as NewCartoon colored by chain. Show all side chain carbon atoms as Licorice colored gray, all side chain nitrogen atoms as Licorice colored blue, and all side chain oxygen atoms as Licorice colored red.
-        Take a screenshot to validate whether the representations and colorings have been applied.
-        Respond with <1> if the backbone is shown as NewCartoon colored by chain, side chain carbon atoms are Licorice gray, side chain nitrogen atoms are Licorice blue, and side chain oxygen atoms are Licorice red, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Selecting and coloring by atom selection - complex distance and element
-- vars:
-    question: |
-        Select all carbon atoms within 4 Angstroms of any nitrogen atom in residues 1 to 15, and color them green. Color all other atoms gray.
-        Take a screenshot to validate whether the selection and coloring has been applied.
-        Respond with <1> if all carbon atoms within 4 Angstroms of any nitrogen atom in residues 1 to 15 are colored green and all other atoms are colored gray, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Selecting and coloring by atom selection - multiple criteria
-- vars:
-    question: |
-        Select all atoms that are either (carbon atoms in residues 1 to 10) or (nitrogen atoms in residues 11 to 20), and color them yellow. Color all other atoms gray.
-        Take a screenshot to validate whether the selection and coloring has been applied.
-        Respond with <1> if all atoms matching the criteria are colored yellow and all other atoms are colored gray, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Selecting and coloring by atom selection - complex multi-criteria
-- vars:
-    question: |
-        Select all atoms that are either (oxygen atoms in residues 1 to 10) or (nitrogen atoms within 3 Angstroms of residue 15), and color them magenta. Color all other atoms gray.
-        Take a screenshot to validate whether the selection and coloring has been applied.
-        Respond with <1> if all atoms matching the complex criteria are colored magenta and all other atoms are colored gray, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Selecting and showing only CA atoms
-- vars:
-    question: |
-        Show only CA (alpha carbon) atoms as Van-der-Waals spheres colored by chain.
-        Take a screenshot to validate whether only alpha carbons are visible.
-        Respond with <1> if only alpha carbon atoms are visible as spheres colored by chain, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Selecting and showing only heteroatoms
-- vars:
-    question: |
-        Show only heteroatoms (non-standard atoms like water, ions, ligands) as Van-der-Waals spheres colored by element.
-        Take a screenshot to validate whether only heteroatoms are visible.
-        Respond with <1> if only heteroatoms (non-standard atoms) are visible as spheres colored by element, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Selecting and coloring by atom selection - multiple element types
-- vars:
-    question: |
-        Select all carbon, nitrogen, and oxygen atoms and color them by element (carbon gray, nitrogen blue, oxygen red). Hide all other atoms.
-        Take a screenshot to validate whether the selection and coloring has been applied.
-        Respond with <1> if only carbon (gray), nitrogen (blue), and oxygen (red) atoms are visible and all other atoms are hidden, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# END OF TASK 13: 1CRN - Multi-Criteria Selection
-# Operations: Multi-representation with element-specific coloring (backbone cartoon + side chain licorice by element), complex distance and element queries (carbon near nitrogen atoms), Boolean logic selection (OR criteria), complex multi-criteria with distance, CA-only visualization, heteroatom isolation, multiple element type filtering

eval_cases/molecular_vis/{workflows/eval_analysis_workflows.yaml → eval_analysis_workflows.yaml}

@@ -2,6 +2,161 @@
 # This test evaluates the ability to complete molecular visualization tasks
 # with detailed requirements and evaluation criteria
 
