Reorganise code

Author: veghp

MANIFEST.in

@@ -1,14 +1,14 @@
 Python Codon Tables
 ===================
 
-.. image:: https://github.com/Edinburgh-Genome-Foundry/codon-usage-tables/actions/workflows/build.yml/badge.svg
-    :target: https://github.com/Edinburgh-Genome-Foundry/codon-usage-tables/actions/workflows/build.yml
+.. image:: https://github.com/Edinburgh-Genome-Foundry/python_codon_tables/actions/workflows/build.yml/badge.svg
+    :target: https://github.com/Edinburgh-Genome-Foundry/python_codon_tables/actions/workflows/build.yml
     :alt: GitHub CI build status
 
-Provides codon usage tables as dictionaries, for Python 3+.
+Provides codon usage tables as dictionaries, for Python.
 
-Tables for the following organisms are provided with the library (any other
-table can be downloaded using a TaxID):
+Tables for the following organisms are provided with the package
+(other tables can be downloaded using a TaxID):
 
 - *B. subtilis*
 - *C. elegans*
@@ -20,15 +20,16 @@ table can be downloaded using a TaxID):
 - *M. musculus domesticus*
 - *S. cerevisiae*
 
-All the tables are from `kazusa.or.jp <http://www.kazusa.or.jp/codon/readme_codon.html>`_
-and here is the original paper to cite:
+All tables are from `kazusa.or.jp <http://www.kazusa.or.jp/codon/readme_codon.html>`_
+(codon usages were computed using NCBI sequence data). The original publication:
 
 .. code::
 
     Codon usage tabulated from the international DNA sequence databases:
     status for the year 2000.
     Nakamura, Y., Gojobori, T. and Ikemura, T. (2000) Nucl. Acids Res. 28, 292.
 
+
 Usage
 -----
 
@@ -58,10 +59,30 @@ Usage
 
 - In ``get_codons_table`` you can also provide a "shorthand" notation ``b_subtilis``, which will be automatically extended to ``b_subtilis_1423`` as it appears so in the built-in table (use this feature at your own risks!)
 
+
+The package can also use codon usage data from a CSV file in the form:
+
+```
+amino_acid,codon,relative_frequency
+*,UAA,0.64
+*,UAG,0.07
+*,UGA,0.29
+A,GCA,0.21
+A,GCC,0.27
+K,AAA,0.76
+K,AAG,0.24
+etc.
+```
+
+
 Contribute
 ----------
 
-This project was started at the Edinburgh Genome Foundry by Zulko and is released on `Github <https://github.com/Edinburgh-Genome-Foundry/codon-usage-tables>`_ under a Public Domain licence (and no warranty whatsoever, please cross-check the codon usage with other sources if you are not sure). Feel free to add other tables if you think of more commonly used species.
+This project was started at the Edinburgh Genome Foundry by Zulko and is released on
+`Github <https://github.com/Edinburgh-Genome-Foundry/python_codon_tables>`_
+under the CC0 (Public Domain) license (and no warranty whatsoever, please cross-check the codon usage with other sources if you are not sure).
+Feel free to add other tables if you think of more commonly used species.
+
 
 Installation
 ------------
@@ -78,6 +99,7 @@ Manual:
 
     python setup.py install
 
+
 More biology software
 ---------------------
 

README.md

@@ -0,0 +1,29 @@
+Python Codon Tables
+===================
+
+Provides codon usage tables as dictionaries, for Python.
+
+
+Infos
+-----
+
+**PIP installation:**
+
+.. code:: bash
+
+  pip install python_codon_tables
+
+**Web documentation:** `<https://edinburgh-genome-foundry.github.io/python_codon_tables/>`_
+
+**Github Page:** `<https://github.com/Edinburgh-Genome-Foundry/python_codon_tables>`_
+
+**License:** CC0
+
+
+More biology software
+---------------------
+
+.. image:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/Edinburgh-Genome-Foundry.github.io/master/static/imgs/logos/egf-codon-horizontal.png
+  :target: https://edinburgh-genome-foundry.github.io/
+
+Python Codon Tables is part of the `EGF Codons <https://edinburgh-genome-foundry.github.io/>`_ synthetic biology software suite for DNA design, manufacturing and validation.

python_codon_tables/README.rst README.rstpython_codon_tables/README.rst renamed to README.rst

@@ -4,22 +4,18 @@ version = "0.1.16"
 license = "CC0-1.0"
 authors = [{ name = "Zulko" }]
 description = "Codon Usage Tables for Python, from kazusa.or.jp"
-readme = "python_codon_tables/README.rst"
+readme = "pypi-readme.rst"
 keywords = ["DNA", "codon", "usage"]
-dependencies = ["biopython"]
 
 [project.urls]
-Homepage = "https://github.com/Edinburgh-Genome-Foundry/codon-usage-tables"
+Homepage = "https://github.com/Edinburgh-Genome-Foundry/python_codon_tables"
 
 [build-system]
 requires = ["setuptools"]
 build-backend = "setuptools.build_meta"
 
-[tool.setuptools]
-include-package-data = true
+[tool.setuptools.packages.find]
+exclude = ["docs*", "examples*", "tests*"]
 
 [tool.setuptools.package-data]
-python_codon_tables = ["../codon_usage_data/*", "../codon_usage_data/**/*"]
-
-[tool.setuptools.packages.find]
-exclude = ["docs"]
+python_codon_tables = ["codon_usage_data/*", "codon_usage_data/**/*"]

codon_usage_data/version.txt

@@ -5,3 +5,5 @@
     get_all_available_codons_tables,
     download_codons_table,
 )
+
+from .version import __version__