From 680ef5967cc9ca457b1bcc5ca946085ecaaabf98 Mon Sep 17 00:00:00 2001
From: milnus <44769523+milnus@users.noreply.github.com>
Date: Thu, 9 Apr 2026 19:56:14 +0200
Subject: [PATCH 01/12] Fix depricated biopython Bio.applications

Use subprocess rather than depricated bio.applications from biopython
---
 .gitignore                            |  3 ++
 Magphi/.gitignore                     |  2 +-
 Magphi/__main__.py                    |  6 +--
 Magphi/search_insertion_sites.py      | 63 ++++++++++++---------------
 functional_tests/test_data/Magphi.log | 25 +++++++++++
 requirements-dev.txt                  |  3 +-
 requirements.txt                      |  3 +-
 setup.py                              |  5 ++-
 8 files changed, 67 insertions(+), 43 deletions(-)
 create mode 100644 functional_tests/test_data/Magphi.log

diff --git a/.gitignore b/.gitignore
index 914c268..d49d898 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,3 +7,6 @@ code_to_transfer/
 extractor.yml
 functional_tests/test_data/test_folder/
 venv/
+CLAUDE.md
+build/
+Magphi.egg-info/
diff --git a/Magphi/.gitignore b/Magphi/.gitignore
index 0d20b64..7e99e36 100644
--- a/Magphi/.gitignore
+++ b/Magphi/.gitignore
@@ -1 +1 @@
-*.pyc
+*.pyc
\ No newline at end of file
diff --git a/Magphi/__main__.py b/Magphi/__main__.py
index b461653..36cb6ae 100644
--- a/Magphi/__main__.py
+++ b/Magphi/__main__.py
@@ -16,9 +16,9 @@
 import logging
 from sys import argv
 from math import ceil
-import pkg_resources
 import concurrent.futures
 from tempfile import TemporaryDirectory
+from importlib.metadata import version, PackageNotFoundError
 
 try:
     from Magphi.commandline_interface import get_commandline_arguments
@@ -79,8 +79,8 @@
 
 
 try:
-    PROGRAM_VERSION = pkg_resources.require(PROGRAM_NAME)[0].version
-except pkg_resources.DistributionNotFound:
+    PROGRAM_VERSION = version(PROGRAM_NAME)
+except PackageNotFoundError:
     PROGRAM_VERSION = "undefined_version"
 
 
diff --git a/Magphi/search_insertion_sites.py b/Magphi/search_insertion_sites.py
index 55c45c6..eddfc74 100644
--- a/Magphi/search_insertion_sites.py
+++ b/Magphi/search_insertion_sites.py
@@ -6,11 +6,7 @@
 import gzip
 from itertools import combinations
 from shutil import copyfile, copyfileobj
-from Bio.Blast.Applications import NcbimakeblastdbCommandline
-from Bio.Blast.Applications import NcbitblastnCommandline
-from Bio.Blast.Applications import NcbiblastnCommandline
-from Bio.Sequencing.Applications import SamtoolsFaidxCommandline
-from Bio.Application import ApplicationError
+import subprocess
 from Bio import SearchIO
 from Bio.Seq import Seq, complement, reverse_complement
 import pybedtools as bedtools
@@ -24,7 +20,6 @@
     from Magphi.split_gff_file import split_single_gff
 except ModuleNotFoundError:
     from split_gff_file import split_single_gff
-# pylint: disable=E1123
 
 
 def tblastn_insertion_site(seeds, genome_file, tmp_name):
@@ -37,22 +32,20 @@ def tblastn_insertion_site(seeds, genome_file, tmp_name):
     """
     # Construct genome_db path and name
     genome_db = f'{genome_file}_tmp_db'
-    # Make blast database command for given genome
-    c_line_makedb = NcbimakeblastdbCommandline(dbtype='nucl', input_file=genome_file, out=genome_db)
-
-    # Run makeblastdb in command line
-    c_line_makedb()
+    # Make blast database command for given genome and run
+    subprocess.run(
+        ['makeblastdb', '-dbtype', 'nucl', '-in', genome_file, '-out', genome_db],
+        check=True, capture_output=True, text=True
+    )
 
     blast_out_xml = f'{tmp_name}.xml'
-    c_line = NcbitblastnCommandline(query=seeds,
-                                   db=genome_db,
-                                   evalue=0.001,
-                                   outfmt=5,
-                                   qcov_hsp_perc=50,
-                                   out=blast_out_xml)
-
     # Run the blast command in commandline blast
-    c_line()
+    subprocess.run(
+        ['tblastn', '-query', seeds, '-db', genome_db,
+         '-evalue', '0.001', '-outfmt', '5', '-qcov_hsp_perc', '50',
+         '-out', blast_out_xml],
+        check=True, capture_output=True, text=True
+    )
 
     # Delete blast database
     file_list = glob.glob(f'{genome_file}_tmp_db.*')
@@ -72,22 +65,20 @@ def blast_insertion_site(seeds, genome_file, tmp_name):
     """
     # Construct genome_db path and name
     genome_db = f'{genome_file}_tmp_db'
-    # Make blast database command for given genome
-    c_line_makedb = NcbimakeblastdbCommandline(dbtype='nucl', input_file=genome_file, out=genome_db)
-
-    # Run makeblastdb in command line
-    c_line_makedb()
+    # Make blast database command for given genome and run
+    subprocess.run(
+        ['makeblastdb', '-dbtype', 'nucl', '-in', genome_file, '-out', genome_db],
+        check=True, capture_output=True, text=True
+    )
 
     blast_out_xml = f'{tmp_name}.xml'
-    c_line = NcbiblastnCommandline(query=seeds,
-                                   db=genome_db,
-                                   evalue=0.001,
-                                   outfmt=5,
-                                   qcov_hsp_perc=50,
-                                   out=blast_out_xml)
-
     # Run the blast command in commandline blast
-    c_line()
+    subprocess.run(
+        ['blastn', '-query', seeds, '-db', genome_db,
+         '-evalue', '0.001', '-outfmt', '5', '-qcov_hsp_perc', '50',
+         '-out', blast_out_xml],
+        check=True, capture_output=True, text=True
+    )
 
     # Delete blast database
     file_list = glob.glob(f'{genome_file}_tmp_db.*')
@@ -428,10 +419,12 @@ def check_seeds_placement(bed_files, seed_pairs, seed_hits, max_seed_dist, genom
     :return: A genome file in the temporary directory and an evidence score for each bed file and its seed connections
     """
     # Produce genome index file using samtools
-    samtools_faidx_cmd = SamtoolsFaidxCommandline(ref=genome_file)
     try:
-        samtools_faidx_cmd()
-    except ApplicationError:
+        subprocess.run(
+            ['samtools', 'faidx', genome_file],
+            check=True, capture_output=True, text=True
+        )
+    except subprocess.CalledProcessError:
         exit_with_error(f"Samtools failed when running the command 'samtools faidx {genome_file}'", EXIT_INPUT_FILE_ERROR)
 