+#simple licorice visualization of a protein 
+- vars:
+    question: |
+        1. I want you to visualize a molecular structure from a CIF file. 
+        2. Load the data/1CRN.cif. 
+        3. Visualize the molecular using a licorice representation. 
+        4. Take a screenshot of the visualization.
+         Q1. Does it show a licorice representation of the protein? (yes/no)
+        5. Answer Q1 in a plain text file "md_analysis/results/answers_basic_vis.txt".
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          1. Q1 correct answer: Yes
+      rs-file: "md_analysis/results/answers_basic_vis.txt"
+
+#simple coloring by element of a protein
+- vars:
+    question: |
+        1. I want you to visualize a molecular structure from a CIF file. 
+        2. Load the data/1CRN.cif. 
+        3. Visualize the molecular using a CPK or similar representation where atoms are colored by their chemical element.
+        4. Take a screenshot of the visualization.
+         Q1. Is the molecule colored according to the chemical element of its atoms (e.g., CPK coloring)? (yes/no)
+        5. Answer Q1 in a plain text file "md_analysis/results/answers_element_coloring.txt".
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          1. Q1 correct answer: Yes
+      rs-file: "md_analysis/results/answers_element_coloring.txt"
+
+#simple selection and coloring of a protein
+- vars:
+    question: |
+        1. I want you to visualize a molecular structure from a CIF file. 
+        2. Load the data/1CRN.cif. 
+        3. Select all carbon atoms and color them cyan.
+        4. Take a screenshot of the visualization.
+         Q1. Are all carbon atoms colored cyan? (yes/no)
+        5. Answer Q1 in a plain text file "md_analysis/results/answers_selection_coloring.txt".
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          1. Q1 correct answer: Yes
+      rs-file: "md_analysis/results/answers_selection_coloring.txt"
+
+#simple coloring by charge of a protein
+- vars:
+    question: |
+        1. I want you to visualize a molecular structure from a CIF file. 
+        2. Load the data/1CRN.cif. 
+        3. Color the molecule according to atomic charge: use one color for positive charges, another for negative charges, and a third for neutral atoms.
+        4. Take a screenshot of the visualization.
+         Q1. Is the molecule colored by atomic charge (differentiating positive, negative, and neutral)? (yes/no)
+        5. Answer Q1 in a plain text file "md_analysis/results/answers_charge_coloring.txt".
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          1. Q1 correct answer: Yes
+      rs-file: "md_analysis/results/answers_charge_coloring.txt"
+
+#simple selection and coloring of specific atoms
+- vars:
+    question: |
+        1. I want you to visualize a molecular structure from a CIF file. 
+        2. Load the data/1CRN.cif. 
+        3. Select all oxygen atoms in residues 1 to 20 and color them red.
+        4. Take a screenshot of the visualization.
+         Q1. Are all oxygen atoms in residues 1 to 20 colored red? (yes/no)
+        5. Answer Q1 in a plain text file "md_analysis/results/answers_complex_selection.txt".
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          1. Q1 correct answer: Yes
+      rs-file: "md_analysis/results/answers_complex_selection.txt"
+
+#simple selection and coloring of aromatic residues
+- vars:
+    question: |
+        1. I want you to visualize a molecular structure from a CIF file. 
+        2. Load the data/1CRN.cif. 
+        3. Select all aromatic residues (PHE, TYR, TRP) and color them purple.
+        4. Take a screenshot of the visualization.
+         Q1. Are all aromatic residues (PHE, TYR, TRP) colored purple? (yes/no)
+        5. Answer Q1 in a plain text file "md_analysis/results/answers_aromatic_selection.txt".
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          1. Q1 correct answer: Yes
+      rs-file: "md_analysis/results/answers_aromatic_selection.txt"
+
+#simple RMSD and RMSF calculation of a protein
+- vars:
+    question: |
+        1. I want you to perform a structural analysis on a molecular structure from a CIF file. 
+        2. Load the data/1CRN.cif. 
+        3. Calculate the Root Mean Square Deviation (RMSD) of the structure against itself.
+        4. Calculate the Root Mean Square Fluctuation (RMSF) for the structure.
+        5. Save the computed RMSD and RMSF values as plain text to "md_analysis/results/answers_rmsd_rmsf.txt".
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          1. Does the output report the calculated RMSD?
+          2. Does the output report the calculated RMSF values or state that it requires a trajectory?
+      rs-file: "md_analysis/results/answers_rmsd_rmsf.txt"
+
+#simple radius of gyration calculation of a protein
+- vars:
+    question: |
+        1. I want you to calculate the compactness of a protein from a CIF file. 
+        2. Load the data/1CRN.cif. 
+        3. Calculate the Radius of Gyration (Rg) of the protein structure.
+        4. Save the calculated Radius of Gyration as plain text to "md_analysis/results/answers_rg.txt".
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          1. Does the output report a numeric value for the calculated Radius of Gyration?
+      rs-file: "md_analysis/results/answers_rg.txt"
+
+- vars:
+    question: |
+        1. I want you to calculate specific geometric properties of a molecular structure from a CIF file. 
+        2. Load the data/1CRN.cif. 
+        3. Calculate the distance between the alpha carbons of residue 1 and residue 10.
+        4. Calculate the backbone dihedral angles (phi and psi) for residue 5.
+        5. Save the computed distance and angles as plain text to "md_analysis/results/answers_distances_angles.txt".
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          1. Does the output report the calculated distance between the alpha carbons of residue 1 and 10?
+          2. Does the output report the calculated phi and psi dihedral angles for residue 5?
+      rs-file: "md_analysis/results/answers_distances_angles.txt"
+
+#simple contact calculation of a protein
+- vars:
+    question: |
+        1. I want you to calculate the number of contacts in a folded protein from a CIF file.
+        2. Load the data/1CRN.cif.
+        3. Calculate the number of contacts within an 8 Angstrom cutoff.
+        4. Save the total count of contacts as plain text to "md_analysis/results/answers_native_contacts.txt".
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          1. Does the output report a numeric count of contacts?
+      rs-file: "md_analysis/results/answers_native_contacts.txt"
+
 # 1. Curved membrane simulation
 # As part of a protocol paper for building membrane using the coarse-grained Martini 3 force field, https://doi.org/10.1016/bs.mie.2024.03.010, a tutorial was developed: https://bbs.llnl.gov/data/building-membranes-data
 # Tutorial 4 is on curved membranes which is used here as an example of bilayer visualization. 
@@ -74,4 +229,4 @@
 # Q1 reason: quite some gray dots from cholesterol ROH headgroup bead can be seen in the center of the bilayer, so the answer is YES.
 # Q2 reason: if you run the flowing VMD selection command (name PO4 ROH) and within 15 of (index 3457 to 35009 and resid 188 to 329)
 # You will find 4 lipids head group beads, so the answer is C. 3-5 
-# Note here it’s important to only count each lipid once, e.g. either use a single reference bead per lipid or center of mass, also selecting the protein can be tricky as the lipids and water also if resid’s in the 188 to 329 range so either exclude other molecule or sub select only the protein residues
+# Note here it’s important to only count each lipid once, e.g. either use a single reference bead per lipid or center of mass, also selecting the protein can be tricky as the lipids and water also if resid’s in the 188 to 329 range so either exclude other molecule or sub select only the protein residues

