From 38cbedf280da695f1aadc585b625b3428cffd684 Mon Sep 17 00:00:00 2001 From: Martin Bernstorff Date: Fri, 30 Aug 2024 11:17:46 +0200 Subject: [PATCH 01/38] initialise_specs_from_primitives From b652623ec3437de7a25802da4e2a0f77f02695a0 Mon Sep 17 00:00:00 2001 From: Martin Bernstorff Date: Fri, 30 Aug 2024 12:51:17 +0200 Subject: [PATCH 02/38] update 5 files --- src/timeseriesflattener/aggregators.py | 44 ++++++++++++++- src/timeseriesflattener/specs/outcome.py | 62 +++++++++++++++++++++- src/timeseriesflattener/specs/static.py | 14 +++++ src/timeseriesflattener/specs/temporal.py | 32 ++++++++++- src/timeseriesflattener/specs/timedelta.py | 21 ++++++++ 5 files changed, 170 insertions(+), 3 deletions(-) diff --git a/src/timeseriesflattener/aggregators.py b/src/timeseriesflattener/aggregators.py index 659a4724..041af936 100644 --- a/src/timeseriesflattener/aggregators.py +++ b/src/timeseriesflattener/aggregators.py @@ -2,9 +2,11 @@ import datetime as dt from abc import ABC, abstractmethod +from typing import Literal, Sequence import polars as pl from attr import dataclass +from timeseriesflattener.specs import timestamp def validate_compatible_fallback_type_for_aggregator( @@ -18,6 +20,46 @@ def validate_compatible_fallback_type_for_aggregator( ) +AggregatorName = Literal[ + "max", + "min", + "mean", + "sum", + "count", + "variance", + "bool", + "change_per_day", + "slope", + "has_values", +] + + +def strings_to_aggregators( + aggregator_names: Sequence[AggregatorName], timestamp_col_name: str +) -> Sequence[Aggregator]: + return [ + string_to_aggregator(name, timestamp_col_name=timestamp_col_name) + for name in aggregator_names + ] + + +def string_to_aggregator(aggregator_name: AggregatorName, timestamp_col_name: str) -> Aggregator: + str2aggr: dict[AggregatorName, Aggregator] = { + "max": MaxAggregator(), + "min": MinAggregator(), + "mean": MeanAggregator(), + "sum": SumAggregator(), + "count": CountAggregator(), + "variance": VarianceAggregator(), + "bool": HasValuesAggregator(), + "change_per_day": SlopeAggregator(timestamp_col_name=timestamp_col_name), + "slope": SlopeAggregator(timestamp_col_name=timestamp_col_name), + "has_values": HasValuesAggregator(), + } + + return str2aggr[aggregator_name] + + class Aggregator(ABC): name: str output_type: type[float | int | bool] @@ -125,7 +167,7 @@ def __call__(self, column_name: str) -> pl.Expr: class HasValuesAggregator(Aggregator): - """Examines whether any values exist in the column. If so, returns True, else False.""" + """Examines whether any values exist in the look window. If so, returns True, else False.""" name: str = "bool" output_type = bool diff --git a/src/timeseriesflattener/specs/outcome.py b/src/timeseriesflattener/specs/outcome.py index 18622081..d33c20fe 100644 --- a/src/timeseriesflattener/specs/outcome.py +++ b/src/timeseriesflattener/specs/outcome.py @@ -8,7 +8,11 @@ from ..validators import validate_col_name_columns_exist from .value import ValueFrame, lookdistance_to_normalised_lookperiod -from ..aggregators import validate_compatible_fallback_type_for_aggregator +from ..aggregators import ( + AggregatorName, + strings_to_aggregators, + validate_compatible_fallback_type_for_aggregator, +) if TYPE_CHECKING: from collections.abc import Sequence @@ -17,6 +21,14 @@ from .timestamp import TimestampValueFrame +def _lookdistance_to_timedelta( + lookdistance: float | tuple[float, float], +) -> tuple[dt.timedelta, dt.timedelta]: + if isinstance(lookdistance, tuple): + return (dt.timedelta(days=lookdistance[0]), dt.timedelta(days=lookdistance[1])) + return (dt.timedelta(days=0), dt.timedelta(days=lookdistance)) + + @dataclass class OutcomeSpec: """Specification for an outcome. If your outcome is binary/boolean, you can use BooleanOutcomeSpec instead.""" @@ -44,6 +56,30 @@ def __post_init__( def df(self) -> pl.DataFrame: return self.value_frame.df + @staticmethod + def from_primitives( + df: pl.DataFrame, + entity_id_col_name: str, + lookahead_days: Sequence[float | tuple[float, float]], + aggregators: Sequence[AggregatorName], + value_timestamp_col_name: str = "timestamp", + column_prefix: str = "outc", + ) -> OutcomeSpec: + """Create an OutcomeSpec from primitives.""" + lookahead_distances = [_lookdistance_to_timedelta(d) for d in lookahead_days] + + return OutcomeSpec( + value_frame=ValueFrame( + init_df=df, + entity_id_col_name=entity_id_col_name, + value_timestamp_col_name=value_timestamp_col_name, + ), + lookahead_distances=lookahead_distances, + aggregators=strings_to_aggregators(aggregators, value_timestamp_col_name), + fallback=0, + column_prefix=column_prefix, + ) + @dataclass class BooleanOutcomeSpec: @@ -81,3 +117,27 @@ def __post_init__(self, init_frame: TimestampValueFrame): @property def df(self) -> pl.DataFrame: return self.value_frame.df + + @staticmethod + def from_primitives( + df: pl.DataFrame, + entity_id_col_name: str, + lookahead_days: Sequence[float | tuple[float, float]], + aggregators: Sequence[AggregatorName], + value_timestamp_col_name: str = "timestamp", + column_prefix: str = "outc", + ) -> BooleanOutcomeSpec: + """Create an OutcomeSpec from primitives.""" + lookahead_distances = [_lookdistance_to_timedelta(d) for d in lookahead_days] + + return BooleanOutcomeSpec( + init_frame=TimestampValueFrame( + init_df=df, + value_timestamp_col_name=value_timestamp_col_name, + entity_id_col_name=entity_id_col_name, + ), + lookahead_distances=lookahead_distances, + aggregators=strings_to_aggregators(aggregators, value_timestamp_col_name), + output_name=column_prefix, + column_prefix=column_prefix, + ) diff --git a/src/timeseriesflattener/specs/static.py b/src/timeseriesflattener/specs/static.py index 63f53c6a..15cab5d0 100644 --- a/src/timeseriesflattener/specs/static.py +++ b/src/timeseriesflattener/specs/static.py @@ -38,3 +38,17 @@ class StaticSpec: value_frame: StaticFrame column_prefix: str fallback: int | float | str | None + + @staticmethod + def from_primitives( + df: pl.DataFrame, + entity_id_col_name: str, + column_prefix: str, + fallback: int | float | str | None, + ) -> StaticSpec: + """Create a StaticSpec from primitives.""" + return StaticSpec( + value_frame=StaticFrame(init_df=df, entity_id_col_name=entity_id_col_name), + column_prefix=column_prefix, + fallback=fallback, + ) diff --git a/src/timeseriesflattener/specs/temporal.py b/src/timeseriesflattener/specs/temporal.py index 829aeaeb..7e9ca930 100644 --- a/src/timeseriesflattener/specs/temporal.py +++ b/src/timeseriesflattener/specs/temporal.py @@ -4,9 +4,15 @@ from dataclasses import InitVar, dataclass from typing import TYPE_CHECKING +from timeseriesflattener.specs.outcome import _lookdistance_to_timedelta + from ..validators import validate_col_name_columns_exist from .value import ValueFrame, lookdistance_to_normalised_lookperiod -from ..aggregators import validate_compatible_fallback_type_for_aggregator +from ..aggregators import ( + AggregatorName, + strings_to_aggregators, + validate_compatible_fallback_type_for_aggregator, +) if TYPE_CHECKING: from collections.abc import Sequence @@ -48,3 +54,27 @@ def __post_init__( @property def df(self) -> pl.DataFrame: return self.value_frame.df + + @staticmethod + def from_primitives( + df: pl.DataFrame, + lookbehind_days: Sequence[float | tuple[float, float]], + aggregators: Sequence[AggregatorName], + value_timestamp_col_name: str = "timestamp", + column_prefix: str = "pred", + fallback: int | float | str | None = 0, + ) -> PredictorSpec: + """Create a PredictorSpec from primitives.""" + lookbehind_distances = [_lookdistance_to_timedelta(d) for d in lookbehind_days] + + return PredictorSpec( + value_frame=ValueFrame( + init_df=df, + entity_id_col_name=df.get_column(df.columns[0]).name, + value_timestamp_col_name=value_timestamp_col_name, + ), + lookbehind_distances=lookbehind_distances, + aggregators=strings_to_aggregators(aggregators, value_timestamp_col_name), + fallback=fallback, + column_prefix=column_prefix, + ) diff --git a/src/timeseriesflattener/specs/timedelta.py b/src/timeseriesflattener/specs/timedelta.py index 21459f54..427ddd55 100644 --- a/src/timeseriesflattener/specs/timedelta.py +++ b/src/timeseriesflattener/specs/timedelta.py @@ -52,3 +52,24 @@ def __post_init__(self): @property def df(self) -> pl.DataFrame: return self.value_frame.df + + @staticmethod + def from_primitives( + df: pl.DataFrame, + entity_id_col_name: str, + output_name: str, + value_timestamp_col_name: str = "timestamp", + column_prefix: str = "pred", + fallback: int | float | str | None = 0, + ) -> TimeDeltaSpec: + """Create a TimeDeltaSpec from primitives.""" + return TimeDeltaSpec( + init_frame=TimestampValueFrame( + init_df=df, + value_timestamp_col_name=value_timestamp_col_name, + entity_id_col_name=entity_id_col_name, + ), + fallback=fallback, + output_name=output_name, + column_prefix=column_prefix, + ) From e245b8a1ef2a2b42892d3f5584bd5b8072b37beb Mon Sep 17 00:00:00 2001 From: Martin Bernstorff Date: Fri, 30 Aug 2024 12:59:14 +0200 Subject: [PATCH 03/38] update 5 files --- docs/tutorials/01_basic.ipynb | 26 +++++++++++++++++++++-- src/timeseriesflattener/aggregators.py | 25 +++++++++++----------- src/timeseriesflattener/specs/__init__.py | 10 +++++++++ src/timeseriesflattener/specs/outcome.py | 9 +------- src/timeseriesflattener/specs/temporal.py | 2 +- 5 files changed, 48 insertions(+), 24 deletions(-) diff --git a/docs/tutorials/01_basic.ipynb b/docs/tutorials/01_basic.ipynb index a83e1571..1ad41332 100644 --- a/docs/tutorials/01_basic.ipynb +++ b/docs/tutorials/01_basic.ipynb @@ -602,6 +602,16 @@ "\n", "test_df = pd.DataFrame({\"entity_id\": [0], \"timestamp\": [pd.Timestamp(\"2020-01-01\")]})\n", "\n", + "outcome_spec = BooleanOutcomeSpec.from_primitives(\n", + " df=test_df,\n", + " entity_id_col_name=\"entity_id\",\n", + " value_timestamp_col_name=\"timestamp\",\n", + " lookahead_days=[365],\n", + " aggregators=[\"max\"],\n", + " column_prefix=\"outc\",\n", + ")\n", + "\n", + "# Alternatively, if you prefer types\n", "outcome_spec = BooleanOutcomeSpec(\n", " init_frame=TimestampValueFrame(\n", " entity_id_col_name=\"entity_id\", init_df=test_df, value_timestamp_col_name=\"timestamp\"\n", @@ -664,6 +674,18 @@ "from timeseriesflattener import PredictorSpec, StaticSpec\n", "from timeseriesflattener.aggregators import MeanAggregator\n", "\n", + "temporal_predictor_spec = PredictorSpec.from_primitives(\n", + " df=df_synth_predictors.rename({\"value\": \"value_1\"}),\n", + " entity_id_col_name=\"entity_id\",\n", + " value_timestamp_col_name=\"timestamp\",\n", + " aggregators=[MeanAggregator()],\n", + " column_prefix=\"pred\",\n", + " fallback=np.nan,\n", + " lookbehind_distances=[dt.timedelta(days=730)],\n", + ")\n", + "\n", + "# Alternatively, if you prefer types\n", + "\n", "temporal_predictor_spec = PredictorSpec(\n", " value_frame=ValueFrame(\n", " entity_id_col_name=\"entity_id\",\n", @@ -802,7 +824,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Note that we don't need to specify which columns to aggregate. Timeseriesflattener aggregates all columns that are not `entity_id_col_name` or `value_timestamp_col_name` and uses the name(s) of the column(s) for the output." + "Note that we don't need to specify which columns to aggregate. Timeseriesflattener aggregates all columns that are not `entity_id_col_name` or `value_timestamp_col_name` and uses the name(s) of the column(s) for the output.\n" ] }, { @@ -1191,4 +1213,4 @@ }, "nbformat": 4, "nbformat_minor": 2 -} \ No newline at end of file +} diff --git a/src/timeseriesflattener/aggregators.py b/src/timeseriesflattener/aggregators.py index 041af936..baa65e39 100644 --- a/src/timeseriesflattener/aggregators.py +++ b/src/timeseriesflattener/aggregators.py @@ -6,7 +6,6 @@ import polars as pl from attr import dataclass -from timeseriesflattener.specs import timestamp def validate_compatible_fallback_type_for_aggregator( @@ -21,16 +20,16 @@ def validate_compatible_fallback_type_for_aggregator( AggregatorName = Literal[ + "bool", + "change_per_day", + "count", + "has_values", "max", - "min", "mean", + "min", + "slope", "sum", - "count", "variance", - "bool", - "change_per_day", - "slope", - "has_values", ] @@ -45,16 +44,16 @@ def strings_to_aggregators( def string_to_aggregator(aggregator_name: AggregatorName, timestamp_col_name: str) -> Aggregator: str2aggr: dict[AggregatorName, Aggregator] = { + "bool": HasValuesAggregator(), + "change_per_day": SlopeAggregator(timestamp_col_name=timestamp_col_name), + "count": CountAggregator(), + "has_values": HasValuesAggregator(), "max": MaxAggregator(), - "min": MinAggregator(), "mean": MeanAggregator(), + "min": MinAggregator(), + "slope": SlopeAggregator(timestamp_col_name=timestamp_col_name), "sum": SumAggregator(), - "count": CountAggregator(), "variance": VarianceAggregator(), - "bool": HasValuesAggregator(), - "change_per_day": SlopeAggregator(timestamp_col_name=timestamp_col_name), - "slope": SlopeAggregator(timestamp_col_name=timestamp_col_name), - "has_values": HasValuesAggregator(), } return str2aggr[aggregator_name] diff --git a/src/timeseriesflattener/specs/__init__.py b/src/timeseriesflattener/specs/__init__.py index e69de29b..1d19fe15 100644 --- a/src/timeseriesflattener/specs/__init__.py +++ b/src/timeseriesflattener/specs/__init__.py @@ -0,0 +1,10 @@ +from __future__ import annotations +import datetime as dt + + +def _lookdistance_to_timedelta( + lookdistance: float | tuple[float, float], +) -> tuple[dt.timedelta, dt.timedelta]: + if isinstance(lookdistance, tuple): + return (dt.timedelta(days=lookdistance[0]), dt.timedelta(days=lookdistance[1])) + return (dt.timedelta(days=0), dt.timedelta(days=lookdistance)) diff --git a/src/timeseriesflattener/specs/outcome.py b/src/timeseriesflattener/specs/outcome.py index d33c20fe..04e3f815 100644 --- a/src/timeseriesflattener/specs/outcome.py +++ b/src/timeseriesflattener/specs/outcome.py @@ -5,6 +5,7 @@ from typing import TYPE_CHECKING import polars as pl +from timeseriesflattener.specs import _lookdistance_to_timedelta from ..validators import validate_col_name_columns_exist from .value import ValueFrame, lookdistance_to_normalised_lookperiod @@ -21,14 +22,6 @@ from .timestamp import TimestampValueFrame -def _lookdistance_to_timedelta( - lookdistance: float | tuple[float, float], -) -> tuple[dt.timedelta, dt.timedelta]: - if isinstance(lookdistance, tuple): - return (dt.timedelta(days=lookdistance[0]), dt.timedelta(days=lookdistance[1])) - return (dt.timedelta(days=0), dt.timedelta(days=lookdistance)) - - @dataclass class OutcomeSpec: """Specification for an outcome. If your outcome is binary/boolean, you can use BooleanOutcomeSpec instead.""" diff --git a/src/timeseriesflattener/specs/temporal.py b/src/timeseriesflattener/specs/temporal.py index 7e9ca930..5eaf56ce 100644 --- a/src/timeseriesflattener/specs/temporal.py +++ b/src/timeseriesflattener/specs/temporal.py @@ -4,7 +4,7 @@ from dataclasses import InitVar, dataclass from typing import TYPE_CHECKING -from timeseriesflattener.specs.outcome import _lookdistance_to_timedelta +from timeseriesflattener.specs import _lookdistance_to_timedelta from ..validators import validate_col_name_columns_exist from .value import ValueFrame, lookdistance_to_normalised_lookperiod From 32387fd8208c3dec6cbd1089fd335814b327eb80 Mon Sep 17 00:00:00 2001 From: Martin Bernstorff Date: Fri, 30 Aug 2024 13:01:32 +0200 Subject: [PATCH 04/38] update outcome.py --- src/timeseriesflattener/specs/outcome.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/timeseriesflattener/specs/outcome.py b/src/timeseriesflattener/specs/outcome.py index 04e3f815..a85a5a21 100644 --- a/src/timeseriesflattener/specs/outcome.py +++ b/src/timeseriesflattener/specs/outcome.py @@ -15,11 +15,12 @@ validate_compatible_fallback_type_for_aggregator, ) +from .timestamp import TimestampValueFrame + if TYPE_CHECKING: from collections.abc import Sequence from ..aggregators import Aggregator - from .timestamp import TimestampValueFrame @dataclass From 431463d6aa48ee9b85923f40235f464efe1720fb Mon Sep 17 00:00:00 2001 From: Martin Bernstorff Date: Fri, 30 Aug 2024 13:05:09 +0200 Subject: [PATCH 05/38] update temporal.py --- src/timeseriesflattener/specs/temporal.