Upgrade SQLAlchemy to 2.0.22 and Pandas to 1.5.3

augur/api/metrics/README.md

@@ -26,7 +26,7 @@ from augur.application.db.engine import engine
 4. Define any queries with the structure show below
 ```py
 repo_sql = s.sql.text(""" SELECT repo.repo_name FROM repo WHERE repo.repo_id = :repo_id """)
-results = pd.read_sql(repo_sql, engine, params={'repo_id': repo_id})
+results = pd.read_sql(repo_sql, engine.connect(), params={'repo_id': repo_id})
 ```
 5. Return either a pandas dataframe, dict, or json.
     - Note: If you return a pandas dataframe or dict it will be automatically converted into json

augur/api/metrics/commit.py

@@ -90,7 +90,7 @@ def committers(repo_group_id, repo_id=None, begin_date=None, end_date=None, peri
             """
         )
 
-    results = pd.read_sql(committersSQL, engine, params={'repo_id': repo_id, 
+    results = pd.read_sql(committersSQL, engine.connect(), params={'repo_id': repo_id, 
         'repo_group_id': repo_group_id,'begin_date': begin_date, 'end_date': end_date, 'period':period})
 
     return results
@@ -167,7 +167,7 @@ def annual_commit_count_ranked_by_new_repo_in_repo_group(repo_group_id, repo_id=
             ORDER BY YEAR ASC
         """.format(table, period))
 
-    results = pd.read_sql(cdRgNewrepRankedCommitsSQL, engine, params={'repo_id': repo_id, 
+    results = pd.read_sql(cdRgNewrepRankedCommitsSQL, engine.connect(), params={'repo_id': repo_id, 
         'repo_group_id': repo_group_id,'begin_date': begin_date, 'end_date': end_date})
     return results
 
@@ -265,7 +265,7 @@ def annual_commit_count_ranked_by_repo_in_repo_group(repo_group_id, repo_id=None
                 LIMIT 10
             """)
 
-    results = pd.read_sql(cdRgTpRankedCommitsSQL, engine, params={ "repo_group_id": repo_group_id,
+    results = pd.read_sql(cdRgTpRankedCommitsSQL, engine.connect(), params={ "repo_group_id": repo_group_id,
     "repo_id": repo_id})
     return results
 
@@ -296,7 +296,7 @@ def top_committers(repo_group_id, repo_id=None, year=None, threshold=0.8):
                 ORDER BY patches DESC) a
         """)
 
-        results = pd.read_sql(total_commits_SQL, engine,
+        results = pd.read_sql(total_commits_SQL, engine.connect(),
                             params={'year': year, 'repo_group_id': repo_group_id})
     else:
         total_commits_SQL = s.sql.text("""
@@ -308,7 +308,7 @@ def top_committers(repo_group_id, repo_id=None, year=None, threshold=0.8):
                 ORDER BY patches DESC) a
         """)
 
-        results = pd.read_sql(total_commits_SQL, engine,
+        results = pd.read_sql(total_commits_SQL, engine.connect(),
                             params={'year': year, 'repo_id': repo_id})
 
     if not results.iloc[0]['sum']:
@@ -334,7 +334,7 @@ def top_committers(repo_group_id, repo_id=None, year=None, threshold=0.8):
             ORDER BY commits DESC
         """)
 
-        results = pd.read_sql(committers_SQL, engine,
+        results = pd.read_sql(committers_SQL, engine.connect(),
                             params={'year': year, 'repo_group_id': repo_group_id})
     else:
         committers_SQL = s.sql.text("""
@@ -353,7 +353,7 @@ def top_committers(repo_group_id, repo_id=None, year=None, threshold=0.8):
             ORDER BY commits DESC
         """)
 
-        results = pd.read_sql(committers_SQL, engine,
+        results = pd.read_sql(committers_SQL, engine.connect(),
                             params={'year': year, 'repo_id': repo_id})
 
     cumsum = 0

augur/api/metrics/contributor.py

@@ -125,7 +125,7 @@ def contributors(repo_group_id, repo_id=None, period='day', begin_date=None, end
             ORDER BY total DESC
         """)
 
-        results = pd.read_sql(contributorsSQL, engine, params={'repo_id': repo_id, 'period': period,
+        results = pd.read_sql(contributorsSQL, engine.connect(), params={'repo_id': repo_id, 'period': period,
                                                                 'begin_date': begin_date, 'end_date': end_date})
     else:
         contributorsSQL = s.sql.text("""
@@ -211,7 +211,7 @@ def contributors(repo_group_id, repo_id=None, period='day', begin_date=None, end
             ORDER BY total DESC
         """)
 
-        results = pd.read_sql(contributorsSQL, engine, params={'repo_group_id': repo_group_id, 'period': period,
+        results = pd.read_sql(contributorsSQL, engine.connect(), params={'repo_group_id': repo_group_id, 'period': period,
                                                             'begin_date': begin_date, 'end_date': end_date})
     return results
 
