feat: add CI and logging

.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 .
+
+# 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 .
+#     - coverage run --source primingsitepredictor -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 .
+    - flake8 --docstring-convention google primingsitepredictor/ # tests/
+    - pylint primingsitepredictor/ # tests/
+    - mypy primingsitepredictor/

img/Images_Max/images.txt

-pepe

primingsitepredictor/.idea/.gitignore

-# Default ignored files
-/shelf/
-/workspace.xml
-# Editor-based HTTP Client requests
-/httpRequests/
-# Datasource local storage ignored files
-/dataSources/
-/dataSources.local.xml

primingsitepredictor/.idea/inspectionProfiles/profiles_settings.xml

-<component name="InspectionProjectProfileManager">
-  <settings>
-    <option name="USE_PROJECT_PROFILE" value="false" />
-    <version value="1.0" />
-  </settings>
-</component>
\ No newline at end of file

primingsitepredictor/.idea/misc.xml

-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.10 (tests)" project-jdk-type="Python SDK" />
-</project>
\ No newline at end of file

primingsitepredictor/.idea/modules.xml

-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="ProjectModuleManager">
-    <modules>
-      <module fileurl="file://$PROJECT_DIR$/.idea/primingsitepredictor.iml" filepath="$PROJECT_DIR$/.idea/primingsitepredictor.iml" />
-    </modules>
-  </component>
-</project>
\ No newline at end of file

primingsitepredictor/.idea/primingsitepredictor.iml

-<?xml version="1.0" encoding="UTF-8"?>
-<module type="PYTHON_MODULE" version="4">
-  <component name="NewModuleRootManager">
-    <content url="file://$MODULE_DIR$" />
-    <orderEntry type="inheritedJdk" />
-    <orderEntry type="sourceFolder" forTests="false" />
-  </component>
-</module>
\ No newline at end of file

primingsitepredictor/.idea/vcs.xml

-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="VcsDirectoryMappings">
-    <mapping directory="$PROJECT_DIR$/.." vcs="Git" />
-  </component>
-</project>
\ No newline at end of file

primingsitepredictor/Primer1.fasta

-<primer1
-TTTTTTTTTTTTTTT

primingsitepredictor/__init__.py

+"""Initialize package."""

primingsitepredictor/cli.py

-# -*- coding: utf-8 -*-
-"""
-Changed on Fr Dec 23 16:49:50 2022
-
-@author: RobinC
-"""
+"""Receive command line arguments."""
 import argparse
 import logging
-import main
-
-class CLI():
-    def create_parser(self):
-        """This function creates the parser"""
-
-        parser = argparse.ArgumentParser(
-            prog = 'PrimingSitePredictor',
-            description = 'Takes a cutoff energy and the predicts location of priming sites of transcripts',
-            epilog = 'To predict or not to predict')
-        parser.add_argument('--float', type=float, required=True, help='A energy-cutoff float number')
-        parsed_args = parser.parse_args()
-        energy_cutoff = parsed_args.float
-        return energy_cutoff
-
-    def letsgo(self):
-        """This function creates a parser and prints the energycutoff"""
-        energy_cutoff = CLI.create_parser()
-        print(f"Your energy cutoff is {energy_cutoff}")
-
-if __name__ == '__main__':
+from primingsitepredictor.prime_site_predictor import CreatePrimer
+from primingsitepredictor.prime_site_predictor import PrimingSitePredictor
+
+LOG = logging.getLogger(__name__)
+
+
+def main():
+    """Use CLI arguments to predict priming sites."""
+    args = parse_args()
+    setup_logging()
+    LOG.info("Starting Priming Site Predictor...")
+
+    if args.primer_sequence is None:
+        primer = CreatePrimer().create_fasta()
+        args.primer_sequence = primer
+
+    predicted_sites = PrimingSitePredictor(
+        args.fasta_file, args.primer_sequence, args.energy_cutoff,
+        args.riblast_output, args.output_filename
+        )
+
+    predicted_sites.generate_gtf()
+
+    LOG.info("Priming Site Predictor finished.")
+
+
+def setup_logging() -> None:
+    """Configure logging.
+
+    Args:
+        verbosity: Level of logging verbosity.
+    """
     logging.basicConfig(
-        format='[%(asctime)s: %(levelname)s] %(message)s (module "%(module)s")',
+        format='[%(asctime)s: %(levelname)s] %(message)s \
+            (module "%(module)s")',
         level=logging.INFO,
+    )
+
+
+def parse_args():
+    """Parse arguments for CLI."""
+    parser = argparse.ArgumentParser(
+        description="Compute potential priming sites using RIBlast."
+        )
+    parser.add_argument(
+        "-f", "--fasta-file",
+        help="Fasta-formatted file of transcript sequences"
+        )
+    parser.add_argument(
+        "-p", "--primer-sequence", default=None,
+        help="Primer sequence"
         )
-    LOG = logging.getLogger(__name__)
+    parser.add_argument(
+        "-e", "--energy-cutoff", type=float,
+        help="Energy cutoff for interactions"
+        )
+    parser.add_argument(
+        "-r", "--riblast-output",
+        help="Path to RIBlast output file"
+        )
+    parser.add_argument(
+        "-o", "--output-filename",
+        help="Path where the output gtf should be written"
+        )
+    args = parser.parse_args()
+
+    return args
+
+
+if __name__ == "__main__":
     main()
 
+
+# def main():
+#     """Execute generate_RIBlast."""
+#     generate_riblast_input()
+
+
+# def generate_riblast_input():
+#     """Create a list of the filenames for the RIBlast."""
+#     my_primer = CreatePrimer()
+#     my_primer.create_fasta()
+#     primer_filename = my_primer.name + ".fasta"
+#     transcripts_filename = "transcripts.fasta"
+
+#     return [primer_filename, transcripts_filename]
+
+
+# def create_gtf():
+#     """Create gtf."""
+#     gtf_file = PostProcessRIBlast().output
+#     print(gtf_file)
+
+
+# def create_parser():
+#     """Create a parser."""
+#     parser = argparse.ArgumentParser(
+#         prog='PrimingSitePredictor',
+#         description='Takes a cutoff energy and the predicts \
+#             location of priming sites of transcripts',
+#         epilog='To predict or not to predict')
+#     parser.add_argument('--float', type=float, required=True,
+#                         help='An energy-cutoff float number')
+#     parsed_args = parser.parse_args()
+#     energy_cutoff = parsed_args.float
+#     return energy_cutoff
+
+
+# def letsgo():
+#     """Create a parser and print the energycutoff."""
+#     energy_cutoff = create_parser()
+#     print(f"Your energy cutoff is {energy_cutoff}")

primingsitepredictor/createprimer.py

-# -*- coding: utf-8 -*-
-"""
-Changed on Fr Dec 23 14:34:20 2022
-
-@author: RobinC
-"""
-
-class CreatePrimer:
-    """This Class creates an instance of a primer of a desired length and primer name
-    which can be saved as a fasta file. By default the length is 15 and name is primer1"""
-    def __init__(self, name='primer1', primerlength=15):
-        self.name = name
-        self.primer_length = primerlength
-        self.primer_sequence = 'T'*self.primer_length
-        self.lines = [f'<{self.name}', self.primer_sequence]
-
-    
-    def create_fasta(self):
-        with open(f'{self.name}.fasta', 'w') as f:
-            for line in self.lines:
-                f.write(line)
-                f.write('\n')
-
-
-
-

primingsitepredictor/main.py

-"""
-Changed on Tue Dec 20 14:06:20 2022
-
-@author: RobinC
-"""
-import sys
-from createprimer import CreatePrimer
-from postprocessing import PostProcessRIBlast
-
-
-def main():
-    generate_RIBlast_input()
-
-        
-
-def generate_RIBlast_input():
-    """This function creates a list of the filenames for the RIBlast"""
-    my_primer = CreatePrimer()
-    my_primer.create_fasta()
-    primer_filename = my_primer.name +".fasta"
-    transcripts_filename = "transcripts.fasta"
-    
-    return [primer_filename, transcripts_filename]
-
-def create_gtf():
-    gtf_file = PostProcessRIBlast().output
-    print(gtf_file)
-
-if __name__ == '__main__':
-    main()

primingsitepredictor/my_primer.fasta

-<my_primer
-TTTTTTTTTTTTTTTTTTTT