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/timeseriesflattener/specs/temporal.py b/src/timeseriesflattener/specs/temporal.py index 5eaf56ce..be45a0fa 100644 --- a/src/timeseriesflattener/specs/temporal.py +++ b/src/timeseriesflattener/specs/temporal.py @@ -58,6 +58,7 @@ def df(self) -> pl.DataFrame: @staticmethod def from_primitives( df: pl.DataFrame, + entity_id_col_name: str, lookbehind_days: Sequence[float | tuple[float, float]], aggregators: Sequence[AggregatorName], value_timestamp_col_name: str = "timestamp", @@ -70,7 +71,7 @@ def from_primitives( return PredictorSpec( value_frame=ValueFrame( init_df=df, - entity_id_col_name=df.get_column(df.columns[0]).name, + entity_id_col_name=entity_id_col_name, value_timestamp_col_name=value_timestamp_col_name, ), lookbehind_distances=lookbehind_distances, From 6cf50781971821f3988d81a44822499fd73d92ee Mon Sep 17 00:00:00 2001 From: Martin Bernstorff Date: Fri, 30 Aug 2024 13:38:15 +0200 Subject: [PATCH 06/38] build(deps): update Dockerfile, 01_basic.ipynb and pyproject.toml --- .dockerignore | 170 ++ Dockerfile | 31 +- docs/tutorials/01_basic.ipynb | 7 + pyproject.toml | 2 +- uv.lock | 3343 +++++++++++++++++++++++++++++++++ 5 files changed, 3524 insertions(+), 29 deletions(-) create mode 100644 .dockerignore create mode 100644 uv.lock diff --git a/.dockerignore b/.dockerignore new file mode 100644 index 00000000..f2ce4167 --- /dev/null +++ b/.dockerignore @@ -0,0 +1,170 @@ +# Byte-compiled / optimized / DLL files +.git +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ +cover/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +.pybuilder/ +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +# For a library or package, you might want to ignore these files since the code is +# intended to run in multiple environments; otherwise, check them in: +# .python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# poetry +# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. +# This is especially recommended for binary packages to ensure reproducibility, and is more +# commonly ignored for libraries. +# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control +poetry.lock + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +*venv*/ +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ + +# pytype static type analyzer +.pytype/ + +# Cython debug symbols +cython_debug/ + +# PyCharm +# JetBrains specific template is maintained in a separate JetBrains.gitignore that can +# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore +# and can be added to the global gitignore or merged into this file. For a more nuclear +# option (not recommended) you can uncomment the following to ignore the entire idea folder. +#.idea/ + +# Testing +pytest-coverage.txt + +# Mac +.DS_Store + +#other +*test_load_data.py +wandb +poetry.lock +*.html + +# PyCharm +/.idea/* +**/tmp/ +**/.tmp/ + +*nbconvert* +.testmondata* +.benchmark_cache/* \ No newline at end of file diff --git a/Dockerfile b/Dockerfile index 16b347ae..165372d1 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,35 +1,10 @@ FROM python:3.9 - -RUN apt-get update && apt-get install -y curl - -# NVM and NPM are required for Graphite -# Install nvm -# Explicitly set HOME environment variable -ENV NVM_DIR=$HOME/.nvm -RUN mkdir -p $NVM_DIR -ENV NODE_VERSION=18.2.0 - -# Install nvm with node and npm -RUN curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.39.5/install.sh | bash \ - && . $NVM_DIR/nvm.sh \ - && nvm install $NODE_VERSION \ - && nvm alias default $NODE_VERSION \ - && nvm use default - -ENV NODE_PATH=$NVM_DIR/v$NODE_VERSION/lib/node_modules -ENV PATH=$NVM_DIR/versions/node/v$NODE_VERSION/bin:$PATH - - -# Install graphite (PR stacking), experimental, can be deleted without notice -RUN npm install -g @withgraphite/graphite-cli@stable - -# Install lefthook (git hooks, e.g. pre-commit) -RUN curl -1sLf 'https://dl.cloudsmith.io/public/evilmartians/lefthook/setup.deb.sh' | bash -RUN apt install lefthook +COPY --from=ghcr.io/astral-sh/uv:0.4.0 /uv /bin/uv # Set the working directory to /app WORKDIR /app VOLUME psycop-common COPY . /app -RUN --mount=type=cache,target=/root/.cache/pip pip install . \ No newline at end of file +RUN --mount=type=cache,target=/root/.cache/uv \ + uv sync --frozen \ No newline at end of file diff --git a/docs/tutorials/01_basic.ipynb b/docs/tutorials/01_basic.ipynb index 1ad41332..08fa7161 100644 --- a/docs/tutorials/01_basic.ipynb +++ b/docs/tutorials/01_basic.ipynb @@ -637,6 +637,13 @@ "Lastly, we specify a name of the outcome which'll be used when generating its column.\n" ] }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + }, { "attachments": {}, "cell_type": "markdown", diff --git a/pyproject.toml b/pyproject.toml index a870ffe4..b8163b92 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,7 +21,7 @@ classifiers = [ "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", ] -requires-python = ">=3.8.0,<3.13.0" +requires-python = ">=3.9.0,<3.13.0" dependencies = [ "scipy>=1.8.0", "scikit-learn>=1.1.2", diff --git a/uv.lock b/uv.lock new file mode 100644 index 00000000..5b9af8c5 --- /dev/null +++ b/uv.lock @@ -0,0 +1,3343 @@ +version = 1 +requires-python = ">=3.9.0, <3.13.0" +resolution-markers = [ + "python_full_version < '3.11'", + "python_full_version == '3.11.*'", + "python_full_version < '3.13'", + "python_full_version >= '3.13'", +] + +[[package]] +name = "alabaster" +version = "0.7.16" +source = { registry = "https://pypi.org/simple" 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index baa65e39..30a470df 100644 --- a/src/timeseriesflattener/aggregators.py +++ b/src/timeseriesflattener/aggregators.py @@ -192,7 +192,7 @@ class SlopeAggregator(Aggregator): def __call__(self, column_name: str) -> pl.Expr: # Convert to days for the slope. Arbitrarily chosen to be the number of days since 1970-01-01. - x_col = (pl.col(self.timestamp_col_name) - dt.datetime(1970, 1, 1)).dt.days() + x_col = (pl.col(self.timestamp_col_name) - dt.datetime(1970, 1, 1)).dt.total_days() y_col = pl.col(column_name) numerator = pl.corr(x_col, y_col, propagate_nans=True) * y_col.std() From d55c2eb38821dc6a563e5b9c9771bffbb26e1d6c Mon Sep 17 00:00:00 2001 From: Martin Bernstorff Date: Fri, 30 Aug 2024 13:44:33 +0200 Subject: [PATCH 08/38] build: update Dockerfile --- Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index e3e34623..f12b2b40 100644 --- a/Dockerfile +++ b/Dockerfile @@ -6,5 +6,5 @@ WORKDIR /app VOLUME psycop-common COPY . /app -RUN --mount=type=cache,target=/root/.cache/pip \ - pip install . \ No newline at end of file +RUN --mount=type=cache,target=/root/.cache/uv \ + uv sync --frozen --all-extras \ No newline at end of file From 9cc48d5bf57942d777ed531c31959ed939a6481d Mon Sep 17 00:00:00 2001 From: Martin Bernstorff Date: Fri, 30 Aug 2024 13:50:14 +0200 Subject: [PATCH 09/38] build: update Dockerfile --- Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/Dockerfile b/Dockerfile index f12b2b40..d8e4d884 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,5 @@ FROM python:3.9 +ENV UV_SYSTEM_PYTHON=true COPY --from=ghcr.io/astral-sh/uv:0.4.0 /uv /bin/uv # Set the working directory to /app From 2dac3fdb830724f31dbbac7be6cba3f4b3d04ef5 Mon Sep 17 00:00:00 2001 From: Martin Bernstorff Date: Fri, 30 Aug 2024 13:52:29 +0200 Subject: [PATCH 10/38] docs: update 01_basic.ipynb --- docs/tutorials/01_basic.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/tutorials/01_basic.ipynb b/docs/tutorials/01_basic.ipynb index 08fa7161..d2c65f60 100644 --- a/docs/tutorials/01_basic.ipynb +++ b/docs/tutorials/01_basic.ipynb @@ -758,7 +758,7 @@ " aggregators=[MeanAggregator()],\n", " column_prefix=\"pred\",\n", " fallback=np.nan,\n", - " lookbehind_distances=[(dt.timedelta(days=10), dt.timedelta(days=365))],\n", + " lookbehind_days=[(dt.timedelta(days=10), dt.timedelta(days=365))],\n", ")" ] }, From 52a11aa46642181bd8ac0af5dfdd20bf37bcd997 Mon Sep 17 00:00:00 2001 From: Martin Bernstorff Date: Fri, 30 Aug 2024 14:03:17 +0200 Subject: [PATCH 11/38] build(deps): update action.yml, 01_basic.ipynb, pyproject.toml and uv.lock --- .github/actions/test/action.yml | 2 +- docs/tutorials/01_basic.ipynb | 6 +- pyproject.toml | 2 + uv.lock | 140 +++++++++++++++++++++++++++++++- 4 files changed, 144 insertions(+), 6 deletions(-) diff --git a/.github/actions/test/action.yml b/.github/actions/test/action.yml index 90525809..c7800d53 100644 --- a/.github/actions/test/action.yml +++ b/.github/actions/test/action.yml @@ -26,4 +26,4 @@ runs: uses: devcontainers/ci@v0.3 with: runCmd: | - inv test --pytest-args "src/" --pytest-args --pytest-args "--cov=src" --pytest-args "--cov-report term-missing" --pytest-args="--color=yes" --pytest-args="-n auto" \ No newline at end of file + inv test --pytest-args="-n auto" \ No newline at end of file diff --git a/docs/tutorials/01_basic.ipynb b/docs/tutorials/01_basic.ipynb index d2c65f60..5791b182 100644 --- a/docs/tutorials/01_basic.ipynb +++ b/docs/tutorials/01_basic.ipynb @@ -685,10 +685,10 @@ " df=df_synth_predictors.rename({\"value\": \"value_1\"}),\n", " entity_id_col_name=\"entity_id\",\n", " value_timestamp_col_name=\"timestamp\",\n", - " aggregators=[MeanAggregator()],\n", + " aggregators=[\"mean\"],\n", " column_prefix=\"pred\",\n", " fallback=np.nan,\n", - " lookbehind_distances=[dt.timedelta(days=730)],\n", + " lookbehind_days=[730],\n", ")\n", "\n", "# Alternatively, if you prefer types\n", @@ -758,7 +758,7 @@ " aggregators=[MeanAggregator()],\n", " column_prefix=\"pred\",\n", " fallback=np.nan,\n", - " lookbehind_days=[(dt.timedelta(days=10), dt.timedelta(days=365))],\n", + " lookbehind_distances=[(dt.timedelta(days=10), dt.timedelta(days=365))],\n", ")" 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'pypy' and os_name == 'nt'" }, + { name = "exceptiongroup", marker = "python_full_version < '3.11'" }, + { name = "idna" }, + { name = "outcome" }, + { name = "sniffio" }, + { name = "sortedcontainers" }, +] +sdist = { url = "https://files.pythonhosted.org/packages/9a/03/ab0e9509be0c6465e2773768ec25ee0cb8053c0b91471ab3854bbf2294b2/trio-0.26.2.tar.gz", hash = "sha256:0346c3852c15e5c7d40ea15972c4805689ef2cb8b5206f794c9c19450119f3a4", size = 561156 } +wheels = [ + { url = "https://files.pythonhosted.org/packages/1c/70/efa56ce2271c44a7f4f43533a0477e6854a0948e9f7b76491de1fd3be7c9/trio-0.26.2-py3-none-any.whl", hash = "sha256:c5237e8133eb0a1d72f09a971a55c28ebe69e351c783fc64bc37db8db8bbe1d0", size = 475996 }, +] + [[package]] name = "typeguard" version = "4.2.1" From a63f636faffd0a8dab7ed7f2960b856e92bd53aa Mon Sep 17 00:00:00 2001 From: Martin Bernstorff Date: Fri, 30 Aug 2024 14:04:22 +0200 Subject: [PATCH 12/38] build(deps): update pyproject.toml and uv.lock --- pyproject.toml | 2 +- uv.lock | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 53b244ad..54fa5b65 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -62,13 +62,13 @@ test = [ "pytest-codspeed==2.2.0", ] docs = [ - "ipykernel", "sphinx==5.3.0", "furo==2023.3.27", "sphinx-copybutton==0.5.2", "sphinxext-opengraph==0.8.2", "myst-nb==0.17.2", "sphinx_design==0.3.0", + "ipykernel>=6.29.5", ] tutorials = ["jupyter>=1.0.0,<1.1.0", "skimpy>=0.0.11"] diff --git a/uv.lock b/uv.lock index ff7b74ec..2a63910b 100644 --- a/uv.lock +++ b/uv.lock @@ -3232,7 +3232,7 @@ requires-dist = [ { name = "frozendict", specifier = ">=2.3.4" }, { name = "furo", marker = "extra == 'docs'", specifier = "==2023.3.27" }, { name = "invoke", marker = "extra == 'dev'", specifier = "==2.1.1" }, - { name = "ipykernel", marker = "extra == 'docs'" }, + { name = "ipykernel", marker = "extra == 'docs'", specifier = ">=6.29.5" }, { name = "ipykernel", extras = ["docs"], specifier = ">=6.29.5" }, { name = "iterpy", specifier = "==1.6.0" }, { name = "jupyter", marker = "extra == 'tutorials'", specifier = ">=1.0.0,<1.1.0" }, From d317a64b00f0d2089bd40bd09095119f20a7b6c0 Mon Sep 17 00:00:00 2001 From: Martin Bernstorff Date: Fri, 30 Aug 2024 14:07:14 +0200 Subject: [PATCH 13/38] update devcontainer.json and post-start.sh --- .devcontainer/post-start.sh | 12 ++---------- 1 file changed, 2 insertions(+), 10 deletions(-) diff --git a/.devcontainer/post-start.sh b/.devcontainer/post-start.sh index 993b8501..99298641 100644 --- a/.devcontainer/post-start.sh +++ b/.devcontainer/post-start.sh @@ -1,10 +1,2 @@ -# Setup lefthook -git init -lefthook install - -# Disable Graphite pager -gt user pager --disable - -# Install dependencies -pip install -e ".[dev, test]" - +#!/bin/bash +uv sync --frozen --all-extras \ No newline at end of file From 584d31c7965e10089f5d53dfd7966af19243a50f Mon Sep 17 00:00:00 2001 From: Martin Bernstorff Date: Fri, 30 Aug 2024 14:20:32 +0200 Subject: [PATCH 14/38] update 7 files --- docs/tutorials/01_basic.ipynb | 394 ++++++++---------- pyproject.toml | 20 +- src/timeseriesflattener/main_test.py | 4 +- .../processors/temporal.py | 7 +- src/timeseriesflattener/specs/outcome.py | 3 +- .../testing/load_synth_data.py | 2 +- uv.lock | 21 +- 7 files changed, 197 insertions(+), 254 deletions(-) diff --git a/docs/tutorials/01_basic.ipynb b/docs/tutorials/01_basic.ipynb index 5791b182..07edf973 100644 --- a/docs/tutorials/01_basic.ipynb +++ b/docs/tutorials/01_basic.ipynb @@ -66,11 +66,11 @@ "│ │ Number of columns │ 2 │ │ datetime64 │ 1 │ │\n", "│ └───────────────────┴────────┘ └─────────────┴───────┘ │\n", "│ number │\n", - "│ ┏━━━━━━━━━━━━━━━━━━┳━━━━━━┳━━━━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━━┓ │\n", - "│ ┃ column_name NA NA % mean sd p0 p25 p50 p75 p100 hist ┃ │\n", - "│ ┡━━━━━━━━━━━━━━━━━━╇━━━━━━╇━━━━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━━┩ │\n", - "│ │ entity_id 0 0 5000 2900 0 2500 4900 7400 10000 ▇▇▇▇▇▇ │ │\n", - "│ └──────────────────┴──────┴─────────┴────────┴────────┴──────┴────────┴────────┴────────┴─────────┴──────────┘ │\n", + "│ ┏━━━━━━━━━━━━━━━━━━┳━━━━━━┳━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━┳━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━━━━┓ │\n", + "│ ┃ column_name NA NA % mean sd p0 p25 p50 p75 p100 hist ┃ │\n", + "│ ┡━━━━━━━━━━━━━━━━━━╇━━━━━━╇━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━╇━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━━━━┩ │\n", + "│ │ entity_id 0 0 4959 2886 0 2485 4922 7443 9999 ▇▇▇▇▇▇ │ │\n", + "│ └──────────────────┴──────┴─────────┴─────────┴────────┴──────┴────────┴────────┴────────┴────────┴──────────┘ │\n", "│ datetime │\n", "│ ┏━━━━━━━━━━━━━━━━━━┳━━━━━━┳━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┓ │\n", "│ ┃ column_name NA NA % first last frequency ┃ │\n", @@ -90,11 +90,11 @@ "│ │ Number of columns │ 2 │ │ datetime64 │ 1 │ │\n", "│ └───────────────────┴────────┘ └─────────────┴───────┘ │\n", "│ \u001b[3m number \u001b[0m │\n", - "│ ┏━━━━━━━━━━━━━━━━━━┳━━━━━━┳━━━━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━━┓ │\n", - "│ ┃\u001b[1m \u001b[0m\u001b[1mcolumn_name \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mNA \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mNA % \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mmean \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1msd \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp0 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp25 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp50 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp75 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp100 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mhist \u001b[0m\u001b[1m \u001b[0m┃ │\n", - "│ ┡━━━━━━━━━━━━━━━━━━╇━━━━━━╇━━━━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━━┩ │\n", - "│ │ \u001b[38;5;141mentity_id \u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 5000\u001b[0m │ \u001b[36m 2900\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 2500\u001b[0m │ \u001b[36m 4900\u001b[0m │ \u001b[36m 7400\u001b[0m │ \u001b[36m 10000\u001b[0m │ \u001b[32m ▇▇▇▇▇▇ \u001b[0m │ │\n", - "│ └──────────────────┴──────┴─────────┴────────┴────────┴──────┴────────┴────────┴────────┴─────────┴──────────┘ │\n", + "│ ┏━━━━━━━━━━━━━━━━━━┳━━━━━━┳━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━┳━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━━━━┓ │\n", + "│ ┃\u001b[1m \u001b[0m\u001b[1mcolumn_name \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mNA \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mNA % \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mmean \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1msd \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp0 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp25 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp50 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp75 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp100 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mhist \u001b[0m\u001b[1m \u001b[0m┃ │\n", + "│ ┡━━━━━━━━━━━━━━━━━━╇━━━━━━╇━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━╇━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━━━━┩ │\n", + "│ │ \u001b[38;5;141mentity_id \u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 4959\u001b[0m │ \u001b[36m 2886\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 2485\u001b[0m │ \u001b[36m 4922\u001b[0m │ \u001b[36m 7443\u001b[0m │ \u001b[36m 9999\u001b[0m │ \u001b[32m ▇▇▇▇▇▇ \u001b[0m │ │\n", + "│ └──────────────────┴──────┴─────────┴─────────┴────────┴──────┴────────┴────────┴────────┴────────┴──────────┘ │\n", "│ \u001b[3m datetime \u001b[0m │\n", "│ ┏━━━━━━━━━━━━━━━━━━┳━━━━━━┳━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┓ │\n", "│ ┃\u001b[1m \u001b[0m\u001b[1mcolumn_name \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mNA \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mNA % \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mfirst \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mlast \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mfrequency \u001b[0m\u001b[1m \u001b[0m┃ │\n", @@ -117,7 +117,7 @@ " white-space: pre-wrap;\n", "}\n", "\n", - "shape: (10_000, 2)
