pydna 6.0.0a3__tar.gz → 6.0.0a15__tar.gz

{pydna-6.0.0a3 → pydna-6.0.0a15}/PKG-INFO

@@ -1,7 +1,8 @@
 Metadata-Version: 2.1
 Name: pydna
-Version: 6.0.0a3
+Version: 6.0.0a15
 Summary: Representing double stranded DNA and functions for simulating cloning and homologous recombination between DNA molecules.
+Home-page: https://github.com/BjornFJohansson/pydna#-pydna
 License: BSD
 Author: BjornFJohansson
 Author-email: bjornjobb@gmail.com
@@ -12,11 +13,11 @@ Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Provides-Extra: clipboard
 Provides-Extra: download
 Provides-Extra: express
 Provides-Extra: gel
-Provides-Extra: gui
 Requires-Dist: appdirs (>=1.4.4)
 Requires-Dist: biopython (>=1.80)
 Requires-Dist: cai2 (>=1.0.5) ; extra == "express"
@@ -25,19 +26,21 @@ Requires-Dist: networkx (>=2.8.8)
 Requires-Dist: pillow (>=8.4.0) ; extra == "gel"
 Requires-Dist: prettytable (>=3.5.0)
 Requires-Dist: pydivsufsort (>=0.0.11)
-Requires-Dist: pyfiglet (>=0.8.post1)
+Requires-Dist: pyfiglet (==0.8.post1)
 Requires-Dist: pyparsing (>=2.4.7) ; extra == "download"
 Requires-Dist: pyperclip (>=1.8.2) ; extra == "clipboard"
-Requires-Dist: pyqt5 (>=5.15.0) ; extra == "gui"
 Requires-Dist: requests (>=2.26.0) ; extra == "download"
-Requires-Dist: scipy (>=1.8.0) ; extra == "gel"
+Requires-Dist: scipy (>=1.9.3) ; extra == "gel"
+Project-URL: Changelog, https://github.com/BjornFJohansson/pydna/blob/master/docs/CHANGELOG.md#changelog
+Project-URL: Documentation, https://pydna.readthedocs.io/?badge=latest
+Project-URL: Repository, https://github.com/BjornFJohansson/pydna/tree/dev_bjorn
 Description-Content-Type: text/markdown
 
 # ![icon](https://raw.githubusercontent.com/bjornFJohansson/pydna/master/docs/pics/pydna.resized.png) pydna
 
-| [![Tests & Coverage](https://github.com/BjornFJohansson/pydna/actions/workflows/pydna_test_and_coverage_workflow.yml/badge.svg?branch=dev_bjorn)](https://github.com/BjornFJohansson/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)              |
-|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------|
-| [![Documentation Status](https://readthedocs.org/projects/pydna/badge/?version=latest)](http://pydna.readthedocs.io/?badge=latest)                                                                   | [![GitHub issues](https://img.shields.io/github/issues/BjornFJohansson/pydna.svg)](https://github.com/BjornFJohansson/pydna/issues)                | [![Anaconda-Server Badge2](https://anaconda.org/bjornfjohansson/pydna/badges/license.svg)](https://anaconda.org/bjornfjohansson/pydna) | [![GitHub stars](https://img.shields.io/github/stars/BjornFJohansson/pydna.svg)](https://github.com/BjornFJohansson/pydna/stargazers) |
+| [![Tests & Coverage](https://github.com/BjornFJohansson/pydna/actions/workflows/pydna_test_and_coverage_workflow.yml/badge.svg?branch=dev_bjorn)](https://github.com/BjornFJohansson/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)              |
+| -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------- |
+| [![Documentation Status](https://readthedocs.org/projects/pydna/badge/?version=latest)](http://pydna.readthedocs.io/?badge=latest)                                                                                                                 | [![GitHub issues](https://img.shields.io/github/issues/BjornFJohansson/pydna.svg)](https://github.com/BjornFJohansson/pydna/issues)                | [![Anaconda-Server Badge2](https://anaconda.org/bjornfjohansson/pydna/badges/license.svg)](https://anaconda.org/bjornfjohansson/pydna) | [![GitHub stars](https://img.shields.io/github/stars/BjornFJohansson/pydna.svg)](https://github.com/BjornFJohansson/pydna/stargazers) |
 
 
 
@@ -62,7 +65,7 @@ Pydna provides simulation of:
 - Gel electrophoresis of DNA with generation of gel images
 - Homologous recombination
 - Gibson assembly
-- Golden gate assembly
+- Golden gate assembly (in progress)
 
 
 Virtually any sub-cloning experiment can be described in pydna, and its execution yield
@@ -73,12 +76,13 @@ Pydna has been designed with the goal of being understandable for biologists wit
 Pydna can formalize planning and sharing of cloning strategies and is especially useful for complex or combinatorial
 DNA molecule constructions.
 
