EvalAccuracyCommand.java

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// SPDX-License-Identifier: Apache-2.0
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// Copyright 2026 Egothor
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// Copyright 2026 Accenture
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package org.egothor.methodatlas.command;
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import java.io.IOException;
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import java.io.PrintWriter;
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import java.nio.file.Path;
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import java.util.Locale;
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import java.util.OptionalDouble;
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import org.egothor.methodatlas.eval.AccuracyEvaluator;
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import org.egothor.methodatlas.eval.AccuracyMetrics;
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import org.egothor.methodatlas.eval.AccuracyReportRenderer;
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/**
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 * Utility CLI mode ({@code -eval-accuracy}) that measures how accurate the AI
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 * classification is against a human-reviewed labelled set.
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 *
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 * <p>
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 * Synopsis:
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 * {@code methodatlas -eval-accuracy <labels.yaml> <predictions.csv> [-eval-format markdown|json] [-eval-min-f1 <0..1>]}
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 * </p>
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 *
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 * <ul>
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 * <li>{@code labels.yaml} — the ground truth, in the {@code -override-file}
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 *     format (the recommended source: those entries are already human-reviewed);</li>
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 * <li>{@code predictions.csv} — a scan CSV produced with {@code -ai} and
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 *     <em>without</em> {@code -override-file}, so the AI columns hold genuine AI
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 *     output;</li>
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 * <li>{@code -eval-format} — {@code markdown} (default) or {@code json};</li>
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 * <li>{@code -eval-min-f1} — optional gate: exit {@code 1} when the F1 of the
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 *     {@code securityRelevant} decision or the micro-averaged tag F1 is below the
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 *     threshold, or when neither could be computed (no labelled data — a gate must
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 *     not pass on no evidence).</li>
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 * </ul>
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 *
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 * <p>
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 * No scan runs and no AI provider is called: the command only reads the two
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 * files, so it is deterministic and offline. The report is written with
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 * {@code \n} line endings regardless of platform.
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 * </p>
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 *
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 * @see AccuracyEvaluator
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 * @see AccuracyMetrics
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 * @since 6.1.0
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 */
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public final class EvalAccuracyCommand implements Command {
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    /** Flag that selects this utility mode; takes two path arguments. */
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    public static final String FLAG_EVAL_ACCURACY = "-eval-accuracy";
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    /** Flag selecting the report format. */
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    public static final String FLAG_EVAL_FORMAT = "-eval-format";
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    /** Flag setting the minimum acceptable F1. */
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    public static final String FLAG_EVAL_MIN_F1 = "-eval-min-f1";
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    private static final int EXIT_GATE_FAILED = 1;
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    private static final String FORMAT_MARKDOWN = "markdown";
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    private static final String FORMAT_JSON = "json";
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    private static final int ARGS_AFTER_FLAG = 2;
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    private final Path labels;
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    private final Path predictions;
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    private final boolean json;
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    private final OptionalDouble minF1;
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    /**
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     * Creates a command.
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     *
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     * @param labels      override-format YAML with the human-reviewed labels
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     * @param predictions scan CSV produced with {@code -ai}
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     * @param json        {@code true} for JSON output, {@code false} for Markdown
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     * @param minF1       minimum acceptable F1 in {@code [0,1]}, or empty for no
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     *                    gate
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     */
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    public EvalAccuracyCommand(Path labels, Path predictions, boolean json, OptionalDouble minF1) {
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        this.labels = labels;
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        this.predictions = predictions;
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        this.json = json;
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        this.minF1 = minF1;
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    }
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    /**
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     * Builds the command from raw command-line arguments.
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     *
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     * @param args raw arguments; must contain {@code -eval-accuracy} followed by
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     *             the labels path and the predictions path
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     * @return a configured command; never {@code null}
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     * @throws IllegalArgumentException if the paths are missing, the format is
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     *                                  neither {@code markdown} nor {@code json},
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     *                                  or the threshold is not a number in
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     *                                  {@code [0,1]}
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     */
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    public static EvalAccuracyCommand fromArgs(String... args) {
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        int at = indexOf(args, FLAG_EVAL_ACCURACY);
98 7 1. fromArgs : removed conditional - replaced comparison check with true → SURVIVED
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        if (at < 0 || at + ARGS_AFTER_FLAG >= args.length) {
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            throw new IllegalArgumentException(
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                    FLAG_EVAL_ACCURACY + " requires two arguments: " + FLAG_EVAL_ACCURACY
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                            + " <labels.yaml> <predictions.csv>");
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        }
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        boolean asJson = false;
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        int fmt = indexOf(args, FLAG_EVAL_FORMAT);
105 3 1. fromArgs : changed conditional boundary → SURVIVED
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        if (fmt >= 0) {
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            String value = valueAfter(args, fmt, FLAG_EVAL_FORMAT).toLowerCase(Locale.ROOT);
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            if (FORMAT_JSON.equals(value)) {
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                asJson = true;
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            } else if (!FORMAT_MARKDOWN.equals(value)) {
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                throw new IllegalArgumentException(
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                        FLAG_EVAL_FORMAT + " must be 'markdown' or 'json', got: " + value);
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            }
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        }
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        OptionalDouble threshold = OptionalDouble.empty();
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        int min = indexOf(args, FLAG_EVAL_MIN_F1);
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        if (min >= 0) {
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            threshold = OptionalDouble.of(parseThreshold(valueAfter(args, min, FLAG_EVAL_MIN_F1)));
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        }
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        return new EvalAccuracyCommand(Path.of(args[at + 1]), Path.of(args[at + 2]), asJson, threshold);
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    }
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    /**
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     * Evaluates the predictions against the labels and writes the report.
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     *
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     * @param out writer that receives the report; never {@code null}
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     * @return {@code 0} on success or when no gate is set; {@code 1} when the
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     *         {@code -eval-min-f1} gate fails
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     * @throws IOException if either input file cannot be read or parsed
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     */
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    @Override
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    public int execute(PrintWriter out) throws IOException {
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        AccuracyEvaluator.Evaluation ev = AccuracyEvaluator.evaluate(labels, predictions);
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        out.print(json ? AccuracyReportRenderer.json(ev) : AccuracyReportRenderer.markdown(ev));
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        out.flush();
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        if (minF1.isEmpty()) {
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            return 0;
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        }
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        return gate(ev.metrics(), minF1.getAsDouble()) ? 0 : EXIT_GATE_FAILED;
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    }
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    /**
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     * Applies the F1 gate: every defined F1 among relevance and micro tags must
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     * reach the threshold, and at least one must be defined.
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     */
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    private static boolean gate(AccuracyMetrics.Result m, double threshold) {
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        OptionalDouble relevanceF1 = m.relevance().f1();
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        OptionalDouble tagF1 = m.tagsMicro().f1();
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        if (relevanceF1.isEmpty() && tagF1.isEmpty()) {
149 1 1. gate : replaced boolean return with true for org/egothor/methodatlas/command/EvalAccuracyCommand::gate → KILLED
 
