.pre-commit-config.yaml

repos:

  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v3.4.0
    hooks:
      - id: trailing-whitespace
        exclude: ^tests/resources/
      - id: end-of-file-fixer
        exclude: ^tests/resources/
      - id: check-yaml
        args: ["--unsafe"]
      - id: check-added-large-files
      - id: check-ast
      - id: check-json
      - id: debug-statements
      - id: detect-aws-credentials
        args: [--allow-missing-credentials]
      - id: detect-private-key
      - id: check-merge-conflict
      - id: check-added-large-files
        args: ['--maxkb=3000']

  - repo: https://github.com/myint/autoflake
    rev: v1.4
    hooks:
      - id: autoflake
        name: Removes unused variables
        args:
          - --in-place
          - --remove-all-unused-imports
          - --expand-star-imports
          - --ignore-init-module-imports

  - repo: https://github.com/pre-commit/mirrors-isort
    rev: v5.10.1
    hooks:
      - id: isort
        name: Sorts imports
        args: [
          # Align isort with black formatting
          "--multi-line=3",
          "--trailing-comma",
          "--force-grid-wrap=0",
          "--use-parentheses",
          "--line-width=99",
        ]

  - repo: https://github.com/psf/black
    rev: 22.3.0
    hooks:
      - id: black
        name: Fixes formatting
        language_version: python3
        args: ["--line-length=99"]


  - repo: https://github.com/pycqa/flake8
    rev: 4.0.1
    hooks:
      - id: flake8
        name: Checks pep8 style
        args: [
          "--max-line-length=99",
          # Ignore imports in init files
          "--per-file-ignores=*/__init__.py:F401,setup.py:E121",
          # ignore long comments (E501), as long lines are formatted by black
          # ignore Whitespace before ':' (E203)
          # ignore Line break occurred before a binary operator (W503)
          "--ignore=E501,E203,W503",
        ]

  - repo: local
    hooks:
      - id: mypy
        name: Checking types
        entry: mypy
        language: system
        types: [ python ]


  - repo: local
    hooks:

      - id: jupyisort
        name: Sorts ipynb imports
        entry: jupytext --pipe-fmt ".py" --pipe "isort - --multi-line=3 --trailing-comma --force-grid-wrap=0 --use-parentheses --line-width=99" --sync
        files: \.ipynb$
        language: python

      - id: jupyblack
        name: Fixes ipynb format
        entry: jupytext --pipe-fmt ".py" --pipe "black - --line-length=99" --sync
        files: \.ipynb$
        language: python

      - id: nbconvert
        name: Removes ipynb content
        entry: jupyter nbconvert
        args:
          [
            "--ClearOutputPreprocessor.enabled=True",
            "--ClearMetadataPreprocessor.enabled=True",
            "--RegexRemovePreprocessor.enabled=True",
            "--to=notebook",
            "--log-level=ERROR",
            "--inplace",
          ]
        files: \.ipynb$
        language: python

gistfile1.txt

FROM docker-repo/rocky

ARG WORKDIR="/workdir"
ARG CONDA_NAME="api-service"

ENV CONDA_NAME=${CONDA_NAME}

USER root

RUN echo "${CONDA_NAME}"

# Setup environment
COPY environment.yml ${WORKDIR}/environment.yml
RUN conda update --all --quiet
RUN yum install libXext libSM libXrender -y # rdkit render dependencies
RUN mamba env create --name ${CONDA_NAME} -f ${WORKDIR}/environment.yml --quiet
RUN conda clean -afy

# Change default conda env
ENV CONDA_DEFAULT_ENV ${CONDA_NAME}
RUN echo "source activate ${CONDA_NAME}" > ~/.bashrc

# Change default conda didn't work, so overwrite path to look for python here
ENV PATH=/home/docker/anaconda/envs/${CONDA_NAME}/bin:${PATH}

# Copy source-code
COPY ./src ${WORKDIR}/src
COPY ./pyproject.toml ${WORKDIR}/pyproject.toml
COPY ./logging.yaml ${WORKDIR}/logging.yaml
COPY ./pytest.ini ${WORKDIR}/pytest.ini
COPY ./tests ${WORKDIR}/tests

RUN python -m pip install ${WORKDIR}

WORKDIR ${WORKDIR}

CMD ["-m", "uvicorn", "--host", "0.0.0.0", "--port", "80", "packagename.service.main:app", "--log-config", "logging.yaml"]

EXPOSE 80

Makefile

.PHONY: format test clean

DOCKERNAME=servicerapp
PACKAGE=packagename


all: env precommit

# Setup

env:
	mamba env create -f ./environment.yml -p ./env --quiet
	./env/bin/python -m pip install -e .

precommit:
	./env/bin/pre-commit install

# Commit work

format:
	pre-commit run --all-files

test:
	python -m pytest -vrs tests

test-cov-html:
	python -m pytest -vrs --cov=${PACKAGE} --cov-report html tests

test-docker:
	docker run --rm -it --entrypoint "pytest" ${DOCKERNAME}

# Build

build-docker:
	docker build -f ./docker/service.Dockerfile . -t ${DOCKERNAME}

# Work

start-api:
	python -m uvicorn \
	${PACKAGE}.service.main:app \
	--reload --port 5000 --log-config logging.dev.yaml

start-docker-api:
	docker run -p 8080:80 ${DOCKERNAME}

start-docker-bash:
	docker run --rm -it --entrypoint bash ${DOCKERNAME}

jupyter:
	jupyter lab

# Post work

clean:

clean-env:
	rm -rf ./env

pyproject.toml

[build-system]
requires = ["setuptools", "setuptools-scm"]
build-backend = "setuptools.build_meta"

[project]
name = "program_name"
dynamic = ["version"]
authors = [
    {name = "Jimmy Kromann", email = "jimmy.kromann@email.com"},
]
requires-python = ">=3.8"

[tool.setuptools.dynamic]
version = {attr = "packagename.__version__"}

[options.packages.find]
where="src"