-To get started, I have compiled some [simple examples](https://github.com/MetabolicEngineeringGroupCBMA/pydna-examples#pydna-examples).
-For more elaborate use, look at some assembly strategies of D-xylose metabolic pathways [MetabolicEngineeringGroupCBMA/ypk-xylose-pathways](https://github.com/MetabolicEngineeringGroupCBMA/ypk-xylose-pathways#pereira-et-al-2016).
-
+Start by looking at the [cookbook](https://github.com/BjornFJohansson/pydna/blob/master/docs/cookbook/cookbook.ipynb).
 
+Some simple examples can be found  [here](https://github.com/MetabolicEngineeringGroupCBMA/pydna-examples#pydna-examples).
 
+For more elaborate use, look at some assembly strategies of D-xylose metabolic pathways [MetabolicEngineeringGroupCBMA/ypk-xylose-pathways](https://github.com/MetabolicEngineeringGroupCBMA/ypk-xylose-pathways#pereira-et-al-2016).
 
+See below for documentation.
 
 ![----]( http://bit.ly/coloredline)
 
@@ -115,11 +119,7 @@ DNA sequences are downloaded from Genbank by accession numbers that are guarante
     lin_vector = vector.linearize(EcoRV)
     rec_vec =  ( lin_vector + pcr_prod ).looped()
 
-Pydna can automate the simulation of [sub cloning](http://en.wikipedia.org/wiki/Subcloning) experiments using
-python. This is helpful to generate examples for teaching purposes.
-
-Read the documentation (below) or the [cookbook](https://github.com/BjornFJohansson/pydna/blob/master/docs/cookbook/cookbook.ipynb) with example files
-for further information.
+Another use case for pydna in the automatic generation of [sub cloning](http://en.wikipedia.org/wiki/Subcloning) examples for teaching purposes. These examples
 
 Feedback & suggestions are very welcome! Please post a message in the [google group](https://groups.google.com/d/forum/pydna) for pydna if you need help or have problems, questions or comments :sos:.
 
@@ -161,11 +161,10 @@ When using pydna.
 
 ![----]( http://bit.ly/coloredline)
 
-## Documentation
+## Documentation :page_with_curl:
 
 Documentation is built using [Sphinx](http://www.sphinx-doc.org/) from [docstrings](https://www.python.org/dev/peps/pep-0257/)
-in the code and displayed at readthedocs [![Documentation Status](https://readthedocs.org/projects/pydna/badge/?version=latest)](http://pydna.readthedocs.io/?badge=latest)
-
+in the code and displayed at readthedocs [![Documentation Status](https://readthedocs.org/projects/pydna/badge/?version=latest)](http://pydna.readthedocs.io/?badge=latest).
 The [numpy](www.numpy.org) [docstring format](https://github.com/numpy/numpy/blob/release/doc/HOWTO_DOCUMENT.rst.txt) is used.
 
 ![----]( http://bit.ly/coloredline)
@@ -185,7 +184,7 @@ or use the --pre switch to get the latest version of pydna.
 
 for optional functionality do:
 
-    pip install pydna[gel,download,express,gui]
+    pip install pydna[clipboard,download,express,gel]
 
 Remove options inside the square brackets as required, but be sure not to leave spaces as pip will not recognize the options. See below under "Optional dependencies".
 
@@ -213,32 +212,65 @@ I am happy to collaborate on new features or bugfixes.
 The list below is the minimal requirements for installing pydna.
 Biopython and pydivsufsort has c-extensions, but the other modules are pure python.
 
-- [Python 3.8, 3.9, 3.10 or 3.11](http://www.python.org)
+- [Python 3.8, 3.9, 3.10, 3.11 or 3.12](http://www.python.org)
 - [appdirs](https://pypi.python.org/pypi/appdirs)
 - [biopython](http://pypi.python.org/pypi/biopython)
 - [networkx](http://pypi.python.org/pypi/networkx)
 - [prettytable](https://pypi.python.org/pypi/PrettyTable)
 - [pydivsufsort](https://pypi.python.org/pypi/pydivsufsort)
+- [pyfiglet](https://pypi.python.org/pypi/pyfiglet)
 
-The above modules are installed as well as pyperclip and pyfiglet.
-Pydna is importable even without these two modules.
+Pydna is importable even without pyfiglet.
 
