From 7bf664b1e8f9b969c5f925ab220dd5e671e338da Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Mon, 23 Sep 2024 14:51:58 -0700
Subject: [PATCH] Set pipefail in setup scripts

This was added in places where it's been necessary. Setting it in shared
setup scripts simplifies tests and allows future tests to use pipes
without the need to set pipefail explicitly.
---
 tests/functional/_setup.sh                      | 1 +
 tests/functional/ancestral/cram/_setup.sh       | 1 +
 tests/functional/curate/cram/_setup.sh          | 1 +
 tests/functional/curate/cram/validate-records.t | 1 -
 tests/functional/export_v2/cram/_setup.sh       | 1 +
 tests/functional/filter/cram/_setup.sh          | 1 +
 tests/functional/frequencies/cram/_setup.sh     | 1 +
 tests/functional/merge/cram/_setup.sh           | 1 +
 tests/functional/merge/cram/merge.t             | 1 -
 tests/functional/refine/cram/_setup.sh          | 1 +
 tests/functional/titers/cram/_setup.sh          | 1 +
 tests/functional/translate/cram/_setup.sh       | 1 +
 tests/functional/tree/cram/_setup.sh            | 1 +
 13 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/tests/functional/_setup.sh b/tests/functional/_setup.sh
index 16e20ca6f..b645edfae 100644
--- a/tests/functional/_setup.sh
+++ b/tests/functional/_setup.sh
@@ -1,2 +1,3 @@
 pushd "$TESTDIR" > /dev/null
 export AUGUR="${AUGUR:-../../bin/augur}"
+set -o pipefail
diff --git a/tests/functional/ancestral/cram/_setup.sh b/tests/functional/ancestral/cram/_setup.sh
index 032447690..9c29b1c17 100644
--- a/tests/functional/ancestral/cram/_setup.sh
+++ b/tests/functional/ancestral/cram/_setup.sh
@@ -1 +1,2 @@
 export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+set -o pipefail
diff --git a/tests/functional/curate/cram/_setup.sh b/tests/functional/curate/cram/_setup.sh
index 032447690..9c29b1c17 100644
--- a/tests/functional/curate/cram/_setup.sh
+++ b/tests/functional/curate/cram/_setup.sh
@@ -1 +1,2 @@
 export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+set -o pipefail
diff --git a/tests/functional/curate/cram/validate-records.t b/tests/functional/curate/cram/validate-records.t
index f5b9bdaa2..7d00a38d7 100644
--- a/tests/functional/curate/cram/validate-records.t
+++ b/tests/functional/curate/cram/validate-records.t
@@ -25,7 +25,6 @@ error when it encounters the record with mismatched fields.
 Passing the records through multiple augur curate commands should raise the
 same error when it encounters the record with mismatched fields.
 
-  $ set -o pipefail
   $ cat records.ndjson \
   >   | ${AUGUR} curate passthru \
   >   | ${AUGUR} curate passthru \
diff --git a/tests/functional/export_v2/cram/_setup.sh b/tests/functional/export_v2/cram/_setup.sh
index 032447690..9c29b1c17 100644
--- a/tests/functional/export_v2/cram/_setup.sh
+++ b/tests/functional/export_v2/cram/_setup.sh
@@ -1 +1,2 @@
 export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+set -o pipefail
diff --git a/tests/functional/filter/cram/_setup.sh b/tests/functional/filter/cram/_setup.sh
index 032447690..9c29b1c17 100644
--- a/tests/functional/filter/cram/_setup.sh
+++ b/tests/functional/filter/cram/_setup.sh
@@ -1 +1,2 @@
 export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+set -o pipefail
diff --git a/tests/functional/frequencies/cram/_setup.sh b/tests/functional/frequencies/cram/_setup.sh
index 032447690..9c29b1c17 100644
--- a/tests/functional/frequencies/cram/_setup.sh
+++ b/tests/functional/frequencies/cram/_setup.sh
@@ -1 +1,2 @@
 export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+set -o pipefail
diff --git a/tests/functional/merge/cram/_setup.sh b/tests/functional/merge/cram/_setup.sh
index 032447690..9c29b1c17 100644
--- a/tests/functional/merge/cram/_setup.sh
+++ b/tests/functional/merge/cram/_setup.sh
@@ -1 +1,2 @@
 export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+set -o pipefail
diff --git a/tests/functional/merge/cram/merge.t b/tests/functional/merge/cram/merge.t
index d40f50e6e..87b29ad79 100644
--- a/tests/functional/merge/cram/merge.t
+++ b/tests/functional/merge/cram/merge.t
@@ -1,7 +1,6 @@
 SETUP
 
   $ source "$TESTDIR"/_setup.sh
-  $ set -o pipefail
 
 
 BASIC USAGE
diff --git a/tests/functional/refine/cram/_setup.sh b/tests/functional/refine/cram/_setup.sh
index 032447690..9c29b1c17 100644
--- a/tests/functional/refine/cram/_setup.sh
+++ b/tests/functional/refine/cram/_setup.sh
@@ -1 +1,2 @@
 export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+set -o pipefail
diff --git a/tests/functional/titers/cram/_setup.sh b/tests/functional/titers/cram/_setup.sh
index 95f4b5dda..a19898b77 100644
--- a/tests/functional/titers/cram/_setup.sh
+++ b/tests/functional/titers/cram/_setup.sh
@@ -1,2 +1,3 @@
 pushd "$TESTDIR" > /dev/null
 export AUGUR="${AUGUR:-../../../../bin/augur}"
+set -o pipefail
diff --git a/tests/functional/translate/cram/_setup.sh b/tests/functional/translate/cram/_setup.sh
index d04045ec2..e53284585 100644
--- a/tests/functional/translate/cram/_setup.sh
+++ b/tests/functional/translate/cram/_setup.sh
@@ -1,2 +1,3 @@
 export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
 export SCRIPTS="$TESTDIR/../../../../scripts"
+set -o pipefail
diff --git a/tests/functional/tree/cram/_setup.sh b/tests/functional/tree/cram/_setup.sh
index 032447690..9c29b1c17 100644
--- a/tests/functional/tree/cram/_setup.sh
+++ b/tests/functional/tree/cram/_setup.sh
@@ -1 +1,2 @@
 export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+set -o pipefail