Format code and sort imports

Author: davenquinn

py-modules/cli/macrostrat/cli/entrypoint.py

@@ -2,15 +2,16 @@
 from pathlib import Path
 
 import typer
-from macrostrat.app_frame import CommandBase
-from macrostrat.utils.shell import run
 from rich import print
 from rich.traceback import install
 from typer import Argument, Typer
 
+from macrostrat.app_frame import CommandBase
 from macrostrat.core import app
 from macrostrat.core.exc import MacrostratError
 from macrostrat.core.main import env_text, set_app_state
+from macrostrat.utils.shell import run
+
 from .database import db_app, db_subsystem
 from .schema_management import schema_app
 from .subsystems.dev import dev_app
@@ -274,6 +275,7 @@ def update_weaver(db):
 
 try:
     from macrostrat.column_ingestion import app as column_app
+
     main.add_typer(
         column_app,
         name="columns",

py-modules/column-ingestion/macrostrat/column_ingestion/__init__.py

@@ -1,23 +1,18 @@
 from pathlib import Path
 
-from typer import Typer, Argument
+from typer import Argument, Typer
 
 app = Typer(
     no_args_is_help=True,
     help="Column ingestion subsystem for Macrostrat",
 )
 
+
 @app.command(name="ingest")
-def ingest_columns(data_file: Path = Argument(..., help="Path to the data file to ingest")):
+def ingest_columns(
+    data_file: Path = Argument(..., help="Path to the data file to ingest")
+):
     """Ingest columns tabular data."""
     from .ingest import ingest_columns_from_file
 
     ingest_columns_from_file(data_file)
-
-
-
-
-
-
-
-

py-modules/column-ingestion/macrostrat/column_ingestion/columns.py

@@ -2,9 +2,10 @@
 from datetime import datetime
 
 import polars as pl
-from macrostrat.database import Database
 from sqlalchemy.dialects.postgresql import insert
 
+from macrostrat.database import Database
+
 from .database import get_macrostrat_table
 from .units import Unit
 

py-modules/column-ingestion/macrostrat/column_ingestion/database.py

@@ -1,9 +1,10 @@
 import re
 from typing import Optional
 
-from macrostrat.core.database import get_database
 from pydantic import BaseModel
 
+from macrostrat.core.database import get_database
+
 
 class ProjectIdentifier(BaseModel):
     id: Optional[int] = None

py-modules/column-ingestion/macrostrat/column_ingestion/ingest.py

@@ -1,11 +1,12 @@
-from macrostrat.core.database import get_database
 from openpyxl import load_workbook
 
+from macrostrat.core.database import get_database
+
 from .columns import (
     get_column_data,
     get_or_create_column,
-    get_or_create_section,
     get_or_create_column_group,
+    get_or_create_section,
 )
 from .database import get_or_create_project
 from .metadata import get_metadata

py-modules/column-ingestion/macrostrat/column_ingestion/lithologies.py

@@ -1,6 +1,6 @@
 from dataclasses import dataclass
 
-from .database import get_all_liths, get_all_lith_attributes
+from .database import get_all_lith_attributes, get_all_liths
 
 
 @dataclass
@@ -11,6 +11,7 @@ class LithAtt:
     def __hash__(self):
         return hash(self.id)
 
+
 @dataclass
 class Lithology:
     name: str
@@ -21,6 +22,7 @@ def __hash__(self):
         """Hash the lithology based on its id and attributes. This allows us to compare lithologies in tests without worrying about object identity."""
         return hash((self.id, frozenset(self.attributes) if self.attributes else None))
 
+
 class LithsProcessor:
     liths = []
     atts = []
@@ -37,30 +39,39 @@ def match_lith_attribute(self, name) -> LithAtt | None:
 
     def find_lith_attribute(self, text) -> tuple[LithAtt | None, str]:
         """Start consuming text word by word, and check for matches at each step.
-        This allows us to match multi-word attributes like "cross-bedded" or "brownish gray"""
+        This allows us to match multi-word attributes like "cross-bedded" or "brownish gray
+        """
         res, remaining_text = _find_target(text, self.atts)
         if res is not None:
-            res = LithAtt(name=res.name, id=res.id)  # create a new LithAtt object without attributes for now
+            res = LithAtt(
+                name=res.name, id=res.id
+            )  # create a new LithAtt object without attributes for now
         return res, remaining_text
 
     def find_lith(self, text) -> tuple[Lithology | None, str]:
         """Start consuming text word by word, and check for matches at each step.
-        This allows us to match multi-word lithologies like "mixed carbonate-siliciclastic"."""
+        This allows us to match multi-word lithologies like "mixed carbonate-siliciclastic".
+        """
         res, remaining_text = _find_target(text, self.liths)
         if res is not None:
-            res = Lithology(name=res.name, id=res.id)  # create a new Lithology object without attributes for now
+            res = Lithology(
+                name=res.name, id=res.id
+            )  # create a new Lithology object without attributes for now
         return res, remaining_text
 
