Clean up tests

tests/builds/zika_compressed.t

@@ -46,148 +46,6 @@ Filter sequences by a minimum date and an exclusion list and only keep one seque
   $ gzip -c -d "$TMP/out/filtered.fasta.gz" | grep "^>" | wc -l
   \s*10 (re)
 
-Align filtered sequences to a specific reference sequence and fill any gaps.
-
-  $ ${AUGUR} align \
-  >  --sequences "results/filtered.fasta" \
-  >  --reference-sequence "config/zika_outgroup.gb" \
-  >  --output "$TMP/out/aligned.fasta" \
-  >  --fill-gaps > /dev/null
-
-  $ diff -u "results/aligned.fasta" "$TMP/out/aligned.fasta"
-
-Build a tree from the multiple sequence alignment.
-
-  $ ${AUGUR} tree \
-  >  --alignment "results/aligned.fasta" \
-  >  --output "$TMP/out/tree_raw.nwk" \
-  >  --method iqtree \
-  >  --tree-builder-args "-seed 314159" > /dev/null
-
-  $ python3 "$TESTDIR/../../scripts/diff_trees.py" "results/tree_raw.nwk" "$TMP/out/tree_raw.nwk" --significant-digits 5
-  {}
-
-Confirm that tree log file exists.
-
-  $ test -e "results/aligned-delim.iqtree.log"
-  $ echo $?
-  0
-
-Build a time tree from the existing tree topology, the multiple sequence alignment, and the strain metadata.
-
-  $ ${AUGUR} refine \
-  >  --tree "results/tree_raw.nwk" \
-  >  --alignment "results/aligned.fasta" \
-  >  --metadata "results/metadata.tsv.gz" \
-  >  --output-tree "$TMP/out/tree.nwk" \
-  >  --output-node-data "$TMP/out/branch_lengths.json" \
-  >  --timetree \
-  >  --coalescent opt \
-  >  --date-confidence \
-  >  --date-inference marginal \
-  >  --clock-filter-iqd 4 \
-  >  --seed 314159 > /dev/null
-
-Confirm that TreeTime trees match expected topology and branch lengths.
-
-  $ python3 "$TESTDIR/../../scripts/diff_trees.py" "results/tree.nwk" "$TMP/out/tree.nwk" --significant-digits 2
-  {}
-
-Branch lengths and other annotations like dates are too stochastic across runs to consistently compare with reasonable precision.
-
-#$ python3 "$TESTDIR/../../scripts/diff_jsons.py" "results/branch_lengths.json" "$TMP/out/branch_lengths.json" --significant-digits 0
-#{}
-
-Calculate tip frequencies from the tree.
-
-  $ ${AUGUR} frequencies \
-  >  --method kde \
-  >  --tree "results/tree.nwk" \
-  >  --metadata "results/metadata.tsv.gz" \
-  >  --pivot-interval 3 \
-  >  --output "$TMP/out/zika_tip-frequencies.json" > /dev/null
-
-  $ diff -u --ignore-matching-lines version "auspice/zika_tip-frequencies.json" "$TMP/out/zika_tip-frequencies.json"
-
-Infer ancestral sequences from the tree.
-
-  $ ${AUGUR} ancestral \
-  >  --tree "results/tree.nwk" \
-  >  --alignment "results/aligned.fasta" \
-  >  --infer-ambiguous \
-  >  --output-node-data "$TMP/out/nt_muts.json" \
-  >  --inference joint > /dev/null
-
-  $ diff -u --ignore-matching-lines version "results/nt_muts.json" "$TMP/out/nt_muts.json"
-
-Infer ancestral traits from the tree.
-
-  $ ${AUGUR} traits \
-  >  --tree "results/tree.nwk" \
-  >  --weights "config/trait_weights.csv" \
-  >  --metadata "results/metadata.tsv.gz" \
-  >  --output-node-data "$TMP/out/traits.json" \
-  >  --columns country region \
-  >  --sampling-bias-correction 3 \
-  >  --confidence > /dev/null
-
-  $ python3 "$TESTDIR/../../scripts/diff_jsons.py" "results/traits.json" "$TMP/out/traits.json" --significant-digits 5
-  {}
-
-Implicit mugration model outputs are not written to the same directory as the traits output, so we cannot test for matching mugration models here.
-See augur issue 541 (https://github.com/nextstrain/augur/issues/541) for more details.
