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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 |
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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 |
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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" | |
+} | |
+ |
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import os, site | |
os.environ["PATH"] = site.PREFIXES[0]+"/bin" + os.pathsep + os.environ["PATH"] |
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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 +++++++----- |
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From 0ac09c0541385289ce6398699ca8e0e2596c8afa 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 last reflog timestamp of tracking branch | |
<https://metasocial.com/@trs/112062359954735355> | |
--- | |
remote.c | 58 +++++++++++++++++++++++++++++++++++++++++++------------- | |
1 file changed, 45 insertions(+), 13 deletions(-) |
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- 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 |
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{ | |
"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 ." | |
} | |
} |
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/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, |
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━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ | |
git -C ./mpox show | |
commit e6a06a2207d46998bca53635f6e4ab26981b00c2 | |
Author: Thomas Sibley <tsibley@fredhutch.org> | |
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 | |
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