diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 3696b4ca..390d4ff0 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -3,32 +3,32 @@ default_stages: [commit] repos: - repo: https://github.com/compilerla/conventional-pre-commit - rev: v2.1.1 + rev: v2.2.0 hooks: - id: conventional-pre-commit stages: [commit-msg] - repo: https://github.com/charliermarsh/ruff-pre-commit - rev: "v0.0.259" + rev: 'v0.0.262' hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] - repo: https://github.com/psf/black - rev: 23.1.0 + rev: 23.3.0 hooks: - id: black-jupyter - repo: https://github.com/PyCQA/docformatter - rev: v1.5.1 + rev: v1.6.3 hooks: - id: docformatter additional_dependencies: [tomli] args: ["--in-place", "--config", "./pyproject.toml"] - repo: https://github.com/pre-commit/mirrors-mypy - rev: v1.1.1 + rev: v1.2.0 hooks: - id: mypy additional_dependencies: ["types-requests"] - repo: https://github.com/pdm-project/pdm - rev: 2.5.2 + rev: 2.5.3 hooks: - id: pdm-lock-check - id: pdm-export diff --git a/CHANGELOG.md b/CHANGELOG.md index 82f3c52a..c4b43bde 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -32,6 +32,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Change embedders and joiners interface to have `.transform` method - Change linter to Ruff and removed flake8, isort, pydocstyle - Change default value inside `transform` function of IntersectionJoiner to not return geometry. +- Make torch and pytorch-lightning as optional dependencies ([#210](https://github.com/srai-lab/srai/issues/210)) ### Deprecated diff --git a/docs/getting_started/README.md b/docs/getting_started/README.md index 249dbb8e..23bb6491 100644 --- a/docs/getting_started/README.md +++ b/docs/getting_started/README.md @@ -19,6 +19,7 @@ The following optional dependencies can be installed to enable additional functi * `srai[voronoi]` - dependencies to use Voronoi-based regionization method * `srai[gtfs]` - dependencies to process GTFS data * `srai[plotting]` - dependencies to plot graphs and maps +* `srai[torch]` - dependencies to use torch-based embedders ## Usage diff --git a/pdm.lock b/pdm.lock index 1f978619..d831bfbf 100644 --- a/pdm.lock +++ b/pdm.lock @@ -69,7 +69,7 @@ dependencies = [ [[package]] name = "astropy" -version = "5.2.1" +version = "5.2.2" requires_python = ">=3.8" summary = "Astronomy and astrophysics core library" dependencies = [ @@ -106,7 +106,7 @@ summary = "Specifications for callback functions passed in to an API" [[package]] name = "beautifulsoup4" -version = "4.12.0" +version = "4.12.2" requires_python = ">=3.6.0" summary = "Screen-scraping library" dependencies = [ @@ -115,7 +115,7 @@ dependencies = [ [[package]] name = "black" -version = "23.1.0" +version = "23.3.0" requires_python = ">=3.7" summary = "The uncompromising code formatter." dependencies = [ @@ -130,12 +130,12 @@ dependencies = [ [[package]] name = "black" -version = "23.1.0" +version = "23.3.0" extras = ["jupyter"] requires_python = ">=3.7" summary = "The uncompromising code formatter." dependencies = [ - "black==23.1.0", + "black==23.3.0", "ipython>=7.8.0", "tokenize-rt>=3.2.0", ] @@ -213,8 +213,8 @@ summary = "Universal encoding detector for Python 3" [[package]] name = "charset-normalizer" -version = "2.1.1" -requires_python = ">=3.6.0" +version = "3.1.0" +requires_python = ">=3.7.0" summary = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." [[package]] @@ -251,7 +251,7 @@ summary = "Extended pickling support for Python objects" [[package]] name = "cmake" -version = "3.26.0" +version = "3.26.3" summary = "CMake is an open-source, cross-platform family of tools designed to build, test and package software" [[package]] @@ -262,7 +262,7 @@ summary = "Cross-platform colored terminal text." [[package]] name = "comm" -version = "0.1.2" +version = "0.1.3" requires_python = ">=3.6" summary = "Jupyter Python Comm implementation, for usage in ipykernel, xeus-python etc." dependencies = [ @@ -291,7 +291,7 @@ summary = "Composable style cycles" [[package]] name = "debugpy" -version = "1.6.6" +version = "1.6.7" requires_python = ">=3.7" summary = "An implementation of the Debug Adapter Protocol for Python" @@ -320,23 +320,23 @@ summary = "Distribution utilities" [[package]] name = "docformatter" -version = "1.5.1" -requires_python = ">=3.6,<4.0" +version = "1.6.3" +requires_python = ">=3.7,<4.0" summary = "Formats docstrings to follow PEP 257" dependencies = [ - "charset-normalizer<3.0.0,>=2.0.0", - "tomli<3.0.0,>=2.0.0; python_version >= \"3.7\"", + "charset-normalizer<4.0.0,>=3.0.0", "untokenize<0.2.0,>=0.1.1", ] [[package]] name = "docformatter" -version = "1.5.1" +version = "1.6.3" extras = ["tomli"] -requires_python = ">=3.6,<4.0" +requires_python = ">=3.7,<4.0" summary = "Formats docstrings to follow PEP 257" dependencies = [ - "docformatter==1.5.1", + "docformatter==1.6.3", + "tomli<3.0.0,>=2.0.0", ] [[package]] @@ -350,6 +350,12 @@ version = "1.1.1" requires_python = ">=3.7" summary = "Backport of PEP 654 (exception groups)" +[[package]] +name = "execnet" +version = "1.9.0" +requires_python = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +summary = "execnet: rapid multi-Python deployment" + [[package]] name = "executing" version = "1.2.0" @@ -372,13 +378,13 @@ dependencies = [ [[package]] name = "filelock" -version = "3.10.0" +version = "3.12.0" requires_python = ">=3.7" summary = "A platform independent file lock." [[package]] name = "fiona" -version = "1.9.2" +version = "1.9.3" requires_python = ">=3.7" summary = "Fiona reads and writes spatial data files" dependencies = [ @@ -405,7 +411,7 @@ dependencies = [ [[package]] name = "fonttools" -version = "4.39.2" +version = "4.39.3" requires_python = ">=3.8" summary = "Tools to manipulate font files" @@ -423,19 +429,19 @@ summary = "A list-like structure which implements collections.abc.MutableSequenc [[package]] name = "fsspec" -version = "2023.3.0" +version = "2023.4.0" requires_python = ">=3.8" summary = "File-system specification" [[package]] name = "fsspec" -version = "2023.3.0" +version = "2023.4.0" extras = ["http"] requires_python = ">=3.8" summary = "File-system specification" dependencies = [ "aiohttp!=4.0.0a0,!=4.0.0a1", - "fsspec==2023.3.0", + "fsspec==2023.4.0", "requests", ] @@ -478,7 +484,7 @@ dependencies = [ [[package]] name = "griffe" -version = "0.25.5" +version = "0.27.1" requires_python = ">=3.7" summary = "Signatures for entire Python programs. Extract the structure, the frame, the skeleton of your project, to generate API documentation or find breaking changes in your API." dependencies = [ @@ -515,7 +521,7 @@ summary = "Calculate the distance between 2 points on Earth." [[package]] name = "identify" -version = "2.5.21" +version = "2.5.22" requires_python = ">=3.7" summary = "File identification library for Python" @@ -527,7 +533,7 @@ summary = "Internationalized Domain Names in Applications (IDNA)" [[package]] name = "importlib-metadata" -version = "6.1.0" +version = "6.6.0" requires_python = ">=3.7" summary = "Read metadata from Python packages" dependencies = [ @@ -572,7 +578,7 @@ dependencies = [ [[package]] name = "ipython" -version = "8.11.0" +version = "8.12.0" requires_python = ">=3.8" summary = "IPython: Productive Interactive Computing" dependencies = [ @@ -588,6 +594,7 @@ dependencies = [ "pygments>=2.4.0", "stack-data", "traitlets>=5", + "typing-extensions; python_version < \"3.10\"", ] [[package]] @@ -597,14 +604,15 @@ summary = "Vestigial utilities from IPython" [[package]] name = "ipywidgets" -version = "7.7.4" +version = "7.7.5" summary = "IPython HTML widgets for Jupyter" dependencies = [ + "ipykernel>=4.5.1", "ipython-genutils~=0.2.0", "ipython>=4.0.0; python_version >= \"3.3\"", "jupyterlab-widgets<3,>=1.0.0; python_version >= \"3.6\"", "traitlets>=4.3.1", - "widgetsnbextension~=3.6.0", + "widgetsnbextension~=3.6.4", ] [[package]] @@ -692,7 +700,7 @@ dependencies = [ [[package]] name = "jupyter-client" -version = "8.1.0" +version = "8.2.0" requires_python = ">=3.8" summary = "Jupyter protocol implementation and client libraries" dependencies = [ @@ -773,7 +781,7 @@ summary = "Pygments theme using JupyterLab CSS variables" [[package]] name = "jupyterlab-widgets" -version = "1.1.3" +version = "1.1.4" requires_python = ">=3.6" summary = "A JupyterLab extension." @@ -845,7 +853,7 @@ dependencies = [ [[package]] name = "lit" -version = "16.0.0" +version = "16.0.2" summary = "A Software Testing Tool" [[package]] @@ -979,8 +987,8 @@ dependencies = [ [[package]] name = "mkdocs-awesome-pages-plugin" -version = "2.8.0" -requires_python = ">=3.6.2" +version = "2.9.0" +requires_python = ">=3.7" summary = "An MkDocs plugin that simplifies configuring page titles and their order" dependencies = [ "mkdocs>=1", @@ -999,7 +1007,7 @@ dependencies = [ [[package]] name = "mkdocs-jupyter" -version = "0.24.0" +version = "0.24.1" requires_python = ">=3.7" summary = "Use Jupyter in mkdocs websites" dependencies = [ @@ -1012,7 +1020,7 @@ dependencies = [ [[package]] name = "mkdocs-material" -version = "9.1.3" +version = "9.1.8" requires_python = ">=3.7" summary = "Documentation that simply works" dependencies = [ @@ -1051,7 +1059,7 @@ dependencies = [ [[package]] name = "mkdocstrings" -version = "0.20.0" +version = "0.21.2" requires_python = ">=3.7" summary = "Automatic documentation from sources, for MkDocs." dependencies = [ @@ -1061,27 +1069,28 @@ dependencies = [ "mkdocs-autorefs>=0.3.1", "mkdocs>=1.2", "pymdown-extensions>=6.3", + "typing-extensions>=4.1; python_version < \"3.10\"", ] [[package]] name = "mkdocstrings-python" -version = "0.8.3" +version = "0.9.0" requires_python = ">=3.7" summary = "A Python handler for mkdocstrings." dependencies = [ "griffe>=0.24", - "mkdocstrings>=0.19", + "mkdocstrings>=0.20", ] [[package]] name = "mkdocstrings" -version = "0.20.0" +version = "0.21.2" extras = ["python"] requires_python = ">=3.7" summary = "Automatic documentation from sources, for MkDocs." dependencies = [ "mkdocstrings-python>=0.5.2", - "mkdocstrings==0.20.0", + "mkdocstrings==0.21.2", ] [[package]] @@ -1128,7 +1137,7 @@ summary = "Simple yet flexible natural sorting in Python." [[package]] name = "nbclassic" -version = "0.5.3" +version = "0.5.5" requires_python = ">=3.7" summary = "Jupyter Notebook as a Jupyter Server extension." dependencies = [ @@ -1153,7 +1162,7 @@ dependencies = [ [[package]] name = "nbclient" -version = "0.7.2" +version = "0.7.4" requires_python = ">=3.7.0" summary = "A client library for executing notebooks. Formerly nbconvert's ExecutePreprocessor." dependencies = [ @@ -1165,7 +1174,7 @@ dependencies = [ [[package]] name = "nbconvert" -version = "7.2.10" +version = "7.3.1" requires_python = ">=3.7" summary = "Converting Jupyter Notebooks" dependencies = [ @@ -1207,7 +1216,7 @@ summary = "Patch asyncio to allow nested event loops" [[package]] name = "networkx" -version = "3.0" +version = "3.1" requires_python = ">=3.8" summary = "Python package for creating and manipulating graphs and networks" @@ -1222,7 +1231,7 @@ dependencies = [ [[package]] name = "notebook" -version = "6.5.3" +version = "6.5.4" requires_python = ">=3.7" summary = "A web-based notebook environment for interactive computing" dependencies = [ @@ -1246,7 +1255,7 @@ dependencies = [ [[package]] name = "notebook-shim" -version = "0.2.2" +version = "0.2.3" requires_python = ">=3.7" summary = "A shim layer for notebook traits and config" dependencies = [ @@ -1255,7 +1264,7 @@ dependencies = [ [[package]] name = "numpy" -version = "1.24.2" +version = "1.24.3" requires_python = ">=3.8" summary = "Fundamental package for array computing in Python" @@ -1393,7 +1402,7 @@ dependencies = [ [[package]] name = "packaging" -version = "23.0" +version = "23.1" requires_python = ">=3.7" summary = "Core utilities for Python packages" @@ -1451,7 +1460,7 @@ summary = "Tiny 'shelve'-like database with concurrency support" [[package]] name = "pillow" -version = "9.4.0" +version = "9.5.0" requires_python = ">=3.7" summary = "Python Imaging Library (Fork)" @@ -1463,16 +1472,17 @@ summary = "Resolve a name to an object." [[package]] name = "platformdirs" -version = "3.1.1" +version = "3.3.0" requires_python = ">=3.7" summary = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." [[package]] name = "plotly" -version = "5.13.1" +version = "5.14.1" requires_python = ">=3.6" summary = "An open-source, interactive data visualization library for Python" dependencies = [ + "packaging", "tenacity>=6.2.0", ] @@ -1512,7 +1522,7 @@ dependencies = [ [[package]] name = "psutil" -version = "5.9.4" +version = "5.9.5" requires_python = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" summary = "Cross-platform lib for process and system monitoring in Python." @@ -1552,11 +1562,11 @@ summary = "C parser in Python" [[package]] name = "pyerfa" -version = "2.0.0.2" +version = "2.0.0.3" requires_python = ">=3.7" summary = "Python bindings for ERFA" dependencies = [ - "numpy>=1.21", + "numpy>=1.17", ] [[package]] @@ -1571,8 +1581,8 @@ dependencies = [ [[package]] name = "pygments" -version = "2.14.0" -requires_python = ">=3.6" +version = "2.15.1" +requires_python = ">=3.7" summary = "Pygments is a syntax highlighting package written in Python." [[package]] @@ -1583,7 +1593,7 @@ summary = "pure Python (no prereqs) coordinate conversions, following convention [[package]] name = "pymdown-extensions" -version = "9.10" +version = "9.11" requires_python = ">=3.7" summary = "Extension pack for Python Markdown." dependencies = [ @@ -1605,7 +1615,7 @@ summary = "pyparsing module - Classes and methods to define and execute parsing [[package]] name = "pyproj" -version = "3.4.1" +version = "3.5.0" requires_python = ">=3.8" summary = "Python interface to PROJ (cartographic projections and coordinate transformations library)" dependencies = [ @@ -1630,11 +1640,10 @@ summary = "Persistent/Functional/Immutable data structures" [[package]] name = "pytest" -version = "7.2.2" +version = "7.3.1" requires_python = ">=3.7" summary = "pytest: simple powerful testing with Python" dependencies = [ - "attrs>=19.2.0", "colorama; sys_platform == \"win32\"", "exceptiongroup>=1.0.0rc8; python_version < \"3.11\"", "iniconfig", @@ -1671,6 +1680,16 @@ dependencies = [ "six", ] +[[package]] +name = "pytest-xdist" +version = "3.2.1" +requires_python = ">=3.7" +summary = "pytest xdist plugin for distributed testing, most importantly across multiple CPUs" +dependencies = [ + "execnet>=1.1", + "pytest>=6.2.0", +] + [[package]] name = "python-dateutil" version = "2.8.2" @@ -1688,7 +1707,7 @@ summary = "A python library adding a json log formatter" [[package]] name = "pytorch-lightning" -version = "2.0.0" +version = "2.0.2" requires_python = ">=3.8" summary = "PyTorch Lightning is the lightweight PyTorch wrapper for ML researchers. Scale your models. Write less boilerplate." dependencies = [ @@ -1705,19 +1724,19 @@ dependencies = [ [[package]] name = "pytz" -version = "2022.7.1" +version = "2023.3" summary = "World timezone definitions, modern and historical" [[package]] name = "pywin32" -version = "305" +version = "306" summary = "Python for Window Extensions" [[package]] name = "pywinpty" version = "2.0.10" requires_python = ">=3.7" -summary = "" +summary = "Pseudo terminal support for Windows from Python." [[package]] name = "pyyaml" @@ -1745,8 +1764,8 @@ dependencies = [ [[package]] name = "regex" -version = "2022.10.31" -requires_python = ">=3.6" +version = "2023.3.23" +requires_python = ">=3.8" summary = "Alternative regular expression module, to replace re." [[package]] @@ -1813,7 +1832,7 @@ summary = "R-Tree spatial index for Python GIS" [[package]] name = "ruff" -version = "0.0.259" +version = "0.0.263" requires_python = ">=3.7" summary = "An extremely fast Python linter, written in Rust." @@ -1876,7 +1895,7 @@ summary = "Send file to trash natively under Mac OS X, Windows and Linux." [[package]] name = "setuptools" -version = "67.6.0" +version = "67.7.2" requires_python = ">=3.7" summary = "Easily download, build, install, upgrade, and uninstall Python packages" @@ -1900,7 +1919,7 @@ summary = "Sniff out which async library your code is running under" [[package]] name = "soupsieve" -version = "2.4" +version = "2.4.1" requires_python = ">=3.7" summary = "A modern CSS selector implementation for Beautiful Soup." @@ -2036,26 +2055,26 @@ dependencies = [ [[package]] name = "tornado" -version = "6.2" -requires_python = ">= 3.7" +version = "6.3.1" +requires_python = ">= 3.8" summary = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed." [[package]] name = "tox" -version = "4.4.7" +version = "4.5.0" requires_python = ">=3.7" summary = "tox is a generic virtualenv management and test command line tool" dependencies = [ "cachetools>=5.3", "chardet>=5.1", "colorama>=0.4.6", - "filelock>=3.9", - "packaging>=23", - "platformdirs>=2.6.2", + "filelock>=3.11", + "packaging>=23.1", + "platformdirs>=3.2", "pluggy>=1", - "pyproject-api>=1.5", + "pyproject-api>=1.5.1", "tomli>=2.0.1; python_version < \"3.11\"", - "virtualenv>=20.17.1", + "virtualenv>=20.21", ] [[package]] @@ -2114,7 +2133,7 @@ dependencies = [ [[package]] name = "types-setuptools" -version = "67.6.0.5" +version = "67.7.0.0" summary = "Typing stubs for setuptools" [[package]] @@ -2152,13 +2171,13 @@ summary = "Flexible version handling" [[package]] name = "virtualenv" -version = "20.21.0" +version = "20.22.0" requires_python = ">=3.7" summary = "Virtual Python Environment builder" dependencies = [ "distlib<1,>=0.3.6", - "filelock<4,>=3.4.1", - "platformdirs<4,>=2.4", + "filelock<4,>=3.11", + "platformdirs<4,>=3.2", ] [[package]] @@ -2183,9 +2202,9 @@ summary = "Measures the displayed width of unicode strings in a terminal" [[package]] name = "webcolors" -version = "1.12" +version = "1.13" requires_python = ">=3.7" -summary = "A library for working with color names and color values formats defined by HTML and CSS." +summary = "A library