Input:
import java.io.ObjectStreamException;
import java.io.Serializable;
import java.util.function.Function;
import edu.uky.cs.nil.sabre.Settings;
import edu.uky.cs.nil.sabre.State;
import edu.uky.cs.nil.sabre.Utilities;
import edu.uky.cs.nil.sabre.io.DefaultParser;
import edu.uky.cs.nil.sabre.util.ImmutableSet;
import edu.uky.cs.nil.sabre.util.Unique;

Context:
src/edu/uky/cs/nil/sabre/logic/Quantified.java
package edu.uky.cs.nil.sabre.logic;

/**
 * A quantified expression is a {@link Proposition proposition} which states
 * that a given {@link #argument} proposition holds for some number of possible
 * values that can be substituted for a {@link #variable}.
 *
 * @author Stephen G. Ware
 */
public class Quantified implements Proposition {

	/** Serial version ID */
	private static final long serialVersionUID = Settings.VERSION_UID;

	/**
	 * A quantifier is a singleton object that specifies for how many possible
	 * values a {@link Quantifier quantifier's} proposition must hold.
	 *
	 * @author Stephen G. Ware
	 */
	public static abstract class Quantifier implements Comparable<Quantifier>, Serializable, Unique {

		/** Serial version ID */
		private static final long serialVersionUID = Quantified.serialVersionUID;

		private Quantifier() {}

		@Override
		public int compareTo(Quantifier other) {
			return hashCode() - other.hashCode();
		}

		/**
		 * Returns the quantifier this quantifier would become when {@link
		 * Quantifier#negate() negating a quantified expression}.
		 *
		 * @return the negated quantifier
		 */
		public abstract Quantifier negate();

		/**
		 * Returns {@link Expression a logical expression} that is logically
		 * equivalent to a {@link Quantified quantified expression} with this
		 * quantifier but which does not contain the quantifier or variable.
		 *
		 * @param variable the quantified variable
		 * @param argument an expression in which the variable appears
		 * @return a logical expression equivalent to a quantified expression
		 * where the variable is quantified with this quantifier but in which
		 * this quantifier and variable do not appear
		 */
		public Expression expand(Variable variable, Expression argument) {
			ImmutableSet<Value> values = variable.type.universe.getValues(variable.type);
			Expression[] arguments = new Expression[values.size()];
			for(int i=0; i<arguments.length; i++)
				arguments[i] = (Expression) argument.substitute(variable, values.get(i));
			return expand(arguments);
		}

		/**
		 * A utility method for {@link #expand(Variable, Expression)} that
		 * creates an expression from an array of arguments which are copies
		 * of a quantified expression with the quantified variable replaced
		 * with every possible value it can have.
		 *
		 * @param arguments copies of a quantified expression where the
		 * variable has been replaced with every possible value
		 * @return a logical expression made from the arguments
		 */
		protected abstract Expression expand(Expression[] arguments);
	}

	/**
	 * The universal {@link Quantifier quantifier} specifies that a quantified
	 * expression must hold for every possible value its variable can have.
	 */
	public static final Quantifier UNIVERSAL = new Quantifier() {

		/** Serial version ID */
		private static final long serialVersionUID = 1;

		@Override
		public int hashCode() {
			return 0;
		}

		@Override
		public String toString() {
			return DefaultParser.UNIVERSAL_QUANTIFICATION_KEYWORD;
		}

		/**
		 * Returns {@link Quantified#EXISTENTIAL the existential quantifier}.
		 *
		 * @returns {@link Quantified#EXISTENTIAL the existential quantifier}
		 */
		@Override
		public Quantifier negate() {
			return EXISTENTIAL;
		}

		/**
		 * Returns a conjunction of its arguments.
		 *
		 * @param arguments copies of a quantified expression where the
		 * variable has been replaced with every possible value
		 * @return a conjunction of the arguments
		 */
		@Override
		protected Conjunction<Expression> expand(Expression[] arguments) {
			return new Conjunction<>(arguments);
		}

		private Object readResolve() throws ObjectStreamException {
			return UNIVERSAL;
		}
	};

	/**
	 * The existential {@link Quantifier quantifier} specifies that a
	 * quantified expression must hold for at least one possible value its
	 * variable can have.
	 */
	public static final Quantifier EXISTENTIAL = new Quantifier() {

		/** Serial version ID */
		private static final long serialVersionUID = 1;

		@Override
		public int hashCode() {
			return 1;
		}

		@Override
		public String toString() {

src/edu/uky/cs/nil/sabre/Utilities.java
public class Utilities {

	/**
	 * A default {@link edu.uky.cs.nil.sabre.io.Printer printer} generally used
	 * for converting objects to strings
	 */
	public static final DefaultPrinter DEFAULT_PRINTER = new DefaultPrinter();

	/**
	 * Checks whether two objects are {@link Object#equals(Object) equal to}
	 * one another without causing a {@link NullPointerException} if one or
	 * both of them is null.
	 *
	 * @param o1 the first object
	 * @param o2 the second object
	 * @return true if they are equal or both null, false otherwise
	 */
	public static final boolean equals(Object o1, Object o2) {
		if(o1 == null)
			return o2 == null;
		else if(o2 == null)
			return false;
		else
			return o1.equals(o2);
	}

	/**
	 * Returns an object's {@link Object#hashCode() hash code} or 0 if the
	 * object is null.
	 *
	 * @param object the object or null
	 * @return the object's hash code or 0 if the object was null
	 */
	public static final int hashCode(Object object) {
		if(object == null)
			return 0;
		else
			return object.hashCode();
	}

	/**
	 * Combines two {@link #hashCode(Object) hash code} values.
	 *
	 * @param hc1 the first hash code
	 * @param hc2 the second hash code
	 * @return the combined hash code
	 */
	public static final int hashCode(int hc1, int hc2) {
		return hc1 * 31 + hc2;
	}

	/**
	 * Combines a {@link #hashCode(Object) hash code} value with the {@link
	 * #hashCode(Object) hash code} of an object.
	 *
	 * @param hc the hash code value
	 * @param o1 the object
	 * @return the combined hash code
	 */
	public static final int hashCode(int hc, Object o1) {
		return hashCode(hc, hashCode(o1));
	}

	/**
	 * Combines the {@link #hashCode(Object) hash code} values of two objects.
	 *
	 * @param o1 the first object
	 * @param o2 the second object
	 * @return the combined hash code
	 */
	public static final int hashCode(Object o1, Object o2) {
		return hashCode(hashCode(o1), hashCode(o2));
	}

	/**
	 * Combines a {@link #hashCode(Object) hash code} value with the {@link
	 * #hashCode(Object) hash code} of two objects.
	 *
	 * @param hc the hash code value
	 * @param o1 the first object
	 * @param o2 the second object
	 * @return the combined hash code
	 */
	public static final int hashCode(int hc, Object o1, Object o2) {
		return hashCode(hashCode(hc, o1), hashCode(o2));
	}

	/**
	 * Combines the {@link #hashCode(Object) hash code} values of three
	 * objects.
	 *
	 * @param o1 the first object
	 * @param o2 the second object
	 * @param o3 the third object
	 * @return the combined hash code
	 */
	public static final int hashCode(Object o1, Object o2, Object o3) {
		return hashCode(hashCode(o1, o2), hashCode(o3));
	}

	/**
	 * Combines a {@link #hashCode(Object) hash code} value with the {@link
	 * #hashCode(Object) hash code} of three objects.
	 *
	 * @param hc the hash code value
	 * @param o1 the first object
	 * @param o2 the second object
	 * @param o3 the third object
	 * @return the combined hash code
	 */
	public static final int hashCode(int hc, Object o1, Object o2, Object o3) {
		return hashCode(hashCode(hc, o1, o2), hashCode(o3));
	}

	/**
	 * Combines the {@link #hashCode(Object) hash code} values of four objects.
	 *
	 * @param o1 the first object
	 * @param o2 the second object
	 * @param o3 the third object
	 * @param o4 the fourth object
	 * @return the combined hash code
	 */
	public static final int hashCode(Object o1, Object o2, Object o3, Object o4) {
		return hashCode(hashCode(o1, o2, o3), hashCode(o4));
	}

	/**
	 * Combines a {@link #hashCode(Object) hash code} value with the {@link
	 * #hashCode(Object) hash code} of four objects.
	 *
	 * @param hc the hash code value
	 * @param o1 the first object
	 * @param o2 the second object
	 * @param o3 the third object
	 * @param o4 the fourth object
	 * @return the combined hash code
	 */
	public static final int hashCode(int hc, Object o1, Object o2, Object o3, Object o4) {
		return hashCode(hashCode(hc, o1, o2, o3), hashCode(o4));
	}

	/**
	 * Combines the {@link #hashCode(Object) hash code} values of five objects.
	 *
	 * @param o1 the first object
	 * @param o2 the second object
	 * @param o3 the third object
	 * @param o4 the fourth object
	 * @param o5 the fifth object
	 * @return the combined hash code
	 */
	public static final int hashCode(Object o1, Object o2, Object o3, Object o4, Object o5) {
		return hashCode(hashCode(o1, o2, o3, o4), hashCode(o5));
	}

	/**
	 * Combines a {@link #hashCode(Object) hash code} value with the {@link
	 * #hashCode(Object) hash code} of five objects.
	 *
	 * @param hc the hash code value
	 * @param o1 the first object
	 * @param o2 the second object
	 * @param o3 the third object
	 * @param o4 the fourth object
	 * @param o5 the fifth object
	 * @return the combined hash code
	 */
	public static final int hashCode(int hc, Object o1, Object o2, Object o3, Object o4, Object o5) {
		return hashCode(hashCode(hc, o1, o2, o3, o4), hashCode(o5));
	}

	/**
	 * Combines the {@link #hashCode(Object) hash code} values of six objects.
	 *
	 * @param o1 the first object
	 * @param o2 the second object
	 * @param o3 the third object
	 * @param o4 the fourth object
	 * @param o5 the fifth object
	 * @param o6 the sixth object
	 * @return the combined hash code
	 */
	public static final int hashCode(Object o1, Object o2, Object o3, Object o4, Object o5, Object o6) {
		return hashCode(hashCode(o1, o2, o3, o4, o5), hashCode(o6));
	}

	/**
	 * Rounds a {@code double} up to the nearest whole number.
	 *
	 * @param value the value to round up
	 * @return the nearest whole number that is greater than or equal to the
	 * value
	 */
	public static final double roundUp(double value) {
		return new BigDecimal(value).setScale(0, RoundingMode.UP).doubleValue();
	}

	/**
	 * Compares a pair of {@link Comparable comparable} objects.
	 *
	 * @param <C1> the type of the objects
	 * @param o1 the first object
	 * @param o2 the second object
	 * @return a negative integer, zero, or a positive integer as the first
	 * object is less than, equal to, or greater than the second object
	 */
	public static final <C1 extends Comparable<C1>> int compare(C1 o1, C1 o2) {
		return o1.compareTo(o2);
	}

	/**
	 * Compares two pairs of {@link Comparable comparable} objects. The first
	 * pair (that is, the first two arguments) is compared. If the result is
	 * not 0, it is returned, otherwise the second pair (that is, the third and
	 * fourth arguments) is compared, and so on.
	 *
	 * @param <C1> the type of the first pair of objects
	 * @param <C2> the type of the second pair of objects
	 * @param o1 the first object in the first pair
	 * @param o2 the second object in the first pair
	 * @param o3 the first object in the second pair
	 * @param o4 the second object in the second pair
	 * @return a negative integer, zero, or a positive integer as the earlier
	 * pairs are less than, equal to, or greater than the later pairs
	 */
	public static final <C1 extends Comparable<C1>, C2 extends Comparable<C2>> int compare(C1 o1, C1 o2, C2 o3, C2 o4) {
		int comparison = compare(o1, o2);
		if(comparison == 0)
			comparison = compare(o3, o4);
		return comparison;
	}

	/**
	 * Compares three pairs of {@link Comparable comparable} objects. The first
	 * pair (that is, the first two arguments) is compared. If the result is not
	 * 0, it is returned, otherwise the second pair (that is, the third and
	 * fourth arguments) is compared, and so on.
	 *
	 * @param <C1> the type of the first pair of objects
	 * @param <C2> the type of the second pair of objects
	 * @param <C3> the type of the third pair of objects
	 * @param o1 the first object in the first pair
	 * @param o2 the second object in the first pair
	 * @param o3 the first object in the second pair
	 * @param o4 the second object in the second pair
	 * @param o5 the first object in the third pair
	 * @param o6 the second object in the third pair
	 * @return a negative integer, zero, or a positive integer as the earlier
	 * pairs are less than, equal to, or greater than the later pairs
	 */
	public static final <C1 extends Comparable<C1>, C2 extends Comparable<C2>, C3 extends Comparable<C3>> int compare(C1 o1, C1 o2, C2 o3, C2 o4, C3 o5, C3 o6) {
		int comparison = compare(o1, o2, o3, o4);
		if(comparison == 0)
			comparison = compare(o5, o6);
		return comparison;
	}

	/**
	 * Compares four pairs of {@link Comparable comparable} objects. The first
	 * pair (that is, the first two arguments) is compared. If the result is
	 * not 0, it is returned, otherwise the second pair (that is, the third and
	 * fourth arguments) is compared, and so on.
	 *
	 * @param <C1> the type of the first pair of objects
	 * @param <C2> the type of the second pair of objects
	 * @param <C3> the type of the third pair of objects
	 * @param <C4> the type of the fourth pair of objects
	 * @param o1 the first object in the first pair
	 * @param o2 the second object in the first pair
	 * @param o3 the first object in the second pair
	 * @param o4 the second object in the second pair
	 * @param o5 the first object in the third pair
	 * @param o6 the second object in the third pair
	 * @param o7 the first object in the fourth pair
	 * @param o8 the second object in the fourth pair
	 * @return a negative integer, zero, or a positive integer as the earlier
	 * pairs are less than, equal to, or greater than the later pairs
	 */
	public static final <C1 extends Comparable<C1>, C2 extends Comparable<C2>, C3 extends Comparable<C3>, C4 extends Comparable<C4>> int compare(C1 o1, C1 o2, C2 o3, C2 o4, C3 o5, C3 o6, C4 o7, C4 o8) {
		int comparison = compare(o1, o2, o3, o4, o5, o6);
		if(comparison == 0)
			comparison = compare(o7, o8);
		return comparison;
	}

	/**
	 * Compares two {@link ImmutableArray arrays} of {@link Logical logical}
	 * objects. The first elements of both arrays are compared. If the result
	 * is not 0, it is returned, otherwise the second elements of both arrays
	 * are compared, and so on.
	 *
	 * @param array1 the first array
	 * @param array2 the second array
	 * @return a negative integer, zero, or a positive integer as the earlier
	 * elements are less than, equal to, or greater than the later elements
	 */
	public static final int compare(ImmutableArray<? extends Logical> array1, ImmutableArray<? extends Logical> array2) {
		int comparison = 0;
		int size = Math.min(array1.size(), array2.size());
		for(int i=0; i<size && comparison==0; i++)
			comparison = array1.get(i).compareTo(array2.get(i));
		if(comparison == 0) {
			if(array1.size() > array2.size())
				return 1;
			else if(array2.size() > array1.size())
				return -1;
		}
		return comparison;
	}

	/**
	 * Iterates through all elements of an {@link Iterable iterable} and places
	 * them into an array of a given type.
	 *
	 * @param <T> the component type of the array
	 * @param iterable the iterable
	 * @param type the class of the component type of the array
	 * @return an array containing all the elements in the iterable
	 */
	public static final <T> T[] toArray(Iterable<? extends T> iterable, Class<T> type) {
		return toArray(iterable.iterator(), 0, type);
	}

	@SuppressWarnings("unchecked")
	private static final <T> T[] toArray(Iterator<? extends T> iterator, int index, Class<T> type) {
		if(iterator.hasNext()) {
			T element = iterator.next();
			T[] array = toArray(iterator, index + 1, type);
			array[index] = element;
			return array;
		}
		else
			return (T[]) Array.newInstance(type, index);
	}

	/**
	 * Iterates through all elements of an {@link Iterable iterable} and places
	 * into a {@link ImmutableSet set} only those items which are of a given
	 * type.
	 *
	 * @param <T> the type of elements to collect
	 * @param type the class object of the type
	 * @param iterable the iterable to iterate through
	 * @return a set of elements from the iterable of the given type
	 */
	@SuppressWarnings("unchecked")
	public static final <T> ImmutableSet<T> collect(Class<T> type, Iterable<?> iterable) {
		LinkedHashSet<T> set = new LinkedHashSet<>();
		for(Object element : iterable)
			if(type.isAssignableFrom(element.getClass()))
				set.add((T) element);
		return new ImmutableSet<>(set);
	}

	/**
	 * Wrap a string in parentheses, unless it is already so wrapped.
	 *
	 * @param string the second
	 * @return the string, wrapped in parentheses
	 */
	public static final String wrap(String string) {
		if(string.startsWith("(") && string.endsWith(")"))
			return string;
		else
			return "(" + string + ")";
	}

	/**
	 * Converts a number of milliseconds into a short string representation
	 * that gives the numbers of days, hours, minutes, seconds, and
	 * milliseconds. For example, {@code "2d1h3m45s20ms"} represents two days,
	 * 1 hour, 3 minutes, fourty-five seconds, and twenty milliseconds.
	 *
	 * @param ms the number of milliseconds
	 * @return a string representation of that amount of time
	 */
	public static final String time(long ms) {
		long days = TimeUnit.MILLISECONDS.toDays(ms);
		ms -= TimeUnit.DAYS.toMillis(days);
		long hours = TimeUnit.MILLISECONDS.toHours(ms);
		ms -= TimeUnit.HOURS.toMillis(hours);
		long minutes = TimeUnit.MILLISECONDS.toMinutes(ms);
		ms -= TimeUnit.MINUTES.toMillis(minutes);
		long seconds = TimeUnit.MILLISECONDS.toSeconds(ms);
		ms -= TimeUnit.SECONDS.toMillis(seconds);
		String string = "";
		if(days > 0)
			string += days + "d";
		if(hours > 0)
			string += hours + "h";
		if(minutes > 0)
			string += minutes + "m";
		if(seconds > 0)
			string += seconds + "s";
		if(ms > 0)
			string += ms + "ms";
		if(string.isEmpty())
			return "0ms";
		return string;
	}
}

Answer: return DefaultParser.EXISTENTIAL_QUANTIFICATION_KEYWORD;

<think>
The code is defining the existential Quantifier anonymous subclass. After overriding hashCode, the next method is toString, which should return the keyword for existential quantification, mirroring the universal quantifier's toString implementation that returns DefaultParser.UNIVERSAL_QUANTIFICATION_KEYWORD. Therefore the next line should return the corresponding constant for existential quantification.
</think>
return DefaultParser.EXISTENTIAL_QUANTIFICATION_KEYWORD;


Input:
import unittest
from reinvent.chemistry import Conversions
from reinvent.chemistry.library_design import (
    FragmentReactionSliceEnumerator,
    BondMaker,
    AttachmentPoints,
)
from reinvent.chemistry.library_design.dtos import FilteringConditionDTO
from reinvent.chemistry.library_design.enums import MolecularDescriptorsEnum
from reinvent.chemistry.library_design.fragment_reactions import FragmentReactions
from tests.chemistry.library_design.fixtures import FRAGMENT_REACTION_SUZUKI, FRAGMENT_REACTIONS
from tests.chemistry.fixtures.test_data import CELECOXIB

Context:
tests/chemistry/library_design/test_fragment_reactions_slice_enumerator.py

        scaffold_conditions = []
        decoration_conditions = []
        self._slice_enumerator = FragmentReactionSliceEnumerator(
            self._suzuki_reaction_dto_list, scaffold_conditions, decoration_conditions
        )

    def test_enumeration_slcing_1(self):
        result = self._slice_enumerator.enumerate(self.suzuki_positive_molecule, 1)

        self.assertEqual(2, len(result))

    def test_enumeration_slicing_2(self):
        result = self._slice_enumerator.enumerate(self.suzuki_positive_molecule, 4)

        self.assertEqual(2, len(result))

        complete_molecules = []
        for sliced in result:
            values = [
                self.chemistry.mol_to_smiles(smi) for num, smi in sorted(sliced.decorations.items())
            ]
            decorations = "|".join(values)
            labeled_scaffold = self._attachment_points.add_attachment_point_numbers(sliced.scaffold)
            molecule = self._bond_maker.join_scaffolds_and_decorations(
                labeled_scaffold, decorations
            )
            complete_smile = self.chemistry.mol_to_smiles(molecule)
            complete_molecules.append(complete_smile)
        self.assertEqual(
            self.chemistry.mol_to_smiles(self.suzuki_positive_molecule),
            list(set(complete_molecules))[0],
        )

class TestMultipleFragmentReactionsSliceEnumerator(unittest.TestCase):
    def setUp(self):
        self._bond_maker = BondMaker()
        self._attachment_points = AttachmentPoints()
        self.chemistry = Conversions()
        self.reactions = FragmentReactions()
        self._fragment_reactions = self.reactions.create_reactions_from_smirks(FRAGMENT_REACTIONS)
        self.positive_smile = CELECOXIB

        self.positive_molecule = self.chemistry.smile_to_mol(self.positive_smile)

        scaffold_conditions = []
        decoartion_conditions = []
        self._slice_enumerator = FragmentReactionSliceEnumerator(
            self._fragment_reactions, scaffold_conditions, decoartion_conditions
        )

    def test_enumeration_slicing_1(self):
        result = self._slice_enumerator.enumerate(self.positive_molecule, 1)

