diff --git a/.github/ISSUE_TEMPLATE/add-request.md b/.github/ISSUE_TEMPLATE/add-request.md deleted file mode 100644 index 63b0672..0000000 --- a/.github/ISSUE_TEMPLATE/add-request.md +++ /dev/null @@ -1,16 +0,0 @@ ---- -name: Add request -about: Suggest an idea for this project -title: "[ADD] " -labels: Add -assignees: fmind - ---- - -**Is your feature request related to a problem? Please describe.** - -**Describe the solution you'd like** - -**Describe alternatives you've considered** - -**Additional context** diff --git a/.github/ISSUE_TEMPLATE/change-request.md b/.github/ISSUE_TEMPLATE/change-request.md deleted file mode 100644 index 5450bb8..0000000 --- a/.github/ISSUE_TEMPLATE/change-request.md +++ /dev/null @@ -1,14 +0,0 @@ ---- -name: Change request -about: Propose a change for this project -title: "[CHANGE] " -labels: Change -assignees: fmind - ---- - -**Describe the problem you encounter** - -**Describe the solution you'd like** - -**Additional context** diff --git a/.github/ISSUE_TEMPLATE/custom-request.md b/.github/ISSUE_TEMPLATE/custom-request.md deleted file mode 100644 index 38075e1..0000000 --- a/.github/ISSUE_TEMPLATE/custom-request.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -name: Custom request -about: Ask anything for this project -title: '' -labels: '' -assignees: '' - ---- - - diff --git a/.github/ISSUE_TEMPLATE/feat-request.md b/.github/ISSUE_TEMPLATE/feat-request.md new file mode 100644 index 0000000..85bdbf0 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/feat-request.md @@ -0,0 +1,22 @@ +--- +name: Feature Request +about: A new feature. +title: "[FEAT] " +labels: feat +assignees: fmind +body: +- type: checkboxes + id: breaking-change + attributes: + label: Breaking change? + options: + - label: Yes + - label: No + - label: Maybe +--- + +## Description + +## Motivation + +## Solutions diff --git a/.github/ISSUE_TEMPLATE/fix-request.md b/.github/ISSUE_TEMPLATE/fix-request.md index 3280bce..39b4d03 100644 --- a/.github/ISSUE_TEMPLATE/fix-request.md +++ b/.github/ISSUE_TEMPLATE/fix-request.md @@ -1,23 +1,24 @@ --- -name: Fix request -about: Request a fix for this project +name: Fix Request +about: A bug fix title: "[FIX] " -labels: Fix +labels: fix assignees: fmind - +body: +- type: checkboxes + id: breaking-change + attributes: + label: Breaking change? + options: + - label: Yes + - label: No + - label: Maybe --- -**Describe the bug** -A clear and concise description of what the bug is. - -**To Reproduce** -Steps to reproduce the behavior: +## Bug Description -**Expected behavior** -A clear and concise description of what you expected to happen. +## Expected Behavior -**Screenshots** -If applicable, add screenshots to help explain your problem. +## Steps to Reproduce -**Additional context** -Add any other context about the problem here. +## Additional Context diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index e1d54d8..4f15536 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -1,3 +1,9 @@ # Changes -- +# Reasons + +# Testing + +# Impacts + +# Notes diff --git a/.github/workflows/on-pull-request.yml b/.github/workflows/check.yml similarity index 84% rename from .github/workflows/on-pull-request.yml rename to .github/workflows/check.yml index 803004c..7351b39 100644 --- a/.github/workflows/on-pull-request.yml +++ b/.github/workflows/check.yml @@ -1,3 +1,4 @@ +name: Check on: pull_request: branches: @@ -11,5 +12,5 @@ jobs: steps: - uses: actions/checkout@v4 - uses: ./.github/actions/setup - - run: poetry install --with dev,checks + - run: poetry install --with checks - run: poetry run invoke checks diff --git a/.github/workflows/on-release-published.yml b/.github/workflows/publish.yml similarity index 96% rename from .github/workflows/on-release-published.yml rename to .github/workflows/publish.yml index 01984c9..d9cc9e1 100644 --- a/.github/workflows/on-release-published.yml +++ b/.github/workflows/publish.yml @@ -1,3 +1,4 @@ +name: Publish on: release: types: [published] @@ -5,7 +6,7 @@ env: DOCKER_IMAGE: ghcr.io/fmind/mlops-python-package:latest concurrency: cancel-in-progress: true - group: on-release-published + group: publish-workflow jobs: pages: runs-on: ubuntu-latest diff --git a/.gitignore b/.gitignore index 06f385d..006fd5a 100644 --- a/.gitignore +++ b/.gitignore @@ -2,6 +2,7 @@ # Build /dist/ +/build/ # Cache .cache/ @@ -16,7 +17,9 @@ .ipynb_checkpoints/ # Environs +.env /.venv/ +poetry.lock # Project /docs/* diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 8921eb0..21cf643 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,5 +1,5 @@ -# See https://pre-commit.com for more information -# See https://pre-commit.com/hooks.html for more hooks +# https://pre-commit.com +# https://pre-commit.com/hooks.html default_language_version: python: python3.12 @@ -13,15 +13,27 @@ repos: - id: check-merge-conflict - id: check-toml - id: check-yaml + - id: debug-statements - id: end-of-file-fixer - id: mixed-line-ending - id: trailing-whitespace - # project - - repo: local + - repo: github.com/PyCQA/bandit + rev: v1.7.7 hooks: - - id: invoke-check - name: invoke checks - language: system - pass_filenames: false - verbose: true - entry: invoke checks + - id: bandit + args: ["--configfile=pyproject.toml"] + - repo: https://github.com/pre-commit/mirrors-mypy + rev: v1.8.0 + hooks: + - id: mypy + - repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.3.0 + hooks: + - id: ruff + - id: ruff-format + - repo: https://github.com/commitizen-tools/commitizen + rev: v3.16.0 + hooks: + - id: commitizen + - id: commitizen-branch + stages: [push] diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 0000000..e69de29 diff --git a/Dockerfile b/Dockerfile index 33adb24..043fa81 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,11 +1,6 @@ # https://docs.docker.com/engine/reference/builder/ -# Define FROM python:3.12 - -# Install COPY dist/*.whl . -RUN pip install --no-cache-dir *.whl - -# Execute +RUN pip install *.whl CMD ["bikes", "--help"] diff --git a/README.md b/README.md index 8966402..9414ba7 100644 --- a/README.md +++ b/README.md @@ -1,10 +1,9 @@ # MLOps Python Package [![on-release-published.yml](https://github.com/fmind/mlops-python-package/actions/workflows/on-release-published.yml/badge.svg)](https://github.com/fmind/mlops-python-package/actions/workflows/on-release-published.yml) -[![Release](https://img.shields.io/github/v/release/fmind/mlops-python-package)](https://github.com/fmind/mlops-python-package/releases) - -[![License](https://img.shields.io/github/license/fmind/mlops-python-package)](https://github.com/fmind/mlops-python-package/blob/main/LICENCE.txt) [![Documentation](https://img.shields.io/badge/documentation-available-brightgreen.svg)](https://fmind.github.io/mlops-python-package/) +[![License](https://img.shields.io/github/license/fmind/mlops-python-package)](https://github.com/fmind/mlops-python-package/blob/main/LICENCE.txt) +[![Release](https://img.shields.io/github/v/release/fmind/mlops-python-package)](https://github.com/fmind/mlops-python-package/releases) This repository contains a Python package implementation designed to support MLOps initiatives. diff --git a/docker-compose.yml b/docker-compose.yml index 7baece6..256fd04 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -1,7 +1,8 @@ # https://docs.docker.com/compose/compose-file/ + services: mlflow: - image: ghcr.io/mlflow/mlflow:v2.10.2 + image: ghcr.io/mlflow/mlflow:v2.11.0 ports: - 5000:5000 environment: diff --git a/mlops-python-package.code-workspace b/mlops-python-package.code-workspace index 3283201..fb7912c 100644 --- a/mlops-python-package.code-workspace +++ b/mlops-python-package.code-workspace @@ -22,9 +22,10 @@ "recommendations": [ "charliermarsh.ruff", "dchanco.vsc-invoke", + "ms-python.mypy-type-checker", "ms-python.python", "ms-python.mypy-type-checker", "ms-python.vscode-pylance", ] } -} +} \ No newline at end of file diff --git a/notebooks/prototype.ipynb b/notebooks/prototype.ipynb index 2c0964e..5eac991 100644 --- a/notebooks/prototype.ipynb +++ b/notebooks/prototype.ipynb @@ -106043,11 +106043,8 @@ ], "source": [ "px.scatter_matrix(\n", - " hour,\n", - " dimensions=[\"registered\", \"casual\", \"cnt\", \"mnth\", \"hr\"],\n", - " color=TARGET,\n", - " height=800,\n", - " title=\"Analysis of top features\",\n", + " hour, dimensions=[\"registered\", \"casual\", \"cnt\", \"mnth\", \"hr\"], color=TARGET,\n", + " height=800, title=\"Analysis of top features\",\n", ")" ] }, @@ -106727,6 +106724,32 @@ "Fitting 4 folds for each of 9 candidates, totalling 36 fits\n" ] }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/home/fmind/mlops-python-package/.venv/lib/python3.12/site-packages/sklearn/pipeline.py:408: UserWarning:\n", + "\n", + "Persisting input arguments took 0.63s to run.If this happens often in your code, it can cause performance problems (results will be correct in all cases). The reason for this is probably some large input arguments for a wrapped function.\n", + "\n", + "/home/fmind/mlops-python-package/.venv/lib/python3.12/site-packages/sklearn/pipeline.py:408: UserWarning:\n", + "\n", + "Persisting input arguments took 0.68s to run.If this happens often in your code, it can cause performance problems (results will be correct in all cases). The reason for this is probably some large input arguments for a wrapped function.