eval_cases/napari/0_actions/eval_basic_napari_functions.yaml

@@ -1,566 +0,0 @@
-# Basic Napari Function Tests - Action Level
-# These tests evaluate individual server functions with simple, single-function calls
-# Each test focuses on testing one specific function with appropriate parameters
-# We suggest using https://www.ebi.ac.uk/bioimage-archive/galleries/S-BIAD7.html IM1 as dataset_001
-# We suggest using https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/pages/S-BIAD573.html IM1 as dataset_002
-#
-# Taxonomy Level: Task (small-scale visualization task involving a few operations)
-# Each task is marked with a comment indicating the end of the task and the task name
-
-# ============================================================
-# TASK 1: Napari - Load & Layer Management
-# ============================================================
-
-# Test: open_file - Load a multi-dimensional image file (T, Z, Y, X, C)
-- vars:
-    question: |
-      Load the file "data/dataset_001/dataset_001.tiff" into the viewer.
-      Respond with <1> if the file was successfully loaded, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Test: delete layers - Delete all loaded layers from the viewer
-- vars:
-    question: |
-      Delete the all currently loaded layers.
-      Respond with <1> if all layers were successfully deleted, or <0> if the operation failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-    
-# Test: open_file - Load a single image file
-- vars:
-    question: |
-      Load the file "data/dataset_002/dataset_002.tif" into the viewer.
-      Respond with <1> if the file was successfully loaded, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Test: list_layers - Get information about loaded layers
-- vars:
-    question: |
-      Retrieve information about all currently loaded layers in the viewer.
-      Respond with <1> if you successfully retrieved layer information, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# END OF TASK 1: Napari - Load & Layer Management
-# Operations: Load multi-dimensional file, delete layers, load single image file, retrieve layer information
-
-# ============================================================
-# TASK 2: Napari - 3D/4D Navigation
-# ============================================================
-
-# Test: Z-stack Navigation - Scroll through different depths
-- vars:
-    question: |
-      Navigate through the z-stack of the loaded image. Use set_z_slice to jump to at least z-slice 0 to examine structures at different depths. 
-      Take a screenshot at each z-slice to verify navigation. 
-      Respond with <1> if you successfully navigated through different z-slices and could see structural changes, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-
-# Test: Time Series Navigation - Navigate through time points
-- vars:
-    question: |
-      If the data has time dimensions, use set_timestep to navigate through different time points.
-      Take screenshots at different time points to show temporal changes.
-      If no time dimension exists, simulate time navigation by adjusting the current view and taking multiple screenshots.
-      Respond with <1> if you successfully navigated through time points or simulated time navigation, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# END OF TASK 2: Napari - 3D/4D Navigation
-# Operations: Z-stack navigation, time series navigation
-
-# ============================================================
-# TASK 3: Napari - Color & Opacity
-# ============================================================
-
-# Test: set_colormap - Change layer colormap
-- vars:
-    question: |
-      Change the colormap of the active image layer (dataset_002_ch1) to 'viridis'.
-      Respond with <1> if the colormap was successfully changed, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Test: set_opacity - Adjust layer transparency
-- vars:
-    question: |
-      Set the opacity of the active layer (dataset_002_ch1) to 0.5 (50% transparent).
-      Respond with <1> if the opacity was successfully changed, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Test: set_blending - Change layer blending mode
-- vars:
-    question: |
-      Change the blending mode of the active layer to 'additive'.
-      Respond with <1> if the blending mode was successfully changed, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# END OF TASK 3: Napari - Color & Opacity
-# Operations: Set colormap, adjust opacity, change blending mode
-
-# ============================================================
-# TASK 4: Napari - Contrast Adjustment
-# ============================================================
-
-# Test: auto_contrast - Auto-adjust contrast
-- vars:
-    question: |
-      Automatically adjust the contrast of the active image layer.
-      Respond with <1> if the contrast was successfully auto-adjusted, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Test: set_contrast_limits - Set specific contrast limits
-- vars:
-    question: |
-      Set the contrast limits of the active layer to min=0.1 and max=0.9.
-      Respond with <1> if the contrast limits were successfully set, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Test: set_gamma - Adjust gamma correction
-- vars:
-    question: |
-      Set the gamma correction of the active layer to 1.5.
-      Respond with <1> if the gamma was successfully adjusted, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Test: set_interpolation - Change interpolation mode - doesn't work
-- vars:
-    question: |
-      Change the interpolation mode of the active layer to 'linear'.
-      Respond with <1> if the interpolation mode was successfully changed, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# END OF TASK 4: Napari - Contrast Adjustment
-# Operations: Auto-adjust contrast, set specific contrast limits, adjust gamma correction, change interpolation mode
-
-# ============================================================
-# TASK 5: Napari - Camera Control
-# ============================================================
-
-# Test: toggle_view - Switch between 2D and 3D view
-- vars:
-    question: |
-      Switch the viewer to 3D mode.
-      Respond with <1> if the view was successfully switched to 3D, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Test: get_dims_info - Get dimension information
-- vars:
-    question: |
-      Get information about the viewer's current dimension settings.
-      Respond with <1> if you successfully retrieved dimension information, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Test: get_camera - Get current camera settings
-- vars:
-    question: |
-      Retrieve the current camera settings of the viewer.
-      Respond with <1> if you successfully retrieved camera settings, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Test: reset_camera - Reset camera to default view
-- vars:
-    question: |
-      Reset the camera to the default view.
-      Respond with <1> if the camera was successfully reset, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Test: set_camera - Adjust camera settings
-- vars:
-    question: |
-      Set the camera zoom to 2.0.
-      Respond with <1> if the camera zoom was successfully set, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# END OF TASK 5: Napari - Camera Control
-# Operations: Switch 2D/3D view, get dimension info, get camera settings, reset camera, adjust camera zoom
-
-# ============================================================
-# TASK 6: Napari - Visibility & Screenshot
-# ============================================================
-
-# Test: set_layer_visibility - Toggle layer visibility
-- vars:
-    question: |
-      Hide the active layer (set visible to false).
-      Respond with <1> if the layer visibility was successfully changed, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Test: set_layer_visibility - Show layer again
-- vars:
-    question: |
-      Show the active layer again (set visible to true).
-      Respond with <1> if the layer visibility was successfully changed, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Test: screenshot - Take a screenshot
-- vars:
-    question: |
-      Take a screenshot of the current view.
-      Respond with <1> if the screenshot was successfully taken, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# END OF TASK 6: Napari - Visibility & Screenshot
-# Operations: Hide layer, show layer, take screenshot
-
-# ============================================================
-# TASK 7: Napari - Annotations
-# ============================================================
-
-# # Test: get_layer_statistics - Get layer statistics
-# - vars:
-#     question: |
-#       Retrieve basic statistics (min, max, mean, std) for the active layer.
-#       Respond with <1> if you successfully retrieved layer statistics, or <0> if it failed. Only respond with <1> or <0>.
-#   assert:
-#     - type: contains-all
-#       value: "<1>"
-#     - type: not-contains
-#       value: "<0>"
-#   options:
-#     cache: false
-#     runSerially: true
-
-# # Test: add_points - Add point annotations - doesn't work
-# - vars:
-#     question: |
-#       Add two point markers at coordinates [[100, 100], [200, 200]] with the name "test_points".
-#       Respond with <1> if the points were successfully added, or <0> if it failed. Only respond with <1> or <0>.
-#   assert:
-#     - type: contains-all
-#       value: "<1>"
-#     - type: not-contains
-#       value: "<0>"
-#   options:
-#     cache: false
-#     runSerially: true
-
-# Test: add_shapes - Add shape annotations
-- vars:
-    question: |
-      Add a rectangle shape with coordinates [[[50, 50], [150, 50], [150, 150], [50, 150]]] and name "test_rectangle".
-      Respond with <1> if the shape was successfully added, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# END OF TASK 7: Napari - Annotations
-# Operations: Add shape annotations
-
-# ============================================================
-# TASK 8: Napari - Scale Bar & Export
-# ============================================================
-
-# # Test: measure_distance - Measure distance between points - doesn't work 
-# - vars:
-#     question: |
-#       Measure the distance between point [100, 100] and point [200, 200].
-#       Respond with <1> if the distance was successfully measured, or <0> if it failed. Only respond with <1> or <0>.
-#   assert:
-#     - type: contains-all
-#       value: "<1>"
-#     - type: not-contains
-#       value: "<0>"
-#   options:
-#     cache: false
-#    runSerially: true
-
-# Test: set_scale_bar - Show scale bar
-- vars:
-    question: |
-      Show the scale bar with unit 'um'.
-      Respond with <1> if the scale bar was successfully shown, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# # Test: set_axis_labels - Set axis labels - doesn't work
-# - vars:
-#     question: |
-#       Set axis labels to ['y', 'x'] for the 2D data.
-#       Respond with <1> if the axis labels were successfully set, or <0> if it failed. Only respond with <1> or <0>.
-#   assert:
-#     - type: contains-all
-#       value: "<1>"
-#     - type: not-contains
-#       value: "<0>"
-#   options:
-#     cache: false
-#     runSerially: true
-
-# Test: screenshot - Save screenshot to file
-- vars:
-    question: |
-      Save a screenshot.
-      Respond with <1> if the screenshot was successfully exported, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# END OF TASK 8: Napari - Scale Bar & Export
-# Operations: Show scale bar with units, save screenshot to file
-
-# ============================================================
-# TASK 9: Napari - Export & Cleanup
-# ============================================================
-
-# Test: save_layers - Save layer to file
-- vars:
-    question: |
-      Save the active layer to the file "test_layer.tif".
-      Respond with <1> if the layer was successfully saved, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Test: remove_layer - Remove a layer
-- vars:
-    question: |
-      Remove the layer named "test_rectangle".
-      Respond with <1> if the layer was successfully removed, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# END OF TASK 9: Napari - Export & Cleanup
-# Operations: Save layer to file, remove layer
-
-# ============================================================
-# TASK 10: Napari - Error Handling
-# ============================================================
-
-# Test: Error handling - Try to load non-existent file
-- vars:
-    question: |
-      Try to load the non-existent file "nonexistent.tif" and handle the error gracefully.
-      Respond with <1> if the error was handled gracefully (no crash), or <0> if it crashed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Test: Error handling - Try to remove non-existent layer
-- vars:
-    question: |
-      Try to remove a layer that doesn't exist named "nonexistent_layer" and handle the error gracefully.
-      Respond with <1> if the error was handled gracefully (no crash), or <0> if it crashed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# END OF TASK 10: Napari - Error Handling
-# Operations: Handle non-existent file, handle non-existent layer removal
-
-# ============================================================
-# TASK 11: Napari - 3D Rendering
-# ============================================================
-
-# Test: 3D View and Iso-surface Rendering
-- vars:
-    question: |
-      Enable iso-surface rendering for the loaded layer.
-      Take a screenshot to verify the 3D iso-surface rendering.
-      Respond with <1> if the 3D iso-surface rendering was successfully set up, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Test: Cleanup - Remove remaining test layers
-- vars:
-    question: |
-      Remove the layer named "test_rectangle" to clean up test annotations.
-      Respond with <1> if the layer was successfully removed, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# END OF TASK 11: Napari - 3D Rendering
-# Operations: Enable iso-surface rendering in 3D, remove test layers for cleanup

