diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 00000000..12515289 --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,41 @@ +version: 2 +updates: + - package-ecosystem: uv + directory: / + cooldown: + default-days: 7 + semver-major-days: 30 + schedule: + interval: weekly + groups: + python-dependencies: + patterns: + - "*" + commit-message: + prefix: "chore(deps):" + + - package-ecosystem: github-actions + directory: / + cooldown: + default-days: 7 + schedule: + interval: weekly + groups: + github-actions: + patterns: + - "*" + commit-message: + prefix: "ci(deps):" + + - package-ecosystem: pre-commit + directory: / + cooldown: + default-days: 7 + schedule: + interval: weekly + groups: + pre-commit: + patterns: + - "*" + commit-message: + prefix: "chore(deps):" diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 8522d212..84078d76 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -7,31 +7,24 @@ on: pull_request: jobs: - test: + ci: runs-on: ubuntu-latest + strategy: + fail-fast: false + matrix: + include: + - name: test + run: uv run --locked --group dev pytest + - name: lint + run: uv run --locked --group dev pre-commit run --all-files steps: - - name: Checkout - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 - - name: Setup Python - uses: actions/setup-python@b64ffcaf5b410884ad320a9cfac8866006a109aa # v4.8.0 - with: - python-version: "3.11" - cache: "pip" - - name: Install dependencies - run: pip install -r requirements.txt - - name: Test collections - run: pytest - lint: - runs-on: ubuntu-latest - steps: - - name: Checkout - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 - - name: Setup Python - uses: actions/setup-python@b64ffcaf5b410884ad320a9cfac8866006a109aa # v4.8.0 + - name: Checkout code + uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 + + - name: Install uv + uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 with: - python-version: "3.11" - cache: "pip" - - name: Install dependencies - run: pip install -r requirements.txt - - name: Run pre-commit hooks - run: pre-commit run --all-files + enable-cache: true + + - name: ${{ matrix.name }} + run: ${{ matrix.run }} diff --git a/.github/workflows/pr.yml b/.github/workflows/pr.yml index a7daedef..e8bbdd13 100644 --- a/.github/workflows/pr.yml +++ b/.github/workflows/pr.yml @@ -35,7 +35,7 @@ jobs: comment_id: ${{ steps.init-comment.outputs.COMMENT_ID }} has_new_files_to_promote: ${{ steps.changed-files.outputs.all_changed_files_count != 0 }} steps: - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 + - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: fetch-depth: 0 @@ -119,7 +119,7 @@ jobs: AIRFLOW_JWT_SECRET: ${{ secrets.AIRFLOW_JWT_SECRET }} AIRFLOW_JWT_SUB: ${{ secrets.AIRFLOW_JWT_SUB }} run: | - pip install -r ./scripts/requirements.txt + uv sync --locked --group scripts # Track successful publications all_failed=true @@ -183,14 +183,10 @@ jobs: $status_message" gh api -X PATCH -H "Authorization: token $GITHUB_TOKEN" /repos/${{ github.repository }}/issues/comments/$COMMENT_ID -f body="$UPDATED_BODY" - - name: Set up Python - uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5.4.0 + - name: Install uv + uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 with: - python-version: '3.9' - - uses: actions/cache@d4323d4df104b026a6aa633fdb11d772146be0bf # v4.2.2 - with: - path: ${{ env.pythonLocation }} - key: ${{ env.pythonLocation }}-pip-${{ hashFiles('requirements.txt') }} + enable-cache: true # If the workflow fails at any point, the PR comment will be updated - name: Update PR comment on overall workflow failure @@ -236,7 +232,7 @@ jobs: run: ls -lah /tmp/upload-artifacts - name: Upload published collections files as directory artifact - uses: actions/upload-artifact@4cec3d8aa04e39d1a68397de0c4cd6fb9dce8ec1 # v4.6.1 + uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1 env: ARTIFACT_RETENTION_DAYS: ${{ vars.ARTIFACT_RETENTION_DAYS }} with: @@ -250,7 +246,7 @@ jobs: echo "${{ github.run_id }}" > run_id.txt - name: Upload Workflow Run ID - uses: actions/upload-artifact@4cec3d8aa04e39d1a68397de0c4cd6fb9dce8ec1 # v4.6.1 + uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1 env: ARTIFACT_RETENTION_DAYS: ${{ vars.ARTIFACT_RETENTION_DAYS }} with: @@ -275,7 +271,7 @@ jobs: skip_mdx_pr_step: ${{ steps.skip_mdx_pr_step_setting.outputs.skip_mdx_pr_step }} steps: - name: Checkout code - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 + uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 - name: Set SKIP_MDX_PR_STEP condition id: skip_mdx_pr_step_setting @@ -292,7 +288,7 @@ jobs: needs: ['mdx-pr-flag-evaluator', 'publish-new-datasets'] steps: - name: Checkout code - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 + uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 - name: Use output from publish-new-datasets run: | @@ -305,7 +301,7 @@ jobs: run: | echo $PUBLISHED_COLLECTION_FILES collection_ids="" - pip install -r ./scripts/requirements.txt + uv sync --locked --group scripts for file in ${PUBLISHED_COLLECTION_FILES}; do collection_id=$(python3 ./scripts/generate_mdx.py "$file") collection_id=$(echo "$collection_id" | sed 's/^["\s]*//;s/["\s]*$//') diff --git a/.github/workflows/promote.yml b/.github/workflows/promote.yml index 1aab7e5d..f237c173 100644 --- a/.github/workflows/promote.yml +++ b/.github/workflows/promote.yml @@ -45,7 +45,12 @@ jobs: environment: production steps: - name: Checkout code - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 + uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 + + - name: Install uv + uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 + with: + enable-cache: true - name: Determine artifact name run: echo "ARTIFACT_NAME=collections-to-promote-from-${{ github.event.inputs.pr_number }}" >> $GITHUB_ENV @@ -70,7 +75,7 @@ jobs: AIRFLOW_JWT_SUB: ${{ secrets.AIRFLOW_JWT_SUB }} run: | - pip install -r ./scripts/requirements.txt + uv sync --locked --group scripts for file in downloaded-files/*.json; do echo "Processing $file" # Check if collection key exists to determine if it's a dataset or collection diff --git a/.github/workflows/promotion-checker.yml b/.github/workflows/promotion-checker.yml index 1da3c698..bdcf5a89 100644 --- a/.github/workflows/promotion-checker.yml +++ b/.github/workflows/promotion-checker.yml @@ -53,7 +53,7 @@ jobs: needs: check-conditions steps: - name: Checkout Repository - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 + uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 - name: Get Workflow Run ID Artifact run: | diff --git a/.markdownlint-cli2.jsonc b/.markdownlint-cli2.jsonc deleted file mode 100644 index e5a00e2c..00000000 --- a/.markdownlint-cli2.jsonc +++ /dev/null @@ -1,8 +0,0 @@ -{ - "config": { - "MD013": false, // disable line length checks - "MD033": { - "allowed_elements": [ "a", "b", "details", "summary" ] - } - } -} \ No newline at end of file diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 9f3482e7..44d308f7 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,22 +1,49 @@ +exclude: ^transformation-scripts/.*$ + repos: - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.5.0 + rev: v6.0.0 hooks: - id: check-yaml - - id: file-contents-sorter - files: ^requirements.in$ - id: trailing-whitespace exclude: ^ingestion-data/.