diff --git a/.github/actions/setup-poetry-environment/action.yml b/.github/actions/setup-poetry-environment/action.yml new file mode 100644 index 0000000..689eabb --- /dev/null +++ b/.github/actions/setup-poetry-environment/action.yml @@ -0,0 +1,39 @@ +name: "Setup test environment" +description: "Sets up Python, Poetry and dependencies" + +inputs: + python: + description: "Python version to use" + default: "3.11" + required: false + poetry: + description: "Poetry version to use" + default: 1.7.1 + required: false + +runs: + using: "composite" + + steps: + - uses: actions/setup-python@v5 + with: + python-version: ${{ inputs.python }} + + - uses: snok/install-poetry@v1 + with: + version: ${{ inputs.poetry }} + virtualenvs-create: true + virtualenvs-in-project: true + + - name: Load cached venv + id: cached-poetry-dependencies + uses: actions/cache@v4 + with: + path: .venv + key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }} + + - if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true' + run: | + poetry lock --no-update + poetry install --no-interaction + shell: bash diff --git a/.github/workflows/pr-report.yml b/.github/workflows/pr-report.yml new file mode 100644 index 0000000..6a37969 --- /dev/null +++ b/.github/workflows/pr-report.yml @@ -0,0 +1,23 @@ +name: PR Report + +on: + pull_request: + branches: + - main + workflow_dispatch: + +env: + PYTHON_VERSION: 3.11 + +jobs: + pre-commit: + name: Linting and type checking + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - name: Setup poetry environment + uses: ./.github/actions/setup-poetry-environment + - name: Run linting, type checking and testing + uses: pre-commit/action@v3.0.0 + with: + extra_args: "--all-files --hook-stage=push" diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..a36970d --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,34 @@ +default_language_version: + python: python3.11 + +repos: + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: f71fa2c1f9cf5cb705f73dffe4b21f7c61470ba9 # 4.4.0 + hooks: + - id: check-yaml + - id: check-json + - id: check-toml + - id: end-of-file-fixer + - id: trailing-whitespace + - repo: https://github.com/pappasam/toml-sort + rev: b9b6210da457c38122995e434b314f4c4a4a923e # 0.23.1 + hooks: + - id: toml-sort-fix + files: ^.+.toml$ + - repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.2.1 + hooks: + - id: ruff + args: + - --fix + - --exit-non-zero-on-fix +# - --ignore=E501 # line-too-long +# - --ignore=F631 # assert-tuple +# - --ignore=E741 # ambiguous-variable-name + - id: ruff-format + files: ^src\/.+\.py$ +# - repo: https://github.com/pre-commit/mirrors-mypy +# rev: v1.8.0 +# hooks: +# - id: mypy +default_stages: [push] diff --git a/dev-setup.sh b/dev-setup.sh new file mode 100755 index 0000000..2f65ff8 --- /dev/null +++ b/dev-setup.sh @@ -0,0 +1,5 @@ +#!/bin/zsh +poetry env use 3.11 # Create the virtual environment if it does not exist +source $(poetry env info --path)/bin/activate # Activate and enter the virtual environment +poetry install --with=dev # Install dev dependencies +pre-commit install --install-hooks --overwrite -t pre-push # Set up pre-commit hooks diff --git a/poetry.lock b/poetry.lock index 97813d2..98ab9f8 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.5.0 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. [[package]] name = "aiohttp" @@ -289,6 +289,17 @@ files = [ [package.dependencies] pycparser = "*" +[[package]] +name = "cfgv" +version = "3.4.0" +description = "Validate configuration and produce human readable error messages." +optional = false +python-versions = ">=3.8" +files = [ + {file = "cfgv-3.4.0-py2.py3-none-any.whl", hash = "sha256:b7265b1f29fd3316bfcd2b330d63d024f2bfd8bcb8b0272f8e19a504856c48f9"}, + {file = "cfgv-3.4.0.tar.gz", hash = "sha256:e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560"}, +] + [[package]] name = "charset-normalizer" version = "3.3.2" @@ -590,6 +601,17 @@ files = [ graph = ["objgraph (>=1.7.2)"] profile = ["gprof2dot (>=2022.7.29)"] +[[package]] +name = "distlib" +version = "0.3.8" +description = "Distribution utilities" +optional = false +python-versions = "*" +files = [ + {file = "distlib-0.3.8-py2.py3-none-any.whl", hash = "sha256:034db59a0b96f8ca18035f36290806a9a6e6bd9d1ff91e45a7f172eb17e51784"}, + {file = "distlib-0.3.8.tar.gz", hash = "sha256:1530ea13e350031b6312d8580ddb6b27a104275a31106523b8f123787f494f64"}, +] + [[package]] name = "embedding-reader" version = "1.7.0" @@ -912,6 +934,20 @@ testing = ["InquirerPy (==0.3.4)", "Jinja2", "Pillow", "aiohttp", "gradio", "jed torch = ["torch"] typing = ["types-PyYAML", "types-requests", "types-simplejson", "types-toml", "types-tqdm", "types-urllib3", "typing-extensions (>=4.8.0)"] +[[package]] +name = "identify" +version = "2.5.34" +description = "File identification library for Python" +optional = false +python-versions = ">=3.8" +files = [ + {file = "identify-2.5.34-py2.py3-none-any.whl", hash = "sha256:a4316013779e433d08b96e5eabb7f641e6c7942e4ab5d4c509ebd2e7a8994aed"}, + {file = "identify-2.5.34.tar.gz", hash = "sha256:ee17bc9d499899bc9eaec1ac7bf2dc9eedd480db9d88b96d123d3b64a9d34f5d"}, +] + +[package.extras] +license = ["ukkonen"] + [[package]] name = "idna" version = "3.6" @@ -1426,6 +1462,20 @@ doc = ["nb2plots (>=0.7)", "nbconvert (<7.9)", "numpydoc (>=1.6)", "pillow (>=9. extra = ["lxml (>=4.6)", "pydot (>=1.4.2)", "pygraphviz (>=1.11)", "sympy (>=1.10)"] test = ["pytest (>=7.2)", "pytest-cov (>=4.0)"] +[[package]] +name = "nodeenv" +version = "1.8.0" +description = "Node.js virtual environment builder" +optional = false +python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*" +files = [ + {file = "nodeenv-1.8.0-py2.py3-none-any.whl", hash = "sha256:df865724bb3c3adc86b3876fa209771517b0cfe596beff01a92700e0e8be4cec"}, + {file = "nodeenv-1.8.0.tar.gz", hash = "sha256:d51e0c37e64fbf47d017feac3145cdbb58836d7eee8c6f6d3b6880c5456227d2"}, +] + +[package.dependencies] +setuptools = "*" + [[package]] name = "numba" version = "0.59.0" @@ -1813,6 +1863,39 @@ tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "pa typing = ["typing-extensions"] xmp = ["defusedxml"] +[[package]] +name = "platformdirs" +version = "4.2.0" +description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." +optional = false +python-versions = ">=3.8" +files = [ + {file = "platformdirs-4.2.0-py3-none-any.whl", hash = "sha256:0614df2a2f37e1a662acbd8e2b25b92ccf8632929bc6d43467e17fe89c75e068"}, + {file = "platformdirs-4.2.0.tar.gz", hash = "sha256:ef0cc731df711022c174543cb70a9b5bd22e5a9337c8624ef2c2ceb8ddad8768"}, +] + +[package.extras] +docs = ["furo (>=2023.9.10)", "proselint (>=0.13)", "sphinx (>=7.2.6)", "sphinx-autodoc-typehints (>=1.25.2)"] +test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4.3)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)"] + +[[package]] +name = "pre-commit" +version = "3.6.1" +description = "A framework for managing and maintaining multi-language pre-commit hooks." +optional = false +python-versions = ">=3.9" +files = [ + {file = "pre_commit-3.6.1-py2.py3-none-any.whl", hash = "sha256:9fe989afcf095d2c4796ce7c553cf28d4d4a9b9346de3cda079bcf40748454a4"}, + {file = "pre_commit-3.6.1.tar.gz", hash = "sha256:c90961d8aa706f75d60935aba09469a6b0bcb8345f127c3fbee4bdc5f114cf4b"}, +] + +[package.dependencies] +cfgv = ">=2.0.0" +identify = ">=1.0.0" +nodeenv = ">=0.11.1" +pyyaml = ">=5.1" +virtualenv = ">=20.10.0" + [[package]] name = "pyarrow" version = "15.0.0" @@ -2076,7 +2159,6 @@ files = [ {file = "PyYAML-6.0.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:69b023b2b4daa7548bcfbd4aa3da05b3a74b772db9e23b982788168117739938"}, {file = "PyYAML-6.0.1-cp310-cp310-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:81e0b275a9ecc9c0c0c07b4b90ba548307583c125f54d5b6946cfee6360c733d"}, {file = "PyYAML-6.0.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:ba336e390cd8e4d1739f42dfe9bb83a3cc2e80f567d8805e11b46f4a943f5515"}, - 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index, self.index_infos = build_index( - embeddings, save_on_disk=False, verbose=logging.ERROR - ) + index, self.index_infos = build_index(embeddings, save_on_disk=False, verbose=logging.ERROR) if index is None: raise ValueError("Failed to build an index for knn search") @@ -71,9 +69,7 @@ def predict(self, embeddings: Embeddings) -> tuple[ProbabilityArray, ClassArray] # We can shape of a factor self.k if we count differently here. weighted_count = np.zeros((n, self.num_classes, self.k), dtype=np.float32) weighted_count[ - np.tile(np.arange(n), (self.k,)).reshape( - -1 - ), # [0, 0, .., 0_k, 1, 1, .., 1_k, ..] + np.tile(np.arange(n), (self.k,)).reshape(-1), # [0, 0, .., 0_k, 1, 1, .., 1_k, ..] nearest_classes.reshape(-1), # [class numbers] np.tile(np.arange(self.k), (n,)), # [0, 1, .., k-1, 0, 1, .., k-1, ..] ] = 1 / dists.reshape(-1) diff --git a/src/evaluation/linear_probe.py b/src/evaluation/linear_probe.py index f859d2c..0bc80b6 100644 --- a/src/evaluation/linear_probe.py +++ b/src/evaluation/linear_probe.py @@ -40,9 +40,7 @@ def __init__( Cs=[1e-3, 1e-2, 1e-1, 1e0, 1e1, 1e2, 1e3], random_state=0, **params ).fit(embeddings, labels) # type: ignore else: - self.classifier = LogisticRegression(random_state=0, **params).fit( - embeddings, labels - ) + self.classifier = LogisticRegression(random_state=0, **params).fit(embeddings, labels) @property def dim(self) -> int: