diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 906cfa26c05a62a1c0b8ceac7c8b1146d85c5fff..2c845cd3fce1bcc5ea4050bad349a96e4b88ee47 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 9665293c6faa57f591a5cd357accce22050be4cc..0000000000000000000000000000000000000000 --- 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 a2d2a784ac40b6efe8587c284c6191e370028fde..0000000000000000000000000000000000000000 --- 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 900b047e7b1602ad39d253eafb94cd85c31eaf69..d52e28bcb202765037b95bf92dd16f5cddd55f85 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 0000000000000000000000000000000000000000..33c2c8a0d01d6d2aac1e871593da4e4edbf945b3 --- /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 9c8c44b77b1a2996548f3cf24ae6b25428e06c57..bb91a4d5103d04661b1cd9c66df88f3780c715ef 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)