Update test to exclude augur version comparison

Exclude the Augur version from the diff, otherwise it'll fail on the
next release. Some of these tests were added via this PR but many
weren't, so it's easier to do it all in a single commit.

<#1355 (comment)>

tests/functional/ancestral/cram/case-sensitive.t

@@ -15,7 +15,8 @@ Change the _reference_ to lowercase
 
   $ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" \
   >   "$TESTDIR/../data/simple-genome/nt_muts.ref-seq.json" \
-  >   "nt_muts.ref-seq.json"
+  >   "nt_muts.ref-seq.json" \
+  >   --exclude-paths "root['meta']['updated']" 
   {}
 
 
@@ -36,5 +37,6 @@ be lowecase which will be compared against the uppercase reference
 
   $ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" \
   >   "$TESTDIR/../data/simple-genome/nt_muts.ref-seq.json" \
-  >   "nt_muts.ref-seq.json"
+  >   "nt_muts.ref-seq.json" \
+  >   --exclude-paths "root['meta']['updated']" 
   {}

tests/functional/ancestral/cram/general.t

@@ -19,7 +19,8 @@ node-data JSON we diff against.
 
   $ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" \
   >   "$TESTDIR/../data/simple-genome/nt_muts.ref-seq.json" \
-  >   "nt_muts.ref-seq.json"
+  >   "nt_muts.ref-seq.json" \
+  >   --exclude-paths "root['meta']['updated']" 
   {}
 
 Same as above but without providing a `--root-sequence`. The effect of this on behaviour is:
@@ -38,5 +39,6 @@ mutations (as there's nothing to compare the root node to)
 
   $ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" \
   >   "$TESTDIR/../data/simple-genome/nt_muts.no-ref-seq.json" \
-  >   "nt_muts.no-ref-seq.json"
+  >   "nt_muts.no-ref-seq.json" \
+  >   --exclude-paths "root['meta']['updated']" 
   {}

tests/functional/ancestral/cram/vcf.t

@@ -21,7 +21,7 @@ but it will have the reference sequence attached.
   $ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" \
   >   "$DATA/nt_muts.ref-seq.json" \
   >   "nt_muts.vcf-input.ref-seq.json" \
-  >   --exclude-regex-paths "root\['nodes'\]\['.+'\]\['sequence'\]"
+  >   --exclude-regex-paths "root\['nodes'\]\['.+'\]\['sequence'\]" "root['meta']['updated']"
   {}
 
 Here's the same mutations as in $DATA/nt_muts.ref-seq.json,

tests/functional/translate/cram/general.t

@@ -19,7 +19,7 @@ which validate the output will fail as it's missing a 'nuc' annotation.
   $ python3 "$SCRIPTS/diff_jsons.py" \
   >   "$DATA/aa_muts.json" \
   >   "aa_muts.json" \
-  >   --exclude-regex-paths "root\['annotations'\]\['.+'\]\['seqid'\]"
+  >   --exclude-regex-paths "root\['annotations'\]\['.+'\]\['seqid'\]" "root['meta']['updated']" 
   {}
 
 Same as above but using a GenBank file. This changes the 'type' of the annotations,
@@ -34,5 +34,5 @@ but this is irrelevant for Auspice's use and simply reflects the reference sourc
   $ python3 "$SCRIPTS/diff_jsons.py" \
   >   "$DATA/aa_muts.json" \
   >   "aa_muts.genbank.json" \
-  >   --exclude-regex-paths "root\['annotations'\]\['.+'\]\['seqid'\]" "root\['annotations'\]\['.+'\]\['type'\]" 
+  >   --exclude-regex-paths "root\['annotations'\]\['.+'\]\['seqid'\]" "root\['annotations'\]\['.+'\]\['type'\]" "root['meta']['updated']" 
   {}

tests/functional/translate/cram/genes.t

@@ -23,7 +23,7 @@ as a feature ('nuc' in this case)
   $ python3 "$SCRIPTS/diff_jsons.py" \
   >   "$DATA/aa_muts.json" \
   >   "aa_muts.genes-args.json" \
-  >   --exclude-regex-paths "seqid" "gene1"
+  >   --exclude-regex-paths "seqid" "gene1" "root['meta']['updated']"
   {}
 Using a text file rather than command line arguments
 
@@ -43,5 +43,6 @@ Using a text file rather than command line arguments
 
   $ python3 "$SCRIPTS/diff_jsons.py" \
   >   "aa_muts.genes-args.json" \
-  >   "aa_muts.genes-txt.json"
+  >   "aa_muts.genes-txt.json" \
+  > --exclude-paths "root['meta']['updated']"
   {}

tests/functional/translate/cram/gff.t

@@ -78,7 +78,7 @@ GFF file with 'region' removed, so the only genome information is the ##sequence
   $ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" \
   >   "$DATA/aa_muts.json" \
   >   "aa_muts.pragma-only.json" \
-  >   --exclude-regex-paths "root\['annotations'\]\['.+'\]\['seqid'\]"
+  >   --exclude-regex-paths "root\['annotations'\]\['.+'\]\['seqid'\]" "root['meta']['updated']"
   {}
 
 GFF file with no genome coordinate information

tests/functional/translate/cram/root-mutations.t

@@ -27,5 +27,5 @@ is unchanged (MPCG*). There is also a mutation E4G at the root node to compensat
   $ python3 "$SCRIPTS/diff_jsons.py" \
   >   "$DATA/aa_muts.json" \
   >   "aa_muts.json" \
-  >   --exclude-regex-paths "root\['annotations'\]\['.+'\]\['seqid'\]"
+  >   --exclude-regex-paths "root\['annotations'\]\['.+'\]\['seqid'\]" "root['meta']['updated']"
   {'values_changed': {"root['reference']['gene1']": {'new_value': 'MPCE*', 'old_value': 'MPCG*'}}, 'iterable_item_added': {"root['nodes']['node_root']['aa_muts']['gene1'][0]": 'E4G'}}

tests/functional/translate/cram/translate-with-genbank.t

@@ -18,5 +18,5 @@ Translate amino acids for genes using a GenBank file.
   amino acid mutations written to .* (re)
 
   $ python3 "$SCRIPTS/diff_jsons.py" $DATA/zika/aa_muts_genbank.json aa_muts.json \
-  >  --exclude-regex-paths "root\['annotations'\]\['.+'\]\['seqid'\]"
+  >  --exclude-regex-paths "root\['annotations'\]\['.+'\]\['seqid'\]" "root['meta']['updated']"
   {}

tests/functional/translate/cram/vcf-with-root-mutation.t

@@ -43,5 +43,5 @@ node is E (and so are all the other nodes))
   $ python3 "$SCRIPTS/diff_jsons.py" \
   >   aa_muts.truth.json \
   >   aa_muts.json \
-  >   --exclude-regex-paths "root\['annotations'\]\['.+'\]\['seqid'\]"
+  >   --exclude-regex-paths "root\['annotations'\]\['.+'\]\['seqid'\]" "root['meta']['updated']"
   {}

tests/functional/translate/cram/vcf.t

@@ -26,7 +26,7 @@ Setup
   $ python3 "$SCRIPTS/diff_jsons.py" \
   >   "$DATA/aa_muts.json" \
   >   aa_muts.json \
-  >   --exclude-regex-paths "root\['annotations'\]\['.+'\]\['seqid'\]"
+  >   --exclude-regex-paths "root\['annotations'\]\['.+'\]\['seqid'\]" "root['meta']['updated']"
   {}
 
 ------------------------------   MISSING TEST   ----------------------------------