\n", + "\n", + "/home/fmind/mlops-python-package/.venv/lib/python3.12/site-packages/sklearn/pipeline.py:408: UserWarning:\n", + "\n", + "Persisting input arguments took 0.75s to run.If this happens often in your code, it can cause performance problems (results will be correct in all cases). The reason for this is probably some large input arguments for a wrapped function.\n", + "\n", + "/home/fmind/mlops-python-package/.venv/lib/python3.12/site-packages/sklearn/pipeline.py:408: UserWarning:\n", + "\n", + "Persisting input arguments took 0.83s to run.If this happens often in your code, it can cause performance problems (results will be correct in all cases). The reason for this is probably some large input arguments for a wrapped function.\n", + "\n", + "/home/fmind/mlops-python-package/.venv/lib/python3.12/site-packages/sklearn/pipeline.py:408: UserWarning:\n", + "\n", + "Persisting input arguments took 0.92s to run.If this happens often in your code, it can cause performance problems (results will be correct in all cases). The reason for this is probably some large input arguments for a wrapped function.\n", + "\n" + ] + }, { "data": { "text/html": [ @@ -107298,10 +107321,10 @@ " \n", " \n", " 4\n", - " 7.874702\n", - " 1.307478\n", - " 0.051198\n", - " 0.010297\n", + " 7.337822\n", + " 0.950208\n", + " 0.047391\n", + " 0.008937\n", " 20\n", " 200\n", " {'regressor__max_depth': 20, 'regressor__n_est...\n", @@ -107315,10 +107338,10 @@ " \n", " \n", " 1\n", - " 6.743718\n", - " 0.591675\n", - " 0.042353\n", - " 0.001662\n", + " 7.093299\n", + " 1.002765\n", + " 0.052084\n", + " 0.005926\n", " 15\n", " 200\n", " {'regressor__max_depth': 15, 'regressor__n_est...\n", @@ -107332,10 +107355,10 @@ " \n", " \n", " 5\n", - " 10.383347\n", - " 1.068664\n", - " 0.071645\n", - " 0.007144\n", + " 9.058873\n", + " 1.212642\n", + " 0.051451\n", + " 0.005104\n", " 20\n", " 250\n", " {'regressor__max_depth': 20, 'regressor__n_est...\n", @@ -107349,10 +107372,10 @@ " \n", " \n", " 7\n", - " 8.013708\n", - " 1.062043\n", - 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-[package.extras] -docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"] -testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"] - -[metadata] -lock-version = "2.0" -python-versions = "^3.12" -content-hash = "f0ed4a3155f5bccd51342798464ceb1f2d9de025677c2a8e027823dcd6eed294" diff --git a/pyproject.toml b/pyproject.toml index 9b226ab..72f5e79 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,11 +1,12 @@ # https://python-poetry.org/docs/pyproject/ -# PACKAGE +# PROJECT [tool.poetry] name = "bikes" -version = "0.5.0" +version = "0.6.0" description = "Predict the number of bikes available." +documentation = "https://fmind.github.io/mlops-python-package/" repository = "https://github.com/fmind/mlops-python-package" authors = ["Médéric HURIER "] readme = "README.md" @@ -22,61 +23,75 @@ bikes = 'bikes.scripts:main' [tool.poetry.dependencies] python = "^3.12" -cloudpathlib = "^0.17.0" codecarbon = "^2.3.4" loguru = "^0.7.2" -mlflow-skinny = "^2.10.2" +mlflow-skinny = "^2.11.0" omegaconf = "^2.3.0" -pandas = "^2.2.0" +pandas = "^2.2.1" pandera = "^0.18.0" -plotly = "^5.18.0" -psutil = "^5.9.8" +plotly = "^5.19.0" pyarrow = "^15.0.0" -pydantic = "^2.5.3" -pydantic-settings = "^2.1.0" -pynvml = "^11.5.0" -scikit-learn = "^1.4.0" +pydantic = "^2.6.3" +pydantic-settings = "^2.2.1" +scikit-learn = "^1.4.1" +mlflow = "^2.11.0" [tool.poetry.group.dev.dependencies] invoke = "^2.2.0" -pre-commit = "^3.6.0" [tool.poetry.group.docs.dependencies] -pdoc = "^13.1.1" +pdoc = "^14.4.0" [tool.poetry.group.checks.dependencies] -coverage = "^7.4.1" +bandit = "^1.7.7" +coverage = "^7.4.3" mypy = "^1.8.0" -pytest = "^8.0.0" +pytest = "^8.0.2" pytest-cov = "^4.1.0" pytest-xdist = "^3.5.0" pandera = { extras = ["mypy"], version = "^0.18.0" } -ruff = "^0.2.2" +ruff = "^0.3.0" + +[tool.poetry.group.commits.dependencies] +commitizen = "^3.16.0" +pre-commit = "^3.6.2" [tool.poetry.group.carbons.dependencies] -dash = "^2.15.0" +dash = "^2.16.0" dash-bootstrap-components = "^1.5.0" fire = "^0.5.0" [tool.poetry.group.notebooks.dependencies] -ipykernel = "^6.29.0" +ipykernel = "^6.29.3" nbformat = "^5.9.2" # CONFIGURATIONS +[tool.bandit] +skips = ["B101"] + +[tool.commitizen] +name = "cz_conventional_commits" +tag_format = "v$version" +version_scheme = "pep440" +version_provider = "poetry" +changelog_start_rev = "v1.0.0" +update_changelog_on_bump = true +major_version_zero = true + [tool.coverage.run] branch = true source = ["src"] omit = ["__main__.py"] [tool.mypy] +pretty = true +strict = true +python_version = "3.12" check_untyped_defs = true ignore_missing_imports = true plugins = ["pandera.mypy", "pydantic.mypy"] -[tool.pytest.ini_options] -addopts = "--numprocesses='auto'" - [tool.ruff] fix = true line-length = 100 diff --git a/src/bikes/configs.py b/src/bikes/configs.py index d5d9184..2d36200 100644 --- a/src/bikes/configs.py +++ b/src/bikes/configs.py @@ -1,10 +1,9 @@ -"""Parse, merge, and convert YAML configs.""" +"""Parse, merge, and convert config objects.""" # %% IMPORTS import typing as T -from cloudpathlib import AnyPath from omegaconf import DictConfig, ListConfig, OmegaConf # %% TYPES @@ -18,22 +17,19 @@ def parse_file(path: str) -> Config: """Parse a config file from a path. Args: - path (str): local or remote path. + path (str): path to local config. Returns: Config: representation of the config file. """ - any_path = AnyPath(path) - text = any_path.read_text() # type: ignore - config = OmegaConf.create(text) - return config + return OmegaConf.load(path) def parse_string(string: str) -> Config: """Parse the given config string. Args: - string (str): configuration string. + string (str): content of config string. Returns: Config: representation of the config string. @@ -45,10 +41,10 @@ def parse_string(string: str) -> Config: def merge_configs(configs: T.Sequence[Config]) -> Config: - """Merge a list of config objects into one. + """Merge a list of config into a single config. Args: - configs (list[Config]): list of config objects. + configs (T.Sequence[Config]): list of configs. Returns: Config: representation of the merged config objects. @@ -59,13 +55,14 @@ def merge_configs(configs: T.Sequence[Config]) -> Config: # %% CONVERTERS -def to_object(config: Config) -> object: +def to_object(config: Config, resolve: bool = True) -> object: """Convert a config object to a python object. Args: config (Config): representation of the config. + resolve (bool): resolve variables. Defaults to True. Returns: object: conversion of the config to a python object. """ - return OmegaConf.to_container(config, resolve=True) + return OmegaConf.to_container(config, resolve=resolve) diff --git a/src/bikes/datasets.py b/src/bikes/datasets.py index 3db6be4..095216c 100644 --- a/src/bikes/datasets.py +++ b/src/bikes/datasets.py @@ -38,7 +38,7 @@ class ParquetReader(Reader): """Read a dataframe from a parquet file. Attributes: - path (str): local or remote path to a dataset. + path (str): local path to the dataset. """ KIND: T.Literal["ParquetReader"] = "ParquetReader" @@ -47,6 +47,7 @@ class ParquetReader(Reader): @T.override def read(self) -> pd.DataFrame: + # can't limit rows at read time data = pd.read_parquet(self.path) if self.limit is not None: data = data.head(self.limit) @@ -80,7 +81,7 @@ class ParquetWriter(Writer): """Writer a dataframe to a parquet file. Attributes: - path (str): local or remote file to a dataset. + path (str): local path to the dataset. """ KIND: T.Literal["ParquetWriter"] = "ParquetWriter" diff --git a/src/bikes/metrics.py b/src/bikes/metrics.py index c7706e3..318c836 100644 --- a/src/bikes/metrics.py +++ b/src/bikes/metrics.py @@ -17,7 +17,7 @@ class Metric(abc.ABC, pdt.BaseModel, strict=True): """Base class for a metric. Use metrics to evaluate model performance. - e.g., accuracy, precision, recall, mae, f1, ... + e.g., accuracy, precision, recall, MAE, F1, ... Attributes: name (str): name of the metric. @@ -36,7 +36,7 @@ def score(self, targets: schemas.Targets, outputs: schemas.Outputs) -> float: outputs (schemas.Outputs): predicted values. Returns: - float: metric result. + float: single result for the metric computation. """ def scorer( @@ -77,7 +77,7 @@ def score(self, targets: schemas.Targets, outputs: schemas.Outputs) -> float: y_true = targets[schemas.TargetsSchema.cnt] y_pred = outputs[schemas.OutputsSchema.prediction] score = metric(y_pred=y_pred, y_true=y_true) * sign - return score + return float(score) MetricKind = SklearnMetric diff --git a/src/bikes/models.py b/src/bikes/models.py index afad913..078b55c 100644 --- a/src/bikes/models.py +++ b/src/bikes/models.py @@ -78,7 +78,7 @@ def predict(self, inputs: schemas.Inputs) -> schemas.Outputs: class BaselineSklearnModel(Model): - """Simple baseline model built on top of sklearn. + """Simple baseline model with sklearn. Attributes: max_depth (int): maximum depth of the random forest. @@ -143,7 +143,7 @@ def fit(self, inputs: schemas.Inputs, targets: schemas.Targets) -> "BaselineSkle @T.override def predict(self, inputs: schemas.Inputs) -> schemas.Outputs: assert self._pipeline is not None, "Model