Pin deepdiff to later version

Pins deepdiff to the latest version (8) which includes a fix a PyYAML
dependency issue with Cython [1]. Also, replaces the deep diff CLI
command in a functional test with a custom Python script that uses the
DeepDiff class, working around an issue where the deep diff CLI did not
properly recognize numeric values and caused the functional test to fail
spuriously. This commit should fix CI for Python versions 3.10 and 3.11.

[1] seperman/deepdiff#406

Author: huddlej

pyproject.toml

@@ -30,7 +30,7 @@ dependencies = [
 test = [
     "coverage[toml] >=5.2.1, ==5.*",
     "cram >=0.7, ==0.*",
-    "deepdiff[cli] >=5.2.0, ==5.*",
+    "deepdiff[cli] >=8.0.0, ==8.*",
     "flake8 >=3.9.0, ==3.*",
     "pylint >=2.14.5, ==2.*",
 ]

scripts/diff_tsv.py

@@ -0,0 +1,39 @@
+"""Compare TSV files line by line with deepdiff
+"""
+import argparse
+import deepdiff
+import pandas as pd
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(
+        description="Compare TSV files line by line with deepdiff",
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter
+    )
+    parser.add_argument("first_tsv", help="first TSV to compare")
+    parser.add_argument("second_tsv", help="second TSV to compare")
+    parser.add_argument("--significant-digits", type=int, default=6, help="number of significant digits to use when comparing numeric values")
+
+    args = parser.parse_args()
+
+    first_tsv = pd.read_csv(
+        args.first_tsv,
+        sep="\t",
+        header=None,
+        na_filter=False,
+    ).to_dict()
+
+    second_tsv = pd.read_csv(
+        args.second_tsv,
+        sep="\t",
+        header=None,
+        na_filter=False,
+    ).to_dict()
+
+    print(
+        deepdiff.DeepDiff(
+            first_tsv,
+            second_tsv,
+            significant_digits=args.significant_digits,
+        )
+    )

tests/functional/forecast.t

@@ -9,7 +9,7 @@ Forecast frequencies with a model trained on simulated data.
   >   --model data/simulated_sample_1/normalized_fitness.json \
   >   --delta-months 12 \
   >   --output-table "$TMP/forecasts.tsv" > /dev/null
-  $ deep diff --significant-digits 6 "data/simulated_sample_1/forecasts.tsv" "$TMP/forecasts.tsv"
+  $ python3 ../../scripts/diff_tsv.py "data/simulated_sample_1/forecasts.tsv" "$TMP/forecasts.tsv"
   {}
   $ rm -f "$TMP/forecasts.tsv"