entity_idtimestamp
i64datetime[μs]
01969-01-11 09:55:00
11965-03-15 07:16:00
21969-09-13 23:18:00
31968-02-04 16:16:00
41965-01-28 12:33:00
51967-10-09 06:22:00
71969-11-17 02:50:00
81965-12-11 02:17:00
91965-08-21 22:00:00
101965-12-26 16:45:00
111966-07-09 13:54:00
121968-01-26 22:35:00
99901965-11-16 21:02:00
99901967-06-09 02:48:00
99911966-07-05 03:18:00
99941965-04-20 06:19:00
99941967-05-07 04:44:00
99951968-08-23 11:30:00
99951965-11-24 05:42:00
99961965-01-30 17:19:00
99961965-07-18 17:12:00
99971967-06-08 07:52:00
99991965-07-19 14:59:00
99991968-02-07 22:24:00
" + "shape: (10_000, 2)
entity_idtimestamp
i64datetime[μs]
01969-01-11 09:55:00
11965-03-15 07:16:00
21969-09-13 23:18:00
31968-02-04 16:16:00
41965-01-28 12:33:00
99961965-01-30 17:19:00
99961965-07-18 17:12:00
99971967-06-08 07:52:00
99991965-07-19 14:59:00
99991968-02-07 22:24:00
" ], "text/plain": [ "shape: (10_000, 2)\n", @@ -177,7 +177,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 2, "metadata": {}, "outputs": [ { @@ -193,12 +193,12 @@ "│ └───────────────────┴────────┘ │ float64 │ 1 │ │\n", "│ └─────────────┴───────┘ │\n", "│ number │\n", - "│ ┏━━━━━━━━━━━━━━━━━┳━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━┳━━━━━━━━┳━━━━━━━━━┓ │\n", - "│ ┃ column_name NA NA % mean sd p0 p25 p50 p75 p100 hist ┃ │\n", - "│ ┡━━━━━━━━━━━━━━━━━╇━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━╇━━━━━━━━╇━━━━━━━━━┩ │\n", - "│ │ entity_id 0 0 5000 2900 0 2500 5000 7500 10000▇▇▇▇▇▇ │ │\n", - "│ │ value 0 0 5 2.9 0.00015 2.5 5 7.5 10▇▇▇▇▇▇ │ │\n", - "│ └─────────────────┴──────┴────────┴────────┴────────┴───────────┴────────┴────────┴───────┴────────┴─────────┘ │\n", + "│ ┏━━━━━━━━━━━━━━━━┳━━━━━┳━━━━━━━┳━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━┳━━━━━━━━┓ │\n", + "│ ┃ column_name NA NA % mean sd p0 p25 p50 p75 p100 hist ┃ │\n", + "│ ┡━━━━━━━━━━━━━━━━╇━━━━━╇━━━━━━━╇━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━╇━━━━━━━━┩ │\n", + "│ │ entity_id 0 0 4994 2887 0 2486 4996 7487 9999▇▇▇▇▇▇ │ │\n", + "│ │ value 0 0 4.983 2.885 0.0001514 2.483 4.975 7.486 10▇▇▇▇▇▇ │ │\n", + "│ └────────────────┴─────┴───────┴─────────┴─────────┴─────────────┴────────┴────────┴────────┴───────┴────────┘ │\n", "│ datetime │\n", "│ ┏━━━━━━━━━━━━━━━━━━┳━━━━━━┳━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┓ │\n", "│ ┃ column_name NA NA % first last frequency ┃ │\n", @@ -219,12 +219,12 @@ "│ └───────────────────┴────────┘ │ float64 │ 1 │ │\n", "│ └─────────────┴───────┘ │\n", "│ \u001b[3m number \u001b[0m │\n", - "│ ┏━━━━━━━━━━━━━━━━━┳━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━┳━━━━━━━━┳━━━━━━━━━┓ │\n", - "│ ┃\u001b[1m \u001b[0m\u001b[1mcolumn_name \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mNA \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mNA % \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mmean \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1msd \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp0 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp25 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp50 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp75 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp100 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mhist \u001b[0m\u001b[1m \u001b[0m┃ │\n", - "│ ┡━━━━━━━━━━━━━━━━━╇━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━╇━━━━━━━━╇━━━━━━━━━┩ │\n", - "│ │ \u001b[38;5;141mentity_id \u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 5000\u001b[0m │ \u001b[36m 2900\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 2500\u001b[0m │ \u001b[36m 5000\u001b[0m │ \u001b[36m 7500\u001b[0m │ \u001b[36m 10000\u001b[0m │ \u001b[32m▇▇▇▇▇▇ \u001b[0m │ │\n", - "│ │ \u001b[38;5;141mvalue \u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 5\u001b[0m │ \u001b[36m 2.9\u001b[0m │ \u001b[36m 0.00015\u001b[0m │ \u001b[36m 2.5\u001b[0m │ \u001b[36m 5\u001b[0m │ \u001b[36m 7.5\u001b[0m │ \u001b[36m 10\u001b[0m │ \u001b[32m▇▇▇▇▇▇ \u001b[0m │ │\n", - "│ └─────────────────┴──────┴────────┴────────┴────────┴───────────┴────────┴────────┴───────┴────────┴─────────┘ │\n", + "│ ┏━━━━━━━━━━━━━━━━┳━━━━━┳━━━━━━━┳━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━┳━━━━━━━━┓ │\n", + "│ ┃\u001b[1m \u001b[0m\u001b[1mcolumn_name \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mNA \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mNA % \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mmean \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1msd \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp0 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp25 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp50 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp75 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp100 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mhist \u001b[0m\u001b[1m \u001b[0m┃ │\n", + "│ ┡━━━━━━━━━━━━━━━━╇━━━━━╇━━━━━━━╇━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━╇━━━━━━━━┩ │\n", + "│ │ \u001b[38;5;141mentity_id \u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 4994\u001b[0m │ \u001b[36m 2887\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 2486\u001b[0m │ \u001b[36m 4996\u001b[0m │ \u001b[36m 7487\u001b[0m │ \u001b[36m 9999\u001b[0m │ \u001b[32m▇▇▇▇▇▇\u001b[0m │ │\n", + "│ │ \u001b[38;5;141mvalue \u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 4.983\u001b[0m │ \u001b[36m 2.885\u001b[0m │ \u001b[36m 0.0001514\u001b[0m │ \u001b[36m 2.483\u001b[0m │ \u001b[36m 4.975\u001b[0m │ \u001b[36m 7.486\u001b[0m │ \u001b[36m 10\u001b[0m │ \u001b[32m▇▇▇▇▇▇\u001b[0m │ │\n", + "│ └────────────────┴─────┴───────┴─────────┴─────────┴─────────────┴────────┴────────┴────────┴───────┴────────┘ │\n", "│ \u001b[3m datetime \u001b[0m │\n", "│ ┏━━━━━━━━━━━━━━━━━━┳━━━━━━┳━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┓ │\n", "│ ┃\u001b[1m \u001b[0m\u001b[1mcolumn_name \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mNA \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mNA % \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mfirst \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mlast \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mfrequency \u001b[0m\u001b[1m \u001b[0m┃ │\n", @@ -247,7 +247,7 @@ " white-space: pre-wrap;\n", "}\n", "\n", - "shape: (100_000, 3)
entity_idtimestampvalue
i64datetime[μs]f64
01967-06-12 14:06:000.174793
01968-04-15 01:45:003.072293
01968-12-09 05:42:001.315754
01969-06-20 18:07:002.812481
01967-11-26 01:59:002.981185
01968-09-07 01:45:000.173205
01969-02-21 03:29:009.943505
01967-11-26 13:45:005.470792
01967-05-12 12:44:000.970382
01965-05-03 05:23:006.630007
01969-10-19 10:29:000.799246
01969-11-25 18:39:002.868688
99991967-12-11 21:34:005.379503
99991968-05-26 12:28:009.645746
99991966-04-23 02:37:008.924175
99991968-10-24 18:47:002.34615
99991967-11-12 07:33:004.414524
99991966-07-15 20:55:000.684468
99991968-01-08 02:41:003.250538
99991968-08-19 10:15:000.671907
99991966-01-03 22:34:004.158796
99991966-06-27 10:55:004.414455
99991968-04-02 12:58:001.552491
99991969-06-24 07:19:004.501553
" + "shape: (100_000, 3)
entity_idtimestampvalue
i64datetime[μs]f64
01967-06-12 14:06:000.174793
01968-04-15 01:45:003.072293
01968-12-09 05:42:001.315754
01969-06-20 18:07:002.812481
01967-11-26 01:59:002.981185
99991968-08-19 10:15:000.671907
99991966-01-03 22:34:004.158796
99991966-06-27 10:55:004.414455
99991968-04-02 12:58:001.552491
99991969-06-24 07:19:004.501553
" ], "text/plain": [ "shape: (100_000, 3)\n", @@ -304,7 +304,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 3, "metadata": {}, "outputs": [ { @@ -319,12 +319,12 @@ "│ │ Number of columns │ 2 │ └─────────────┴───────┘ │\n", "│ └───────────────────┴────────┘ │\n", "│ number │\n", - "│ ┏━━━━━━━━━━━━━━━━━━┳━━━━━━┳━━━━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━━┓ │\n", - "│ ┃ column_name NA NA % mean sd p0 p25 p50 p75 p100 hist ┃ │\n", - "│ ┡━━━━━━━━━━━━━━━━━━╇━━━━━━╇━━━━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━━┩ │\n", - "│ │ entity_id 0 0 5000 2900 0 2500 5000 7500 10000 ▇▇▇▇▇▇ │ │\n", - "│ │ female 0 0 0.5 0.5 0 0 0 1 1 ▇ ▇ │ │\n", - "│ └──────────────────┴──────┴─────────┴────────┴────────┴──────┴────────┴────────┴────────┴─────────┴──────────┘ │\n", + "│ ┏━━━━━━━━━━━━━━━━━━┳━━━━━━┳━━━━━━━━┳━━━━━━━━━━━┳━━━━━━━━┳━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━━━┓ │\n", + "│ ┃ column_name NA NA % mean sd p0 p25 p50 p75 p100 hist ┃ │\n", + "│ ┡━━━━━━━━━━━━━━━━━━╇━━━━━━╇━━━━━━━━╇━━━━━━━━━━━╇━━━━━━━━╇━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━━━┩ │\n", + "│ │ entity_id 0 0 4999 2887 0 2500 4999 7500 9999▇▇▇▇▇▇ │ │\n", + "│ │ female 0 0 0.4984 0.5 0 0 0 1 1▇ ▇ │ │\n", + "│ └──────────────────┴──────┴────────┴───────────┴────────┴──────┴────────┴────────┴────────┴────────┴─────────┘ │\n", "╰────────────────────────────────────────────────────── End ──────────────────────────────────────────────────────╯\n", "\n" ], @@ -338,12 +338,12 @@ "│ │ Number of columns │ 2 │ └─────────────┴───────┘ │\n", "│ └───────────────────┴────────┘ │\n", "│ \u001b[3m number \u001b[0m │\n", - "│ ┏━━━━━━━━━━━━━━━━━━┳━━━━━━┳━━━━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━━┓ │\n", - "│ ┃\u001b[1m \u001b[0m\u001b[1mcolumn_name \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mNA \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mNA % \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mmean \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1msd \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp0 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp25 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp50 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp75 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp100 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mhist \u001b[0m\u001b[1m \u001b[0m┃ │\n", - "│ ┡━━━━━━━━━━━━━━━━━━╇━━━━━━╇━━━━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━━┩ │\n", - "│ │ \u001b[38;5;141mentity_id \u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 5000\u001b[0m │ \u001b[36m 2900\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 2500\u001b[0m │ \u001b[36m 5000\u001b[0m │ \u001b[36m 7500\u001b[0m │ \u001b[36m 10000\u001b[0m │ \u001b[32m ▇▇▇▇▇▇ \u001b[0m │ │\n", - "│ │ \u001b[38;5;141mfemale \u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0.5\u001b[0m │ \u001b[36m 0.5\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 1\u001b[0m │ \u001b[36m 1\u001b[0m │ \u001b[32m ▇ ▇ \u001b[0m │ │\n", - "│ └──────────────────┴──────┴─────────┴────────┴────────┴──────┴────────┴────────┴────────┴─────────┴──────────┘ │\n", + "│ ┏━━━━━━━━━━━━━━━━━━┳━━━━━━┳━━━━━━━━┳━━━━━━━━━━━┳━━━━━━━━┳━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━━━┓ │\n", + "│ ┃\u001b[1m \u001b[0m\u001b[1mcolumn_name \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mNA \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mNA % \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mmean \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1msd \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp0 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp25 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp50 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp75 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp100 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mhist \u001b[0m\u001b[1m \u001b[0m┃ │\n", + "│ ┡━━━━━━━━━━━━━━━━━━╇━━━━━━╇━━━━━━━━╇━━━━━━━━━━━╇━━━━━━━━╇━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━━━┩ │\n", + "│ │ \u001b[38;5;141mentity_id \u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 4999\u001b[0m │ \u001b[36m 2887\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 2500\u001b[0m │ \u001b[36m 4999\u001b[0m │ \u001b[36m 7500\u001b[0m │ \u001b[36m 9999\u001b[0m │ \u001b[32m▇▇▇▇▇▇ \u001b[0m │ │\n", + "│ │ \u001b[38;5;141mfemale \u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0.4984\u001b[0m │ \u001b[36m 0.5\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 1\u001b[0m │ \u001b[36m 1\u001b[0m │ \u001b[32m▇ ▇ \u001b[0m │ │\n", + "│ └──────────────────┴──────┴────────┴───────────┴────────┴──────┴────────┴────────┴────────┴────────┴─────────┘ │\n", "╰────────────────────────────────────────────────────── End ──────────────────────────────────────────────────────╯\n" ] }, @@ -360,7 +360,7 @@ " white-space: pre-wrap;\n", "}\n", "\n", - "shape: (9_999, 2)
entity_idfemale
i64i64
00
11
21
31
40
50
60
70
81
90
100
110
99881
99890
99901
99910
99920
99930
99941
99950
99960
99971
99981
99990
" + "shape: (9_999, 2)
entity_idfemale
i64i64
00
11
21
31
40
99950
99960
99971
99981
99990
