Save some lines in test files by excluding all generated_by by default

Author: corneliusroemer

Diff for: scripts/diff_jsons.py

@@ -16,7 +16,7 @@
     parser.add_argument("first_json", help="first JSON to compare")
     parser.add_argument("second_json", help="second JSON to compare")
     parser.add_argument("--significant-digits", type=int, default=5, help="number of significant digits to use when comparing numeric values")
-    parser.add_argument("--exclude-paths", nargs="+", action=ExtendOverwriteDefault, help="list of paths to exclude from consideration when performing a diff", default=["root['generated_by']['version']", "root['meta']['updated']"])
+    parser.add_argument("--exclude-paths", nargs="+", action=ExtendOverwriteDefault, help="list of paths to exclude from consideration when performing a diff", default=["root['generated_by']", "root['meta']['updated']"])
     parser.add_argument("--exclude-regex-paths", nargs="+", action="extend", help="list of path regular expressions to exclude from consideration when performing a diff")
     parser.add_argument("--ignore-numeric-type-changes", action="store_true", help="ignore numeric type changes in the diff (e.g., int of 1 to float of 1.0)")
 

Diff for: tests/functional/ancestral/cram/case-sensitive.t

@@ -15,8 +15,7 @@ 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" \
-  >   --exclude-paths "root['generated_by']"
+  >   "nt_muts.ref-seq.json" 
   {}
 
 
@@ -37,6 +36,5 @@ 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" \
-  >   --exclude-paths "root['generated_by']"
+  >   "nt_muts.ref-seq.json"
   {}

Diff for: tests/functional/ancestral/cram/general.t

@@ -19,8 +19,7 @@ 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" \
-  >   --exclude-paths "root['generated_by']"
+  >   "nt_muts.ref-seq.json"
   {}
 
 Same as above but without providing a `--root-sequence`. The effect of this on behaviour is:
@@ -39,6 +38,5 @@ 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" \
-  >   --exclude-paths "root['generated_by']"
+  >   "nt_muts.no-ref-seq.json"
   {}

Diff for: tests/functional/clades/cram/membership-and-label.t

@@ -13,6 +13,5 @@ Test custom membership key + label key. The only change should be the key names
 
   $ cat clades_custom.json | sed "s/lineage/clade_membership/" | sed "s/origin/clade/" > clades_sed.json
 
-  $ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" "$TESTDIR/../data/clades.json" clades_sed.json \
-  >   --exclude-paths "root['generated_by']"
+  $ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" "$TESTDIR/../data/clades.json" clades_sed.json
   {}

Diff for: tests/functional/clades/cram/no-label.t

@@ -11,6 +11,5 @@ Test the ability to _not_ export a branch label (same logic as not exporting the
   >   --label-name none \
   >   --output-node-data clades_no-labels.json &>/dev/null
 
-  $ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" "$TESTDIR/../data/clades.json" clades_no-labels.json \
-  >   --exclude-paths "root['generated_by']"
+  $ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" "$TESTDIR/../data/clades.json" clades_no-labels.json
   {'dictionary_item_removed': [root['branches']]}

Diff for: tests/functional/clades/cram/root-clade-identification.t

@@ -12,8 +12,7 @@ This is an oversight and ideally would be fixed
   >   --clades "$TESTDIR/../data/toy_clades_nuc.tsv" \
   >   --output-node-data toy_clades_1.json &>/dev/null
 
-  $ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" "$TESTDIR/../data/toy_clades_1.json" toy_clades_1.json \
-  >   --exclude-paths "root['generated_by']"
+  $ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" "$TESTDIR/../data/toy_clades_1.json" toy_clades_1.json
   {}
 
 A clade which exists at the root is identified (and correctly propogated) if the root sequence
@@ -25,8 +24,7 @@ is explicitly set.
   >   --clades "$TESTDIR/../data/toy_clades_nuc.tsv" \
   >   --output-node-data toy_clades_2a.json &>/dev/null
 
-  $ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" "$TESTDIR/../data/toy_clades_2.json" toy_clades_2a.json \
-  >   --exclude-paths "root['generated_by']"
+  $ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" "$TESTDIR/../data/toy_clades_2.json" toy_clades_2a.json
   {}
 
 A clade which exists at the root is identified (and correctly propogated) without a root sequence
@@ -38,6 +36,5 @@ if the (branch leading to the) root has the clade-defining mutation.
   >   --clades "$TESTDIR/../data/toy_clades_nuc.tsv" \
   >   --output-node-data toy_clades_2b.json &>/dev/null
 
-  $ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" "$TESTDIR/../data/toy_clades_2.json" toy_clades_2b.json \
-  >   --exclude-paths "root['generated_by']"
+  $ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" "$TESTDIR/../data/toy_clades_2.json" toy_clades_2b.json
   {}

Diff for: tests/functional/refine/cram/not-timetree-mutations-per-site.t

@@ -28,5 +28,5 @@ Confirm that trees match expected topology and branch lengths, given that the ou
   >   "$TESTDIR/../data/mutations_per_site_branch_lengths.json" \
   >   branch_lengths.json \
   >   --significant-digits 0 \
-  >   --exclude-paths "root['generated_by']['version']" "root['input_tree']"
+  >   --exclude-paths "generated_by" "input_tree"
   {}

Diff for: tests/functional/refine/cram/not-timetree-mutations.t

@@ -29,5 +29,5 @@ Confirm that trees match expected topology and branch lengths, given that the ou
   >   "$TESTDIR/../data/integer_branch_lengths.json" \
   >   branch_lengths.json \
   >   --significant-digits 0 \
-  >   --exclude-paths "root['generated_by']['version']" "root['input_tree']" "root['alignment']"
+  >   --exclude-paths "generated_by" "input_tree" "alignment"
   {}