     # Initialise the dict to hold the support for a seed hit
diff --git a/functional_tests/test_data/Magphi.log b/functional_tests/test_data/Magphi.log
new file mode 100644
index 0000000..66c7394
--- /dev/null
+++ b/functional_tests/test_data/Magphi.log
@@ -0,0 +1,25 @@
+[2026-04-09T19:50:49+0200] INFO - __main__ - command line: /Users/magnus.jespersen/miniforge3/envs/Magphi/bin/Magphi -g test_fasta.fna test_GFF.gff -S -s empty_file
+[2026-04-09T19:50:50+0200] WARNING - __main__ - Some dependencies are untested version(s)
+[2026-04-09T19:50:50+0200] INFO - __main__ - Processing started
+[2026-04-09T19:50:50+0200] ERROR - check_inputs - Input files were found to be of mixed type with some being recognised as fasta!
+Please make sure that all your input files are only either Fasta or GFF3, not mixed
+[2026-04-09T19:50:51+0200] INFO - __main__ - command line: /Users/magnus.jespersen/miniforge3/envs/Magphi/bin/Magphi -g test_fasta.fna random_text.txt -S -s empty_file
+[2026-04-09T19:50:51+0200] WARNING - __main__ - Some dependencies are untested version(s)
+[2026-04-09T19:50:51+0200] INFO - __main__ - Processing started
+[2026-04-09T19:50:51+0200] ERROR - check_inputs - Input files were found to be of mixed type with some being recognised as fasta!
+Please make sure that all your input files are only either Fasta or GFF3, not mixed
+[2026-04-09T19:50:52+0200] INFO - __main__ - command line: /Users/magnus.jespersen/miniforge3/envs/Magphi/bin/Magphi -g test_GFF.gff random_text.txt -S -s empty_file
+[2026-04-09T19:50:52+0200] WARNING - __main__ - Some dependencies are untested version(s)
+[2026-04-09T19:50:52+0200] INFO - __main__ - Processing started
+[2026-04-09T19:50:52+0200] ERROR - check_inputs - Input files were found to be of mixed type with some being recognised as GFF!
+Please make sure that all your input files are only either Fasta or GFF3, not mixed
+[2026-04-09T19:50:52+0200] INFO - __main__ - command line: /Users/magnus.jespersen/miniforge3/envs/Magphi/bin/Magphi -g random_text.txt -S -s empty_file
+[2026-04-09T19:50:52+0200] WARNING - __main__ - Some dependencies are untested version(s)
+[2026-04-09T19:50:52+0200] INFO - __main__ - Processing started
+[2026-04-09T19:50:52+0200] ERROR - check_inputs - The given input files could not be recognised as either Fasta or GFF3 with a genome.
+NoneType: None
+[2026-04-09T19:50:53+0200] INFO - __main__ - command line: /Users/magnus.jespersen/miniforge3/envs/Magphi/bin/Magphi -g empty_file -S -s empty_file
+[2026-04-09T19:50:53+0200] WARNING - __main__ - Some dependencies are untested version(s)
+[2026-04-09T19:50:53+0200] INFO - __main__ - Processing started
+[2026-04-09T19:50:53+0200] ERROR - check_inputs - The given input files could not be recognised as either Fasta or GFF3 with a genome.
+NoneType: None
diff --git a/requirements-dev.txt b/requirements-dev.txt
index c54010e..d53e981 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -1,5 +1,6 @@
 # Dependencies, with versions explicitly declared for development and testing
-biopython>=1.79
+biopython>=1.87
 pybedtools==0.8.2
+setuptools
 # Packages that are not dependencies but used for building or testing
 pylint
diff --git a/requirements.txt b/requirements.txt
index 9a51a45..1da197c 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,5 +1,6 @@
 # Dependencies, with versions explicitly declared for development and testing
-biopython==1.79
+biopython==1.87
 pybedtools==0.8.2
+setuptools
 # Packages that are not dependencies but used for building or testing
 pylint
diff --git a/setup.py b/setup.py
index 87fdaa6..d6b95fb 100644
--- a/setup.py
+++ b/setup.py
@@ -24,8 +24,9 @@
     license='MIT license',
     description=('A bioinformatics tool allowing for examnination and extraction of genomic features using seed sequences.'),
     long_description=LONG_DESCRIPTION,
-    install_requires=['biopython>=1.79',
-                      'pybedtools==0.8.2'],
+    install_requires=['biopython>=1.87',
+                      'setuptools',
+                      'pybedtools>=0.12.0'],
     keywords=['Genomic', 'extraction', 'bacteria', 'prokaryotes', 'bioinformatics'],
     classifiers=[
         'Programming Language :: Python :: 3.9',

From f3be420521ac191fc3de7dc01fe4d28fb3eb7039 Mon Sep 17 00:00:00 2001
From: milnus <44769523+milnus@users.noreply.github.com>
Date: Thu, 9 Apr 2026 20:09:11 +0200
Subject: [PATCH 02/12] Update check_depencies.py

Improve dependency version check
---
 Magphi/check_depencies.py | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/Magphi/check_depencies.py b/Magphi/check_depencies.py
index 4630c93..0be271a 100644
--- a/Magphi/check_depencies.py
+++ b/Magphi/check_depencies.py
@@ -2,6 +2,8 @@
 import warnings
 import sys
 
+from packaging.version import Version
+
 try:
     from Magphi.exit_with_error import exit_with_error
 except ModuleNotFoundError:
@@ -20,10 +22,10 @@ def check_for_biopython(verbose):
         if verbose:
             print("Biopython was successfully found")
 
-        if float(Bio.__version__) >= 1.78:
+        if Version(Bio.__version__) >= Version('1.78'):
             if verbose:
                 print("Biopython version is valid")
-            return float(Bio.__version__)
+            return Bio.__version__
 
         warnings.warn('Biopython seems to be an untested version! Make sure it is version = 1.78 or above.')
         return False
@@ -44,7 +46,7 @@ def check_for_pybedtools(verbose):
         if verbose:
             print("pybedtools was successfully found")
 
-        if pybedtools.__version__ >= '0.8.2':
+        if Version(pybedtools.__version__) >= Version('0.8.2'):
             if verbose:
                 print("pybedtools version is valid")
             return pybedtools.__version__
@@ -72,7 +74,7 @@ def check_for_bedtools(verbose):
 
             cmd_return = subprocess.run(['bedtools', '-version'], capture_output=True)
             version = cmd_return.stdout.decode().rsplit('v', 1)[-1]
-            if version >= '2.29.2':
+            if Version(version) >= Version('2.29.2'):
                 if verbose:
                     print("Bedtools version is valid")
                 return version
@@ -111,7 +113,7 @@ def check_for_samtools(verbose):
             version = cmd_return.stdout.decode().split(' ', 1)[-1]
             version = version.split('\n', 1)[0]
 
-            if version >= '1.11':
+            if Version(version) >= Version('1.11'):
                 if verbose:
                     print("Samtools version is valid")
                 return version
@@ -149,7 +151,7 @@ def check_for_blast_plus(verbose=False):
             version = version.split(' ')[3]
             version = version.rsplit(',', 1)[0]
 
-            if version == '2.6.0' or version >= '2.11.0':
+            if Version(version) == Version('2.6.0') or Version(version) >= Version('2.11.0'):
                 if verbose:
                     print("Blast+ version is valid")
                 return version

