From 4134a5e665e99b54c8e8f99cf1074b5d3ca7a1d3 Mon Sep 17 00:00:00 2001
From: Francis Charette Migneault <francis.charette.migneault@gmail.com>
Date: Wed, 6 Dec 2023 18:02:12 -0500
Subject: [PATCH] fix module resolution for pytest

---
 .github/workflows/tests.yml                         | 4 +++-
 nlp/notebooks/nl2q_eval/query_eval.py               | 2 +-
 nlp/notebooks/nl2query/V1/Vars_values_textsearch.py | 2 +-
 nlp/notebooks/stac_wrapper/query_handler.py         | 3 ++-
 nlp/tests/test_MetricsClasses.py                    | 3 ++-
 nlp/tests/test_query_eval.py                        | 3 ++-
 setup.cfg                                           | 4 ++--
 7 files changed, 13 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 80cee9e..259e81c 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -101,4 +101,6 @@ jobs:
 
       - name: Run Tests
         if: ${{ steps.check_tests.outputs.HAS_TEST_DIR == 'true' }}
-        run: pytest -vvv ${{ matrix.domain }}/tests
+        run: |
+          cd ${{ matrix.domain }}/notebooks
+          python -m pytest -vvv ../tests
diff --git a/nlp/notebooks/nl2q_eval/query_eval.py b/nlp/notebooks/nl2q_eval/query_eval.py
index 59f12fe..862bf8e 100644
--- a/nlp/notebooks/nl2q_eval/query_eval.py
+++ b/nlp/notebooks/nl2q_eval/query_eval.py
@@ -11,7 +11,6 @@
 import sys
 from typing import Any, Dict, List, MutableMapping, Tuple
 
-from typedefs import JSON
 from nl2q_eval.MetricsClasses import (
     ANNOTATION_TYPES,
     DATA_TYPES,
@@ -23,6 +22,7 @@
     SpanMeasures,
     ValueMeasures
 )
+from typedefs import JSON
 
 
 def eval_query(gold: JSON, test: JSON) -> (DataMeasures, SpanMeasures, AttributeMeasures, ValueMeasures):
diff --git a/nlp/notebooks/nl2query/V1/Vars_values_textsearch.py b/nlp/notebooks/nl2query/V1/Vars_values_textsearch.py
index 74f79bb..8bb2bee 100644
--- a/nlp/notebooks/nl2query/V1/Vars_values_textsearch.py
+++ b/nlp/notebooks/nl2query/V1/Vars_values_textsearch.py
@@ -1,6 +1,5 @@
 from textsearch import TextSearch
 
-from nl2query.V1.vocab.Vocabulary import Vocabulary
 from nl2query.NL2QueryInterface import (
     LocationAnnotation,
     NL2QueryInterface,
@@ -9,6 +8,7 @@
     TargetAnnotation,
     TemporalAnnotation
 )
+from nl2query.V1.vocab.Vocabulary import Vocabulary
 
 
 class Vars_values_textsearch(NL2QueryInterface):
diff --git a/nlp/notebooks/stac_wrapper/query_handler.py b/nlp/notebooks/stac_wrapper/query_handler.py
index b984cb5..17a10f5 100644
--- a/nlp/notebooks/stac_wrapper/query_handler.py
+++ b/nlp/notebooks/stac_wrapper/query_handler.py
@@ -4,9 +4,10 @@
 from configparser import ConfigParser
 
 import ipywidgets as widgets
-from typedefs import JSON
 from pystac_client import Client
 
+from typedefs import JSON
+
 
 class STAC_query_handler:
     """ class to handle running a stac query"""
diff --git a/nlp/tests/test_MetricsClasses.py b/nlp/tests/test_MetricsClasses.py
index f472034..bed6cb5 100644
--- a/nlp/tests/test_MetricsClasses.py
+++ b/nlp/tests/test_MetricsClasses.py
@@ -1,9 +1,10 @@
 import unittest
 
-from tests import GOLD_FILE, TEST_FILE
 from nl2q_eval.MetricsClasses import AttributeMeasures, DataMeasures, SpanMeasures, ValueMeasures
 from nl2q_eval.query_eval import read_files
 
+from ..tests import GOLD_FILE, TEST_FILE
+
 
 class MetricsClassesTests(unittest.TestCase):
 
diff --git a/nlp/tests/test_query_eval.py b/nlp/tests/test_query_eval.py
index a3a58a0..3388d6f 100644
--- a/nlp/tests/test_query_eval.py
+++ b/nlp/tests/test_query_eval.py
@@ -1,6 +1,5 @@
 import unittest
 
-from tests import GOLD_FILE, TEST_FILE
 from nl2q_eval.MetricsClasses import (
     ANNOTATION_TYPES,
     VALUE_TYPES,
@@ -11,6 +10,8 @@
 )
 from nl2q_eval.query_eval import global_stats, read_files
 
+from ..tests import GOLD_FILE, TEST_FILE
+
 annot_counts = {"property": 20, "location": 6, "tempex": 3, "target": 5, "global": 34}
 
 
diff --git a/setup.cfg b/setup.cfg
index f763949..6917156 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -10,6 +10,6 @@ treat_all_comments_as_code = true
 default_section = THIRDPARTY
 sections = FUTURE,STDLIB,THIRDPARTY,FIRSTPARTY,LOCALFOLDER
 extra_standard_library = posixpath,typing,typing_extensions
-known_third_party = cornice_swagger,cwltool,cwt,docker,mock
-known_first_party = nl2q_eval,nl2query,stac_wrapper,tests
+known_third_party = docker,mock
+known_first_party = nl2q_eval,nl2query,stac_wrapper,typedefs,tests
 skip = *.egg*,build,env,src,venv,reports,node_modules