From dab5293be41c5185c9df6eefcd0b5a0cee727242 Mon Sep 17 00:00:00 2001
From: JLSteenwyk <jlsteenwyk@gmail.com>
Date: Thu, 8 Aug 2024 17:11:02 -0700
Subject: [PATCH] added confttest to define slow and fast tests

---
 change_log.txt    | 30 ++++++++++++++++++++++++++++++
 docs/setup.py     | 35 +++++++++++++++++++++++++++++++++++
 tests/conftest.py |  7 +++++++
 3 files changed, 72 insertions(+)
 create mode 100644 change_log.txt
 create mode 100644 docs/setup.py
 create mode 100644 tests/conftest.py

diff --git a/change_log.txt b/change_log.txt
new file mode 100644
index 0000000..5ec8551
--- /dev/null
+++ b/change_log.txt
@@ -0,0 +1,30 @@
+Major changes to ClipKIT are summarized here.
+
+2.2.3
+Fixed gap character handling. The help message was incongruent
+with what was happening underneath the hood.
+
+2.2.1
+Removed "Processing" block from CLI output. Reordered CLI output to 
+put user arguments first followed by outputs. Added original length of
+the alignment to output statistics.
+
+2.2.0
+Incorporated C3 trimming, which can be evoked using the c3 trimming mode.
+
+2.1.2
+Incorporate codon-based trimming. When one position in a codon gets trimmed based on the mode
+being used, the whole codon will get trimmed from the alignment.
+
+2.0.0 through 2.1.0
+Introduce and refactor MSA class. Rely on Numpy functionality to accelerate processes.
+
+1.3.0
+long description of sequences, rather than identifiers, are kept in the ClipKIT output
+
+1.1.5
+carried over code base to biopython, v1.79
+
+1.1.0
+smart-gap trimming is introduced and is now the default trimming approach used in ClipKIT.
+smart-gap trimming is a dynamic approach to determine the appropriate gaps threshold for an alignment.
diff --git a/docs/setup.py b/docs/setup.py
new file mode 100644
index 0000000..31fd7ff
--- /dev/null
+++ b/docs/setup.py
@@ -0,0 +1,35 @@
+from os import path
+from setuptools import setup
+
+here = path.abspath(path.dirname(__file__))
+
+with open(path.join(here, "README.md"), encoding="utf-8") as f:
+    long_description = f.read()
+
+CLASSIFIERS = [
+    "Operating System :: OS Independent",
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3.6",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Topic :: Scientific/Engineering",
+]
+
+REQUIRES = ["biopython==1.76", "numpy==1.21.0"]
+
+setup(
+    name="clipkit",
+    description="Alignment trimming software for phylogenetics.",
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    author="Jacob L. Steenwyk",
+    author_email="jlsteenwyk@gmail.com",
+    url="https://github.com/jlsteenwyk/clipkit",
+    packages=["clipkit"],
+    classifiers=CLASSIFIERS,
+    entry_points={"console_scripts": ["clipkit = clipkit.clipkit:main"]},
+    version="0.1.3",
+    include_package_data=True,
+    install_requires=REQUIRES,
+)
diff --git a/tests/conftest.py b/tests/conftest.py
new file mode 100644
index 0000000..22c7cab
--- /dev/null
+++ b/tests/conftest.py
@@ -0,0 +1,7 @@
+# global fixtures can go here
+import pytest
+
+
+def pytest_configure(config):
+    config.addinivalue_line("markers", "integration: mark as integration test")
+    config.addinivalue_line("markers", "slow: mark as slow test")