pydna 5.5.2__py3-none-any.whl → 5.5.4__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (14) hide show
  1. pydna/__init__.py +1 -1
  2. pydna/assembly2.py +1116 -135
  3. pydna/cre_lox.py +130 -0
  4. pydna/dseqrecord.py +50 -2
  5. pydna/gateway.py +154 -152
  6. pydna/opencloning_models.py +553 -0
  7. pydna/parsers.py +23 -0
  8. pydna/seqrecord.py +1 -1
  9. pydna/sequence_regex.py +44 -0
  10. pydna/types.py +5 -2
  11. {pydna-5.5.2.dist-info → pydna-5.5.4.dist-info}/METADATA +14 -56
  12. {pydna-5.5.2.dist-info → pydna-5.5.4.dist-info}/RECORD +14 -11
  13. {pydna-5.5.2.dist-info → pydna-5.5.4.dist-info}/WHEEL +1 -1
  14. {pydna-5.5.2.dist-info → pydna-5.5.4.dist-info/licenses}/LICENSE.txt +0 -0
{pydna-5.5.2.dist-info → pydna-5.5.4.dist-info}/METADATA RENAMED
@@ -1,11 +1,12 @@
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- Metadata-Version: 2.3
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+ Metadata-Version: 2.4
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  Name: pydna
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- Version: 5.5.2
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+ Version: 5.5.4
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  Summary: Representing double stranded DNA and functions for simulating cloning and homologous recombination between DNA molecules.
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  License: BSD
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+ License-File: LICENSE.txt
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  Author: Björn F. Johansson
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  Author-email: bjornjobb@gmail.com
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- Requires-Python: >=3.9,<4.0
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+ Requires-Python: >=3.10,<4.0
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  Classifier: Development Status :: 4 - Beta
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  Classifier: Environment :: Console
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  Classifier: Intended Audience :: Education
@@ -13,7 +14,6 @@ Classifier: Intended Audience :: Developers
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  Classifier: Intended Audience :: Science/Research
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  Classifier: License :: OSI Approved :: BSD License
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  Classifier: Operating System :: OS Independent
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- Classifier: Programming Language :: Python :: 3.9
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  Classifier: Programming Language :: Python :: 3.10
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  Classifier: Programming Language :: Python :: 3.11
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  Classifier: Programming Language :: Python :: 3.12
@@ -24,12 +24,13 @@ Provides-Extra: download
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  Provides-Extra: express
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  Provides-Extra: gel
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  Requires-Dist: appdirs (>=1.4.4)
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- Requires-Dist: biopython (>=1.85)
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+ Requires-Dist: biopython (==1.85)
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  Requires-Dist: cai2 (>=1.0.5) ; extra == "express"
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  Requires-Dist: matplotlib (>=3.4.3) ; extra == "gel"
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  Requires-Dist: networkx (>=2.8.8)
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  Requires-Dist: numpy (>1.26) ; python_version < "3.12"
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  Requires-Dist: numpy (>=2.3.0) ; python_version >= "3.12"
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+ Requires-Dist: opencloning-linkml (==0.4.5)
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  Requires-Dist: pillow (>=8.4.0) ; extra == "gel"
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  Requires-Dist: prettytable (>=3.5.0)
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  Requires-Dist: pydivsufsort (>=0.0.14)
@@ -49,9 +50,9 @@ Description-Content-Type: text/markdown
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  # ![icon](https://github.com/pydna-group/pydna/blob/master/docs/_static/banner.png?raw=true)
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- | [![Tests & Coverage](https://github.com/pydna-group/pydna/actions/workflows/pydna_test_and_coverage_workflow.yml/badge.svg?branch=dev_bjorn)](https://github.com/pydna-group/pydna/actions/workflows/pydna_test_and_coverage_workflow.yml) | [![codecov](https://codecov.io/gh/BjornFJohansson/pydna/branch/master/graph/badge.svg)](https://codecov.io/gh/BjornFJohansson/pydna/branch/master) | [![PyPI version](https://badge.fury.io/py/pydna.svg)](https://badge.fury.io/py/pydna) | [![Google group : pydna](https://img.shields.io/badge/Google%20Group-pydna-blue.svg)](https://groups.google.com/g/pydna) |