From a732236336b8aab350d93a8c0c3a42de4adf0e18 Mon Sep 17 00:00:00 2001
From: milnus <44769523+milnus@users.noreply.github.com>
Date: Thu, 9 Apr 2026 20:09:30 +0200
Subject: [PATCH 03/12] Pump version

---
 setup.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index d6b95fb..b6ae16c 100644
--- a/setup.py
+++ b/setup.py
@@ -12,7 +12,7 @@
 
 setup(
     name='Magphi',
-    version='2.0.1',
+    version='2.0.3',
     author='Magnus Ganer Jespersen',
     author_email='magnus.ganer.j@gmail.com',
     packages=['Magphi'],
@@ -26,6 +26,7 @@
     long_description=LONG_DESCRIPTION,
     install_requires=['biopython>=1.87',
                       'setuptools',
+                      'packaging',
                       'pybedtools>=0.12.0'],
     keywords=['Genomic', 'extraction', 'bacteria', 'prokaryotes', 'bioinformatics'],
     classifiers=[

From 82e6d183cb626429a44ec777ff61bfcb1d0b36a7 Mon Sep 17 00:00:00 2001
From: milnus <44769523+milnus@users.noreply.github.com>
Date: Thu, 9 Apr 2026 20:34:42 +0200
Subject: [PATCH 04/12] Update CI workflows

---
 .github/workflows/Compile_paper.yml     |  4 +--
 .github/workflows/Mapghi_test_suite.yml | 16 ---------
 .github/workflows/build_n_publish.yml   | 29 +++++----------
 .github/workflows/test.yml              | 48 +++++++++++++++++++------
 .travis.yml                             | 18 ----------
 .travis/install-dependencies.sh         |  9 -----
 .travis/unit-test.sh                    | 23 ------------
 7 files changed, 48 insertions(+), 99 deletions(-)
 delete mode 100644 .github/workflows/Mapghi_test_suite.yml
 delete mode 100644 .travis.yml
 delete mode 100755 .travis/install-dependencies.sh
 delete mode 100755 .travis/unit-test.sh

diff --git a/.github/workflows/Compile_paper.yml b/.github/workflows/Compile_paper.yml
index 8535d32..4f94eb4 100644
--- a/.github/workflows/Compile_paper.yml
+++ b/.github/workflows/Compile_paper.yml
@@ -6,7 +6,7 @@ jobs:
     name: Paper Draft
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: Build draft PDF
         uses: openjournals/openjournals-draft-action@master
         with:
@@ -14,7 +14,7 @@ jobs:
           # This should be the path to the paper within your repo.
           paper-path: paper/paper.md
       - name: Upload
-        uses: actions/upload-artifact@v1
+        uses: actions/upload-artifact@v4
         with:
           name: paper
           # This is the output path where Pandoc will write the compiled
diff --git a/.github/workflows/Mapghi_test_suite.yml b/.github/workflows/Mapghi_test_suite.yml
deleted file mode 100644
index 81a125c..0000000
--- a/.github/workflows/Mapghi_test_suite.yml
+++ /dev/null
@@ -1,16 +0,0 @@
-name: 'Magphi_test_suite'
-on:
-  push:
-    branches:
-      - dev
-jobs:
-  build:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      - name: 'Build Docker image'
-        run: docker build -t magphi .
-      - name: 'Run unit tests'
-        run: docker run --entrypoint /Magphi/.travis/unit-test.sh magphi
-      - name: 'Run functional tests'
-        run: docker run --entrypoint /Magphi/functional_tests/Magphi-test.sh magphi -p Magphi -d /Magphi/functional_tests/test_data -v
diff --git a/.github/workflows/build_n_publish.yml b/.github/workflows/build_n_publish.yml
index b60aa50..a0f42d6 100644
--- a/.github/workflows/build_n_publish.yml
+++ b/.github/workflows/build_n_publish.yml
@@ -7,31 +7,18 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@main
+    - uses: actions/checkout@v4
     - name: Set up Python 3.9
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: '3.9'
+        cache: 'pip'
     - name: Install pypa/build
-      run: >-
-        python -m
-        pip install
-        build
-        --user
-    - name: Build a binary wheel and a source tarball
-      run: >-
-        python -m
-        build
-        --sdist
-        --wheel
-        --outdir dist/
-#    - name: Publish distribution 📦 to Test PyPI
-#      uses: pypa/gh-action-pypi-publish@master
-#      with:
-#        password: ${{ secrets.TEST_PYPI_TOKEN_CICD }}
-#        repository_url: https://test.pypi.org/legacy/
+      run: python -m pip install build --user
+    - name: Publish distribution 📦 to Test PyPI
+      run: python -m build --sdist --wheel --outdir dist/
     - name: Publish distribution 📦 to PyPI
       if: startsWith(github.ref, 'refs/tags')
-      uses: pypa/gh-action-pypi-publish@master
+      uses: pypa/gh-action-pypi-publish@release/v1
       with:
         password: ${{ secrets.PYPI_API_TOKEN_SECRET }}
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 3fda51b..e2b4de8 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -1,17 +1,45 @@
-name: 'Test'
+name: Test
+
 on:
   push:
+    branches: [main, dev]
   pull_request:
-    branches:
-      - main
+    branches: [main]
+
 jobs:
   test:
     runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.9', '3.10', '3.11', '3.12']
+
     steps:
-      - uses: actions/checkout@v2
-      - name: 'Build Docker image'
-        run: docker build -t magphi .
-      - name: 'Run unit tests'
-        run: docker run --entrypoint /Magphi/.travis/unit-test.sh magphi
-      - name: 'Run functional tests'
-        run: docker run --entrypoint /Magphi/functional_tests/Magphi-test.sh magphi -p Magphi -d /Magphi/functional_tests/test_data -v
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+
+      - name: Install system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y bedtools samtools ncbi-blast+
+
+      - name: Install Python dependencies
+        run: |
+          pip install --upgrade pip
+          pip install .
+          pip install -r requirements-dev.txt
+
+      - name: Run unit tests
+        working-directory: unit_tests
+        run: python Magphi_test.py
+
+      - name: Run pylint
+        run: pylint -E Magphi/*.py
+
+      - name: Run functional tests
+        run: bash functional_tests/Magphi-test.sh -p Magphi -d functional_tests/test_data -v
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index ac17947..0000000
--- a/.travis.yml
+++ /dev/null
@@ -1,18 +0,0 @@
-sudo: true
-dist: xenial 
-services:
-  - docker
-language: python 
-python:
-  - "3.9"
-
-before_install:
-  - pip3 install cwltool
-  - docker build -t magphi .
-
-script:
-  # Both of these same tests, in Docker
-  # Functional tests
-  - docker run --entrypoint /Magphi/.travis/unit-test.sh magphi
-  # Unit tests
-  - docker run --entrypoint /Magphi/functional_tests/Magphi-test.sh magphi -p Magphi -d /Magphi/functional_tests/test_data -v
diff --git a/.travis/install-dependencies.sh b/.travis/install-dependencies.sh
deleted file mode 100755
index bef6e6c..0000000
--- a/.travis/install-dependencies.sh
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/bin/sh
-
-# Install Python dependencies
-
-echo 'Python install'
-(
-   pip install -r requirements-dev.txt
-   pip install .
-)
diff --git a/.travis/unit-test.sh b/.travis/unit-test.sh
deleted file mode 100755
index 9110506..0000000
--- a/.travis/unit-test.sh
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/bin/bash
-
-set -e
-errors=0
-
-# Run unit tests
-python unit_tests/Magphi_test.py || {
-    echo "'python python/Magphi/Magphi_test.py' failed"
-    let errors+=1
-}
-
-# Check program style
-pylint -E Magphi/*.py || {
-    echo 'pylint -E Magphi/*.py failed'
-    let errors+=1
-}
-
-[ "$errors" -gt 0 ] && {
-    echo "There were $errors errors found"
-    exit 1
-}
-
-echo "Ok : Python specific tests"

