added setup for cdiff component

install.sh

@@ -76,12 +76,12 @@ git pull origin main --tags
 LATEST_COMMIT=$(git rev-parse HEAD)
 echo "Updated commit hash of cdiff_fbi after update: $LATEST_COMMIT"
 
-# print the latest tag of ecoli_fbi
+# print the latest tag of cdiff_fbi
 LATEST_TAG_COMMIT=$(git tag --sort=-creatordate --format '%(objectname)'|head -1)
 LATEST_TAG=$(git tag --sort=-creatordate|head -1)
 
-echo "Checking commit hash for the latest tag of ecoli_fbi: $LATEST_TAG_COMMIT"
-echo "Checking the lastest tag of ecoli_fbi: $LATEST_TAG"
+echo "Checking commit hash for the latest tag of cdiff_fbi: $LATEST_TAG_COMMIT"
+echo "Checking the lastest tag of cdiff_fbi: $LATEST_TAG"
 
 git checkout $LATEST_TAG_COMMIT
 

setup.cfg

@@ -0,0 +1,31 @@
+[bumpversion]
+current_version = 0.0.1
+parse = ((?P<major>\d+))(.(?P<minor>\d+))(.(?P<patch>\d+))
+serialize = {major}.{minor}.{patch}
+commit = True
+tag = True
+
+[metadata]
+description-file = README.md
+
+[bumpversion:file:setup.py]
+search = version='{current_version}'
+replace = version='{new_version}'
+
+[bumpversion:file:bifrost_sp_cdiff/config.yaml]
+search = {current_version}
+replace = {new_version}
+
+[bumpversion:file:bifrost_sp_cdiff/__init__.py]
+search = __version__ = '{current_version}'
+replace = __version__ = '{new_version}'
+
+[bumpversion:file:tests/test_simple.py]
+search = component_name = "sp_cdiff__v{current_version}"
+replace = component_name = "sp_cdiff__v{new_version}"
+
+[tool:pytest]
+minversion = 6.0
+addopts = -ra -q --durations=0
+testpaths = 
+	tests

setup.py

@@ -0,0 +1,19 @@
+from setuptools import setup, find_namespace_packages
+
+setup(
+    name='bifrost_sp_cdiff',
+    version='0.0.1',
+    description='Cdiff serotyping and stx typing for Bifrost',
+    url='https://github.com/ssi-dk/bifrost_sp_cdiff',
+    author='Rasmus',
+    author_email='[email protected]',
+    license='MIT',
+    packages=find_namespace_packages(),
+    install_requires=[
+        'bifrostlib >= 2.1.9',
+        'biopython>=1.77'
+    ],
+    python_requires='>=3.11',
+    package_data={'bifrost_sp_cdiff': ['config.yaml', 'pipeline.smk']},
+    include_package_data=True
+)