tsibley

import json
import os
from subprocess import run, PIPE, STDOUT

for prog in ["conda", "mamba", "micromamba"]:
    for arch in [None, "x86_64", ""]:
        env = {**os.environ}

        if arch is None:
            try:

tsibley

#!/usr/bin/env python3
import doctest
import sys

try:
    script = sys.argv[1]
except IndexError:
    sys.stderr.write(f"error: no script given\n")
    sys.stderr.write(f"usage: {sys.argv[0]} <script>\n")
    sys.exit(1)

tsibley

 rules/config.smk | 22 ----------------------
 rules/genome.smk | 11 +++--------
 rules/main.smk   | 11 +++--------
 3 files changed, 6 insertions(+), 38 deletions(-)

diff --git a/rules/config.smk b/rules/config.smk
index 38cc55e..89ea2dd 100644
--- a/rules/config.smk
+++ b/rules/config.smk
@@ -179,28 +179,6 @@ def resolve_config_path(*fields):

tsibley

repo	workflow_name	workflow_path	html_url	created_at	conclusion	status	duration
forecasts-ncov	Run models	.github/workflows/run-models.yaml	https://github.com/nextstrain/forecasts-ncov/actions/runs/14074997682/attempts/1	2025-03-26T03:40:56+00:00	success	completed	PT1M3S
forecasts-ncov	Run models	.github/workflows/run-models.yaml	https://github.com/nextstrain/forecasts-ncov/actions/runs/14051269800/attempts/1	2025-03-25T03:50:35+00:00	success	completed	PT59S
mpox	Fetch and ingest	.github/workflows/fetch-and-ingest.yaml	https://github.com/nextstrain/mpox/actions/runs/14134150778/attempts/1	2025-03-28T17:06:07+00:00	success	completed	PT50S
mpox	Fetch and ingest	.github/workflows/fetch-and-ingest.yaml	https://github.com/nextstrain/mpox/actions/runs/14112517891/attempts/1	2025-03-27T17:05:57+00:00	success	completed	PT51S
mpox	Fetch and ingest	.github/workflows/fetch-and-ingest.yaml	https://github.com/nextstrain/mpox/actions/runs/14089260513/attempts/1	2025-03-26T17:06:13+00:00	success	completed	PT45S
mpox	Fetch a

tsibley

#!/bin/bash
set -euo pipefail

main() {
    pick | parse | convert | tee >(copy >/dev/null) | format
}

pick() {
    gdbus call --session \
        --dest org.gnome.Shell.Screenshot \

tsibley

$ cat /tmp/x
        declare -a config;
        if [[ "$TRIAL_NAME" ]]; then
          config+=(
            deploy_url="s3://nextstrain-staging/avian-flu_trials_${TRIAL_NAME}_"
          )
        fi;
        if [[ "$BUILDS" = "h5n1-d1.1" ]]; then
          config+=(

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}.