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Set pipefail in setup scripts
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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.

A couple calls with non-zero exit codes have been exposed. These still
fall under expected behavior.
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victorlin committed Sep 23, 2024
1 parent 4bc6cfc commit 56e7657
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Showing 15 changed files with 13 additions and 2 deletions.
1 change: 1 addition & 0 deletions tests/functional/_setup.sh
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@@ -1,2 +1,3 @@
pushd "$TESTDIR" > /dev/null
export AUGUR="${AUGUR:-../../bin/augur}"
set -o pipefail
1 change: 1 addition & 0 deletions tests/functional/ancestral/cram/_setup.sh
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@@ -1 +1,2 @@
export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
set -o pipefail
1 change: 1 addition & 0 deletions tests/functional/curate/cram/_setup.sh
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@@ -1 +1,2 @@
export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
set -o pipefail
1 change: 0 additions & 1 deletion tests/functional/curate/cram/validate-records.t
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Expand Up @@ -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 \
> | ${AUGUR} curate passthru \
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1 change: 1 addition & 0 deletions tests/functional/export_v2/cram/_setup.sh
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@@ -1 +1,2 @@
export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
set -o pipefail
1 change: 1 addition & 0 deletions tests/functional/filter/cram/_setup.sh
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@@ -1 +1,2 @@
export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
set -o pipefail
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Expand Up @@ -39,6 +39,7 @@ Repeat with sequence and strain outputs. We should get the same results.
\s*0 .* (re)
$ grep "^>" filtered.fasta | wc -l
\s*0 (re)
[1]

Repeat without any sequence-based filters.
Since we expect metadata to be filtered by presence of strains in input sequences, this should produce no results because the intersection of metadata and sequences is empty.
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1 change: 1 addition & 0 deletions tests/functional/frequencies/cram/_setup.sh
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@@ -1 +1,2 @@
export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
set -o pipefail
1 change: 1 addition & 0 deletions tests/functional/merge/cram/_setup.sh
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@@ -1 +1,2 @@
export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
set -o pipefail
1 change: 0 additions & 1 deletion tests/functional/merge/cram/merge.t
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@@ -1,7 +1,6 @@
SETUP

$ source "$TESTDIR"/_setup.sh
$ set -o pipefail


BASIC USAGE
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1 change: 1 addition & 0 deletions tests/functional/parse.t
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Expand Up @@ -106,6 +106,7 @@ This should use the first field as the id field and the metadata should not have
- strain\tvirus\taccession\tdate\tregion\tcountry\tdivision\tcity\tdb\tsegment\tauthors\turl\ttitle\tjournal\tpaper_url (esc)
---
+ col1\tvirus\tcol3\tdate\tregion\tcountry\tdivision\tcity\tdb\tsegment\tauthors\turl\ttitle\tjournal\tpaper_url (esc)
[1]
$ rm -f "$TMP/sequences.fasta" "$TMP/metadata.tsv"

Parse compressed Zika sequences into sequences and metadata.
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1 change: 1 addition & 0 deletions tests/functional/refine/cram/_setup.sh
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@@ -1 +1,2 @@
export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
set -o pipefail
1 change: 1 addition & 0 deletions tests/functional/titers/cram/_setup.sh
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@@ -1,2 +1,3 @@
pushd "$TESTDIR" > /dev/null
export AUGUR="${AUGUR:-../../../../bin/augur}"
set -o pipefail
1 change: 1 addition & 0 deletions tests/functional/translate/cram/_setup.sh
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@@ -1,2 +1,3 @@
export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
export SCRIPTS="$TESTDIR/../../../../scripts"
set -o pipefail
1 change: 1 addition & 0 deletions tests/functional/tree/cram/_setup.sh
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@@ -1 +1,2 @@
export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
set -o pipefail

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