From 76d6a9af91a71401d158bc150518b3c9366030ac Mon Sep 17 00:00:00 2001 From: EugeneTorap Date: Wed, 17 Aug 2022 16:36:36 +0300 Subject: [PATCH] chore: Support Python 3.10 and bump pandas 1.4 and pyarrow 6 (#21002) * Bump pandas 1.4 and pyarrow 6 * Use engine="pyarrow" for pd.read_csv() * Refactoring * Refactoring * Refactoring * Use bytes in pd.read_json() * Fix test_contribution * Fix pandas issue when 'arrays' are empty but 'names' contain values * fix: ValueError: For argument "ascending" expected type bool, received type NoneType. * Remove engine="pyarrow" and convert bytes to string * make copy of selected df to fix regression * Simplify pd.read_json() and pd.read_csv() for example data Co-authored-by: Ville Brofeldt --- CONTRIBUTING.md | 2 +- Makefile | 6 +++--- UPDATING.md | 1 + requirements/base.txt | 4 ++-- setup.py | 5 +++-- superset/examples/bart_lines.py | 6 +++--- superset/examples/birth_names.py | 5 +++-- superset/examples/country_map.py | 8 +++----- superset/examples/energy.py | 6 +++--- superset/examples/flights.py | 10 +++++----- superset/examples/helpers.py | 16 ++-------------- superset/examples/long_lat.py | 6 +++--- superset/examples/multiformat_time_series.py | 6 +++--- superset/examples/paris.py | 6 +++--- superset/examples/random_time_series.py | 6 +++--- superset/examples/sf_population_polygons.py | 6 +++--- superset/examples/world_bank.py | 6 +++--- superset/result_set.py | 3 +++ .../utils/pandas_postprocessing/contribution.py | 3 +++ superset/viz.py | 4 ++-- 20 files changed, 55 insertions(+), 60 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 304038346..3acf5c2da 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -420,7 +420,7 @@ Commits to `master` trigger a rebuild and redeploy of the documentation site. Su Make sure your machine meets the [OS dependencies](https://superset.apache.org/docs/installation/installing-superset-from-scratch#os-dependencies) before following these steps. You also need to install MySQL or [MariaDB](https://mariadb.com/downloads). -Ensure that you are using Python version 3.8 or 3.9, then proceed with: +Ensure that you are using Python version 3.8, 3.9 or 3.10, then proceed with: ```bash # Create a virtual environment and activate it (recommended) diff --git a/Makefile b/Makefile index 84ecd69e9..3caac1b55 100644 --- a/Makefile +++ b/Makefile @@ -15,8 +15,8 @@ # limitations under the License. # -# Python version installed; we need 3.8-3.9 -PYTHON=`command -v python3.9 || command -v python3.8` +# Python version installed; we need 3.8-3.10 +PYTHON=`command -v python3.10 || command -v python3.9 || command -v python3.8` .PHONY: install superset venv pre-commit @@ -70,7 +70,7 @@ update-js: venv: # Create a virtual environment and activate it (recommended) - if ! [ -x "${PYTHON}" ]; then echo "You need Python 3.8 or 3.9 installed"; exit 1; fi + if ! [ -x "${PYTHON}" ]; then echo "You need Python 3.8, 3.9 or 3.10 installed"; exit 1; fi test -d venv || ${PYTHON} -m venv venv # setup a python3 virtualenv . venv/bin/activate diff --git a/UPDATING.md b/UPDATING.md index 6c6ffff64..d53f7cae9 100644 --- a/UPDATING.md +++ b/UPDATING.md @@ -26,6 +26,7 @@ assists people when migrating to a new version. - [20606](https://github.com/apache/superset/pull/20606): When user clicks on chart title or "Edit chart" button in Dashboard page, Explore opens in the same tab. Clicking while holding cmd/ctrl opens Explore in a new tab. To bring back the old behaviour (always opening Explore in a new tab), flip feature flag `DASHBOARD_EDIT_CHART_IN_NEW_TAB` to `True`. - [20799](https://github.com/apache/superset/pull/20799): Presto and Trino engine will now display tracking URL for running queries in SQL Lab. If for some reason