*$ + + - repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.16.1 + hooks: + - id: ruff-check + args: [--fix] + - id: ruff-format + types_or: [python, pyi, pyproject] + - repo: https://github.com/DavidAnson/markdownlint-cli2 - rev: v0.10.0 + rev: v0.23.2 hooks: - id: markdownlint-cli2 - - repo: https://github.com/psf/black-pre-commit-mirror - rev: 24.3.0 + args: + - "--fix" + - "--config" + - "pyproject.toml" + - "--configPointer" + - "/tool/markdownlint-cli2" + + - repo: https://github.com/astral-sh/uv-pre-commit + rev: 0.12.5 hooks: - - id: black - - id: black-jupyter - - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.0.292 + - id: uv-lock + + - repo: https://github.com/DavidAnson/markdownlint-cli2 + rev: v0.23.2 + hooks: + - id: markdownlint-cli2 + args: + - "--fix" + - "--config" + - "pyproject.toml" + - "--configPointer" + - "/tool/markdownlint-cli2" + + - repo: https://github.com/astral-sh/uv-pre-commit + rev: 0.12.5 hooks: - - id: ruff + - id: uv-lock diff --git a/CODEOWNERS b/CODEOWNERS index 296e5839..ebb5e4f4 100644 --- a/CODEOWNERS +++ b/CODEOWNERS @@ -1,5 +1 @@ -* @anayeaye -* @gadomski -* @ividito -* @slesaad -* @smohiudd +* @NASA-IMPACT/veda-data-services diff --git a/README.md b/README.md index 39918351..41cece2d 100644 --- a/README.md +++ b/README.md @@ -20,7 +20,7 @@ To add data to VEDA you will: ### Step 1: Stage your files -Upload files to the staging bucket `s3://veda-data-store-staging` (which you can do with a VEDA JupyterHub account--request access [here](https://docs.openveda.cloud/user-guide/scientific-computing/getting-access.html)) or a self-hosted bucket in s3 has shared read access to VEDA service. [See docs.openveda.cloud for additional details on preparing files.](https://docs.openveda.cloud/user-guide/content-curation/dataset-ingestion/file-preparation.html) +Upload files to the staging bucket `s3://veda-data-store-staging` (which you can do with a VEDA JupyterHub account--request [access here](https://docs.openveda.cloud/user-guide/scientific-computing/getting-access.html)) or a self-hosted bucket in s3 has shared read access to VEDA service. [See docs.openveda.cloud for additional details on preparing files.](https://docs.openveda.cloud/user-guide/content-curation/dataset-ingestion/file-preparation.html) ### Step 2: Generate STAC metadata in the staging catalog diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 00000000..0761cc55 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,56 @@ +[project] +name = "veda-data" +version = "0.1.0" +description = "Config data used to load datasets into the VEDA catalog" +readme = "README.md" +requires-python = ">=3.11" +dependencies = [] + +[dependency-groups] +dev = [ + "pre-commit==4.6.1", + "pystac[validation]==1.8.4", + "pytest==9.0.3", +] +scripts = [ + "pyyaml", + "PyJWT", +] + +[tool.uv] +default-groups = ["dev"] + +[tool.ruff] +line-length = 88 + +[tool.ruff.lint] +select = [ + "E", # pycodestyle errors + "W", # pycodestyle warnings + "F", # Pyflakes + "I", # isort + "UP", # pyupgrade + "B", # flake8-bugbear + "C4", # flake8-comprehensions + "SIM", # flake8-simplify + "PTH", # flake8-use-pathlib + "RET", # flake8-return + "TID", # flake8-tidy-imports + "TC", # flake8-type-checking + "ISC", # flake8-implicit-str-concat + "ICN", # flake8-import-conventions +] +ignore = [ + "BLE001", # Blind Exceptions +] + +[tool.ruff.format] +docstring-code-format = true +docstring-code-line-length = "dynamic" + +[tool.markdownlint-cli2.config] +MD013 = false +MD033 = { allowed_elements = ["a", "b", "details", "summary"] } + +[tool.ruff.lint.isort] +combine-as-imports = true diff --git a/requirements.in b/requirements.in deleted file mode 100644 index 8f9b6370..00000000 --- a/requirements.in +++ /dev/null @@ -1,6 +0,0 @@ -black[jupyter] -pip-tools -pre-commit -pystac[validation] -pytest -ruff diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 64c91392..00000000 --- a/requirements.txt +++ /dev/null @@ -1,123 +0,0 @@ -# -# This file is autogenerated by pip-compile with Python 3.11 -# by the following command: -# -# pip-compile -# -asttokens==2.4.0 - # via stack-data -attrs==23.1.0 - # via - # jsonschema - # referencing -backcall==0.2.0 - # via ipython -black[jupyter]==23.10.0 - # via -r requirements.in -build==1.0.3 - # via pip-tools -cfgv==3.4.0 - # via pre-commit -click==8.1.7 - # via - # black - # pip-tools -decorator==5.1.1 - # via ipython -distlib==0.3.7 - # via virtualenv -executing==2.0.0 - # via stack-data -filelock==3.12.4 - # via virtualenv -identify==2.5.30 - # via pre-commit -iniconfig==2.0.0 - # via pytest -ipython==8.16.1 - # via black -jedi==0.19.1 - # via ipython -jsonschema==4.19.1 - # via pystac -jsonschema-specifications==2023.7.1 - # via jsonschema -matplotlib-inline==0.1.6 - # via ipython -mypy-extensions==1.0.0 - # via black -nodeenv==1.8.0 - # via pre-commit -packaging==23.2 - # via - # black - # build - # pytest -parso==0.8.3 - # via jedi -pathspec==0.11.2 - # via black -pexpect==4.8.0 - # via ipython -pickleshare==0.7.5 - # via ipython -pip-tools==7.3.0 - # via -r requirements.in -platformdirs==3.11.0 - # via - # black - # virtualenv -pluggy==1.3.0 - # via pytest -pre-commit==3.5.0 - # via -r requirements.in -prompt-toolkit==3.0.39 - # via ipython -ptyprocess==0.7.0 - # via pexpect -pure-eval==0.2.2 - # via stack-data -pygments==2.16.1 - # via ipython -pyproject-hooks==1.0.0 - # via build -pystac[validation]==1.8.4 - # via -r requirements.in -pytest==7.4.2 - # via -r requirements.in -python-dateutil==2.8.2 - # via pystac -pyyaml==6.0.1 - # via pre-commit -referencing==0.30.2 - # via - # jsonschema - # jsonschema-specifications -rpds-py==0.10.6 - # via - # jsonschema - # referencing -ruff==0.1.0 - # via -r requirements.in -six==1.16.0 - # via - # asttokens - # python-dateutil -stack-data==0.6.3 - # via ipython -tokenize-rt==5.2.0 - # via black -traitlets==5.11.2 - # via - # ipython - # matplotlib-inline -virtualenv==20.26.6 - # via pre-commit -wcwidth==0.2.8 - # via prompt-toolkit -wheel==0.41.2 - # via pip-tools - -# The following packages are considered to be unsafe in a requirements file: -# pip -# setuptools diff --git a/scripts/airflow_api.py b/scripts/airflow_api.py index 583f840a..ae7f8c7a 100644 --- a/scripts/airflow_api.py +++ b/scripts/airflow_api.py @@ -2,13 +2,12 @@ Supports Airflow 2 and 3 (API v1 / v2) """ +import http.client +import json import os import uuid -import json -import http.client - -from typing import Dict, Any from base64 import b64encode +from typing import Any class AirflowAPIError(Exception): @@ -20,8 +19,8 @@ def __init__(self, msg, status_code=None): def _build_request_body( - conf: Dict[str, Any], dag_id: str, note: str = "", api_version: str = "2" -) -> Dict[str, Any]: + conf: dict[str, Any], dag_id: str, note: str = "", api_version: str = "2" +) -> dict[str, Any]: """Build the request body for the DagRun""" run_id = os.getenv("GITHUB_RUN_ID") if run_id: @@ -45,9 +44,10 @@ def _build_request_body( def _generate_jwt_token(secret: str, sub: str, expiration_time: int = 3600) -> str: """Generate a HS512 JWT Token for Airflow API authentication""" - import jwt import time + import jwt + payload = { "iss": "airflow", "sub": sub, @@ -62,11 +62,11 @@ def _generate_jwt_token(secret: str, sub: str, expiration_time: int = 3600) -> s def trigger_dag_run( base_api_url: str, dag_id: str, - conf: Dict[str, Any], + conf: dict[str, Any], username: str, password: str, api_version: str = None, -) -> Dict[str, Any]: +) -> dict[str, Any]: """ Trigger a DAG run with version-aware API handling @@ -120,4 +120,4 @@ def trigger_dag_run( except AirflowAPIError: raise except Exception as e: - raise AirflowAPIError(f"Failed to trigger