From 9a1bf3cd43eb043e5650f27b5ab834b9e019a917 Mon Sep 17 00:00:00 2001
From: milnus <44769523+milnus@users.noreply.github.com>
Date: Thu, 9 Apr 2026 20:39:21 +0200
Subject: [PATCH 05/12] relax biopython and install setuptools

---
 .github/workflows/test.yml | 1 +
 setup.py                   | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index e2b4de8..ce8ef41 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -31,6 +31,7 @@ jobs:
       - name: Install Python dependencies
         run: |
           pip install --upgrade pip
+          pip install setuptools
           pip install .
           pip install -r requirements-dev.txt
 
diff --git a/setup.py b/setup.py
index b6ae16c..149000f 100644
--- a/setup.py
+++ b/setup.py
@@ -24,7 +24,7 @@
     license='MIT license',
     description=('A bioinformatics tool allowing for examnination and extraction of genomic features using seed sequences.'),
     long_description=LONG_DESCRIPTION,
-    install_requires=['biopython>=1.87',
+    install_requires=['biopython>=1.79',
                       'setuptools',
                       'packaging',
                       'pybedtools>=0.12.0'],

From d3aa04f0828bfcbda69eddd9ba3258e5089cda02 Mon Sep 17 00:00:00 2001
From: milnus <44769523+milnus@users.noreply.github.com>
Date: Fri, 10 Apr 2026 06:16:14 +0200
Subject: [PATCH 06/12] change dependency requirements

---
 requirements-dev.txt | 2 +-
 requirements.txt     | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/requirements-dev.txt b/requirements-dev.txt
index d53e981..3be827d 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -1,6 +1,6 @@
 # Dependencies, with versions explicitly declared for development and testing
 biopython>=1.87
-pybedtools==0.8.2
+pybedtools==0.12.0
 setuptools
 # Packages that are not dependencies but used for building or testing
 pylint
diff --git a/requirements.txt b/requirements.txt
index 1da197c..921907c 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,6 +1,6 @@
 # Dependencies, with versions explicitly declared for development and testing
 biopython==1.87
-pybedtools==0.8.2
+pybedtools==0.12.0
 setuptools
 # Packages that are not dependencies but used for building or testing
 pylint

From 554e59d5b8cc01f64ee9eeb9f5a48235f3332246 Mon Sep 17 00:00:00 2001
From: milnus <44769523+milnus@users.noreply.github.com>
Date: Fri, 10 Apr 2026 06:46:12 +0200
Subject: [PATCH 07/12] Fix setup

---
 Magphi/search_insertion_sites.py | 1 +
 requirements-dev.txt             | 2 +-
 requirements.txt                 | 2 +-
 setup.py                         | 4 ++--
 4 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/Magphi/search_insertion_sites.py b/Magphi/search_insertion_sites.py
index eddfc74..3adbc4f 100644
--- a/Magphi/search_insertion_sites.py
+++ b/Magphi/search_insertion_sites.py
@@ -935,6 +935,7 @@ def screen_genome_for_seeds(genome_file, seed_pairs, seed_path, tmp_folder,
     tmp_genome_folder = os.path.join(tmp_folder, genome_name)
     os.mkdir(tmp_genome_folder)
 
+    annotation_file = None
     if file_type == 'fasta':
         tmp_genome = os.path.join(tmp_genome_folder, genome_file.rsplit('/')[-1])
 
diff --git a/requirements-dev.txt b/requirements-dev.txt
index 3be827d..a6b4f86 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -1,5 +1,5 @@
 # Dependencies, with versions explicitly declared for development and testing
-biopython>=1.87
+biopython>=1.85
 pybedtools==0.12.0
 setuptools
 # Packages that are not dependencies but used for building or testing
diff --git a/requirements.txt b/requirements.txt
index 921907c..b76b0f2 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,5 +1,5 @@
 # Dependencies, with versions explicitly declared for development and testing
-biopython==1.87
+biopython==1.85
 pybedtools==0.12.0
 setuptools
 # Packages that are not dependencies but used for building or testing
diff --git a/setup.py b/setup.py
index 149000f..83b7c85 100644
--- a/setup.py
+++ b/setup.py
@@ -24,13 +24,13 @@
     license='MIT license',
     description=('A bioinformatics tool allowing for examnination and extraction of genomic features using seed sequences.'),
     long_description=LONG_DESCRIPTION,
-    install_requires=['biopython>=1.79',
+    install_requires=['biopython>=1.85',
                       'setuptools',
                       'packaging',
                       'pybedtools>=0.12.0'],
     keywords=['Genomic', 'extraction', 'bacteria', 'prokaryotes', 'bioinformatics'],
     classifiers=[
-        'Programming Language :: Python :: 3.9',
+        'Programming Language :: Python :: 3.10',
         'License :: OSI Approved :: MIT License',
         'Operating System :: OS Independent',
         'Intended Audience :: Science/Research',

From 692e4b69487eb0cc85676a73cbcc7e16e7186a3a Mon Sep 17 00:00:00 2001
From: milnus <44769523+milnus@users.noreply.github.com>
Date: Fri, 10 Apr 2026 06:55:09 +0200
Subject: [PATCH 08/12] Make help message test more dynamic

---
 functional_tests/Magphi-test.sh | 39 +++++++++++++++++++++++++++++++--
 1 file changed, 37 insertions(+), 2 deletions(-)

diff --git a/functional_tests/Magphi-test.sh b/functional_tests/Magphi-test.sh
index 789b45f..7e2a20b 100755
--- a/functional_tests/Magphi-test.sh
+++ b/functional_tests/Magphi-test.sh
@@ -164,6 +164,41 @@ function test_exit_status {
     fi 
 }
 