        complete_molecules = []
        for sliced in result:
            values = [
                self.chemistry.mol_to_smiles(smi) for num, smi in sorted(sliced.decorations.items())
            ]
            decorations = "|".join(values)
            labeled_scaffold = self._attachment_points.add_attachment_point_numbers(sliced.scaffold)
            molecule = self._bond_maker.join_scaffolds_and_decorations(
                labeled_scaffold, decorations
            )
            complete_smile = self.chemistry.mol_to_smiles(molecule)
            complete_molecules.append(complete_smile)
        reference = self.chemistry.mol_to_smiles(self.chemistry.smile_to_mol(self.positive_smile))
        self.assertEqual(reference, list(set(complete_molecules))[0])

        self.assertEqual(6, len(result))

    def test_enumeration_slicing_2(self):
        result = self._slice_enumerator.enumerate(self.positive_molecule, 2)
        self.assertEqual(12, len(result))

    def test_enumeration_slicing_3(self):
        result = self._slice_enumerator.enumerate(self.positive_molecule, 3)

        complete_molecules = []
        for sliced in result:
            values = [self.chemistry.mol_to_smiles(smi) for num, smi in sliced.decorations.items()]
            decorations = "|".join(values)
            labeled_scaffold = self._attachment_points.add_attachment_point_numbers(sliced.scaffold)
            molecule = self._bond_maker.join_scaffolds_and_decorations(
                labeled_scaffold, decorations
            )
            complete_smile = self.chemistry.mol_to_smiles(molecule)
            complete_molecules.append(complete_smile)
        reference = self.chemistry.mol_to_smiles(self.chemistry.smile_to_mol(self.positive_smile))
        self.assertEqual(reference, list(set(complete_molecules))[0])
        self.assertEqual(1, len(list(set(complete_molecules))))
        self.assertEqual(12, len(result))

class TestReactionsSliceEnumeratorWithFilters(unittest.TestCase):
    def setUp(self):
        self.chemistry = Conversions()
        self.reactions = FragmentReactions()
        self._suzuki_reactions = self.reactions.create_reactions_from_smirks(
            FRAGMENT_REACTION_SUZUKI
        )
        self.positive_smile = CELECOXIB

        self.positive_molecule = self.chemistry.smile_to_mol(self.positive_smile)
        descriptors_enum = MolecularDescriptorsEnum()

        scaffold_condition_1 = FilteringConditionDTO(descriptors_enum.RING_COUNT, min=1)
        scaffold_condition_2 = FilteringConditionDTO(descriptors_enum.MOLECULAR_WEIGHT, max=600)
        decoartion_condition_1 = FilteringConditionDTO(
            descriptors_enum.HYDROGEN_BOND_ACCEPTORS, max=3
        )
        decoartion_condition_2 = FilteringConditionDTO(descriptors_enum.HYDROGEN_BOND_DONORS, max=3)
        scaffold_conditions = [scaffold_condition_1, scaffold_condition_2]
        decoartion_conditions = [decoartion_condition_1, decoartion_condition_2]
        self._slice_enumerator = FragmentReactionSliceEnumerator(
            self._suzuki_reactions, scaffold_conditions, decoartion_conditions
        )

    def test_enumeration_slicing_1(self):

reinvent/chemistry/library_design/fragment_reactions.py
class FragmentReactions:
    def __init__(self):
        self._conversions = Conversions()
        self._tokens = TransformationTokens()
        self._bond_mapper = BondMapper()

    def create_reactions_from_smarts(self, smarts: List[str]) -> List[ChemicalReaction]:
        reactions = [AllChem.ReactionFromSmarts(smirks) for smirks in smarts]
        return reactions

    def create_reaction_from_smirk(self, smirks: str) -> ReactionDTO:
        reaction = ReactionDTO(smirks, AllChem.ReactionFromSmarts(smirks))
        return reaction

    def create_reactions_from_smirks(self, smirks: List[str]) -> List[ReactionDTO]:
        reactions = [self.create_reaction_from_smirk(smirk) for smirk in smirks]
        return reactions

    def slice_molecule_to_fragments(
        self, molecule: Mol, reaction_dtos: List[ReactionDTO]
    ) -> List[Tuple[Mol]]:
        """
        This method applies a list of chemical reactions on a molecule and
        decomposes the input molecule to complementary fragments.
        :param molecule:
        :param reaction_dtos:
        :return: Different slicing combinations are returned.
        """
        list_of_outcomes = self.apply_reactions_on_molecule(molecule, reaction_dtos)
        all_outcomes = []

        for outcome in list_of_outcomes:
            all_outcomes.extend(outcome.reaction_outcomes)
        # TODO: the overall data processing is extremely slow. consider reducing redundancy here.
        return all_outcomes

    def apply_reactions_on_molecule(
        self, molecule: Mol, reaction_dtos: List[ReactionDTO]
    ) -> List[ReactionOutcomeDTO]:
        """Build list of possible splits of a molecule given multiple reactions."""
        list_of_outcomes = []
        for reaction_dto in reaction_dtos:
            outcome_dto = self.apply_reaction_on_molecule(molecule, reaction_dto)
            purged_outcome_dto = self._filter_pairs_with_no_ring_count_change(outcome_dto)
            list_of_outcomes.append(purged_outcome_dto)
        return list_of_outcomes

    def apply_reaction_on_molecule(
        self, molecule: Mol, reaction_dto: ReactionDTO
    ) -> ReactionOutcomeDTO:
        """Build list of possible splits of a molecule given a single reaction."""
        molecule = self._conversions.copy_mol(molecule)
        outcomes = reaction_dto.chemical_reaction.RunReactant(molecule, 0)
        outcome_dto = ReactionOutcomeDTO(reaction_dto.reaction_smarts, list(outcomes), molecule)
        return outcome_dto

    def _filter_pairs_with_no_ring_count_change(
        self, outcome_dto: ReactionOutcomeDTO
    ) -> ReactionOutcomeDTO:
        molecule_rings = RingCount(outcome_dto.targeted_molecule)
        acceptable_pairs = []
        for pair in outcome_dto.reaction_outcomes:
            if not self._detect_ring_break(molecule_rings, pair) and len(pair) == 2:
                acceptable_pairs.append(pair)
        outcome_dto.reaction_outcomes = acceptable_pairs
        return outcome_dto

    def _detect_ring_break(self, molecule_ring_count: int, pair: Tuple[Mol]) -> bool:
        reagent_rings = 0
        for reagent in pair:
            reagent_smiles = self._conversions.mol_to_smiles(reagent)
            reagent_mol = self._conversions.smile_to_mol(reagent_smiles)
            try:
                reagent_rings = reagent_rings + RingCount(reagent_mol)
            except:
                return True
        return molecule_ring_count != reagent_rings

tests/chemistry/fixtures/test_data.py
CELECOXIB = 'O=S(=O)(c3ccc(n1nc(cc1c2ccc(cc2)C)C(F)(F)F)cc3)N'

reinvent/chemistry/library_design/attachment_points.py
class AttachmentPoints:
    def __init__(self):
        self._conversions = Conversions()
        self._tokens = TransformationTokens()

    def add_attachment_point_numbers(self, mol_or_smi, canonicalize=True):
        """
        Adds the numbers for the attachment points throughout the molecule.
        :param mol_or_smi: SMILES string to convert.
        :param canonicalize: Canonicalize the SMILES so that the attachment points are always in the same order.
        :return : A converted SMILES string.
        """
        if isinstance(mol_or_smi, str):
            smi = mol_or_smi
            if canonicalize:
                smi = self._conversions.mol_to_smiles(self._conversions.smile_to_mol(mol_or_smi))
            # only add numbers ordered by the SMILES ordering
            num = -1

            def _ap_callback(_):
                nonlocal num
                num += 1
                return "[{}:{}]".format(self._tokens.ATTACHMENT_POINT_TOKEN, num)

            return re.sub(self._tokens.ATTACHMENT_POINT_REGEXP, _ap_callback, smi)
        else:
            mol = mol_or_smi
            if canonicalize:
                mol = self._conversions.smile_to_mol(self._conversions.mol_to_smiles(mol))
            idx = 0
            for atom in mol.GetAtoms():
                if atom.GetSymbol() == self._tokens.ATTACHMENT_POINT_TOKEN:
                    atom.SetProp("molAtomMapNumber", str(idx))
                    idx += 1
            return self._conversions.mol_to_smiles(mol)

    def get_attachment_points(self, smile: str) -> List:
        """
        Gets all attachment points from SMILES string.
        :param smile: A SMILES string
        :return : A list with the numbers ordered by appearance.
        """
        return [
            int(match.group(1))
            for match in re.finditer(self._tokens.ATTACHMENT_POINT_NUM_REGEXP, smile)
        ]

    def get_attachment_points_for_molecule(self, molecule: Mol) -> List:
        """
        Gets all attachment points from RDKit Mol.
        :param molecule: A Mol object.
        :return : A list with the numbers ordered by appearance.
        """
        if isinstance(molecule, Mol):
            return [
                int(atom.GetProp("molAtomMapNumber"))
                for atom in molecule.GetAtoms()
                if atom.GetSymbol() == self._tokens.ATTACHMENT_POINT_TOKEN
                and atom.HasProp("molAtomMapNumber")
            ]

    def add_first_attachment_point_number(self, smi, num):
        """
        Changes/adds a number to the first attachment point.
        :param smi: SMILES string with the molecule.
        :param num: Number to add.
        :return: A SMILES string with the number added.
        """
        return re.sub(
            self._tokens.ATTACHMENT_POINT_REGEXP,
            "[{}:{}]".format(self._tokens.ATTACHMENT_POINT_TOKEN, num),
            smi,
            count=1,
        )

    def remove_attachment_point_numbers(self, smile: str) -> str:
        """
        Removes the numbers for the attachment points throughout the molecule.
        :param smile: SMILES string.
        :return : A converted SMILES string.
        """
        result = re.sub(
            self._tokens.ATTACHMENT_POINT_NUM_REGEXP,
            "[{}]".format(self._tokens.ATTACHMENT_POINT_TOKEN),
            smile,
        )
        return result

    def remove_attachment_point_numbers_from_mol(self, molecule: Mol) -> Mol:
        """
        Removes the numbers for the attachment points throughout the molecule.
        :param molecule: RDKit molecule.
        :return : A molecule.
        """
        if isinstance(molecule, Mol):
            for atom in molecule.GetAtoms():
                atom.ClearProp("molAtomMapNumber")
        return molecule

    def add_brackets_to_attachment_points(self, scaffold: str):
        """
        Adds brackets to the attachment points (if they don't have them).
        :param scaffold: SMILES string.
        :return: A SMILES string with attachments in brackets.
        """
        return re.sub(
            self._tokens.ATTACHMENT_POINT_NO_BRACKETS_REGEXP,
            "[{}]".format(self._tokens.ATTACHMENT_POINT_TOKEN),
            scaffold,
        )

reinvent/chemistry/conversions.py
class Conversions:
    @staticmethod
    def smiles_to_mols_and_indices(query_smiles: List[str]) -> Tuple[List[Mol], List[int]]:
        mols = [MolFromSmiles(smile) for smile in query_smiles]
        valid_mask = [mol is not None for mol in mols]
        valid_idxs = [idx for idx, is_valid in enumerate(valid_mask) if is_valid]
        valid_mols = [mols[idx] for idx in valid_idxs]
        return valid_mols, valid_idxs