+
 def _match_target(name, liths):
     for lith in liths:
         if lith.name == name:
             return lith
     return None
 
+
 def _find_target(text, target_list) -> tuple[Lithology | LithAtt | None, str]:
     """Start consuming text word by word, and check for matches at each step.
     Return the first match found, along with remaining text that was not part of the match.
-    This allows us to match multi-word lithologies like "mixed carbonate-siliciclastic" or attributes like "brownish gray"."""
+    This allows us to match multi-word lithologies like "mixed carbonate-siliciclastic" or attributes like "brownish gray".
+    """
     remaining_words = text.split()
     text_to_match = []
     while len(remaining_words) > 0:
@@ -72,16 +83,19 @@ def _find_target(text, target_list) -> tuple[Lithology | LithAtt | None, str]:
     # Return None if no match was found, along with an empty string for remaining text
     return None, text
 
+
 liths_processor = LithsProcessor()
 
 split_words = {"and", "or"}
 
+
 def split_domains(text) -> list[str]:
     """Splits text into parts within which we will search for lithologies and attributes."""
     for split_word in split_words:
         text = text.replace(f" {split_word} ", ";")
     return text.split(";")
 
+
 def process_liths_text(lith) -> set[Lithology]:
     # Process the lithology string to extract information about the rock type, grainsize, color, etc.
     split_lith = split_domains(lith)
@@ -91,7 +105,8 @@ def process_liths_text(lith) -> set[Lithology]:
         output.update(res)
     return output
 
-def process_lith_domain(lith_text) -> set[Lithology] :
+
+def process_lith_domain(lith_text) -> set[Lithology]:
     """
     This function processes a single lithology block that doesn't have a strong separator (semicolon) from other lithologies.
     It looks for a single lithology and any attributes that are associated with it.

py-modules/column-ingestion/macrostrat/column_ingestion/test_lithologies.py

@@ -2,7 +2,7 @@
 
 from pytest import mark
 
-from .lithologies import Lithology, LithAtt, process_liths_text
+from .lithologies import LithAtt, Lithology, process_liths_text
 
 
 @dataclass
@@ -11,22 +11,19 @@ class LithologyTestCase:
     output: set[Lithology]
     expect_error: bool = False
 