you don't want to show the tracking URL (for example, when your data warehouse hasn't enable access for to Presto or Trino UI), update `TRACKING_URL_TRANSFORMER` in `config.py` to return `None`. +- [21002](https://github.com/apache/superset/pull/21002): Support Python 3.10 and bump pandas 1.4 and pyarrow 6. ### Breaking Changes diff --git a/requirements/base.txt b/requirements/base.txt index 505f601ae..ead18fba5 100644 --- a/requirements/base.txt +++ b/requirements/base.txt @@ -185,7 +185,7 @@ packaging==21.3 # via # bleach # deprecation -pandas==1.3.4 +pandas==1.4.3 # via apache-superset parsedatetime==2.6 # via apache-superset @@ -197,7 +197,7 @@ prison==0.2.1 # via flask-appbuilder prompt-toolkit==3.0.28 # via click-repl -pyarrow==5.0.0 +pyarrow==6.0.1 # via apache-superset pycparser==2.20 # via cffi diff --git a/setup.py b/setup.py index 4dfd66dea..1ca612691 100644 --- a/setup.py +++ b/setup.py @@ -100,7 +100,7 @@ setup( "markdown>=3.0", "msgpack>=1.0.0, <1.1", "numpy==1.22.1", - "pandas>=1.3.0, <1.4", + "pandas>=1.4.3, <1.5", "parsedatetime", "pgsanity", "polyline", @@ -108,7 +108,7 @@ setup( "python-dateutil", "python-dotenv", "python-geohash", - "pyarrow>=5.0.0, <6.0", + "pyarrow>=6.0.1, <7", "pyyaml>=5.4", "PyJWT>=2.4.0, <3.0", "redis", @@ -183,5 +183,6 @@ setup( classifiers=[ "Programming Language :: Python :: 3.8", "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", ], ) diff --git a/superset/examples/bart_lines.py b/superset/examples/bart_lines.py index bcdf3589a..91257058b 100644 --- a/superset/examples/bart_lines.py +++ b/superset/examples/bart_lines.py @@ -23,7 +23,7 @@ from sqlalchemy import inspect, String, Text from superset import db from ..utils.database import get_example_database -from .helpers import get_example_data, get_table_connector_registry +from .helpers import get_example_url, get_table_connector_registry def load_bart_lines(only_metadata: bool = False, force: bool = False) -> None: @@ -34,8 +34,8 @@ def load_bart_lines(only_metadata: bool = False, force: bool = False) -> None: table_exists = database.has_table_by_name(tbl_name) if not only_metadata and (not table_exists or force): - content = get_example_data("bart-lines.json.gz") - df = pd.read_json(content, encoding="latin-1") + url = get_example_url("bart-lines.json.gz") + df = pd.read_json(url, encoding="latin-1", compression="gzip") df["path_json"] = df.path.map(json.dumps) df["polyline"] = df.path.map(polyline.encode) del df["path"] diff --git a/superset/examples/birth_names.py b/superset/examples/birth_names.py index b86f7a25c..f8b8a8ecf 100644 --- a/superset/examples/birth_names.py +++ b/superset/examples/birth_names.py @@ -33,7 +33,7 @@ from superset.utils.core import DatasourceType from ..utils.database import get_example_database from .helpers import ( - get_example_data, + get_example_url, get_slice_json, get_table_connector_registry, merge_slice, @@ -66,7 +66,8 @@ def gen_filter( def load_data(tbl_name: str, database: Database, sample: bool = False) -> None: - pdf = pd.read_json(get_example_data("birth_names2.json.gz")) + url = get_example_url("birth_names2.json.gz") + pdf = pd.read_json(url, compression="gzip") # TODO(bkyryliuk): move load examples data into the pytest fixture if database.backend == "presto": pdf.ds = pd.to_datetime(pdf.ds, unit="ms") diff --git a/superset/examples/country_map.py b/superset/examples/country_map.py index c959a9208..302b55180 100644 --- a/superset/examples/country_map.py +++ b/superset/examples/country_map.py @@ -27,7 +27,7 @@ from superset.models.slice import Slice from superset.utils.core import DatasourceType from .helpers import ( - get_example_data, + get_example_url, get_slice_json, get_table_connector_registry, merge_slice, @@ -44,10 +44,8 @@ def load_country_map_data(only_metadata: bool = False, force: bool = False) -> N table_exists = database.has_table_by_name(tbl_name) if not only_metadata and (not table_exists or force): - csv_bytes = get_example_data( - "birth_france_data_for_country_map.csv", is_gzip=False, make_bytes=True - ) - data = pd.read_csv(csv_bytes, encoding="utf-8") + url = get_example_url("birth_france_data_for_country_map.csv") + data = pd.read_csv(url, encoding="utf-8") data["dttm"] = datetime.datetime.now().date() data.to_sql( tbl_name, diff --git a/superset/examples/energy.py b/superset/examples/energy.py index d88d69365..72b22525f 100644 --- a/superset/examples/energy.py +++ b/superset/examples/energy.py @@ -28,7 +28,7 @@ from superset.models.slice import Slice from superset.utils.core import DatasourceType from .helpers import ( - get_example_data, + get_example_url, get_table_connector_registry, merge_slice, misc_dash_slices, @@ -46,8 +46,8 @@ def load_energy( table_exists = database.has_table_by_name(tbl_name) if not only_metadata and (not table_exists or force): - data = get_example_data("energy.json.gz") - pdf = pd.read_json(data) + url = get_example_url("energy.json.gz") + pdf = pd.read_json(url, compression="gzip") pdf = pdf.head(100) if sample else pdf pdf.to_sql( tbl_name, diff --git a/superset/examples/flights.py b/superset/examples/flights.py index 46fdc5c1d..1389c65c9 100644 --- a/superset/examples/flights.py +++ b/superset/examples/flights.py @@ -20,7 +20,7 @@ from sqlalchemy import DateTime, inspect import superset.utils.database as database_utils from superset import db -from .helpers import get_example_data, get_table_connector_registry +from .helpers import get_example_url, get_table_connector_registry def load_flights(only_metadata: bool = False, force: bool = False) -> None: @@ -32,12 +32,12 @@ def load_flights(only_metadata: bool = False, force: bool = False) -> None: table_exists = database.has_table_by_name(tbl_name) if not only_metadata and (not table_exists or force): - data = get_example_data("flight_data.csv.gz", make_bytes=True) - pdf = pd.read_csv(data, encoding="latin-1") + flight_data_url = get_example_url("flight_data.csv.gz") + pdf = pd.read_csv(flight_data_url, encoding="latin-1", compression="gzip") # Loading airports info to join and get lat/long - airports_bytes = get_example_data("airports.csv.gz", make_bytes=True) - airports = pd.read_csv(airports_bytes, encoding="latin-1") + airports_url = get_example_url("airports.csv.gz") + airports = pd.read_csv(airports_url, encoding="latin-1", compression="gzip") airports = airports.set_index("IATA_CODE") pdf[ # pylint: disable=unsupported-assignment-operation,useless-suppression diff --git a/superset/examples/helpers.py b/superset/examples/helpers.py index 8c2ad29f4..e26e05e49 100644 --- a/superset/examples/helpers.py +++ b/superset/examples/helpers.py @@ -17,10 +17,7 @@ """Loads datasets, dashboards and slices in a new superset instance""" import json import os -import zlib -from io import BytesIO from typing import Any, Dict, List, Set -from urllib import request from superset import app, db from superset.connectors.sqla.models import SqlaTable @@ -73,14 +70,5 @@ def get_slice_json(defaults: Dict[Any, Any], **kwargs: Any) -> str: return json.dumps(defaults_copy, indent=4, sort_keys=True) -def get_example_data( - filepath: str, is_gzip: bool = True, make_bytes: bool = False -) -> BytesIO: - content = request.urlopen( # pylint: disable=consider-using-with - f"{BASE_URL}{filepath}?raw=true" - ).read() - if is_gzip: - content = zlib.decompress(content, zlib.MAX_WBITS | 16) - if make_bytes: - content = BytesIO(content) - return content +def get_example_url(filepath: str) -> str: + return f"{BASE_URL}{filepath}?raw=true" diff --git a/superset/examples/long_lat.py b/superset/examples/long_lat.py index ba9824bb4..76f51a615 100644 --- a/superset/examples/long_lat.py +++ b/superset/examples/long_lat.py @@ -27,7 +27,7 @@ from superset.models.slice import Slice from superset.utils.core import DatasourceType from .helpers import ( - get_example_data, + get_example_url, get_slice_json, get_table_connector_registry, merge_slice, @@ -44,8 +44,8 @@ def load_long_lat_data(only_metadata: bool = False, force: bool = False) -> None table_exists = database.has_table_by_name(tbl_name) if not only_metadata and (not table_exists or force): - data = get_example_data("san_francisco.csv.gz", make_bytes=True) - pdf = pd.read_csv(data, encoding="utf-8") + url = get_example_url("san_francisco.csv.gz") + pdf = pd.read_csv(url, encoding="utf-8", compression="gzip") start = datetime.datetime.now().replace( hour=0, minute=0, second=0, microsecond=0 ) diff --git a/superset/examples/multiformat_time_series.py b/superset/examples/multiformat_time_series.py index 9b8bb22c9..62e16d2cb 100644 --- a/superset/examples/multiformat_time_series.py +++ b/superset/examples/multiformat_time_series.py @@ -25,7 +25,7 @@ from superset.utils.core import DatasourceType from ..utils.database import get_example_database from .helpers import ( - get_example_data, + get_example_url, get_slice_json, get_table_connector_registry, merge_slice, @@ -44,8 +44,8 @@ def load_multiformat_time_series( # pylint: disable=too-many-locals table_exists = database.has_table_by_name(tbl_name) if not only_metadata and (not table_exists or force): - data = get_example_data("multiformat_time_series.json.gz") - pdf = pd.read_json(data) + url = get_example_url("multiformat_time_series.json.gz") + pdf = pd.read_json(url, compression="gzip") # TODO(bkyryliuk): move load examples data into the pytest fixture if database.backend == "presto": pdf.ds = pd.to_datetime(pdf.ds, unit="s") diff --git a/superset/examples/paris.py b/superset/examples/paris.py index 264d80fee..c32300702 100644 --- a/superset/examples/paris.py +++ b/superset/examples/paris.py @@ -22,7 +22,7 @@ from sqlalchemy import inspect, String, Text import superset.utils.database as database_utils from superset import db -from .helpers import get_example_data, get_table_connector_registry +from .helpers import get_example_url, get_table_connector_registry def load_paris_iris_geojson(only_metadata: bool = False, force: bool = False) -> None: @@ -33,8 +33,8 @@ def load_paris_iris_geojson(only_metadata: bool = False, force: bool = False) -> table_exists = database.has_table_by_name(tbl_name) if not only_metadata and (not table_exists or force): - data = get_example_data("paris_iris.json.gz") - df = pd.read_json(data) + url = get_example_url("paris_iris.json.gz") + df = pd.read_json(url, compression="gzip") df["features"] = df.features.map(json.dumps) df.to_sql( diff --git a/superset/examples/random_time_series.py b/superset/examples/random_time_series.py index 152b63e1c..4a2628df7 100644 --- a/superset/examples/random_time_series.py +++ b/superset/examples/random_time_series.py @@ -24,7 +24,7 @@ from superset.models.slice import Slice from superset.utils.core import DatasourceType from .helpers import ( - get_example_data, + get_example_url, get_slice_json, get_table_connector_registry, merge_slice, @@ -42,8 +42,8 @@ def load_random_time_series_data( table_exists = database.has_table_by_name(tbl_name) if not only_metadata and (not table_exists or force): - data = get_example_data("random_time_series.json.gz") - pdf = pd.read_json(data) + url = get_example_url("random_time_series.json.gz") + pdf = pd.read_json(url, compression="gzip") if database.backend == "presto": pdf.ds = pd.to_datetime(pdf.ds, unit="s") pdf.ds = pdf.ds.dt.strftime("%Y-%m-%d %H:%M%:%S") diff --git a/superset/examples/sf_population_polygons.py b/superset/examples/sf_population_polygons.py index 6e60d6012..71ba34401 100644 --- a/superset/examples/sf_population_polygons.py +++ b/superset/examples/sf_population_polygons.py @@ -22,7 +22,7 @@ from sqlalchemy import BigInteger, Float, inspect, Text import superset.utils.database as database_utils from superset import db -from .helpers import get_example_data, get_table_connector_registry +from .helpers import get_example_url, get_table_connector_registry def load_sf_population_polygons( @@ -35,8 +35,8 @@ def load_sf_population_polygons( table_exists = database.has_table_by_name(tbl_name) if not only_metadata and (not table_exists or force): - data = get_example_data("sf_population.json.gz") - df = pd.read_json(data) + url = get_example_url("sf_population.json.gz") + df = pd.read_json(url, compression="gzip") df["contour"] = df.contour.map(json.dumps) df.to_sql( diff --git a/superset/examples/world_bank.py b/superset/examples/world_bank.py index 39b982aa5..4a18f806e 100644 --- a/superset/examples/world_bank.py +++ b/superset/examples/world_bank.py @@ -33,7 +33,7 @@ from superset.utils.core import DatasourceType from ..connectors.base.models import BaseDatasource from .helpers import ( - get_example_data, + get_example_url, get_examples_folder, get_slice_json, get_table_connector_registry, @@ -56,8 +56,8 @@ def load_world_bank_health_n_pop( # pylint: disable=too-many-locals, too-many-s table_exists = database.has_table_by_name(tbl_name) if not only_metadata and (not table_exists or force): - data = get_example_data("countries.json.gz") - pdf = pd.read_json(data) + url = get_example_url("countries.json.gz") + pdf = pd.read_json(url, compression="gzip") pdf.columns = [col.replace(".", "_") for col in pdf.columns] if database.backend == "presto": pdf.year = pd.to_datetime(pdf.year) diff --git a/superset/result_set.py b/superset/result_set.py index 725bf1449..b8a5abb6d 100644 --- a/superset/result_set.py +++ b/superset/result_set.py @@ -161,6 +161,9 @@ class SupersetResultSet: except Exception as ex: # pylint: disable=broad-except logger.exception(ex) + if not pa_data: + column_names = [] + self.table = pa.Table.from_arrays(pa_data, names=column_names) self._type_dict: Dict[str, Any] = {} try: diff --git a/superset/utils/pandas_postprocessing/contribution.py b/superset/utils/pandas_postprocessing/contribution.py index 2bfc6f4be..86ef27139 100644 --- a/superset/utils/pandas_postprocessing/contribution.py +++ b/superset/utils/pandas_postprocessing/contribution.py @@ -49,6 +49,9 @@ def contribution( """ contribution_df = df.copy() numeric_df = contribution_df.select_dtypes(include=["number", Decimal]) + # TODO: copy needed due to following regression in 1.4, remove if not needed: + # https://github.com/pandas-dev/pandas/issues/48090 + numeric_df = numeric_df.copy() numeric_df.fillna(0, inplace=True) # verify column selections if columns: diff --git a/superset/viz.py b/superset/viz.py index 8da909875..42de86497 100644 --- a/superset/viz.py +++ b/superset/viz.py @@ -2172,14 +2172,14 @@ class FilterBoxViz(BaseViz): if df is not None and not df.empty: if metric: df = df.sort_values( - utils.get_metric_name(metric), ascending=flt.get("asc") + utils.get_metric_name(metric), ascending=flt.get("asc", False) ) data[col] = [ {"id": row[0], "text": row[0], "metric": row[1]} for row in df.itertuples(index=False) ] else: - df = df.sort_values(col, ascending=flt.get("asc")) + df = df.sort_values(col, ascending=flt.get("asc", False)) data[col] = [ {"id": row[0], "text": row[0]} for row in df.itertuples(index=False)