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+ | [![Tests & Coverage](https://github.com/pydna-group/pydna/actions/workflows/pydna_test_and_coverage_workflow.yml/badge.svg?branch=master)](https://github.com/pydna-group/pydna/actions/workflows/pydna_test_and_coverage_workflow.yml) | [![codecov](https://codecov.io/gh/pydna-group/pydna/branch/master/graph/badge.svg)](https://codecov.io/gh/pydna-group/pydna/branch/master) | [![PyPI version](https://badge.fury.io/py/pydna.svg)](https://badge.fury.io/py/pydna) | [![Google group : pydna](https://img.shields.io/badge/Google%20Group-pydna-blue.svg)](https://groups.google.com/g/pydna) |
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  | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | -------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------- |
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- | [![Documentation Status](https://github.com/pydna-group/pydna/actions/workflows/publish-docs.yml/badge.svg)](https://github.com/pydna-group/pydna/actions/workflows/publish-docs.yml) | [![GitHub issues](https://img.shields.io/github/issues/BjornFJohansson/pydna.svg)](https://github.com/pydna-group/pydna/issues) | [![GitHub stars](https://img.shields.io/github/stars/BjornFJohansson/pydna.svg)](https://github.com/pydna-group/pydna/stargazers) | |
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+ | [![Documentation Status](https://github.com/pydna-group/pydna/actions/workflows/publish-docs.yml/badge.svg)](https://github.com/pydna-group/pydna/actions/workflows/publish-docs.yml) | [![GitHub issues](https://img.shields.io/github/issues/pydna-group/pydna.svg)](https://github.com/pydna-group/pydna/issues) | [![GitHub stars](https://img.shields.io/github/stars/pydna-group/pydna.svg)](https://github.com/pydna-group/pydna/stargazers) | |
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  <!-- docs/index.rst-start -->
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@@ -438,15 +439,11 @@ Feedback & suggestions are very welcome! Please create an issue with your questi
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  If you don't have a github account, you can get in touch through the [google group](https://groups.google.com/d/forum/pydna) for pydna.
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- Below are the instructions for developers who want to contribute to pydna. Please direct pull requests towards the `dev_bjorn` branch.
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+ Below are the instructions for developers who want to contribute to pydna. Please direct pull requests towards the `master` branch.
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  ### Fork the repository and set up a dev branch 🍴
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- Fork the entire repository (not just the `master` branch by unticking the "Copy the `master` branch only" box)
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- ![Fork](https://github.com/pydna-group/pydna/blob/master/docs/_static/create-fork.png?raw=true)
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- Create your branch starting from `dev_bjorn`, and if your changes are related to an issue, call the branch `issue_<number>`.
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+ Fork the repository. Create your branch starting from `master`, and if your changes are related to an issue, call the branch `issue_<number>`.
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  ```bash
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  # Clone the repository
@@ -455,12 +452,6 @@ git clone https://github.com/<your-username>/pydna.git
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  # Change to the repository directory
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  cd pydna
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- # Go to the dev_bjorn branch
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- git checkout -b dev_bjorn
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-
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- # Pull the current version of dev_bjorn
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- git pull origin dev_bjorn
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-
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  # Create your own branch
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  git checkout -b issue_<number>
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  ```
@@ -494,27 +485,6 @@ poetry shell
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  poetry run pre-commit install
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  ```
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- #### Alternative method (using `pip`) 🐍
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- Use this for a small contribution or if you don't manage to set up the dev environment.