+# Run a command and check that all expected strings appear in the output
+# ARG1: command we want to test as a string
+# ARG2: expected exit status
+# ARG3+: strings that must appear in the output
+function test_stdout_contains {
+    let num_tests+=1
+    local cmd=$1
+    local expected_exit_status=$2
+    shift 2
+    local expected_strings=("$@")
+    output=$(eval $cmd 2>&1)
+    exit_status=$?
+    verbose_message "Testing stdout contains strings: $cmd"
+    local failed=0
+    for s in "${expected_strings[@]}"; do
+        if [[ "$output" != *"$s"* ]]; then
+            let num_errors+=1
+            echo "TEST FAILED!"
+            echo "Test output failed (missing expected string): $cmd"
+            echo "Expected to find: $s"
+            echo "Actual output:"
+            echo "$output"
+            failed=1
+            break
+        fi
+    done
+    if [ "$failed" -eq 0 ] && [ "$exit_status" -ne "$expected_exit_status" ]; then
+        let num_errors+=1
+        echo "TEST FAILED!"
+        echo "Test exit status failed: $cmd"
+        echo "Actual exit status: $exit_status"
+        echo "Expected exit status: $expected_exit_status"
+    fi
+}
+
 function call_new_test {
   echo ''
   echo $1
@@ -177,10 +212,10 @@ cd $test_data_dir
 ## Test commandline exit status
 # Test output for no arguments
 call_new_test "Test output for no arguments"
-test_stdout_exit "$test_program" no_input.expected 2
+test_stdout_contains "$test_program" 2 "Magphi" "Welcome to Magphi" "--input_genomes" "--input_seeds" "--help"
 # Test output for -help argument given
 call_new_test "Test output for -help argument given"
-test_stdout_exit "$test_program -help" no_input.expected 0
+test_stdout_contains "$test_program -help" 0 "Magphi" "Welcome to Magphi" "--input_genomes" "--input_seeds" "--help"
 # Test exit status for a bad command line invocation
 call_new_test "Test exit status for a bad command line invocation"
 test_exit_status "$test_program --this_is_not_a_valid_argument > /dev/null 2>&1" 2

From 9c6e17b9cc6a08a592ddbba8dd4202c5f2beec56 Mon Sep 17 00:00:00 2001
From: milnus <44769523+milnus@users.noreply.github.com>
Date: Fri, 10 Apr 2026 07:33:04 +0200
Subject: [PATCH 09/12] Fix up CI workflow

---
 .github/workflows/test.yml            | 10 +++++-
 functional_tests/Magphi-test.sh       | 50 +++++++++++++--------------
 functional_tests/test_data/Magphi.log | 25 ++++++++++++++
 3 files changed, 59 insertions(+), 26 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index ce8ef41..dfd4fa8 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -8,7 +8,7 @@ on:
 
 jobs:
   test:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     strategy:
       fail-fast: false
       matrix:
@@ -35,6 +35,14 @@ jobs:
           pip install .
           pip install -r requirements-dev.txt
 
+      - name: Verify installation
+        run: |
+          which Magphi
+          Magphi --check
+          blastn -version
+          samtools --version | head -1
+          bedtools --version
+
       - name: Run unit tests
         working-directory: unit_tests
         run: python Magphi_test.py
diff --git a/functional_tests/Magphi-test.sh b/functional_tests/Magphi-test.sh
index 7e2a20b..c66a145 100755
--- a/functional_tests/Magphi-test.sh
+++ b/functional_tests/Magphi-test.sh
@@ -207,7 +207,7 @@ function call_new_test {
 # 1. Parse command line arguments.
 parse_args $@
 # 2. Change to test directory
-cd $test_data_dir
+cd "$test_data_dir" || exit_with_error "could not cd to $test_data_dir" 1
 # 2. Run tests
 ## Test commandline exit status
 # Test output for no arguments
@@ -240,61 +240,61 @@ test_exit_status "$test_program -g empty_file -S -s empty_file > /dev/null 2>&1"
 
 # Run test for evidence level when no seed hits are found
 call_new_test "Run test for evidence level when no seed hits are found"
-Magphi -g evidence_levels_simple_genome.fasta -S -s no_primers_match_primers.fasta -o test_out_folder
+$test_program -g evidence_levels_simple_genome.fasta -S -s no_primers_match_primers.fasta -o test_out_folder
 test_output_file test_out_folder/master_seed_evidence.csv no_primers_match_evidence_levels.expected
 rm -r test_out_folder
 
 # Run test for evidence level when a single seed hit is found
 call_new_test "Test for evidence level when a single seed hit is found"
-Magphi -g evidence_levels_simple_genome.fasta -S -s single_primer_match_primers.fasta -o test_out_folder
+$test_program -g evidence_levels_simple_genome.fasta -S -s single_primer_match_primers.fasta -o test_out_folder
 test_output_file test_out_folder/master_seed_evidence.csv one_primer_match_evidence_level.expected
 rm -r test_out_folder
 
 # Run test for evidence level when two primers hit multiple times on same contig, but cannot connect
 call_new_test "Test for evidence level when two primers hit multiple times on same contig, but cannot connect"
-Magphi -g evidence_levels_simple_genome.fasta -S -s two_primers_simple_match_primers.fasta -o test_out_folder -md 1
+$test_program -g evidence_levels_simple_genome.fasta -S -s two_primers_simple_match_primers.fasta -o test_out_folder -md 1
 test_output_file test_out_folder/master_seed_evidence.csv two_primers_multiple_hits_single_contig_no_connections.expected
 rm -r test_out_folder
 
 # Run test for evidence level when two primers hit the same contig multiple times and they can connect multiple ways
 call_new_test "Test for evidence level when two primers hit the same contig multiple times and they can connect multiple ways"
-Magphi -g evidence_levels_simple_genome.fasta -S -s two_primers_simple_match_primers.fasta -o test_out_folder -md 1000
+$test_program -g evidence_levels_simple_genome.fasta -S -s two_primers_simple_match_primers.fasta -o test_out_folder -md 1000
 test_output_file test_out_folder/master_seed_evidence.csv two_primers_multiple_hits_single_contig_multiple_connections.expected
 rm -r test_out_folder
 
 # Run test for evidence level when two primers hit multiple contigs multiple times and no connection between them
 call_new_test "Test for evidence level when two primers hit multiple contigs multiple times and no connection between them"
-Magphi -g evidence_levels_simple_two_contigs.fasta -S -s two_primers_simple_match_primers.fasta -o test_out_folder -md 1
+$test_program -g evidence_levels_simple_two_contigs.fasta -S -s two_primers_simple_match_primers.fasta -o test_out_folder -md 1
 test_output_file test_out_folder/master_seed_evidence.csv two_primers_two_contigs_multipe_hits_no_connection.expected
 rm -r test_out_folder
 
 # run test for evidence level when two seeds hit multiple contigs multiple times and multiple connections
 call_new_test "Test for evidence level when two seeds hit multiple contigs multiple times and multiple connections"
-Magphi -g evidence_levels_simple_two_contigs.fasta -S -s two_primers_simple_match_primers.fasta -o test_out_folder -md 1000
+$test_program -g evidence_levels_simple_two_contigs.fasta -S -s two_primers_simple_match_primers.fasta -o test_out_folder -md 1000
 test_output_file test_out_folder/master_seed_evidence.csv two_primers_two_contigs_multi_hit_multi_connect.expected
 rm -r test_out_folder
 
 # Run test for evidence level when two seeds overlap and are excluded because primers are deleted
 call_new_test "Test for evidence level when two seeds overlap and are excluded because primers are deleted"
-Magphi -g evidence_levels_overlap_two_contigs.fasta -S -s overlap_primers.fasta -o test_out_folder -md 1
+$test_program -g evidence_levels_overlap_two_contigs.fasta -S -s overlap_primers.fasta -o test_out_folder -md 1
 test_output_file test_out_folder/master_seed_evidence.csv evidence_levels_overlapping_seeds.expected
 rm -r test_out_folder
 