should be fitted first!" - prediction = self._pipeline.predict(inputs) # return an np.ndarray, not a dataframe! + prediction = self._pipeline.predict(inputs) # return an np.ndarray outputs = schemas.Outputs( {schemas.OutputsSchema.prediction: prediction}, index=inputs.index ) diff --git a/src/bikes/schemas.py b/src/bikes/schemas.py index 62193b5..54283ea 100644 --- a/src/bikes/schemas.py +++ b/src/bikes/schemas.py @@ -2,6 +2,8 @@ # %% IMPORTS +import typing as T + import pandas as pd import pandera as pa import pandera.typing as papd @@ -28,8 +30,8 @@ class Config: strict: bool = True @classmethod - def check(cls, data: pd.DataFrame, **kwargs): - """Check the data with this schema. + def check(cls, data: pd.DataFrame, **kwargs: T.Any) -> T.Any: + """Check the dataframe with this schema. Args: data (pd.DataFrame): dataframe to check. diff --git a/src/bikes/services.py b/src/bikes/services.py index 1485e74..aa477f8 100644 --- a/src/bikes/services.py +++ b/src/bikes/services.py @@ -83,6 +83,8 @@ def start(self) -> None: class CarbonService(Service): """Service for tracking carbon emissions. + https://mlco2.github.io/codecarbon/parameters.html + Attributes: log_level (str): Level of logging to output. project_name (str): Name of the project to track. @@ -97,6 +99,7 @@ class CarbonService(Service): # - inputs log_level: str = "ERROR" project_name: str = "bikes" + tracking_mode: str = "machine" measure_power_secs: int = 5 # - outputs output_dir: str = "outputs" @@ -107,13 +110,15 @@ class CarbonService(Service): # private _tracker: cc.OfflineEmissionsTracker | None = None - def start(self): + @T.override + def start(self) -> None: """Start the carbon service.""" - os.makedirs(self.output_dir, exist_ok=True) # create output dir - self._tracker = cc.OfflineEmissionsTracker(**self.model_dump()) + params = self.model_dump() + os.makedirs(self.output_dir, exist_ok=True) + self._tracker = cc.OfflineEmissionsTracker(**params) self._tracker.start() - def stop(self): + def stop(self) -> None: """Stop the carbon service.""" assert self._tracker, "Carbon tracker should be started!" self._tracker.flush() @@ -151,13 +156,16 @@ class MLflowService(Service): # system enable_system_metrics: bool = True # tracking - tracking_uri: str = "http://localhost:5000" + # tracking_uri: str = "http://localhost:5000" + tracking_uri: str = "./mlruns" experiment_name: str = "bikes" # registry - registry_uri: str = "http://localhost:5000" + # registry_uri: str = "http://localhost:5000" + registry_uri: str = "./mlruns" registry_name: str = "bikes" - def start(self): + @T.override + def start(self) -> None: """Start the mlflow service.""" # uri mlflow.set_tracking_uri(uri=self.tracking_uri) diff --git a/tasks/__init__.py b/tasks/__init__.py index 26f3ad6..f5ec5a1 100644 --- a/tasks/__init__.py +++ b/tasks/__init__.py @@ -6,7 +6,7 @@ from invoke import Collection -from . import carbons, checks, cleans, containers, dags, docs, formats, installs, packages +from . import carbons, checks, cleans, commits, containers, dags, docs, formats, installs, packages # %% NAMESPACES @@ -17,8 +17,9 @@ ns.add_collection(carbons) ns.add_collection(checks) ns.add_collection(cleans) -ns.add_collection(dags, default=True) +ns.add_collection(commits) ns.add_collection(containers) +ns.add_collection(dags, default=True) ns.add_collection(docs) ns.add_collection(formats) ns.add_collection(installs) diff --git a/tasks/carbons.py b/tasks/carbons.py index 8873991..82c0684 100644 --- a/tasks/carbons.py +++ b/tasks/carbons.py @@ -10,7 +10,7 @@ @task def board(ctx: Context, filepath: str = "outputs/emissions.csv", port: int = 8050) -> None: - """Visualize caron emissions data at file path from the carbon board app.""" + """Visualize carbon emissions data from file path with the carbon board app.""" ctx.run(f"poetry run carbonboard --filepath={filepath} --port={port}") diff --git a/tasks/checks.py b/tasks/checks.py index a3f53fb..bd78698 100644 --- a/tasks/checks.py +++ b/tasks/checks.py @@ -5,10 +5,6 @@ from invoke import task from invoke.context import Context -# %% CONFIGS - -COVERAGE_FAIL_UNDER = 80 - # %% TASKS @@ -39,15 +35,21 @@ def code(ctx: Context) -> None: @task def test(ctx: Context) -> None: """Check the tests with pytest.""" - ctx.run("poetry run pytest tests/") + ctx.run("poetry run pytest --numprocesses='auto' tests/") + + +@task +def bandit(ctx: Context) -> None: + """Check the security with bandit.""" + ctx.run("poetry run bandit --recursive --configfile=pyproject.toml src/") @task def coverage(ctx: Context) -> None: """Check the coverage with coverage.""" - ctx.run(f"poetry run pytest --cov=src/ --cov-fail-under={COVERAGE_FAIL_UNDER} tests/") + ctx.run(f"poetry run pytest --numprocesses='auto' --cov=src/ tests/") -@task(pre=[poetry, format, type, code, coverage], default=True) +@task(pre=[poetry, format, type, code, bandit, coverage], default=True) def all(_: Context) -> None: """Run all check tasks.""" diff --git a/tasks/cleans.py b/tasks/cleans.py index d455d0f..0e6f220 100644 --- a/tasks/cleans.py +++ b/tasks/cleans.py @@ -19,7 +19,7 @@ def mypy(ctx: Context) -> None: @task def ruff(ctx: Context) -> None: """Clean the ruff tool.""" - ctx.run("ruff clean") + ctx.run("rm -rf .ruff_cache/") @task diff --git a/tasks/commits.py b/tasks/commits.py new file mode 100644 index 0000000..2ef2400 --- /dev/null +++ b/tasks/commits.py @@ -0,0 +1,31 @@ +"""Commits tasks for pyinvoke.""" + +# %% IMPORTS + +from invoke import task +from invoke.context import Context + +# %% TASKS + + +@task +def info(ctx: Context) -> None: + """Print a guide for messages.""" + ctx.run("poetry run cz info") + + +@task +def bump(ctx: Context) -> None: + """Bump the version of the package.""" + ctx.run("poetry run cz bump", pty=True) + + +@task +def commit(ctx: Context) -> None: + """Commit all changes with a message.""" + ctx.run("poetry run cz commit", pty=True) + + +@task(pre=[commit], default=True) +def all(_: Context) -> None: + """Run all commit tasks.""" diff --git a/tasks/containers.py b/tasks/containers.py index 4b65154..f1714c8 100644 --- a/tasks/containers.py +++ b/tasks/containers.py @@ -1,4 +1,4 @@ -"""Docker tasks for pyinvoke.""" +"""Container tasks for pyinvoke.""" # %% IMPORTS @@ -16,22 +16,22 @@ @task def compose(ctx: Context) -> None: - """Start docker compose.""" + """Start up docker compose.""" ctx.run("docker compose up") @task(pre=[packages.build]) -def build(ctx: Context) -> None: - """Build the container image.""" - ctx.run(f"docker build -t {ctx.project.name}:{IMAGE_TAG} .") +def build(ctx: Context, tag: str = IMAGE_TAG) -> None: + """Build the container image with the given tag.""" + ctx.run(f"docker build --tag={ctx.project.name}:{tag} .") @task -def run(ctx: Context) -> None: - """Run the container image.""" - ctx.run(f"docker run --rm {ctx.project.name}:{IMAGE_TAG}") +def run(ctx: Context, tag: str = IMAGE_TAG) -> None: + """Run the container image with the given tag.""" + ctx.run(f"docker run --rm {ctx.project.name}:{tag}") -@task(pre=[build], default=True) +@task(pre=[build, run], default=True) def all(_: Context) -> None: """Run all container tasks.""" diff --git a/tasks/docs.py b/tasks/docs.py index d18d656..a3d8da1 100644 --- a/tasks/docs.py +++ b/tasks/docs.py @@ -16,17 +16,17 @@ @task -def api(ctx: Context) -> None: - """Document the API with pdoc.""" - ctx.run( - f"poetry run pdoc --docformat={DOC_FORMAT} --output-directory={OUTPUT_DIR} src/{ctx.project.name}" - ) +def serve(ctx: Context, format: str = DOC_FORMAT, port: int = 8088) -> None: + """Serve the API docs with pdoc using the given format and computer port.""" + ctx.run(f"poetry run pdoc --docformat={format} --port={port} src/{ctx.project.name}") @task -def serve(ctx: Context) -> None: - """Document the API with pdoc.""" - ctx.run(f"poetry run pdoc --docformat={DOC_FORMAT} src/{ctx.project.name}") +def api(ctx: Context, format: str = DOC_FORMAT, output_dir: str = OUTPUT_DIR) -> None: + """Document the API with pdoc using the given format and output directory.""" + ctx.run( + f"poetry run pdoc --docformat={format} --output-directory={output_dir} src/{ctx.project.name}" + ) @task(pre=[cleans.docs, api], default=True) diff --git a/tasks/installs.py b/tasks/installs.py index f8f78bc..1bcce41 100644 --- a/tasks/installs.py +++ b/tasks/installs.py @@ -10,14 +10,15 @@ @task def poetry(ctx: Context) -> None: - """Run poetry install.""" + """Install poetry packages.""" ctx.run("poetry install") @task def pre_commit(ctx: Context) -> None: """Run pre-commit install.""" - ctx.run("poetry run pre-commit install") + ctx.run("poetry run pre-commit install --hook-type pre-push") + ctx.run("poetry run pre-commit install --hook-type commit-msg") @task(pre=[poetry, pre_commit], default=True) diff --git a/tasks/packages.py b/tasks/packages.py index fe6ddce..8bb2d54 100644 --- a/tasks/packages.py +++ b/tasks/packages.py @@ -15,9 +15,9 @@ @task(pre=[cleans.dist]) -def build(ctx: Context) -> None: - """Build a wheel package.""" - ctx.run(f"poetry build --format={BUILD_FORMAT}") +def build(ctx: Context, format: str = BUILD_FORMAT) -> None: + """Build a python package with the given format.""" + ctx.run(f"poetry build --format={format}") @task(pre=[build], default=True) diff --git a/tests/test_configs.py