more linting

.pre-commit-config.yaml

@@ -4,6 +4,7 @@ repos:
   rev: v2.3.0
   hooks:
     - id: check-yaml
+      args: [--allow-multiple-documents]
     - id: end-of-file-fixer
     - id: trailing-whitespace
 
@@ -13,7 +14,7 @@ repos:
   hooks:
     # Run the linter.
     - id: ruff
-      args: [ --fix ]
+      args: [--fix]
     # Run the formatter.
     - id: ruff-format
 

Dockerfile

@@ -1,7 +1,5 @@
 FROM python:3.12
 
-MAINTAINER Daniel Reeves "[email protected]"
-
 ADD --chmod=755 https://astral.sh/uv/install.sh /install.sh
 RUN /install.sh && rm /install.sh
 

alembic/env.py

@@ -61,6 +61,7 @@ def run_migrations_online():
     In this scenario we need to create an Engine and associate a connection
     with the context.
     """
+
     # If you use Alembic revision's --autogenerate flag this function will
     # prevent Alembic from creating an empty migration file if nothing changed.
     # Source: https://alembic.sqlalchemy.org/en/latest/cookbook.html
@@ -80,7 +81,7 @@ def process_revision_directives(context, revision, directives):
         context.configure(
             connection=connection,
             target_metadata=target_metadata,
-            process_revision_directives=process_revision_directives
+            process_revision_directives=process_revision_directives,
         )
 
         with context.begin_transaction():

alembic/versions/rev001.py

@@ -8,6 +8,7 @@
 Create Date: 2022-01-22 15:49:40.837695
 
 """
+
 import sqlalchemy as sa
 from sqlalchemy import schema
 from sqlalchemy.engine.reflection import Inspector
@@ -17,7 +18,7 @@
 
 
 # revision identifiers, used by Alembic.
-revision = '016fff145273'
+revision = "016fff145273"
 down_revision = None
 branch_labels = None
 depends_on = None
@@ -35,44 +36,47 @@ def upgrade():
     # - model_outputs
     # These are rewritten each time; their data doesn't need to be persisted.
 
-    if 'boathouses' not in tables:
-        op.execute(schema.CreateSequence(schema.Sequence('boathouses_id_seq')))
+    if "boathouses" not in tables:
+        op.execute(schema.CreateSequence(schema.Sequence("boathouses_id_seq")))
         op.create_table(
-            'boathouses',
+            "boathouses",
             sa.Column(
-                'id', sa.Integer(), autoincrement=True, nullable=False,
-                server_default=sa.text("nextval('boathouses_id_seq'::regclass)")
+                "id",
+                sa.Integer(),
+                autoincrement=True,
+                nullable=False,
+                server_default=sa.text("nextval('boathouses_id_seq'::regclass)"),
             ),
-            sa.Column('boathouse', sa.String(length=255), nullable=False),
-            sa.Column('reach', sa.Integer(), nullable=True),
-            sa.Column('latitude', sa.Numeric(), nullable=True),
-            sa.Column('longitude', sa.Numeric(), nullable=True),
-            sa.Column('overridden', sa.Boolean(), nullable=True),
-            sa.Column('reason', sa.String(length=255), nullable=True),
-            sa.PrimaryKeyConstraint('boathouse')
+            sa.Column("boathouse", sa.String(length=255), nullable=False),
+            sa.Column("reach", sa.Integer(), nullable=True),
+            sa.Column("latitude", sa.Numeric(), nullable=True),
+            sa.Column("longitude", sa.Numeric(), nullable=True),
+            sa.Column("overridden", sa.Boolean(), nullable=True),
+            sa.Column("reason", sa.String(length=255), nullable=True),
+            sa.PrimaryKeyConstraint("boathouse"),
         )
-        with open(QUERIES_DIR + '/override_event_triggers_v1.sql', 'r') as f:
+        with open(QUERIES_DIR + "/override_event_triggers_v1.sql", "r") as f:
             sql = sa.text(f.read())
             conn.execute(sql)
-    if 'live_website_options' not in tables:
+    if "live_website_options" not in tables:
         op.create_table(
-            'live_website_options',
-            sa.Column('id', sa.Integer(), nullable=False),
-            sa.Column('flagging_message', sa.Text(), nullable=True),
-            sa.Column('boating_season', sa.Boolean(), nullable=False),
-            sa.PrimaryKeyConstraint('id')
+            "live_website_options",
+            sa.Column("id", sa.Integer(), nullable=False),
+            sa.Column("flagging_message", sa.Text(), nullable=True),
+            sa.Column("boating_season", sa.Boolean(), nullable=False),
+            sa.PrimaryKeyConstraint("id"),
         )
-    if 'override_history' not in tables:
+    if "override_history" not in tables:
         op.create_table(
-            'override_history',
-            sa.Column('time', sa.TIMESTAMP(), nullable=True),
-            sa.Column('boathouse', sa.TEXT(), nullable=True),
-            sa.Column('overridden', sa.BOOLEAN(), nullable=True),
-            sa.Column('reason', sa.TEXT(), nullable=True)
+            "override_history",
+            sa.Column("time", sa.TIMESTAMP(), nullable=True),
+            sa.Column("boathouse", sa.TEXT(), nullable=True),
+            sa.Column("overridden", sa.BOOLEAN(), nullable=True),
+            sa.Column("reason", sa.TEXT(), nullable=True),
         )
 