" ], "text/plain": [ "shape: (9_999, 2)\n", @@ -423,7 +423,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 4, "metadata": {}, "outputs": [ { @@ -438,12 +438,12 @@ "│ │ Number of columns │ 3 │ │ datetime64 │ 1 │ │\n", "│ └───────────────────┴────────┘ └─────────────┴───────┘ │\n", "│ number │\n", - "│ ┏━━━━━━━━━━━━━━━━━━┳━━━━━━┳━━━━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━━┓ │\n", - "│ ┃ column_name NA NA % mean sd p0 p25 p50 p75 p100 hist ┃ │\n", - "│ ┡━━━━━━━━━━━━━━━━━━╇━━━━━━╇━━━━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━━┩ │\n", - "│ │ entity_id 0 0 5000 2900 4 2500 5100 7600 10000 ▇▇▇▇▇▇ │ │\n", - "│ │ value 0 0 1 0 1 1 1 1 1 │ │\n", - "│ └──────────────────┴──────┴─────────┴────────┴────────┴──────┴────────┴────────┴────────┴─────────┴──────────┘ │\n", + "│ ┏━━━━━━━━━━━━━━━━━━┳━━━━━━┳━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━┳━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━━━━┓ │\n", + "│ ┃ column_name NA NA % mean sd p0 p25 p50 p75 p100 hist ┃ │\n", + "│ ┡━━━━━━━━━━━━━━━━━━╇━━━━━━╇━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━╇━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━━━━┩ │\n", + "│ │ entity_id 0 0 5032 2900 4 2499 5109 7555 9992 ▇▇▇▇▇▇ │ │\n", + "│ │ value 0 0 1 0 1 1 1 1 1 │ │\n", + "│ └──────────────────┴──────┴─────────┴─────────┴────────┴──────┴────────┴────────┴────────┴────────┴──────────┘ │\n", "│ datetime │\n", "│ ┏━━━━━━━━━━━━━━━━━━┳━━━━━━┳━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┓ │\n", "│ ┃ column_name NA NA % first last frequency ┃ │\n", @@ -463,12 +463,12 @@ "│ │ Number of columns │ 3 │ │ datetime64 │ 1 │ │\n", "│ └───────────────────┴────────┘ └─────────────┴───────┘ │\n", "│ \u001b[3m number \u001b[0m │\n", - "│ ┏━━━━━━━━━━━━━━━━━━┳━━━━━━┳━━━━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━━┓ │\n", - "│ ┃\u001b[1m \u001b[0m\u001b[1mcolumn_name \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mNA \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mNA % \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mmean \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1msd \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp0 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp25 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp50 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp75 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp100 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mhist \u001b[0m\u001b[1m \u001b[0m┃ │\n", - "│ ┡━━━━━━━━━━━━━━━━━━╇━━━━━━╇━━━━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━━┩ │\n", - "│ │ \u001b[38;5;141mentity_id \u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 5000\u001b[0m │ \u001b[36m 2900\u001b[0m │ \u001b[36m 4\u001b[0m │ \u001b[36m 2500\u001b[0m │ \u001b[36m 5100\u001b[0m │ \u001b[36m 7600\u001b[0m │ \u001b[36m 10000\u001b[0m │ \u001b[32m ▇▇▇▇▇▇ \u001b[0m │ │\n", - "│ │ \u001b[38;5;141mvalue \u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 1\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 1\u001b[0m │ \u001b[36m 1\u001b[0m │ \u001b[36m 1\u001b[0m │ \u001b[36m 1\u001b[0m │ \u001b[36m 1\u001b[0m │ \u001b[32m ▇ \u001b[0m │ │\n", - "│ └──────────────────┴──────┴─────────┴────────┴────────┴──────┴────────┴────────┴────────┴─────────┴──────────┘ │\n", + "│ ┏━━━━━━━━━━━━━━━━━━┳━━━━━━┳━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━┳━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━━━━┓ │\n", + "│ ┃\u001b[1m \u001b[0m\u001b[1mcolumn_name \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mNA \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mNA % \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mmean \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1msd \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp0 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp25 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp50 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp75 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp100 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mhist \u001b[0m\u001b[1m \u001b[0m┃ │\n", + "│ ┡━━━━━━━━━━━━━━━━━━╇━━━━━━╇━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━╇━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━━━━┩ │\n", + "│ │ \u001b[38;5;141mentity_id \u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 5032\u001b[0m │ \u001b[36m 2900\u001b[0m │ \u001b[36m 4\u001b[0m │ \u001b[36m 2499\u001b[0m │ \u001b[36m 5109\u001b[0m │ \u001b[36m 7555\u001b[0m │ \u001b[36m 9992\u001b[0m │ \u001b[32m ▇▇▇▇▇▇ \u001b[0m │ │\n", + "│ │ \u001b[38;5;141mvalue \u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 1\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 1\u001b[0m │ \u001b[36m 1\u001b[0m │ \u001b[36m 1\u001b[0m │ \u001b[36m 1\u001b[0m │ \u001b[36m 1\u001b[0m │ \u001b[32m ▇ \u001b[0m │ │\n", + "│ └──────────────────┴──────┴─────────┴─────────┴────────┴──────┴────────┴────────┴────────┴────────┴──────────┘ │\n", "│ \u001b[3m datetime \u001b[0m │\n", "│ ┏━━━━━━━━━━━━━━━━━━┳━━━━━━┳━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┓ │\n", "│ ┃\u001b[1m \u001b[0m\u001b[1mcolumn_name \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mNA \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mNA % \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mfirst \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mlast \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mfrequency \u001b[0m\u001b[1m \u001b[0m┃ │\n", @@ -491,7 +491,7 @@ " white-space: pre-wrap;\n", "}\n", "\n", - "shape: (3_103, 3)
entity_idtimestampvalue
i64datetime[μs]i64
17271966-08-01 07:08:001
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60501969-10-28 22:11:001
22301966-10-06 16:26:001
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31651965-03-03 18:44:001
96021968-07-01 03:24:001
95691968-02-07 11:17:001
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92241967-12-01 09:23:001
26381966-12-11 07:07:001
34151968-06-20 21:58:001
96791967-12-11 09:25:001
33761969-03-23 02:20:001
83481966-02-10 10:22:001
33701969-07-01 12:05:001
45761968-02-04 19:26:001
36231968-02-13 14:43:001
55911967-03-13 02:57:001
95631969-03-07 08:20:001
8991967-07-30 06:03:001
79791967-02-13 12:39:001
84791965-09-11 10:29:001
16551966-05-21 13:06:001
" + "shape: (3_103, 3)
entity_idtimestampvalue
i64datetime[μs]i64
96141968-07-25 20:32:001
75181967-05-22 15:26:001
61631967-09-21 17:10:001
60681967-01-22 22:27:001
55081969-08-29 18:27:001
31291966-10-12 14:42:001
40491966-05-05 03:52:001
39151969-04-28 04:43:001
77261967-07-28 07:27:001
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" ], "text/plain": [ "shape: (3_103, 3)\n", @@ -500,17 +500,17 @@ "│ --- ┆ --- ┆ --- │\n", "│ i64 ┆ datetime[μs] ┆ i64 │\n", "╞═══════════╪═════════════════════╪═══════╡\n", - "│ 1727 ┆ 1966-08-01 07:08:00 ┆ 1 │\n", - "│ 2269 ┆ 1965-09-07 11:14:00 ┆ 1 │\n", - "│ 6050 ┆ 1969-10-28 22:11:00 ┆ 1 │\n", - "│ 2230 ┆ 1966-10-06 16:26:00 ┆ 1 │\n", - "│ 6449 ┆ 1966-02-06 14:18:00 ┆ 1 │\n", + "│ 9614 ┆ 1968-07-25 20:32:00 ┆ 1 │\n", + "│ 7518 ┆ 1967-05-22 15:26:00 ┆ 1 │\n", + "│ 6163 ┆ 1967-09-21 17:10:00 ┆ 1 │\n", + "│ 6068 ┆ 1967-01-22 22:27:00 ┆ 1 │\n", + "│ 5508 ┆ 1969-08-29 18:27:00 ┆ 1 │\n", "│ … ┆ … ┆ … │\n", - "│ 9563 ┆ 1969-03-07 08:20:00 ┆ 1 │\n", - "│ 899 ┆ 1967-07-30 06:03:00 ┆ 1 │\n", - "│ 7979 ┆ 1967-02-13 12:39:00 ┆ 1 │\n", - "│ 8479 ┆ 1965-09-11 10:29:00 ┆ 1 │\n", - "│ 1655 ┆ 1966-05-21 13:06:00 ┆ 1 │\n", + "│ 3129 ┆ 1966-10-12 14:42:00 ┆ 1 │\n", + "│ 4049 ┆ 1966-05-05 03:52:00 ┆ 1 │\n", + "│ 3915 ┆ 1969-04-28 04:43:00 ┆ 1 │\n", + "│ 7726 ┆ 1967-07-28 07:27:00 ┆ 1 │\n", + "│ 7294 ┆ 1968-11-13 14:03:00 ┆ 1 │\n", "└───────────┴─────────────────────┴───────┘" ] }, @@ -579,20 +579,9 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 5, "metadata": {}, - "outputs": [ - { - "ename": "", - "evalue": "", - "output_type": "error", - "traceback": [ - "\u001b[1;31mRunning cells with '.venv' requires the ipykernel package.\n", - "\u001b[1;31mRun the following command to install 'ipykernel' into the Python environment. \n", - "\u001b[1;31mCommand: '/Users/au554730/Desktop/Projects/timeseriesflattener/.venv/bin/python -m pip install ipykernel -U --force-reinstall'" - ] - } - ], + "outputs": [], "source": [ "import datetime as dt\n", "\n", @@ -662,20 +651,9 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 6, "metadata": {}, - "outputs": [ - { - "ename": "", - "evalue": "", - "output_type": "error", - "traceback": [ - "\u001b[1;31mRunning cells with '.venv' requires the ipykernel package.\n", - "\u001b[1;31mRun the following command to install 'ipykernel' into the Python environment. \n", - "\u001b[1;31mCommand: '/Users/au554730/Desktop/Projects/timeseriesflattener/.venv/bin/python -m pip install ipykernel -U --force-reinstall'" - ] - } - ], + "outputs": [], "source": [ "import numpy as np\n", "from timeseriesflattener import PredictorSpec, StaticSpec\n", @@ -734,20 +712,9 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 7, "metadata": {}, - "outputs": [ - { - "ename": "", - "evalue": "", - "output_type": "error", - "traceback": [ - "\u001b[1;31mRunning cells with '.venv' requires the ipykernel package.\n", - "\u001b[1;31mRun the following command to install 'ipykernel' into the Python environment. \n", - "\u001b[1;31mCommand: '/Users/au554730/Desktop/Projects/timeseriesflattener/.venv/bin/python -m pip install ipykernel -U --force-reinstall'" - ] - } - ], + "outputs": [], "source": [ "temporal_interval_predictor_spec = PredictorSpec(\n", " value_frame=ValueFrame(\n", @@ -775,7 +742,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 8, "metadata": {}, "outputs": [ { @@ -788,7 +755,7 @@ " white-space: pre-wrap;\n", "}\n", "\n", - "shape: (9_999, 2)
entity_idfemale
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" + "shape: (9_999, 2)
entity_idfemale
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" ], "text/plain": [ "shape: (9_999, 2)\n", @@ -869,21 +836,18 @@ }, { "cell_type": "code", - "execution_count": 16, + "execution_count": 10, "metadata": {}, "outputs": [ { "data": { - "text/html": [ - "
/Users/au484925/Desktop/Git/timeseriesflattener/.venv/lib/python3.9/site-packages/rich/live.py:231: UserWarning: \n",
-                            "install \"ipywidgets\" for Jupyter support\n",
-                            "  warnings.warn('install \"ipywidgets\" for Jupyter support')\n",
-                            "
\n" - ], + "application/vnd.jupyter.widget-view+json": { + "model_id": "f25333ef77e543b88cd5420e89c48571", + "version_major": 2, + "version_minor": 0 + }, "text/plain": [ - "/Users/au484925/Desktop/Git/timeseriesflattener/.venv/lib/python3.9/site-packages/rich/live.py:231: UserWarning: \n", - "install \"ipywidgets\" for Jupyter support\n", - " warnings.warn('install \"ipywidgets\" for Jupyter support')\n" + "Output()" ] }, "metadata": {}, @@ -892,11 +856,11 @@ { "data": { "text/html": [ - "
Processing spec: female\n",
+                            "
Processing spec: ['female']\n",
                             "
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+                            "
Processing spec: ['value_1']\n",
                             "
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Processing spec: value_2\n",
+                            "
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                             "
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Processing spec: value\n",
+                            "
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                             "
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\n" ], @@ -1028,21 +972,22 @@ "│ │ string │ 1 │ │\n", "│ └─────────────┴───────┘ │\n", "│ \u001b[3m number \u001b[0m │\n", - "│ ┏━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━┳━━━━━━━┳━━━━━━━━━┳━━━━━━━┳━━━━━━━┳━━━━━━━┳━━━━━━━┳━━━━━━┳━━━━━━━┳━━━━━━━━┓ │\n", - "│ ┃\u001b[1m \u001b[0m\u001b[1mcolumn_name \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mNA \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mNA % \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mmean \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1msd \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp0 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp25 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp50 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp75 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp100 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mhist \u001b[0m\u001b[1m \u001b[0m┃ │\n", - "│ ┡━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━╇━━━━━━━╇━━━━━━━━━╇━━━━━━━╇━━━━━━━╇━━━━━━━╇━━━━━━━╇━━━━━━╇━━━━━━━╇━━━━━━━━┩ │\n", - "│ │ \u001b[38;5;141mentity_id \u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 5000\u001b[0m │ \u001b[36m 2900\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 2500\u001b[0m │ \u001b[36m 4900\u001b[0m │ \u001b[36m7400\u001b[0m │ \u001b[36m10000\u001b[0m │ \u001b[32m▇▇▇▇▇▇\u001b[0m │ │\n", - "│ │ \u001b[38;5;141mpred_female_fallback_na\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0.49\u001b[0m │ \u001b[36m 0.5\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 1\u001b[0m │ \u001b[36m 1\u001b[0m │ \u001b[32m▇ ▇\u001b[0m │ │\n", - "│ │ \u001b[38;5;141mn \u001b[0m │ │ │ │ │ │ │ │ │ │ │ │\n", - "│ │ \u001b[38;5;141mpred_value_1_within_0_t\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 5\u001b[0m │ \u001b[36m 0.97\u001b[0m │ \u001b[36m 0.66\u001b[0m │ \u001b[36m 4.3\u001b[0m │ \u001b[36m 5\u001b[0m │ \u001b[36m 5.6\u001b[0m │ \u001b[36m 9\u001b[0m │ \u001b[32m ▁▇▇▂ \u001b[0m │ │\n", - "│ │ \u001b[38;5;141mo_730_days_mean_fallbac\u001b[0m │ │ │ │ │ │ │ │ │ │ │ │\n", - "│ │ \u001b[38;5;141mk_nan \u001b[0m │ │ │ │ │ │ │ │ │ │ │ │\n", - "│ │ \u001b[38;5;141mpred_value_2_within_10_\u001b[0m │ \u001b[36m 10000\u001b[0m │ \u001b[36m 100\u001b[0m │ \u001b[36m nan\u001b[0m │ \u001b[36m nan\u001b[0m │ \u001b[36m nan\u001b[0m │ \u001b[36m nan\u001b[0m │ \u001b[36m nan\u001b[0m │ \u001b[36m nan\u001b[0m │ \u001b[36m nan\u001b[0m │ \u001b[32m \u001b[0m │ │\n", - "│ │ \u001b[38;5;141mto_365_days_mean_fallba\u001b[0m │ │ │ │ │ │ │ │ │ │ │ │\n", - "│ │ \u001b[38;5;141mck_nan \u001b[0m │ │ │ │ │ │ │ │ │ │ │ │\n", - "│ │ \u001b[38;5;141moutc_value_within_0_to_\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0.0001\u001b[0m │ \u001b[36m 0.01\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 1\u001b[0m │ \u001b[32m ▇ \u001b[0m │ │\n", - "│ │ \u001b[38;5;141m365_days_max_fallback_0\u001b[0m │ │ │ │ │ │ │ │ │ │ │ │\n", - "│ └─────────────────────────┴────────┴───────┴─────────┴───────┴───────┴───────┴───────┴──────┴───────┴────────┘ │\n", + "│ ┏━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━┳━━━━━━━┳━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━┳━━━━━━━┳━━━━━━━┳━━━━━━━┳━━━━━━━┳━━━━━━━━┓ │\n", + "│ ┃\u001b[1m \u001b[0m\u001b[1mcolumn_name \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mNA \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mNA % \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mmean \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1msd \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp0 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp25 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp50 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp75 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mp100 \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mhist \u001b[0m\u001b[1m \u001b[0m┃ │\n", + "│ ┡━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━╇━━━━━━━╇━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━╇━━━━━━━╇━━━━━━━╇━━━━━━━╇━━━━━━━╇━━━━━━━━┩ │\n", + "│ │ \u001b[38;5;141mentity_id \u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 4959\u001b[0m │ \u001b[36m 2886\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 2485\u001b[0m │ \u001b[36m 4922\u001b[0m │ \u001b[36m 7443\u001b[0m │ \u001b[36m 9999\u001b[0m │ \u001b[32m▇▇▇▇▇▇\u001b[0m │ │\n", + "│ │ \u001b[38;5;141mpred_female_fallback_\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m0.4931\u001b[0m │ \u001b[36m 0.5\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 1\u001b[0m │ \u001b[36m 1\u001b[0m │ \u001b[32m▇ ▇\u001b[0m │ │\n", + "│ │ \u001b[38;5;141mnan \u001b[0m │ │ │ │ │ │ │ │ │ │ │ │\n", + "│ │ \u001b[38;5;141mpred_value_1_within_0\u001b[0m │ \u001b[36m1072\u001b[0m │ \u001b[36m10.72\u001b[0m │ \u001b[36m 5.01\u001b[0m │ \u001b[36m1.842\u001b[0m │ \u001b[36m 0.01491\u001b[0m │ \u001b[36m3.851\u001b[0m │ \u001b[36m5.023\u001b[0m │ \u001b[36m6.178\u001b[0m │ \u001b[36m9.946\u001b[0m │ \u001b[32m▁▃▇▇▃▁\u001b[0m │ │\n", + "│ │ \u001b[38;5;141m_to_730_days_mean_fal\u001b[0m │ │ │ │ │ │ │ │ │ │ │ │\n", + "│ │ \u001b[38;5;141mlback_nan \u001b[0m │ │ │ │ │ │ │ │ │ │ │ │\n", + "│ │ \u001b[38;5;141mpred_value_2_within_1\u001b[0m │ \u001b[36m2060\u001b[0m │ \u001b[36m 20.6\u001b[0m │ \u001b[36m 5.008\u001b[0m │ \u001b[36m2.222\u001b[0m │ \u001b[36m0.0003901\u001b[0m │ \u001b[36m 3.52\u001b[0m │ \u001b[36m5.014\u001b[0m │ \u001b[36m 6.56\u001b[0m │ \u001b[36m9.997\u001b[0m │ \u001b[32m▂▅▇▇▅▂\u001b[0m │ │\n", + "│ │ \u001b[38;5;141m0_to_365_days_mean_fa\u001b[0m │ │ │ │ │ │ │ │ │ │ │ │\n", + "│ │ \u001b[38;5;141mllback_nan \u001b[0m │ │ │ │ │ │ │ │ │ │ │ │\n", + "│ │ \u001b[38;5;141moutc_outcome_within_0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[32m ▇ \u001b[0m │ │\n", + "│ │ \u001b[38;5;141m_to_365_days_max_fall\u001b[0m │ │ │ │ │ │ │ │ │ │ │ │\n", + "│ │ \u001b[38;5;141mback_0 \u001b[0m │ │ │ │ │ │ │ │ │ │ │ │\n", + "│ └───────────────────────┴──────┴───────┴────────┴───────┴───────────┴───────┴───────┴───────┴───────┴────────┘ │\n", "│ \u001b[3m datetime \u001b[0m │\n", "│ ┏━━━━━━━━━━━━━━━━━━┳━━━━━━┳━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┓ │\n", "│ ┃\u001b[1m \u001b[0m\u001b[1mcolumn_name \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mNA \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mNA % \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mfirst \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mlast \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mfrequency \u001b[0m\u001b[1m \u001b[0m┃ │\n", @@ -1050,11 +995,11 @@ "│ │ \u001b[38;5;141mtimestamp \u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[31m 1965-01-02 09:35:00 \u001b[0m │ \u001b[31m 1969-12-31 21:42:00 \u001b[0m │ \u001b[38;5;141mNone \u001b[0m │ │\n", "│ └──────────────────┴──────┴─────────┴────────────────────────────┴────────────────────────────┴──────────────┘ │\n", "│ \u001b[3m string \u001b[0m │\n", - "│ ┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━┓ │\n", - "│ ┃\u001b[1m \u001b[0m\u001b[1mcolumn_name \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mNA \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mNA % \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mwords per row \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mtotal words \u001b[0m\u001b[1m \u001b[0m┃ │\n", - "│ ┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━╇━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━┩ │\n", - "│ │ \u001b[38;5;141mpred_time_uuid \u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 2\u001b[0m │ \u001b[36m 20000\u001b[0m │ │\n", - "│ └───────────────────────────────┴────────┴────────────┴─────────────────────────────┴────────────────────────┘ │\n", + "│ ┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓ │\n", + "│ ┃\u001b[1m \u001b[0m\u001b[1mcolumn_name \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mNA \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mNA % \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mwords per row \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mtotal words \u001b[0m\u001b[1m \u001b[0m┃ │\n", + "│ ┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩ │\n", + "│ │ \u001b[38;5;141mprediction_time_uuid \u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 0\u001b[0m │ \u001b[36m 2\u001b[0m │ \u001b[36m 20000\u001b[0m │ │\n", + "│ └───────────────────────────────────────┴───────┴───────────┴──────────────────────────┴─────────────────────┘ │\n", "╰────────────────────────────────────────────────────── End ──────────────────────────────────────────────────────╯\n" ] }, @@ -1066,14 +1011,14 @@ "text/plain": [ "['entity_id',\n", " 'timestamp',\n", - " 'pred_time_uuid',\n", + " 'prediction_time_uuid',\n", " 'pred_female_fallback_nan',\n", " 'pred_value_1_within_0_to_730_days_mean_fallback_nan',\n", " 'pred_value_2_within_10_to_365_days_mean_fallback_nan',\n", - " 'outc_value_within_0_to_365_days_max_fallback_0']" + " 'outc_outcome_within_0_to_365_days_max_fallback_0']" ] }, - "execution_count": 16, + "execution_count": 10, "metadata": {}, "output_type": "execute_result" } @@ -1095,7 +1040,7 @@ }, { "cell_type": "code", - "execution_count": 17, + "execution_count": 11, "metadata": {}, "outputs": [ { @@ -1108,51 +1053,51 @@ " white-space: pre-wrap;\n", "}\n", "\n", - "shape: (10_000, 7)
entity_idtimestamppred_time_uuidpred_female_fallback_nanpredXpredX_30_to_90outc_Y
i64datetime[μs]stri64f64f64i32
99031968-05-09 21:24:00"9903-1968-05-0…03.197213NaN0
74651966-05-24 01:23:00"7465-1966-05-2…14.243969NaN0
64471967-09-25 18:08:00"6447-1967-09-2…15.260492NaN0
21211966-05-05 20:52:00"2121-1966-05-0…04.798062NaN0
49271968-06-30 12:13:00"4927-1968-06-3…04.040067NaN0
54751967-01-09 03:09:00"5475-1967-01-0…05.953548NaN0
31571969-10-07 05:01:00"3157-1969-10-0…15.068696NaN0
97931968-12-15 12:59:00"9793-1968-12-1…06.93591NaN0
59621965-11-08 17:03:00"5962-1965-11-0…04.112929NaN0
97681967-07-04 23:09:00"9768-1967-07-0…15.053019NaN0
98611969-01-22 17:34:00"9861-1969-01-2…03.828896NaN0
6571969-04-14 15:47:00"657-1969-04-14…05.124361NaN0
65421967-04-15 14:37:00"6542-1967-04-1…16.099213NaN0
56071966-02-14 02:15:00"5607-1966-02-1…04.235413NaN0
42281967-02-26 05:45:00"4228-1967-02-2…05.181058NaN0
83371965-07-14 08:14:00"8337-1965-07-1…05.184373NaN0
97451969-02-04 01:18:00"9745-1969-02-0…16.005186NaN0
72221966-06-07 16:10:00"7222-1966-06-0…04.666051NaN0
33851967-07-17 19:18:00"3385-1967-07-1…16.98234NaN0
71591966-12-12 16:32:00"7159-1966-12-1…05.022668NaN0
1471965-03-12 05:32:00"147-1965-03-12…15.927239NaN0
14211968-04-15 15:53:00"1421-1968-04-1…06.061767NaN0
33531966-01-15 10:04:00"3353-1966-01-1…06.108344NaN0
19401968-05-17 10:49:00"1940-1968-05-1…04.909043NaN0
" + "shape: (10_000, 7)
entity_idtimestampprediction_time_uuidpred_female_fallback_nanpredXpredX_30_to_90outc_Y
i64datetime[μs]stri64f64f64i32
98521965-01-02 09:35:00"9852-1965-01-02 09:35:00.00000…1NaNNaN0
14671965-01-02 10:05:00"1467-1965-01-02 10:05:00.00000…0NaNNaN0
11251965-01-02 12:55:00"1125-1965-01-02 12:55:00.00000…0NaNNaN0
6491965-01-02 14:01:00"649-1965-01-02 14:01:00.000000"0NaNNaN0
20701965-01-03 08:01:00"2070-1965-01-03 08:01:00.00000…1NaNNaN0
3341969-12-31 16:32:00"334-1969-12-31 16:32:00.000000"17.252526NaN0
33631969-12-31 17:52:00"3363-1969-12-31 17:52:00.00000…13.6796672.4096640
79291969-12-31 18:22:00"7929-1969-12-31 18:22:00.00000…04.9435857.4759790
60021969-12-31 20:07:00"6002-1969-12-31 20:07:00.00000…15.5935837.0765980
8641969-12-31 21:42:00"864-1969-12-31 21:42:00.000000"15.520416NaN0
" ], "text/plain": [ "shape: (10_000, 7)\n", "┌───────────┬────────────────┬────────────────┬────────────────┬──────────┬───────────────┬────────┐\n", - "│ entity_id ┆ timestamp ┆ pred_time_uuid ┆ pred_female_fa ┆ predX ┆ predX_30_to_9 ┆ outc_Y │\n", - "│ --- ┆ --- ┆ --- ┆ llback_nan ┆ --- ┆ 0 ┆ --- │\n", - "│ i64 ┆ datetime[μs] ┆ str ┆ --- ┆ f64 ┆ --- ┆ i32 │\n", - "│ ┆ ┆ ┆ i64 ┆ ┆ f64 ┆ │\n", + "│ entity_id ┆ timestamp ┆ prediction_tim ┆ pred_female_fa ┆ predX ┆ predX_30_to_9 ┆ outc_Y │\n", + "│ --- ┆ --- ┆ e_uuid ┆ llback_nan ┆ --- ┆ 0 ┆ --- │\n", + "│ i64 ┆ datetime[μs] ┆ --- ┆ --- ┆ f64 ┆ --- ┆ i32 │\n", + "│ ┆ ┆ str ┆ i64 ┆ ┆ f64 ┆ │\n", "╞═══════════╪════════════════╪════════════════╪════════════════╪══════════╪═══════════════╪════════╡\n", - "│ 9903 ┆ 1968-05-09 ┆ 9903-1968-05-0 ┆ 0 ┆ 3.197213 ┆ NaN ┆ 0 │\n", - "│ ┆ 21:24:00 ┆ 9 21:24:00.000 ┆ ┆ ┆ ┆ │\n", - "│ ┆ ┆ 000 ┆ ┆ ┆ ┆ │\n", - "│ 7465 ┆ 1966-05-24 ┆ 7465-1966-05-2 ┆ 1 ┆ 4.243969 ┆ NaN ┆ 0 │\n", - "│ ┆ 01:23:00 ┆ 4 01:23:00.000 ┆ ┆ ┆ ┆ │\n", - "│ ┆ ┆ 000 ┆ ┆ ┆ ┆ │\n", - "│ 6447 ┆ 1967-09-25 ┆ 6447-1967-09-2 ┆ 1 ┆ 5.260492 ┆ NaN ┆ 0 │\n", - "│ ┆ 18:08:00 ┆ 5 18:08:00.000 ┆ ┆ ┆ ┆ │\n", - "│ ┆ ┆ 000 ┆ ┆ ┆ ┆ │\n", - "│ 2121 ┆ 1966-05-05 ┆ 2121-1966-05-0 ┆ 0 ┆ 4.798062 ┆ NaN ┆ 0 │\n", - "│ ┆ 20:52:00 ┆ 5 20:52:00.000 ┆ ┆ ┆ ┆ │\n", - "│ ┆ ┆ 000 ┆ ┆ ┆ ┆ │\n", - "│ 4927 ┆ 1968-06-30 ┆ 4927-1968-06-3 ┆ 0 ┆ 4.040067 ┆ NaN ┆ 0 │\n", - "│ ┆ 12:13:00 ┆ 0 12:13:00.000 ┆ ┆ ┆ ┆ │\n", - "│ ┆ ┆ 000 ┆ ┆ ┆ ┆ │\n", + "│ 9852 ┆ 1965-01-02 ┆ 9852-1965-01-0 ┆ 1 ┆ NaN ┆ NaN ┆ 0 │\n", + "│ ┆ 09:35:00 ┆ 2 09:35:00.000 ┆ ┆ ┆ ┆ │\n", + "│ ┆ ┆ 00… ┆ ┆ ┆ ┆ │\n", + "│ 1467 ┆ 1965-01-02 ┆ 1467-1965-01-0 ┆ 0 ┆ NaN ┆ NaN ┆ 0 │\n", + "│ ┆ 10:05:00 ┆ 2 10:05:00.000 ┆ ┆ ┆ ┆ │\n", + "│ ┆ ┆ 00… ┆ ┆ ┆ ┆ │\n", + "│ 1125 ┆ 1965-01-02 ┆ 1125-1965-01-0 ┆ 0 ┆ NaN ┆ NaN ┆ 0 │\n", + "│ ┆ 12:55:00 ┆ 2 12:55:00.000 ┆ ┆ ┆ ┆ │\n", + "│ ┆ ┆ 00… ┆ ┆ ┆ ┆ │\n", + "│ 649 ┆ 1965-01-02 ┆ 649-1965-01-02 ┆ 0 ┆ NaN ┆ NaN ┆ 0 │\n", + "│ ┆ 14:01:00 ┆ 14:01:00.00000 ┆ ┆ ┆ ┆ │\n", + "│ ┆ ┆ 0 ┆ ┆ ┆ ┆ │\n", + "│ 2070 ┆ 1965-01-03 ┆ 2070-1965-01-0 ┆ 1 ┆ NaN ┆ NaN ┆ 0 │\n", + "│ ┆ 08:01:00 ┆ 3 08:01:00.000 ┆ ┆ ┆ ┆ │\n", + "│ ┆ ┆ 00… ┆ ┆ ┆ ┆ │\n", "│ … ┆ … ┆ … ┆ … ┆ … ┆ … ┆ … │\n", - "│ 7159 ┆ 1966-12-12 ┆ 7159-1966-12-1 ┆ 0 ┆ 5.022668 ┆ NaN ┆ 0 │\n", - "│ ┆ 16:32:00 ┆ 2 16:32:00.000 ┆ ┆ ┆ ┆ │\n", - "│ ┆ ┆ 000 ┆ ┆ ┆ ┆ │\n", - "│ 147 ┆ 1965-03-12 ┆ 147-1965-03-12 ┆ 1 ┆ 5.927239 ┆ NaN ┆ 0 │\n", - "│ ┆ 05:32:00 ┆ 05:32:00.00000 ┆ ┆ ┆ ┆ │\n", + "│ 334 ┆ 1969-12-31 ┆ 334-1969-12-31 ┆ 1 ┆ 7.252526 ┆ NaN ┆ 0 │\n", + "│ ┆ 16:32:00 ┆ 16:32:00.00000 ┆ ┆ ┆ ┆ │\n", + "│ ┆ ┆ 0 ┆ ┆ ┆ ┆ │\n", + "│ 3363 ┆ 1969-12-31 ┆ 3363-1969-12-3 ┆ 1 ┆ 3.679667 ┆ 2.409664 ┆ 0 │\n", + "│ ┆ 17:52:00 ┆ 1 17:52:00.000 ┆ ┆ ┆ ┆ │\n", + "│ ┆ ┆ 00… ┆ ┆ ┆ ┆ │\n", + "│ 7929 ┆ 1969-12-31 ┆ 7929-1969-12-3 ┆ 0 ┆ 4.943585 ┆ 7.475979 ┆ 0 │\n", + "│ ┆ 18:22:00 ┆ 1 18:22:00.000 ┆ ┆ ┆ ┆ │\n", + "│ ┆ ┆ 00… ┆ ┆ ┆ ┆ │\n", + "│ 6002 ┆ 1969-12-31 ┆ 6002-1969-12-3 ┆ 1 ┆ 5.593583 ┆ 7.076598 ┆ 0 │\n", + "│ ┆ 20:07:00 ┆ 1 20:07:00.000 ┆ ┆ ┆ ┆ │\n", + "│ ┆ ┆ 00… ┆ ┆ ┆ ┆ │\n", + "│ 864 ┆ 1969-12-31 ┆ 864-1969-12-31 ┆ 1 ┆ 5.520416 ┆ NaN ┆ 0 │\n", + "│ ┆ 21:42:00 ┆ 21:42:00.00000 ┆ ┆ ┆ ┆ │\n", "│ ┆ ┆ 0 ┆ ┆ ┆ ┆ │\n", - "│ 1421 ┆ 1968-04-15 ┆ 1421-1968-04-1 ┆ 0 ┆ 6.061767 ┆ NaN ┆ 0 │\n", - "│ ┆ 15:53:00 ┆ 5 15:53:00.000 ┆ ┆ ┆ ┆ │\n", - "│ ┆ ┆ 000 ┆ ┆ ┆ ┆ │\n", - "│ 3353 ┆ 1966-01-15 ┆ 3353-1966-01-1 ┆ 0 ┆ 6.108344 ┆ NaN ┆ 0 │\n", - "│ ┆ 10:04:00 ┆ 5 10:04:00.000 ┆ ┆ ┆ ┆ │\n", - "│ ┆ ┆ 000 ┆ ┆ ┆ ┆ │\n", - "│ 1940 ┆ 1968-05-17 ┆ 1940-1968-05-1 ┆ 0 ┆ 4.909043 ┆ NaN ┆ 0 │\n", - "│ ┆ 10:49:00 ┆ 7 10:49:00.000 ┆ ┆ ┆ ┆ │\n", - "│ ┆ ┆ 000 ┆ ┆ ┆ ┆ │\n", "└───────────┴────────────────┴────────────────┴────────────────┴──────────┴───────────────┴────────┘" ] }, - "execution_count": 17, + "execution_count": 11, "metadata": {}, "output_type": "execute_result" } @@ -1187,6 +1132,11 @@ "5. Our outcome columns, prefixed with `outc_`\n" ] }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [] + }, { "cell_type": "markdown", "metadata": {}, diff --git a/pyproject.toml b/pyproject.toml index 54fa5b65..eb2d1bca 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -35,7 +35,7 @@ dependencies = [ "frozendict>=2.3.4", "coloredlogs>14.0.0", "tqdm>4.1.0", - "polars>0.19.0", + "polars>=0.19.0", "iterpy==1.6.0", "rich>=13.0.0", "ipykernel[docs]>=6.29.5", @@ -70,7 +70,7 @@ docs = [ "sphinx_design==0.3.0", "ipykernel>=6.29.5", ] -tutorials = ["jupyter>=1.0.0,<1.1.0", "skimpy>=0.0.11"] +tutorials = ["jupyter>=1.0.0,<1.1.0", "skimpy==0.0.15"] [project.readme] file = "README.md" @@ -81,20 +81,8 @@ homepage = "https://github.com/Aarhus-Psychiatry-Research/timeseriesflattener" repository = "https://github.com/Aarhus-Psychiatry-Research/timeseriesflattener" documentation = "https://aarhus-psychiatry-research.github.io/timeseriesflattener/" -[tool] -rye = { dev-dependencies = [ - "pytest>=7.1.3, <7.3.0", - "pytest-cov>=3.0.0, <3.1.0", - "pytest-xdist>=3.0.0, <3.2.0", - "pytest-sugar>=0.9.4, <0.10.0", - "pytest-testmon==2.1.0", - "pytest-benchmark==4.0.0", - "pytest-codspeed==2.2.0", - "invoke==2.1.1", - "pyright==1.1.330.post0", - "pandas-stubs>=2.0.3.230814", - "ruff>=0.2.2", -] } +[tool.uv] +override-dependencies = ["polars >= 1.0"] [tool.pyright] exclude = [".*venv*/", ".venv38/", ".tox", ".benchmark_cache"] diff --git a/src/timeseriesflattener/main_test.py b/src/timeseriesflattener/main_test.py index eb26b33b..ec521163 100644 --- a/src/timeseriesflattener/main_test.py +++ b/src/timeseriesflattener/main_test.py @@ -45,8 +45,8 @@ def assert_frame_equal( result: pl.DataFrame, expected: pl.DataFrame, ignore_colums: Sequence[str] = () ): polars_testing.assert_frame_equal( - result.drop(ignore_colums), - expected.drop(ignore_colums), + result.drop(ignore_colums, strict=False), + expected.drop(ignore_colums, strict=False), check_dtypes=False, check_column_order=False, ) diff --git a/src/timeseriesflattener/processors/temporal.py b/src/timeseriesflattener/processors/temporal.py index 8624037a..07f4a608 100644 --- a/src/timeseriesflattener/processors/temporal.py +++ b/src/timeseriesflattener/processors/temporal.py @@ -130,9 +130,10 @@ def _aggregate_masked_frame( ) rename_mapping = dict(value_columns) - with_fallback = grouped_frame.with_columns( - cs.contains(masked_frame.value_col_names).fill_null(fallback) - ).rename(rename_mapping) + for col in masked_frame.value_col_names: + with_fallback = grouped_frame.with_columns(cs.contains(col).fill_null(fallback)).rename( + rename_mapping + ) return with_fallback diff --git a/src/timeseriesflattener/specs/outcome.py b/src/timeseriesflattener/specs/outcome.py index a85a5a21..11ae545e 100644 --- a/src/timeseriesflattener/specs/outcome.py +++ b/src/timeseriesflattener/specs/outcome.py @@ -4,6 +4,7 @@ from dataclasses import InitVar, dataclass from typing import TYPE_CHECKING +import pandas as pd import polars as pl from timeseriesflattener.specs import _lookdistance_to_timedelta @@ -114,7 +115,7 @@ def df(self) -> pl.DataFrame: @staticmethod def from_primitives( - df: pl.DataFrame, + df: pl.DataFrame | pd.DataFrame, entity_id_col_name: str, lookahead_days: Sequence[float | tuple[float, float]], aggregators: Sequence[AggregatorName], diff --git a/src/timeseriesflattener/testing/load_synth_data.py b/src/timeseriesflattener/testing/load_synth_data.py index c7f26ddf..cff859a4 100644 --- a/src/timeseriesflattener/testing/load_synth_data.py +++ b/src/timeseriesflattener/testing/load_synth_data.py @@ -37,7 +37,7 @@ def synth_predictor_binary() -> pl.DataFrame: def load_synth_outcome() -> pl.DataFrame: # Get first row for each id df = load_raw_test_csv("synth_raw_binary_2.csv") - df = df.groupby("entity_id").last() + df = df.group_by("entity_id").last() # Drop all rows with a value equal to 1 df = df.filter(pl.col("value") == 1) diff --git a/uv.lock b/uv.lock index 2a63910b..917dcfe5 100644 --- a/uv.lock +++ b/uv.lock @@ -9,6 +9,9 @@ resolution-markers = [ "python_full_version >= '3.13'", ] +[manifest] +overrides = [{ name = "polars", specifier = ">=1.0" }] + [[package]] name = "accessible-pygments" version = "0.0.5" @@ -1911,15 +1914,15 @@ wheels = [ [[package]] name = "polars" -version = "0.20.31" +version = "1.6.0" source = { registry = "https://pypi.org/simple" } -sdist = { url = "https://files.pythonhosted.org/packages/10/cb/447d8ba0d38df42bf247ade1fb7ad1ba61f09a95144ee8c4ab0314d38703/polars-0.20.31.tar.gz", hash = "sha256:00f62dec6bf43a4e2a5db58b99bf0e79699fe761c80ae665868eaea5168f3bbb", size = 3666354 } +sdist = { url = "https://files.pythonhosted.org/packages/2b/a9/cf169ce361224d4b397f52d6fcceb191452ecdc50813ce2aa6c60ff46e04/polars-1.6.0.tar.gz", hash = "sha256:d7e8d5e577883a9755bc3be92ecbf6f20bced68267bdb8bdb440120e905cc19c", size = 3929590 } wheels = [ - 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{ name = "polars", specifier = ">0.19.0" }, + { name = "polars", specifier = ">=0.19.0" }, { name = "pre-commit", marker = "extra == 'dev'", specifier = "==3.4.0" }, { name = "protobuf", specifier = "<=4.24.4" }, { name = "pyarrow", specifier = ">=8.0.0" }, @@ -3257,7 +3260,7 @@ requires-dist = [ { name = "ruff", marker = "extra == 'dev'", specifier = "==0.2.1" }, { name = "scikit-learn", specifier = ">=1.1.2" }, { name = "scipy", specifier = ">=1.8.0" }, - { name = "skimpy", marker = "extra == 'tutorials'", specifier = ">=0.0.11" }, + { name = "skimpy", marker = "extra == 'tutorials'", specifier = "==0.0.15" }, { name = "sphinx", marker = "extra == 'docs'", specifier = "==5.3.0" }, { name = "sphinx-copybutton", marker = "extra == 'docs'", specifier = "==0.5.2" }, { name = "sphinx-design", marker = "extra == 'docs'", specifier = "==0.3.0" }, From 3dddca6a064ae2179fb9b703b1458a59842d5fe3 Mon Sep 17 00:00:00 2001 From: Martin Bernstorff Date: Fri, 30 Aug 2024 14:21:00 +0200 Subject: [PATCH 15/38] update post-start.sh and Dockerfile --- .devcontainer/post-start.sh | 2 +- Dockerfile | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.devcontainer/post-start.sh b/.devcontainer/post-start.sh index 99298641..95312aa4 100644 --- a/.devcontainer/post-start.sh +++ b/.devcontainer/post-start.sh @@ -1,2 +1,2 @@ #!/bin/bash -uv sync --frozen --all-extras \ No newline at end of file +uv sync --all-extras \ No newline at end of file diff --git a/Dockerfile b/Dockerfile index d8e4d884..6cffc0a0 100644 --- a/Dockerfile +++ b/Dockerfile @@ -8,4 +8,4 @@ VOLUME psycop-common COPY . /app RUN --mount=type=cache,target=/root/.cache/uv \ - uv sync --frozen --all-extras \ No newline at end of file + uv sync --all-extras \ No newline at end of file From 77ba0325dbd6ac28bcf1bfb09428093b0a50c54f Mon Sep 17 00:00:00 2001 From: Martin Bernstorff Date: Fri, 30 Aug 2024 14:34:48 +0200 Subject: [PATCH 16/38] update 5 files update 5 files update post-start.sh, Makefile and tasks.py --- .devcontainer/post-start.sh | 1 + .pre-commit-config.yaml | 12 +- Makefile | 26 +- lefthook.yml | 2 +- .../processors/temporal.py | 7 +- tasks.py | 261 +----------------- 6 files changed, 21 insertions(+), 288 deletions(-) diff --git a/.devcontainer/post-start.sh b/.devcontainer/post-start.sh index 95312aa4..7f4398ef 100644 --- a/.devcontainer/post-start.sh +++ b/.devcontainer/post-start.sh @@ -1,2 +1,3 @@ #!