diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml new file mode 100644 index 0000000000000000000000000000000000000000..a723cb2646f30787e15af359702cc3e992f0aeca --- /dev/null +++ b/.gitlab-ci.yml @@ -0,0 +1,23 @@ +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/ diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..9665293c6faa57f591a5cd357accce22050be4cc --- /dev/null +++ b/Dockerfile @@ -0,0 +1,9 @@ +FROM python:3.10-slim-buster + +MAINTAINER Samuel Mondal + +ENV PATH=$PATH:/usr/local/ + +COPY . . + +RUN pip install -e . diff --git a/tests/test_files/test_1.fa b/tests/test_files/test_1.fa new file mode 100644 index 0000000000000000000000000000000000000000..f92bb2b84f79e445dcda17c45ae0e6f34aa64c82 --- /dev/null +++ b/tests/test_files/test_1.fa @@ -0,0 +1,8 @@ +>ENST00000673477::1:1471765-1472089 +TTTCGCCTGCGCAGTGGTCCTGGCCACCGGCTCGCGGCGCGTGGAGGCTGCTCCCAGCCGCGCCCGAGTCAGACTCGGGTGGGGGTCCCGGCGGCGGTAGCGGCGGCGGCGGTGCGAGCATGTCGTGGCTCTTCGGCGTTAACAAGGGCCCCAAGGGTGAAGGCGCGGGGCCGCCGCCGCCTTTGCCGCCCGCGCAGCCCGGGGCCGAGGGCGGCGGGGACCGCGGTTTGGGAGACCGGCCGGCGCCCAAGGACAAATGGAGCAACTTCGACCCCACCGGCCTGGAGCGCGCCGCCAAGGCGGCGCGCGAGCTGGAGCACTCGC +>ENST00000673477::1:1477274-1477350 +TTACGCCAAGGAGGCCCTGAATCTGGCGCAGATGCAGGAGCAGACGCTGCAGTTGGAGCAACAGTCCAAGCTCAAA +>ENST00000378391::1:3244087-3244137 +AAATACTGACGGACGTGGAAGTGTCGCCCCAGGAAGGCTGCATCACAAAG +>ENST00000378391::1:3385152-3385286 +TCTCCGAAGACCTGGGCAGTGAGAAGTTCTGCGTGGATGCAAATCAGGCGGGGGCTGGCAGCTGGCTCAAGTACATCCGTGTGGCGTGCTCCTGCGATGACCAGAACCTCACCATGTGTCAGATCAGTGAGCAG diff --git a/tests/test_files/test_2.fa b/tests/test_files/test_2.fa new file mode 100644 index 0000000000000000000000000000000000000000..7b8ebb26c52072dc4431535d5a0eae56fee268ee --- /dev/null +++ b/tests/test_files/test_2.fa @@ -0,0 +1,7 @@ +>ENST00000673477::1:1482545-1482614 +ACGGCTGGCACCTTGTTTGGGGAAGGATTCCGTGCCTTTGTGACAGACCGGGACAAAGTGACAGCCACG +>ENST00000673477::1:1485016-1485171 +TGGCTGGGCTGACGCTGCTGGCTGTCGGGGTCTACTCAGCCAAGAATGCGACAGCCGTCACTGGCCGCTTCATCGAGGCTCGGCTGGGGAAGCCGTCCCTAGTGAGGGAGACGTCCCGCATCACGGTGCTGGAGGCGCTGCGGCACCCCATCCAG +>ENST00000673477::1:1485782-1485838 +TCAGCCGGCGGCTCCTCAGTCGACCCCAGGACGTGCTGGAGGGTGTTGTGCTTAGT +>ENST00000673477::1:1486110-1486235