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- ```bash
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- # Create a new virtual environment
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- python -m venv .venv
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-
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- # Activate the virtual environment
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- source .venv/bin/activate
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-
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- # Install all dependencies (library deps + dev and test requirements)
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- pip install -r requirements.txt
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-
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- # Install the project as editable dependency
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- pip install -e .
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-
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- # Install the pre-commit hooks
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- pre-commit install
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- ```
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-
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  #### Contributing code 💻
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  1. Make your changes.
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  ### Creating a PR 🔗
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- * From your fork, make a PR towards the branch `dev_bjorn` in the original repository.
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+ * From your fork, make a PR towards the branch `master` in the original repository.
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  * Mention the issue number in the PR description (e.g., `Closes #123`).
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  * Remember to click the "Allow edits from maintainers" checkbox so that we can make some changes to the PR if necessary.
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@@ -551,22 +521,10 @@ supported python versions.
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  ### Building the documentation locally 📚
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- Documentation is built using [Sphinx](http://www.sphinx-doc.org/) from [docstrings](https://www.python.org/dev/peps/pep-0257/)
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- using a GitHub [action](https://github.com/pydna-group/pydna/actions/workflows/publish-docs.yml).
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+ Documentation is built using [Sphinx](http://www.sphinx-doc.org/) from [docstrings](https://www.python.org/dev/peps/pep-0257/) using a GitHub [action](https://github.com/pydna-group/pydna/actions/workflows/publish-docs.yml) and also built in readthedocs.
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  The [numpy](https://www.numpy.org) [docstring format](https://numpy.org/doc/stable/dev/howto-docs.html#docstring-intro) is used.
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- Below the commands to run a local sphinx server that auto-updated when files are changed.
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- ```bash
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- # Install docs dependency group
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- poetry install --with docs
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- # Start the sphinx server to see docs live by default at http://127.0.0.1:8000/
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- sphinx-autobuild --watch src/ docs docs/_build/html
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- ```
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- More info about how to contribute to the documentation can be found [here](docs/README.md)
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+ To work locally with the documentation, check the [documentation README](docs/README.md) for instructions.
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  ## Release process 🚀
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@@ -596,7 +554,7 @@ Wang, Y., Xue, H., Pourcel, C., Du, Y., & Gautheret, D. (2021).
