tsibley

# Example of an OS-specific installer for Windows.
#
# XXX FIXME: Replace hardcoded URL below with something like https://nextstrain.org/download/cli/windows
$ErrorActionPreference = "Stop"

if (!$IsWindows -and !$env:TESTING) {
    echo "This is not Windows.  Aborting!"
    exit 1
}

tsibley

commit 18010940faba6c5d20fbf19e37bcb3faf79f0b4b
Author: Thomas Sibley <tsibley@fredhutch.org>
Date:   Fri Dec 7 12:33:17 2018 -0800

    titers tree: Add a --branch-filter option allowing for a custom function
    
    Sidney and I talked about this as a way to support a custom branch
    "criterium" function.  In her dengue work, she only includes
    interserotype branches in the model.

tsibley

diff --git a/augur/__init__.py b/augur/__init__.py
index 31ee6826..a69dcf44 100644
--- a/augur/__init__.py
+++ b/augur/__init__.py
@@ -142,4 +142,9 @@ def command_name(command):
     package     = command.__package__
     module_name = command.__name__
 
+    # If the command module is also a package, e.g. augur/x/__init__.py instead
+    # of augur/x.py, then use the parent package.

tsibley

#!/bin/bash
# Extract changelog for a specified version (or __NEXT__ if no version
# specified).
set -euo pipefail

cd "$(dirname "$0")/.."

version="${1:-__NEXT__}"
export version

tsibley

#!/bin/bash
set -euo pipefail

main() {
    local domain="$1"
    shift
    local paths=("$@")
    local distribution invalidation

    echo "-> Finding CloudFront distribution"

tsibley

2022-06-10T19:36:39.0592611Z Software Licensing Summary
2022-06-10T19:36:39.0593298Z ==========================
2022-06-10T19:36:39.0593757Z 
2022-06-10T19:36:39.0594119Z 87 distinct software components
2022-06-10T19:36:39.0594432Z 0 lack a known software license
2022-06-10T19:36:39.0594733Z 22 have unknown license expressions
2022-06-10T19:36:39.0594978Z 15 distinct SPDX licenses
2022-06-10T19:36:39.0595262Z 2 components in the public domain
2022-06-10T19:36:39.0595517Z 2 have copyleft licenses
2022-06-10T19:36:39.0595670Z 

tsibley

#!/usr/bin/env python3
from netrc import netrc
from os.path import basename
from sys import argv, exit, stderr

if len(argv) < 2:
    print(f"usage: {basename(__file__)} <machine> [login [password]]")
    exit(1)

machine = argv[1]

tsibley

# Example of a compact, OS-specific installer for Linux.
#
# XXX FIXME: Replace hardcoded URL below with something like https://nextstrain.org/download/cli/linux
dest="${XDG_DATA_HOME:-$HOME/.local/share}/nextstrain/cli/standalone" &&
mkdir -p "${dest}-new" &&
curl -fsSL --proto "=https" https://github.com/nextstrain/cli/releases/download/4.1.1/nextstrain-cli-4.1.1-standalone-x86_64-unknown-linux-gnu.tar.gz \
   | tar xzf - -C "${dest}-new" &&
if [[ -d "$dest" ]]; then mv "$dest" "${dest}-old"; fi &&
mv "${dest}-new" "$dest" &&
printf 'Please add PATH="%s:$PATH" to your shell initialization files.\n' "$dest"

tsibley

# This file defines how PyOxidizer application building and packaging is
# performed.  See PyOxidizer's documentation at
# https://pyoxidizer.readthedocs.io/en/stable/ for details of this
# configuration file format.


# Define how to bundle a Python interpreter + our Python code + shared
# libraries + other resources into an executable and adjacent filesystem "lib/"
# tree.
def make_exe():

tsibley

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