 ## Optional dependencies
 
-If the modules listed below in the first column are installed, they will provide the functionality listed in the second column.
+These can be installed `pip install pydna[clipboard,gel,download,express]`
+where `[clipboard,gel,download,express]` is the list of options available. Any
+combination of the words inside the square brackets are allowed, but no white space.
+
+
+### `clipboard`
+
+Enables the `pydna.dseqrecord.Dseqrecord.copy_gb_to_clipboard()` and `pydna.dseqrecord.Dseqrecord.copy_fasta_to_clipboard()`
+
+These methods will put a copy the sequence on the clipboard in either Genbank (gb) or fasta format.
+
 
 | Dependency                                          | Function in pydna                                      |
-|-----------------------------------------------------|--------------------------------------------------------|
-| [scipy](https://www.scipy.org)                      | gel simulation with pydna.gel                          |
-| [matplotlib](http://matplotlib.org)                 | “                                                      |
-| [pillow](https://github.com/python-pillow/Pillow)   | “                                                      |
-| [numpy](http://www.numpy.org)                       | "                                                      |
+| --------------------------------------------------- | ------------------------------------------------------ |
+| [pyperclip](https://pypi.python.org/pypi/pyperclip) | copy sequence to clipboard                             |
+
+### download
+
+Pyparsing enables the `pydna.genbankfixer.gbtext_clean()` function that can automatically
+correct malformed sequence files in Genbank format. These are often found online, so this option also installs requests to enable the  `pydna.genbankfixer.download.download_text()` function which can be used to get cleaned up text from a URL.
+
+
+| Dependency                                          | Function in pydna                                      |
+| --------------------------------------------------- | ------------------------------------------------------ |
 | [pyparsing](https://pypi.python.org/pypi/pyparsing) | fix corrupt Genbank files with pydna.genbankfixer      |
 | [requests](https://pypi.org/project/requests)       | download sequences with pydna.download                 |
+
+### express
+
+This option enables the `pydna.utils.cai()` function and the `cai()` method
+available from subclasses of `pydna.seqrecord.SeqRecord`, such as
+`pydna.dseqrecord.Dseqrecord`.
+
 | [cai2](https://pypi.python.org/pypi/cai2)           | codon adaptation index calculations in several modules |
-| [pyqt5](https://pypi.python.org/pypi/pyqt5)         | future plan for gui                                    |
-| [pyperclip](https://pypi.python.org/pypi/pyperclip) | copy sequence to clipboard                             |
-| [pyfiglet](https://pypi.python.org/pypi/pyfiglet)   | print nice logotype (pydna.logo()                      |
+
+### gel
+
+Scipy, matplotlib and pillow (PIL) enable the generation of gel images. Numpy is also
+needed, but usually installed as a dependency of biopython.
+
+
+| Dependency                                          | Function in pydna                                      |
+| --------------------------------------------------- | ------------------------------------------------------ |
+| [scipy](https://www.scipy.org)                      | gel simulation with pydna.gel                          |
+| [matplotlib](http://matplotlib.org)                 | “                                                      |
+| [pillow](https://github.com/python-pillow/Pillow)   | “                                                      |
+
 
 ## Requirements for running tests, coverage and profiling
 
@@ -252,7 +284,7 @@ If the modules listed below in the first column are installed, they will provide
 
 for instance by `pip install pytest pytest-cov pytest-doctestplus pytest-profiling coverage nbval requests-mock`
 
-Running the antire test suite also require:
+Running the entire test suite also require:
 
 - scipy
 - matplotlib
@@ -260,35 +292,64 @@ Running the antire test suite also require:
 - pyparsing
 - requests
 - cai2
-- pyqt5
 
-That can be installed by `pip install pydna[gel,gui,download,express]`
+That can be installed by `pip install pydna[clipboard,gel,download,express]`
 
-or by `pip install scipy matplotlib pillow pyparsing requests cai2 pyqt5`
+or by `pip install pyparsing requests cai2 scipy matplotlib pillow`
 
 
 ![----]( http://bit.ly/coloredline)
 
-## Releases
+## Contributing
 
-See the [releases](https://github.com/BjornFJohansson/pydna/releases) for changes and releases.
+Please direct pull requests towards the `develop` branch.
 
-![----]( http://bit.ly/coloredline)
+
+### Local development
+
+1. Use [Poetry](https://pypi.org/project/poetry) to install dependencies and activate virtual environment.
+
+    ```bash
+    # If you want the virtual environment to be created in this folder
+    poetry config virtualenvs.in-project true
+
+    # Install dependencies (extras are required for tests to pass)
+    poetry install --all-extras
+
+    # Activate virtual environment
+    poetry shell
+    ```
+
+2. Make your changes.
+3. Add the necessary tests in `tests/`.
+4. Run the tests from the root directory with `python run_test.py`.
+
+#### Building the documentation locally
+
+Below the commands to run a local sphinx server that auto-updated when files are changed.
+
+```
+# 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
+
+```
 
 ## Automatic testing & Release process
 
+See the [releases](https://github.com/BjornFJohansson/pydna/releases) for changes and releases.
+
 There are two github actions for this package:
 
-- `pydna_test_and_coverage_workflow.yml`
-- `pydna_pypi_build_workflow.yml`
+- `.github/workflows/pydna_test_and_coverage_workflow.yml`
+- `.github/workflows/pydna_pypi_build_workflow.yml`
 
-The `pydna_test_and_coverage_workflow.yml` is triggered on all pushed commits for all branches.
-This workflow run tests, doctests and a series of Jupyter notebooks using pytest on Linux, Windows and macOS and all
+The test_and_coverage workflow is triggered on all pushed commits for all branches except the `master` branch. This workflow run tests, doctests and a series of Jupyter notebooks using pytest on Linux, Windows and macOS with all
 supported python versions.
 