eval_cases/napari/1_workflows/eval_analysis_workflows.yaml

@@ -1,104 +0,0 @@
-# Analysis Workflow Tests for napari-mcp
-# These tests evaluate complex analysis workflows that combine multiple napari functions
-# Each test focuses on performing specific analysis tasks
-
-# Test: Cell Counting and Measurement Analysis
-- vars:
-    question: |
-      Load the image "data/dataset_001/dataset_001.tiff" and set it to magenta colormap.
-      Take a screenshot and analyze it to count how many complete cells are visible (not cut off by edges).
-      Add point annotations to mark the center of each counted cell.
-      Measure the distance between the two most distant cells.
-      Q1: answer with the number of complete cells you counted, for example "5" if you see 5 complete cells.
-      Save the answer of Q1 to the questions in plain text as "eval_analysis_workflows/Q1_answer.txt".
-  assert:
-    - type: llm-rubric
-      subtype: text
-      value: |
-        1. Q1 correct answer: 2
-      rs-file: eval_analysis_workflows/Q1_answer.txt
-  options:
-    cache: false
-    runSerially: true
-
-# Test: Statistical Analysis and Data Export
-- vars:
-    question: |
-      Get basic statistics (min, max, mean, std) for the loaded layer.
-      Extract the raw layer data and examine its properties.
-      Save the current layer to a file for further analysis.
-      Export a screenshot of the current view for documentation.
-      Respond with <1> if the statistical analysis and data export were successful, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Test: Annotation and Measurement Workflow
-- vars:
-    question: |
-      1. Add point annotations to mark specific features of interest in the image.
-      2. Add shape annotations (rectangles or circles) to highlight regions of interest.
-      3. Measure distances between multiple pairs of points.
-      4. Take a screenshot showing all annotations and measurements, save it to "eval_analysis_workflows/screenshot_1.png".
-  assert:
-    - type: llm-rubric
-      value: |
-          1. The screenshot shows the point and shape annotations, and measurements
-      rs-file: eval_analysis_workflows/screenshot_1.png
-  options:
-    cache: false
-    runSerially: true
-
-# Test: Time Series Analysis (if applicable)
-- vars:
-    question: |
-      If the data has time dimensions, navigate through different time points.
-      Compare cellular structures between different time points.
-      Take screenshots at different time points to show temporal changes.
-      If no time dimension exists, simulate time series analysis by adjusting the current view and taking multiple screenshots.
-      Respond with <1> if the time series analysis was successful, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true
-
-# Test: Data Cropping and Region of Interest Analysis
-- vars:
-    question: |
-      1. Define a region of interest by cropping the layer to a specific area.
-      2. Analyze the cropped region separately from the full dataset.
-      3. Compare statistics between the full dataset and the cropped region.
-      4. Take a screenshot of the full view and save it to "eval_analysis_workflows/screenshot_2.png".
-      5. Take a screenshot of the cropped region and save it to "eval_analysis_workflows/screenshot_3.png".
-  assert:
-    - type: llm-rubric
-      subtype: vision
-      value: |
-          1. This screenshot shows the full dataset with the cropped region highlighted.
-      rs-file: eval_analysis_workflows/screenshot_2.png
-  options:
-    cache: false
-    runSerially: true
-
-# Test: Cleanup - Reset for next test run
-- vars:
-    question: |
-      Delete all loaded layers and remove any annotations to prepare for the next test run.
-      Respond with <1> if all layers and annotations were successfully removed, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true

eval_cases/napari/1_workflows/eval_figure_recreation.yaml

@@ -1,28 +0,0 @@
-# Figure Recreation Tests for napari-mcp
-# These tests evaluate the agent's ability to recreate scientific figures from papers
-# Focus: Loading data, applying appropriate visualization settings, and matching target figures
-
-#Test: Recreate a figure from a dataset. 
-- vars:
-    question: |
-      1. Load the dataset into napari: data/dataset_001/dataset_001.tiff
-      2. Read the target figure: data/dataset_001/dataset_001.png but don't load it into napari.
-      3. Read the dataset description: data/dataset_001/dataset_001.yaml. 
-      4. Set the same colormaps and blending modes as the target figure.
-      5. Adjust contrast and gamma as needed to match the target figure.
-      6. Take a screenshot of your recreation.
-      7. If the recreation does not match the target figure, adjust the visualization settings and take a screenshot again.
-      8. Stop when the recreation matches the target figure or you have tried five different visualization settings.
-      9. Save the final screenshot to "eval_figure_recreation/screenshot.png".
-  assert:
-    - type: llm-rubric
-      subtype: vision
-      value: |
-          1. Does the result screenshot look similar to the ground truth image?
-          2. Are the same colormaps and blending modes used as in the target figure?
-          3. Is the contrast and gamma adjusted to match the target figure?
-      gs-file: GS/dataset_001.png
-      rs-file: eval_figure_recreation/screenshot.png                 
-  options:
-    cache: false
-    runSerially: true