            return false;
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        }
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        boolean relevanceOk = relevanceF1.isEmpty() || relevanceF1.getAsDouble() >= threshold;
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        boolean tagOk = tagF1.isEmpty() || tagF1.getAsDouble() >= threshold;
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        return relevanceOk && tagOk;
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    }
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    private static double parseThreshold(String text) {
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        double value;
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        try {
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            value = Double.parseDouble(text);
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        } catch (NumberFormatException e) {
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            throw new IllegalArgumentException(FLAG_EVAL_MIN_F1 + " must be a number in [0,1], got: " + text, e);
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        }
163 8 1. parseThreshold : removed conditional - replaced comparison check with true → SURVIVED
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        if (Double.isNaN(value) || value < 0.0 || value > 1.0) {
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            throw new IllegalArgumentException(FLAG_EVAL_MIN_F1 + " must be in [0,1], got: " + text);
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        }
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        return value;
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    }
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    private static String valueAfter(String[] args, int flagIndex, String flag) {
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        if (flagIndex + 1 >= args.length) {
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            throw new IllegalArgumentException(flag + " requires a value");
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        }
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        return args[flagIndex + 1];
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    }
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    private static int indexOf(String[] args, String flag) {
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        for (int i = 0; i < args.length; i++) {
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            if (flag.equals(args[i])) {
179 1 1. indexOf : replaced int return with 0 for org/egothor/methodatlas/command/EvalAccuracyCommand::indexOf → KILLED
 
                return i;
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            }
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        }
182 1 1. indexOf : replaced int return with 0 for org/egothor/methodatlas/command/EvalAccuracyCommand::indexOf → KILLED
 
        return -1;
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    }
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}

Mutations

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1.1
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2.2
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3.3
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4.4
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5.5
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2.2
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3.3
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2.2
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2.2
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3.3
Location : fromArgs
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2.2
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3.3
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2.2
Location : execute
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2.2
Location : execute
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2.2
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3.3
Location : execute
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148

1.1
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2.2
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3.3
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4.4
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3.3
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4.4
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5.5
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152

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2.2
Location : gate
Killed by : org.egothor.methodatlas.command.EvalAccuracyCommandTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.command.EvalAccuracyCommandTest]/[method:gateFailsBelowThresholdAndPassesAtOrAbove()] changed conditional boundary → KILLED

3.3
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4.4
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2.2
Location : gate
Killed by : org.egothor.methodatlas.command.EvalAccuracyCommandTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.command.EvalAccuracyCommandTest]/[method:gateFailsBelowThresholdAndPassesAtOrAbove()] removed conditional - replaced equality check with false → KILLED

