tsibley

diff --git a/src/reference/ca-certificates.rst b/src/reference/ca-certificates.rst
index 086e37e..583d030 100644
--- a/src/reference/ca-certificates.rst
+++ b/src/reference/ca-certificates.rst
@@ -68,7 +68,8 @@ OpenSSL is the most common library used to provide TLS/SSL support in
 application software.  Its `default locations of trusted CA certificates
 <https://docs.openssl.org/3.0/man3/SSL_CTX_load_verify_locations/>`__ can be
 overridden by setting the ``SSL_CERT_FILE`` and/or ``SSL_CERT_DIR`` environment
-variables.
+variables.  Filenames in the latter must be hashed with OpenSSL's ``c_rehash``

tsibley

/* Revert *some* of what RTD's force-readthedocs-addons.js does.
 *
 * <https://github.com/readthedocs/common/blob/c766aa84a01b74d83c5fac061d92e31d512df99f/dockerfiles/force-readthedocs-addons.js#L96-L118>
 */
let esc = text => String(text).replace(/[&<>"']/g, x => `&#${x.charCodeAt(0)};`);

// This HTML is very specific to sphinx_rtd_theme.
let rstVersions = `
  <div class="rst-versions" data-toggle="rst-versions" role="note" aria-label="Versions">
    <span class="rst-current-version" data-toggle="rst-current-version">

tsibley

diff --git a/cram/_main.py b/cram/_main.py
index 11d457b..cdbf8db 100644
--- a/cram/_main.py
+++ b/cram/_main.py
@@ -42,14 +42,14 @@ class _OptionParser(optparse.OptionParser):
         option = optparse.OptionParser.add_option(self, *args, **kwargs)
         if option.dest and option.dest != 'version':
             key = option.dest.replace('_', '-')
-            self._config_opts[key] = option.action == 'store_true'
+            self._config_opts[key] = (option.dest, option.action == 'store_true')

tsibley

# Create Conda env with ctng-compiler-activation package installed.
$ micromamba create -p /tmp/conda -c conda-forge --override-channels gcc_linux-64

# Set HOST as a *shell variable*.
$ HOST=whunk

# It's visible to the shell…
$ echo $HOST
whunk

tsibley

#!/bin/bash
set -euo pipefail

app_db="${1:?usage: $(basename "$0") <app-name>[/<database-name>]}"
shift

app="${app_db%%/*}"
db="${app_db#*/}"

url="$(heroku redis:credentials -a "$app" "$db")"

tsibley

From 4b07dc59f847f08a51addf7a9826d572484accf2 Mon Sep 17 00:00:00 2001
From: Thomas Sibley <[email protected]>
Date: Tue, 3 Sep 2024 12:55:14 -0700
Subject: [PATCH] wip! merge: concurrent import

---
 augur/merge.py | 146 ++++++++++++++++++++++++++++++-------------------
 1 file changed, 90 insertions(+), 56 deletions(-)

diff --git a/augur/merge.py b/augur/merge.py

tsibley

import express from 'express';

const app = express();

// Middleware to parse req.body from application/x-www-form-urlencoded to an object
app.use(express.urlencoded({ extended: false }));

// Shared state that the server has access to.  Could be a database or some
// other external service.
let counter = 0;

tsibley

diff --git a/nextstrain/cli/remote/nextstrain_dot_org.py b/nextstrain/cli/remote/nextstrain_dot_org.py
index c57c83d..08a2a7e 100644
--- a/nextstrain/cli/remote/nextstrain_dot_org.py
+++ b/nextstrain/cli/remote/nextstrain_dot_org.py
@@ -69,6 +69,7 @@ from collections import defaultdict
 from email.message import EmailMessage
 from pathlib import Path, PurePosixPath
 from requests.utils import parse_dict_header
+from shlex import quote as shquote
 from tempfile import NamedTemporaryFile

tsibley

#!/bin/bash
# usage: git diff-rebase
#        git diff-rebase u[pstream]
#        git diff-rebase <a> [<b>] [<branch>]
#        git diff-rebase -h
#
# Display the differences in a branch after rebasing it.
#
# Immediately after a rebase, running this command with no arguments displays
# differences between the pre- and post-rebase versions of the current branch

tsibley

diff --git a/augur/io/json.py b/augur/io/json.py
index 2a4678ea..5eae5d1b 100644
--- a/augur/io/json.py
+++ b/augur/io/json.py
@@ -32,7 +32,7 @@ The LICENSE file included in ID3C's repo is copied below verbatim::
     SOFTWARE.
 """
 import json
-from datetime import datetime
+from datetime import date, datetime