tsibley

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


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

    try:

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#!/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 \

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#!/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}")"

tsibley

diff --git a/ingest/defaults/config.yaml b/ingest/defaults/config.yaml
index 7bd0362..dfddd22 100644
--- a/ingest/defaults/config.yaml
+++ b/ingest/defaults/config.yaml
@@ -39,9 +39,11 @@ curate:
   # For the Nextstrain team, this is currently
   # "https://raw.githubusercontent.com/nextstrain/ncov-ingest/master/source-data/gisaid_geoLocationRules.tsv"
   geolocation_rules_url: "https://raw.githubusercontent.com/nextstrain/ncov-ingest/master/source-data/gisaid_geoLocationRules.tsv"
-  # The path to the local geolocation rules within the pathogen repo
+  # General global defaults are sourced from the geolocation_rules_url URL above.

tsibley

#!/bin/bash
set -euo pipefail

REPO="$(basename $PWD)"

mkdir -p .github

cat > .github/dependabot.yml <<~~
# Dependabot configuration file
# <https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file>

tsibley

/* Color values from RTD's Doc Diff addon's CSS */
.doc-diff-added   { --bgcolor: rgb(171, 242, 188) }
.doc-diff-removed { --bgcolor: rgba(255, 129, 130, 0.4) }

/* Doesn't work in Firefox 131… not sure why… *//*
.doc-diff-removed {
  --bgcolor: color(
    from rgba(255, 129, 130, 0.4)
    srgb
    calc(((1 - alpha) * 255) + (alpha * r))

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defaults:
  a:
    x: 1
    y: 2
  b:
    z: 3

builds:
  global:
    a: