Merge pull request #1637: Use shared setup script for all Cram tests

nextstrain · Sep 24, 2024 · 9c92458 · 9c92458
2 parents d10c3fb + 4bc6cfc
commit 9c92458
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Showing 34 changed files with 37 additions and 49 deletions.
diff --git a/tests/functional/_setup.sh b/tests/functional/_setup.sh
@@ -0,0 +1,2 @@
+pushd "$TESTDIR" > /dev/null
+export AUGUR="${AUGUR:-../../bin/augur}"
diff --git a/tests/functional/clades.t b/tests/functional/clades.t
@@ -1,7 +1,6 @@
 Integration tests for augur clades.
 
-  $ pushd "$TESTDIR" > /dev/null
-  $ export AUGUR="${AUGUR:-../../bin/augur}"
+  $ source "$TESTDIR"/_setup.sh
 
 Test augur clades with simple Zika input files and hierarchical clades.
 

diff --git a/tests/functional/mask.t b/tests/functional/mask.t
@@ -1,7 +1,6 @@
 Integration tests for augur mask.
 
-  $ pushd "$TESTDIR" > /dev/null
-  $ export AUGUR="${AUGUR:-../../bin/augur}"
+  $ source "$TESTDIR"/_setup.sh
 
 Try masking a VCF without any specified mask.
 

diff --git a/tests/functional/merge/cram/_setup.sh b/tests/functional/merge/cram/_setup.sh
@@ -0,0 +1 @@
+export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
diff --git a/tests/functional/merge/cram/merge.t b/tests/functional/merge/cram/merge.t
@@ -1,6 +1,6 @@
 SETUP
 
-  $ export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+  $ source "$TESTDIR"/_setup.sh
   $ set -o pipefail
 
 

diff --git a/tests/functional/parse.t b/tests/functional/parse.t
@@ -1,7 +1,6 @@
 Integration tests for augur parse.
 
-  $ pushd "$TESTDIR" > /dev/null
-  $ export AUGUR="${AUGUR:-../../bin/augur}"
+  $ source "$TESTDIR"/_setup.sh
 
 Try to parse Zika sequences without specifying fields.
 This should fail.

diff --git a/tests/functional/titers/cram/_setup.sh b/tests/functional/titers/cram/_setup.sh
@@ -0,0 +1,2 @@
+pushd "$TESTDIR" > /dev/null
+export AUGUR="${AUGUR:-../../../../bin/augur}"
diff --git a/tests/functional/titers/cram/titers-sub-with-tree-and-custom-prefix.t b/tests/functional/titers/cram/titers-sub-with-tree-and-custom-prefix.t
@@ -1,7 +1,6 @@
 Setup
 
-  $ pushd "$TESTDIR" > /dev/null
-  $ export AUGUR="${AUGUR:-../../../../bin/augur}"
+  $ source "$TESTDIR"/_setup.sh
 
 Test titer substitution model with alignment and tree inputs and a custom prefix for the node data attributes in the output.
 

diff --git a/tests/functional/titers/cram/titers-sub-with-tree.t b/tests/functional/titers/cram/titers-sub-with-tree.t
@@ -1,7 +1,6 @@
 Setup
 
-  $ pushd "$TESTDIR" > /dev/null
-  $ export AUGUR="${AUGUR:-../../../../bin/augur}"
+  $ source "$TESTDIR"/_setup.sh
 
 Test titer substitution model with alignment and tree inputs.
 

diff --git a/tests/functional/titers/cram/titers-tree-with-custom-prefix.t b/tests/functional/titers/cram/titers-tree-with-custom-prefix.t
@@ -1,7 +1,6 @@
 Setup
 
-  $ pushd "$TESTDIR" > /dev/null
-  $ export AUGUR="${AUGUR:-../../../../bin/augur}"
+  $ source "$TESTDIR"/_setup.sh
 
 Test titer tree model with a custom prefix for the node data attributes in the output.
 

diff --git a/tests/functional/titers/cram/titers-tree.t b/tests/functional/titers/cram/titers-tree.t
@@ -1,7 +1,6 @@
 Setup
 
-  $ pushd "$TESTDIR" > /dev/null
-  $ export AUGUR="${AUGUR:-../../../../bin/augur}"
+  $ source "$TESTDIR"/_setup.sh
 
 Test titer tree model.
 

diff --git a/tests/functional/traits.t b/tests/functional/traits.t
@@ -1,7 +1,6 @@
 Integration tests for augur traits.
 
-  $ pushd "$TESTDIR" > /dev/null
-  $ export AUGUR="${AUGUR:-../../bin/augur}"
+  $ source "$TESTDIR"/_setup.sh
 
 Infer the ancestral region for a given tree and metadata.
 

diff --git a/tests/functional/translate/cram/_setup.sh b/tests/functional/translate/cram/_setup.sh
@@ -0,0 +1,2 @@
+export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+export SCRIPTS="$TESTDIR/../../../../scripts"
diff --git a/tests/functional/translate/cram/basic-error-checking.t b/tests/functional/translate/cram/basic-error-checking.t
@@ -1,7 +1,6 @@
 Setup
 
-  $ export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
-  $ export SCRIPTS="$TESTDIR/../../../../scripts"
+  $ source "$TESTDIR"/_setup.sh
   $ export ANC_DATA="$TESTDIR/../../ancestral/data/simple-genome"
   $ export DATA="$TESTDIR/../data/simple-genome"
 

diff --git a/tests/functional/translate/cram/genbank.t b/tests/functional/translate/cram/genbank.t
@@ -1,6 +1,6 @@
 Setup
 
-  $ export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+  $ source "$TESTDIR"/_setup.sh
   $ export ANC_DATA="$TESTDIR/../../ancestral/data/simple-genome"
   $ export DATA="$TESTDIR/../data/simple-genome"
 

diff --git a/tests/functional/translate/cram/general.t b/tests/functional/translate/cram/general.t
@@ -1,7 +1,6 @@
 Setup
 
-  $ export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
-  $ export SCRIPTS="$TESTDIR/../../../../scripts"
+  $ source "$TESTDIR"/_setup.sh
   $ export ANC_DATA="$TESTDIR/../../ancestral/data/simple-genome"
   $ export DATA="$TESTDIR/../data/simple-genome"
 

diff --git a/tests/functional/translate/cram/genes.t b/tests/functional/translate/cram/genes.t
@@ -1,7 +1,6 @@
 Setup
 
-  $ export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
-  $ export SCRIPTS="$TESTDIR/../../../../scripts"
+  $ source "$TESTDIR"/_setup.sh
   $ export ANC_DATA="$TESTDIR/../../ancestral/data/simple-genome"
   $ export DATA="$TESTDIR/../data/simple-genome"
 

diff --git a/tests/functional/translate/cram/gff.t b/tests/functional/translate/cram/gff.t
@@ -1,7 +1,6 @@
 Setup
 
-  $ export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
-  $ export SCRIPTS="$TESTDIR/../../../../scripts"
+  $ source "$TESTDIR"/_setup.sh
   $ export ANC_DATA="$TESTDIR/../../ancestral/data/simple-genome"
   $ export DATA="$TESTDIR/../data/simple-genome"
 

diff --git a/tests/functional/translate/cram/invalid-args.t b/tests/functional/translate/cram/invalid-args.t
@@ -1,7 +1,6 @@
 Setup
 
-  $ export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
-  $ export SCRIPTS="$TESTDIR/../../../../scripts"
+  $ source "$TESTDIR"/_setup.sh
   $ export ANC_DATA="$TESTDIR/../../ancestral/data/simple-genome"
   $ export DATA="$TESTDIR/../data/simple-genome"
 

diff --git a/tests/functional/translate/cram/root-mutations.t b/tests/functional/translate/cram/root-mutations.t
@@ -1,7 +1,6 @@
 Setup
 
-  $ export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
-  $ export SCRIPTS="$TESTDIR/../../../../scripts"
+  $ source "$TESTDIR"/_setup.sh
   $ export ANC_DATA="$TESTDIR/../../ancestral/data/simple-genome"
   $ export DATA="$TESTDIR/../data/simple-genome"
 

diff --git a/tests/functional/translate/cram/translate-with-genbank.t b/tests/functional/translate/cram/translate-with-genbank.t
@@ -1,8 +1,7 @@
 Setup
 
-  $ export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+  $ source "$TESTDIR"/_setup.sh
   $ export DATA="$TESTDIR/../data"
-  $ export SCRIPTS="$TESTDIR/../../../../scripts"
 
 Translate amino acids for genes using a GenBank file.
 

diff --git a/tests/functional/translate/cram/translate-with-gff-and-gene-name.t b/tests/functional/translate/cram/translate-with-gff-and-gene-name.t
@@ -1,8 +1,7 @@
 Setup
 
-  $ export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+  $ source "$TESTDIR"/_setup.sh
   $ export DATA="$TESTDIR/../data"
-  $ export SCRIPTS="$TESTDIR/../../../../scripts"
 
 Translate amino acids for genes using a GFF3 file where the gene names are stored in a qualifier named "gene_name".
 

diff --git a/tests/functional/translate/cram/translate-with-gff-and-gene.t b/tests/functional/translate/cram/translate-with-gff-and-gene.t
@@ -1,8 +1,7 @@
 Setup
 
-  $ export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+  $ source "$TESTDIR"/_setup.sh
   $ export DATA="$TESTDIR/../data"
-  $ export SCRIPTS="$TESTDIR/../../../../scripts"
 
 Translate amino acids for genes using a GFF3 file where the gene names are stored in a qualifier named "gene".
 

diff --git a/tests/functional/translate/cram/translate-with-gff-and-locus-tag.t b/tests/functional/translate/cram/translate-with-gff-and-locus-tag.t
@@ -1,8 +1,7 @@
 Setup
 
-  $ export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+  $ source "$TESTDIR"/_setup.sh
   $ export DATA="$TESTDIR/../data"
-  $ export SCRIPTS="$TESTDIR/../../../../scripts"
 
 This is an identical test setup as `translate-with-gff-and-gene.t` but using locus_tag instead of gene in the GFF
 

diff --git a/tests/functional/translate/cram/vcf-with-root-mutation.t b/tests/functional/translate/cram/vcf-with-root-mutation.t
@@ -1,7 +1,6 @@
 Setup
 
-  $ export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
-  $ export SCRIPTS="$TESTDIR/../../../../scripts"
+  $ source "$TESTDIR"/_setup.sh
   $ export ANC_DATA="$TESTDIR/../../ancestral/data/simple-genome"
   $ export DATA="$TESTDIR/../data/simple-genome"
 

diff --git a/tests/functional/translate/cram/vcf.t b/tests/functional/translate/cram/vcf.t
@@ -1,7 +1,6 @@
 Setup
 
-  $ export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
-  $ export SCRIPTS="$TESTDIR/../../../../scripts"
+  $ source "$TESTDIR"/_setup.sh
   $ export ANC_DATA="$TESTDIR/../../ancestral/data/simple-genome"
   $ export DATA="$TESTDIR/../data/simple-genome"
 

diff --git a/tests/functional/tree/cram/_setup.sh b/tests/functional/tree/cram/_setup.sh
@@ -0,0 +1 @@
+export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
diff --git a/tests/functional/tree/cram/iqtree-compressed-input.t b/tests/functional/tree/cram/iqtree-compressed-input.t
@@ -1,6 +1,6 @@
 Setup
 
-  $ export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+  $ source "$TESTDIR"/_setup.sh
 
 Build a tree with excluded sites using a compressed input file.
 

diff --git a/tests/functional/tree/cram/iqtree-extend-args.t b/tests/functional/tree/cram/iqtree-extend-args.t
@@ -1,6 +1,6 @@
 Setup
 
-  $ export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+  $ source "$TESTDIR"/_setup.sh
 
 Build a tree, augmenting existing default arguments with custom arguments.
 

diff --git a/tests/functional/tree/cram/iqtree-model-auto.t b/tests/functional/tree/cram/iqtree-model-auto.t
@@ -1,6 +1,6 @@
 Setup
 
-  $ export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+  $ source "$TESTDIR"/_setup.sh
 
 Try building a tree with IQ-TREE using its ModelTest functionality, by supplying a substitution model of "auto".
 

diff --git a/tests/functional/tree/cram/iqtree-more-threads.t b/tests/functional/tree/cram/iqtree-more-threads.t
@@ -1,6 +1,6 @@
 Setup
 
-  $ export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+  $ source "$TESTDIR"/_setup.sh
 
 Try building a tree with IQ-TREE with more threads (4) than there are input sequences (3).
 

diff --git a/tests/functional/tree/cram/iqtree-override-args.t b/tests/functional/tree/cram/iqtree-override-args.t
@@ -1,6 +1,6 @@
 Setup
 
-  $ export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+  $ source "$TESTDIR"/_setup.sh
 
 Build a tree, replacing existing default arguments with custom arguments.
 Since the following custom arguments are incompatible with the default IQ-TREE arguments, this command will only work with the `--override-default-args` flag.

diff --git a/tests/functional/tree/cram/iqtree-preserve-fa.t b/tests/functional/tree/cram/iqtree-preserve-fa.t
@@ -1,6 +1,6 @@
 Setup
 
-  $ export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+  $ source "$TESTDIR"/_setup.sh
 
 Build a tree with an input file that doesn't end in .fasta, and ensure it's not overwritten.
 

diff --git a/tests/functional/tree/cram/iqtree.t b/tests/functional/tree/cram/iqtree.t
@@ -1,6 +1,6 @@
 Setup
 
-  $ export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+  $ source "$TESTDIR"/_setup.sh
 
 Try building a tree with IQ-TREE.