first draft of tests + CI/CD

.gitlab-ci.yml

+default:         # Set default
+  tags:
+    - docker
+  image: python:3.10-slim-buster
+
+stages:          # List of stages for jobs, and their order of execution
+  - build
+  - test
+
+build-job:       # This job runs in the build stage, which runs first.
+  stage: build
+  script:
+    - pip install -r requirements.txt
+    - pip install -r requirements-dev.txt
+    - pip install -e .
+
+unit-test-job:   # This job runs in the test stage.
+  stage: test    # It only starts when the job in the build stage completes successfully.
+  script:
+    - pip install -r requirements.txt
+    - pip install -r requirements-dev.txt
+    - pip install -e .
+    - coverage run --source term_frag_sel -m pytest
+    - coverage report -m
+
+lint-test-job:   # This job also runs in the test stage.
+  stage: test    # It can run at the same time as unit-test-job (in parallel).
+  script:
+    - pip install -r requirements.txt
+    - pip install -r requirements-dev.txt
+    - pip install -e .
+    #- flake8 --docstring-convention google readsequencer/ tests/
+    #- pylint readsequencer/ tests/

term_frag_sel/cli.py

@@ -6,8 +6,8 @@ import numpy as np
 import pandas as pd
 from pathlib import Path
 
-from fragmentation import fragmentation
-from utils import check_positive, check_prob
+from term_frag_sel.fragmentation import fragmentation
+from term_frag_sel.utils import check_positive, check_prob
 
 
 def main(args: argparse.Namespace):
@@ -62,7 +62,7 @@ def file_validation(fasta_file: str,
     with open(fasta_file, "r") as handle:
         fasta = SeqIO.parse(handle, "fasta")
     if not any(fasta):
-        logger.exception("Input FASTA file is either empty or \
+        raise ValueError("Input FASTA file is either empty or \
             incorrect file type.")
 
     count_path = Path(counts_file)

term_frag_sel/utils.py

@@ -42,6 +42,6 @@ def check_prob(value: str) -> float:
     """
     pvalue = float(value)
     if pvalue <= 0 or pvalue > 1:
-        raise argparse.ArgumentTypeError("""%s is an invalid positive int
-                                         value""" % value)
+        raise argparse.ArgumentTypeError("""Expected a positive float between
+                                         0 and 1, but got {value}""")
     return pvalue

tests/test_cli.py

+"""Test cli.py functions."""
+import pytest
+from Bio import SeqIO
+
+from term_frag_sel.cli import file_validation
+
+with open("./test_files/test.fasta", "r") as handle:
+    fasta = SeqIO.parse(handle, "fasta")
+
+
+def test_file():
+    """Test check_positive function."""
+    assert file_validation(fasta, "", ",") == 1
+    with pytest.raises(FileNotFoundError):
+        file_validation("", "", ",")

tests/test_frag.py

+"""Test utils.py functions."""
+import pytest
+from Bio import SeqIO
+
+from term_frag_sel.fragmentation import fragmentation
+
+with open("./test_files/test.fasta", "r") as handle:
+    fasta = SeqIO.parse(handle, "fasta")
+
+# have to create the counts file
+
+mu = 100
+std = 10
+a_prob = 0.22
+c_prob = 0.28
+t_prob = 0.25
+g_prob = 0.25
+
+
+def test_frag():
+    """Test fragmentation function."""
+    with pytest.raises(TypeError):
+        fragmentation()

tests/test_utils.py

 """Test utils.py functions."""
 import pytest
+import argparse
 
-from 
+from term_frag_sel.utils import check_positive, check_prob
+
+
+def test_positive():
+    """Test check_positive function."""
+    assert check_positive("1") == 1
+    assert check_positive("100") == 100
+    assert check_positive("0") == 100
+    assert check_positive("2.2") == 2
+    assert check_positive("2.6") == 3
+    with pytest.raises(argparse.ArgumentTypeError):
+        check_positive("-1")
+    with pytest.raises(argparse.ArgumentTypeError):
+        check_positive("string")
+    with pytest.raises(argparse.ArgumentTypeError):
+        check_positive("")
+
+
+def test_prob():
+    """Test check_prob function."""
+    assert check_prob("0.1") == 0.1
+    assert check_prob("1") == 1.0
+    with pytest.raises(argparse.ArgumentTypeError):
+        check_prob("0")
+    with pytest.raises(argparse.ArgumentTypeError):
+        check_prob("10")
+    with pytest.raises(argparse.ArgumentTypeError):
+        check_prob("-1")
+    with pytest.raises(argparse.ArgumentTypeError):
+        check_prob("string")
+    with pytest.raises(argparse.ArgumentTypeError):
+        check_prob("")