diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index fa1ae223..215da6a7 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -11,57 +11,79 @@ permissions: contents: write jobs: - test: + lint: runs-on: ubuntu-latest steps: - name: Check out repository code uses: actions/checkout@v4 - - name: Install poetry - shell: bash - run: pipx install poetry==1.8.2 + - name: Install uv + uses: astral-sh/setup-uv@v3 + with: + enable-cache: true + cache-dependency-glob: "uv.lock" - - name: Install python or load from cache with dependencies + - name: Install Python or load from cache with dependencies uses: actions/setup-python@v5 with: - python-version-file: .python-version - cache: poetry + python-version-file: "pyproject.toml" - - name: Install dependencies - run: poetry install --with dev + - name: Install the project + run: uv sync --all-extras --dev - name: Lint run: | - poetry run pre-commit install - poetry run pre-commit run --all-files --show-diff-on-failure + uv run pre-commit install + uv run pre-commit run --all-files --show-diff-on-failure + + test: + runs-on: ubuntu-latest + steps: + - name: Check out repository code + uses: actions/checkout@v4 + + - name: Install uv + uses: astral-sh/setup-uv@v3 + with: + enable-cache: true + cache-dependency-glob: "uv.lock" + + - name: Install Python or load from cache with dependencies + uses: actions/setup-python@v5 + with: + python-version-file: "pyproject.toml" + + - name: Install the project + run: uv sync --all-extras --dev - name: Test - run: poetry run pytest -v + run: uv run pytest -v deploy: if: github.ref == 'refs/heads/main' - needs: [test] + needs: [lint, test] runs-on: ubuntu-latest steps: - name: Check out repository code uses: actions/checkout@v4 - - name: Install poetry - shell: bash - run: pipx install poetry==1.8.2 + - name: Install uv + uses: astral-sh/setup-uv@v3 + with: + enable-cache: true + cache-dependency-glob: "uv.lock" - - name: Install python or load from cache with dependencies + - name: Install Python or load from cache with dependencies uses: actions/setup-python@v5 with: - python-version-file: .python-version - cache: poetry + python-version-file: "pyproject.toml" - - name: Install dependencies - run: poetry install + - name: Install the project + run: uv sync --all-extras --dev - name: Deploy docs working-directory: ./docs - run: poetry run mkdocs gh-deploy --force + run: uv run mkdocs gh-deploy --force - name: Deploy more run: echo 'this is a placeholder' diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index b6ed4732..d5253711 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -26,8 +26,3 @@ repos: files: ^src/ types: [python] additional_dependencies: ['pyright@1.1.294'] - - repo: https://github.com/python-poetry/poetry - rev: 1.8.0 - hooks: - - id: poetry-check - diff --git a/.python-version b/.python-version deleted file mode 100644 index c8cfe395..00000000 --- a/.python-version +++ /dev/null @@ -1 +0,0 @@ -3.10 diff --git a/flows/inference.py b/flows/inference.py index 06d0eaf2..d2b7416e 100644 --- a/flows/inference.py +++ b/flows/inference.py @@ -3,6 +3,7 @@ from dataclasses import dataclass from io import BytesIO from pathlib import Path +from typing import Optional import boto3 from cpr_sdk.parser_models import BaseParserOutput @@ -158,8 +159,8 @@ def determine_classifier_ids( @flow(log_prints=True) def classifier_inference( - document_ids: list[str] = None, - classifier_spec: list[tuple[WikibaseID, str]] = None, + document_ids: Optional[list[str]] = None, + classifier_spec: Optional[list[tuple[WikibaseID, str]]] = None, ): """ Flow to run inference on documents within a bucket prefix diff --git a/justfile b/justfile index 78d8d482..44dad666 100644 --- a/justfile +++ b/justfile @@ -2,57 +2,57 @@ set dotenv-load # install dependencies and set up the project install: - poetry install --with dev - poetry run pre-commit install - poetry run ipython kernel install --user + uv sync --extra dev + uv run pre-commit install + uv run ipython kernel install --user # test the project test: - poetry run pytest + uv run pytest # update the snapshots for the tests test-snapshot-update: - poetry run pytest --snapshot-update + uv run pytest --snapshot-update # run linters and code formatters lint: - poetry run pre-commit run --all-files --show-diff-on-failure + uv run pre-commit run --all-files --show-diff-on-failure # build a dataset of passages build-dataset: - poetry run python scripts/build_dataset.py + uv run python scripts/build_dataset.py # fetch metadata and labelled passages for a specific wikibase ID get-concept id: - poetry run python scripts/get_concept.py --wikibase-id {{id}} + uv run python scripts/get_concept.py --wikibase-id {{id}} # train a model for a specific wikibase ID train id +OPTS="": - poetry run train --wikibase-id {{id}} {{OPTS}} + uv run scripts/train.py --wikibase-id {{id}} {{OPTS}} # evaluate a model for a specific wikibase ID evaluate id: - poetry run python scripts/evaluate.py --wikibase-id {{id}} + uv run python scripts/evaluate.py --wikibase-id {{id}} # promote a model for a specific wikibase ID promote id +OPTS="": - poetry run promote --wikibase-id {{id}} {{OPTS}} + uv run scripts/promote.py --wikibase-id {{id}} {{OPTS}} # run a model for a specific wikibase ID on a supplied string label id string: - poetry run python scripts/label.py --wikibase-id {{id}} --input-string {{string}} + uv run python scripts/label.py --wikibase-id {{id}} --input-string {{string}} # find instances of the concept in a set of passages for a specific wikibase ID predict id: - poetry run python scripts/predict.py --wikibase-id {{id}} + uv run python scripts/predict.py --wikibase-id {{id}} # sample a set of passages from the dataset for a specific wikibase ID sample id: - poetry run python scripts/sample.py --wikibase-id {{id}} + uv run python scripts/sample.py --wikibase-id {{id}} # push a sampled set of passages to argilla for a specific wikibase ID push-to-argilla id usernames workspace: - poetry run python scripts/push_to_argilla.py --wikibase-id {{id}} --usernames {{usernames}} --workspace {{workspace}} + uv run python scripts/push_to_argilla.py --wikibase-id {{id}} --usernames {{usernames}} --workspace {{workspace}} # run the full pipeline for a specific wikibase ID create-labelling-task id usernames workspace: @@ -64,6 +64,6 @@ create-labelling-task id usernames workspace: # visualise IAA, model vs gold-standard agreement, and positive predictions on the full dataset visualise-labels id: - poetry run python scripts/visualise_labels.py --wikibase-id {{id}} + uv run python scripts/visualise_labels.py --wikibase-id {{id}} analyse-classifier id: (get-concept id) (train id) (predict id) (evaluate id) (visualise-labels id) diff --git a/pyproject.toml b/pyproject.toml index 6dbe3938..17babaa9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,70 +1,46 @@ -[tool.poetry] +[project] name = "knowledge-graph" version = "0.1.0" -description = "" -authors = ["CPR Data Science "] -license = "Apache 2.0" +description = "Add your description here" readme = "README.md" -packages = [ - { include = "src", from = "." }, - { include = "tests", from = "." }, - { include = "scripts", from = "." }, +requires-python = ">=3.11" +dependencies = [ + "argilla==1.29.1", + "azure-pdf-parser", + "boto3==1.35.31", + "cpr-sdk==1.9.1", + "griffe==0.48.0", + "httpx==0.26.0", + "ipykernel==6.29.3", + "more-itertools==10.3.0", + "neomodel==5.3.3", + "prefect==2.16.8", + "python-dotenv==1.0.1", + "rapidfuzz==3.10.0", + "rich==13.7.0", + "sentence-transformers==3.1.1", + "tqdm>=4.66.5", + "typer==0.9.4", + "wandb==0.18.3", + # The following is to work around the fact that pytorch stopped supported intel-macs after 2.2.2 + # See: https://github.com/pytorch/pytorch/issues/114602 + "torch==2.2.2; sys_platform == 'darwin' and platform_machine == 'x86_64'", + "torch==2.4.1; sys_platform != 'darwin' or platform_machine != 'x86_64'", ] -[tool.poetry.dependencies] -python = ">=3.10,<3.11" -httpx = "^0.26.0" -rich = "^13.7.0" -tqdm = "^4.66.2" -ipykernel = "^6.29.3" -azure_pdf_parser = { git = "https://github.com/climatepolicyradar/azure-pdf-parser.git", tag = "v0.4.3" } -# navigator_document_parser = { git = "https://github.com/climatepolicyradar/navigator-document-parser.git" } -neomodel = "^5.3.3" -typer = "0.9.4" -rapidfuzz = "^3.10.0" -python-dotenv = "^1.0.1" -hypothesis = "^6.112.2" -more-itertools = "^10.3.0" -argilla = "1.29.1" -prefect = "2.16.8" -griffe = "0.48.0" -cpr-sdk = "^1.7.1" -sentence-transformers = "^3.1.1" -wandb = "^0.18.3" -boto3 = "^1.35.31" -moto = {extras = ["s3"], version = "^5.0.16"} -# The following is to work around the fact that pytorch stopped supported intel-macs after 2.2.2 -# See: https://github.com/pytorch/pytorch/issues/114602 -torch = [ - {version = "2.2.2", markers = "sys_platform == 'darwin' and platform_machine == 'x86_64'"}, - {version = "2.4.1", markers = "sys_platform != 'darwin' and platform_machine != 'x86_64'"}, - ] - - -[[tool.poetry.source]] -name = "pytorch" -url = "https://download.pytorch.org/whl/cpu" -priority = "explicit" - - -[tool.poetry.scripts] -train = "scripts.train:app" -promote = "scripts.promote:app" - -[tool.poetry.group.dev] -optional = true - -[tool.poetry.group.dev.dependencies] -pytest = "^8.3.2" -mkdocs-material = "^9.5.39" -pre-commit = "^3.8.0" -boto3 = "^1.35.32" -syrupy = "^4.7.1" -moto = {extras = ["s3"], version = "^5.0.16"} +[project.optional-dependencies] +dev = [ + "hypothesis==6.112.2", + "mkdocs-material==9.5.39", + "moto[s3]==5.0.16", + "pre-commit>=4.0.1", + "pytest>=8.3.3", + "ruff>=0.7.0", + "syrupy>=4.7.2", +] -[build-system] -requires = ["poetry-core"] -build-backend = "poetry.core.masonry.api" +[tool.uv.sources] +azure-pdf-parser = { git = "https://github.com/climatepolicyradar/azure-pdf-parser.git", tag = "v0.4.3" } [tool.ruff] lint.select = ["E", "F", "D", "I"] diff --git 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