+
 sandstone = Lithology(name="sandstone", id=10)
 limestone = Lithology(name="limestone", id=30)
 cross_bedded_sandstone = Lithology(
-    name="sandstone",
-    id=10,
-    attributes={LithAtt(name="cross-bedded", id=17)}
+    name="sandstone", id=10, attributes={LithAtt(name="cross-bedded", id=17)}
 )
 cross_bedded_red_sandstone = Lithology(
     name="sandstone",
     id=10,
-    attributes={LithAtt(name="cross-bedded", id=17), LithAtt(name="red", id=112)}
+    attributes={LithAtt(name="cross-bedded", id=17), LithAtt(name="red", id=112)},
 )
 stromatolitic_dolomite = Lithology(
-    name="dolomite",
-    id=31,
-    attributes={LithAtt(name="stromatolitic", id=78)}
+    name="dolomite", id=31, attributes={LithAtt(name="stromatolitic", id=78)}
 )
 dolomite = Lithology(name="dolomite", id=31)
 chert = Lithology(name="chert", id=45)
@@ -37,31 +34,59 @@ class LithologyTestCase:
     LithologyTestCase("sandstone", {sandstone}),
     LithologyTestCase("limestone; sandstone", {sandstone, limestone}),
     LithologyTestCase("cross-bedded sandstone", {cross_bedded_sandstone}),
-    LithologyTestCase("limestone; cross-bedded sandstone", {limestone, cross_bedded_sandstone}),
+    LithologyTestCase(
+        "limestone; cross-bedded sandstone", {limestone, cross_bedded_sandstone}
+    ),
     LithologyTestCase("cross-bedded, red sandstone", {cross_bedded_red_sandstone}),
-    LithologyTestCase("cross-bedded, red sandstone; stromatolitic dolomite",
-                      {cross_bedded_red_sandstone, stromatolitic_dolomite}),
+    LithologyTestCase(
+        "cross-bedded, red sandstone; stromatolitic dolomite",
+        {cross_bedded_red_sandstone, stromatolitic_dolomite},
+    ),
     LithologyTestCase("stromatolitic dolomite", {stromatolitic_dolomite}),
     #  "stromatoporoid" is not a valid attribute right now)
     # TODO: print a warning for unrecognized attributes, or return them
     LithologyTestCase("stromatoporoid dolomite", {dolomite}),
     # Handle common case where multiple liths are listed with commas instead of semicolons
-    LithologyTestCase("dolomite, limestone, chert, cross-bedded sandstone", {dolomite, limestone, chert, cross_bedded_sandstone}),
+    LithologyTestCase(
+        "dolomite, limestone, chert, cross-bedded sandstone",
+        {dolomite, limestone, chert, cross_bedded_sandstone},
+    ),
     # Play around with some special cases for separators
-    LithologyTestCase("dolomite; limestone; chert; cross-bedded, red sandstone", {dolomite, limestone, chert, cross_bedded_red_sandstone}),
-    LithologyTestCase("dolomite, limestone, chert; cross-bedded, red sandstone", {dolomite, limestone, chert, cross_bedded_red_sandstone}),
-    LithologyTestCase("dolomite, limestone, chert, cross-bedded, red sandstone", {dolomite, limestone, chert, cross_bedded_red_sandstone}),
-    LithologyTestCase("cross-bedded sandstone and chert", {cross_bedded_sandstone, chert}),
+    LithologyTestCase(
+        "dolomite; limestone; chert; cross-bedded, red sandstone",
+        {dolomite, limestone, chert, cross_bedded_red_sandstone},
+    ),
+    LithologyTestCase(
+        "dolomite, limestone, chert; cross-bedded, red sandstone",
+        {dolomite, limestone, chert, cross_bedded_red_sandstone},
+    ),
+    LithologyTestCase(
+        "dolomite, limestone, chert, cross-bedded, red sandstone",
+        {dolomite, limestone, chert, cross_bedded_red_sandstone},
+    ),
+    LithologyTestCase(
+        "cross-bedded sandstone and chert", {cross_bedded_sandstone, chert}
+    ),
     LithologyTestCase("mixed carbonate-siliciclastic", {mixed_carbonate}),
     LithologyTestCase("some rocks and stuff", set()),
-    LithologyTestCase("fractured, brownish gray siltstone, sand, and mixed carbonate-siliciclastic", {
-        mixed_carbonate,
-        sand,
-        Lithology(name="siltstone", id=9, attributes={LithAtt(name="fractured", id=169), LithAtt(name="brownish gray", id=133)})
-    }),
-
+    LithologyTestCase(
+        "fractured, brownish gray siltstone, sand, and mixed carbonate-siliciclastic",
+        {
+            mixed_carbonate,
+            sand,
+            Lithology(
+                name="siltstone",
+                id=9,
+                attributes={
+                    LithAtt(name="fractured", id=169),
+                    LithAtt(name="brownish gray", id=133),
+                },
+            ),
+        },
+    ),
 ]
 
+
 @mark.parametrize("test_case", test_cases)
 def test_process_liths_text(test_case):
     liths = process_liths_text(test_case.input)

py-modules/core/macrostrat/core/config.py

@@ -3,12 +3,13 @@
 
 from dotenv import load_dotenv
 from dynaconf import Dynaconf, Validator
-from macrostrat.app_frame.control_command import BackendType
-from macrostrat.utils import get_logger
 from sqlalchemy.engine import make_url
 from sqlalchemy.engine.url import URL
 from toml import load as load_toml
 
+from macrostrat.app_frame.control_command import BackendType
+from macrostrat.utils import get_logger
+
 from .resolvers import cast_sources, setup_source_roots_environment
 from .utils import convert_to_string, find_macrostrat_config, path_list_resolver
 

py-modules/core/macrostrat/core/main.py

@@ -4,6 +4,9 @@
 
 import toml
 from dynaconf import Dynaconf
+from rich.console import Console
+from typer import Context, Option, get_app_dir
+
 from macrostrat.app_frame import (
     Application,
     ControlCommand,
@@ -12,8 +15,6 @@
 )
 from macrostrat.app_frame.control_command import CommandBase
 from macrostrat.utils import get_logger
-from rich.console import Console
-from typer import Context, Option, get_app_dir
 
 from .console import console_theme
 from .exc import MacrostratError