 # Run test for evidence level when one seed is on the edge of a contig and is deleted due to being excluded
 call_new_test "Test for evidence level when one seed is on the edge of a contig and is deleted due to being excluded"
-Magphi -g evidence_levels_overlap_two_contigs.fasta -S -s contig_edge_primers.fasta -o test_out_folder -md 180
+$test_program -g evidence_levels_overlap_two_contigs.fasta -S -s contig_edge_primers.fasta -o test_out_folder -md 180
 test_output_file test_out_folder/master_seed_evidence.csv evidence_levels_contig_edge.expected
 rm -r test_out_folder
 
 # Run test for evidence level when only two unique seeds hit but can not connect
 call_new_test "Test for evidence level when only two unique seeds hit but can not connect"
-Magphi -g two_contigs_two_primers_single_hit.fasta -S -s two_primers_simple_match_primers.fasta -o test_out_folder -md 1
+$test_program -g two_contigs_two_primers_single_hit.fasta -S -s two_primers_simple_match_primers.fasta -o test_out_folder -md 1
 test_output_file test_out_folder/master_seed_evidence.csv evidence_levels_simple_hits_cross_contig_no_connect.expected
 rm -r test_out_folder
 
 # Run test for evidence level when only two unique seeds hit with connection but no annotation
 call_new_test "Test for evidence level when only two unique seeds hit with connection but no annotation"
-Magphi -g two_contigs_two_primers_single_hit.fasta -S -s two_primers_simple_match_primers.fasta -o test_out_folder -b -md 70
+$test_program -g two_contigs_two_primers_single_hit.fasta -S -s two_primers_simple_match_primers.fasta -o test_out_folder -b -md 70
 test_output_file test_out_folder/master_seed_evidence.csv evidence_levels_simple_hits_cross_contig_connected/master_seed_evidence.csv
 test_output_file test_out_folder/inter_seed_distance.csv evidence_levels_simple_hits_cross_contig_connected/inter_seed_distance.csv
 test_output_file test_out_folder/two_primers_simple/two_contigs_two_primers_single_hit-two_primers_simple_1_break.fasta evidence_levels_simple_hits_cross_contig_connected/two_contigs_two_primers_single_hit-two_primers_simple_1_break.fasta
@@ -303,7 +303,7 @@ rm -r test_out_folder
 
 # Run test for evidence level when only two unique seeds hit with connection and annotation
 call_new_test "Test for evidence level when only two unique seeds hit with connection and annotation"
-Magphi -g two_contigs_two_primers_single_hit.gff -S -s two_seeds_w_annotation_between.fasta -o test_out_folder -b -md 375
+$test_program -g two_contigs_two_primers_single_hit.gff -S -s two_seeds_w_annotation_between.fasta -o test_out_folder -b -md 375
 test_output_file test_out_folder/master_seed_evidence.csv evidence_levels_simple_primers_connect_cross_contig_with_annotations/master_seed_evidence.csv
 test_output_file test_out_folder/inter_seed_distance.csv evidence_levels_simple_primers_connect_cross_contig_with_annotations/inter_seed_distance.csv
 test_output_file test_out_folder/annotation_num_matrix.csv evidence_levels_simple_primers_connect_cross_contig_with_annotations/annotation_num_matrix.csv
@@ -315,13 +315,13 @@ rm -r test_out_folder
 
 # Run test on a gff with a single contig no connection between primers
 call_new_test 'Test of a gff with a single contig no connection between primers'
-Magphi -g evidence_levels_single_contig.gff -S -s two_primers_simple_match_primers.fasta -o test_out_folder -md 1
+$test_program -g evidence_levels_single_contig.gff -S -s two_primers_simple_match_primers.fasta -o test_out_folder -md 1
 test_output_file test_out_folder/master_seed_evidence.csv evidence_levels_single_contig_no_connection/master_seed_evidence.csv
 rm -r test_out_folder
 
 # Run test on a gff with a single contig with connection between primers
 call_new_test "Test of a gff with a single contig with connection between primers"
-Magphi -g evidence_levels_single_contig.gff -S -s two_primers_simple_match_primers.fasta -o test_out_folder -md 100
+$test_program -g evidence_levels_single_contig.gff -S -s two_primers_simple_match_primers.fasta -o test_out_folder -md 100
 test_output_file test_out_folder/master_seed_evidence.csv evidence_levels_single_contig_connection/master_seed_evidence.csv
 test_output_file test_out_folder/inter_seed_distance.csv evidence_levels_single_contig_connection/inter_seed_distance.csv
 test_output_file test_out_folder/two_primers_simple/evidence_levels_single_contig-two_primers_simple.fasta evidence_levels_single_contig_connection/evidence_levels_single_contig-two_primers_simple.fasta
@@ -330,7 +330,7 @@ rm -r test_out_folder
 
 # Run test on a gff with a single contig with connection and annotation between primers - exclude seeds
 call_new_test "Test of a gff with a single contig with connection and annotation between primers - exclude seeds"
-Magphi -g evidence_levels_single_contig.gff -S -s two_seeds_w_annotation_between.fasta -o test_out_folder -md 750 -is
+$test_program -g evidence_levels_single_contig.gff -S -s two_seeds_w_annotation_between.fasta -o test_out_folder -md 750 -is
 test_output_file test_out_folder/master_seed_evidence.csv evidence_level_single_contigs_connect_annotations_include_seeds/master_seed_evidence.csv
 test_output_file test_out_folder/inter_seed_distance.csv evidence_level_single_contigs_connect_annotations_include_seeds/inter_seed_distance.csv
 test_output_file test_out_folder/annotation_primers/evidence_levels_single_contig-annotation_primers.gff evidence_level_single_contigs_connect_annotations_include_seeds/evidence_levels_single_contig-annotation_primers.gff
@@ -340,7 +340,7 @@ rm -r test_out_folder
 
 # Test output when seeds hit multiple times and one and only one connection can be made between seeds on same contig
 call_new_test "Test output when seeds hit multiple times and one and only one connection can be made between seeds on same contig"
-Magphi -g evidence_levels_simple_two_contigs.fasta -S -s two_primers_simple_match_primers.fasta -o test_out_folder -md 130
+$test_program -g evidence_levels_simple_two_contigs.fasta -S -s two_primers_simple_match_primers.fasta -o test_out_folder -md 130
 test_output_file test_out_folder/master_seed_evidence.csv evidence_level_multi_hit_multi_contig_single_same_contig_overlap/master_seed_evidence.csv
 test_output_file test_out_folder/inter_seed_distance.csv evidence_level_multi_hit_multi_contig_single_same_contig_overlap/inter_seed_distance.csv
 test_output_file test_out_folder/contig_hit_matrix.csv evidence_level_multi_hit_multi_contig_single_same_contig_overlap/contig_hit_matrix.csv
@@ -349,7 +349,7 @@ rm -r test_out_folder
 
