dmyersturnbull

# SPDX-FileCopyrightText: Copyright 2020-2024, Contributors
# SPDX-PackageHomePage: https://gist.github.com/dmyersturnbull
# SPDX-License-Identifier: Apache-2.0

"""
Tool to diff two order-independent sets of lines.
"""

import math
import sys

dmyersturnbull

/**
 * Recommended exit codes from {@code /usr/include/sysexits.h}.
 */
public final class ExitStatus {
    public static final int OK = 0;
    public static final int GENERIC_ERROR = 1;
    public static final int BASE = 64;
    public static final int USAGE = 64;
    public static final int NO_DATA = 65;
    public static final int NO_INPUT = 66;

dmyersturnbull

*.backup
/data

dmyersturnbull

[metadata]
description-file = "README.md"

[build-system]
requires = ["poetry>=1.0", "coverage[toml]"]
build-backend = "poetry.masonry.api"


#########################################################################################
# Poetry metadata

dmyersturnbull

import argparse, sys, re, logging
from pathlib import Path
from typing import Mapping, Any, Sequence, Collection
from typing import Tuple as Tup

logger = logging.getLogger('paperpile-latex')


class Paperpiler:

dmyersturnbull

[
    {
        "code": "100",
        "phrase": "Continue",
        "description": "The initial part of a request has been received and has not yet been rejected by the server.",
        "spec_title": "RFC7231#6.2.1",
        "spec_href": "https://tools.ietf.org/html/rfc7231#section-6.2.1"
    },
    {
        "code": "101",

dmyersturnbull

import sys
import re
from pathlib import Path

def fix(path: Path, accent_file: Path, output_path: Path) -> None:
    """
    Reformat my bib file.
    
    * Remove PMC and DOI URLs because they're listed as IDs anyway.
    * Replace accent-like escape characters with their UTF equivalents. I mean, it's 2020.

dmyersturnbull

See https://github.com/dmyersturnbull/genomics-io/tree/master/core/src/main/java/org/pharmgkb/parsers/escape

package org.pharmgkb.parsers.escape;

import com.google.common.base.Preconditions;
import com.google.common.collect.ImmutableSet;

import javax.annotation.Nonnull;
import javax.annotation.concurrent.NotThreadSafe;
import javax.annotation.concurrent.ThreadSafe;

dmyersturnbull

// copied from https://github.com/dmyersturnbull/genomics-io/blob/master/core/src/main/java/org/pharmgkb/parsers/utils/HttpHeadResponse.java
package org.pharmgkb.parsers.utils;

import com.google.common.collect.ImmutableMap;

import javax.annotation.Nonnegative;
import javax.annotation.Nonnull;
import javax.annotation.concurrent.Immutable;
import java.io.IOException;
import java.net.HttpURLConnection;

dmyersturnbull

// copied from https://github.com/dmyersturnbull/genomics-io/blob/master/core/src/main/java/org/pharmgkb/parsers/utils/Try.java

package org.pharmgkb.parsers.utils;

import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import java.util.Objects;
import java.util.Optional;
import java.util.function.Function;
import java.util.function.Supplier;