dockerfile addition

.gitlab-ci.yml

+default:         # Set default
+  tags:
+    - docker
+  image: python:3.10-slim-buster
+
+stages:          # List of employment runs, starts with build ends with deploy.
+  - build
+  - test
+
+build-job:       # First stage deployment and installation of dependencies.
+  stage: build   # Build Stage
+  script:
+    - pip install -r requirements.txt
+    - pip install -r requirements_dev.txt
+    - pip install -e .
+    - echo "Dependencies successfully deployed."
+
+lint-test-job:   # Test Stage
+  stage: test    # Deploys and runs all 3 linters.
+  script:
+    - flake8 --docstring-convention google sequence_extractor/ gtf_processing/
+    - pylint sequence_extractor/ gtf_processing/
+    - mypy sequence_extractor/ gtf_processing/

Dockerfile

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

tests/test_files/test_1.fa

+>ENST00000673477::1:1471765-1472089
+TTTCGCCTGCGCAGTGGTCCTGGCCACCGGCTCGCGGCGCGTGGAGGCTGCTCCCAGCCGCGCCCGAGTCAGACTCGGGTGGGGGTCCCGGCGGCGGTAGCGGCGGCGGCGGTGCGAGCATGTCGTGGCTCTTCGGCGTTAACAAGGGCCCCAAGGGTGAAGGCGCGGGGCCGCCGCCGCCTTTGCCGCCCGCGCAGCCCGGGGCCGAGGGCGGCGGGGACCGCGGTTTGGGAGACCGGCCGGCGCCCAAGGACAAATGGAGCAACTTCGACCCCACCGGCCTGGAGCGCGCCGCCAAGGCGGCGCGCGAGCTGGAGCACTCGC
+>ENST00000673477::1:1477274-1477350
+TTACGCCAAGGAGGCCCTGAATCTGGCGCAGATGCAGGAGCAGACGCTGCAGTTGGAGCAACAGTCCAAGCTCAAA
+>ENST00000378391::1:3244087-3244137
+AAATACTGACGGACGTGGAAGTGTCGCCCCAGGAAGGCTGCATCACAAAG
+>ENST00000378391::1:3385152-3385286
+TCTCCGAAGACCTGGGCAGTGAGAAGTTCTGCGTGGATGCAAATCAGGCGGGGGCTGGCAGCTGGCTCAAGTACATCCGTGTGGCGTGCTCCTGCGATGACCAGAACCTCACCATGTGTCAGATCAGTGAGCAG

tests/test_files/test_2.fa

+>ENST00000673477::1:1482545-1482614
+ACGGCTGGCACCTTGTTTGGGGAAGGATTCCGTGCCTTTGTGACAGACCGGGACAAAGTGACAGCCACG
+>ENST00000673477::1:1485016-1485171
+TGGCTGGGCTGACGCTGCTGGCTGTCGGGGTCTACTCAGCCAAGAATGCGACAGCCGTCACTGGCCGCTTCATCGAGGCTCGGCTGGGGAAGCCGTCCCTAGTGAGGGAGACGTCCCGCATCACGGTGCTGGAGGCGCTGCGGCACCCCATCCAG
+>ENST00000673477::1:1485782-1485838
+TCAGCCGGCGGCTCCTCAGTCGACCCCAGGACGTGCTGGAGGGTGTTGTGCTTAGT
+>ENST00000673477::1:1486110-1486235