 # Test output when seeds hit multiple times and one and only one connection can be made between seeds on different contig
 call_new_test "Test output when seeds hit multiple times and one and only one connection can be made between seeds on different contig"
-Magphi -g evidence_levels_simple_two_contigs_cross_conenct.fasta -S -s two_primers_simple_match_primers.fasta -o test_out_folder -b -md 180
+$test_program -g evidence_levels_simple_two_contigs_cross_conenct.fasta -S -s two_primers_simple_match_primers.fasta -o test_out_folder -b -md 180
 test_output_file test_out_folder/master_seed_evidence.csv evidence_level_multi_seed_hit_cross_contig_connect/master_seed_evidence.csv
 test_output_file test_out_folder/inter_seed_distance.csv evidence_level_multi_seed_hit_cross_contig_connect/inter_seed_distance.csv
 test_output_file test_out_folder/contig_hit_matrix.csv evidence_level_multi_seed_hit_cross_contig_connect/contig_hit_matrix.csv
@@ -359,7 +359,7 @@ rm -r test_out_folder
 
 # Test gzipped gff file
 call_new_test 'Test gzipped file'
-test_exit_status "Magphi -g evidence_levels_single_contig.gff.gz -S -s two_seeds_w_annotation_between.fasta -o test_out_folder -md 750 -is" 0
+test_exit_status "$test_program -g evidence_levels_single_contig.gff.gz -S -s two_seeds_w_annotation_between.fasta -o test_out_folder -md 750 -is" 0
 test_output_file test_out_folder/master_seed_evidence.csv evidence_level_single_contigs_connect_annotations_include_seeds/master_seed_evidence.csv
 test_output_file test_out_folder/inter_seed_distance.csv evidence_level_single_contigs_connect_annotations_include_seeds/inter_seed_distance.csv
 test_output_file test_out_folder/annotation_primers/evidence_levels_single_contig-annotation_primers.gff evidence_level_single_contigs_connect_annotations_include_seeds/evidence_levels_single_contig-annotation_primers.gff
@@ -369,7 +369,7 @@ rm -r test_out_folder
 
 # Test gzipped fasta file evidence level when only two unique seeds hit with connection but no annotation
 call_new_test "Test gzipped fasta file evidence level when only two unique seeds hit with connection but no annotation"
-Magphi -g two_contigs_two_primers_single_hit.fasta.gz -S -s two_primers_simple_match_primers.fasta -o test_out_folder -b -md 70
+$test_program -g two_contigs_two_primers_single_hit.fasta.gz -S -s two_primers_simple_match_primers.fasta -o test_out_folder -b -md 70
 test_output_file test_out_folder/master_seed_evidence.csv evidence_levels_simple_hits_cross_contig_connected/master_seed_evidence.csv
 test_output_file test_out_folder/inter_seed_distance.csv evidence_levels_simple_hits_cross_contig_connected/inter_seed_distance.csv
 test_output_file test_out_folder/two_primers_simple/two_contigs_two_primers_single_hit-two_primers_simple_1_break.fasta evidence_levels_simple_hits_cross_contig_connected/two_contigs_two_primers_single_hit-two_primers_simple_1_break.fasta
@@ -379,7 +379,7 @@ rm -r test_out_folder
 
 # Chaws problem.
 call_new_test "Test larger mock up of problem reported in emm4"
-Magphi -g \
+$test_program -g \
 gff3_files_larger_test/*.gff -S -s larger_test_primers.fa -o test_out_folder -md 15000 -is
 test_output_file test_out_folder/annotation_num_matrix.csv larger_Magphi_test/annotation_num_matrix.csv
 test_output_file test_out_folder/inter_seed_distance.csv larger_Magphi_test/inter_seed_distance.csv
@@ -390,7 +390,7 @@ rm -r test_out_folder
 
 # Test input seeds being proteins and the tblastn function
 call_new_test "Test input seeds being proteins and the tblastn function - with correct -p flag"
-Magphi -g tblasn_test/tblastn_genome.fasta -S -s tblasn_test/prot_seeds.fasta -o test_out_folder -md 140 -p
+$test_program -g tblasn_test/tblastn_genome.fasta -S -s tblasn_test/prot_seeds.fasta -o test_out_folder -md 140 -p
 test_output_file test_out_folder/master_seed_evidence.csv tblastn_simple_expected/master_seed_evidence.expected
 test_output_file test_out_folder/inter_seed_distance.csv tblastn_simple_expected/inter_seed_distance.expected
 test_output_file test_out_folder/contig_hit_matrix.csv tblastn_simple_expected/contig_hit_matrix.expected
@@ -398,7 +398,7 @@ rm -r test_out_folder
 
 # Test input seeds being proteins and the tblastn function
 call_new_test "Test input seeds being proteins and the tblastn function - No -p flag"
-Magphi -g tblasn_test/tblastn_genome.fasta -S -s tblasn_test/prot_seeds.fasta -o test_out_folder -md 140
+$test_program -g tblasn_test/tblastn_genome.fasta -S -s tblasn_test/prot_seeds.fasta -o test_out_folder -md 140
 test_output_file test_out_folder/master_seed_evidence.csv tblastn_simple_expected/master_seed_evidence.expected
 test_output_file test_out_folder/inter_seed_distance.csv tblastn_simple_expected/inter_seed_distance.expected
 test_output_file test_out_folder/contig_hit_matrix.csv tblastn_simple_expected/contig_hit_matrix.expected
@@ -406,7 +406,7 @@ rm -r test_out_folder
 
 # Test output fasta when they are reverse complemented to orient seed
 call_new_test "Test output fasta when they are reverse complemented to orient seed"
-Magphi -g Fix_start_genome.fasta -s fixstart_seeds.fasta -o test_out_folder -b -md 5
+$test_program -g Fix_start_genome.fasta -s fixstart_seeds.fasta -o test_out_folder -b -md 5
 test_output_file test_out_folder/fixstart/Fix_start_genome-fixstart.fasta fix_start/Fix_start_genome-fixstart_rev_comp.fasta.expected
 rm -r test_out_folder
 
@@ -424,7 +424,7 @@ rm -r test_out_folder
 
 # Test output gff when they are reverse complemented to orient seed
 call_new_test "Test output gff when they are reverse complemented to orient seed"
-Magphi -g Fix_start_genome.gff -s fixstart_seeds.fasta -o test_out_folder -b -md 5
+$test_program -g Fix_start_genome.gff -s fixstart_seeds.fasta -o test_out_folder -b -md 5
 test_output_file test_out_folder/fixstart/Fix_start_genome-fixstart.gff fix_start/Fix_start_genome-fixstart_reverse_complemented.gff.expected
 rm -r test_out_folder
 
