Merge pull request #1636: Set pipefail for Cram tests

nextstrain · Oct 2, 2024 · 129fd7e · 129fd7e
2 parents 5c746dd + 8cac61c
commit 129fd7e
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Showing 15 changed files with 13 additions and 2 deletions.
diff --git a/tests/functional/_setup.sh b/tests/functional/_setup.sh
@@ -1 +1,2 @@
 export AUGUR="${AUGUR:-$TESTDIR/../../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/filter/cram/filter-mismatched-sequences-error.t b/tests/functional/filter/cram/filter-mismatched-sequences-error.t
@@ -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.

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/parse.t b/tests/functional/parse.t
@@ -107,6 +107,7 @@ 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.

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