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Define two asv configurations for pip and latest-github dependencies (#…
…110) * prototype dependency install from github * Run asv check in CI with the two new configs * Check asv benchmarks without existing flag * Fix existing flag * Setup conda * Activate environment * Add python version to conda setup * Fix path to latest-github requirements in asv config * Fix typo * Use action with old version of conda * Clean up conda approach * Second benchmark job should fail * Time Python approach * Fix and time python approach * Revert "Second benchmark job should fail" This reverts commit 3f067d5. * add all brainglobe dev requirements * Update README * Add pip list to install command in both asv config files * Small edits to README * Feedback from Igor --------- Co-authored-by: sfmig <[email protected]>
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@@ -79,27 +79,46 @@ jobs: | |
| benchmarks: | ||
| name: Check benchmarks | ||
| runs-on: ubuntu-latest | ||
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| # Set shell in login mode as global setting for the job | ||
| defaults: | ||
| run: | ||
| shell: bash -l {0} | ||
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| strategy: | ||
| matrix: | ||
| python-version: ["3.10"] | ||
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| steps: | ||
| - uses: actions/checkout@v4 | ||
| - uses: actions/setup-python@v5 | ||
| - name: Checkout brainglobe-workflows repository | ||
| uses: actions/checkout@v4 | ||
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| - name: Create and activate conda environment # we need conda for asv management of environments | ||
| uses: conda-incubator/[email protected] # see https://github.com/conda-incubator/setup-miniconda/issues/261 | ||
| with: | ||
| python-version: "3.10" | ||
| miniconda-version: py310_24.1.2-0 # we need conda<24.3, see https://github.com/airspeed-velocity/asv/pull/1397 | ||
| python-version: ${{ matrix.python-version }} | ||
| activate-environment: asv-only | ||
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| - name: Install asv | ||
| shell: bash | ||
| run: | | ||
| python -mpip install --upgrade pip | ||
| pip install --upgrade pip | ||
| pip install asv | ||
| - name: Run asv check with pip dependencies | ||
| working-directory: ${{ github.workspace }}/benchmarks | ||
| run: | | ||
| # check benchmarks with pip dependencies | ||
| asv check -v --config $GITHUB_WORKSPACE/benchmarks/asv.pip.conf.json | ||
| # We install the project to benchmark because we run `asv check` with the `existing` flag. | ||
| python -mpip install . | ||
| python -mpip install asv | ||
| - name: Run asv check | ||
| shell: bash | ||
| - name: Run asv check with latest-github dependencies | ||
| working-directory: ${{ github.workspace }}/benchmarks | ||
| run: | | ||
| cd benchmarks | ||
| # With `existing`, the benchmarked project must be already installed, including all dependencies. | ||
| # see https://asv.readthedocs.io/en/v0.6.3/commands.html#asv-check | ||
| asv check -v -E existing | ||
| # check benchmarks with latest-github dependencies | ||
| asv check -v --config $GITHUB_WORKSPACE/benchmarks/asv.latest-github.conf.json | ||
| build_sdist_wheels: | ||
| name: Build source distribution | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,185 @@ | ||
| { | ||
| // 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": "brainglobe-workflows", | ||
| // The project's homepage | ||
| "project_url": "https://github.com/brainglobe/brainglobe-workflows", | ||
| // The URL or local path of the source code repository for the | ||
| // project being benchmarked | ||
| "repo": "..", | ||
| // "repo": "https://github.com/brainglobe/brainglobe-workflows.git", | ||
| // 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", | ||
| "PIP_NO_BUILD_ISOLATION=false python -mpip wheel --no-deps --no-index -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", | ||
| // "PIP_NO_BUILD_ISOLATION=false python -mpip wheel --no-deps --no-index -w {build_cache_dir} {build_dir}" | ||
| // ], | ||
| // Customizable commands for installing and uninstalling the project. | ||
| // See asv.conf.json documentation. | ||
| // overwrite dependencies from PyPi with latest `main` version from GitHub | ||
| "install_command": [ | ||
| "in-dir={env_dir} python -mpip install --force-reinstall '{wheel_file}'", | ||
| "in-dir={env_dir} python -mpip install -r {conf_dir}/latest-github-requirements.txt", | ||
| "in-dir={env_dir} python -mpip list" // print dependencies' versions if asv ran with -v | ||
| ], | ||
| "uninstall_command": [ | ||
| "return-code=any python -mpip uninstall -y {project}" | ||
| ], | ||
| // List of branches to benchmark. If not provided, defaults to "master" | ||
| // (for git) or "default" (for mercurial). | ||
| "branches": [ | ||
| "HEAD" | ||
| ], // 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": "conda", | ||
| // 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": "https://github.com/brainglobe/brainglobe-workflows/commit/", | ||
| // The Pythons you'd like to test against. If not provided, defaults | ||
| // to the current version of Python used to run `asv`. | ||
| "pythons": [ | ||
| "3.10" | ||
| ], | ||
| // 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 python2.7 | ||
| // {"python": "2.7", "req": {"numpy": "1.8"}, "env_nobuild": {"FOO": "123"}}, | ||
| // // additional env if run on windows+conda | ||
| // {"platform": "win32", "environment_type": "conda", "python": "2.7", "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": "results", | ||
| // The directory (relative to the current directory) that the html tree | ||
| // should be written to. If not provided, defaults to "html". | ||
| "html_dir": "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% | ||
| // }, | ||
| } |
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