pydna 5.5.3__tar.gz → 5.5.5__tar.gz

{pydna-5.5.3 → pydna-5.5.5}/PKG-INFO

@@ -1,11 +1,12 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: pydna
-Version: 5.5.3
+Version: 5.5.5
 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
@@ -23,15 +23,18 @@ Provides-Extra: clipboard
 Provides-Extra: download
 Provides-Extra: express
 Provides-Extra: gel
+Provides-Extra: primer-screen
 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 (>=0.4.9,<0.5.0)
 Requires-Dist: pillow (>=8.4.0) ; extra == "gel"
 Requires-Dist: prettytable (>=3.5.0)
+Requires-Dist: pyahocorasick (>=2.2.0) ; extra == "primer-screen"
 Requires-Dist: pydivsufsort (>=0.0.14)
 Requires-Dist: pyfiglet (==0.8.post1)
 Requires-Dist: pyparsing (>=2.4.7) ; extra == "download"
@@ -484,27 +487,6 @@ 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.
@@ -526,7 +508,7 @@ pre-commit install
 > =================================== FAILURES ===================================
 > ___________________ [doctest] pydna.assembly2.blunt_overlap ____________________
 > ```
-> This means that the doctest of the function `blunt_overlap` failed. You can run the same test locally with `python -m doctest src/pydna/assembly2.py` (use the appropriate path to the module file). That will give you information of what's failing. Fix, and re-run until it passes!
+> This means that the doctest of the function `blunt_overlap` failed. You can run the same test locally with `pytest src/pydna --doctest-modules` (use the appropriate path to the module file). That will give you information of what's failing. Fix, and re-run until it passes!
 
 ### Creating a PR 🔗
 
@@ -541,39 +523,25 @@ 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 🚀
 
 See the [releases](https://github.com/pydna-group/pydna/releases) for changes and releases.
 
 The build workflow builds a PyPI packages using poetry. This workflow is triggered by publishing a Github release manually from the Github web interface.
+We keep future release names [here](https://docs.google.com/document/d/1PrBYKzDh6QBcqfH9ksjpgArJo3ibDhMRNcibfXtYmCc/edit?tab=t.0). Please edit to
+reflect used release names.
 
-![----]( http://bit.ly/coloredline)
+![----](http://bit.ly/coloredline)
 
 ## History 📜
 
 Pydna was made public in 2012 on [Google code](https://code.google.com/archive/p/pydna).
 
-:microbe:
-
-:portugal:
-
 ## Who is using pydna? 🧪
 
 Taylor, L. J., & Strebel, K. (2017).

{pydna-5.5.3 → pydna-5.5.5}/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.
@@ -477,7 +456,7 @@ pre-commit install
 > =================================== FAILURES ===================================
 > ___________________ [doctest] pydna.assembly2.blunt_overlap ____________________
 > ```
-> This means that the doctest of the function `blunt_overlap` failed. You can run the same test locally with `python -m doctest src/pydna/assembly2.py` (use the appropriate path to the module file). That will give you information of what's failing. Fix, and re-run until it passes!
+> This means that the doctest of the function `blunt_overlap` failed. You can run the same test locally with `pytest src/pydna --doctest-modules` (use the appropriate path to the module file). That will give you information of what's failing. Fix, and re-run until it passes!
 
 ### Creating a PR 🔗
 
@@ -492,39 +471,25 @@ 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 🚀
 
 See the [releases](https://github.com/pydna-group/pydna/releases) for changes and releases.
 
 The build workflow builds a PyPI packages using poetry. This workflow is triggered by publishing a Github release manually from the Github web interface.
+We keep future release names [here](https://docs.google.com/document/d/1PrBYKzDh6QBcqfH9ksjpgArJo3ibDhMRNcibfXtYmCc/edit?tab=t.0). Please edit to
+reflect used release names.
 
-![----]( http://bit.ly/coloredline)
+![----](http://bit.ly/coloredline)
 
 ## History 📜
 
 Pydna was made public in 2012 on [Google code](https://code.google.com/archive/p/pydna).
 
-:microbe:
-
-:portugal:
-
 ## Who is using pydna? 🧪
 
 Taylor, L. J., & Strebel, K. (2017).

{pydna-5.5.3 → pydna-5.5.5}/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 = "5.5.5"
 [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"
@@ -53,19 +52,22 @@ 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 }
+pyahocorasick = { version = ">=2.2.0", optional = true }
 scipy = [
   { version = ">=1.11.3", python = ">=3.12", optional = true },
   { version = ">=1.9.3", python = "<3.12", optional = true },
 ]
 seguid = ">=0.0.5"
 regex = "^2024.11.6"
+opencloning-linkml = "^0.4.9"
 [tool.poetry.extras]
 clipboard = ["pyperclip"]
 download = ["pyparsing", "requests"]
 express = ["cai2"]
 gel = ["scipy", "matplotlib", "pillow"]
+primer_screen = ["pyahocorasick"]
 [build-system]
 build-backend = "poetry_dynamic_versioning.backend"
 requires = ["poetry-core", "poetry-dynamic-versioning"]
@@ -87,38 +89,34 @@ 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"
 black = "^25.1.0"
 pre-commit = ">3.6"
-nbstripout = "^0.7.1"
+nbstripout = "^0.9"
 flake8-bugbear = "^24.12.12"
 
