Add asv benchmark code (#784)

* init for asv

* ignore asv folder

* add basic benchmarks

* improve cluster_blobs creation time

* update readme

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* lint code

* pass pre-commit by ignore benchmark files.

* add n_transcripts_per_cell to benchmark

* lower benchmark size

* add more benchmark documentation

* add more benchmark documentation

* updates from feedback

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* minor edits docstrings

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: LucaMarconato <2664412+LucaMarconato@users.noreply.github.com>

.gitignore

@@ -47,3 +47,5 @@ _version.py
 
 # other
 node_modules/
+
+.asv/

asv.conf.json

@@ -0,0 +1,203 @@
+{
+    // The version of the config file format.  Do not change, unless
+    // you know what you are doing.
+    "version": 1,
+
+    // The name of the project being benchmarked
+    "project": "spatialdata",
+
+    // The project's homepage
+    "project_url": "https://spatialdata.scverse.org/",
+
+    // The URL or local path of the source code repository for the
+    // project being benchmarked
+    "repo": ".",
+
+    // The Python project's subdirectory in your repo.  If missing or
+    // the empty string, the project is assumed to be located at the root
+    // of the repository.
+    // "repo_subdir": "",
+
+    // Customizable commands for building the project.
+    // See asv.conf.json documentation.
+    // To build the package using pyproject.toml (PEP518), uncomment the following lines
+    // "build_command": [
+    //     "python -m pip install build",
+    //     "python -m build",
+    //     "python -mpip wheel -w {build_cache_dir} {build_dir}"
+    // ],
+    // To build the package using setuptools and a setup.py file, uncomment the following lines
+    // "build_command": [
+    //     "python setup.py build",
+    //     "python -mpip wheel -w {build_cache_dir} {build_dir}"
+    // ],
+    "build_command": ["python -V"], // skip build stage
+
+    // Customizable commands for installing and uninstalling the project.
+    // See asv.conf.json documentation.
+    // "install_command": ["in-dir={env_dir} python -mpip install {wheel_file}"],
+    // "uninstall_command": ["return-code=any python -mpip uninstall -y {project}"],
+
+    // Install using default install
+    "install_command": [
+        "in-dir={env_dir} python -m pip install {build_dir}[test]"
+    ],
+    "uninstall_command": [
+        "in-dir={env_dir} python -m pip uninstall -y {project}"
+    ],
+
+    // List of branches to benchmark. If not provided, defaults to "main"
+    // (for git) or "default" (for mercurial).
+    "branches": ["main"], // for git
+    // "branches": ["default"],    // for mercurial
+
+    // The DVCS being used.  If not set, it will be automatically
+    // determined from "repo" by looking at the protocol in the URL
+    // (if remote), or by looking for special directories, such as
+    // ".git" (if local).
+    // "dvcs": "git",
+
+    // The tool to use to create environments.  May be "conda",
+    // "virtualenv", "mamba" (above 3.8)
+    // or other value depending on the plugins in use.
+    // If missing or the empty string, the tool will be automatically
+    // determined by looking for tools on the PATH environment
+    // variable.
+    "environment_type": "virtualenv",
+
+    // timeout in seconds for installing any dependencies in environment
+    // defaults to 10 min
+    // "install_timeout": 600,
+
+    // the base URL to show a commit for the project.
+    // "show_commit_url": "http://github.com/owner/project/commit/",
+
+    // The Pythons you'd like to test against.  If not provided, defaults
+    // to the current version of Python used to run `asv`.
+    "pythons": ["3.12"],
+
+    // The list of conda channel names to be searched for benchmark
+    // dependency packages in the specified order
+    // "conda_channels": ["conda-forge", "defaults"],
+
+    // A conda environment file that is used for environment creation.
+    // "conda_environment_file": "environment.yml",
+
+    // The matrix of dependencies to test.  Each key of the "req"
+    // requirements dictionary is the name of a package (in PyPI) and
+    // the values are version numbers.  An empty list or empty string
+    // indicates to just test against the default (latest)
+    // version. null indicates that the package is to not be
+    // installed. If the package to be tested is only available from
+    // PyPi, and the 'environment_type' is conda, then you can preface
+    // the package name by 'pip+', and the package will be installed
+    // via pip (with all the conda available packages installed first,
+    // followed by the pip installed packages).
+    //
