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Commit 6bb2c59a authored by Christoph Harmel's avatar Christoph Harmel
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feat: updated CI, setup.py and requirements.txt

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2 merge requests!31Ci,!30feat: updated CI, setup.py and requirements.txt
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# This file is a template, and might need editing before it works on your project.
# This is a sample GitLab CI/CD configuration file that should run without any modifications.
# It demonstrates a basic 3 stage CI/CD pipeline. Instead of real tests or scripts,
# it uses echo commands to simulate the pipeline execution.
#
# A pipeline is composed of independent jobs that run scripts, grouped into stages.
# Stages run in sequential order, but jobs within stages run in parallel.
#
# For more information, see: https://docs.gitlab.com/ee/ci/yaml/index.html#stages
#
# You can copy and paste this template into a new `.gitlab-ci.yml` file.
# You should not add this template to an existing `.gitlab-ci.yml` file by using the `include:` keyword.
#
# To contribute improvements to CI/CD templates, please follow the Development guide at:
# https://docs.gitlab.com/ee/development/cicd/templates.html
# This specific template is located at:
# https://gitlab.com/gitlab-org/gitlab/-/blob/master/lib/gitlab/ci/templates/Getting-Started.gitlab-ci.yml
#default:
# tags:
# - docker
# image: python:3.10-slim-buster
default: # Set default
tags:
- docker
image: python:3.10-slim-buster
stages: # List of stages for jobs, and their order of execution
- build
......@@ -29,22 +11,20 @@ stages: # List of stages for jobs, and their order of execution
build-job: # This job runs in the build stage, which runs first.
stage: build
script:
- echo "Compiling the code..."
- echo "Compile complete."
- pip install requirements.txt requirements-dev.txt
- pip install -e .
unit-test-job: # This job runs in the test stage.
stage: test # It only starts when the job in the build stage completes successfully.
script:
- echo "Running unit tests... This will take about 60 seconds."
- sleep 60
- echo "Code coverage is 90%"
- coverage run --source readsequencer -m pytest
- coverage report -m
lint-test-job: # This job also runs in the test stage.
stage: test # It can run at the same time as unit-test-job (in parallel).
script:
- echo "Linting code... This will take about 10 seconds."
- sleep 10
- echo "No lint issues found."
- flake8 --docstring-convention google readsequencer/ tests/
- pylint readsequencer/ tests/
deploy-job: # This job runs in the deploy stage.
stage: deploy # It only runs when *both* jobs in the test stage complete successfully.
......
Bio
argparse
\ No newline at end of file
from setuptools import setup, find_packages
with open(project_root_dir / "requirements.txt", "r", encoding="utf-8") as _file:
INSTALL_REQUIRES = _file.read().splitlines()
setup(
name='readsequencer',
version='0.1.1',
......@@ -9,6 +12,6 @@ setup(
author_email='christoph.harmel@unibas.ch',
description='Simulates sequencing with a specified read length from sequences specified by a FASTA file.',
packages=find_packages(),
install_requires=['Bio','argparse'],
install_requires=INSTALL_REQUIRES,
entry_points={'console_scripts': ['readsequencer=readsequencer.cli:main']}
)
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