Made a separate libcodonusage library.

See https://stackoverflow.com/a/17864475/1878788

.gitignore

+# Compiled python modules.
+*.pyc
+
+# Setuptools distribution folder.
+/dist/
+
+# Python egg metadata, regenerated from source files by setuptools.
+/*.egg-info
+
+# Backups
+*~

README.md

+# Utilities to analyse codon usage
+
+This is a very preliminary version, with very few utilities.
+
+
+## Installing
+
+Get the source using `git clone git@gitlab.pasteur.fr:bli/libcodonusage.git`, `cd` into it and run `python3 -m pip install .`
+
+It might also work directly:
+
+    python3 -m pip install git+ssh://git@gitlab.pasteur.fr/bli/libcodonusage.git
+

libcodonusage/__init__.py

+__copyright__ = "Copyright (C) 2022 Blaise Li"
+__licence__ = "GNU GPLv3"
+__version__ = 0.1
+from .libcodonusage import (
+    aa2colour,
+    columns_by_aa,
+    load_bias_table,
+    violin_usage,
+    violin_usage_vertical,
+    violin_usage_by_clusters,
+    violin_with_thresh,
+    )

common.py → libcodonusage/libcodonusage.py

 #!/usr/bin/env python3
-# Copyright (C) 2021 Blaise Li
+# Copyright (C) 2021-2022 Blaise Li
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

pyproject.toml

+[build-system]
+requires = [
+    "setuptools",
+]
+build-backend = "setuptools.build_meta"

setup.py

+# Copyright (C) 2022 Blaise Li
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+from setuptools import setup, find_packages
+#from Cython.Build import cythonize
+#from distutils.extension import Extension
+
+name = "libcodonusage"
+
+# Adapted from Biopython
+__version__ = "Undefined"
+for line in open("%s/__init__.py" % name):
+    if (line.startswith('__version__')):
+        exec(line.strip())
+
+
+# https://github.com/cython/cython/blob/master/docs/src/reference/compilation.rst#configuring-the-c-build
+#extensions = [
+#    Extension(
+#        "libreads.libbamutils", ["libreads/libbamutils.pyx"],
+#        include_dirs=pysam_get_include()),
+#    ]
+
+setup(
+    name=name,
+    version=__version__,
+    description="Miscellaneous things to analyse codon usage.",
+    author="Blaise Li",
+    author_email="blaise.li__git@nsup.org",
+    license="GNU GPLv3",
+    python_requires=">=3.6, <4",
+    packages=find_packages(),
+    #scripts=["bin/ali2consensus.py"],
+    #ext_modules = extensions,
+    setup_requires=[
+        #"wheel",
+        #"cython",
+        #"pysam",
+    ],
+    install_requires=[
+        "biotite",
+        "cytoolz",
+        "matplotlib",
+        "numpy",
+        "pandas",
+        "seaborn"
+    ],
+)