test: Creation of a test suite #85
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style: formatting with isort & black
…hes--main--components--AmpliGone chore(main): release 1.3.1
chore: sync main to dev
test: tests/unit/ - added unit test for argument parsing, cutlery and fasta2bed test: tests/data/ - added files to GitHub LFS for testing purposes fix: .gitignore - added *:Zone.Identifier fix: improved static type checking, linting, and formatting for all files
feat: test-requirements- added seperate test reqs feat: .github.workflows.tests - created automatic testing workflow chore: __main__ - bandit B101 says that assert should not be used directly, because they are removed when compiling. chore: alignmentpreset - removed asserts (bandit B101) chore: args.py - removed asserts (bandit B101), and trailing whitespace chore: cut_reads - mypy didnt get the ignore comment chore: fasta2bed - no need to return chore: reports/ - linting reports for sonarcloud chore: test_e2e - bandit B101 chore: test_args - bandit B101 chore: test_cutlery - bandit B101 chore: test_fasta2bed - bandit B101 chore: .gitignore - removed coverage.xml so it goed in the reports folder
…a2bed. test: finished e2e tests
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There are some e2e tests that fail. While I did not find a solution for them yet, I am quite sure that they are not faulty tests but actual issues. |
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Major Update: Complete Test Suite Integration
This pull request introduces a comprehensive test suite, alongside minor improvements in the AmpliGone package to enhance static analysis and ease of testing. Below is a summary of the major new features included:
New GitHub Actions Workflow for Static Analysis and Testing
This workflow automates code quality checks and testing through the following steps:
Unit Tests for Core Modules
Detailed unit tests have been implemented for the following modules:
args.pycut_readscutleryfasta2bedEnd-to-End (E2E) Testing Framework
A modular and easily extendable framework to simulate real-world scenarios, currently covering:
.fastaand.bedprimer files.