+    // The ``@env`` and ``@env_nobuild`` keys contain the matrix of
+    // environment variables to pass to build and benchmark commands.
+    // An environment will be created for every combination of the
+    // cartesian product of the "@env" variables in this matrix.
+    // Variables in "@env_nobuild" will be passed to every environment
+    // during the benchmark phase, but will not trigger creation of
+    // new environments.  A value of ``null`` means that the variable
+    // will not be set for the current combination.
+    //
+    // "matrix": {
+    //     "req": {
+    //         "numpy": ["1.6", "1.7"],
+    //         "six": ["", null],  // test with and without six installed
+    //         "pip+emcee": [""]   // emcee is only available for install with pip.
+    //     },
+    //     "env": {"ENV_VAR_1": ["val1", "val2"]},
+    //     "env_nobuild": {"ENV_VAR_2": ["val3", null]},
+    // },
+
+    // Combinations of libraries/python versions can be excluded/included
+    // from the set to test. Each entry is a dictionary containing additional
+    // key-value pairs to include/exclude.
+    //
+    // An exclude entry excludes entries where all values match. The
+    // values are regexps that should match the whole string.
+    //
+    // An include entry adds an environment. Only the packages listed
+    // are installed. The 'python' key is required. The exclude rules
+    // do not apply to includes.
+    //
+    // In addition to package names, the following keys are available:
+    //
+    // - python
+    //     Python version, as in the *pythons* variable above.
+    // - environment_type
+    //     Environment type, as above.
+    // - sys_platform
+    //     Platform, as in sys.platform. Possible values for the common
+    //     cases: 'linux2', 'win32', 'cygwin', 'darwin'.
+    // - req
+    //     Required packages
+    // - env
+    //     Environment variables
+    // - env_nobuild
+    //     Non-build environment variables
+    //
+    // "exclude": [
+    //     {"python": "3.2", "sys_platform": "win32"}, // skip py3.2 on windows
+    //     {"environment_type": "conda", "req": {"six": null}}, // don't run without six on conda
+    //     {"env": {"ENV_VAR_1": "val2"}}, // skip val2 for ENV_VAR_1
+    // ],
+    //
+    // "include": [
+    //     // additional env for python3.12
+    //     {"python": "3.12", "req": {"numpy": "1.26"}, "env_nobuild": {"FOO": "123"}},
+    //     // additional env if run on windows+conda
+    //     {"platform": "win32", "environment_type": "conda", "python": "3.12", "req": {"libpython": ""}},
+    // ],
+
+    // The directory (relative to the current directory) that benchmarks are
+    // stored in.  If not provided, defaults to "benchmarks"
+    // "benchmark_dir": "benchmarks",
+
+    // The directory (relative to the current directory) to cache the Python
+    // environments in.  If not provided, defaults to "env"
+    "env_dir": ".asv/env",
+
+    // The directory (relative to the current directory) that raw benchmark
+    // results are stored in.  If not provided, defaults to "results".
+    "results_dir": ".asv/results",
+
+    // The directory (relative to the current directory) that the html tree
+    // should be written to.  If not provided, defaults to "html".
+    "html_dir": ".asv/html",
+
+    // The number of characters to retain in the commit hashes.
+    "hash_length": 8,
+
+    // `asv` will cache results of the recent builds in each
+    // environment, making them faster to install next time.  This is
+    // the number of builds to keep, per environment.
+    "build_cache_size": 2
+
+    // The commits after which the regression search in `asv publish`
+    // should start looking for regressions. Dictionary whose keys are
+    // regexps matching to benchmark names, and values corresponding to
+    // the commit (exclusive) after which to start looking for
+    // regressions.  The default is to start from the first commit
+    // with results. If the commit is `null`, regression detection is
+    // skipped for the matching benchmark.
+    //
+    // "regressions_first_commits": {
+    //    "some_benchmark": "352cdf",  // Consider regressions only after this commit
+    //    "another_benchmark": null,   // Skip regression detection altogether
+    // },
+
+    // The thresholds for relative change in results, after which `asv
+    // publish` starts reporting regressions. Dictionary of the same
+    // form as in ``regressions_first_commits``, with values
+    // indicating the thresholds.  If multiple entries match, the
+    // maximum is taken. If no entry matches, the default is 5%.
+    //
+    // "regressions_thresholds": {
+    //    "some_benchmark": 0.01,     // Threshold of 1%
+    //    "another_benchmark": 0.5,   // Threshold of 50%
+    // },
+}