for working with the color formats defined by HTML and CSS." [[package]] name = "webencodings" @@ -2206,7 +2225,7 @@ summary = "A built-package format for Python" [[package]] name = "widgetsnbextension" -version = "3.6.3" +version = "3.6.4" summary = "IPython HTML widgets for Jupyter" dependencies = [ "notebook>=4.4.1", @@ -2214,7 +2233,7 @@ dependencies = [ [[package]] name = "yarl" -version = "1.8.2" +version = "1.9.1" requires_python = ">=3.7" summary = "Yet another URL library" dependencies = [ @@ -2230,8 +2249,8 @@ summary = "Backport of pathlib-compatible object wrapper for zip files" [metadata] lock_version = "4.2" -groups = ["default", "all", "dev", "docs", "gtfs", "license", "lint", "osm", "performance", "plotting", "test", "visualization", "voronoi"] -content_hash = "sha256:0a1cc165f764516cab6a99b789b18c110e0f797523d1bd4d79794dcde4156fd8" +groups = ["default", "all", "dev", "docs", "gtfs", "license", "lint", "osm", "performance", "plotting", "test", "torch", "visualization", "voronoi"] +content_hash = 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a/pyproject.toml b/pyproject.toml index 36ec009b..caa90d1c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -5,7 +5,7 @@ description = "A set of python modules for geospatial machine learning and data authors = [{ name = "srai", email = "spatialrepresentationsforai@gmail.com" }] # pdm add dependencies = [ - "pandas>=1.3", + "pandas>=1.3, <2", "geopandas>=0.11.1", "shapely>=1.8.5.post1", "h3>=4.0.0b1", @@ -18,8 +18,6 @@ dependencies = [ "topojson>=1.5", "tqdm>=4.64.1", "s2>=0.1.9", - "pytorch-lightning>=1.0.0", - "torch", "typeguard>=3.0.2", ] requires-python = ">=3.8" @@ -47,6 +45,10 @@ Documentation = "https://srai-lab.github.io/srai" Changelog = "https://github.com/srai-lab/srai/blob/main/CHANGELOG.md" [project.optional-dependencies] +# Make sure to edit test_optional_dependencies.py: +# add entries to optional packages +# add tests + # pdm add -G osm osm = ["osmium>=3.4.1", "osmnx>=1.2.2", "overpass>=0.7"] # pdm add -G voronoi @@ -55,7 +57,10 @@ voronoi = ["pymap3d>=2.9.1", "haversine>=2.7.0", "spherical-geometry>=1.2.23"] gtfs = ["gtfs-kit>=5.0.0"] # pdm add -G plotting plotting = ["folium>=0.14.0", "mapclassify>=2.5.0", "plotly>=5.10.0", "kaleido==0.2.1"] -all = ["srai[osm,voronoi,gtfs,plotting]"] +# pdm add -G torch +torch = ["pytorch-lightning>=1.0.0", "torch"] +all = ["srai[osm,voronoi,gtfs,plotting,torch]"] + [build-system] requires = ["pdm-pep517>=1.0.0"] @@ -82,6 +87,7 @@ test = [ "requests-mock>=1.10.0", "pytest-check>=2.1.4", "pytest-parametrization>=2022.2.1", + "pytest-xdist>=3.2.1", ] # pdm add -dG visualization visualization = [ @@ -175,6 +181,7 @@ push = false [tool.pytest.ini_options] addopts = ["--import-mode=importlib"] markers = ["slow: marks tests as slow (deselect with '-m \"not slow\"')"] +log_cli = true [tool.licensecheck] using = "requirements" diff --git a/srai/embedders/gtfs2vec/embedder.py b/srai/embedders/gtfs2vec/embedder.py index 5f187c4d..a8da61a9 100644 --- a/srai/embedders/gtfs2vec/embedder.py +++ b/srai/embedders/gtfs2vec/embedder.py @@ -14,14 +14,12 @@ import geopandas as gpd import numpy as np import pandas as pd -import pytorch_lightning as pl -import torch -from torch.utils.data import DataLoader from srai.embedders import Embedder from srai.embedders.gtfs2vec.model import GTFS2VecModel from srai.exceptions import ModelNotFitException from srai.loaders.gtfs_loader import GTFS2VEC_DIRECTIONS_PREFIX, GTFS2VEC_TRIPS_PREFIX +from srai.utils._optional import import_optional_dependencies class GTFS2VecEmbedder(Embedder): @@ -39,6 +37,9 @@ def __init__( skip_autoencoder (bool, optional): Skip using autoencoder as part of embedding. Defaults to False. """ + import_optional_dependencies( + dependency_group="torch", modules=["torch", "pytorch_lightning"] + ) self._model: Optional[GTFS2VecModel] = None self._hidden_size = hidden_size self._embedding_size = embedding_size @@ -230,6 +231,9 @@ def _train_model_unsupervised(self, features: pd.DataFrame) -> GTFS2VecModel: Args: features (pd.DataFrame): Features. """ + import pytorch_lightning as pl + from torch.utils.data import DataLoader + model = GTFS2VecModel( n_features=len(features.columns), n_hidden=self._hidden_size, @@ -253,6 +257,8 @@ def _embed(self, features: pd.DataFrame) -> pd.DataFrame: Returns: pd.DataFrame: Embeddings. """ + import torch + model = self._maybe_get_model() if len(features.columns) != model.n_features: raise ValueError( diff --git a/srai/embedders/gtfs2vec/model.py b/srai/embedders/gtfs2vec/model.py index 4928037c..8658775b 100644 --- a/srai/embedders/gtfs2vec/model.py +++ b/srai/embedders/gtfs2vec/model.py @@ -6,12 +6,19 @@ References: 1. https://doi.org/10.1145/3486640.3491392 """ -from typing import Any +from typing import TYPE_CHECKING, Any -import torch -from pytorch_lightning import LightningModule -from torch import nn -from torch.nn import functional as F +from srai.utils._optional import import_optional_dependencies + +if TYPE_CHECKING: # pragma: no cover + import torch + + +try: # pragma: no cover + from pytorch_lightning import LightningModule + +except ImportError: + from srai.utils._pytorch_stubs import LightningModule class GTFS2VecModel(LightningModule): # type: ignore @@ -32,6 +39,11 @@ def __init__( n_embed (int, optional): Embedding size. Defaults to 64. """ super().__init__() + import_optional_dependencies( + dependency_group="torch", modules=["torch", "pytorch_lightning"] + ) + from torch import nn + self.n_features = n_features self.encoder = nn.Sequential( @@ -41,22 +53,24 @@ def __init__( nn.Linear(n_embed, n_hidden), nn.ReLU(), nn.Linear(n_hidden, n_features) ) - def forward(self, x: torch.Tensor) -> torch.Tensor: + def forward(self, x: "torch.Tensor") -> "torch.Tensor": """ Forward pass. Args: x (torch.Tensor): Input tensor. """ - embedding: torch.Tensor = self.encoder(x) + embedding: "torch.Tensor" = self.encoder(x) return embedding - def configure_optimizers(self) -> torch.optim.Optimizer: + def configure_optimizers(self) -> "torch.optim.Optimizer": """Configure optimizer.""" + import torch + optimizer = torch.optim.Adam(self.parameters(), lr=1e-3) return optimizer - def training_step(self, batch: torch.Tensor, batch_idx: Any) -> torch.Tensor: + def training_step(self, batch: "torch.Tensor", batch_idx: Any) -> "torch.Tensor": """ Training step. @@ -64,6 +78,8 @@ def training_step(self, batch: torch.Tensor, batch_idx: Any) -> torch.Tensor: batch (torch.Tensor): Batch. batch_idx (Any): Batch index. """ + from torch.nn import functional as F + x = batch z = self.encoder(x) x_hat = self.decoder(z) diff --git a/srai/embedders/highway2vec/embedder.py b/srai/embedders/highway2vec/embedder.py index cc81673b..6c52f46f 100644 --- a/srai/embedders/highway2vec/embedder.py +++ b/srai/embedders/highway2vec/embedder.py @@ -10,12 +10,10 @@ import geopandas as gpd import pandas as pd -import pytorch_lightning as pl -import torch -from torch.utils.data import DataLoader from srai.embedders import Embedder from srai.exceptions import ModelNotFitException +from srai.utils._optional import import_optional_dependencies from .model import Highway2VecModel @@ -31,6 +29,10 @@ def __init__(self, hidden_size: int = 64, embedding_size: int = 30) -> None: hidden_size (int, optional): Hidden size in encoder and decoder. Defaults to 64. embedding_size (int, optional): Embedding size. Defaults to 30. """ + import_optional_dependencies( + dependency_group="torch", modules=["torch", "pytorch_lightning"] + ) + self._model: Optional[Highway2VecModel] = None self._hidden_size = hidden_size self._embedding_size = embedding_size @@ -58,6 +60,8 @@ def transform( ValueError: If joint_gdf.index is not of type pd.MultiIndex or doesn't have 2 levels. ValueError: If index levels in gdfs don't overlap correctly. """ + import torch + self._validate_indexes(regions_gdf, features_gdf, joint_gdf) self._check_is_fitted() features_df = self._remove_geometry_if_present(features_gdf) @@ -94,6 +98,10 @@ def fit( ValueError: If joint_gdf.index is not of type pd.MultiIndex or doesn't have 2 levels. ValueError: If index levels in gdfs don't overlap correctly. """ + import pytorch_lightning as pl + import torch + from torch.utils.data import DataLoader + self._validate_indexes(regions_gdf, features_gdf, joint_gdf) features_df = self._remove_geometry_if_present(features_gdf) diff --git a/srai/embedders/highway2vec/model.py b/srai/embedders/highway2vec/model.py index 19e6e2a6..badd752d 100644 --- a/srai/embedders/highway2vec/model.py +++ b/srai/embedders/highway2vec/model.py @@ -6,13 +6,22 @@ References: 1. https://doi.org/10.1145/3557918.3565865 """ -import pytorch_lightning as pl -import torch -import torch.nn.functional as F -from torch import nn, optim +from typing import TYPE_CHECKING +from srai.utils._optional import import_optional_dependencies -class Highway2VecModel(pl.LightningModule): # type: ignore +if TYPE_CHECKING: # pragma: no cover + import torch + + +try: # pragma: no cover + from pytorch_lightning import LightningModule + +except ImportError: + from srai.utils._pytorch_stubs import LightningModule + + +class Highway2VecModel(LightningModule): # type: ignore """Autoencoder based embedding model for highway2vec.""" def __init__(self, n_features: int, n_hidden: int = 64, n_embed: int = 30, lr: float = 1e-3): @@ -25,6 +34,11 @@ def __init__(self, n_features: int, n_hidden: int = 64, n_embed: int = 30, lr: f n_embed (int, optional): Embedding size. Defaults to 30. lr (float, optional): Learning rate. Defaults to 1e-3. """ + import_optional_dependencies( + dependency_group="torch", modules=["torch", "pytorch_lightning"] + ) + from torch import nn + super().__init__() self.save_hyperparameters() @@ -41,17 +55,17 @@ def __init__(self, n_features: int, n_hidden: int = 64, n_embed: int = 30, lr: f ) self.lr = lr - def forward(self, x: torch.Tensor) -> torch.Tensor: + def forward(self, x: "torch.Tensor") -> "torch.Tensor": """ Forward pass. Args: x (torch.Tensor): Input tensor. """ - z: torch.Tensor = self.encoder(x) + z: "torch.Tensor" = self.encoder(x) return z - def training_step(self, batch: torch.Tensor, batch_idx: int) -> torch.Tensor: + def training_step(self, batch: "torch.Tensor", batch_idx: int) -> "torch.Tensor": """ Training step. @@ -61,7 +75,7 @@ def training_step(self, batch: torch.Tensor, batch_idx: int) -> torch.Tensor: """ return self._common_step(batch, batch_idx, "train") - def _common_step(self, batch: torch.Tensor, batch_idx: int, stage: str) -> torch.Tensor: + def _common_step(self, batch: "torch.Tensor", batch_idx: int, stage: str) -> "torch.Tensor": """ Perform common step. @@ -70,6 +84,8 @@ def _common_step(self, batch: torch.Tensor, batch_idx: int, stage: str) -> torch batch_idx (int): Batch index. stage (str): Name of the stage - e.g. train, valid, test. """ + import torch.nn.functional as F + x = batch z = self.encoder(x) x_hat = self.decoder(z) @@ -79,7 +95,9 @@ def _common_step(self, batch: torch.Tensor, batch_idx: int, stage: str) -> torch return loss - def configure_optimizers(self) -> torch.optim.Optimizer: + def configure_optimizers(self) -> "torch.optim.Optimizer": """Configure optimizer.""" - optimizer = optim.Adam(self.parameters(), lr=self.lr) + import torch + + optimizer = torch.optim.Adam(self.parameters(), lr=self.lr) return optimizer diff --git a/srai/loaders/osm_loaders/pbf_file_downloader.py b/srai/loaders/osm_loaders/pbf_file_downloader.py index 787c19ae..ae18aa74 100644 --- a/srai/loaders/osm_loaders/pbf_file_downloader.py +++ b/srai/loaders/osm_loaders/pbf_file_downloader.py @@ -218,8 +218,8 @@ def _prepare_polygon_for_download(self, polygon: Polygon) -> Polygon: Function buffers the polygon, closes internal holes and simplifies its boundary to 1000 points. - Makes sure that the generated polygon will fully cover the original one by increasing - the buffer size incrementally. + Makes sure that the generated polygon will fully cover the original one by increasing the + buffer size incrementally. """ is_fully_covered = False buffer_size_meters = 50 diff --git a/srai/neighbourhoods/_base.py b/srai/neighbourhoods/_base.py index b7cfa6ae..df4dfcc5 100644 --- a/srai/neighbourhoods/_base.py +++ b/srai/neighbourhoods/_base.py @@ -13,16 +13,14 @@ class Neighbourhood(ABC, Generic[IndexType]): """ Neighbourhood interface. - This class abstracts away getting the neighbours of a region. - It allows to get the neighbours at a certain distance or up to a certain distance. - It is worth noting, that the distance here is not a metric distance, but a number of hops. - This definition makes most sense semantically for grid systems such as H3 or S2 but should work - for arbitrary neighbourhoods as well. + This class abstracts away getting the neighbours of a region. It allows to get the neighbours at + a certain distance or up to a certain distance. It is worth noting, that the distance here is + not a metric distance, but a number of hops. This definition makes most sense semantically for + grid systems such as H3 or S2 but should work for arbitrary neighbourhoods as well. The subclasses only need to implement the `get_neighbours` method, but can also override the `get_neighbours_up_to_distance` and `get_neighbours_at_distance` methods for performance - reasons. - See the `H3Neighbourhood` class for an example. + reasons. See the `H3Neighbourhood` class for an example. """ @abstractmethod diff --git