diff --git a/CHANGELOG.md b/CHANGELOG.md index 8fafb06..0cef9b7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,16 @@ # Changelog -## [Unreleased] +## [2.2.0] - 2024-01-04 + +- Update application for Python 3.11 +- Update dependencies including SQLAlchemy 2 + +## [2.0.0] + +- Switch dependency management to Poetry +- Break into submodules + +## [Unknown] - New [notebooks](notebooks) showing [usage in Python](notebooks/Corelle-Basic-Usage.ipynb) and building towards diff --git a/README.md b/README.md index 6c40c85..f306368 100644 --- a/README.md +++ b/README.md @@ -91,9 +91,16 @@ To build (and continuously watch) the frontend, run `make dev`. A backend API server will be started and proxied, so you don't have to run `corelle serve`. -### Installation with Docker +### Testing -Simply install Docker and run `docker-compose up --build` in the root directory. +Corelle contains an extensive set of conformance tests to ensure that it has +GPlates-compatible rotation handling, and to ensure that rotation APIs perform +correctly and performantly in both Python and PostGIS. To run the test suite, +run `make test-docker` in the application directory. + +### Running the web app with Docker + +Install Docker and run `docker-compose up --build` in the root directory. This will build the application, install test data, and spin up the development server. You can run a development version by creating a `.env` file containing @@ -104,8 +111,8 @@ for auto-rebuilding. ## Todo - [x] Fix subtle math bugs! -- [ ] On-database cache of rotations (say, at 1 Ma increments?) -- [ ] Return pre-rotated feature datasets (rather than just modern versions) +- [x] On-database cache of rotations (say, at 1 Ma increments?) +- [x] Return pre-rotated feature datasets (rather than just modern versions) - [x] Materialized view for split feature datasets - [x] Allow feature datasets to be listed - [x] Create a dockerized version diff --git a/bin/test-docker b/bin/test-docker index 5968fce..e5eed35 100755 --- a/bin/test-docker +++ b/bin/test-docker @@ -3,6 +3,12 @@ set -e +# Check if we're in a TTY +TTY_FLAG="" +if [ -t 1 ]; then + TTY_FLAG="-it" +fi + # Load dotenv if it exists if [ -f .env ]; then set -o allexport @@ -44,7 +50,7 @@ docker run --rm \ EOF # Run the tests -docker run -t --rm --link corelle-db:database corelle /code/bin/run-tests $@ +docker run $TTY_FLAG --rm --link corelle-db:database corelle /code/bin/run-tests $@ # Stop the database docker stop corelle-db diff --git a/poetry.lock b/poetry.lock index 5a5cb32..b586b06 100644 --- a/poetry.lock +++ b/poetry.lock @@ -25,20 +25,6 @@ files = [ {file = "annotated_types-0.6.0.tar.gz", hash = "sha256:563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d"}, ] -[package.dependencies] -typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.9\""} - -[[package]] -name = "appnope" -version = "0.1.3" -description = "Disable App Nap on macOS >= 10.9" -optional = false -python-versions = "*" -files = [ - {file = "appnope-0.1.3-py2.py3-none-any.whl", hash = "sha256:265a455292d0bd8a72453494fa24df5a11eb18373a60c7c0430889f22548605e"}, - {file = "appnope-0.1.3.tar.gz", hash = "sha256:02bd91c4de869fbb1e1c50aafc4098827a7a54ab2f39d9dcba6c9547ed920e24"}, -] - [[package]] name = "asttokens" version = "2.4.1" @@ -57,16 +43,6 @@ six = ">=1.12.0" astroid = ["astroid 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-3,18 +3,18 @@ authors = ["Daven Quinn "] description = "An API server application for the Corelle plate-rotation system" license = "MIT" name = "corelle.client" -version = "2.0.0" +version = "2.1.0" packages = [{ include = "corelle" }] [tool.poetry.dependencies] -geopandas = "^0.12.0" +geopandas = "^0.14.1" numpy = "^1.23.4" numpy-quaternion = "^2022.4.2" pandas = "^1.5.1||^2.0.0" -python = "^3.8" -shapely = "^1.8.5.post1||^2.0.0" +python = "^3.9" +shapely = "^2.0.0" [tool.poetry.dev-dependencies] diff --git a/py-packages/engine/corelle/engine/load_data.py b/py-packages/engine/corelle/engine/load_data.py index ce63eb7..d394218 100644 --- a/py-packages/engine/corelle/engine/load_data.py +++ b/py-packages/engine/corelle/engine/load_data.py @@ -13,9 +13,10 @@ from macrostrat.utils import working_directory from wget import download from contextlib import contextmanager -from geoalchemy2 import func as gfunc +from geoalchemy2 import functions as gfunc from geoalchemy2.shape import from_shape from shapely.geometry import shape, MultiPolygon +from macrostrat.database import run_sql from .database import db from .query import get_sql @@ -118,14 +119,13 @@ def import_plates(model_id, datafile, fields={}): # Run database transaction conn = connect() - trans = conn.begin() conn.execute(insert(__plate).values(plates)) for poly in plate_polygons: conn.execute(insert(__plate_polygon).values(poly)) - trans.commit() + conn.commit() # For faster updates, this materialized view could become an actual table - conn.execute("REFRESH MATERIALIZED VIEW corelle.plate_polygon_cache") + run_sql(conn, "REFRESH MATERIALIZED VIEW corelle.plate_polygon_cache") def create_feature(dataset, feature): @@ -151,9 +151,8 @@ def import_features(name, features, overwrite=False): for i, feature in enumerate(src): vals.append(create_feature(name, feature)) - trans = conn.begin() conn.execute(insert(__feature).values(vals)) - trans.commit() + conn.commit() step1 = perf_counter() elapsed = step1 - start @@ -164,9 +163,8 @@ def import_features(name, features, overwrite=False): ) sql = get_sql("cache-feature-dataset") - trans = conn.begin() - conn.execute(sql, dataset_id=name) - trans.commit() + conn.execute(sql, dict(dataset_id=name)) + conn.commit() elapsed = perf_counter() - step1 echo(f" cached transformed features in {elapsed:.2f} seconds") @@ -250,7 +248,7 @@ def import_model( print("Importing model", name) conn = connect() q = text("SELECT count(*) FROM corelle.model WHERE name=:name") - res = conn.execute(q, name=name).scalar() + res = conn.execute(q, dict(name=name)).scalar() if res == 1 and not overwrite: print("Model has already been imported.") return @@ -330,7 +328,7 @@ def load_basic_data(): q = text( "SELECT count(*) FROM (SELECT DISTINCT dataset_id FROM corelle.feature WHERE dataset_id=:name) AS a" ) - res = connect().execute(q, name=dsn).scalar() + res = connect().execute(q, dict(name=dsn)).scalar() if res == 1: continue diff --git a/py-packages/engine/corelle/engine/rotate.py b/py-packages/engine/corelle/engine/rotate.py index a3e9195..75202b4 100644 --- a/py-packages/engine/corelle/engine/rotate.py +++ b/py-packages/engine/corelle/engine/rotate.py @@ -89,7 +89,7 @@ def get_rotation( break else: # Fall back to fetching the data ourselves - pairs = conn.execute(__sql, **params).fetchall() + pairs = conn.execute(__sql, params).fetchall() if len(pairs) == 0: return __cache(None) if verbose: @@ -138,14 +138,14 @@ def get_rotation( def plates_for_model(model): sql = get_sql("plates-for-model") - for row in conn.execute(sql, model_name=model): + for row in conn.execute(sql, dict(model_name=model)): yield row[0] def get_plate_id(point, model, time): sql = get_sql("plate-for-point") return conn.execute( - sql, lon=point[0], lat=point[1], model_name=model, time=time + sql, dict(lon=point[0], lat=point[1], model_name=model, time=time) ).scalar() @@ -170,7 +170,7 @@ def rotate_point(point, model, time): def plates_for_model(model): """Returns a list of plate IDs for a given model""" - return [k[0] for k in conn.execute(__model_plates_sql, model_name=model)] + return [k[0] for k in conn.execute(__model_plates_sql, dict(model_name=model))] def get_all_rotations( @@ -191,14 +191,14 @@ def get_all_rotations( """ if plates is None: if active_only: - res = conn.execute(__active_plates_sql, time=time, model_name=model) + res = conn.execute(__active_plates_sql, dict(time=time, model_name=model)) plates = [p[0] for p in res] else: plates = plates_for_model(model) if rowset is None: _rowset = conn.execute( - __tstep_rotation_pairs, time=time, model_name=model + __tstep_rotation_pairs, dict(time=time, model_name=model) ).fetchall() else: _rowset = [ @@ -228,14 +228,16 @@ def get_rotation_series(model, *times, **kwargs): plate_ages = conn.execute( __plate_time_ranges, - model_name=model, + dict(model_name=model), ).fetchall() rowset = conn.execute( __model_rotation_pairs, - model_name=model, - early_age=float(max(times)), - late_age=float(min(times)), + dict( + model_name=model, + early_age=float(max(times)), + late_age=float(min(times)), + ), ).fetchall() for t in times: t = float(t) diff --git a/py-packages/engine/corelle/tests/rotation_testing_functions.py b/py-packages/engine/corelle/tests/rotation_testing_functions.py index d32baab..ba1dc7e 100644 --- a/py-packages/engine/corelle/tests/rotation_testing_functions.py +++ b/py-packages/engine/corelle/tests/rotation_testing_functions.py @@ -8,6 +8,7 @@ from corelle.engine.database import db from geoalchemy2.shape import to_shape from geoalchemy2.elements import WKBElement +from sqlalchemy import text from corelle.math import sph2cart, cart2sph identity_quaternion = Q.from_float_array([1, 0, 0, 0]) @@ -41,7 +42,7 @@ def rotate_point(point, quaternion, func="corelle.rotate_geometry"): sql = f"SELECT {func}(ST_SetSRID(ST_MakePoint(:lon, :lat), 4326), :quaternion)" # Get the result of the rotation as a WKBElement result = db.session.execute( - sql, + text(sql), params=dict( lon=point[0], lat=point[1], @@ -60,7 +61,7 @@ def rotate_with_ob_tran(start_pos, lon_p, lat_p, lon_0): # Get the result of the rotation as a WKBElement with db.session_scope() as session: result = session.execute( - sql, + text(sql), params=dict( x=start_pos[0], y=start_pos[1], diff --git a/py-packages/engine/corelle/tests/test_database_rotations.py b/py-packages/engine/corelle/tests/test_database_rotations.py index 57fd598..48805b7 100644 --- a/py-packages/engine/corelle/tests/test_database_rotations.py +++ b/py-packages/engine/corelle/tests/test_database_rotations.py @@ -14,6 +14,7 @@ from corelle.math import euler_to_quaternion, sph2cart, cart2sph from pytest import mark from corelle.engine.rotate import get_plate_id, get_rotation +from sqlalchemy import text from .rotation_testing_functions import ( rotation_functions, postgis_rotation_functions, @@ -28,7 +29,7 @@ def test_postgis_noop_rotation(): sql = "SELECT corelle.rotate_geometry(ST_GeomFromText('POINT(0 0)', 4326), :quaternion)" # Get the result of the rotation as a WKBElement result = db.session.execute( - sql, params=dict(quaternion=list(N.array(identity, dtype=float))) + text(sql), params=dict(quaternion=list(N.array(identity, dtype=float))) ).scalar() # Convert the WKBElement to a Shapely geometry geom = to_shape(WKBElement(result)) @@ -91,7 +92,7 @@ def test_postgis_euler_recovery(case): euler = (*case.pole, case.angle) q = euler_to_quaternion(euler) result = db.session.execute( - sql, params=dict(quaternion=[q.w, q.x, q.y, q.z]) + text(sql), params=dict(quaternion=[q.w, q.x, q.y, q.z]) ).scalar() if case.angle == 0: assert result is None @@ -138,7 +139,7 @@ def test_postgis_geometry_rotation(func, geom): assert wkt.loads(geom).is_valid result = session.execute( - sql, params=dict(geom=geom, quaternion=[q.w, q.x, q.y, q.z]) + text(sql), params=dict(geom=geom, quaternion=[q.w, q.x, q.y, q.z]) ).scalar() geom = to_shape(WKBElement(result)) print(geom.wkt) @@ -152,7 +153,7 @@ def test_postgis_geometry_rotation_invalid(geom): with db.session_scope() as session: g0 = wkt.loads(geom) result = session.execute( - sql, params=dict(geom=geom, quaternion=[q.w, q.x, q.y, q.z]) + text(sql), params=dict(geom=geom, quaternion=[q.w, q.x, q.y, q.z]) ).scalar() assert result is not None geom = to_shape(WKBElement(result)) @@ -163,7 +164,7 @@ def _rotate_geom(geom, q, func="corelle.rotate_geometry"): sql = f"SELECT {func}(ST_GeomFromText(:geom, 4326), :quaternion)" with db.session_scope() as session: result = session.execute( - sql, params=dict(geom=geom, quaternion=[q.w, q.x, q.y, q.z]) + text(sql), params=dict(geom=geom, quaternion=[q.w, q.x, q.y, q.z]) ).scalar() assert result is not None return to_shape(WKBElement(result)) @@ -190,7 +191,7 @@ def test_inverse_rotation(geom, func): # Check validity of the input geometry g0 = wkt.loads(geom) result = session.execute( - sql, params=dict(geom=geom, quaternion=[q.w, q.x, q.y, q.z]) + text(sql), params=dict(geom=geom, quaternion=[q.w, q.x, q.y, q.z]) ).scalar() assert result is not None geom = to_shape(WKBElement(result)) @@ -199,7 +200,7 @@ def test_inverse_rotation(geom, func): print(g0.wkt, geom.wkt) # Check that the geometry is the same as the original - assert g0.almost_equals(geom) + assert g0.equals_exact(geom, tolerance=1e-10) def make_quaternion(*arr): @@ -275,7 +276,7 @@ def test_postgis_vector_rotation(q, direction): vx0 = Q.rotate_vectors(q, vx) result = db.session.execute( - "SELECT corelle.rotate_vector(:vector, :quaternion)::float[]", + text("SELECT corelle.rotate_vector(:vector, :quaternion)::float[]"), params=dict(quaternion=[q.w, q.x, q.y, q.z], vector=list(vx)), ).scalar() coords = list(result) diff --git a/py-packages/engine/poetry.lock b/py-packages/engine/poetry.lock index f4e900e..ba4a085 100644 --- a/py-packages/engine/poetry.lock +++ b/py-packages/engine/poetry.lock @@ -11,20 +11,6 @@ files = [ {file = 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modern plate polygons query """ q = get_sql("modern-plate-polygons") - results = conn.execute(q, model_name=model) + results = conn.execute(q, dict(model_name=model)) for row in results: props = dict(row) geom = loads(props.pop("geometry")) @@ -43,7 +43,7 @@ def get_plate_polygons(model): def get_plate_polygons_cached(model): q = get_sql("modern-plate-polygons-cached") - return conn.execute(q, model_name=model).scalar() + return conn.execute(q, dict(model_name=model)).scalar() class ModelResource(Resource): @@ -63,7 +63,7 @@ class Features(ModelResource): def get(self, dataset): args = self.parser.parse_args() q = get_sql("feature-dataset-cached") - return conn.execute(q, model_name=args["model"], dataset=dataset).scalar() + return conn.execute(q, dict(model_name=args["model"], dataset=dataset)).scalar() class ModernPlates(ModelResource): @@ -110,7 +110,7 @@ def get(self): return list(self.get_all(args)) def get_all(self, args): - for (plate_id, q) in get_all_rotations(args["model"], args["time"]): + for plate_id, q in get_all_rotations(args["model"], args["time"]): yield self.reducer(q, args, plate_id) def get_single(self, args): diff --git a/py-packages/server/poetry.lock b/py-packages/server/poetry.lock index df069da..4fb8a7e 100644 --- a/py-packages/server/poetry.lock +++ b/py-packages/server/poetry.lock @@ -25,20 +25,6 @@ files = [ {file = "annotated_types-0.6.0.tar.gz", hash = "sha256:563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d"}, ] -[package.dependencies] -typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.9\""} - -[[package]] -name = "appnope" -version = "0.1.3" -description = "Disable App Nap on macOS >= 10.9" -optional = false -python-versions = "*" -files = [ - {file = "appnope-0.1.3-py2.py3-none-any.whl", hash = "sha256:265a455292d0bd8a72453494fa24df5a11eb18373a60c7c0430889f22548605e"}, - {file = "appnope-0.1.3.tar.gz", hash = "sha256:02bd91c4de869fbb1e1c50aafc4098827a7a54ab2f39d9dcba6c9547ed920e24"}, -] - 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-python-versions = "^3.8" -content-hash = "74162420d0d8500a816c120d49ef189038498b867a81049e6f65ad52d4966685" +python-versions = "^3.9" +content-hash = "4b79e55d53dfa27853098b3ad8c5c9b5f8ea5801e1a3715490822a7bd2cda551" diff --git a/py-packages/server/pyproject.toml b/py-packages/server/pyproject.toml index a903ee6..9d8476d 100644 --- a/py-packages/server/pyproject.toml +++ b/py-packages/server/pyproject.toml @@ -18,8 +18,8 @@ MarkupSafe = "2.0.1" "corelle.engine" = {path = "../engine", develop = true} itsdangerous = "<2.1.0" jinja2 = "<3.1.0" -numpy = "^1.23.4" -python = "^3.8" +numpy = "^1.26.3" +python = "^3.9" simplejson = "^3.17.6" "werkzeug" = "2.0.3" diff --git a/pyproject.toml b/pyproject.toml index acecd2e..81d83b0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -2,19 +2,19 @@ authors = ["Daven Quinn "] description = "An API service to support plate rotations on the web" name = "corelle" -version = "2.1.0" +version = "2.2.0" [tool.poetry.dependencies] -python = ">=3.8,<4.0" 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