    @staticmethod
    def mols_to_fingerprints(
        molecules: List[Mol], radius: int = 3, use_counts: bool = True, use_features: bool = True
    ) -> List[UIntSparseIntVect]:
        fingerprints = [
            AllChem.GetMorganFingerprint(
                mol, radius, useCounts=use_counts, useFeatures=use_features
            )
            for mol in molecules
        ]
        return fingerprints

    @staticmethod
    def smiles_to_mols(query_smiles: List[str]) -> List[Mol]:
        mols = [MolFromSmiles(smile) for smile in query_smiles]
        valid_mask = [mol is not None for mol in mols]
        valid_idxs = [idx for idx, is_valid in enumerate(valid_mask) if is_valid]
        valid_mols = [mols[idx] for idx in valid_idxs]
        return valid_mols

    def smiles_to_fingerprints(
        self, query_smiles: List[str], radius=3, use_counts=True, use_features=True
    ) -> List[UIntSparseIntVect]:
        mols = self.smiles_to_mols(query_smiles)
        fingerprints = self.mols_to_fingerprints(
            mols, radius=radius, use_counts=use_counts, use_features=use_features
        )
        return fingerprints

    def smile_to_mol(self, smile: str) -> Mol:
        """
        Creates a Mol object from a SMILES string.
        :param smile: SMILES string.
        :return: A Mol object or None if it's not valid.
        """
        if smile:
            return MolFromSmiles(smile)

    def mols_to_smiles(
        self, molecules: List[Mol], isomericSmiles=False, canonical=True
    ) -> List[str]:
        """This method assumes that all molecules are valid."""
        valid_smiles = [
            MolToSmiles(mol, isomericSmiles=isomericSmiles, canonical=canonical)
            for mol in molecules
        ]
        return valid_smiles

    def mol_to_smiles(self, molecule: Mol, isomericSmiles=False, canonical=True) -> str:
        """
        Converts a Mol object into a canonical SMILES string.
        :param molecule: Mol object.
        :return: A SMILES string.
        """
        if molecule:
            return MolToSmiles(molecule, isomericSmiles=isomericSmiles, canonical=canonical)

    def mol_to_random_smiles(self, molecule: Mol) -> str:
        """
        Converts a Mol object into a random SMILES string.
        :return: A SMILES string.
        """
        if molecule:
            new_atom_order = list(range(molecule.GetNumAtoms()))
            random.shuffle(new_atom_order)
            random_mol = RenumberAtoms(molecule, newOrder=new_atom_order)
            return MolToSmiles(random_mol, canonical=False, isomericSmiles=False)

    def convert_to_rdkit_smiles(
        self, smiles: str, allowTautomers=True, sanitize=False, isomericSmiles=False
    ) -> str:
        """
        :param smiles: Converts a smiles string into a canonical SMILES string.
        :type allowTautomers: allows having same molecule represented in different tautomeric forms
        """
        if allowTautomers:
            return MolToSmiles(
                MolFromSmiles(smiles, sanitize=sanitize), isomericSmiles=isomericSmiles
            )
        else:
            return MolStandardize.canonicalize_tautomer_smiles(smiles)

    def convert_to_standardized_smiles(self, smiles: str) -> Optional[str]:
        """Standardize SMILES for Mol2Mol

        This should only be used to validate and transform user input
        because the code will abort execution on any error it finds.

        param smiles: single SMILES string
        return: single SMILES string
        """

        mol = MolFromSmiles(smiles, sanitize=True)

        if not mol:  # RDKit fails silently
            raise RuntimeError(f"RDKit does not accept SMILES: {smiles}")

        standardizer = Standardizer()  # MolVS

        try:
            smol = standardizer(mol)  # runs SanitizeMol() first
            smol = standardizer.charge_parent(smol)  # largest fragment uncharged
            smi = MolToSmiles(smol, isomericSmiles=True)
        except Exception as error:  # RDKit may raise multiple exceptions
            raise RuntimeError(f"RDKit does not accept SMILES: {smiles} {error}")

        # Sometimes when standardizing ChEMBL [H] are not removed so try a
        # second call
        if "[H]" in smi:
            return self.convert_to_standardized_smiles(smi)
        else:
            return smi

    def copy_mol(self, molecule: Mol) -> Mol:
        """
        Copies, sanitizes, canonicalizes and cleans a molecule.
        :param molecule: A Mol object to copy.
        :return : Another Mol object copied, sanitized, canonicalized and cleaned.
        """
        return self.smile_to_mol(self.mol_to_smiles(molecule))

    def randomize_smiles(self, smiles: str) -> str:
        """
        Returns a random SMILES given a SMILES of a molecule.
        :param smiles: A smiles string
        :returns: A random SMILES string of the same molecule or None if the molecule is invalid.
        """
        mol = MolFromSmiles(smiles)
        if mol:
            new_atom_order = list(range(mol.GetNumHeavyAtoms()))
            random.shuffle(new_atom_order)
            random_mol = RenumberAtoms(mol, newOrder=new_atom_order)
            return MolToSmiles(random_mol, canonical=False, isomericSmiles=False)

    def mol_to_inchi_key(self, molecule: Mol) -> str:
        """Returns the standard InChI key for a molecule"""
        if molecule:
            inchi_key = MolToInchiKey(molecule)
            return inchi_key

    def mol_to_sdf(self, molecules: List, input_sdf_path: str):
        """Write a set of molecules to sdf file"""
        writer = SDWriter(input_sdf_path)
        for mol in molecules:
            writer.write(mol)

reinvent/chemistry/library_design/fragment_reaction_slice_enumerator.py
class FragmentReactionSliceEnumerator:
    def __init__(
        self,
        chemical_reactions: List[ReactionDTO],
        scaffold_conditions: List[FilteringConditionDTO],
        decoration_conditions: List[FilteringConditionDTO],
    ):
        """
        Class to enumerate slicings given certain conditions.
        :param chemical_reactions: A list of ChemicalReaction objects.
        :param scaffold_conditions: Conditions to use when filtering scaffolds obtained from slicing molecules (see FragmentFilter).
        :param decoration_conditions: Conditions to use when filtering decorations obtained from slicing molecules.
        """
        self._tockens = TransformationTokens()
        self._chemical_reactions = chemical_reactions
        self._scaffold_filter = FragmentFilter(scaffold_conditions)
        self._decoration_filter = FragmentFilter(decoration_conditions)
        self._reactions = FragmentReactions()
        self._conversions = Conversions()

    def enumerate(self, molecule: Mol, cuts: int) -> List[FragmentedMolecule]:
        """
        Enumerates all possible combination of slicings of a molecule given a number of cuts.
        :param molecule: A mol object with the molecule to slice.
        :param cuts: The number of cuts to perform.
        :return : A list with all the possible (scaffold, decorations) pairs as SlicedMol objects.
        """
        original_smiles = self._conversions.mol_to_smiles(molecule)
        sliced_mols = set()
        for cut in range(1, cuts + 1):
            if cut == 1:
                fragment_pairs = self._reactions.slice_molecule_to_fragments(
                    molecule, self._chemical_reactions
                )

                for pair in fragment_pairs:
                    for indx, _ in enumerate(pair):
                        decorations = self._select_all_except(pair, indx)
                        decoration = self._conversions.copy_mol(decorations[0])
                        labeled_decoration = OrderedDict()
                        labeled_decoration[0] = decoration  # [ for decoration in decorations]

                        scaffold = self._conversions.copy_mol(pair[indx])
                        labeled_scaffold = self._label_scaffold(scaffold)

                        # TODO: filtering should take place after scaffold is generated
                        sliced_mol = FragmentedMolecule(
                            labeled_scaffold, labeled_decoration, original_smiles
                        )
                        if sliced_mol.original_smiles == sliced_mol.reassembled_smiles:
                            sliced_mols.add(sliced_mol)
            else:
                for slice in sliced_mols:
                    to_add = self._scaffold_slicing(slice, cut)
                    sliced_mols = sliced_mols.union(to_add)

        return list(filter(self._filter, sliced_mols))

    def _scaffold_slicing(self, slice: FragmentedMolecule, cut: int) -> Set[FragmentedMolecule]:
        to_add = set()
        if slice.decorations_count() == cut - 1:
            fragment_pairs = self._reactions.slice_molecule_to_fragments(
                slice.scaffold, self._chemical_reactions
            )

            for pair in fragment_pairs:
                scaffold, decoration = self._split_scaffold_from_decorations(pair, cut)
                if scaffold:
                    labeled_scaffold = self._label_scaffold(scaffold)
                    labeled_scaffold = self._conversions.copy_mol(labeled_scaffold)
                    decoration = self._conversions.copy_mol(decoration)
                    sliced_mol = self._create_sliced_molecule(slice, labeled_scaffold, decoration)

                    if sliced_mol.original_smiles == sliced_mol.reassembled_smiles:
                        to_add.add(sliced_mol)
        return to_add

    def _select_all_except(self, fragments: Tuple[Mol], to_exclude: int) -> List[Mol]:
        return [fragment for indx, fragment in enumerate(fragments) if indx != to_exclude]

    def _filter(self, sliced_mol: FragmentedMolecule) -> bool:
        return self._scaffold_filter.filter(sliced_mol.scaffold) and all(
            self._decoration_filter.filter(dec) for dec in sliced_mol.decorations.values()
        )

    def _split_scaffold_from_decorations(self, pair: Tuple[Mol], cuts: int) -> Tuple[Mol, Mol]:
        decoration = None
        scaffold = None
        for frag in pair:
            num_att = len(
                [
                    atom
                    for atom in frag.GetAtoms()
                    if atom.GetSymbol() == self._tockens.ATTACHMENT_POINT_TOKEN
                ]
            )
            # detect whether there is one fragment with as many attachment points as cuts (scaffold)
            # the rest are decorations
            if num_att == cuts and not scaffold:
                scaffold = frag
            if num_att == 1:
                decoration = frag
        if decoration and scaffold:
            return scaffold, decoration
        else:
            return (None, None)

    def _label_scaffold(self, scaffold: Mol) -> Mol:
        highest_number = self._find_highest_number(scaffold)

        for atom in scaffold.GetAtoms():
            if atom.GetSymbol() == self._tockens.ATTACHMENT_POINT_TOKEN:
                try:
                    atom_number = int(atom.GetProp("molAtomMapNumber"))
                except:
                    highest_number += 1
                    num = atom.GetIsotope()
                    atom.SetIsotope(0)
                    atom.SetProp("molAtomMapNumber", str(highest_number))
        scaffold.UpdatePropertyCache()

