Merge pull request #19 from UW-Macrostrat/cli-speed

Fixes to CLI app for quicker importing

Author: davenquinn

.gitignore

@@ -2,4 +2,5 @@
 .pytest_cache
 .ipynb_checkpoints
 .env
-.venv
+.venv
+.idea

py-packages/engine/corelle/engine/cache.py

@@ -2,10 +2,12 @@
 Mapped database models. These would ideally be in the database module, but
 they need to be here to avoid initialization issues.
 """
+
 from sqlalchemy.sql import select
 
 from rich.progress import Progress
 from sqlalchemy.dialects.postgresql import insert
+from sqlalchemy.sql import text
 import numpy as N
 
 from corelle.math import quaternion_to_euler
@@ -47,16 +49,16 @@ def build_rotation_caches():
 def build_rotation_cache(model, time_step=1):
     # Get the time span of the model
 
-    min_age = model["min_age"] or 0
-    max_age = model["max_age"] or 1000
+    min_age = model.min_age or 0
+    max_age = model.max_age or 1000
 
     # Get model steps every 1 Myr
     t_steps = list(range(int(min_age), int(max_age) + 1, time_step))
 
     session = db.session()
 
     session.execute(
-        "DELETE FROM corelle.rotation_cache WHERE model_id = :model_id",
+        text("DELETE FROM corelle.rotation_cache WHERE model_id = :model_id"),
         dict(model_id=model.id),
     )
     session.commit()

py-packages/engine/corelle/engine/cli.py

@@ -1,11 +1,9 @@
 import warnings
 
-import numpy as N
 from IPython import embed
 from os import environ
 import click
 from click import group, argument, option, echo
-from corelle.math import quaternion_to_euler
 from macrostrat.utils import working_directory
 from pathlib import Path
 
@@ -104,6 +102,8 @@ def rotate(model, plate, time, verbose=False):
     """
     Rotate a plate to a time
     """
+    import numpy as N
+    from corelle.math import quaternion_to_euler
     from .rotate import get_rotation
 
     q = get_rotation(model, plate, time, verbose=verbose)
@@ -124,6 +124,7 @@ def rotate_all(model, time, verbose=False):
     """
     Rotate all plates in a model to a time
     """
+    import numpy as N
     from .rotate import get_all_rotations
 
     for plate_id, q in get_all_rotations(model, time, verbose=verbose):

py-packages/engine/pyproject.toml

@@ -3,7 +3,7 @@ authors = ["Daven Quinn <[email protected]>"]
 description = "An API server application for the Corelle plate-rotation system"
 license = "MIT"
 name = "corelle.engine"
-version = "2.0.0"
+version = "2.0.1"
 
 packages = [{ include = "corelle" }]
 
@@ -21,9 +21,9 @@ numpy-quaternion = "^2022.4.2"
 psycopg2-binary = "^2.9.5"
 python = "^3.9"
 rich = "^12.6.0||^13.0.0"
-typer = "^0.7.0||^0.8.0||^0.9.0"
+typer = "^0.7.0||^0.8.0||^0.9.0||^0.10.0||^0.11.0||^0.12.0"
 wget = "^3.2"
-geoalchemy2 = "^0.14.0"
+geoalchemy2 = "^0.14.0||^0.15.0"
 
 [tool.poetry.dev-dependencies]