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  In Cold Spring Harbor Laboratory (p. 2021.01.17.427048). [DOI](https://doi.org/10.1101/2021.01.17.427048)
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  [PubMed](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8180056)
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- [ShareYourCloning](https://shareyourcloning.org), a web application for designing and documenting DNA cloning strategies.
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+ [OpenCloning](https://opencloning.org), a web application for designing and documenting DNA cloning strategies.
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  [An Automated Protein Synthesis Pipeline with Transcriptic and Snakemake](http://blog.booleanbiotech.com/transcriptic_protein_synthesis_pipeline.html)
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{pydna-5.5.2.dist-info → pydna-5.5.4.dist-info}/RECORD RENAMED
@@ -1,23 +1,24 @@
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- pydna/__init__.py,sha256=a08F6v_bfQLzTDkNEbjeSa3hadO_cuKH0mIAkoG1AtU,12867
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+ pydna/__init__.py,sha256=Fb-8yiWHmQwChAGIXW38c0iWfPw4Cm3tQLHTiBOU9pc,12867
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  pydna/_pretty.py,sha256=foRAxdL3Jiupuz7l38THBQZ7tu-5vQvLm1cKdDa7n6A,923
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  pydna/_thermodynamic_data.py,sha256=9_w-97DpkbsWbJGHVijscMvUS_SFt7GxzrxspMRPZSg,10903
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  pydna/all.py,sha256=xwkbR5Hn52xVfgLAXaEfIgtNwaBiGDbJFTQfa3Zi6HQ,1781
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  pydna/amplicon.py,sha256=X4rCSanhlx1sPN0eAtcdAWg4Lw0WKrGQhv-cgZKtM3s,5343
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  pydna/amplify.py,sha256=XRwmSMQ2d8Y379zcl56yU6rt1xWbSulWWHLqp-HRDc0,19260
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  pydna/assembly.py,sha256=LM3-s3YysFvvkl1oooxoBjYLt0iMc3E1YLoqE05i8bs,19936
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- pydna/assembly2.py,sha256=IN5tP5-FgdqLpIkAEKy9tXDG8x58iIgc6FUZSMr5kS0,73307
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+ pydna/assembly2.py,sha256=A_agqF57amqquwaYuEJmzhU8qn6XjGiNh1vHeDNcpC4,106017
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  pydna/codon.py,sha256=Nxa_03n2wxXKACkzi55bUN1t5xUU_DBRRwh_ZLIb9_o,2568
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  pydna/common_sub_strings.py,sha256=A-gJeA2cEyxKKGQSFoC0BKvcXUGJZcnTUU7x2xlAovc,11574
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  pydna/conftest.py,sha256=T5-WmHWLZH3U3ifxnbxd_oOiIFibIrkYpwNacCHlvsY,999
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  pydna/contig.py,sha256=m0XV0LO2AbArPZkjyNCf8c7_b1EkXFtYwXHJVG4eTY8,8168
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+ pydna/cre_lox.py,sha256=sOj9R8_oFPGWs68vc4jf6LqWOXjMsVSwtJaeKl6ZF2M,4476
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  pydna/crispr.py,sha256=iwu0Cjskzdb2r-In9633QIxQYKGmSNVOEM_dLK6lC54,3619
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  pydna/design.py,sha256=BAoPb4M47yMkF1p4gGmbomZPFyTl0WuXkv8sLSY_Tg0,29067
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  pydna/download.py,sha256=7tT8LAEy2Vg05spGfbCea_sol6pUOOBVbxOtyk2mnlQ,1085
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  pydna/dseq.py,sha256=2N_dXX36niJItQzN61PoVweee0xxP04_amJ3cSExAtU,54232
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- pydna/dseqrecord.py,sha256=9OSuxLqcJse3aIVZCVeN7bZCyohGt7WEXnnv1qBIcB0,47983
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+ pydna/dseqrecord.py,sha256=MMc6nWUqFfc8KmnDWKDeb2bze8qv9X2rSbZXSS-AXrU,49885
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  pydna/fakeseq.py,sha256=uxyu1PXF-sVasEqhmyhMcsbpTy84uUtubDiZuxHNb9c,1174
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  pydna/fusionpcr.py,sha256=tfIfGGkNoZjg_dodcEx9wTc12aLRnC7J3g-Vg3Jg1uA,2821
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- pydna/gateway.py,sha256=9OL6o9J_FQoQ5VExmHMIPDtDiJs3_4-whcS755BPCG0,8451
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+ pydna/gateway.py,sha256=iwNHrDIOqKl6_3Rdz7z7c8n_kcLQZuuu72oxNIjyyL8,8686