 [tool.pytest.ini_options]
 minversion = "6.0.2"
 python_files = "test_*.py"
-testpaths = ["tests", "src"]
+testpaths = ["tests", "src/pydna"]
+norecursedirs = ["*"]
+
 [tool.black]
 include = '\.pyi?$'
 line-length = 88
 target-version = ["py38", "py39", "py310", "py311", "py312"]
-# 'extend-exclude' excludes files or directories in addition to the defaults
-extend-exclude = '''
-(
-  ^/foo.py         # exclude a file named foo.py in the root of the project
-  | .*_pb2.py      # exclude autogenerated Protocol Buffer files anywhere in the project
-  | ^docs/         # exclude all files in the docs/ directory
-  | ^tests/        # exclude all files in the tests/ directory
-)
-'''
 
 [tool.poetry.requires-plugins]
 poetry-plugin-export = ">=1.9"

pydna-5.5.5/src/pydna/__init__.py

@@ -0,0 +1,229 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# Copyright 2013-2023 by Björn Johansson.  All rights reserved.
+# This code is part of the Python-dna distribution and governed by its
+# license.  Please see the LICENSE.txt file that should have been included
+# as part of this package.
+
+
+"""
+:copyright: Copyright 2013-2023 by Björn Johansson. All rights reserved.
+:license:   This code is part of the pydna package, governed by the
+            license in LICENSE.txt that should be included as part
+            of this package.
+
+pydna
+=====
+Pydna is a python package providing code for simulation of the creation of
+recombinant DNA molecules using
+`molecular biology <https://en.wikipedia.org/wiki/Molecular_biology>`_
+techniques. Development of pydna happens in this Github `repository <https://github.com/pydna-group/pydna>`_.
+
+Provided:
+  1. PCR simulation
+  2. Assembly simulation based on shared identical sequences
+  3. Primer design for amplification of a given sequence
+  4. Automatic design of primer tails for Gibson assembly
+     or homologous recombination.
+  5. Restriction digestion and cut&paste cloning
+  6. Agarose gel simulation
+  7. Download sequences from Genbank
+  8. Parsing various sequence formats including the capacity to
+     handle broken Genbank format
+
+pydna package layout
+--------------------
+
+The most important modules and how to import functions or classes from
+them are listed below. Class names starts with a capital letter,
+functions with a lowercase letter:
+
+::
+
+      from pydna.module import function
+      from pydna.module import Class
+
+      Example: from pydna.gel import Gel
+
+      pydna
+         ├── amplify
+         │         ├── Anneal
+         │         └── pcr
+         ├── assembly
+         │          └── Assembly
+         ├── design
+         │        ├── assembly_fragments
+         │        └── primer_design
+         ├── download
+         │          └── download_text
+         ├── dseqrecord
+         │            └── Dseqrecord
+         ├── gel
+         │     └── Gel
+         ├── genbank
+         │         ├── genbank
+         │         └── Genbank
+         ├── parsers
+         │         ├── parse
+         │         └── parse_primers
+         └── readers
+                   ├── read
+                   └── read_primers
+
+
+
+How to use the documentation
+----------------------------
+Documentation is available as docstrings provided in the source code for
+each module.
+These docstrings can be inspected by reading the source code directly.
+See further below on how to obtain the code for pydna.
+
+In the python shell, use the built-in ``help`` function to view a
+function's docstring::
+
+  >>> from pydna import readers
+  >>> help(readers.read)
+  ... # doctest: +SKIP
+
+The doctrings are also used to provide an automaticly generated reference
+manual available online at
+`read the docs <https://pydna-group.github.io/pydna>`_.
+
+Docstrings can be explored using `IPython <http://ipython.org/>`_, an
+advanced Python shell with
+TAB-completion and introspection capabilities. To see which functions
+are available in `pydna`,
+type `pydna.<TAB>` (where `<TAB>` refers to the TAB key).
+Use `pydna.open_config_folder?<ENTER>`to view the docstring or
+`pydna.open_config_folder??<ENTER>` to view the source code.
+
+In the `Spyder IDE <https://github.com/spyder-ide/spyder>`_ it is possible
+to place the cursor immediately before the name of a module,class or
+function and press ctrl+i to bring up docstrings in a separate window in Spyder
+
+Code snippets are indicated by three greater-than signs::
+
+    >>> x=41
+    >>> x=x+1
+    >>> x
+    42
+
+pydna source code
+-----------------
+
+The pydna source code is
+`available on Github <https://github.com/pydna-group/pydna>`_.
+
+How to get more help
+--------------------
+
+Please join the
+`Google group <https://groups.google.com/forum/#!forum/pydna>`_
+for pydna, this is the preferred location for help. If you find bugs
+in pydna itself, open an issue at the
+`Github repository <https://github.com/pydna-group/pydna/issues>`_.
+
+Examples of pydna in use
+------------------------
+
+See this repository for a collection of
+ `examples <https://github.com/MetabolicEngineeringGroupCBMA/pydna-examples?tab=readme-ov-file#pydna-examples>`_.
+
+"""
+
+from pydna._pretty import PrettyTable
+from Bio.Restriction import FormattedSeq
+import os
+
+__author__ = "Björn Johansson"
+__copyright__ = "Copyright 2013 - 2023 Björn Johansson"
+__credits__ = ["Björn Johansson", "Mark Budde"]
+__license__ = "BSD"
+__maintainer__ = "Björn Johansson"
+__email__ = "bjorn_johansson@bio.uminho.pt"
+__status__ = "Development"  # "Production" #"Prototype"
+__version__ = "5.5.5"
+
+
+class _PydnaWarning(Warning):
+    """Pydna warning.
+
+    Pydna uses this warning (or subclasses of it), to make it easy to
+    silence all warning messages:
+
+    >>> import warnings
+    >>> from pydna import _PydnaWarning
+    >>> warnings.simplefilter('ignore', _PydnaWarning)
+
+    Consult the warnings module documentation for more details.
+    """
+
+    pass
+
+
+class _PydnaDeprecationWarning(_PydnaWarning):
+    """pydna deprecation warning.
+
+    Pydna uses this warning instead of the built in DeprecationWarning
+    since those are ignored by default since Python 2.7.
+
+    To silence all our deprecation warning messages, use:
+
+    >>> import warnings
+    >>> from pydna import _PydnaDeprecationWarning
+    >>> warnings.simplefilter('ignore', _PydnaDeprecationWarning)
+
+    Code marked as deprecated will be removed in a future version
+    of Pydna. This can be discussed in the Pydna google group:
+    https://groups.google.com/forum/#!forum/pydna
+
+    """
+
+    pass
+
+
+def get_env():
+    """Print a an ascii table containing all environmental variables.
+
+    Pydna related variables have names that starts with `pydna_`
+    """
+    _table = PrettyTable(["Variable", "Value"])
+    # _table.set_style(_prettytable.DEFAULT)
+    _table.align["Variable"] = "l"  # Left align
+    _table.align["Value"] = "l"  # Left align
+    _table.padding_width = 1  # One space between column edges and contents
+    for k, v in sorted(os.environ.items()):
+        if k.lower().startswith("pydna"):
+            _table.add_row([k, v])
+    return _table
+
+
+def logo():
+    """Ascii-art logotype of pydna."""
+    from pydna._pretty import pretty_str
+
+    message = f"pydna {__version__}"
+    try:
+        from pyfiglet import Figlet
+    except ModuleNotFoundError:
+        pass
+    else:
+        f = Figlet()
+        message = f.renderText(message)
+    return pretty_str(message)
+
+
+## Override Bio.Restriction.FormattedSeq._table
+
+
+def _make_FormattedSeq_table() -> bytes:
+    table = bytearray(256)
+    upper_to_lower = ord("A") - ord("a")
+    for c in b"ABCDEFGHIJKLMNOPQRSTUVWXYZ":  # Only allow IUPAC letters
+        table[c] = c  # map uppercase to uppercase
+        table[c - upper_to_lower] = c  # map lowercase to uppercase
+    return bytes(table)
+
+
+FormattedSeq._table = _make_FormattedSeq_table()