@@ -442,7 +442,7 @@ rm -r test_out_folder
 
 # Test output gff when two genes are present and they are reverse complemented to orient seed
 call_new_test "Test output gff when two genes are present and they are reverse complemented to orient seed"
-Magphi -g Fix_start_genome_2.gff -s fixstart_seeds.fasta -o test_out_folder -b -md 5
+$test_program -g Fix_start_genome_2.gff -s fixstart_seeds.fasta -o test_out_folder -b -md 5
 test_output_file test_out_folder/fixstart/Fix_start_genome_2-fixstart.gff fix_start/Fix_start_genome_2-fixstart_reverse_complement.gff.expected
 rm -r test_out_folder
 
diff --git a/functional_tests/test_data/Magphi.log b/functional_tests/test_data/Magphi.log
index 66c7394..6006626 100644
--- a/functional_tests/test_data/Magphi.log
+++ b/functional_tests/test_data/Magphi.log
@@ -23,3 +23,28 @@ NoneType: None
 [2026-04-09T19:50:53+0200] INFO - __main__ - Processing started
 [2026-04-09T19:50:53+0200] ERROR - check_inputs - The given input files could not be recognised as either Fasta or GFF3 with a genome.
 NoneType: None
+[2026-04-10T06:57:43+0200] INFO - __main__ - command line: /Users/magnus.jespersen/miniforge3/envs/Magphi/bin/Magphi -g test_fasta.fna test_GFF.gff -S -s empty_file
+[2026-04-10T06:57:44+0200] WARNING - __main__ - Some dependencies are untested version(s)
+[2026-04-10T06:57:44+0200] INFO - __main__ - Processing started
+[2026-04-10T06:57:44+0200] ERROR - check_inputs - Input files were found to be of mixed type with some being recognised as fasta!
+Please make sure that all your input files are only either Fasta or GFF3, not mixed
+[2026-04-10T06:57:44+0200] INFO - __main__ - command line: /Users/magnus.jespersen/miniforge3/envs/Magphi/bin/Magphi -g test_fasta.fna random_text.txt -S -s empty_file
+[2026-04-10T06:57:44+0200] WARNING - __main__ - Some dependencies are untested version(s)
+[2026-04-10T06:57:44+0200] INFO - __main__ - Processing started
+[2026-04-10T06:57:44+0200] ERROR - check_inputs - Input files were found to be of mixed type with some being recognised as fasta!
+Please make sure that all your input files are only either Fasta or GFF3, not mixed
+[2026-04-10T06:57:45+0200] INFO - __main__ - command line: /Users/magnus.jespersen/miniforge3/envs/Magphi/bin/Magphi -g test_GFF.gff random_text.txt -S -s empty_file
+[2026-04-10T06:57:45+0200] WARNING - __main__ - Some dependencies are untested version(s)
+[2026-04-10T06:57:45+0200] INFO - __main__ - Processing started
+[2026-04-10T06:57:45+0200] ERROR - check_inputs - Input files were found to be of mixed type with some being recognised as GFF!
+Please make sure that all your input files are only either Fasta or GFF3, not mixed
+[2026-04-10T06:57:46+0200] INFO - __main__ - command line: /Users/magnus.jespersen/miniforge3/envs/Magphi/bin/Magphi -g random_text.txt -S -s empty_file
+[2026-04-10T06:57:46+0200] WARNING - __main__ - Some dependencies are untested version(s)
+[2026-04-10T06:57:46+0200] INFO - __main__ - Processing started
+[2026-04-10T06:57:46+0200] ERROR - check_inputs - The given input files could not be recognised as either Fasta or GFF3 with a genome.
+NoneType: None
+[2026-04-10T06:57:47+0200] INFO - __main__ - command line: /Users/magnus.jespersen/miniforge3/envs/Magphi/bin/Magphi -g empty_file -S -s empty_file
+[2026-04-10T06:57:47+0200] WARNING - __main__ - Some dependencies are untested version(s)
+[2026-04-10T06:57:47+0200] INFO - __main__ - Processing started
+[2026-04-10T06:57:47+0200] ERROR - check_inputs - The given input files could not be recognised as either Fasta or GFF3 with a genome.
+NoneType: None

From 5b72fbd6c3138c11f5694265065b4b2e06e715c7 Mon Sep 17 00:00:00 2001
From: milnus <44769523+milnus@users.noreply.github.com>
Date: Fri, 10 Apr 2026 07:36:36 +0200
Subject: [PATCH 10/12] Fix utf-8 problem

---
 Magphi/check_depencies.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/Magphi/check_depencies.py b/Magphi/check_depencies.py
index 0be271a..69b4b59 100644
--- a/Magphi/check_depencies.py
+++ b/Magphi/check_depencies.py
@@ -73,7 +73,7 @@ def check_for_bedtools(verbose):
                 print("Bedtools was successfully found")
 
             cmd_return = subprocess.run(['bedtools', '-version'], capture_output=True)
-            version = cmd_return.stdout.decode().rsplit('v', 1)[-1]
+            version = cmd_return.stdout.decode('utf-8', errors='ignore').rsplit('v', 1)[-1]
             if Version(version) >= Version('2.29.2'):
                 if verbose:
                     print("Bedtools version is valid")
@@ -110,7 +110,7 @@ def check_for_samtools(verbose):
 
             cmd_return = subprocess.run(['samtools', '--version'], capture_output=True)
             # Isolate version tag
-            version = cmd_return.stdout.decode().split(' ', 1)[-1]
+            version = cmd_return.stdout.decode('utf-8', errors='ignore').split(' ', 1)[-1]
             version = version.split('\n', 1)[0]
 
             if Version(version) >= Version('1.11'):
@@ -147,7 +147,7 @@ def check_for_blast_plus(verbose=False):
                 print("Blast+ was successfully found")
 
             # Isolate version tag
-            version = cmd_return.stdout.decode().split('\n')[1]
+            version = cmd_return.stdout.decode('utf-8', errors='ignore').split('\n')[1]
             version = version.split(' ')[3]
             version = version.rsplit(',', 1)[0]
 

From b3aff7a47a5100069222d7d8838f8603fe4a1cc4 Mon Sep 17 00:00:00 2001
From: milnus <44769523+milnus@users.noreply.github.com>
Date: Fri, 10 Apr 2026 08:30:02 +0200
Subject: [PATCH 11/12] Update actions for deprication

---
 .github/workflows/build_n_publish.yml | 6 +++---
 .github/workflows/test.yml            | 4 ++--
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/build_n_publish.yml b/.github/workflows/build_n_publish.yml
index a0f42d6..eb28321 100644
--- a/.github/workflows/build_n_publish.yml
+++ b/.github/workflows/build_n_publish.yml
@@ -8,10 +8,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v5
+    - name: Set up Python 3.13
+      uses: actions/setup-python@v6
       with:
-        python-version: '3.9'
+        python-version: '3.13'
         cache: 'pip'
     - name: Install pypa/build
       run: python -m pip install build --user
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index dfd4fa8..71c84ac 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -15,10 +15,10 @@ jobs:
         python-version: ['3.9', '3.10', '3.11', '3.12']
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
           cache: 'pip'

From b8ba4935229391eac1a184e81c4a7f08aa8aa244 Mon Sep 17 00:00:00 2001
From: milnus <44769523+milnus@users.noreply.github.com>
Date: Fri, 10 Apr 2026 08:34:52 +0200
Subject: [PATCH 12/12] Bump version

Indicate with version that there are some major changes, without interface changing
---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 83b7c85..e066f9b 100644
--- a/setup.py
+++ b/setup.py
@@ -12,7 +12,7 @@
 
 setup(
     name='Magphi',
-    version='2.0.3',
+    version='2.1.0',
     author='Magnus Ganer Jespersen',
     author_email='magnus.ganer.j@gmail.com',
     packages=['Magphi'],