eval_cases/napari/1_workflows/eval_iso_surface_determination.yaml

@@ -1,25 +0,0 @@
-# finding iso surface value for a dataset
-# These tests evaluate the agent's ability to recreate scientific figures from papers
-
-# Test: Iso surface determination for a target
-- vars:
-    question: |
-      1. Read the file "data/dataset_003/eval_iso_surface_determination_target_1.txt" to get the target iso-surface values for different tooth structures.
-      2. Load data/dataset_003/dataset_003.tif into napari. 
-      3. Switch to 3D view mode and set the rendering to iso. 
-      4. Find the iso surface value that shows the target clearly.
-      5. Rotate the camera to several angles and take a screenshot of the result each time to check if the target structure is clearly visible from different angles.
-      6. If the target structure is not clearly visible, adjust the iso surface value and take a screenshot again.
-      7. Stop when the target structure is clearly visible or you have tried five different iso surface values.
-      8. Save the final screenshot to "eval_iso_surface_determination/screenshot.png".
-  assert:
-    - type: llm-rubric
-      subtype: vision
-      value: |
-          1. Does the result rendering look similar to ground truth? 
-          2. Does the visualization show the target structure clearly?
-      gs-file: GS/dataset_003.png
-      rs-file: eval_iso_surface_determination/screenshot.png                          
-  options:
-    cache: false
-    runSerially: true

eval_cases/napari/1_workflows/eval_visualization_workflows.yaml

@@ -1,79 +0,0 @@
-# Basic Visualization Workflow Tests
-# Use https://www.ebi.ac.uk/bioimage-archive/galleries/S-BIAD573.html IM1 to test the workflows.
-
-# Test: Multi-channel Overlay with Colormaps with channels
-- vars:
-    question: |
-      1. Load the "data/dataset_002/dataset_002.tif" dataset into napari. 
-      2. Depending on the number of channels, set the colormap for the first channel 0 to red and channel 1 to green.
-      3. Switch to the 3D view. 
-      4. Use additive blending for all channels to create an overlay visualization.
-      5. Go the timestep 14. 
-        Q1: Does the cell show protrusions? (Yes/No)
-      6. Take a screenshot of the result, save it to "eval_visualization_workflows/screenshot_1.png"
-      7. Answer Q1 in a plain text file "eval_visualization_workflows/Q1_answer.txt".
-  assert:
-    - type: llm-rubric
-      subtype: vision
-      value: |
-          1. Does the visualization show a green cell with red blobs on the inside? 
-          2. Does the result rendering look similar to ground truth?
-      gs-file: GS/dataset_002_1.png
-      rs-file: eval_visualization_workflows/screenshot_1.png
-    - type: llm-rubric
-      subtype: text
-      value: |
-          1. Q1 correct answer: Yes
-      rs-file: eval_visualization_workflows/Q1_answer.txt                    
-  options:
-    cache: false
-    runSerially: true
-
-# Test: Hide All Channels Except for the Channel with the Cells
-- vars:
-    question: |
-      1. Set all layers invisible except for the layer that contains the individual cells. 
-      2. Take a screenshots of the result, save it to "eval_visualization_workflows/screenshot_2.png".
-  assert:
-    - type: llm-rubric
-      subtype: vision
-      value: |
-          1. Are there only the green cells visible with no red blobs on the inside?
-      rs-file: eval_visualization_workflows/screenshot_2.png
-  options:
-    cache: false
-    runSerially: true
-
-# Test: Advanced 3D Camera Control and Navigation
-- vars:
-    question: |
-      1. Start in the 3D view
-      2. Zoom into the cell with protrusions until the cell fills up the entire viewport. 
-      3. Rotate the camera to show the 3D data from a different perspective (side view).
-      4. Take a screenshot of the result, save it to "eval_visualization_workflows/screenshot_3.png".
-  assert:
-    - type: llm-rubric
-      subtype: vision
-      value: |
-          1. Does the visualization show the green cell from the side? 
-          2. Does the result rendering look similar to the ground truth image?
-      gs-file: GS/dataset_002_2.jpg
-      rs-file: eval_visualization_workflows/screenshot_3.png
-             
-  options:
-    cache: false
-    runSerially: true
-
-# Test: Cleanup - Reset for next test run
-- vars:
-    question: |
-      Delete all loaded layers and reset the view to 2D mode to prepare for the next test run.
-      Respond with <1> if all layers were successfully deleted and the view was reset, or <0> if it failed. Only respond with <1> or <0>.
-  assert:
-    - type: contains-all
-      value: "<1>"
-    - type: not-contains
-      value: "<0>"
-  options:
-    cache: false
-    runSerially: true

