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.
nextstrain · Sep 23, 2024 · 7bf664b · 7bf664b
1 parent 4bc6cfc
commit 7bf664b
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Showing 13 changed files with 11 additions and 2 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -1,2 +1,3 @@
 export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
 export SCRIPTS="$TESTDIR/../../../../scripts"
+set -o pipefail
diff --git a/tests/functional/tree/cram/_setup.sh b/tests/functional/tree/cram/_setup.sh
@@ -1 +1,2 @@
 export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+set -o pipefail