benchmarks/README.md

@@ -0,0 +1,75 @@
+# Benchmarking SpatialData code
+
+This `benchmarks/` folder contains code to benchmark the performance of the SpatialData code. You can use it to see how code behaves for different options or data sizes. For more information, check the [SpatialData Contributing Guide](https://spatialdata.scverse.org/en/stable/contributing.html).
+
+Note that to run code, your current working directory should be the SpatialData repo, not this `benchmarks/` folder.
+
+## Installation
+
+The benchmarks use the [airspeed velocity](https://asv.readthedocs.io/en/stable/) (asv) framework. Install it with the `benchmark` option:
+
+```
+pip install -e '.[docs,test,benchmark]'
+```
+
+## Usage
+
+Running all the benchmarks is usually not needed. You run the benchmark using `asv run`. See the [asv documentation](https://asv.readthedocs.io/en/stable/commands.html#asv-run) for interesting arguments, like selecting the benchmarks you're interested in by providing a regex pattern `-b` or `--bench` that links to a function or class method e.g. the option `-b timeraw_import_inspect` selects the function `timeraw_import_inspect` in `benchmarks/spatialdata_benchmark.py`. You can run the benchmark in your current environment with `--python=same`. Some example benchmarks:
+
+Importing the SpatialData library can take around 4 seconds:
+
+```
+PYTHONWARNINGS="ignore" asv run --python=same --show-stderr -b timeraw_import_inspect
+Couldn't load asv.plugins._mamba_helpers because
+No module named 'conda'
+· Discovering benchmarks
+· Running 1 total benchmarks (1 commits * 1 environments * 1 benchmarks)
+[ 0.00%] ·· Benchmarking existing-py_opt_homebrew_Caskroom_mambaforge_base_envs_spatialdata2_bin_python3.12
+[50.00%] ··· Running (spatialdata_benchmark.timeraw_import_inspect--).
+[100.00%] ··· spatialdata_benchmark.timeraw_import_inspect                                                                            3.65±0.2s
+```
+
+Querying using a bounding box without a spatial index is highly impacted by large amounts of points (transcripts), more than table rows (cells).
+
+```
+$ PYTHONWARNINGS="ignore" asv run --python=same --show-stderr -b time_query_bounding_box
+
+[100.00%] ··· ======== ============ ============= ============= ==============
+              --                filter_table / n_transcripts_per_cell
+              -------- -------------------------------------------------------
+               length   True / 100   True / 1000   False / 100   False / 1000
+              ======== ============ ============= ============= ==============
+                100      177±5ms       195±4ms      168±0.5ms      186±2ms
+                1000     195±3ms       402±2ms       187±3ms       374±4ms
+               10000     722±3ms      2.65±0.01s     389±3ms      2.22±0.02s
+              ======== ============ ============= ============= ==============
+```
+
+You can use `asv` to run all the benchmarks in their own environment. This can take a long time, so it is not recommended for regular use:
+
+```
+$ asv run
+Couldn't load asv.plugins._mamba_helpers because
+No module named 'conda'
+· Creating environments....
+· Discovering benchmarks..
+·· Uninstalling from virtualenv-py3.12
+·· Building a89d16d8 <v0.2.6-pre0~7> for virtualenv-py3.12
+·· Installing a89d16d8 <v0.2.6-pre0~7> into virtualenv-py3.12.............
+· Running 6 total benchmarks (1 commits * 1 environments * 6 benchmarks)
+[ 0.00%] · For spatialdata commit a89d16d8 <v0.2.6-pre0~7>:
+[ 0.00%] ·· Benchmarking virtualenv-py3.12
+[25.00%] ··· Running (spatialdata_benchmark.TimeMapRaster.time_map_blocks--)...
+...
+[100.00%] ··· spatialdata_benchmark.timeraw_import_inspect                                                                                                                                    3.33±0.06s
+```
+
+## Notes
+
+When using PyCharm, remember to set [Configuration](https://www.jetbrains.com/help/pycharm/run-debug-configuration.html) to include the benchmark module, as this is separate from the main code module.
+
+In Python, you can run a module using the following command:
+
+```
+python -m benchmarks.spatialdata_benchmark
+```

benchmarks/spatialdata_benchmark.py

@@ -0,0 +1,75 @@
+# type: ignore
+
+# Write the benchmarking functions here.
+# See "Writing benchmarks" in the asv docs for more information.
+import spatialdata as sd
+
+from .utils import cluster_blobs
+
+
+class MemorySpatialData:
+    # TODO: see what the memory overhead is e.g. Python interpreter...
+    """Calculate the peak memory usage is for artificial datasets with increasing channels."""
+
+    def peakmem_list(self):
+        sdata: sd.SpatialData = sd.datasets.blobs(n_channels=1)
+        return sdata
+
+    def peakmem_list2(self):
+        sdata: sd.SpatialData = sd.datasets.blobs(n_channels=2)
+        return sdata
+
+
+def timeraw_import_inspect():
+    """Time the import of the spatialdata module."""
+    return """
+    import spatialdata
+    """
+
+
+class TimeMapRaster:
+    """Time the."""
+
+    params = [100, 1000, 10_000]
+    param_names = ["length"]
+
+    def setup(self, length):
+        self.sdata = cluster_blobs(length=length)
+
+    def teardown(self, _):
+        del self.sdata
+
+    def time_map_blocks(self, _):
+        sd.map_raster(self.sdata["blobs_image"], lambda x: x + 1)
+
+
+class TimeQueries:
+
+    params = ([100, 1_000, 10_000], [True, False], [100, 1_000])
+    param_names = ["length", "filter_table", "n_transcripts_per_cell"]
+
+    def setup(self, length, filter_table, n_transcripts_per_cell):
+        import shapely
+
+        self.sdata = cluster_blobs(length=length, n_transcripts_per_cell=n_transcripts_per_cell)
+        self.polygon = shapely.box(0, 0, length // 2, length // 2)
+
+    def teardown(self, length, filter_table, n_transcripts_per_cell):
+        del self.sdata
+
+    def time_query_bounding_box(self, length, filter_table, n_transcripts_per_cell):
+        self.sdata.query.bounding_box(
+            axes=["x", "y"],
+            min_coordinate=[0, 0],
+            max_coordinate=[length // 2, length // 2],
+            target_coordinate_system="global",
+            filter_table=filter_table,
+        )
+
+    def time_query_polygon_box(self, length, filter_table, n_transcripts_per_cell):
+        sd.polygon_query(
+            self.sdata,
+            self.polygon,
+            target_coordinate_system="global",
+            filter_table=filter_table,
+        )