{pydna-5.5.3 → pydna-5.5.5}/src/pydna/_pretty.py

@@ -6,10 +6,10 @@ The pretty_str class is similar to str but has a _repr_pretty_ method
 for for nicer string output in the IPython shell and Jupyter notebook.
 """
 
-from prettytable import PrettyTable as _Pt
-from prettytable import TableStyle as _TableStyle
-from copy import copy as _copy
-from typing import List as _List
+from prettytable import PrettyTable as Pt
+from prettytable import TableStyle
+from copy import copy
+from typing import List
 
 
 class pretty_str(str):
@@ -19,10 +19,10 @@ class pretty_str(str):
         p.text(self)
 
 
-class PrettyTable(_Pt):
+class PrettyTable(Pt):
     """docstring."""
 
-    def lol(self) -> _List[list]:
+    def lol(self) -> List[list]:
         """docstring."""
         return [self._field_names] + self._rows
 
@@ -31,6 +31,6 @@ class PrettyTable(_Pt):
         return self.get_string()
 
     def _repr_markdown_(self) -> pretty_str:
-        c = _copy(self)
-        c.set_style(_TableStyle.MARKDOWN)
+        c = copy(self)
+        c.set_style(TableStyle.MARKDOWN)
         return pretty_str(c.get_string())

{pydna-5.5.3 → pydna-5.5.5}/src/pydna/_thermodynamic_data.py

@@ -5,10 +5,10 @@
 # license.  Please see the LICENSE.txt file that should have been included
 # as part of this package.
 
-import collections as _collections
+import collections
 
-dHBr = _collections.defaultdict(dict)
-dSBr = _collections.defaultdict(dict)
+dHBr = collections.defaultdict(dict)
+dSBr = collections.defaultdict(dict)
 
 dHBr[0][0] = -9100
 dSBr[0][0] = -24