refactor: update setup.py, delete files

.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/

Dockerfile

-FROM python:3.10-slim-buster
-
-MAINTAINER Samuel Mondal
-
-ENV PATH=$PATH:/usr/local/
-
-COPY . .
-
-RUN pip install -e .

environment.yml

-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

setup.py

 """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",

tests/__init__.py

+"""Initalise tests."""

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)