eval_cases/napari/eval_visualization_workflows.yaml

@@ -0,0 +1,236 @@
+# Basic Visualization Workflow Tests
+# Use https://www.ebi.ac.uk/bioimage-archive/galleries/S-BIAD573.html IM1 to test the workflows.
+
+# Test: Multi-channel Overlay with Colormaps with channels
+- vars:
+    question: |
+      1. Load the "data/dataset_002/dataset_002_ch0.tif" dataset into napari as channel 0 and "data/dataset_002/dataset_002_ch1.tif" as channel 1. 
+      2. Set the colormap for channel 0 to red and channel 1 to green.
+      3. Switch to the 3D view. 
+      4. Use additive blending for all channels to create an overlay visualization.
+      5. Go the timestep 14. 
+        Q1: Does the cell show protrusions? (Yes/No)
+      6. Take a screenshot of the result, save it to "eval_visualization_workflows/screenshot_1.png"
+      7. Answer Q1 in a plain text file "eval_visualization_workflows/multi_channel_answer.txt".
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Does the visualization show a green cell with red blobs on the inside? 
+          2. Does the result rendering look similar to ground truth?
+      gs-file: GS/dataset_002_1.png
+      rs-file: eval_visualization_workflows/screenshot_1.png
+    - type: llm-rubric
+      subtype: text
+      value: |
+          1. Q1 correct answer: Yes
+      rs-file: eval_visualization_workflows/multi_channel_answer.txt                    
+  options:
+    cache: false
+    runSerially: true
+
+
+# Test: ingesting points
+- vars:
+    question: |
+      1. Load the "data/dataset_002/Points.csv" dataset into napari.
+      2. Check if the points layer has been created.
+        Q1: Was the points layer created successfully? (Yes/No)
+      3. Answer Q1 in a plain text file "eval_visualization_workflows/points_answer.txt".
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          1. Q1 correct answer: Yes
+      rs-file: eval_visualization_workflows/points_answer.txt
+  options:
+    cache: false
+    runSerially: true
+
+# Test: ingesting shapes
+- vars:
+    question: |
+      1. Load the "data/dataset_002/Shapes.csv" dataset into napari.
+      2. Check if the shapes layer has been created.
+        Q1: Was the shapes layer created successfully? (Yes/No)
+      3. Answer Q1 in a plain text file "eval_visualization_workflows/shapes_answer.txt".
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          1. Q1 correct answer: Yes
+      rs-file: eval_visualization_workflows/shapes_answer.txt
+  options:
+    cache: false
+    runSerially: true
+
+# Test: ingesting labels
+- vars:
+    question: |
+      1. Load the "data/dataset_002/Labels.tif" dataset into napari.
+      2. Check if a new layer called "Labels" has been created.
+        Q1: Was the layer created successfully? (Yes/No)
+      3. Answer Q1 in a plain text file "eval_visualization_workflows/labels_answer.txt".
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+        1. Q1 correct answer: Yes
+      rs-file: eval_visualization_workflows/labels_answer.txt
+  options:
+    cache: false
+    runSerially: true
+
+
+#Test: Recreate a figure from a dataset. 
+- vars:
+    question: |
+      1. Load the dataset into napari: data/dataset_001/dataset_001.tiff
+      2. Read the target figure: data/dataset_001/dataset_001.png but don't load it into napari.
+      3. Read the dataset description: data/dataset_001/dataset_001.yaml. 
+      4. Set the same colormaps and blending modes as the target figure.
+      5. Adjust contrast and gamma as needed to match the target figure.
+      6. Take a screenshot of your recreation.
+      7. If the recreation does not match the target figure, adjust the visualization settings and take a screenshot again.
+      8. Stop when the recreation matches the target figure or you have tried five different visualization settings.
+      9. Save the final screenshot to "eval_figure_recreation/screenshot.png".
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Does the result screenshot look similar to the ground truth image?
+          2. Are the same colormaps and blending modes used as in the target figure?
+          3. Is the contrast and gamma adjusted to match the target figure?
+      gs-file: GS/dataset_001.png
+      rs-file: eval_figure_recreation/screenshot.png                 
+  options:
+    cache: false
+    runSerially: true
+
+# Test: Iso surface determination for a target
+- vars:
+    question: |
+      1. Read the file "data/dataset_003/eval_iso_surface_determination_target_1.txt" to get the target iso-surface values for different tooth structures.
+      2. Load data/dataset_003/dataset_003.tif into napari. 
+      3. Switch to 3D view mode and set the rendering to iso. 
+      4. Find the iso surface value that shows the target clearly.
+      5. Rotate the camera to several angles and take a screenshot of the result each time to check if the target structure is clearly visible from different angles.
+      6. If the target structure is not clearly visible, adjust the iso surface value and take a screenshot again.
+      7. Stop when the target structure is clearly visible or you have tried five different iso surface values.
+      8. Save the final screenshot to "eval_iso_surface_determination/screenshot.png".
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Does the result rendering look similar to ground truth? 
+          2. Does the visualization show the target structure clearly?
+      gs-file: GS/dataset_003.png
+      rs-file: eval_iso_surface_determination/screenshot.png                          
+  options:
+    cache: false
+    runSerially: true
+
+
+# Test: Cell Counting and Measurement Analysis
+- vars:
+    question: |
+      1. Load the image "data/dataset_002/dataset_002_ch0.tif" and set channel 0 to a magenta colormap.
+      2. Switch to a 3D MIP view. 
+      3. Take a screenshot and analyze it to count how many complete cells are visible (not cut off by edges).
+      Q1: answer with the number of complete cells you counted, for example "5" if you see 5 complete cells.
+      4. Save the answer of Q1 to the questions in plain text as "eval_analysis_workflows/Q1_answer.txt".
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+        1. Q1 correct answer: 2
+      rs-file: eval_analysis_workflows/Q1_answer.txt
+  options:
+    cache: false
+    runSerially: true
+
+# Test: Statistical Analysis and Data Export
+- vars:
+    question: |
+      1. Load the image "data/dataset_001/dataset_001.tiff". 
+      2. Get basic statistics (min, max, mean, std) for the loaded layer.
+      3. Extract the raw layer data and examine its properties.
+      4. Save the current layer to a file for further analysis.
+       Q1: Was the statistical analysis and data export successful? (Yes/No)
+      6. Save the answer of Q1 in plain text as "eval_analysis_workflows/layer_statistics_answer.txt".
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+        1. Q1 correct answer: Yes
+      rs-file: eval_analysis_workflows/layer_statistics_answer.txt
+  options:
+    cache: false
+    runSerially: true
+
+# Test: Annotation Workflow
+- vars:
+    question: |
+      1. Load the image "data/dataset_001/dataset_001.tiff". 
+      2. Add point annotations at random locations on the image.
+      3. Add shape annotations (rectangles or circles) at random locations on the image.
+       Q1: Check if layers have been generated. (Yes/No)
+      4. Save the answer of Q1 in plain text as "eval_analysis_workflows/annotation_answer.txt".
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          1. Q1 correct answer: Yes
+      rs-file: eval_analysis_workflows/annotation_answer.txt
+  options:
+    cache: false
+    runSerially: true
+
+# Test: Advanced Annotation Workflow: Cell Surface Trace (This will likely fail)
+- vars:
+    question: |
+      1. Load the image "data/dataset_002/dataset_002_ch0.tif" into napari.
+      2. Trace the cell surface on the current slice by adding a polygon shape in a new shape layer.
+      3. Use a screenshot to validate whether the polygon correctly traces the cell surface.
+      4. If the trace is not accurate, adjust the polygon and take a new screenshot to validate.
+      5. Stop when the trace is accurate or you have tried five different attempts.
+      6. Save the results and the final screenshot to "eval_annotation_workflows/cell_surface_trace.png".
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Does the final screenshot show a polygon shape that accurately traces the outline of the cell surface?
+          2. Is the polygon layer correctly overlaid on the image?
+      rs-file: eval_annotation_workflows/cell_surface_trace.png
+  options:
+    cache: false
+    runSerially: true
+
+# Test: Camera Operations (Zoom and Rotate)
+- vars:
+    question: |
+      1. Load the "data/dataset_002/dataset_002_ch0.tif" dataset into napari as channel 0 and "data/dataset_002/dataset_002_ch1.tif" as channel 1.
+      2. Depending on the number of channels, set the colormap for the first channel 0 to red and channel 1 to green.
+      3. Switch to the 3D view. 
+      4. Zoom in to the cell in the middle.
+      5. Rotate the camera to a side view.
+      6. Take a screenshot of the zoomed-in view and save it to "eval_camera_operations/zoom_screenshot.png".
+      7. Take a screenshot of the side view and save it to "eval_camera_operations/rotate_screenshot.png".
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Does the visualization show a zoomed-in view of the cell in the middle?
+          2. Does the result rendering look similar to ground truth?
+      gs-file: GS/dataset_002_zoom.jpg
+      rs-file: eval_camera_operations/zoom_screenshot.png
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Does the visualization show a side view of the cell?
+          2. Does the result rendering look similar to ground truth?
+      gs-file: GS/dataset_002_camera_side.png
+      rs-file: eval_camera_operations/rotate_screenshot.png
+  options:
+    cache: false
+    runSerially: true

