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@tsibley
tsibley / heroku-redis-cli
Created September 19, 2024 21:07
#!/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
tsibley / 0001-wip-merge-concurrent-import.patch
Created September 3, 2024 19:58
From 4b07dc59f847f08a51addf7a9826d572484accf2 Mon Sep 17 00:00:00 2001
From: Thomas Sibley <tsibley@fredhutch.org>
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
tsibley / demo.js
Last active August 23, 2024 22:14
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
tsibley / err.diff
Created August 15, 2024 22:24
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
tsibley / git-diff-rebase
Created August 1, 2024 17:10
#!/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
tsibley / excel.patch
Created July 12, 2024 06:28
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
@tsibley
tsibley / 0001-wip-.import-nulls.patch
Last active July 11, 2024 21:33
From 10bc706b2630cb9f607f2b5d55923fdfc7c6da6e Mon Sep 17 00:00:00 2001
From: Thomas Sibley <tsibley@fredhutch.org>
Date: Tue, 18 Jun 2024 13:27:03 -0700
Subject: [PATCH] wip! .import --nulls
---
src/shell.c.in | 10 +++++++++-
1 file changed, 9 insertions(+), 1 deletion(-)
diff --git a/src/shell.c.in b/src/shell.c.in
@tsibley
tsibley / iam-user-secrets.patch
Created June 14, 2024 20:14
diff --git a/env/production/aws-iam-user-NextstrainPathogenNcov.tf b/env/production/aws-iam-user-NextstrainPathogenNcov.tf
new file mode 100644
index 0000000..966023a
--- /dev/null
+++ b/env/production/aws-iam-user-NextstrainPathogenNcov.tf
@@ -0,0 +1,18 @@
+resource "aws_iam_user" "NextstrainPathogenNcov" {
+ name = "NextstrainPathogen@ncov"
+}
+
@tsibley
tsibley / sitecustomize.py
Created June 10, 2024 22:17
import os, site
os.environ["PATH"] = site.PREFIXES[0]+"/bin" + os.pathsep + os.environ["PATH"]
@tsibley
tsibley / 0001-wip-status-show-when-tracking-branch-was-last-fetche.patch
Last active March 9, 2024 06:32
From c7caebe7d19d43bd8dad98afd28ee703e04ab806 Mon Sep 17 00:00:00 2001
From: Thomas Sibley <tom@zulutango.org>
Date: Fri, 8 Mar 2024 16:42:45 -0800
Subject: [PATCH] wip! status: show when tracking branch was last fetched
<https://metasocial.com/@trs/112062359954735355>
fetch now logs no-ops as "up-to-date" reflog entries to support this
---
builtin/fetch.c | 17 +++++++-----