a/srai/utils/_pytorch_stubs.py b/srai/utils/_pytorch_stubs.py new file mode 100644 index 00000000..46ec64e3 --- /dev/null +++ b/srai/utils/_pytorch_stubs.py @@ -0,0 +1,4 @@ +class LightningModule: # pragma: no cover + """LightningModule class stub.""" + + ... diff --git a/tests/miscellaneous/test_optional_dependencies.py b/tests/miscellaneous/test_optional_dependencies.py index 188bc4e2..743dcf50 100644 --- a/tests/miscellaneous/test_optional_dependencies.py +++ b/tests/miscellaneous/test_optional_dependencies.py @@ -11,6 +11,26 @@ from srai.utils._optional import ImportErrorHandle, import_optional_dependency +@pytest.fixture # type: ignore +def optional_packages() -> List[str]: + """Get a list with optional packages.""" + return [ + "osmium", + "osmnx", + "overpass", + "pymap3d", + "haversine", + "spherical_geometry", + "gtfs_kit", + "folium", + "mapclassify", + "plotly", + "kaleido", + "pytorch-lightning", + "torch", + ] + + @pytest.fixture(autouse=True) # type: ignore def cleanup_imports(): """Clean imports.""" @@ -32,23 +52,10 @@ def find_spec(self, fullname, path, target=None) -> None: # type: ignore @pytest.fixture # type: ignore -def no_optional_dependencies(monkeypatch): +def no_optional_dependencies(monkeypatch, optional_packages): """Mock environment without optional dependencies.""" d = PackageDiscarder() - optional_packages = [ - "osmium", - "osmnx", - "overpass", - "pymap3d", - "haversine", - "spherical_geometry", - "gtfs_kit", - "folium", - "mapclassify", - "plotly", - "kaleido", - ] for package in optional_packages: sys.modules.pop(package, None) d.pkgnames.append(package) @@ -57,9 +64,9 @@ def no_optional_dependencies(monkeypatch): sys.meta_path.remove(d) -def _test_voronoi_regionizer() -> None: +def _test_voronoi() -> None: import geopandas as gpd - from shapely.geometry import Point, box + from shapely.geometry import Point from srai.regionizers import VoronoiRegionizer @@ -75,42 +82,35 @@ def _test_voronoi_regionizer() -> None: index=[1, 2, 3, 4], crs=WGS84_CRS, ) - vr = VoronoiRegionizer(seeds=seeds_gdf) - vr.transform( - gdf=gpd.GeoDataFrame( - {GEOMETRY_COLUMN: [box(minx=-180, maxx=180, miny=-90, maxy=90)]}, crs=WGS84_CRS - ) - ) + VoronoiRegionizer(seeds=seeds_gdf) -def _test_administrative_boundary_regionizer() -> None: - from srai.regionizers.administrative_boundary_regionizer import ( - AdministrativeBoundaryRegionizer, - ) +def _test_plotting() -> None: + from srai.plotting import folium_wrapper, plotly_wrapper - asia_bbox = box( - minx=69.73278412113555, - miny=24.988848422533074, - maxx=88.50230949587835, - maxy=34.846427760404225, - ) - asia_bbox_gdf = gpd.GeoDataFrame({GEOMETRY_COLUMN: [asia_bbox]}, crs=WGS84_CRS) - abr = AdministrativeBoundaryRegionizer( - admin_level=2, return_empty_region=True, toposimplify=0.001 - ) - abr.transform(gdf=asia_bbox_gdf) + folium_wrapper.plot_regions(_get_regions_gdf()) + plotly_wrapper.plot_regions(_get_regions_gdf(), return_plot=True) -def _test_plotting_folium_module() -> None: - from srai.plotting import folium_wrapper +def _test_torch() -> None: + from srai.embedders import GTFS2VecEmbedder, Highway2VecEmbedder - folium_wrapper.plot_regions(_get_regions_gdf()) + Highway2VecEmbedder() + GTFS2VecEmbedder() + + +def _test_osm() -> None: + from srai.loaders.osm_loaders import OSMPbfLoader + from srai.regionizers import AdministrativeBoundaryRegionizer + + AdministrativeBoundaryRegionizer(2) + OSMPbfLoader() -def _test_plotting_plotly_module() -> None: - from srai.plotting import plotly_wrapper +def _test_gtfs() -> None: + from srai.loaders import GTFSLoader - plotly_wrapper.plot_regions(_get_regions_gdf()) + GTFSLoader() def _get_regions_gdf() -> gpd.GeoDataFrame: @@ -133,10 +133,11 @@ def _get_regions_gdf() -> gpd.GeoDataFrame: @pytest.mark.parametrize( # type: ignore "test_fn", [ - (_test_voronoi_regionizer), - (_test_administrative_boundary_regionizer), - (_test_plotting_folium_module), - (_test_plotting_plotly_module), + (_test_voronoi), + (_test_plotting), + (_test_torch), + (_test_osm), + (_test_gtfs), ], ) def test_optional_available(test_fn): @@ -148,10 +149,11 @@ def test_optional_available(test_fn): @pytest.mark.parametrize( # type: ignore "test_fn", [ - (_test_voronoi_regionizer), - (_test_administrative_boundary_regionizer), - (_test_plotting_folium_module), - (_test_plotting_plotly_module), + (_test_voronoi), + (_test_plotting), + (_test_torch), + (_test_osm), + (_test_gtfs), ], ) def test_optional_missing(test_fn):