@@ -281,7 +281,7 @@ def contributors_new(repo_group_id, repo_id=None, period='day', begin_date=None,
             GROUP BY date, repo.repo_id, repo_name
             """)
 
-        results = pd.read_sql(contributorsNewSQL, engine, params={'repo_id': repo_id, 'period': period,
+        results = pd.read_sql(contributorsNewSQL, engine.connect(), params={'repo_id': repo_id, 'period': period,
                                                                 'begin_date': begin_date, 'end_date': end_date})
     else:
         contributorsNewSQL = s.sql.text("""
@@ -330,7 +330,7 @@ def contributors_new(repo_group_id, repo_id=None, period='day', begin_date=None,
             GROUP BY date, repo.repo_id, repo_name
             """)
 
-        results = pd.read_sql(contributorsNewSQL, engine, params={'repo_group_id': repo_group_id, 'period': period,
+        results = pd.read_sql(contributorsNewSQL, engine.connect(), params={'repo_group_id': repo_group_id, 'period': period,
                                                                    'begin_date': begin_date, 'end_date': end_date})
     return results
 
@@ -351,7 +351,7 @@ def lines_changed_by_author(repo_group_id, repo_id=None):
             GROUP BY commits.repo_id, date_trunc('week', cmt_author_date::date), cmt_author_affiliation, cmt_author_email, repo_name
             ORDER BY date_trunc('week', cmt_author_date::date) ASC;
         """)
-        results = pd.read_sql(linesChangedByAuthorSQL, engine, params={"repo_id": repo_id})
+        results = pd.read_sql(linesChangedByAuthorSQL, engine.connect(), params={"repo_id": repo_id})
         return results
     else:
         linesChangedByAuthorSQL = s.sql.text("""
@@ -362,7 +362,7 @@ def lines_changed_by_author(repo_group_id, repo_id=None):
             GROUP BY repo_id, date_trunc('week', cmt_author_date::date), cmt_author_affiliation, cmt_author_email
             ORDER BY date_trunc('week', cmt_author_date::date) ASC;
         """)
-        results = pd.read_sql(linesChangedByAuthorSQL, engine, params={"repo_group_id": repo_group_id})
+        results = pd.read_sql(linesChangedByAuthorSQL, engine.connect(), params={"repo_group_id": repo_group_id})
         return results
 
 @register_metric()
@@ -420,7 +420,7 @@ def contributors_code_development(repo_group_id, repo_id=None, period='all', beg
             GROUP BY a.email, a.repo_id, repo_name
         """)
 
-        results = pd.read_sql(contributorsSQL, engine, params={'repo_id': repo_id, 'period': period,
+        results = pd.read_sql(contributorsSQL, engine.connect(), params={'repo_id': repo_id, 'period': period,
                                                                 'begin_date': begin_date, 'end_date': end_date})
     else:
         contributorsSQL = s.sql.text("""
@@ -455,6 +455,6 @@ def contributors_code_development(repo_group_id, repo_id=None, period='all', beg
             ORDER BY commits desc, email
         """)
 
-        results = pd.read_sql(contributorsSQL, engine, params={'repo_group_id': repo_group_id, 'period': period,
+        results = pd.read_sql(contributorsSQL, engine.connect(), params={'repo_group_id': repo_group_id, 'period': period,
                                                                 'begin_date': begin_date, 'end_date': end_date})
     return results

augur/api/metrics/deps.py

@@ -6,6 +6,7 @@
 import sqlalchemy as s
 import pandas as pd
 from augur.api.util import register_metric
+import datetime
 
 from ..server import engine
 
@@ -45,7 +46,7 @@ def deps(repo_group_id, repo_id=None, period='day', begin_date=None, end_date=No
             AND repo_dependencies.repo_id = :repo_id
             """)
 
-        results = pd.read_sql(depsSQL, engine)    	
+        results = pd.read_sql(depsSQL, engine.connect())    	
 
     else:
 
@@ -69,7 +70,7 @@ def deps(repo_group_id, repo_id=None, period='day', begin_date=None, end_date=No
             AND repo.repo_group_id = :repo_group_id
             """)
 
-        results = pd.read_sql(depsSQL, engine)
+        results = pd.read_sql(depsSQL, engine.connect())
     return results
 
 

augur/api/metrics/insight.py

@@ -29,5 +29,5 @@ def top_insights(repo_group_id, num_repos=6):
             LIMIT :num_repos
         )
     """)
-    results = pd.read_sql(topInsightsSQL, engine, params={'repo_group_id': repo_group_id, 'num_repos': num_repos})
+    results = pd.read_sql(topInsightsSQL, engine.connect(), params={'repo_group_id': repo_group_id, 'num_repos': num_repos})
     return results