tsibley

From 10bc706b2630cb9f607f2b5d55923fdfc7c6da6e Mon Sep 17 00:00:00 2001
From: Thomas Sibley <[email protected]>
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

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

import os, site
os.environ["PATH"] = site.PREFIXES[0]+"/bin" + os.pathsep + os.environ["PATH"]

tsibley

From c7caebe7d19d43bd8dad98afd28ee703e04ab806 Mon Sep 17 00:00:00 2001
From: Thomas Sibley <[email protected]>
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 +++++++-----

tsibley

From 0ac09c0541385289ce6398699ca8e0e2596c8afa Mon Sep 17 00:00:00 2001
From: Thomas Sibley <[email protected]>
Date: Fri, 8 Mar 2024 16:42:45 -0800
Subject: [PATCH] wip! status: show last reflog timestamp of tracking branch

<https://metasocial.com/@trs/112062359954735355>
---
 remote.c | 58 +++++++++++++++++++++++++++++++++++++++++++-------------
 1 file changed, 45 insertions(+), 13 deletions(-)

tsibley

- workflow: ./mpox/.github/workflows/fetch-and-ingest-branch.yaml
  jobs:
    fetch-and-ingest:
      needs: [set_config_overrides]
      permissions:
        id-token: write
      uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
      secrets: inherit
      with:
        runtime: aws-batch

tsibley

{
    "ref": "trs/pathogen-repo-build/wait-for-aws-batch-job",
    "inputs": {
        "repo": "nextstrain/zika-tutorial",
        "runtime": "aws-batch",
        "run": "perl -pi -e 's/(?=augur tree)/sleep 240;/' Snakefile; nextstrain build --detach --env X=X ."
    }
}

tsibley

/usr/lib/ruby/gems/2.7.0/gems/rdoc-6.2.1.1/exe/rdoc:                                                                     ELF 64-bit LSB executable, x86-64, version 1 (SYSV), statically linked, for GNU/Linux 2.6.9, stripped
/usr/local/bin/csv2tsv:                                                                                                  ELF 64-bit LSB executable, x86-64, version 1 (SYSV), statically linked, for GNU/Linux 2.6.32, BuildID[sha1]=27e53e1f84df7ba7c2091839d557184036a919cc, with debug_info, not stripped
/usr/local/bin/gofasta:                                                                                                  ELF 64-bit LSB executable, x86-64, version 1 (SYSV), statically linked, Go BuildID=yWxujNqjWDT1QiN3FnJ4/6ffI4jRMnWBSC3oi7Hsy/lnvl60FmDO6xJu-A3bjQ/cjeAl372Ux4t_LQsCQ3g, not stripped
/usr/local/bin/iqtree:                                                                                                   ELF 64-bit LSB executable, x86-64, version 1 (GNU/Linux), statically linked, 

tsibley

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git -C ./mpox show
commit e6a06a2207d46998bca53635f6e4ab26981b00c2
Author: Thomas Sibley <[email protected]>
Date:   Tue Jan 30 10:51:26 2024 -0800

    Automatically check for new GitHub actions versions
    
    Configure Dependabot to do this for us,¹ as discussed in Slack.²
    

tsibley

#!/usr/bin/env python3
import boto3
import logging
from argparse import ArgumentParser
from logging import info, error
from operator import attrgetter, itemgetter
from sys import exit

argparser = ArgumentParser()
argparser.add_argument("bucket")