/bin/bash +git init uv sync --all-extras \ No newline at end of file diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index c0b0446a..85705fd7 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -17,14 +17,4 @@ repos: ] types_or: [ python, pyi, jupyter ] - id: ruff-format - types_or: [ python, pyi, jupyter ] - - - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v2.3.0 - hooks: - - id: check-yaml - - - repo: https://github.com/repo-helper/pyproject-parser - rev: v0.7.0 - hooks: - - id: check-pyproject + types_or: [ python, pyi, jupyter ] \ No newline at end of file diff --git a/Makefile b/Makefile index da782e6c..e9f93efc 100644 --- a/Makefile +++ b/Makefile @@ -1,12 +1,14 @@ -.DEFAULT_GOAL := help -help: - @echo "This project uses Invoke (pyinvoke.org) for task management." - @echo Install it via - @echo - @echo " pip install invoke" - @echo - @echo and then run - @echo - @echo " inv --list" - @echo - @echo to get available tasks. \ No newline at end of file +test-tutorials: + find docs/tutorials -name '*.ipynb' | grep -v 'nbconvert' | xargs jupyter nbconvert --to notebook --execute + +types: + uv run pyright src + +lint: + uv run pre-commit run --all-files + +test: + uv run pytest src -n auto -rfE --failed-first --benchmark-disable + +qtest: + uv run pytest src -n auto -rfE --failed-first --benchmark-disable --testmon \ No newline at end of file diff --git a/lefthook.yml b/lefthook.yml index 14034829..cb1277dd 100644 --- a/lefthook.yml +++ b/lefthook.yml @@ -16,5 +16,5 @@ pre-commit: commands: format: glob: "*.{py}" - run: inv lint + run: make lint stage_fixed: true \ No newline at end of file diff --git a/src/timeseriesflattener/processors/temporal.py b/src/timeseriesflattener/processors/temporal.py index 07f4a608..76282a79 100644 --- a/src/timeseriesflattener/processors/temporal.py +++ b/src/timeseriesflattener/processors/temporal.py @@ -130,10 +130,9 @@ def _aggregate_masked_frame( ) rename_mapping = dict(value_columns) - for col in masked_frame.value_col_names: - with_fallback = grouped_frame.with_columns(cs.contains(col).fill_null(fallback)).rename( - rename_mapping - ) + with_fallback = grouped_frame.with_columns( + cs.contains(*masked_frame.value_col_names).fill_null(fallback) + ).rename(rename_mapping) return with_fallback diff --git a/tasks.py b/tasks.py index 3f45cdf3..6da1e472 100644 --- a/tasks.py +++ b/tasks.py @@ -1,28 +1,11 @@ """ -This project uses Invoke (pyinvoke.org) for task management. -Install it via: - -``` -pip install invoke -``` - -And then run: - -``` -inv --list -``` - -If you do not wish to use invoke you can simply delete this file. +Most tasks are in the makefile. """ from __future__ import annotations -import platform -import re from dataclasses import dataclass from pathlib import Path -from invoke import Context, Result, task # type: ignore - def echo_header(msg: str): print(f"\n--- {msg} ---") @@ -42,206 +25,6 @@ class Emo: EXAMINE = "🔍" -def git_init(c: Context, branch: str = "main"): - """Initialize a git repository if it does not exist yet.""" - # If no .git directory exits - if not Path(".git").exists(): - echo_header(f"{Emo.DO} Initializing Git repository") - c.run(f"git init -b {branch}") - c.run("git add .") - c.run("git commit -m 'Initial commit'") - print(f"{Emo.GOOD} Git repository initialized") - else: - print(f"{Emo.GOOD} Git repository already initialized") - - -def setup_venv(c: Context, python_version: str) -> str: - venv_name = f'.venv{python_version.replace(".", "")}' - - if not Path(venv_name).exists(): - echo_header(f"{Emo.DO} Creating virtual environment for {python_version}{Emo.PY}") - c.run(f"python{python_version} -m venv {venv_name}") - print(f"{Emo.GOOD} Virtual environment created") - else: - print(f"{Emo.GOOD} Virtual environment already exists") - - c.run(f"source {venv_name}/bin/activate") - - return venv_name - - -def _add_commit(c: Context, msg: str | None = None): - print("🔨 Adding and committing changes") - c.run("git add .") - - if msg is None: - msg = input("Commit message: ") - - c.run(f'git commit -m "{msg}"', pty=True, hide=True) - print("\n🤖 Changes added and committed\n") - - -def is_uncommitted_changes(c: Context) -> bool: - git_status_result: Result = c.run("git status --porcelain", pty=True, hide=True) # type: ignore - - uncommitted_changes = git_status_result.stdout != "" - return uncommitted_changes - - -def add_and_commit(c: Context, msg: str | None = None): - """Add and commit all changes.""" - if is_uncommitted_changes(c): - uncommitted_changes_descr = c.run("git status --porcelain", pty=True, hide=True).stdout - - echo_header(f"{Emo.WARN} Uncommitted changes detected") - - for line in uncommitted_changes_descr.splitlines(): - print(f" {line.strip()}") - print("\n") - _add_commit(c, msg=msg) - - -def branch_exists_on_remote(c: Context) -> bool: - branch_name = Path(".git/HEAD").read_text().split("/")[-1].strip() - - branch_exists_result: Result = c.run(f"git ls-remote --heads origin {branch_name}", hide=True) # type: ignore - - return branch_name in branch_exists_result.stdout - - -def update_branch(c: Context): - echo_header(f"{Emo.SYNC} Syncing branch with remote") - - if not branch_exists_on_remote(c): - c.run("git push --set-upstream origin HEAD") - else: - print("Pulling") - c.run("git pull") - print("Pushing") - c.run("git push") - - -def create_pr(c: Context): - c.run("gh pr create --web", pty=True) - - -def update_pr(c: Context): - echo_header(f"{Emo.COMMUNICATE} Syncing PR") - # Get current branch name - branch_name = Path(".git/HEAD").read_text().split("/")[-1].strip() - pr_result: Result = c.run("gh pr list --state OPEN", pty=False, hide=True) # type: ignore - - if branch_name not in pr_result.stdout: - create_pr(c) - else: - open_web = input("Open in browser? [y/n] ") - if "y" in open_web.lower(): - c.run("gh pr view --web", pty=True) - - -def exit_if_error_in_stdout(result: Result): - # Find N remaining using regex - - if "error" in result.stdout: - try: - errors_remaining = re.findall(r"\d+(?=( remaining))", result.stdout)[0] # testing - if errors_remaining != "0": - exit(0) - except IndexError: - pass - - -def pre_commit(c: Context): - """Run pre-commit checks.""" - - # Essential to have a clean working directory before pre-commit to avoid committing - # heterogenous files under a "style: linting" commit - echo_header(f"{Emo.CLEAN} Running pre-commit checks") - pre_commit_cmd = "pre-commit run --all-files" - result = c.run(pre_commit_cmd, pty=True, warn=True) - - exit_if_error_in_stdout(result) # type: ignore - - -@task -def types(c: Context): - echo_header(f"{Emo.CLEAN} Running static type checks") - c.run("pyright .", pty=True) - - -@task -def install(c: Context): - """Install the project in editable mode using pip install""" - echo_header(f"{Emo.DO} Installing project") - c.run("pip install -e '.[dev,test,docs,tutorials]'") - - -@task -def setup(c: Context, python_version: str = "3.9"): - """Confirm that a git repo exists and setup a virtual environment.""" - git_init(c) - venv_name = setup_venv(c, python_version=python_version) - print( - f"{Emo.DO} Activate your virtual environment by running: \n\n\t\t source {venv_name}/bin/activate \n" - ) - print(f"{Emo.DO} Then install the project by running: \n\n\t\t inv install\n") - - -@task -def update(c: Context): - """Update dependencies.""" - echo_header(f"{Emo.DO} Updating project") - c.run("pip install --upgrade -e '.[dev,tests,docs]'") - - -@task(iterable="pytest_args") -def test( - c: Context, - pytest_args: list[str] = [], # noqa - testmon: bool = True, -): - """Run tests""" - echo_header(f"{Emo.TEST} Running tests") - - if len(pytest_args) == 0: - pytest_args = [ - "src", - "-n auto", - "-rfE", - "--failed-first", - "-p no:cov", - "--disable-warnings", - "-q", - "--testmon", - "--benchmark-disable", - ] - if testmon: - pytest_args.append("--testmon") - - pytest_arg_str = " ".join(pytest_args) - - test_result: Result = c.run(f"pytest {pytest_arg_str}", warn=True, pty=True) # type: ignore - - # If "failed" in the pytest results - if "failed" in test_result.stdout: - print("\n\n\n") - echo_header("Failed tests") - - # Get lines with "FAILED" in them from the .pytest_results file - failed_tests = [line for line in test_result.stdout if line.startswith("FAILED")] - - for line in failed_tests: - # Remove from start of line until /test_ - line_sans_prefix = line[line.find("test_") :] - - # Keep only that after :: - line_sans_suffix = line_sans_prefix[line_sans_prefix.find("::") + 2 :] - print(f"FAILED {Emo.FAIL} #{line_sans_suffix} ") - - if test_result.return_code != 0: - exit(test_result.return_code) - - def test_for_rej(): # Get all paths in current directory or subdirectories that end in .rej rej_files = list(Path().rglob("*.rej")) @@ -252,45 +35,3 @@ def test_for_rej(): print(f" /{file}") print("\nResolve the conflicts and try again. \n") exit(1) - - -@task -def lint(c: Context): - """Lint the project using the pre-commit hooks and mypy.""" - test_for_rej() - pre_commit(c=c) - - -@task -def test_tutorials(c: Context): - c.run( - "find docs/tutorials -name '*.ipynb' | grep -v 'nbconvert' | xargs jupyter nbconvert --to notebook --execute" - ) - - -@task -def pr(c: Context): - """Run all checks and update the PR.""" - add_and_commit(c) - lint(c) - test(c) - test_tutorials(c) - update_branch(c) - update_pr(c) - - -@task -def docs(c: Context, view: bool = False, view_only: bool = False): - """ - Build and view docs. If neither build or view are specified, both are run. - """ - if not view_only: - echo_header(f"{Emo.DO} Building docs") - c.run("sphinx-build -b html docs docs/_build/html") - if view or view_only: - echo_header(f"{Emo.EXAMINE} open docs in browser") - # check the OS and open the docs in the browser - if platform.system() == "Windows": - c.run("start docs/_build/html/index.html") - else: - c.run("open docs/_build/html/index.html") From 02fc7221339eb87c685f395a20d58b52969d3567 Mon Sep 17 00:00:00 2001 From: Martin Bernstorff Date: Fri, 30 Aug 2024 14:35:31 +0200 Subject: [PATCH 17/38] chore: update action.yml --- .github/actions/test/action.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/actions/test/action.yml b/.github/actions/test/action.yml index c7800d53..74a13b7e 100644 --- a/.github/actions/test/action.yml +++ b/.github/actions/test/action.yml @@ -26,4 +26,4 @@ runs: uses: devcontainers/ci@v0.3 with: runCmd: | - inv test --pytest-args="-n auto" \ No newline at end of file + make test \ No newline at end of file From 8ad9ef785c01c41c6029a7fc5b0a791b68c33b47 Mon Sep 17 00:00:00 2001 From: Martin Bernstorff Date: Fri, 30 Aug 2024 14:39:48 +0200 Subject: [PATCH 18/38] update action.yml, static_type_checks.yml and Makefile --- .github/actions/test_tutorials/action.yml | 19 +++++++++---------- .github/workflows/static_type_checks.yml | 5 +++-- Makefile | 3 +++ 3 files changed, 15 insertions(+), 12 deletions(-) diff --git a/.github/actions/test_tutorials/action.yml b/.github/actions/test_tutorials/action.yml index 0f65e059..c18b0f59 100644 --- a/.github/actions/test_tutorials/action.yml +++ b/.github/actions/test_tutorials/action.yml @@ -8,27 +8,26 @@ runs: using: "composite" steps: ### Setup prerequisites + - name: Set up uv + shell: bash + # Install a specific uv version using the installer + run: curl -LsSf https://astral.sh/uv/0.4.0/install.sh | sh + - name: Set up Python - uses: actions/setup-python@v4 - with: - python-version: ${{ inputs.python-version }} + shell: bash + run: uv python install # Installing - name: Install dependencies shell: bash run: | - pip install invoke - inv install + make install ### Run tests - - name: Install jupyter - shell: bash - run: | - pip install jupyter - name: Compile notebooks and check for errors shell: bash run: | - inv test-tutorials + make test-tutorials for notebook in tutorials/*.ipynb; do if grep -q "\"cell_type\": \"error\"" $notebook; then echo "Error cell found in $notebook" diff --git a/.github/workflows/static_type_checks.yml b/.github/workflows/static_type_checks.yml index 94d3e281..46a3d774 100644 --- a/.github/workflows/static_type_checks.yml +++ b/.github/workflows/static_type_checks.yml @@ -18,7 +18,8 @@ jobs: uses: actions/checkout@v4 - name: Create github hosts file - run: | # If this file is not created, the dev container fails because of non-existent mount + run: + | # If this file is not created, the dev container fails because of non-existent mount mkdir -p ~/.config/gh touch ~/.config/gh/hosts.yml @@ -26,4 +27,4 @@ jobs: uses: devcontainers/ci@v0.3 with: runCmd: | - inv types \ No newline at end of file + make types diff --git a/Makefile b/Makefile index e9f93efc..08b37f2b 100644 --- a/Makefile +++ b/Makefile @@ -4,6 +4,9 @@ test-tutorials: types: uv run pyright src +install: + uv sync --all-extras + lint: uv run pre-commit run --all-files From a2b5438acf00fa5f4a0287dc2f6106fe0f8561ee Mon Sep 17 00:00:00 2001 From: Martin Bernstorff Date: Fri, 30 Aug 2024 14:42:03 +0200 Subject: [PATCH 19/38] build: update Makefile --- Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Makefile b/Makefile index 08b37f2b..e0f1fa03 100644 --- a/Makefile +++ b/Makefile @@ -1,5 +1,5 @@ test-tutorials: - find docs/tutorials -name '*.ipynb' | grep -v 'nbconvert' | xargs jupyter nbconvert --to notebook --execute + find docs/tutorials -name '*.ipynb' | grep -v 'nbconvert' | xargs uv run jupyter nbconvert --to notebook --execute types: uv run pyright src From 35deb509df705332007df55a363a8222ba16f1b0 Mon Sep 17 00:00:00 2001 From: Martin Bernstorff Date: Fri, 30 Aug 2024 14:42:43 +0200 Subject: [PATCH 20/38] build: update Dockerfile --- Dockerfile | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/Dockerfile b/Dockerfile index 6cffc0a0..d115ee2a 100644 --- a/Dockerfile +++ b/Dockerfile @@ -2,6 +2,25 @@ FROM python:3.9 ENV UV_SYSTEM_PYTHON=true COPY --from=ghcr.io/astral-sh/uv:0.4.0 /uv /bin/uv +RUN apt-get update && apt-get install -y curl + +# NVM and NPM are required for pyright +# Install nvm +# Explicitly set HOME environment variable +ENV NVM_DIR=$HOME/.nvm +RUN mkdir -p $NVM_DIR +ENV NODE_VERSION=18.2.0 + +# Install nvm with node and npm +RUN curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.39.5/install.sh | bash \ + && . $NVM_DIR/nvm.sh \ + && nvm install $NODE_VERSION \ + && nvm alias default $NODE_VERSION \ + && nvm use default + +ENV NODE_PATH=$NVM_DIR/v$NODE_VERSION/lib/node_modules +ENV PATH=$NVM_DIR/versions/node/v$NODE_VERSION/bin:$PATH + # Set the working directory to /app WORKDIR /app VOLUME psycop-common From aa780c14a34b1f34bfc60b4976b8909fe5aa95f6 Mon Sep 17 00:00:00 2001 From: Martin Bernstorff Date: Fri, 30 Aug 2024 14:47:15 +0200 Subject: [PATCH 21/38] docs: update 03_text.ipynb --- docs/tutorials/03_text.ipynb | 101 +++++++++++++---------------------- 1 file changed, 38 insertions(+), 63 deletions(-) diff --git a/docs/tutorials/03_text.ipynb b/docs/tutorials/03_text.ipynb index f05175a5..eec2d047 100644 --- a/docs/tutorials/03_text.ipynb +++ b/docs/tutorials/03_text.ipynb @@ -9,7 +9,7 @@ "\n", "So far, the tutorials have dealt with _tabular_ data only. This tutorial will show you to make predictors out of text features, such as clinical notes, within `timeseriesflattener`.\n", "\n", - "Specifically, this tutorial will cover *how to generate flattened predictors from already embedded text.*" + "Specifically, this tutorial will cover _how to generate flattened predictors from already embedded text._\n" ] }, { @@ -19,7 +19,7 @@ "source": [ "## The dataset\n", "\n", - "To start out, let's load a synthetic dataset containing text. As with all other features, each row in the dataset needs an ID, a timestamp, and the feature value. " + "To start out, let's load a synthetic dataset containing text. As with all other features, each row in the dataset needs an ID, a timestamp, and the feature value.\n" ] }, { @@ -48,21 +48,21 @@ " white-space: pre-wrap;\n", "}\n", "\n", - "shape: (5, 3)
