tsibley

From ac5609c2f0cb65886fe6e7e8f41971b3ce1807f3 Mon Sep 17 00:00:00 2001
From: Thomas Sibley <[email protected]>
Date: Wed, 12 Feb 2025 13:24:59 -0800
Subject: [PATCH] Excise Vercel's sponsorship

It's no more.
---
 README.md                                     | 20 -------------------
 .../src/assets/img/powered-by-vercel.svg      |  1 -
 .../src/components/Layout/Footer.tsx          |  5 -----

tsibley

$ augur export v2 --tree test.nwk --metadata test.tsv --metadata-columns accession url --output test.json
WARNING: You didn't provide information on who is maintaining this analysis.

Validating produced JSON
Validating schema of 'test.json'...
Validating that the JSON is internally consistent...
Validation of 'test.json' succeeded.

tsibley

#!/usr/bin/env python3
from copy import copy
from shutil import copyfileobj
from sys import argv, stderr
from zipfile import ZipFile

zi = ZipFile(argv[1], "r")
zo = ZipFile(argv[2], "w")
xform = argv[3]

tsibley

def pathogen_version_for_setup(name_version_url: str) -> "PathogenVersion":
    # XXX FIXME docstring
    """
    TKTK
    """
    name, version, url = spec = PathogenSpec.parse(name_version_url)

    if not name:
        raise UserError(f"""
            No name specified in {name_version_url!r}.

tsibley

#!/bin/python3
from argparse import ArgumentParser, ArgumentError
from contextlib import contextmanager


@contextmanager
def scoped_setattr(obj, name, value):
    dne = object()

    try:

tsibley

#!/bin/python3
import argparse


class OverloadAction(argparse.Action):
    class OverloadParser(argparse.ArgumentParser):
        def exit(self, status = 0, message = None):
            raise argparse.ArgumentError(None, message)

        def _print_message(self, message, file = None):

tsibley

"""
For Cécile, re: <https://bedfordlab.slack.com/archives/C0K3GS3J8/p1731108015913239>.

The rule-of-thumb is: if you need to read from a file output by rule A in order
to determine what rule B will declare as input, then rule A needs to be a
checkpoint and rule B needs to use an input function that reads from the file.

In this example, the intermediate rule is naive to the checkpoint and input
function: it's a basic rule that uses two wildcards. The final rule uses an
input function to declare input files that "pass thru" the global {scenario}

tsibley

#!/usr/bin/env python3
import xml.etree.ElementTree as ET
from sys import argv, stdin, stdout

layer = argv[1]
doc = ET.parse(stdin)
root = doc.getroot()

for g in root.findall(".//{http://www.w3.org/2000/svg}g[@id]"):
    id = g.get("id")

tsibley

#!/bin/bash
# usage: clockins [<since>]
#
# <since> defaults to "yesterday".
set -euo pipefail

since="${1:-yesterday}${1:+ ago}"

{
    journalctl \

tsibley

#!/bin/bash
# usage: plx install <module> [args…]
#        plx link <module>
#        plx ls [<module>]
#        plx --help
#
# Install Perl programs into isolated environments.
set -euo pipefail

PREFIX="$(realpath "${PREFIX:-$HOME/.local}")"