Initialize package

.github/workflows/build.yml

@@ -0,0 +1,30 @@
+name: build
+
+on: [workflow_dispatch]
+
+jobs:
+ build:
+
+ runs-on: ubuntu-latest
+
+ steps:
+ - uses: actions/checkout@v2
+ - name: Set up Python 3.9
+ uses: actions/setup-python@v2
+ with:
+ python-version: '3.9'
+ - name: Install dependencies
+ run: |
+ python -m pip install --upgrade pip
+ pip install pytest pytest-cov coveralls
+ - name: Test pip installation
+ run: |
+ pip install -e .
+ - name: Test with pytest
+ run: |
+ python -m pytest --cov seqreport --cov-report term-missing
+ - name: Coveralls
+ run: coveralls
+ env:
+ GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+ COVERALLS_SERVICE_NAME: github

.gitignore

@@ -0,0 +1,129 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+# Usually these files are written by a python script from a template
+# before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+# However, in case of collaboration, if having platform-specific dependencies or dependencies
+# having no cross-platform support, pipenv may install dependencies that don't work, or not
+# install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2024 Edinburgh Genome Foundry
+Copyright (c) 2024 Edinburgh Genome Foundry, University of Edinburgh
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -1,2 +1,36 @@
-# Seq_Report
-Simple reporting on a set of sequences for documentation purposes
+<p align="center">
+<img alt="EGF logo" title="EGF" src="images/egf.png" width="120">
+</p>
+
+# Seq Report
+
+<!-- [![build](https://github.com/Edinburgh-Genome-Foundry/Seq_Report/actions/workflows/build.yml/badge.svg)](https://github.com/Edinburgh-Genome-Foundry/Seq_Report/actions/workflows/build.yml) -->
+
+<!-- [![coverage](https://coveralls.io/repos/github/Edinburgh-Genome-Foundry/Seq_Report/badge.svg?branch=main)](https://coveralls.io/github/Edinburgh-Genome-Foundry/Seq_Report?branch=main) -->
+
+Simple reporting on a set of sequences for documentation purposes.
+
+## Install
+
+```bash
+pip install git+https://github.com/Edinburgh-Genome-Foundry/Seq_Report.git
+```
+
+## Usage
+
+```python
+import seqreport
+```
+
+## Versioning
+
+Seq Report uses the [semantic versioning](https://semver.org) scheme.
+
+## License = MIT
+
+Seq Report is free/libre and open-source software, which means the users have the freedom to run, study, change and distribute the software.
+
+Seq Report was written at the [Edinburgh Genome Foundry](https://edinburgh-genome-foundry.github.io/)
+by [Peter Vegh](https://github.com/veghp).
+
+Copyright 2024 Edinburgh Genome Foundry, University of Edinburgh

pypi-readme.rst

@@ -0,0 +1,33 @@
+Seq Report
+==========
+
+Simple reporting on a set of sequences for documentation purposes
+
+
+**Install:**
+
+.. code:: bash
+
+ pip install git+https://github.com/Edinburgh-Genome-Foundry/Seq_Report.git
+
+
+**Web documentation:**
+
+`<https://edinburgh-genome-foundry.github.io/Seq_Report/>`_
+
+
+**Github page:**
+
+`<https://github.com/Edinburgh-Genome-Foundry/Seq_Report>`_
+
+
+**License:** MIT, Copyright 2024 Edinburgh Genome Foundry, University of Edinburgh
+
+
+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/
+
+Seq Report is part of the `EGF Codons <https://edinburgh-genome-foundry.github.io/>`_ synthetic biology software suite for DNA design, manufacturing and validation.

seqreport/version.py

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+__version__ = "0.1.0"

setup.py

@@ -0,0 +1,19 @@
+from setuptools import setup, find_packages
+
+version = {}
+with open("seqreport/version.py") as fp:
+ exec(fp.read(), version)
+
+setup(
+ name="seqreport",
+ version=version["__version__"],
+ author="Peter Vegh",
+ description="Simple reporting on a set of sequences for documentation purposes",
+ long_description=open("pypi-readme.rst").read(),
+ long_description_content_type="text/x-rst",
+ license="MIT",
+ keywords="biology dna",
+ packages=find_packages(exclude="docs"),
+ include_package_data=True,
+ install_requires=[],
+)