        return scaffold

    def _find_highest_number(self, cut_mol: Mol) -> int:
        highest_number = -1

        for atom in cut_mol.GetAtoms():
            if atom.GetSymbol() == self._tockens.ATTACHMENT_POINT_TOKEN:
                try:
                    atom_number = int(atom.GetProp("molAtomMapNumber"))
                    if highest_number < atom_number:
                        highest_number = atom_number
                except:
                    pass
        return highest_number

    def _create_sliced_molecule(
        self, original_sliced_mol: FragmentedMolecule, scaffold: Mol, decoration: Mol
    ) -> FragmentedMolecule:
        old_decorations = OrderedDict()
        for k, v in original_sliced_mol.decorations.items():
            old_decorations[k] = v
        old_decorations[original_sliced_mol.decorations_count()] = decoration
        sliced_mol = FragmentedMolecule(
            scaffold, old_decorations, original_sliced_mol.original_smiles
        )
        return sliced_mol

reinvent/chemistry/library_design/bond_maker.py
class BondMaker:
    def __init__(self):
        self._conversions = Conversions()
        self._tokens = TransformationTokens()
        self._attachment_points = AttachmentPoints()

    def join_scaffolds_and_decorations(
        self, scaffold_smi: str, decorations_smi, keep_labels_on_atoms=False
    ) -> Optional[Mol]:
        decorations_smi = [
            self._attachment_points.add_first_attachment_point_number(dec, i)
            for i, dec in enumerate(decorations_smi.split(self._tokens.ATTACHMENT_SEPARATOR_TOKEN))
        ]
        num_attachment_points = len(self._attachment_points.get_attachment_points(scaffold_smi))
        if len(decorations_smi) != num_attachment_points:
            return None

        mol = self._conversions.smile_to_mol(scaffold_smi)
        for decoration in decorations_smi:
            mol = self.join_molecule_fragments(
                mol,
                self._conversions.smile_to_mol(decoration),
                keep_label_on_atoms=keep_labels_on_atoms,
            )
            if not mol:
                return None
        return mol

    def join_molecule_fragments(self, scaffold: Mol, decoration: Mol, keep_label_on_atoms=False):
        """
        Joins a RDKit MOL scaffold with a decoration. They must be labelled.
        :param scaffold: RDKit MOL of the scaffold.
        :param decoration: RDKit MOL of the decoration.
        :param keep_label_on_atoms: Add the labels to the atoms after attaching the molecule.
        This is useful when debugging, but it can give problems.
        :return: A Mol object of the joined scaffold.
        """

        if scaffold and decoration:
            # obtain id in the decoration
            try:
                attachment_points = [
                    atom.GetProp("molAtomMapNumber")
                    for atom in decoration.GetAtoms()
                    if atom.GetSymbol() == self._tokens.ATTACHMENT_POINT_TOKEN
                ]
                if len(attachment_points) != 1:
                    return None  # more than one attachment point...
                attachment_point = attachment_points[0]
            except KeyError:
                return None

            combined_scaffold = RWMol(CombineMols(decoration, scaffold))
            attachments = [
                atom
                for atom in combined_scaffold.GetAtoms()
                if atom.GetSymbol() == self._tokens.ATTACHMENT_POINT_TOKEN
                and atom.HasProp("molAtomMapNumber")
                and atom.GetProp("molAtomMapNumber") == attachment_point
            ]
            if len(attachments) != 2:
                return None  # something weird

            neighbors = []
            for atom in attachments:
                if atom.GetDegree() != 1:
                    return None  # the attachment is wrongly generated
                neighbors.append(atom.GetNeighbors()[0])

            bonds = [atom.GetBonds()[0] for atom in attachments]
            bond_type = BondType.SINGLE
            if any(bond for bond in bonds if bond.GetBondType() == BondType.DOUBLE):
                bond_type = BondType.DOUBLE

            combined_scaffold.AddBond(neighbors[0].GetIdx(), neighbors[1].GetIdx(), bond_type)
            combined_scaffold.RemoveAtom(attachments[0].GetIdx())
            combined_scaffold.RemoveAtom(attachments[1].GetIdx())

            if keep_label_on_atoms:
                for neigh in neighbors:
                    self._add_attachment_point_num(neigh, attachment_point)

            # Label the atoms in the bond
            bondNumbers = [
                int(atom.GetProp("bondNum"))
                for atom in combined_scaffold.GetAtoms()
                if atom.HasProp("bondNum")
            ]

            if bondNumbers:
                bondNum = max(bondNumbers) + 1
            else:
                bondNum = 0

            for neighbor in neighbors:
                idx = neighbor.GetIdx()
                atom = combined_scaffold.GetAtomWithIdx(idx)
                atom.SetIntProp("bondNum", bondNum)
            ##########################################

            scaffold = combined_scaffold.GetMol()
            try:
                SanitizeMol(scaffold)
            except ValueError:  # sanitization error
                return None
        else:
            return None

        return scaffold

    def _add_attachment_point_num(self, atom, idx):
        idxs = []
        if atom.HasProp("molAtomMapNumber"):
            idxs = atom.GetProp("molAtomMapNumber").split(",")
        idxs.append(str(idx))
        idxs = sorted(list(set(idxs)))
        atom.SetProp("molAtomMapNumber", ",".join(idxs))
        # Fixme: This way of annotating fails in case of several attachment points when the mol is converted back to a
        #  SMILES string (RuntimeError: boost::bad_any_cast: failed conversion using boost::any_cast)
        #  For example combining scaffold '*C(*)CC' and  warhead pair '*OC|*C' would result in
        #  C[O:0][CH:0,1]([CH3:1])CC, which results in an error due to the '0,1'

    def randomize_scaffold(self, scaffold: Mol):
        smi = self._conversions.mol_to_random_smiles(scaffold)
        conv_smi = None
        if smi:
            conv_smi = self._attachment_points.add_brackets_to_attachment_points(smi)
        return conv_smi

Answer: result = self._slice_enumerator.enumerate(self.positive_molecule, 1)

<think>
In the TestReactionsSliceEnumeratorWithFilters class, after defining the test method 'def test_enumeration_slicing_1(self):' the next logical line is to invoke the slice enumerator on the positive molecule with a single cut, mirroring other test methods. This starts the test body.
The appropriate line, respecting indentation, is:
        result = self._slice_enumerator.enumerate(self.positive_molecule, 1)
</think>
result = self._slice_enumerator.enumerate(self.positive_molecule, 1)


Input:
import edu.wpi.first.math.Matrix;
import edu.wpi.first.math.geometry.Pose2d;
import edu.wpi.first.math.geometry.Rotation2d;
import edu.wpi.first.math.kinematics.ChassisSpeeds;
import edu.wpi.first.math.kinematics.SwerveModuleState;
import edu.wpi.first.math.numbers.N1;
import edu.wpi.first.math.numbers.N3;
import edu.wpi.first.wpilibj.DriverStation;
import edu.wpi.first.wpilibj2.command.Command;
import edu.wpi.first.wpilibj2.command.Subsystem;
import frc.robot.Robot;
import frc.robot.RobotTelemetry;
import frc.robot.swerve.configs.MUSICDISC2023;
import frc.robot.swerve.configs.NOTEBLOCK2023;
import frc.spectrumLib.swerve.Drivetrain;
import frc.spectrumLib.swerve.Drivetrain.DriveState;
import frc.spectrumLib.swerve.Request;
import frc.spectrumLib.swerve.config.SwerveConfig;
import java.util.concurrent.locks.ReadWriteLock;
import java.util.concurrent.locks.ReentrantReadWriteLock;
import java.util.function.Consumer;
import java.util.function.DoubleSupplier;
import java.util.function.Supplier;
import org.littletonrobotics.junction.Logger;

Context:
src/main/java/frc/robot/swerve/Swerve.java
package frc.robot.swerve;

public class Swerve implements Subsystem {
    public final SwerveConfig config;
    private final Drivetrain drivetrain;
    private final RotationController rotationController;
    private double OdometryUpdateFrequency = 250;
    private double targetHeading = 0;
    private ReadWriteLock m_stateLock = new ReentrantReadWriteLock();
    private SwerveModuleState[] Setpoints = new SwerveModuleState[] {};

    public Swerve() {
        RobotTelemetry.print("Swerve Subsystem Starting: ");

        // Choose the correct swerve configuration
        switch (Robot.config.getRobotType()) {
            case NOTEBLOCK:
                config = NOTEBLOCK2023.config;
                break;
            case MUSICDISC:
                config = MUSICDISC2023.config;
                break;
            case SIM: // runs in simulation
                OdometryUpdateFrequency = 50;
                config = NOTEBLOCK2023.config;
                break;
            default:
                config = NOTEBLOCK2023.config;
                break;
        }

src/main/java/frc/robot/swerve/configs/MUSICDISC2023.java
public class MUSICDISC2023 {
    // Angle Offsets
    private static final double kFrontLeftCANcoderOffset = 20;
    private static final double kFrontRightCANncoderOffset = 20;
    private static final double kBackLeftCANcoderOffset = 20;
    private static final double kBackRightCANcoderOffset = 20;

    // Device Setup
    private static final String kCANbusName = "rio";
    private static final boolean supportsPro = false;
    private static final SwerveModuleSteerFeedbackType steerFeedbackType =
            SwerveModuleSteerFeedbackType.RemoteCANcoder;

    public static final ModuleConfig FrontLeft =
            NOTEBLOCK2023.FrontLeft.withCANcoderOffset(kFrontLeftCANcoderOffset)
                    .withFeedbackSource(steerFeedbackType);
    public static final ModuleConfig FrontRight =
            NOTEBLOCK2023.FrontRight.withCANcoderOffset(kFrontRightCANncoderOffset)
                    .withFeedbackSource(steerFeedbackType);
    public static final ModuleConfig BackLeft =
            NOTEBLOCK2023.BackLeft.withCANcoderOffset(kBackLeftCANcoderOffset)
                    .withFeedbackSource(steerFeedbackType);
    public static final ModuleConfig BackRight =
            NOTEBLOCK2023.BackRight.withCANcoderOffset(kBackRightCANcoderOffset)
                    .withFeedbackSource(steerFeedbackType);

    public static final ModuleConfig[] ModuleConfigs = {FrontLeft, FrontRight, BackLeft, BackRight};

    public static final SwerveConfig config =
            DefaultConfig.DrivetrainConstants.withCANbusName(kCANbusName)
                    .withSupportsPro(supportsPro)
                    .withModules(ModuleConfigs);
}

src/main/java/frc/robot/RobotTelemetry.java
public class RobotTelemetry extends Telemetry {

    /* What to publish over networktables for telemetry */
    NetworkTableInstance inst = NetworkTableInstance.getDefault();

    /* Robot pose for field positioning */
    NetworkTable table = inst.getTable("Pose");
    DoubleArrayPublisher fieldPub = table.getDoubleArrayTopic("robotPose").publish();
    StringPublisher fieldTypePub = table.getStringTopic(".type").publish();