the DAG run: {str(e)}") + raise AirflowAPIError(f"Failed to trigger the DAG run: {str(e)}") from e diff --git a/scripts/generate_mdx.py b/scripts/generate_mdx.py index e8726d53..a5f3ddcf 100644 --- a/scripts/generate_mdx.py +++ b/scripts/generate_mdx.py @@ -5,10 +5,11 @@ Dependency: `dataset.mdx` file """ -import yaml -import os import json import sys +from pathlib import Path + +import yaml def create_frontmatter(input_data): @@ -91,39 +92,37 @@ def create_frontmatter(input_data): json_data["layers"].append(layer) # Convert json to yaml for frontmatter - yaml_data = yaml.dump(json_data, sort_keys=False) - - return yaml_data + return yaml.dump(json_data, sort_keys=False) def safe_open_w(path): """Open "path" for writing, creating any parent directories as needed.""" - os.makedirs(os.path.dirname(path), exist_ok=True) - return open(path, "w") + Path(path).parent.mkdir(parents=True, exist_ok=True) + return Path(path).open("w") if __name__ == "__main__": - input_data = json.load(open(sys.argv[1])) + with Path(sys.argv[1]).open() as f: + input_data = json.load(f) dataset_config = create_frontmatter(input_data) front_matter = f"---\n{dataset_config}---\n" # Path to the existing file - curr_directory = os.path.dirname(os.path.abspath(__file__)) - file_path = os.path.join(curr_directory, "dataset.mdx") + curr_directory = Path(__file__).parent + file_path = curr_directory / "dataset.mdx" # Read the existing content of the file - with open(file_path, "r") as file: - existing_content = file.read() + existing_content = file_path.read_text() # Combine front matter and existing content new_content = front_matter + existing_content # Write the combined content back to the file - output_filepath = os.path.join( - curr_directory, - f"../ingestion-data/dataset-mdx/{input_data['collection']}.data.mdx", + output_filepath = ( + curr_directory + / f"../ingestion-data/dataset-mdx/{input_data['collection']}.data.mdx" ) - with safe_open_w(output_filepath) as ofile: + with safe_open_w(str(output_filepath)) as ofile: ofile.write(new_content) collection_id = input_data["collection"] diff --git a/scripts/promote_collection.py b/scripts/promote_collection.py index 80d6dd2e..106a7741 100644 --- a/scripts/promote_collection.py +++ b/scripts/promote_collection.py @@ -1,13 +1,13 @@ -from typing import Dict, Any - import json -import sys import os +import sys +from pathlib import Path +from typing import Any from airflow_api import AirflowAPIError, trigger_dag_run -def trigger_collection_dag(payload: Dict[str, Any], stage: str): +def trigger_collection_dag(payload: dict[str, Any], stage: str): """ Triggers the veda_collection_pipeline DAG in either staging or production SM2A. """ @@ -53,7 +53,7 @@ def trigger_collection_dag(payload: Dict[str, Any], stage: str): if __name__ == "__main__": try: - with open(sys.argv[1], "r") as file: + with Path(sys.argv[1]).open("r") as file: input_data = json.load(file) stage = sys.argv[2] dag_payload = {"conf": input_data} diff --git a/scripts/promote_dataset.py b/scripts/promote_dataset.py index 1cd3e20d..07a54b88 100644 --- a/scripts/promote_dataset.py +++ b/scripts/promote_dataset.py @@ -1,8 +1,8 @@ -from typing import Dict, Any - import json -import sys import os +import sys +from pathlib import Path +from typing import Any from airflow_api import AirflowAPIError, trigger_dag_run @@ -11,7 +11,7 @@ class MissingFieldError(Exception): pass -def validate_discovery_item_config(item: Dict[str, Any]) -> Dict[str, Any]: +def validate_discovery_item_config(item: dict[str, Any]) -> dict[str, Any]: required_fields = ["bucket", "discovery", "filename_regex", "prefix"] for field in required_fields: if field not in item: @@ -81,7 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