 
 def downgrade():
-    op.drop_table('live_website_options')
-    op.drop_table('boathouses')
-    op.drop_table('override_history')
+    op.drop_table("live_website_options")
+    op.drop_table("boathouses")
+    op.drop_table("override_history")

alembic/versions/rev002.py

@@ -6,6 +6,7 @@
 Create Date: 2022-01-22 17:03:23.094306
 
 """
+
 import sqlalchemy as sa
 from sqlalchemy.engine.reflection import Inspector
 
@@ -14,8 +15,8 @@
 
 
 # revision identifiers, used by Alembic.
-revision = '39a4e575f68c'
-down_revision = '016fff145273'
+revision = "39a4e575f68c"
+down_revision = "016fff145273"
 branch_labels = None
 depends_on = None
 
@@ -27,65 +28,68 @@ def upgrade():
 
     # Create reach association table
     op.create_table(
-        'reach',
-        sa.Column('id', sa.Integer(), nullable=False),
-        sa.PrimaryKeyConstraint('id'),
-        sa.UniqueConstraint('id')
+        "reach",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.PrimaryKeyConstraint("id"),
+        sa.UniqueConstraint("id"),
     )
 
     # We need to make sure that we can add the foreign key constraint to the
     # boathouse relation. If the boathouse table is already populated, this
     # necessitates running this now before adding the constraint.
-    num_boathouses = conn.execute(sa.text('select * from boathouses;')).scalar()
+    num_boathouses = conn.execute(sa.text("select * from boathouses;")).scalar()
     if num_boathouses is not None and num_boathouses > 0:
-        with open(QUERIES_DIR + '/define_reach.sql', 'r') as f:
+        with open(QUERIES_DIR + "/define_reach.sql", "r") as f:
             sql = sa.text(f.read())
             conn.execute(sql)
 
     # Migrate predictions
     # Technically speaking, the types won't match the SQLA schema because Pandas
     # overwrites the tables.
-    if 'model_outputs' in tables:
-        op.alter_column('model_outputs', 'reach', new_column_name='reach_id')
-        op.drop_column('model_outputs', 'log_odds')
-        op.rename_table('model_outputs', 'prediction')
+    if "model_outputs" in tables:
+        op.alter_column("model_outputs", "reach", new_column_name="reach_id")
+        op.drop_column("model_outputs", "log_odds")
+        op.rename_table("model_outputs", "prediction")
     else:
         op.create_table(
-            'prediction',
-            sa.Column('reach_id', sa.Integer(), nullable=False),
-            sa.Column('time', sa.DateTime(), nullable=False),
-            sa.Column('probability', sa.Numeric(), nullable=True),
-            sa.Column('safe', sa.Boolean(), nullable=True),
-            sa.ForeignKeyConstraint(['reach_id'], ['reach.id'], ),
-            sa.PrimaryKeyConstraint('reach_id', 'time')
+            "prediction",
+            sa.Column("reach_id", sa.Integer(), nullable=False),
+            sa.Column("time", sa.DateTime(), nullable=False),
+            sa.Column("probability", sa.Numeric(), nullable=True),
+            sa.Column("safe", sa.Boolean(), nullable=True),
+            sa.ForeignKeyConstraint(
+                ["reach_id"],
+                ["reach.id"],
+            ),
+            sa.PrimaryKeyConstraint("reach_id", "time"),
         )
 
     # Migrate override history.
-    op.alter_column('override_history', 'boathouse', new_column_name='boathouse_name')
+    op.alter_column("override_history", "boathouse", new_column_name="boathouse_name")
 
     # Migrate website options.
-    op.rename_table('live_website_options', 'website_options')
+    op.rename_table("live_website_options", "website_options")
 
     # Migrate boathouse table
-    op.alter_column('boathouses', 'boathouse', new_column_name='name')
-    op.alter_column('boathouses', 'reach', new_column_name='reach_id')
-    op.alter_column('boathouses', 'overridden', server_default='f')
-    op.create_unique_constraint(None, 'boathouses', ['name'])
-    op.create_foreign_key(None, 'boathouses', 'reach', ['reach_id'], ['id'])
-    op.rename_table('boathouses', 'boathouse')
-    with open(QUERIES_DIR + '/override_event_triggers_v2.sql', 'r') as f:
+    op.alter_column("boathouses", "boathouse", new_column_name="name")
+    op.alter_column("boathouses", "reach", new_column_name="reach_id")
+    op.alter_column("boathouses", "overridden", server_default="f")
+    op.create_unique_constraint(None, "boathouses", ["name"])
+    op.create_foreign_key(None, "boathouses", "reach", ["reach_id"], ["id"])
+    op.rename_table("boathouses", "boathouse")
+    with open(QUERIES_DIR + "/override_event_triggers_v2.sql", "r") as f:
         sql = sa.text(f.read())
         conn.execute(sql)
 
 
 def downgrade():
-    op.rename_table('boathouse', 'boathouses')
-    op.drop_constraint(None, 'boathouses', type_='foreignkey')
-    op.drop_constraint(None, 'boathouses', type_='unique')
-    op.alter_column('boathouses', 'name', new_column_name='boathouse')
-    op.alter_column('boathouses', 'reach_id', new_column_name='reach')
-    op.alter_column('boathouses', 'overridden', server_default=None)
-
-    op.drop_table('model_outputs')
-    op.drop_table('prediction')
-    op.drop_table('reach')
+    op.rename_table("boathouse", "boathouses")
+    op.drop_constraint(None, "boathouses", type_="foreignkey")
+    op.drop_constraint(None, "boathouses", type_="unique")
+    op.alter_column("boathouses", "name", new_column_name="boathouse")
+    op.alter_column("boathouses", "reach_id", new_column_name="reach")
+    op.alter_column("boathouses", "overridden", server_default=None)
+
+    op.drop_table("model_outputs")
+    op.drop_table("prediction")
+    op.drop_table("reach")

alembic/versions/rev003.py

@@ -6,19 +6,20 @@
 Create Date: 2023-04-17 17:42:44.755320
 
 """
+
 from alembic import op
 
 
 # revision identifiers, used by Alembic.
-revision = '793fab3b5438'
-down_revision = '39a4e575f68c'
+revision = "793fab3b5438"
+down_revision = "39a4e575f68c"
 branch_labels = None
 depends_on = None
 
 
 def upgrade():
-    op.alter_column('prediction', 'probability', new_column_name='predicted_ecoli_cfu_100ml')
+    op.alter_column("prediction", "probability", new_column_name="predicted_ecoli_cfu_100ml")
 
 
 def downgrade():
-    op.alter_column('prediction', 'predicted_ecoli_cfu_100ml', new_column_name='probability')
+    op.alter_column("prediction", "predicted_ecoli_cfu_100ml", new_column_name="probability")

alembic/versions/rev004.py

@@ -6,19 +6,20 @@
 Create Date: 2023-05-21 12:57:25.545426
 
 """
+
 from alembic import op
 
 
 # revision identifiers, used by Alembic.
-revision = 'e433f34dd4bd'
-down_revision = '793fab3b5438'
+revision = "e433f34dd4bd"
+down_revision = "793fab3b5438"
 branch_labels = None
 depends_on = None
 
 
 def upgrade():
-    op.alter_column('prediction', 'predicted_ecoli_cfu_100ml', new_column_name='probability')
+    op.alter_column("prediction", "predicted_ecoli_cfu_100ml", new_column_name="probability")
 
 
 def downgrade():
-    op.alter_column('prediction', 'probability', new_column_name='predicted_ecoli_cfu_100ml')
+    op.alter_column("prediction", "probability", new_column_name="predicted_ecoli_cfu_100ml")

app/README.md

@@ -1,4 +1,4 @@
-# `/app` Content 
+# `/app` Content
 
   - `/blueprints`: custom endpoints for the flagging website (all the logic that helps to render the HTML pages or JSONs.)
   - `/data`: database, predictive models, and functions to retrieve live data.