    /* Robot speeds for general checking */
    NetworkTable driveStats = inst.getTable("Drive");
    DoublePublisher velocityX = driveStats.getDoubleTopic("Velocity X").publish();
    DoublePublisher velocityY = driveStats.getDoubleTopic("Velocity Y").publish();
    DoublePublisher speed = driveStats.getDoubleTopic("Speed").publish();
    DoublePublisher odomPeriod = driveStats.getDoubleTopic("Odometry Period").publish();

    /* Keep a reference of the last pose to calculate the speeds */
    Pose2d m_lastPose = new Pose2d();
    double lastTime = Utils.getCurrentTimeSeconds();

    /* Mechanisms to represent the swerve module states */
    Mechanism2d[] m_moduleMechanisms =
            new Mechanism2d[] {
                new Mechanism2d(1, 1),
                new Mechanism2d(1, 1),
                new Mechanism2d(1, 1),
                new Mechanism2d(1, 1),
            };
    /* A direction and length changing ligament for speed representation */
    MechanismLigament2d[] m_moduleSpeeds =
            new MechanismLigament2d[] {
                m_moduleMechanisms[0]
                        .getRoot("RootSpeed", 0.5, 0.5)
                        .append(new MechanismLigament2d("Speed", 0.5, 0)),
                m_moduleMechanisms[1]
                        .getRoot("RootSpeed", 0.5, 0.5)
                        .append(new MechanismLigament2d("Speed", 0.5, 0)),
                m_moduleMechanisms[2]
                        .getRoot("RootSpeed", 0.5, 0.5)
                        .append(new MechanismLigament2d("Speed", 0.5, 0)),
                m_moduleMechanisms[3]
                        .getRoot("RootSpeed", 0.5, 0.5)
                        .append(new MechanismLigament2d("Speed", 0.5, 0)),
            };
    /* A direction changing and length constant ligament for module direction */
    MechanismLigament2d[] m_moduleDirections =
            new MechanismLigament2d[] {
                m_moduleMechanisms[0]
                        .getRoot("RootDirection", 0.5, 0.5)
                        .append(
                                new MechanismLigament2d(
                                        "Direction", 0.1, 0, 0, new Color8Bit(Color.kWhite))),
                m_moduleMechanisms[1]
                        .getRoot("RootDirection", 0.5, 0.5)
                        .append(
                                new MechanismLigament2d(
                                        "Direction", 0.1, 0, 0, new Color8Bit(Color.kWhite))),
                m_moduleMechanisms[2]
                        .getRoot("RootDirection", 0.5, 0.5)
                        .append(
                                new MechanismLigament2d(
                                        "Direction", 0.1, 0, 0, new Color8Bit(Color.kWhite))),
                m_moduleMechanisms[3]
                        .getRoot("RootDirection", 0.5, 0.5)
                        .append(
                                new MechanismLigament2d(
                                        "Direction", 0.1, 0, 0, new Color8Bit(Color.kWhite))),
            };

    public RobotTelemetry() {
        super();
        Logger.recordMetadata("RobotType", Robot.config.getRobotType().name());

        Robot.swerve.registerTelemetry((b) -> telemeterize(b));
    }

    /* Accept the swerve drive state and telemeterize it to smartdashboard */
    public void telemeterize(DriveState state) {
        /* Telemeterize the pose */
        Pose2d pose = state.Pose;
        fieldTypePub.set("Field2d");
        fieldPub.set(new double[] {pose.getX(), pose.getY(), pose.getRotation().getDegrees()});

        /* Telemeterize the robot's general speeds */
        double currentTime = Utils.getCurrentTimeSeconds();
        double diffTime = currentTime - lastTime;
        lastTime = currentTime;
        Translation2d distanceDiff = pose.minus(m_lastPose).getTranslation();
        m_lastPose = pose;

        Translation2d velocities = distanceDiff.div(diffTime);

        speed.set(velocities.getNorm());
        velocityX.set(velocities.getX());
        velocityY.set(velocities.getY());
        odomPeriod.set(state.OdometryPeriod);

        /* Telemeterize the module's states */
        for (int i = 0; i < 4; ++i) {
            m_moduleSpeeds[i].setAngle(state.ModuleStates[i].angle);
            m_moduleDirections[i].setAngle(state.ModuleStates[i].angle);
            m_moduleSpeeds[i].setLength(state.ModuleStates[i].speedMetersPerSecond / (2 * 6));

            SmartDashboard.putData("Module " + i, m_moduleMechanisms[i]);
        }
    }
}

src/main/java/frc/robot/swerve/configs/NOTEBLOCK2023.java
public class NOTEBLOCK2023 {

    // Angle Offsets
    private static final double kFrontLeftCANcoderOffset = -0.407958984375;
    private static final double kFrontRightCANncoderOffset = -0.181396484375;
    private static final double kBackLeftCANcoderOffset = -0.8779296875;
    private static final double kBackRightCANcoderOffset = -0.84130859375;

    // Physical Config
    private static final double wheelBaseInches = 21.5;
    private static final double trackWidthInches = 18.5;
    private static final double kDriveGearRatio = 6.746;
    private static final double kSteerGearRatio = 21.428;

    // Tuning Config
    // Estimated at first, then fudge-factored to make odom match record
    private static final double kWheelRadiusInches = 2;
    private static final double speedAt12VoltsMps = 6;
    private static final double slipCurrent = 800;
    private static final SlotGains steerGains = new SlotGains(100, 0, 0.05, 0, 0);
    private static final SlotGains driveGains = new SlotGains(0.4, 0, 0, 0, 0);

    /*Rotation Controller*/
    private static final double kPRotationController = 0.0;
    private static final double kIRotationController = 0.0;
    private static final double kDRotationController = 0.0;

    /*Profiling Configs*/
    private static final double maxVelocity = speedAt12VoltsMps;
    private static final double maxAccel = maxVelocity * 1.5; // take 1/2 sec to get to max speed.
    private static final double maxAngularVelocity =
            maxVelocity
                    / Units.inchesToMeters(
                            Math.hypot(wheelBaseInches / 2.0, trackWidthInches / 2.0));
    private static final double maxAngularAcceleration = Math.pow(maxAngularVelocity, 2);

    // Device Setup
    private static final String kCANbusName = "3847";
    private static final boolean supportsPro = true;
    private static final SwerveModuleSteerFeedbackType steerFeedbackType =
            SwerveModuleSteerFeedbackType.FusedCANcoder;

    // Wheel Positions
    private static final double kFrontLeftXPos = Units.inchesToMeters(wheelBaseInches / 2.0);
    private static final double kFrontLeftYPos = Units.inchesToMeters(trackWidthInches / 2.0);
    private static final double kFrontRightXPos = Units.inchesToMeters(wheelBaseInches / 2.0);
    private static final double kFrontRightYPos = Units.inchesToMeters(-trackWidthInches / 2.0);
    private static final double kBackLeftXPos = Units.inchesToMeters(-wheelBaseInches / 2.0);
    private static final double kBackLeftYPos = Units.inchesToMeters(trackWidthInches / 2.0);
    private static final double kBackRightXPos = Units.inchesToMeters(-wheelBaseInches / 2.0);
    private static final double kBackRightYPos = Units.inchesToMeters(-trackWidthInches / 2.0);

    public static final ModuleConfig FrontLeft =
            DefaultConfig.FrontLeft.withCANcoderOffset(kFrontLeftCANcoderOffset)
                    .withLocationX(kFrontLeftXPos)
                    .withLocationY(kFrontLeftYPos)
                    .withSlipCurrent(slipCurrent)
                    .withSpeedAt12VoltsMps(speedAt12VoltsMps)
                    .withDriveMotorGearRatio(kDriveGearRatio)
                    .withSteerMotorGearRatio(kSteerGearRatio)
                    .withDriveMotorGains(driveGains)
                    .withSteerMotorGains(steerGains)
                    .withWheelRadius(kWheelRadiusInches)
                    .withFeedbackSource(steerFeedbackType);

    public static final ModuleConfig FrontRight =
            DefaultConfig.FrontRight.withCANcoderOffset(kFrontRightCANncoderOffset)
                    .withLocationX(kFrontRightXPos)
                    .withLocationY(kFrontRightYPos)
                    .withSlipCurrent(slipCurrent)
                    .withSpeedAt12VoltsMps(speedAt12VoltsMps)
                    .withDriveMotorGearRatio(kDriveGearRatio)
                    .withSteerMotorGearRatio(kSteerGearRatio)
                    .withDriveMotorGains(driveGains)
                    .withSteerMotorGains(steerGains)
                    .withWheelRadius(kWheelRadiusInches)
                    .withFeedbackSource(steerFeedbackType);

    public static final ModuleConfig BackLeft =
            DefaultConfig.BackLeft.withCANcoderOffset(kBackLeftCANcoderOffset)
                    .withLocationX(kBackLeftXPos)
                    .withLocationY(kBackLeftYPos)
                    .withSlipCurrent(slipCurrent)
                    .withSpeedAt12VoltsMps(speedAt12VoltsMps)
                    .withDriveMotorGearRatio(kDriveGearRatio)
                    .withSteerMotorGearRatio(kSteerGearRatio)
                    .withDriveMotorGains(driveGains)
                    .withSteerMotorGains(steerGains)
                    .withWheelRadius(kWheelRadiusInches)
                    .withFeedbackSource(steerFeedbackType);

    public static final ModuleConfig BackRight =
            DefaultConfig.BackRight.withCANcoderOffset(kBackRightCANcoderOffset)
                    .withLocationX(kBackRightXPos)
                    .withLocationY(kBackRightYPos)
                    .withSlipCurrent(slipCurrent)
                    .withSpeedAt12VoltsMps(speedAt12VoltsMps)
                    .withDriveMotorGearRatio(kDriveGearRatio)
                    .withSteerMotorGearRatio(kSteerGearRatio)
                    .withDriveMotorGains(driveGains)
                    .withSteerMotorGains(steerGains)
                    .withWheelRadius(kWheelRadiusInches)
                    .withFeedbackSource(steerFeedbackType);

    public static final ModuleConfig[] ModuleConfigs = {FrontLeft, FrontRight, BackLeft, BackRight};

    public static final SwerveConfig config =
            DefaultConfig.DrivetrainConstants.withCANbusName(kCANbusName)
                    .withSupportsPro(supportsPro)
                    .withModules(ModuleConfigs)
                    .withRotationGains(
                            kPRotationController, kIRotationController, kDRotationController)
                    .withProfilingConfigs(
                            maxVelocity, maxAccel, maxAngularVelocity, maxAngularAcceleration);
}

src/main/java/frc/spectrumLib/swerve/config/SwerveConfig.java
public class SwerveConfig {
    /** CAN ID of the Pigeon2 on the drivetrain */
    public int Pigeon2Id = 0;
    /** Name of CANivore the swerve drive is on */
    public String CANbusName = "rio";