eval_cases/selected_15_cases.yaml

@@ -1,87 +0,0 @@
-# Selected 15 Cases for Human Evaluation
-# These cases represent diverse visualization capabilities across the benchmark
-#
-# Each case specifies:
-#   - name: The case directory name
-#   - path: Path to the case directory (relative to workspace root)
-#   - yaml: Path to the YAML file containing evaluation criteria
-#   - description: Brief description of what the case tests
-
-cases:
-  # From main benchmark (7 cases)
-  - name: argon-bubble
-    path: SciVisAgentBench-tasks/main/argon-bubble
-    yaml: benchmark/eval_cases/paraview/main_cases.yaml
-    description: Color & Opacity Mapping, Volume Rendering
-
-  - name: bonsai
-    path: SciVisAgentBench-tasks/main/bonsai
-    yaml: benchmark/eval_cases/paraview/main_cases.yaml
-    description: Volume Rendering
-
-  - name: trl-velocity_streamline
-    path: SciVisAgentBench-tasks/main/trl-velocity_streamline
-    yaml: benchmark/eval_cases/paraview/main_cases.yaml
-    description: Temporal Processing (Streamline)
-
-  - name: tornado
-    path: SciVisAgentBench-tasks/main/tornado
-    yaml: benchmark/eval_cases/paraview/main_cases.yaml
-    description: Glyph & Marker Placement
-
-  - name: tgc-velocity_contour
-    path: SciVisAgentBench-tasks/main/tgc-velocity_contour
-    yaml: benchmark/eval_cases/paraview/main_cases.yaml
-    description: Surface & Contour Extraction
-
-  - name: rti-velocity_slices
-    path: SciVisAgentBench-tasks/main/rti-velocity_slices
-    yaml: benchmark/eval_cases/paraview/main_cases.yaml
-    description: View & Camera Control, Data Subsetting & Extraction
-
-  - name: supernova-velocity_isosurface
-    path: SciVisAgentBench-tasks/main/supernova-velocity_isosurface
-    yaml: benchmark/eval_cases/paraview/main_cases.yaml
-    description: Surface & Contour Extraction (isosurface)
-
-  # From chatvis_bench (6 cases)
-  - name: time-varying
-    path: SciVisAgentBench-tasks/chatvis_bench/time-varying
-    yaml: benchmark/eval_cases/paraview/chatvis_bench_cases.yaml
-    description: Temporal Processing
-
-  - name: chart-opacity
-    path: SciVisAgentBench-tasks/chatvis_bench/chart-opacity
-    yaml: benchmark/eval_cases/paraview/chatvis_bench_cases.yaml
-    description: Plot & Chart Generation
-
-  - name: climate
-    path: SciVisAgentBench-tasks/chatvis_bench/climate
-    yaml: benchmark/eval_cases/paraview/chatvis_bench_cases.yaml
-    description: Field Computation
-
-  - name: materials
-    path: SciVisAgentBench-tasks/chatvis_bench/materials
-    yaml: benchmark/eval_cases/paraview/chatvis_bench_cases.yaml
-    description: Scientific Insight Derivation
-
-  - name: subseries-of-time-series
-    path: SciVisAgentBench-tasks/chatvis_bench/subseries-of-time-series
-    yaml: benchmark/eval_cases/paraview/chatvis_bench_cases.yaml
-    description: Dataset Restructuring
-
-  - name: shrink-sphere
-    path: SciVisAgentBench-tasks/chatvis_bench/shrink-sphere
-    yaml: benchmark/eval_cases/paraview/chatvis_bench_cases.yaml
-    description: Geometric & Topological Transformation
-
-  # From molecular_vis/workflows (2 cases)
-  - name: curved-membrane
-    path: SciVisAgentBench-tasks/molecular_vis/workflows/curved-membrane
-    yaml: benchmark/eval_cases/molecular_vis/workflows/eval_analysis_workflows.yaml
-    description: Data Subsetting & Extraction
-
-  - name: ras-raf-membrane
-    path: SciVisAgentBench-tasks/molecular_vis/workflows/ras-raf-membrane
-    yaml: benchmark/eval_cases/molecular_vis/workflows/eval_analysis_workflows.yaml
-    description: View & Camera Control