b/tests/test_configs.py index 7e85251..8d14498 100644 --- a/tests/test_configs.py +++ b/tests/test_configs.py @@ -5,10 +5,10 @@ from bikes import configs from omegaconf import OmegaConf -# %% LOADERS +# %% PARSERS -def test_parse_file(tmp_path: str): +def test_parse_file(tmp_path: str) -> None: # given text = """ a: 1 @@ -28,7 +28,7 @@ def test_parse_file(tmp_path: str): }, "File config should be loaded correctly!" -def test_parse_string(): +def test_parse_string() -> None: # given text = """{"a": 1, "b": 2, "data": [3, 4]}""" # when @@ -41,7 +41,10 @@ def test_parse_string(): }, "String config should be loaded correctly!" -def test_merge_configs(): +# %% MERGERS + + +def test_merge_configs() -> None: # given confs = [OmegaConf.create({"x": i, i: i}) for i in range(3)] # when @@ -58,7 +61,7 @@ def test_merge_configs(): # %% CONVERTERS -def test_to_object(): +def test_to_object() -> None: # given values = { "a": 1, diff --git a/tests/test_datasets.py b/tests/test_datasets.py index 14c8d86..f4b6d7b 100644 --- a/tests/test_datasets.py +++ b/tests/test_datasets.py @@ -9,7 +9,7 @@ @pytest.mark.parametrize("limit", [None, 50]) -def test_parquet_reader(limit: int | None, inputs_path: str): +def test_parquet_reader(limit: int | None, inputs_path: str) -> None: # given reader = datasets.ParquetReader(path=inputs_path, limit=limit) # when @@ -23,7 +23,7 @@ def test_parquet_reader(limit: int | None, inputs_path: str): # %% WRITERS -def test_parquet_writer(targets: schemas.Targets, tmp_outputs_path: str): +def test_parquet_writer(targets: schemas.Targets, tmp_outputs_path: str) -> None: # given writer = datasets.ParquetWriter(path=tmp_outputs_path) # when diff --git a/tests/test_jobs.py b/tests/test_jobs.py index 3fc8bc1..04650f6 100644 --- a/tests/test_jobs.py +++ b/tests/test_jobs.py @@ -18,7 +18,7 @@ def test_tuning_job( logger_service: services.LoggerService, carbon_service: services.CarbonService, mlflow_service: services.MLflowService, -): +) -> None: # given run_name = "TuningTest" job = jobs.TuningJob( @@ -85,7 +85,7 @@ def test_training_job( logger_service: services.LoggerService, carbon_service: services.CarbonService, mlflow_service: services.MLflowService, -): +) -> None: # given run_name = "TrainingTest" scorers = [default_metric] @@ -193,7 +193,7 @@ def test_inference_job( logger_service: services.LoggerService, carbon_service: services.CarbonService, mlflow_service: services.MLflowService, -): +) -> None: # given registry_alias = "Testing" job = jobs.InferenceJob( diff --git a/tests/test_metrics.py b/tests/test_metrics.py index e6fe617..05b6fa8 100644 --- a/tests/test_metrics.py +++ b/tests/test_metrics.py @@ -17,11 +17,11 @@ def test_sklearn_metric( name: str, interval: tuple[int, int], greater_is_better: bool, - default_model: models.Model, inputs: schemas.Inputs, targets: schemas.Targets, outputs: schemas.Outputs, -): + default_model: models.Model, +) -> None: # given low, high = interval metric = metrics.SklearnMetric(name=name, greater_is_better=greater_is_better) diff --git a/tests/test_models.py b/tests/test_models.py index dd5fdaf..adea3c1 100644 --- a/tests/test_models.py +++ b/tests/test_models.py @@ -7,9 +7,9 @@ # %% MODELS -def test_model(): +def test_model() -> None: # given - class MyModel(models.Model): + class MyModel(models.Model): # type: ignore KIND: T.Literal["MyModel"] = "MyModel" # public @@ -18,10 +18,10 @@ class MyModel(models.Model): # private _c: int = 3 - def fit(self, inputs, targets): - pass + def fit(self, inputs: schemas.Inputs, targets: schemas.Targets) -> T.Self: + return self - def predict(self, inputs): + def predict(self, inputs: schemas.Inputs) -> schemas.Outputs: pass # when @@ -38,7 +38,7 @@ def predict(self, inputs): def test_baseline_sklearn_model( train_test_sets: tuple[schemas.Inputs, schemas.Targets, schemas.Inputs, schemas.Targets], -): +) -> None: # given params = {"max_depth": 3, "n_estimators": 5, "random_state": 0} inputs_train, targets_train, inputs_test, _ = train_test_sets diff --git a/tests/test_registers.py b/tests/test_registers.py index eae3bb5..0ca7ed9 100644 --- a/tests/test_registers.py +++ b/tests/test_registers.py @@ -8,7 +8,7 @@ # %% ADAPTERS -def test_custom_adapter(default_model: models.Model, inputs: schemas.Inputs): +def test_custom_adapter(default_model: models.Model, inputs: schemas.Inputs) -> None: # given adapter = registers.CustomAdapter(model=default_model) # when @@ -20,7 +20,7 @@ def test_custom_adapter(default_model: models.Model, inputs: schemas.Inputs): # %% SIGNERS -def test_infer_signer(inputs: schemas.Inputs, outputs: schemas.Outputs): +def test_infer_signer(inputs: schemas.Inputs, outputs: schemas.Outputs) -> None: # given signer = registers.InferSigner() # when @@ -39,7 +39,7 @@ def test_infer_signer(inputs: schemas.Inputs, outputs: schemas.Outputs): def test_custom_saver( inputs: schemas.Inputs, default_model: models.Model, default_signature: registers.Signature -): +) -> None: # given path = "custom" saver = registers.CustomSaver(path=path) @@ -60,7 +60,7 @@ def test_custom_loader( inputs: schemas.Inputs, mlflow_service: services.MLflowService, default_mlflow_model_version: registers.Version, -): +) -> None: # given name = mlflow_service.registry_name version = default_mlflow_model_version.version diff --git a/tests/test_schemas.py b/tests/test_schemas.py index f26ef83..a64cfc3 100644 --- a/tests/test_schemas.py +++ b/tests/test_schemas.py @@ -5,7 +5,7 @@ # %% SCHEMAS -def test_inputs_schema(inputs_reader: datasets.Reader): +def test_inputs_schema(inputs_reader: datasets.Reader) -> None: # given schema = schemas.InputsSchema # when @@ -14,7 +14,7 @@ def test_inputs_schema(inputs_reader: datasets.Reader): assert schema.check(data) is not None, "Inputs data should be valid!" -def test_targets_schema(targets_reader: datasets.Reader): +def test_targets_schema(targets_reader: datasets.Reader) -> None: # given schema = schemas.TargetsSchema # when @@ -23,7 +23,7 @@ def test_targets_schema(targets_reader: datasets.Reader): assert schema.check(data) is not None, "Targets data should be valid!" -def test_output_schema(outputs_reader: datasets.Reader): +def test_output_schema(outputs_reader: datasets.Reader) -> None: # given schema = schemas.OutputsSchema # when diff --git a/tests/test_scripts.py b/tests/test_scripts.py index 80e408e..0170c4f 100644 --- a/tests/test_scripts.py +++ b/tests/test_scripts.py @@ -2,6 +2,7 @@ import json import os +import typing as T import pytest from bikes import scripts @@ -9,7 +10,7 @@ # %% SCRIPTS -def test_schema(capsys): +def test_schema(capsys: T.Any) -> None: # given argv = ["prog", "--schema"] # when @@ -29,7 +30,7 @@ def test_schema(capsys): pytest.param("invalid", marks=pytest.mark.xfail), ], ) -def test_main(scenario: str, confs_path: str, extra_config: str): +def test_main(scenario: str, confs_path: str, extra_config: str) -> None: # given root = os.path.join(confs_path, scenario) # when diff --git a/tests/test_searchers.py b/tests/test_searchers.py index d0821a0..161a61c 100644 --- a/tests/test_searchers.py +++ b/tests/test_searchers.py @@ -11,7 +11,7 @@ def test_grid_cv_searcher( time_series_splitter: splitters.Splitter, inputs: schemas.Inputs, targets: schemas.Targets, -): +) -> None: # given param_grid = {"max_depth": [3, 5, 7]} searcher = searchers.GridCVSearcher(param_grid=param_grid) diff --git a/tests/test_services.py b/tests/test_services.py index 55a60c0..a8b2796 100644 --- a/tests/test_services.py +++ b/tests/test_services.py @@ -1,6 +1,7 @@ # %% IMPORTS import os +import typing as T import mlflow import pytest @@ -10,7 +11,7 @@ # %% SERVICES -def test_logger_service(capsys): +def test_logger_service(capsys: T.Any) -> None: # given service = services.LoggerService(sink="stdout", level="INFO") # when @@ -24,7 +25,7 @@ def test_logger_service(capsys): assert "DEBUG" not in capture.out, "Debug should not be logged!" -def test_carbon_service(tmp_carbon_path: str): +def test_carbon_service(tmp_carbon_path: str) -> None: # given output_dir = tmp_carbon_path output_file = "emissions-test.csv" @@ -39,7 +40,9 @@ def test_carbon_service(tmp_carbon_path: str): @pytest.mark.parametrize("enable_system_metrics", [True, False]) -def test_mlflow_service(enable_system_metrics: bool, mlflow_service: services.MLflowService): +def test_mlflow_service( + enable_system_metrics: bool, mlflow_service: services.MLflowService +) -> None: # given service = mlflow_service service.enable_system_metrics = enable_system_metrics diff --git a/tests/test_splitters.py b/tests/test_splitters.py index 611f379..46a0ea6 100644 --- a/tests/test_splitters.py +++ b/tests/test_splitters.py @@ -5,7 +5,7 @@ # %% SPLITTERS -def test_train_test_splitter(inputs: schemas.Inputs, targets: schemas.Targets): +def test_train_test_splitter(inputs: schemas.Inputs, targets: schemas.Targets) -> None: # given shuffle = True test_size = 50 @@ -27,7 +27,7 @@ def test_train_test_splitter(inputs: schemas.Inputs, targets: schemas.Targets): assert not inputs.iloc[train_index].empty, "Train index should be a subset of the inputs!" -def test_time_series_splitter(inputs: schemas.Inputs, targets: schemas.Targets): +def test_time_series_splitter(inputs: schemas.Inputs, targets: schemas.Targets) -> None: # given gap = 0 n_splits = 3