3.3
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4.4
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5.5
Location : gate
Killed by : org.egothor.methodatlas.command.EvalAccuracyCommandTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.command.EvalAccuracyCommandTest]/[method:gateFailsBelowThresholdAndPassesAtOrAbove()] replaced boolean return with true for org/egothor/methodatlas/command/EvalAccuracyCommand::gate → KILLED

163

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2.2
Location : parseThreshold
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3.3
Location : parseThreshold
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4.4
Location : parseThreshold
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5.5
Location : parseThreshold
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6.6
Location : parseThreshold
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7.7
Location : parseThreshold
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8.8
Location : parseThreshold
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166

1.1
Location : parseThreshold
Killed by : org.egothor.methodatlas.command.EvalAccuracyCommandTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.command.EvalAccuracyCommandTest]/[method:gateFailsBelowThresholdAndPassesAtOrAbove()] replaced double return with 0.0d for org/egothor/methodatlas/command/EvalAccuracyCommand::parseThreshold → KILLED

170

1.1
Location : valueAfter
Killed by : org.egothor.methodatlas.command.EvalAccuracyCommandTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.command.EvalAccuracyCommandTest]/[method:invalidArgumentsAreRejected()] removed conditional - replaced comparison check with false → KILLED

2.2
Location : valueAfter
Killed by : org.egothor.methodatlas.command.EvalAccuracyCommandTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.command.EvalAccuracyCommandTest]/[method:invalidArgumentsAreRejected()] Replaced integer addition with subtraction → KILLED

3.3
Location : valueAfter
Killed by : org.egothor.methodatlas.command.EvalAccuracyCommandTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.command.EvalAccuracyCommandTest]/[method:jsonFormatIsSelectable()] removed conditional - replaced comparison check with true → KILLED

4.4
Location : valueAfter
Killed by : org.egothor.methodatlas.command.EvalAccuracyCommandTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.command.EvalAccuracyCommandTest]/[method:invalidArgumentsAreRejected()] changed conditional boundary → KILLED

173

1.1
Location : valueAfter
Killed by : org.egothor.methodatlas.command.EvalAccuracyCommandTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.command.EvalAccuracyCommandTest]/[method:jsonFormatIsSelectable()] Replaced integer addition with subtraction → KILLED

2.2
Location : valueAfter
Killed by : org.egothor.methodatlas.command.EvalAccuracyCommandTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.command.EvalAccuracyCommandTest]/[method:jsonFormatIsSelectable()] replaced return value with "" for org/egothor/methodatlas/command/EvalAccuracyCommand::valueAfter → KILLED

177

1.1
Location : indexOf
Killed by : org.egothor.methodatlas.command.EvalAccuracyCommandTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.command.EvalAccuracyCommandTest]/[method:defaultsToMarkdownAndExitsZeroWithoutGate()] removed conditional - replaced comparison check with false → KILLED

2.2
Location : indexOf
Killed by : org.egothor.methodatlas.command.EvalAccuracyCommandTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.command.EvalAccuracyCommandTest]/[method:invalidArgumentsAreRejected()] changed conditional boundary → KILLED

3.3
Location : indexOf
Killed by : org.egothor.methodatlas.command.EvalAccuracyCommandTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.command.EvalAccuracyCommandTest]/[method:invalidArgumentsAreRejected()] removed conditional - replaced comparison check with true → KILLED

178

1.1
Location : indexOf
Killed by : org.egothor.methodatlas.command.EvalAccuracyCommandTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.command.EvalAccuracyCommandTest]/[method:defaultsToMarkdownAndExitsZeroWithoutGate()] removed conditional - replaced equality check with true → KILLED

2.2
Location : indexOf
Killed by : org.egothor.methodatlas.command.EvalAccuracyCommandTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.command.EvalAccuracyCommandTest]/[method:defaultsToMarkdownAndExitsZeroWithoutGate()] removed conditional - replaced equality check with false → KILLED

179

1.1
Location : indexOf
Killed by : org.egothor.methodatlas.command.EvalAccuracyCommandTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.command.EvalAccuracyCommandTest]/[method:jsonFormatIsSelectable()] replaced int return with 0 for org/egothor/methodatlas/command/EvalAccuracyCommand::indexOf → KILLED

182

1.1
Location : indexOf
Killed by : org.egothor.methodatlas.command.EvalAccuracyCommandTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.command.EvalAccuracyCommandTest]/[method:defaultsToMarkdownAndExitsZeroWithoutGate()] replaced int return with 0 for org/egothor/methodatlas/command/EvalAccuracyCommand::indexOf → KILLED

Active mutators

Tests examined


Report generated by PIT 1.30.1 support