From c3debb20e4736299038ca83d94ef3d71038d3fcf Mon Sep 17 00:00:00 2001
From: Mate Balajti <mate.balajti@unibas.ch>
Date: Tue, 19 Sep 2023 12:41:55 +0000
Subject: [PATCH] refactor: update setup.py, delete files
---
.gitlab-ci.yml | 7 +++----
Dockerfile | 9 ---------
environment.yml | 19 -------------------
setup.py | 2 +-
tests/__init__.py | 1 +
tests/test_exon_concatenation.py | 16 +++++++++++++---
6 files changed, 18 insertions(+), 36 deletions(-)
delete mode 100644 Dockerfile
delete mode 100644 environment.yml
create mode 100644 tests/__init__.py
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 906cfa2..2c845cd 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -13,7 +13,6 @@ build-job: # First stage deployment and installation of dependencies.
- pip install -r requirements.txt
- pip install -r requirements_dev.txt
- pip install -e .
- - echo "Dependencies successfully deployed."
unit-test-job: # This job runs in the test stage.
stage: test # It only starts when the job in the build stage completes successfully.
@@ -30,6 +29,6 @@ lint-test-job: # Test Stage
- pip install -r requirements.txt
- pip install -r requirements_dev.txt
- pip install -e .
- - flake8 --docstring-convention google sequence_extractor/
- - pylint sequence_extractor/
- - mypy sequence_extractor/
+ - flake8 --docstring-convention google sequence_extractor/ tests/
+ - pylint sequence_extractor/ tests/
+ - mypy sequence_extractor/ tests/
diff --git a/Dockerfile b/Dockerfile
deleted file mode 100644
index 9665293..0000000
--- a/Dockerfile
+++ /dev/null
@@ -1,9 +0,0 @@
-FROM python:3.10-slim-buster
-
-MAINTAINER Samuel Mondal
-
-ENV PATH=$PATH:/usr/local/
-
-COPY . .
-
-RUN pip install -e .
diff --git a/environment.yml b/environment.yml
deleted file mode 100644
index a2d2a78..0000000
--- a/environment.yml
+++ /dev/null
@@ -1,19 +0,0 @@
-name: transcript-sequence-extractor
-channels:
- - defaults
- - conda-forge
- - bioconda
-dependencies:
- - python=3.10
- - pandas=1.5
- - numpy=1.23
- - gtfparse=1.2
- - pip=22.3
- - pytest=7.2
- - coverage=6.5
- - black=22.10
- - flake8=6.0
- - flake8-docstrings=1.6
- - mypy=0.991
- - pylint=2.15
- - bedtools=2.30
diff --git a/setup.py b/setup.py
index 900b047..d52e28b 100644
--- a/setup.py
+++ b/setup.py
@@ -1,6 +1,6 @@
"""Set up project."""
from pathlib import Path
-from setuptools import setup, find_packages
+from setuptools import setup, find_packages # type: ignore
project_root_dir = Path(__file__).parent.resolve()
with open(project_root_dir / "requirements.txt",
diff --git a/tests/__init__.py b/tests/__init__.py
new file mode 100644
index 0000000..33c2c8a
--- /dev/null
+++ b/tests/__init__.py
@@ -0,0 +1 @@
+"""Initalise tests."""
diff --git a/tests/test_exon_concatenation.py b/tests/test_exon_concatenation.py
index 9c8c44b..bb91a4d 100644
--- a/tests/test_exon_concatenation.py
+++ b/tests/test_exon_concatenation.py
@@ -12,8 +12,14 @@ def test_exon_concatenation():
"""Test exon_concatenation function."""
# Test for test_fasta_1
expected_fasta_1 = [
- (">ENST00000673477", "TTTCGCCTGCGCAGTGGTCCTGGCCACCGGCTCGCGGCGCGTGGAGGCTGCTCCCAGCCGCGCCCGAGTCAGACTCGGGTGGGGGTCCCGGTTACGCCAAGGAGGCCCTGAATCTGGCGCAGATGCAGGAGCAGACGCTGCAGTTGGAGCAACAGTCCAAGCTCAAA"),
- (">ENST00000378391", "AAATACTGACGGACGTGGAAGTGTCGCCCCAGGAAGGCTGCATCACAAAGTCTCCGAAGACCTGGGCAGTGAGAAGTTCTGCGTGGATGCAAATCAGGCGGGGG"),
+ (">ENST00000673477",
+ "TTTCGCCTGCGCAGTGGTCCTGGCCACCGGCTCGCGGCGCGTGGAGGCTGC"
+ "TCCCAGCCGCGCCCGAGTCAGACTCGGGTGGGGGTCCCGGTTACGCCAAGG"
+ "AGGCCCTGAATCTGGCGCAGATGCAGGAGCAGACGCTGCAGTTGGAGCAAC"
+ "AGTCCAAGCTCAAA"),
+ (">ENST00000378391",
+ "AAATACTGACGGACGTGGAAGTGTCGCCCCAGGAAGGCTGCATCACAAAGTC"
+ "TCCGAAGACCTGGGCAGTGAGAAGTTCTGCGTGGATGCAAATCAGGCGGGGG"),
]
result_fasta_1 = exon_concatenation(test_fasta_1)
@@ -21,7 +27,11 @@ def test_exon_concatenation():
# Test for test_fasta_2
expected_fasta_2 = [
- (">ENST00000673477", "ACGGCTGGCACCTTGTTTGGGGAAGGATTCCGTGCCTTTGTGACAGACCGGGACAAAGTGACTGGCTGGGCTGACGCTGCTGGCTGTCGGGGTCTACTCAGCCAAGAATGCGATCAGCCGGCGGCTCCTCAGTCGACCCCAGGACGTGCTGGAGGGTGTTGTGCTTAGT"),
+ (">ENST00000673477",
+ "ACGGCTGGCACCTTGTTTGGGGAAGGATTCCGTGCCTTTGTGACAGACCGGGA"
+ "CAAAGTGACTGGCTGGGCTGACGCTGCTGGCTGTCGGGGTCTACTCAGCCAAG"
+ "AATGCGATCAGCCGGCGGCTCCTCAGTCGACCCCAGGACGTGCTGGAGGGTGT"
+ "TGTGCTTAGT"),
]
result_fasta_2 = exon_concatenation(test_fasta_2)
--
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