pydna 5.5.3__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 (9) hide show
  1. pydna/__init__.py +1 -1
  2. pydna/assembly2.py +415 -159
  3. pydna/dseqrecord.py +50 -2
  4. pydna/opencloning_models.py +553 -0
  5. pydna/types.py +5 -2
  6. {pydna-5.5.3.dist-info → pydna-5.5.4.dist-info}/METADATA +8 -40
  7. {pydna-5.5.3.dist-info → pydna-5.5.4.dist-info}/RECORD +9 -8
  8. {pydna-5.5.3.dist-info → pydna-5.5.4.dist-info}/WHEEL +1 -1
  9. {pydna-5.5.3.dist-info → pydna-5.5.4.dist-info/licenses}/LICENSE.txt +0 -0
{pydna-5.5.3.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: 5.5.3
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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)
@@ -484,27 +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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-
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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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-
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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.
@@ -541,22 +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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-
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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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-
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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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- ```
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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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{pydna-5.5.3.dist-info → pydna-5.5.4.dist-info}/RECORD RENAMED
@@ -1,11 +1,11 @@
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- pydna/__init__.py,sha256=aHQGRBpQdABGgHMwN6CfDMKGvsOpCVSs2f5I5ir5DMw,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=gyn-R2Jz3D6Pze27iE3IZ6JLvnqg72my9r-J34ZjWqI,98202
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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
@@ -15,7 +15,7 @@ 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=iwNHrDIOqKl6_3Rdz7z7c8n_kcLQZuuu72oxNIjyyL8,8686
@@ -27,6 +27,7 @@ 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/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
@@ -36,10 +37,10 @@ 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-5.5.3.dist-info/LICENSE.txt,sha256=u8QfcsnNXZM0UCexerK_MvyA2lPWgeGyUtSYXvLG6Oc,6119
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- pydna-5.5.3.dist-info/METADATA,sha256=Orph3mLdDMwKy21DsEucxGYPyLHX9p9FimxYMiaidYU,25090
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- pydna-5.5.3.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
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- pydna-5.5.3.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-5.5.3.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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  Root-Is-Purelib: true
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  Tag: py3-none-any