pydna 5.5.3__tar.gz → 5.5.4__tar.gz

{pydna-5.5.3 → pydna-5.5.4}/PKG-INFO

@@ -1,11 +1,12 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: pydna
-Version: 5.5.3
+Version: 5.5.4
 Summary: Representing double stranded DNA and functions for simulating cloning and homologous recombination between DNA molecules.
 License: BSD
+License-File: LICENSE.txt
 Author: Björn F. Johansson
 Author-email: bjornjobb@gmail.com
-Requires-Python: >=3.9,<4.0
+Requires-Python: >=3.10,<4.0
 Classifier: Development Status :: 4 - Beta
 Classifier: Environment :: Console
 Classifier: Intended Audience :: Education
@@ -13,7 +14,6 @@ Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
@@ -24,12 +24,13 @@ Provides-Extra: download
 Provides-Extra: express
 Provides-Extra: gel
 Requires-Dist: appdirs (>=1.4.4)
-Requires-Dist: biopython (>=1.85)
+Requires-Dist: biopython (==1.85)
 Requires-Dist: cai2 (>=1.0.5) ; extra == "express"
 Requires-Dist: matplotlib (>=3.4.3) ; extra == "gel"
 Requires-Dist: networkx (>=2.8.8)
 Requires-Dist: numpy (>1.26) ; python_version < "3.12"
 Requires-Dist: numpy (>=2.3.0) ; python_version >= "3.12"
+Requires-Dist: opencloning-linkml (==0.4.5)
 Requires-Dist: pillow (>=8.4.0) ; extra == "gel"
 Requires-Dist: prettytable (>=3.5.0)
 Requires-Dist: pydivsufsort (>=0.0.14)
@@ -484,27 +485,6 @@ poetry shell
 poetry run pre-commit install
 ```
 
-#### Alternative method (using `pip`) 🐍
-
-Use this for a small contribution or if you don't manage to set up the dev environment.
-
-```bash
-# Create a new virtual environment
-python -m venv .venv
-
-# Activate the virtual environment
-source .venv/bin/activate
-
-# Install all dependencies (library deps + dev and test requirements)
-pip install -r requirements.txt
-
-# Install the project as editable dependency
-pip install -e .
-
-# Install the pre-commit hooks
-pre-commit install
-```
-
 #### Contributing code 💻
 
 1. Make your changes.
@@ -541,22 +521,10 @@ supported python versions.
 
 ### Building the documentation locally 📚
 
-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).
+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.
 The [numpy](https://www.numpy.org) [docstring format](https://numpy.org/doc/stable/dev/howto-docs.html#docstring-intro) is used.
 
-Below the commands to run a local sphinx server that auto-updated when files are changed.
-
-```bash
-# Install docs dependency group
-poetry install --with docs
-
-# Start the sphinx server to see docs live by default at http://127.0.0.1:8000/
-sphinx-autobuild --watch src/ docs docs/_build/html
-
-```
-
-More info about how to contribute to the documentation can be found [here](docs/README.md)
+To work locally with the documentation, check the [documentation README](docs/README.md) for instructions.
 
 ## Release process 🚀
 

{pydna-5.5.3 → pydna-5.5.4}/README.md

@@ -435,27 +435,6 @@ poetry shell
 poetry run pre-commit install
 ```
 
-#### Alternative method (using `pip`) 🐍
-
-Use this for a small contribution or if you don't manage to set up the dev environment.
-
-```bash
-# Create a new virtual environment
-python -m venv .venv
-
-# Activate the virtual environment
-source .venv/bin/activate
-
-# Install all dependencies (library deps + dev and test requirements)
-pip install -r requirements.txt
-
-# Install the project as editable dependency
-pip install -e .
-
-# Install the pre-commit hooks
-pre-commit install
-```
-
 #### Contributing code 💻
 
 1. Make your changes.
@@ -492,22 +471,10 @@ supported python versions.
 
 ### Building the documentation locally 📚
 
-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).
+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.
 The [numpy](https://www.numpy.org) [docstring format](https://numpy.org/doc/stable/dev/howto-docs.html#docstring-intro) is used.
 
-Below the commands to run a local sphinx server that auto-updated when files are changed.
-
-```bash
-# Install docs dependency group
-poetry install --with docs
-
-# Start the sphinx server to see docs live by default at http://127.0.0.1:8000/
-sphinx-autobuild --watch src/ docs docs/_build/html
-
-```
-
-More info about how to contribute to the documentation can be found [here](docs/README.md)
+To work locally with the documentation, check the [documentation README](docs/README.md) for instructions.
 
 ## Release process 🚀
 

{pydna-5.5.3 → pydna-5.5.4}/pyproject.toml

@@ -11,7 +11,6 @@ classifiers = [
   "Intended Audience :: Science/Research",
   "License :: OSI Approved :: BSD License",
   "Operating System :: OS Independent",
-  "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
@@ -36,10 +35,10 @@ license = "BSD"
 name = "pydna"
 readme = "README.md"
 repository = "https://github.com/pydna-group/pydna/tree/master"
-version = "5.5.3"
+version = "5.5.4"
 [tool.poetry.dependencies]
 appdirs = ">=1.4.4"
-biopython = ">=1.85"
+biopython = "1.85"
 cai2 = { version = ">=1.0.5", optional = true }
 matplotlib = { version = ">=3.4.3", optional = true }
 networkx = ">=2.8.8"
@@ -53,7 +52,7 @@ pydivsufsort = ">=0.0.14"
 pyfiglet = "0.8.post1"
 pyparsing = { version = ">=2.4.7", optional = true }
 pyperclip = { version = ">=1.8.2", optional = true }
-python = ">=3.9,<4.0"
+python = ">=3.10,<4.0"
 requests = { version = ">=2.26.0", optional = true }
 scipy = [
   { version = ">=1.11.3", python = ">=3.12", optional = true },
@@ -61,6 +60,7 @@ scipy = [
 ]
 seguid = ">=0.0.5"
 regex = "^2024.11.6"
+opencloning-linkml = "0.4.5"
 [tool.poetry.extras]
 clipboard = ["pyperclip"]
 download = ["pyparsing", "requests"]
@@ -87,13 +87,16 @@ requests-mock = ">=1.10.0"
 
 [tool.poetry.group.docs.dependencies]
 numpydoc = "^1.6.0"
-sphinx-autobuild = "^2021.3.14"
-sphinx-rtd-theme = ">=1.3,<4.0"
-nbconvert = "^7.16.4"
-myst-parser = [
-  { version = ">3.0.0", python = "<3.10" },
-  { version = ">=4.0.0", python = ">=3.10" },
-]
+sphinx = "*"
+# sphinx-rtd-theme = ">=1.3,<4.0"
+# nbconvert = "^7.16.4"
+# myst-parser = [
+#   { version = ">3.0.0", python = "<3.10" },
+#   { version = ">=4.0.0", python = ">=3.10" },
+# ]
+myst-nb = "*"
+sphinx-book-theme = "*"
+pandas = "*"
 
 [tool.poetry.group.dev.dependencies]
 autopep8 = "^2.1.0"

{pydna-5.5.3 → pydna-5.5.4}/src/pydna/__init__.py

@@ -151,7 +151,7 @@ __license__ = "BSD"
 __maintainer__ = "Björn Johansson"
 __email__ = "bjorn_johansson@bio.uminho.pt"
 __status__ = "Development"  # "Production" #"Prototype"
-__version__ = "5.5.3"
+__version__ = "5.5.4"
 
 
 # obtain config directory from env or appdirs