eval_cases/selected_cases.yaml

@@ -0,0 +1,200 @@
+# Selected 15 Cases for Human Evaluation
+# These cases represent diverse visualization capabilities across the benchmark
+#
+# Each case specifies:
+#   - name: The case directory name
+#   - path: Path to the case directory (relative to workspace root)
+#   - yaml: Path to the YAML file containing evaluation criteria
+#   - description: Brief description of what the case tests
+
+cases:
+  - name: argon-bubble
+    path: SciVisAgentBench-tasks/paraview/argon-bubble
+    yaml: benchmark/eval_cases/paraview/paraview_cases.yaml
+    description: Color & Opacity Mapping, Volume Rendering
+    agent_mode: paraview_mcp_claude-sonnet-4-5_exp1
+
+  - name: richtmyer
+    path: SciVisAgentBench-tasks/paraview/richtmyer
+    yaml: benchmark/eval_cases/paraview/paraview_cases.yaml
+    description: Color & Opacity Mapping, Volume Rendering
+    agent_mode: paraview_mcp_claude-sonnet-4-5_exp1
+
+  - name: foot
+    path: SciVisAgentBench-tasks/paraview/foot
+    yaml: benchmark/eval_cases/paraview/paraview_cases.yaml
+    description: Volume Rendering
+    agent_mode: paraview_mcp_claude-sonnet-4-5_exp1
+
+  - name: crayfish_streamline
+    path: SciVisAgentBench-tasks/paraview/crayfish_streamline
+    yaml: benchmark/eval_cases/paraview/paraview_cases.yaml
+    description: Surface & Contour Extraction
+    agent_mode: chatvis_claude-sonnet-4-5_exp1
+
+  - name: twoswirls_streamribbon
+    path: SciVisAgentBench-tasks/paraview/twoswirls_streamribbon
+    yaml: benchmark/eval_cases/paraview/paraview_cases.yaml
+    description: Surface & Contour Extraction
+    agent_mode: chatvis_claude-sonnet-4-5_exp1
+
+  - name: tornado
+    path: SciVisAgentBench-tasks/paraview/tornado
+    yaml: benchmark/eval_cases/paraview/paraview_cases.yaml
+    description: Surface & Contour Extraction, Glyph & Marker Placement
+    agent_mode: chatvis_claude-sonnet-4-5_exp1
+
+  - name: tgc-velocity_contour
+    path: SciVisAgentBench-tasks/paraview/tgc-velocity_contour
+    yaml: benchmark/eval_cases/paraview/paraview_cases.yaml
+    description: Surface & Contour Extraction
+    agent_mode: paraview_mcp_claude-sonnet-4-5_exp1
+
+  - name: rti-velocity_slices
+    path: SciVisAgentBench-tasks/paraview/rti-velocity_slices
+    yaml: benchmark/eval_cases/paraview/paraview_cases.yaml
+    description: View & Camera Control, Data Subsetting & Extraction
+    agent_mode: paraview_mcp_claude-sonnet-4-5_exp1
+
+  - name: rti-velocity_glyph
+    path: SciVisAgentBench-tasks/paraview/rti-velocity_glyph
+    yaml: benchmark/eval_cases/paraview/paraview_cases.yaml
+    description: Glyph & Marker Placement, Data Subsetting & Extraction
+    agent_mode: chatvis_claude-sonnet-4-5_exp1
+
+  - name: supernova_isosurface
+    path: SciVisAgentBench-tasks/paraview/supernova_isosurface
+    yaml: benchmark/eval_cases/paraview/paraview_cases.yaml
+    description: Surface & Contour Extraction (isosurface)
+    agent_mode: chatvis_claude-sonnet-4-5_exp1
+
+  - name: time-varying
+    path: SciVisAgentBench-tasks/paraview/time-varying
+    yaml: benchmark/eval_cases/paraview/paraview_cases.yaml
+    description: Temporal Processing
+    agent_mode: chatvis_claude-sonnet-4-5_exp1
+
+  - name: chart-opacity
+    path: SciVisAgentBench-tasks/paraview/chart-opacity
+    yaml: benchmark/eval_cases/paraview/paraview_cases.yaml
+    description: Plot & Chart Generation
+    agent_mode: chatvis_claude-sonnet-4-5_exp1
+
+  - name: climate
+    path: SciVisAgentBench-tasks/paraview/climate
+    yaml: benchmark/eval_cases/paraview/paraview_cases.yaml
+    description: Field Computation
+    agent_mode: chatvis_claude-sonnet-4-5_exp1
+
+  # - name: subseries-of-time-series
+  #   path: SciVisAgentBench-tasks/paraview/subseries-of-time-series
+  #   yaml: benchmark/eval_cases/paraview/paraview_cases.yaml
+  #   description: Dataset Restructuring
+  #   agent_mode: chatvis_claude-sonnet-4-5_exp1
+
+  - name: shrink-sphere
+    path: SciVisAgentBench-tasks/paraview/shrink-sphere
+    yaml: benchmark/eval_cases/paraview/paraview_cases.yaml
+    description: Geometric & Topological Transformation
+    agent_mode: chatvis_claude-sonnet-4-5_exp1
+
+  - name: import-gltf
+    path: SciVisAgentBench-tasks/paraview/import-gltf
+    yaml: benchmark/eval_cases/paraview/paraview_cases.yaml
+    description: Dataset Restructuring, View & Camera Control
+    agent_mode: paraview_mcp_claude-sonnet-4-5_exp1
+
+  - name: render-histogram
+    path: SciVisAgentBench-tasks/paraview/render-histogram
+    yaml: benchmark/eval_cases/paraview/paraview_cases.yaml
+    description: Plot & Chart Generation, Color & Opacity Mapping
+    agent_mode: chatvis_claude-sonnet-4-5_exp1
+
+  # From molecular_vis/workflows (2 cases)
+  - name: curved-membrane
+    path: SciVisAgentBench-tasks/molecular_vis/workflows/curved-membrane
+    yaml: benchmark/eval_cases/molecular_vis/workflows/eval_analysis_workflows.yaml
+    description: Data Subsetting & Extraction
+    agent_mode: gmx_vmd_mcp_claude-sonnet-4-5_exp1
+
+  - name: ras-raf-membrane
+    path: SciVisAgentBench-tasks/molecular_vis/workflows/ras-raf-membrane
+    yaml: benchmark/eval_cases/molecular_vis/workflows/eval_analysis_workflows.yaml
+    description: View & Camera Control
+    agent_mode: gmx_vmd_mcp_claude-sonnet-4-5_exp1
+
+  - name: bio_isosurface-determination
+    path: SciVisAgentBench-tasks\bioimage_data\eval_iso_surface_determination\operation_1
+    yaml: benchmark\eval_cases\napari\1_workflows\eval_iso_surface_determination.yaml
+    description: Surface & Contour Extraction (isosurface)
+    agent_mode: napari_mcp_claude-sonnet-4-5_exp_default
+    task_description:
+      1. Read the file "data/dataset_003/eval_iso_surface_determination_target_1.txt" to get the target iso-surface values for different tooth structures.
+
+      2. Load data/dataset_003/dataset_003.tif into napari. 
+
+      3. Switch to 3D view mode and set the rendering to iso. 
+
+      4. Find the iso surface value that shows the target clearly.
+
+      5. Rotate the camera to several angles and take a screenshot of the result each time to check if the target structure is clearly visible from different angles.
+
+      6. If the target structure is not clearly visible, adjust the iso surface value and take a screenshot again.
+
+      7. Stop when the target structure is clearly visible or you have tried five different iso surface values.
+
+      8. Save the final screenshot to "eval_iso_surface_determination/screenshot.png".
+    vision-rubrics:
+        1. Does the result rendering look similar to ground truth? 
+        2. Does the visualization show the target structure clearly?
+
+  - name: bio_visualization-workflows
+    path: SciVisAgentBench-tasks\bioimage_data\eval_visualization_workflows\operation_1
+    yaml: benchmark\eval_cases\napari\1_workflows\eval_visualization_workflows.yaml
+    description: Color & Opacity Mapping, Volume Rendering, Temporal Processing
+    agent_mode: napari_mcp_claude-sonnet-4-5_exp_default
+    task_description:
+      1. Load the "data/dataset_002/dataset_002.tif" dataset into napari. 
+
+      2. Depending on the number of channels, set the colormap for the first channel 0 to red and channel 1 to green.
+
+      3. Switch to the 3D view. 
+
+      4. Use additive blending for all channels to create an overlay visualization.
+
+      5. Go the timestep 14. 
+        Q1. Does the cell show protrusions? (Yes/No)
+
+      6. Take a screenshot of the result, save it to "eval_visualization_workflows/screenshot_1.png"
+
+      7. Answer Q1 in a plain text file "eval_visualization_workflows/Q1_answer.txt".
+    vision-rubrics:
+        1. Does the visualization show a green cell with red blobs on the inside? 
+        2. Does the result rendering look similar to ground truth?
+
+  - name: bio_figure-recreation
+    path: SciVisAgentBench-tasks\bioimage_data\eval_figure_recreation\operation_1
+    yaml: benchmark\eval_cases\napari\1_workflows\eval_figure_recreation.yaml
+    description: Color & Opacity Mapping, Volume Rendering
+    agent_mode: napari_mcp_claude-sonnet-4-5_exp_default
+    task_description:
+      1. Load the dataset into napari "data/dataset_001/dataset_001.tiff"
+
+      2. Read the target figure "data/dataset_001/dataset_001.png" but don't load it into napari.
+
+      3. Read the dataset description "data/dataset_001/dataset_001.yaml".
+
+      4. Set the same colormaps and blending modes as the target figure.
+
+      5. Adjust contrast and gamma as needed to match the target figure.
+
+      6. Take a screenshot of your recreation.
+
+      7. If the recreation does not match the target figure, adjust the visualization settings and take a screenshot again.
+
+      8. Stop when the recreation matches the target figure or you have tried five different visualization settings.
+
+      9. Save the final screenshot to "eval_figure_recreation/screenshot.png".
+    vision-rubrics:
+        1. Does the visualization show a green cell with red blobs on the inside? 
+        2. Does the result rendering look similar to ground truth?