    /** If using Pro, specify this as true to make use of all the Pro features */
    public boolean SupportsPro = false;

    public ModuleConfig[] modules = new ModuleConfig[0];

    /*Rotation Controller*/
    public double kPRotationController = 0.0;
    public double kIRotationController = 0.0;
    public double kDRotationController = 0.0;

    /*Profiling Configs*/
    public double maxVelocity = 0;
    public double maxAccel = maxVelocity * 1.5; // take 1/2 sec to get to max speed.
    public double maxAngularVelocity = Math.PI * 2;
    public double maxAngularAcceleration = Math.pow(maxAngularVelocity, 2);

    public SwerveConfig withPigeon2Id(int id) {
        this.Pigeon2Id = id;
        return this;
    }

    public SwerveConfig withCANbusName(String name) {
        this.CANbusName = name;
        return this;
    }

    public SwerveConfig withSupportsPro(boolean supportsPro) {
        this.SupportsPro = supportsPro;
        return this;
    }

    public SwerveConfig withModules(ModuleConfig[] modules) {
        this.modules = modules;
        return this;
    }

    public SwerveConfig withRotationGains(double kP, double kI, double kD) {
        this.kPRotationController = kP;
        this.kIRotationController = kI;
        this.kDRotationController = kD;
        return this;
    }

    public SwerveConfig withProfilingConfigs(
            double maxVelocity,
            double maxAccel,
            double maxAngularVelocity,
            double maxAngularAcceleration) {
        this.maxVelocity = maxVelocity;
        this.maxAccel = maxAccel;
        this.maxAngularVelocity = maxAngularVelocity;
        this.maxAngularAcceleration = maxAngularAcceleration;
        return this;
    }
}

src/main/java/frc/spectrumLib/swerve/Drivetrain.java
public class DriveState {
    public int SuccessfulDaqs;
    public int FailedDaqs;
    public Pose2d Pose = new Pose2d();
    public SwerveModuleState[] ModuleStates = new SwerveModuleState[] {};
    public double OdometryPeriod;
}

src/main/java/frc/spectrumLib/swerve/Request.java
public interface Request {

    /*
     * Contains everything the control requests need to calculate the module state
     */
    public class ControlRequestParameters {
        public SwerveDriveKinematics kinematics;
        public Pose2d currentPose;
        public double timestamp;
        public Translation2d[] swervePositions;
        public double updatePeriod;
    }

    public StatusCode apply(ControlRequestParameters parameters, Module... modulesToApply);

    /**
     * Does nothing to the swerve module state. This is the default state of a newly created swerve
     * drive mechanism.
     */
    public class Idle implements Request {

        /** True to use open-loop control while stopped. */
        public boolean IsOpenLoop = false;

        public StatusCode apply(ControlRequestParameters parameters, Module... modulesToApply) {

            return StatusCode.OK;
        }

        public Idle withIsOpenLoop(boolean isOpenLoop) {
            this.IsOpenLoop = isOpenLoop;
            return this;
        }
    }
}

src/main/java/frc/spectrumLib/swerve/Drivetrain.java
public class Drivetrain {
    protected final int ModuleCount;
    protected final double UpdateFrequency;
    protected final Module[] Modules;

    protected Pigeon2 m_pigeon2;
    protected SwerveDriveKinematics m_kinematics;
    protected SwerveDrivePoseEstimator m_odometry;
    protected SwerveModulePosition[] m_modulePositions;
    protected Translation2d[] m_moduleLocations;
    protected OdometryThread m_odometryThread;
    protected Rotation2d m_fieldRelativeOffset;
    protected StatusSignal<Double> m_yawGetter;
    protected StatusSignal<Double> m_angularZGetter;

    protected Request m_requestToApply = new Request.Idle();
    protected ControlRequestParameters m_requestParameters = new ControlRequestParameters();

    protected ReadWriteLock m_stateLock = new ReentrantReadWriteLock();

    protected final SimDrivetrain m_simDrive;
    protected final boolean IsOnCANFD;

    /**
     * Plain-Old-Data class holding the state of the swerve drivetrain. This encapsulates most data
     * that is relevant for telemetry or decision-making from the Swerve Drive.
     */
    public class DriveState {
        public int SuccessfulDaqs;
        public int FailedDaqs;
        public Pose2d Pose = new Pose2d();
        public SwerveModuleState[] ModuleStates = new SwerveModuleState[] {};
        public double OdometryPeriod;
    }

    protected Consumer<DriveState> m_telemetryFunction = null;
    protected DriveState m_cachedState = new DriveState();

    /* Perform swerve module updates in a separate thread to minimize latency */
    public class OdometryThread extends Thread {
        private final int START_THREAD_PRIORITY =
                1; // Testing shows 1 (minimum realtime) is sufficient for tighter
        // odometry loops.
        // If the odometry period is far away from the desired frequency,
        // increasing this may help

        private BaseStatusSignal[] m_allSignals;
        public int SuccessfulDaqs = 0;
        public int FailedDaqs = 0;
        MedianFilter peakRemover = new MedianFilter(3);
        LinearFilter lowPass = LinearFilter.movingAverage(50);
        double lastTime = 0;
        double currentTime = 0;
        double averageLoopTime = 0;

        int lastThreadPriority = START_THREAD_PRIORITY;
        int threadPriorityToSet = START_THREAD_PRIORITY;

        public OdometryThread() {
            super();
            // 4 signals for each module + 2 for Pigeon2
            m_allSignals = new BaseStatusSignal[(ModuleCount * 4) + 2];
            for (int i = 0; i < ModuleCount; ++i) {
                BaseStatusSignal[] signals = Modules[i].getSignals();
                m_allSignals[(i * 4) + 0] = signals[0];
                m_allSignals[(i * 4) + 1] = signals[1];
                m_allSignals[(i * 4) + 2] = signals[2];
                m_allSignals[(i * 4) + 3] = signals[3];
            }
            m_allSignals[m_allSignals.length - 2] = m_yawGetter;
            m_allSignals[m_allSignals.length - 1] = m_angularZGetter;
        }

        @Override
        public void run() {
            /* Make sure all signals update at around 250hz */
            for (BaseStatusSignal sig : m_allSignals) {
                sig.setUpdateFrequency(UpdateFrequency);
            }
            Threads.setCurrentThreadPriority(true, START_THREAD_PRIORITY);

            /* Run as fast as possible, our signals will control the timing */
            while (true) {
                /* Synchronously wait for all signals in drivetrain */
                /* Wait up to twice the period of the update frequency */
                StatusCode status;
                if (IsOnCANFD) {
                    status = BaseStatusSignal.waitForAll(2.0 / UpdateFrequency, m_allSignals);
                } else {
                    try {
                        /* Wait for the signals to update */
                        Thread.sleep((long) ((1.0 / UpdateFrequency) * 1000.0));
                    } catch (InterruptedException ex) {
                    }
                    status = BaseStatusSignal.refreshAll(m_allSignals);
                }
                m_stateLock.writeLock().lock();

                lastTime = currentTime;
                currentTime = Utils.getCurrentTimeSeconds();
                /* We don't care about the peaks, as they correspond to GC events, and we want the period generally low passed */
                averageLoopTime = lowPass.calculate(peakRemover.calculate(currentTime - lastTime));

                /* Get status of first element */
                if (status.isOK()) {
                    SuccessfulDaqs++;
                } else {
                    FailedDaqs++;
                }

                /* Now update odometry */
                /* Keep track of the change in azimuth rotations */
                for (int i = 0; i < ModuleCount; ++i) {
                    m_modulePositions[i] = Modules[i].getPosition(false);
                }
                // Assume Pigeon2 is flat-and-level so latency compensation can be performed
                double yawDegrees =
                        BaseStatusSignal.getLatencyCompensatedValue(m_yawGetter, m_angularZGetter);

                /* Keep track of previous and current pose to account for the carpet vector */
                m_odometry.update(Rotation2d.fromDegrees(yawDegrees), m_modulePositions);

                /* And now that we've got the new odometry, update the controls */
                m_requestParameters.currentPose =
                        m_odometry
                                .getEstimatedPosition()
                                .relativeTo(new Pose2d(0, 0, m_fieldRelativeOffset));
                m_requestParameters.kinematics = m_kinematics;
                m_requestParameters.swervePositions = m_moduleLocations;
                m_requestParameters.timestamp = currentTime;
                m_requestParameters.updatePeriod = 1.0 / UpdateFrequency;

                m_requestToApply.apply(m_requestParameters, Modules);

                /* Update our cached state with the newly updated data */
                m_cachedState.FailedDaqs = FailedDaqs;
                m_cachedState.SuccessfulDaqs = SuccessfulDaqs;
                m_cachedState.ModuleStates = new SwerveModuleState[Modules.length];
                for (int i = 0; i < Modules.length; ++i) {
                    m_cachedState.ModuleStates[i] = Modules[i].getCurrentState();
                }
                m_cachedState.Pose = m_odometry.getEstimatedPosition();
                m_cachedState.OdometryPeriod = averageLoopTime;

                if (m_telemetryFunction != null) {
                    /* Log our state */
                    m_telemetryFunction.accept(m_cachedState);
                }

                m_stateLock.writeLock().unlock();
                /**
                 * This is inherently synchronous, since lastThreadPriority is only written here and
                 * threadPriorityToSet is only read here
                 */
                if (threadPriorityToSet != lastThreadPriority) {
                    Threads.setCurrentThreadPriority(true, threadPriorityToSet);
                    lastThreadPriority = threadPriorityToSet;
                }
            }
        }

        public boolean odometryIsValid() {
            return SuccessfulDaqs > 2; // Wait at least 3 daqs before saying the odometry is valid
        }

        /**
         * Sets the DAQ thread priority to a real time priority under the specified priority level
         *
         * @param priority Priority level to set the DAQ thread to. This is a value between 0 and
         *     99, with 99 indicating higher priority and 0 indicating lower priority.
         */
        public void setThreadPriority(int priority) {
            threadPriorityToSet = priority;
        }
    }

    protected boolean checkIsOnCanFD(String canbusName) {
        return Unmanaged.isNetworkFD(canbusName);
    }

    /**
     * Constructs a CTRSwerveDrivetrain using the specified constants.
     *
     * <p>This constructs the underlying hardware devices, so user should not construct the devices
     * themselves. If they need the devices, they can access them through getters in the classes.
     *
     * @param swerveConfig Drivetrain-wide constants for the swerve drive
     * @param modules Constants for each specific module
     */
    public Drivetrain(SwerveConfig swerveConfig) {
        this(swerveConfig, 250);
    }