entity_idtimestampvalue
i64datetime[μs]str
46471967-07-19 00:22:00"The patient we…
20071966-11-25 02:02:00"The patient is…
57991967-09-19 12:31:00"The patient, d…
13191969-07-21 23:16:00"The patient ha…
42341966-04-14 22:04:00"The patient ha…
" + "shape: (5, 3)
entity_idtimestampvalue
i64datetime[μs]str
46471967-07-19 00:22:00"The patient went into a medica…
20071966-11-25 02:02:00"The patient is taken to the em…
57991967-09-19 12:31:00"The patient, described as a 7-…
13191969-07-21 23:16:00"The patient had been left on a…
42341966-04-14 22:04:00"The patient had had some sever…
" ], "text/plain": [ "shape: (5, 3)\n", - "┌───────────┬─────────────────────┬───────────────────────────────────┐\n", - "│ entity_id ┆ timestamp ┆ value │\n", - "│ --- ┆ --- ┆ --- │\n", - "│ i64 ┆ datetime[μs] ┆ str │\n", - "╞═══════════╪═════════════════════╪═══════════════════════════════════╡\n", - "│ 4647 ┆ 1967-07-19 00:22:00 ┆ The patient went into a medicall… │\n", - "│ 2007 ┆ 1966-11-25 02:02:00 ┆ The patient is taken to the emer… │\n", - "│ 5799 ┆ 1967-09-19 12:31:00 ┆ The patient, described as a 7-mo… │\n", - "│ 1319 ┆ 1969-07-21 23:16:00 ┆ The patient had been left on a b… │\n", - "│ 4234 ┆ 1966-04-14 22:04:00 ┆ The patient had had some severe … │\n", - "└───────────┴─────────────────────┴───────────────────────────────────┘" + "┌───────────┬─────────────────────┬─────────────────────────────────┐\n", + "│ entity_id ┆ timestamp ┆ value │\n", + "│ --- ┆ --- ┆ --- │\n", + "│ i64 ┆ datetime[μs] ┆ str │\n", + "╞═══════════╪═════════════════════╪═════════════════════════════════╡\n", + "│ 4647 ┆ 1967-07-19 00:22:00 ┆ The patient went into a medica… │\n", + "│ 2007 ┆ 1966-11-25 02:02:00 ┆ The patient is taken to the em… │\n", + "│ 5799 ┆ 1967-09-19 12:31:00 ┆ The patient, described as a 7-… │\n", + "│ 1319 ┆ 1969-07-21 23:16:00 ┆ The patient had been left on a… │\n", + "│ 4234 ┆ 1966-04-14 22:04:00 ┆ The patient had had some sever… │\n", + "└───────────┴─────────────────────┴─────────────────────────────────┘" ] }, "execution_count": 2, @@ -83,14 +83,14 @@ "\n", "As generating text embeddings can often take a while, it can be an advantageous to embed the text before using `timeseriesflattener` to speed up the computation if you're generating multiple datasets. This first block will show you how to format a dataframe with embedded text for `timeseriesflattener`.\n", "\n", - "To start, let's embed the synthetic text data using TF-IDF. You can use any form of text-embedding you want - the only constraint is that the result of the embedding function should be a dataframe with an `entity_id_col`, `timestamp_col` and any number of columns containing the embeddings, with a single value in each column. \n", + "To start, let's embed the synthetic text data using TF-IDF. You can use any form of text-embedding you want - the only constraint is that the result of the embedding function should be a dataframe with an `entity_id_col`, `timestamp_col` and any number of columns containing the embeddings, with a single value in each column.\n", "\n", - "For purposes of demonstration, we will fit a small TF-IDF model to the data and use it to embed the text." + "For purposes of demonstration, we will fit a small TF-IDF model to the data and use it to embed the text.\n" ] }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 8, "metadata": {}, "outputs": [], "source": [ @@ -109,51 +109,26 @@ "# embed text\n", "embedded_text = embed_text_to_df(text=synth_text[\"value\"].to_list())\n", "# drop the text column from the original dataframe\n", - "metadata_only = synth_text.drop(columns=[\"value\"])\n", + "metadata_only = synth_text.drop([\"value\"])\n", "# concatenate the metadata and the embedded text\n", "embedded_text_with_metadata = pl.concat([metadata_only, embedded_text], how=\"horizontal\")" ] }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 4, "metadata": {}, "outputs": [ { - "data": { - "text/html": [ - "
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" + "Let's make some features!\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "We are creating 10*2=20 features: 1 for each embedding for each lookbehind (365 and 730 days), using the mean aggregation function." + "We are creating 10\\*2=20 features: 1 for each embedding for each lookbehind (365 and 730 days), using the mean aggregation function.\n" ] }, { "cell_type": "code", - "execution_count": 16, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -285,12 +260,12 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Let's check the output." + "Let's check the output.\n" ] }, { "cell_type": "code", - "execution_count": 29, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -356,7 +331,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "And just like that, you're ready to make a prediction model!" + "And just like that, you're ready to make a prediction model!\n" ] }, { @@ -381,7 +356,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.2" + "version": "3.9.18" }, "orig_nbformat": 4, "vscode": { @@ -392,4 +367,4 @@ }, "nbformat": 4, "nbformat_minor": 2 -} \ No newline at end of file +} From bd5be7c0e933d8020784faf01f17200f255a4709 Mon Sep 17 00:00:00 2001 From: Martin Bernstorff Date: Fri, 30 Aug 2024 14:51:28 +0200 Subject: [PATCH 22/38] docs: update 03_text.ipynb --- docs/tutorials/03_text.ipynb | 144 ++++++++++++++++++----------------- 1 file changed, 76 insertions(+), 68 deletions(-) diff --git a/docs/tutorials/03_text.ipynb b/docs/tutorials/03_text.ipynb index eec2d047..64cb46b9 100644 --- a/docs/tutorials/03_text.ipynb +++ b/docs/tutorials/03_text.ipynb @@ -24,7 +24,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": 10, "metadata": {}, "outputs": [], "source": [ @@ -35,7 +35,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 11, "metadata": {}, "outputs": [ { @@ -65,7 +65,7 @@ "└───────────┴─────────────────────┴─────────────────────────────────┘" ] }, - "execution_count": 2, + "execution_count": 11, "metadata": {}, "output_type": "execute_result" } @@ -90,7 +90,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 12, "metadata": {}, "outputs": [], "source": [ @@ -116,19 +116,44 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 13, "metadata": {}, "outputs": [ { - "ename": "NameError", - "evalue": "name 'embedded_text_with_metadata' is not defined", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)", - "Cell \u001b[0;32mIn[4], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43membedded_text_with_metadata\u001b[49m\u001b[38;5;241m.\u001b[39mhead()\n", - "\u001b[0;31mNameError\u001b[0m: name 'embedded_text_with_metadata' is not defined" - ] + "data": { + "text/html": [ + "
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"│ ┆ ┆ 000000 ┆ ┆ ┆ ┆ ┆ ┆ │\n", + "│ 6840 ┆ 1965-11-0 ┆ 6840-1965 ┆ 0.155821 ┆ … ┆ 0.096561 ┆ 0.28581 ┆ 0.45603 ┆ 0.092896 │\n", + "│ ┆ 2 ┆ -11-02 ┆ ┆ ┆ ┆ ┆ ┆ │\n", + "│ ┆ 07:17:00 ┆ 07:17:00. ┆ ┆ ┆ ┆ ┆ ┆ │\n", + "│ ┆ ┆ 00000… ┆ ┆ ┆ ┆ ┆ ┆ │\n", + "│ 2039 ┆ 1966-04-2 ┆ 2039-1966 ┆ 0.108015 ┆ … ┆ 0.133872 ┆ 0.693431 ┆ 0.210747 ┆ 0.257581 │\n", + "│ ┆ 0 ┆ -04-20 ┆ ┆ ┆ ┆ ┆ ┆ │\n", + "│ ┆ 05:06:00 ┆ 05:06:00. ┆ ┆ ┆ ┆ ┆ ┆ │\n", + "│ ┆ ┆ 00000… ┆ ┆ ┆ ┆ ┆ ┆ │\n", + "│ 9496 ┆ 1966-12-0 ┆ 9496-1966 ┆ 0.279955 ┆ … ┆ 0.0 ┆ 0.513498 ┆ 0.546216 ┆ 0.3338 │\n", + "│ ┆ 6 ┆ -12-06 ┆ ┆ ┆ ┆ ┆ ┆ │\n", + "│ ┆ 06:44:00 ┆ 06:44:00. ┆ ┆ ┆ ┆ ┆ ┆ │\n", + "│ ┆ ┆ 00000… ┆ ┆ ┆ ┆ ┆ ┆ │\n", + "│ 7281 ┆ 1967-06-0 ┆ 7281-1967 ┆ 0.289663 ┆ … ┆ 0.269251 ┆ 0.464891 ┆ 0.211934 ┆ 0.388547 │\n", + "│ ┆ 5 ┆ -06-05 ┆ ┆ ┆ ┆ ┆ ┆ │\n", + "│ ┆ 00:41:00 ┆ 00:41:00. ┆ ┆ ┆ ┆ ┆ ┆ │\n", + "│ ┆ ┆ 00000… ┆ ┆ ┆ ┆ ┆ ┆ │\n", + "│ 7424 ┆ 1967-07-1 ┆ 7424-1967 ┆ 0.153907 ┆ … ┆ 0.063583 ┆ 0.682222 ┆ 0.475452 ┆ 0.0 │\n", + "│ ┆ 3 ┆ -07-13 ┆ ┆ ┆ ┆ ┆ ┆ │\n", + "│ ┆ 15:01:00 ┆ 15:01:00. ┆ ┆ ┆ ┆ ┆ ┆ │\n", + "│ ┆ ┆ 00000… ┆ ┆ ┆ ┆ ┆ ┆ │\n", "└───────────┴───────────┴───────────┴───────────┴───┴───────────┴───────────┴───────────┴──────────┘" ] }, - "execution_count": 29, + "execution_count": 16, "metadata": {}, "output_type": "execute_result" } From bd7c0fcd8458ffa022e47d303375ba7af5dd4224 Mon Sep 17 00:00:00 2001 From: Martin Bernstorff Date: Mon, 2 Sep 2024 08:20:54 +0200 Subject: [PATCH 23/38] update settings.json, test_specs.py and timedelta.py --- .vscode/settings.json | 1 + src/timeseriesflattener/specs/test_specs.py | 57 +++++++++++++++++++-- src/timeseriesflattener/specs/timedelta.py | 4 +- 3 files changed, 56 insertions(+), 6 deletions(-) diff --git a/.vscode/settings.json b/.vscode/settings.json index 6ae01a5a..2d8e9055 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -6,4 +6,5 @@ "python.testing.pytestEnabled": true, "python.analysis.typeCheckingMode": "standard", "python.analysis.diagnosticMode": "workspace", + "restructuredtext.pythonRecommendation.disabled": true, } \ No newline at end of file diff --git a/src/timeseriesflattener/specs/test_specs.py b/src/timeseriesflattener/specs/test_specs.py index 4ef58eb5..790f4f43 100644 --- a/src/timeseriesflattener/specs/test_specs.py +++ b/src/timeseriesflattener/specs/test_specs.py @@ -8,14 +8,14 @@ from timeseriesflattener.aggregators import MeanAggregator from .value import ValueFrame -from .outcome import OutcomeSpec +from .outcome import BooleanOutcomeSpec, OutcomeSpec from .temporal import PredictorSpec from .timedelta import TimeDeltaSpec from .timestamp import TimestampValueFrame +from .static import StaticSpec -MockValueFrame = ValueFrame( - init_df=pl.DataFrame({"value": [1], "timestamp": ["2021-01-01"], "entity_id": [1]}) -) +MockDF = pl.DataFrame({"value": [1], "timestamp": ["2021-01-01"], "entity_id": [1]}) +MockValueFrame = ValueFrame(init_df=MockDF) def test_predictor_spec_post_init(): @@ -60,3 +60,52 @@ def test_timedelta_spec_error_if_non_unique_ids(): fallback=0, output_name="timedelta", ) + + +def test_predictor_from_primitives(): + predictor_spec = PredictorSpec.from_primitives( + df=MockDF, + entity_id_col_name="entity_id", + value_timestamp_col_name="timestamp", + lookbehind_days=[10], + aggregators=["mean"], + fallback=0, + ) + + assert predictor_spec.normalised_lookperiod[0].first == dt.timedelta(days=-10) + assert predictor_spec.normalised_lookperiod[0].last == dt.timedelta(days=0) + + +def test_static_spec_from_primitives(): + static_spec = StaticSpec.from_primitives( + df=MockDF, entity_id_col_name="entity_id", column_prefix="static", fallback=0 + ) + + assert static_spec.value_frame.df.shape == MockDF.shape + assert static_spec.value_frame.df.columns == MockDF.columns + + +def test_boolean_outcome_spec_correct_dates(): + boolean_outcome_spec = BooleanOutcomeSpec.from_primitives( + df=MockDF, + entity_id_col_name="entity_id", + lookahead_days=[10], + aggregators=["mean"], + column_prefix="boolean_outcome", + ) + + assert boolean_outcome_spec.normalised_lookperiod[0].first == dt.timedelta(days=0) + assert boolean_outcome_spec.normalised_lookperiod[0].last == dt.timedelta(days=10) + + +def test_boolean_outcome_spec_from_primitives(): + boolean_outcome_spec = BooleanOutcomeSpec.from_primitives( + df=MockDF, + entity_id_col_name="entity_id", + lookahead_days=[10], + aggregators=["mean"], + column_prefix="boolean_outcome", + ) + + assert boolean_outcome_spec.normalised_lookperiod[0].first == dt.timedelta(days=0) + assert boolean_outcome_spec.normalised_lookperiod[0].last == dt.timedelta(days=10) diff --git a/src/timeseriesflattener/specs/timedelta.py b/src/timeseriesflattener/specs/timedelta.py index 427ddd55..ea0ad5d4 100644 --- a/src/timeseriesflattener/specs/timedelta.py +++ b/src/timeseriesflattener/specs/timedelta.py @@ -20,8 +20,8 @@ class TimeDeltaSpec: output_name: str column_prefix: str = "pred" time_format: Literal["seconds", "minutes", "hours", "days", "years"] = "days" - """Specification for a time delta feature, i.e. the time between a prediction timestamp and a value timestamp. - Useful for e.g. calculating age or the time since a certain event. + """Specification for a time delta featre for an entity, i.e. the time between a prediction timestamp and a birthdate. + Useful for e.g. calculating age or the time since a certain event. Joins on the entity_id column. init_frame must contain columns: entity_id_col_name: The name of the column containing the entity ids. Must be a string, and the column's values must be strings which are unique. From b8f23641025a9b5bc15772a2e03a1c1c6f5e496c Mon Sep 17 00:00:00 2001 From: Martin Bernstorff Date: Mon, 2 Sep 2024 08:31:22 +0200 Subject: [PATCH 24/38] update 5 files --- .github/actions/test/action.yml | 22 +++++++------- .github/actions/test_tutorials/action.yml | 2 +- .github/workflows/documentation.yml | 12 ++++++-- Dockerfile | 2 +- Makefile | 35 ++++++++++++++++++----- 5 files changed, 50 insertions(+), 23 deletions(-) diff --git a/.github/actions/test/action.yml b/.github/actions/test/action.yml index 74a13b7e..7884fe77 100644 --- a/.github/actions/test/action.yml +++ b/.github/actions/test/action.yml @@ -11,19 +11,17 @@ runs: - name: Checkout (GitHub) uses: actions/checkout@v4 - - name: Replace python version in Dockerfile + - name: Set up uv shell: bash - run: | - sed -i '/python:.*/c\FROM python:${{ inputs.python-version }}' Dockerfile + # Install a specific uv version using the installer + run: curl -LsSf https://astral.sh/uv/0.4.0/install.sh | sh - - name: Create github hosts file + - name: Set up Python shell: bash - run: | # If this file is not created, the dev container fails because of non-existent mount - mkdir -p ~/.config/gh - touch ~/.config/gh/hosts.yml + run: uv python install - - name: Pre-build dev container image - uses: devcontainers/ci@v0.3 - with: - runCmd: | - make test \ No newline at end of file + # Installing + - name: Install dependencies + shell: bash + run: | + make test \ No newline at end of file diff --git a/.github/actions/test_tutorials/action.yml b/.github/actions/test_tutorials/action.yml index c18b0f59..1247c434 100644 --- a/.github/actions/test_tutorials/action.yml +++ b/.github/actions/test_tutorials/action.yml @@ -21,7 +21,7 @@ runs: - name: Install dependencies shell: bash run: | - make install + make install-tutorials ### Run tests - name: Compile notebooks and check for errors diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml index e3c03b76..26b9d6d1 100644 --- a/.github/workflows/documentation.yml +++ b/.github/workflows/documentation.yml @@ -16,11 +16,19 @@ jobs: fetch-depth: 0 # otherwise, you will failed to push refs to dest repo token: ${{ secrets.PAT }} + - name: Set up uv + shell: bash + # Install a specific uv version using the installer + run: curl -LsSf https://astral.sh/uv/0.4.0/install.sh | sh + + - name: Set up Python + shell: bash + run: uv python install + - name: Install dependencies shell: bash run: | - python -m pip install --upgrade pip - pip install -e ".[docs,tutorials,text]" + make install - name: Build and Commit uses: sphinx-notes/pages@2.1 diff --git a/Dockerfile b/Dockerfile index d115ee2a..b95c1017 100644 --- a/Dockerfile +++ b/Dockerfile @@ -27,4 +27,4 @@ VOLUME psycop-common COPY . /app RUN --mount=type=cache,target=/root/.cache/uv \ - uv sync --all-extras \ No newline at end of file + uv sync \ No newline at end of file diff --git a/Makefile b/Makefile index e0f1fa03..d788aeb8 100644 --- a/Makefile +++ b/Makefile @@ -1,17 +1,38 @@ +# Install environments +install: + uv sync --all-extras + +install-tests: + uv sync --no-dev --extra test + +install-tutorials: + uv sync --no-dev --extra tutorials + +install-docs: + uv sync --no-dev --extra docs --extra tutorials + +# Tests test-tutorials: + make install-tutorials find docs/tutorials -name '*.ipynb' | grep -v 'nbconvert' | xargs uv run jupyter nbconvert --to notebook --execute +test: + make install-tests + uv run pytest src -n auto -rfE --failed-first --benchmark-disable + +qtest: + uv run pytest src -n auto -rfE --failed-first --benchmark-disable --testmon + +# Lint and types types: + make install uv run pyright src -install: - uv sync --all-extras - lint: + make install uv run pre-commit run --all-files -test: - uv run pytest src -n auto -rfE --failed-first --benchmark-disable +docs: + make install-docs + uv run sphinx-build docs docs/_build -qtest: - uv run pytest src -n auto -rfE --failed-first --benchmark-disable --testmon \ No newline at end of file From c76ed25de7762609711d5e4f5be5645c34df32cf Mon Sep 17 00:00:00 2001 From: Martin Bernstorff Date: Mon, 2 Sep 2024 08:37:54 +0200 Subject: [PATCH 25/38] ci: update documentation.yml --- .github/workflows/documentation.yml | 12 ++---------- 1 file changed, 2 insertions(+), 10 deletions(-) diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml index 26b9d6d1..96b16c90 100644 --- a/.github/workflows/documentation.yml +++ b/.github/workflows/documentation.yml @@ -16,19 +16,11 @@ jobs: fetch-depth: 0 # otherwise, you will failed to push refs to dest repo token: ${{ secrets.PAT }} - - name: Set up uv - shell: bash - # Install a specific uv version using the installer - run: curl -LsSf https://astral.sh/uv/0.4.0/install.sh | sh - - - name: Set up Python - shell: bash - run: uv python install - - name: Install dependencies shell: bash run: | - make install + python -m pip install --upgrade pip + pip install -e ".