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  pydna/gel.py,sha256=QE1uhnjWXLl2nXgbLs_1TWbPixgUa0-z_UR8jZaByS4,3371
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  pydna/genbank.py,sha256=rH677VRklVKBpPoFRsl7Az8fZvrC8TD2lNrNoHO1wU8,8856
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  pydna/genbankfile.py,sha256=ii0_RjNGnsfUThTN01c5PRLSZkQT3WlYDvoC6R6ozAA,1451
@@ -26,18 +27,20 @@ pydna/genbankrecord.py,sha256=u9RNBifT0j8rrA2bSdWajodtwm42P52_VlXsxKeOvq0,5566
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  pydna/goldengate.py,sha256=LvUWAzhG9OhN1wil7osJIkjfqwBLh355a18wCZO1TvI,1778
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  pydna/ladders.py,sha256=fKfWwezxQpX4qon9YCMIwchMBkGVOu8-C02xXk90J-E,3310
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  pydna/ligate.py,sha256=ap8xgS4aL9cH4w38e-kpw1Ixa7DtpYF_ipezrVXiHG0,1965
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- pydna/parsers.py,sha256=RFYBCKrlqWzZbRWhg5lQE3pp31KjUNAarpAgHJuUpaU,6690
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+ pydna/opencloning_models.py,sha256=DOvoaG4eQSslguZQDWBsfYhKX1xxy4fYHQUqrdfMhmA,19535
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+ pydna/parsers.py,sha256=FW2RhZrxWX9wUYJcmt0qi1n7DZP0RfsNaXHhG0eVTWg,7319
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  pydna/primer.py,sha256=k9Z_fHfBcY_rGnOtfys806rQBDtvyKwKl2ceSx3_w9A,2272
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  pydna/readers.py,sha256=tKoonGlIB9ACeOMnzjhbCya1ooqhFMQIO_G36azN81E,1575
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  pydna/seq.py,sha256=82gR1g2D8jfPy1So1pSJvlXYk4zkcKx_qmgvcydxth4,7579
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- pydna/seqrecord.py,sha256=rzUUecmf9RkQdYHL0b9Pu8ofXM3Q6KThm-wv43jH0SA,23368
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+ pydna/seqrecord.py,sha256=haLp1316KQkROkQ0HkJp-RfgWN-eDyLPzTGFLjgXwHk,23363
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  pydna/sequence_picker.py,sha256=Pco9IrUwNSiS0wQ5hp5FMfE9kIN9XOwXasKLF9OA6DM,1402
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+ pydna/sequence_regex.py,sha256=DYuAJkWm_GqEGMpd0pE-Mad_B6POUP8gwjSCFR8RfXw,1259
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  pydna/threading_timer_decorator_exit.py,sha256=D91kqjKSavWDnXyc1Fo-CwPYtbmR2DjTXnBYSRXKmSA,2793
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  pydna/tm.py,sha256=0r4Aqjt_qanfqR8GNvqNh8us7AKM6JvaQKqHYsswAz4,11143
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- pydna/types.py,sha256=OE7iwA3b7f_T6EoBnYbRl9CFrY6OrSkAfuyY-R5kins,1389
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+ pydna/types.py,sha256=Y9HxQ0wd-1AGuBzCSIU9JwZhGSrAIZBAFYjmEdOyL3M,1490
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  pydna/user_cloning.py,sha256=VSpYX1tdbcD_PzEt69Jz6Lud-yAkYMVXnzVd4v2usnE,692
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  pydna/utils.py,sha256=BwBOcr2HyLAPAVdpXEEDiwJ5MeWW096EOekvfyXxbDM,25227
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- pydna-5.5.2.dist-info/LICENSE.txt,sha256=u8QfcsnNXZM0UCexerK_MvyA2lPWgeGyUtSYXvLG6Oc,6119
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- pydna-5.5.2.dist-info/METADATA,sha256=TsRUcktnk2S-D4iZncIM54BSgQJ3XYv8EyTRfAAOgJI,25439
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- pydna-5.5.2.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
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- pydna-5.5.2.dist-info/RECORD,,
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+ pydna-5.5.4.dist-info/METADATA,sha256=01RQRwIOoehyk7LNVpLSmQGgFynAyTZ97Di4juPnm0w,24379
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+ pydna-5.5.4.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
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+ pydna-5.5.4.dist-info/licenses/LICENSE.txt,sha256=u8QfcsnNXZM0UCexerK_MvyA2lPWgeGyUtSYXvLG6Oc,6119
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+ pydna-5.5.4.dist-info/RECORD,,
{pydna-5.5.2.dist-info → pydna-5.5.4.dist-info}/WHEEL RENAMED
@@ -1,4 +1,4 @@
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  Wheel-Version: 1.0
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- Generator: poetry-core 2.1.3
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+ Generator: poetry-core 2.2.1
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  Tag: py3-none-any