    /**
     * Constructs a CTRSwerveDrivetrain using the specified constants.
     *
     * <p>This constructs the underlying hardware devices, so user should not construct the devices
     * themselves. If they need the devices, they can access them through getters in the classes.
     *
     * @param swerveConfig Drivetrain-wide constants for the swerve drive
     * @param OdometryUpdateFrequency The frequency to run the odometry loop. If unspecified, this
     *     is 250 hz.
     * @param modules Constants for each specific module
     */
    public Drivetrain(SwerveConfig swerveConfig, double OdometryUpdateFrequency) {
        ModuleConfig[] moduleConfigs = swerveConfig.modules;
        UpdateFrequency = OdometryUpdateFrequency;
        ModuleCount = moduleConfigs.length;

        IsOnCANFD = checkIsOnCanFD(swerveConfig.CANbusName);

        m_pigeon2 = new Pigeon2(swerveConfig.Pigeon2Id, swerveConfig.CANbusName);
        m_yawGetter = m_pigeon2.getYaw().clone();
        m_angularZGetter = m_pigeon2.getAngularVelocityZ().clone();

        Modules = new Module[ModuleCount];
        m_modulePositions = new SwerveModulePosition[ModuleCount];
        m_moduleLocations = new Translation2d[ModuleCount];

        int iteration = 0;
        for (ModuleConfig module : moduleConfigs) {
            Modules[iteration] =
                    new Module(module, swerveConfig.CANbusName, swerveConfig.SupportsPro);
            m_moduleLocations[iteration] = new Translation2d(module.LocationX, module.LocationY);
            m_modulePositions[iteration] = Modules[iteration].getPosition(true);

            iteration++;
        }
        m_kinematics = new SwerveDriveKinematics(m_moduleLocations);
        m_odometry =
                new SwerveDrivePoseEstimator(
                        m_kinematics, new Rotation2d(), m_modulePositions, new Pose2d());

        m_fieldRelativeOffset = new Rotation2d();

        m_simDrive = new SimDrivetrain(m_moduleLocations, m_pigeon2, swerveConfig, moduleConfigs);

        m_odometryThread = new OdometryThread();
        RobotTelemetry.print("Starting Odometry Thread: ");
        m_odometryThread.start();
    }

    /**
     * Gets a reference to the data acquisition thread.
     *
     * @return DAQ thread
     */
    public OdometryThread getDaqThread() {
        return m_odometryThread;
    }

    /**
     * Applies the specified control request to this swerve drivetrain.
     *
     * @param request Request to apply
     */
    public void setControl(Request request) {
        try {
            m_stateLock.writeLock().lock();

            m_requestToApply = request;
        } finally {
            m_stateLock.writeLock().unlock();
        }
    }

    /**
     * Zero's this swerve drive's odometry entirely.
     *
     * <p>This will zero the entire odometry, and place the robot at 0,0
     */
    public void tareEverything() {
        try {
            m_stateLock.writeLock().lock();

            for (int i = 0; i < ModuleCount; ++i) {
                Modules[i].resetPosition();
                m_modulePositions[i] = Modules[i].getPosition(true);
            }
            m_odometry.resetPosition(m_pigeon2.getRotation2d(), m_modulePositions, new Pose2d());
        } finally {
            m_stateLock.writeLock().unlock();
        }
    }

    /**
     * Takes the current orientation of the robot and makes it X forward for field-relative
     * maneuvers.
     */
    public void seedFieldRelative() {
        try {
            m_stateLock.writeLock().lock();

            m_fieldRelativeOffset = getState().Pose.getRotation();
        } finally {
            m_stateLock.writeLock().unlock();
        }
    }

    /**
     * Takes the current orientation of the robot plus an angle offset and makes it X forward for
     * field-relative maneuvers.
     */
    public void seedFieldRelative(double offsetDegrees) {
        try {
            m_stateLock.writeLock().lock();

            m_fieldRelativeOffset =
                    getState().Pose.getRotation().plus(Rotation2d.fromDegrees(offsetDegrees));
        } finally {
            m_stateLock.writeLock().unlock();
        }
    }

    /**
     * Takes the specified location and makes it the current pose for field-relative maneuvers
     *
     * @param location Pose to make the current pose at.
     */
    public void seedFieldRelative(Pose2d location) {
        try {
            m_stateLock.writeLock().lock();

            m_odometry.resetPosition(
                    Rotation2d.fromDegrees(m_yawGetter.getValue()), m_modulePositions, location);
        } finally {
            m_stateLock.writeLock().unlock();
        }
    }

    /**
     * Check if the odometry is currently valid
     *
     * @return True if odometry is valid
     */
    public boolean odometryIsValid() {
        try {
            m_stateLock.readLock().lock();

            return m_odometryThread.odometryIsValid();
        } finally {
            m_stateLock.readLock().unlock();
        }
    }

    /**
     * Get a reference to the module at the specified index. The index corresponds to the module
     * described in the constructor
     *
     * @param index Which module to get
     * @return Reference to SwerveModule
     */
    public Module getModule(int index) {
        if (index >= Modules.length) return null;
        return Modules[index];
    }

    /**
     * Gets the current state of the swerve drivetrain.
     *
     * @return Current state of the drivetrain
     */
    public DriveState getState() {
        try {
            m_stateLock.readLock().lock();

            return m_cachedState;
        } finally {
            m_stateLock.readLock().unlock();
        }
    }

    /**
     * Get the current module states from the cached state
     *
     * @return
     */
    public SwerveModuleState[] getModuleStates() {
        return getState().ModuleStates;
    }

    /**
     * Get the current chassis speeds from the cached state
     *
     * @return
     */
    public ChassisSpeeds getChassisSpeeds() {
        return m_kinematics.toChassisSpeeds(getModuleStates());
    }

    /**
     * Adds a vision measurement to the Kalman Filter. This will correct the odometry pose estimate
     * while still accounting for measurement noise.
     *
     * <p>This method can be called as infrequently as you want, as long as you are calling {@link
     * SwerveDrivePoseEstimator#update} every loop.
     *
     * <p>To promote stability of the pose estimate and make it robust to bad vision data, we
     * recommend only adding vision measurements that are already within one meter or so of the
     * current pose estimate.
     *
     * <p>Note that the vision measurement standard deviations passed into this method will continue
     * to apply to future measurements until a subsequent call to {@link
     * SwerveDrivePoseEstimator#setVisionMeasurementStdDevs(Matrix)} or this method.
     *
     * @param visionRobotPoseMeters The pose of the robot as measured by the vision camera.
     * @param timestampSeconds The timestamp of the vision measurement in seconds. Note that if you
     *     don't use your own time source by calling {@link
     *     SwerveDrivePoseEstimator#updateWithTime(double,Rotation2d,SwerveModulePosition[])}, then
     *     you must use a timestamp with an epoch since FPGA startup (i.e., the epoch of this
     *     timestamp is the same epoch as {@link edu.wpi.first.wpilibj.Timer#getFPGATimestamp()}).
     *     This means that you should use {@link edu.wpi.first.wpilibj.Timer#getFPGATimestamp()} as
     *     your time source in this case.
     * @param visionMeasurementStdDevs Standard deviations of the vision pose measurement (x
     *     position in meters, y position in meters, and heading in radians). Increase these numbers
     *     to trust the vision pose measurement less.
     */
    public void addVisionMeasurement(
            Pose2d visionRobotPoseMeters,
            double timestampSeconds,
            Matrix<N3, N1> visionMeasurementStdDevs) {
        try {
            m_stateLock.writeLock().lock();
            m_odometry.addVisionMeasurement(
                    visionRobotPoseMeters, timestampSeconds, visionMeasurementStdDevs);
        } finally {
            m_stateLock.writeLock().unlock();
        }
    }

    /**
     * Adds a vision measurement to the Kalman Filter. This will correct the odometry pose estimate
     * while still accounting for measurement noise.
     *
     * <p>This method can be called as infrequently as you want, as long as you are calling {@link
     * SwerveDrivePoseEstimator#update} every loop.
     *
     * <p>To promote stability of the pose estimate and make it robust to bad vision data, we
     * recommend only adding vision measurements that are already within one meter or so of the
     * current pose estimate.
     *
     * @param visionRobotPoseMeters The pose of the robot as measured by the vision camera.
     * @param timestampSeconds The timestamp of the vision measurement in seconds. Note that if you
     *     don't use your own time source by calling {@link
     *     SwerveDrivePoseEstimator#updateWithTime(double,Rotation2d,SwerveModulePosition[])} then
     *     you must use a timestamp with an epoch since FPGA startup (i.e., the epoch of this
     *     timestamp is the same epoch as {@link edu.wpi.first.wpilibj.Timer#getFPGATimestamp()}.)
     *     This means that you should use {@link edu.wpi.first.wpilibj.Timer#getFPGATimestamp()} as
     *     your time source or sync the epochs.
     */
    public void addVisionMeasurement(Pose2d visionRobotPoseMeters, double timestampSeconds) {
        try {
            m_stateLock.writeLock().lock();
            m_odometry.addVisionMeasurement(visionRobotPoseMeters, timestampSeconds);
        } finally {
            m_stateLock.writeLock().unlock();
        }
    }

    /**
     * Sets the pose estimator's trust of global measurements. This might be used to change trust in
     * vision measurements after the autonomous period, or to change trust as distance to a vision
     * target increases.
     *
     * @param visionMeasurementStdDevs Standard deviations of the vision measurements. Increase
     *     these numbers to trust global measurements from vision less. This matrix is in the form
     *     [x, y, theta]ᵀ, with units in meters and radians.
     */
    public void setVisionMeasurementStdDevs(Matrix<N3, N1> visionMeasurementStdDevs) {
        try {
            m_stateLock.writeLock().lock();
            m_odometry.setVisionMeasurementStdDevs(visionMeasurementStdDevs);
        } finally {
            m_stateLock.writeLock().unlock();
        }
    }

    /**
     * Updates all the simulation state variables for this drivetrain class. User provides the
     * update variables for the simulation.
     *
     * @param dtSeconds time since last update call
     * @param supplyVoltage voltage as seen at the motor controllers
     */
    public void updateSimState(double dtSeconds, double supplyVoltage) {
        m_simDrive.update(dtSeconds, supplyVoltage, Modules);
    }

    /**
     * Register the specified lambda to be executed whenever our SwerveDriveState function is
     * updated in our odometry thread.
     *
     * <p>It is imperative that this function is cheap, as it will be executed along with the
     * odometry call, and if this takes a long time, it may negatively impact the odometry of this
     * stack.
     *
     * <p>This can also be used for logging data if the function performs logging instead of
     * telemetry
     *
     * @param telemetryFunction Function to call for telemetry or logging
     */
    public void registerTelemetry(Consumer<DriveState> telemetryFunction) {
        m_telemetryFunction = telemetryFunction;
    }
}

Answer: drivetrain = new Drivetrain(config, OdometryUpdateFrequency);

<think>
After the switch that selects the appropriate SwerveConfig and possibly adjusts OdometryUpdateFrequency, the constructor needs to create the drivetrain using those values. The Drivetrain class has a constructor taking a SwerveConfig and an update frequency, so the next line should instantiate it and assign to the drivetrain field.
</think>
drivetrain = new Drivetrain(config, OdometryUpdateFrequency);