-
-#$ diff -u "results/treecountry.mugration_model.txt" "$TMP/out/treecountry.mugration_model.txt"
-#$ diff -u "results/treeregion.mugration_model.txt" "$TMP/out/treeregion.mugration_model.txt"
-
-Translate inferred ancestral and observed nucleotide sequences to amino acid mutations.
-
-  $ ${AUGUR} translate \
-  >  --tree "results/tree.nwk" \
-  >  --ancestral-sequences "$TMP/out/nt_muts.json" \
-  >  --reference-sequence "config/zika_outgroup.gb" \
-  >  --output-node-data "$TMP/out/aa_muts.json" > /dev/null
-
-  $ diff -u --ignore-matching-lines version "results/aa_muts.json" "$TMP/out/aa_muts.json"
-
-Export JSON files as v1 auspice outputs.
-
-  $ ${AUGUR} export v1 \
-  >  --tree "results/tree.nwk" \
-  >  --metadata "results/metadata.tsv.gz" \
-  >  --node-data "$TMP/out/branch_lengths.json" \
-  >              "$TMP/out/traits.json" \
-  >              "$TMP/out/nt_muts.json" \
-  >              "$TMP/out/aa_muts.json" \
-  >  --colors "config/colors.tsv" \
-  >  --auspice-config "config/auspice_config_v1.json" \
-  >  --output-tree "$TMP/out/v1_zika_tree.json" \
-  >  --output-meta "$TMP/out/v1_zika_meta.json" \
-  >  --output-sequence "$TMP/out/v1_zika_seq.json" > /dev/null
-
-  $ ${AUGUR} validate export-v1 "$TMP/out/v1_zika_meta.json" "$TMP/out/v1_zika_tree.json" > /dev/null
-
-Compare auspice metadata files, but ignore the "updated" field since this changes with the date the export command is run.
-
-  $ diff -u --ignore-matching-lines updated "auspice/v1_zika_meta.json" "$TMP/out/v1_zika_meta.json"
-
-Export JSON files as v2 auspice outputs.
-
-  $ ${AUGUR} export v2 \
-  >  --tree "results/tree.nwk" \
-  >  --metadata "results/metadata.tsv.gz" \
-  >  --node-data "$TMP/out/branch_lengths.json" \
-  >              "$TMP/out/traits.json" \
-  >              "$TMP/out/nt_muts.json" \
-  >              "$TMP/out/aa_muts.json" \
-  >  --colors "config/colors.tsv" \
-  >  --auspice-config "config/auspice_config_v2.json" \
-  >  --output "$TMP/out/v2_zika.json" \
-  >  --title 'Real-time tracking of Zika virus evolution -- v2 JSON' \
-  >  --panels tree map entropy frequencies > /dev/null
-
-  $ ${AUGUR} validate export-v2 "$TMP/out/v2_zika.json" > /dev/null
-
 Switch back to the original directory where testing started.
 
   $ popd > /dev/null

tests/functional/tree.t

@@ -20,4 +20,7 @@ Try building a tree with IQ-TREE with more threads (4) than there are input sequ
   >  --nthreads 4 > /dev/null
   WARNING: more threads requested than there are sequences; falling back to IQ-TREE's `-nt AUTO` mode.
 
+Clean up tree log files.
+
+  $ rm -f tree/*.log
   $ popd > /dev/null

tests/test_align.py

@@ -448,13 +448,7 @@ def test_run_fill_gaps(self, test_file, ref_file, run, fill_gaps):
         assert output["SUFFIX"].seq.endswith(expected_char*3)
         if fill_gaps:
             assert all("-" not in record.seq for record in output.values())
-
-    def test_run_error_during_alignment(self, test_file, argparser, mp_context):
-        """Not a great test - we can't be sure we're not failing some other check somewhere along the way, but it's all we can do"""
-        mp_context.setattr(align, "run_shell_command", lambda i: False)
-        args = argparser("-s %s" % test_file)
-        assert align.run(args) == 1
-
+
     def test_run_debug_files(self, test_file, out_file, run):
         run("-s %s --debug" % test_file)
         assert os.path.isfile(out_file + ".pre_aligner.fasta")