[docs,tutorials]" - name: Build and Commit uses: sphinx-notes/pages@2.1 From 76c285890af1fa1ad7975c347cf253171d538b7d Mon Sep 17 00:00:00 2001 From: Martin Bernstorff Date: Mon, 2 Sep 2024 08:40:10 +0200 Subject: [PATCH 26/38] chore: update action.yml --- .github/actions/test/action.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/actions/test/action.yml b/.github/actions/test/action.yml index 7884fe77..2f1fa5e2 100644 --- a/.github/actions/test/action.yml +++ b/.github/actions/test/action.yml @@ -18,7 +18,7 @@ runs: - name: Set up Python shell: bash - run: uv python install + run: uv python install ${{ inputs.python-version }} # Installing - name: Install dependencies From d39a00d5f79561f8325eddba2d79517e026e074d Mon Sep 17 00:00:00 2001 From: Martin Bernstorff Date: Mon, 2 Sep 2024 08:40:54 +0200 Subject: [PATCH 27/38] update action.yml and static_type_checks.yml --- .github/workflows/static_type_checks.yml | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/.github/workflows/static_type_checks.yml b/.github/workflows/static_type_checks.yml index 46a3d774..396e5a21 100644 --- a/.github/workflows/static_type_checks.yml +++ b/.github/workflows/static_type_checks.yml @@ -16,15 +16,15 @@ jobs: steps: - name: Checkout (GitHub) uses: actions/checkout@v4 + + - name: Set up uv + shell: bash + run: curl -LsSf https://astral.sh/uv/0.4.0/install.sh | sh - - name: Create github hosts file - run: - | # If this file is not created, the dev container fails because of non-existent mount - mkdir -p ~/.config/gh - touch ~/.config/gh/hosts.yml + - name: Set up Python + shell: bash + run: uv python install - - name: Pre-build dev container image - uses: devcontainers/ci@v0.3 - with: - runCmd: | - make types + - name: Run static type checks + shell: bash + run: make types From 415bf4039be218db265be1258177090f4e937521 Mon Sep 17 00:00:00 2001 From: Martin Bernstorff Date: Mon, 2 Sep 2024 08:41:17 +0200 Subject: [PATCH 28/38] ci: update benchmark.yml --- .github/workflows/benchmark.yml | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml index 7e389003..231582d6 100644 --- a/.github/workflows/benchmark.yml +++ b/.github/workflows/benchmark.yml @@ -18,8 +18,16 @@ jobs: with: python-version: "3.9" + - name: Set up uv + shell: bash + run: curl -LsSf https://astral.sh/uv/0.4.0/install.sh | sh + + - name: Set up Python + shell: bash + run: uv python install + - name: Install dependencies - run: pip install .[test] + run: make install - name: Run benchmarks uses: CodSpeedHQ/action@v2 From 3e3eca0e009099be2d60f0fd5ba2aeba1ceae231 Mon Sep 17 00:00:00 2001 From: Martin Bernstorff Date: Mon, 2 Sep 2024 08:43:25 +0200 Subject: [PATCH 29/38] ci: update benchmark.yml --- .github/workflows/benchmark.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml index 231582d6..e2f114f3 100644 --- a/.github/workflows/benchmark.yml +++ b/.github/workflows/benchmark.yml @@ -33,4 +33,4 @@ jobs: uses: CodSpeedHQ/action@v2 with: token: ${{ secrets.CODSPEED_TOKEN }} - run: pytest . --codspeed \ No newline at end of file + run: uv run pytest src --codspeed \ No newline at end of file From 1cc4e535bc100f4b3a21f11ac2af1bd2f283c8ed Mon Sep 17 00:00:00 2001 From: Martin Bernstorff Date: Mon, 2 Sep 2024 08:44:05 +0200 Subject: [PATCH 30/38] update benchmark.yml and Makefile --- .github/workflows/benchmark.yml | 5 +---- Makefile | 4 ++++ 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml index e2f114f3..22aa8f99 100644 --- a/.github/workflows/benchmark.yml +++ b/.github/workflows/benchmark.yml @@ -26,11 +26,8 @@ jobs: shell: bash run: uv python install - - name: Install dependencies - run: make install - - name: Run benchmarks uses: CodSpeedHQ/action@v2 with: token: ${{ secrets.CODSPEED_TOKEN }} - run: uv run pytest src --codspeed \ No newline at end of file + run: make benchmark \ No newline at end of file diff --git a/Makefile b/Makefile index d788aeb8..02c8c3f5 100644 --- a/Makefile +++ b/Makefile @@ -20,6 +20,10 @@ test: make install-tests uv run pytest src -n auto -rfE --failed-first --benchmark-disable +benchmark: + make install + uv run pytest src --codspeed + qtest: uv run pytest src -n auto -rfE --failed-first --benchmark-disable --testmon From c7fd6ae5d041e7891560248081eb8d03ffd6b909 Mon Sep 17 00:00:00 2001 From: Martin Bernstorff Date: Mon, 2 Sep 2024 08:50:54 +0200 Subject: [PATCH 31/38] build: update Makefile --- Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Makefile b/Makefile index 02c8c3f5..e21d8027 100644 --- a/Makefile +++ b/Makefile @@ -14,7 +14,7 @@ install-docs: # Tests test-tutorials: make install-tutorials - find docs/tutorials -name '*.ipynb' | grep -v 'nbconvert' | xargs uv run jupyter nbconvert --to notebook --execute + find docs/tutorials -name '*.ipynb' | grep -v 'nbconvert' | xargs -P 4 -I {} uv run jupyter nbconvert {} --to notebook --execute test: make install-tests From c2ad6a8560365bbb95968405a7a4fab6de652fae Mon Sep 17 00:00:00 2001 From: Martin Bernstorff Date: Mon, 2 Sep 2024 08:54:35 +0200 Subject: [PATCH 32/38] ci: update benchmark.yml --- .github/workflows/benchmark.yml | 3 --- 1 file changed, 3 deletions(-) diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml index 22aa8f99..351b016c 100644 --- a/.github/workflows/benchmark.yml +++ b/.github/workflows/benchmark.yml @@ -14,9 +14,6 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v4 - - uses: actions/setup-python@v3 - with: - python-version: "3.9" - name: Set up uv shell: bash From 91fe6b6f1150c87e4c11b9605575575a3c4606ca Mon Sep 17 00:00:00 2001 From: Martin Bernstorff Date: Mon, 2 Sep 2024 08:55:02 +0200 Subject: [PATCH 33/38] ci: update benchmark.yml --- .github/workflows/benchmark.yml | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml index 351b016c..4dd0a0f0 100644 --- a/.github/workflows/benchmark.yml +++ b/.github/workflows/benchmark.yml @@ -14,14 +14,12 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v4 + - uses: actions/setup-python@v3 + with: + python-version: "3.9" - - name: Set up uv - shell: bash - run: curl -LsSf https://astral.sh/uv/0.4.0/install.sh | sh - - - name: Set up Python - shell: bash - run: uv python install + - name: Install dependencies + run: pip install .[test] - name: Run benchmarks uses: CodSpeedHQ/action@v2 From 34f29f9f4f6292d0d19e9c6bcb3c8c0e6b737d0a Mon Sep 17 00:00:00 2001 From: Martin Bernstorff Date: Mon, 2 Sep 2024 08:56:30 +0200 Subject: [PATCH 34/38] ci: update benchmark.yml --- .github/workflows/benchmark.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml index 4dd0a0f0..7e389003 100644 --- a/.github/workflows/benchmark.yml +++ b/.github/workflows/benchmark.yml @@ -25,4 +25,4 @@ jobs: uses: CodSpeedHQ/action@v2 with: token: ${{ secrets.CODSPEED_TOKEN }} - run: make benchmark \ No newline at end of file + run: pytest . --codspeed \ No newline at end of file From 453a578ad939c222d0fe0c40be9ff7513584c759 Mon Sep 17 00:00:00 2001 From: Martin Bernstorff Date: Mon, 2 Sep 2024 09:04:28 +0200 Subject: [PATCH 35/38] build: update Makefile --- Makefile | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/Makefile b/Makefile index e21d8027..87ce3a44 100644 --- a/Makefile +++ b/Makefile @@ -1,24 +1,26 @@ # Install environments install: - uv sync --all-extras + uv sync --all-extras -q install-tests: - uv sync --no-dev --extra test + uv sync --no-dev --extra test -q install-tutorials: - uv sync --no-dev --extra tutorials + uv sync --no-dev --extra tutorials -q install-docs: - uv sync --no-dev --extra docs --extra tutorials + uv sync --no-dev --extra docs --extra tutorials -q # Tests test-tutorials: make install-tutorials find docs/tutorials -name '*.ipynb' | grep -v 'nbconvert' | xargs -P 4 -I {} uv run jupyter nbconvert {} --to notebook --execute + make install test: make install-tests uv run pytest src -n auto -rfE --failed-first --benchmark-disable + make install benchmark: make install @@ -39,4 +41,5 @@ lint: docs: make install-docs uv run sphinx-build docs docs/_build + make install From 57e50d88883433ca7f052c82014f480a3af7a41a Mon Sep 17 00:00:00 2001 From: Lasse Date: Mon, 2 Sep 2024 13:32:16 +0200 Subject: [PATCH 36/38] tutorials: add `to_primitives` examples for all specs --- docs/tutorials/01_basic.ipynb | 16 ++++++++++++++++ docs/tutorials/03_text.ipynb | 11 +++++++++++ 2 files changed, 27 insertions(+) diff --git a/docs/tutorials/01_basic.ipynb b/docs/tutorials/01_basic.ipynb index 07edf973..c7a602b5 100644 --- a/docs/tutorials/01_basic.ipynb +++ b/docs/tutorials/01_basic.ipynb @@ -716,6 +716,17 @@ "metadata": {}, "outputs": [], "source": [ + "temporal_interval_predictor_spec = PredictorSpec.from_primitives(\n", + " df=df_synth_predictors.rename({\"value\": \"value_2\"}),\n", + " entity_id_col_name=\"entity_id\",\n", + " value_timestamp_col_name=\"timestamp\",\n", + " aggregators=[\"mean\"],\n", + " column_prefix=\"pred\",\n", + " fallback=np.nan,\n", + " lookbehind_days=[(10, 365)],\n", + ")\n", + "\n", + "# Alternatively, if you prefer types\n", "temporal_interval_predictor_spec = PredictorSpec(\n", " value_frame=ValueFrame(\n", " entity_id_col_name=\"entity_id\",\n", @@ -786,6 +797,11 @@ "source": [ "from timeseriesflattener import StaticFrame\n", "\n", + "sex_predictor_spec = StaticSpec.from_primitives(\n", + " df=df_synth_sex, entity_id_col_name=\"entity_id\", column_prefix=\"pred\", fallback=np.nan\n", + ")\n", + "\n", + "# Alternatively, if you prefer types\n", "sex_predictor_spec = StaticSpec(\n", " value_frame=StaticFrame(init_df=df_synth_sex), column_prefix=\"pred\", fallback=np.nan\n", ")\n", diff --git a/docs/tutorials/03_text.ipynb b/docs/tutorials/03_text.ipynb index 64cb46b9..ce4c55df 100644 --- a/docs/tutorials/03_text.ipynb +++ b/docs/tutorials/03_text.ipynb @@ -179,6 +179,17 @@ "from timeseriesflattener import PredictorSpec, ValueFrame\n", "from timeseriesflattener.aggregators import MeanAggregator\n", "\n", + "text_spec = PredictorSpec.from_primitives(\n", + " df=embedded_text_with_metadata,\n", + " entity_id_col_name=\"entity_id\",\n", + " value_timestamp_col_name=\"timestamp\",\n", + " lookbehind_days=[365, 730],\n", + " aggregators=[\"mean\"],\n", + " column_prefix=\"pred_tfidf\",\n", + " fallback=np.nan,\n", + ")\n", + "\n", + "# Alternatively, if you prefer types\n", "text_spec = PredictorSpec(\n", " ValueFrame(\n", " init_df=embedded_text_with_metadata,\n", From 0c7413fa42180735528b861836d696b4b4d4b8cd Mon Sep 17 00:00:00 2001 From: Lasse Date: Mon, 2 Sep 2024 13:33:11 +0200 Subject: [PATCH 37/38] chore: rename function --- src/timeseriesflattener/specs/__init__.py | 3 ++- src/timeseriesflattener/specs/outcome.py | 12 ++++++------ src/timeseriesflattener/specs/temporal.py | 8 ++++---- 3 files changed, 12 insertions(+), 11 deletions(-) diff --git a/src/timeseriesflattener/specs/__init__.py b/src/timeseriesflattener/specs/__init__.py index 1d19fe15..e5430234 100644 --- a/src/timeseriesflattener/specs/__init__.py +++ b/src/timeseriesflattener/specs/__init__.py @@ -1,8 +1,9 @@ from __future__ import annotations + import datetime as dt -def _lookdistance_to_timedelta( +def _lookdistance_to_timedelta_days( lookdistance: float | tuple[float, float], ) -> tuple[dt.timedelta, dt.timedelta]: if isinstance(lookdistance, tuple): diff --git a/src/timeseriesflattener/specs/outcome.py b/src/timeseriesflattener/specs/outcome.py index 11ae545e..066df33e 100644 --- a/src/timeseriesflattener/specs/outcome.py +++ b/src/timeseriesflattener/specs/outcome.py @@ -6,17 +6,17 @@ import pandas as pd import polars as pl -from timeseriesflattener.specs import _lookdistance_to_timedelta -from ..validators import validate_col_name_columns_exist -from .value import ValueFrame, lookdistance_to_normalised_lookperiod +from timeseriesflattener.specs import _lookdistance_to_timedelta_days + from ..aggregators import ( AggregatorName, strings_to_aggregators, validate_compatible_fallback_type_for_aggregator, ) - +from ..validators import validate_col_name_columns_exist from .timestamp import TimestampValueFrame +from .value import ValueFrame, lookdistance_to_normalised_lookperiod if TYPE_CHECKING: from collections.abc import Sequence @@ -61,7 +61,7 @@ def from_primitives( column_prefix: str = "outc", ) -> OutcomeSpec: """Create an OutcomeSpec from primitives.""" - lookahead_distances = [_lookdistance_to_timedelta(d) for d in lookahead_days] + lookahead_distances = [_lookdistance_to_timedelta_days(d) for d in lookahead_days] return OutcomeSpec( value_frame=ValueFrame( @@ -123,7 +123,7 @@ def from_primitives( column_prefix: str = "outc", ) -> BooleanOutcomeSpec: """Create an OutcomeSpec from primitives.""" - lookahead_distances = [_lookdistance_to_timedelta(d) for d in lookahead_days] + lookahead_distances = [_lookdistance_to_timedelta_days(d) for d in lookahead_days] return BooleanOutcomeSpec( init_frame=TimestampValueFrame( diff --git a/src/timeseriesflattener/specs/temporal.py b/src/timeseriesflattener/specs/temporal.py index be45a0fa..3713688b 100644 --- a/src/timeseriesflattener/specs/temporal.py +++ b/src/timeseriesflattener/specs/temporal.py @@ -4,15 +4,15 @@ from dataclasses import InitVar, dataclass from typing import TYPE_CHECKING -from timeseriesflattener.specs import _lookdistance_to_timedelta +from timeseriesflattener.specs import _lookdistance_to_timedelta_days -from ..validators import validate_col_name_columns_exist -from .value import ValueFrame, lookdistance_to_normalised_lookperiod from ..aggregators import ( AggregatorName, strings_to_aggregators, validate_compatible_fallback_type_for_aggregator, ) +from ..validators import validate_col_name_columns_exist +from .value import ValueFrame, lookdistance_to_normalised_lookperiod if TYPE_CHECKING: from collections.abc import Sequence @@ -66,7 +66,7 @@ def from_primitives( fallback: int | float | str | None = 0, ) -> PredictorSpec: """Create a PredictorSpec from primitives.""" - lookbehind_distances = [_lookdistance_to_timedelta(d) for d in lookbehind_days] + lookbehind_distances = [_lookdistance_to_timedelta_days(d) for d in lookbehind_days] return PredictorSpec( value_frame=ValueFrame( From 95608f356e63f506eab941fe6cdf7c984bb24fcc Mon Sep 17 00:00:00 2001 From: Lasse Hansen Date: Mon, 2 Sep 2024 13:33:30 +0200 Subject: [PATCH 38/38] Update src/timeseriesflattener/specs/timedelta.py --- src/timeseriesflattener/specs/timedelta.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/timeseriesflattener/specs/timedelta.py b/src/timeseriesflattener/specs/timedelta.py index ea0ad5d4..fd0fb9ea 100644 --- a/src/timeseriesflattener/specs/timedelta.py +++ b/src/timeseriesflattener/specs/timedelta.py @@ -20,7 +20,7 @@ class TimeDeltaSpec: output_name: str column_prefix: str = "pred" time_format: Literal["seconds", "minutes", "hours", "days", "years"] = "days" - """Specification for a time delta featre for an entity, i.e. the time between a prediction timestamp and a birthdate. + """Specification for a time delta feature for an entity, i.e. the time between a prediction timestamp and a value timestamp (e.g. a birthdate). Useful for e.g. calculating age or the time since a certain event. Joins on the entity_id column. init_frame must contain columns: