filter: Reorganize Cram test files

.github/workflows/ci.yaml

@@ -43,7 +43,7 @@ jobs:
     - run: conda info
     - run: conda list
     - run: pytest -c pytest.python3.ini --cov=augur
-    - run: cram --shell=/bin/bash tests/functional/*.t tests/builds/*.t
+    - run: cram --shell=/bin/bash tests/
       env:
         AUGUR: coverage run -a ${{ github.workspace }}/bin/augur
         COVERAGE_FILE: ${{ github.workspace }}/.coverage

augur/io.py

@@ -62,19 +62,19 @@ def read_metadata(metadata_file, id_columns=("strain", "name"), chunk_size=None)
 
     For standard use, request a metadata file and get a pandas DataFrame.
 
-    >>> read_metadata("tests/functional/filter/metadata.tsv").index.values[0]
+    >>> read_metadata("tests/functional/filter/data/metadata.tsv").index.values[0]
     'COL/FLR_00024/2015'
 
     Requesting an index column that doesn't exist should produce an error.
 
-    >>> read_metadata("tests/functional/filter/metadata.tsv", id_columns=("Virus name",))
+    >>> read_metadata("tests/functional/filter/data/metadata.tsv", id_columns=("Virus name",))
     Traceback (most recent call last):
       ...
     Exception: None of the possible id columns (('Virus name',)) were found in the metadata's columns ('strain', 'virus', 'accession', 'date', 'region', 'country', 'division', 'city', 'db', 'segment', 'authors', 'url', 'title', 'journal', 'paper_url')
 
     We also allow iterating through metadata in fixed chunk sizes.
 
-    >>> for chunk in read_metadata("tests/functional/filter/metadata.tsv", chunk_size=5):
+    >>> for chunk in read_metadata("tests/functional/filter/data/metadata.tsv", chunk_size=5):
     ...     print(chunk.shape)
     ...
     (5, 14)

run_tests.sh

@@ -22,7 +22,7 @@ python3 -m pytest -c pytest.python3.ini $coverage_arg "$@"
 # Only run functional tests if we are not running a subset of tests for pytest.
 if [ "$partial_test" = 0 ]; then
     echo "Running functional tests with cram"
-    cram --shell=/bin/bash tests/functional/*.t tests/builds/*.t
+    cram --shell=/bin/bash tests/
 else
     echo "Skipping functional tests when running a subset of unit tests"
 fi