From 14f70b34235dbf43d68ad72ea74a2020af890072 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Tue, 14 Dec 2021 13:46:40 +0300
Subject: mypy: ignore some imports and errors

* Ignore some missing library stubs
* Ignore some typing errors
* Fix obvious typing errors
---
 gn3/computations/partial_correlations.py |  9 +++++----
 gn3/db/correlations.py                   |  2 +-
 mypy.ini                                 | 12 ++++++++++++
 3 files changed, 18 insertions(+), 5 deletions(-)

diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py
index 95eb5e9..91e953a 100644
--- a/gn3/computations/partial_correlations.py
+++ b/gn3/computations/partial_correlations.py
@@ -259,8 +259,9 @@ def partial_correlations_fast(# pylint: disable=[R0913, R0914]
     ## `correlation_type` parameter
     return len(all_correlations), tuple(
         corr + (
-            (fetched_correlations[corr[0]],) if correlation_type == "literature"
-            else fetched_correlations[corr[0]][0:2])
+            (fetched_correlations[corr[0]],) # type: ignore[index]
+            if correlation_type == "literature"
+            else fetched_correlations[corr[0]][0:2]) # type: ignore[index]
         for idx, corr in enumerate(all_correlations))
 
 def build_data_frame(
@@ -372,7 +373,7 @@ def partial_correlations_normal(# pylint: disable=R0913
             return tuple(item) + (trait_database[1], trait_database[2])
         return item
 
-    target_trait_names, target_trait_vals = reduce(
+    target_trait_names, target_trait_vals = reduce(# type: ignore[var-annotated]
         lambda acc, item: (acc[0]+(item[0],), acc[1]+(item[data_start_pos:],)),
         trait_database, (tuple(), tuple()))
 
@@ -425,7 +426,7 @@ def partial_corrs(# pylint: disable=[R0913]
         data_start_pos, dataset, method)
 
 def literature_correlation_by_list(
-        conn: Any, species: str, trait_list: Tuple[dict]) -> Tuple[dict]:
+        conn: Any, species: str, trait_list: Tuple[dict]) -> Tuple[dict, ...]:
     """
     This is a migration of the
     `web.webqtl.correlation.CorrelationPage.getLiteratureCorrelationByList`
diff --git a/gn3/db/correlations.py b/gn3/db/correlations.py
index 268cfdd..338c0f2 100644
--- a/gn3/db/correlations.py
+++ b/gn3/db/correlations.py
@@ -422,7 +422,7 @@ def fetch_sample_ids(
 
 def build_query_sgo_lit_corr(
         db_type: str, temp_table: str, sample_id_columns: str,
-        joins: Tuple[str, ...]) -> str:
+        joins: Tuple[str, ...]) -> Tuple[str, int]:
     """
     Build query for `SGO Literature Correlation` data, when querying the given
     `temp_table` temporary table.
diff --git a/mypy.ini b/mypy.ini
index b0c48df..ef93008 100644
--- a/mypy.ini
+++ b/mypy.ini
@@ -19,4 +19,16 @@ ignore_missing_imports = True
 ignore_missing_imports = True
 
 [mypy-requests.*]
+ignore_missing_imports = True
+
+[mypy-flask.*]
+ignore_missing_imports = True
+
+[mypy-werkzeug.*]
+ignore_missing_imports = True
+
+[mypy-SPARQLWrapper.*]
+ignore_missing_imports = True
+
+[mypy-pandas.*]
 ignore_missing_imports = True
\ No newline at end of file
-- 
cgit v1.2.3