app/blueprints/README.md

@@ -1,5 +1,5 @@
 # Contents of blueprints
 
 - `__init__.py`: required to treat directory as a module
-- `frontend.py`: render public facing frontend stuff 
+- `frontend.py`: render public facing frontend stuff
 - `api.py`: provide info and updates on api status

app/blueprints/openapi/boathouse.yml

@@ -37,4 +37,4 @@ responses:
               reason:
                 description: If overridden, we may provide a reason why.
                 type: string
-                x-nullable: true
+                x-nullable: true

app/data/README.md

@@ -3,7 +3,7 @@
 - `/_store`: contains pickle files used to test webpage offline using data provided already from usgus.pickle and hobolink.pickle
 - `__init__.py`: required to treat directory as a package
 - `database.py`: file handling database connection
-- `hobolink.py`: retrieve hobolink by requesting a response and parsing data from hobolink 
-- `model.py`: outputs table model by processing usgs and hobolink data 
-- `task_queue`: set up task queue 
+- `hobolink.py`: retrieve hobolink by requesting a response and parsing data from hobolink
+- `model.py`: outputs table model by processing usgs and hobolink data
+- `task_queue`: set up task queue
 - `usgs.py`: retrieve hobolink by requesting a response and parsing data from usgs

app/static/favicon/site.webmanifest

@@ -1 +1 @@
-{"name":"","short_name":"","icons":[{"src":"/android-chrome-192x192.png","sizes":"192x192","type":"image/png"},{"src":"/android-chrome-512x512.png","sizes":"512x512","type":"image/png"}],"theme_color":"#ffffff","background_color":"#ffffff","display":"standalone"}
+{"name":"","short_name":"","icons":[{"src":"/android-chrome-192x192.png","sizes":"192x192","type":"image/png"},{"src":"/android-chrome-512x512.png","sizes":"512x512","type":"image/png"}],"theme_color":"#ffffff","background_color":"#ffffff","display":"standalone"}

app/static/style.css

@@ -165,7 +165,7 @@ nav a:hover {
   border-top: thin solid #dce9f2;
   box-shadow: 0 4px 10px -2px #dce9f2;
   overflow: hidden;
-  
+
   max-height: 300px; /* exclusively for transition */
   transition: padding 0.3s, max-height 0.3s, border-top-width 0.3s;
 }
@@ -288,7 +288,7 @@ nav a:hover {
   border: 1px solid black;
   border-collapse: collapse;
   padding: 15px;
-  margin: 0 auto;            
+  margin: 0 auto;
 }
 
 .twitter-tweet {

docs/README.md

@@ -10,7 +10,7 @@ There are a lot of extensions included in this documentation in addition to Mate
 
 - Most of the extensions come from [PyMdown Extensions](https://facelessuser.github.io/pymdown-extensions/).
 - We use a tool called [Mermaid](https://mermaid-js.github.io/mermaid-live-editor/) for our flow charts.
-- We use the [macros plugin](https://squidfunk.github.io/mkdocs-material/reference/variables/) but only to parameterize the flagging website URL (the `flagging_website_url` field inside of `mkdocs.yml`). 
+- We use the [macros plugin](https://squidfunk.github.io/mkdocs-material/reference/variables/) but only to parameterize the flagging website URL (the `flagging_website_url` field inside of `mkdocs.yml`).
 
 All of these tools are added and configured inside `mkdocs.yml`. Note you need to pip install them for them to work when you deploy; see deployment script below.
 

docs/mkdocs.yml

@@ -46,7 +46,7 @@ markdown_extensions:
     custom_fences:
     - name: mermaid
       class: mermaid
-      format: !!python/name:pymdownx.superfences.fence_div_format
+      format: "!!python/name:pymdownx.superfences.fence_div_format"
 - sane_lists
 extra:
   flagging_website_url: https://crwa-flagging.herokuapp.com

docs/src/about.md

@@ -29,4 +29,3 @@ The Charles River Watershed Association ("CRWA") was formed in 1965, the same ye
 > CRWA is one of the country’s oldest watershed organizations and has figured prominently in major cleanup and protection efforts. Since our earliest days of advocacy, we have worked with government officials and citizen groups from 35 Massachusetts watershed towns from Hopkinton to Boston.
 
 The EPA also relies on sample data collected by the CRWA to construct its report card.
-