-The other workflow builds a PyPI packages using poetry on
-
-These are triggered by publishing a github release manually from the github interface.
+The build workflow builds a PyPI packages using poetry. This workflow is triggered by publishing a Github release manually from the Github web interface.
 
 ![----]( http://bit.ly/coloredline)
 
@@ -323,9 +384,7 @@ These are triggered by publishing a github release manually from the github inte
 
 Pydna was made public in 2012 on [Google code](https://code.google.com/archive/p/pydna).
 
-
 :microbe:
 
-
 :portugal:
 

{pydna-6.0.0a3 → pydna-6.0.0a15}/README.md

@@ -1,8 +1,8 @@
 # ![icon](https://raw.githubusercontent.com/bjornFJohansson/pydna/master/docs/pics/pydna.resized.png) pydna
 
-| [![Tests & Coverage](https://github.com/BjornFJohansson/pydna/actions/workflows/pydna_test_and_coverage_workflow.yml/badge.svg?branch=dev_bjorn)](https://github.com/BjornFJohansson/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)              |
-|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------|
-| [![Documentation Status](https://readthedocs.org/projects/pydna/badge/?version=latest)](http://pydna.readthedocs.io/?badge=latest)                                                                   | [![GitHub issues](https://img.shields.io/github/issues/BjornFJohansson/pydna.svg)](https://github.com/BjornFJohansson/pydna/issues)                | [![Anaconda-Server Badge2](https://anaconda.org/bjornfjohansson/pydna/badges/license.svg)](https://anaconda.org/bjornfjohansson/pydna) | [![GitHub stars](https://img.shields.io/github/stars/BjornFJohansson/pydna.svg)](https://github.com/BjornFJohansson/pydna/stargazers) |
+| [![Tests & Coverage](https://github.com/BjornFJohansson/pydna/actions/workflows/pydna_test_and_coverage_workflow.yml/badge.svg?branch=dev_bjorn)](https://github.com/BjornFJohansson/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)              |
+| -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------- |
+| [![Documentation Status](https://readthedocs.org/projects/pydna/badge/?version=latest)](http://pydna.readthedocs.io/?badge=latest)                                                                                                                 | [![GitHub issues](https://img.shields.io/github/issues/BjornFJohansson/pydna.svg)](https://github.com/BjornFJohansson/pydna/issues)                | [![Anaconda-Server Badge2](https://anaconda.org/bjornfjohansson/pydna/badges/license.svg)](https://anaconda.org/bjornfjohansson/pydna) | [![GitHub stars](https://img.shields.io/github/stars/BjornFJohansson/pydna.svg)](https://github.com/BjornFJohansson/pydna/stargazers) |
 
 
 
@@ -27,7 +27,7 @@ Pydna provides simulation of:
 - Gel electrophoresis of DNA with generation of gel images
 - Homologous recombination
 - Gibson assembly
-- Golden gate assembly
+- Golden gate assembly (in progress)
 
 
 Virtually any sub-cloning experiment can be described in pydna, and its execution yield
@@ -38,12 +38,13 @@ Pydna has been designed with the goal of being understandable for biologists wit
 Pydna can formalize planning and sharing of cloning strategies and is especially useful for complex or combinatorial
 DNA molecule constructions.
 
-To get started, I have compiled some [simple examples](https://github.com/MetabolicEngineeringGroupCBMA/pydna-examples#pydna-examples).
-For more elaborate use, look at some assembly strategies of D-xylose metabolic pathways [MetabolicEngineeringGroupCBMA/ypk-xylose-pathways](https://github.com/MetabolicEngineeringGroupCBMA/ypk-xylose-pathways#pereira-et-al-2016).
-
+Start by looking at the [cookbook](https://github.com/BjornFJohansson/pydna/blob/master/docs/cookbook/cookbook.ipynb).
 
+Some simple examples can be found  [here](https://github.com/MetabolicEngineeringGroupCBMA/pydna-examples#pydna-examples).
 
+For more elaborate use, look at some assembly strategies of D-xylose metabolic pathways [MetabolicEngineeringGroupCBMA/ypk-xylose-pathways](https://github.com/MetabolicEngineeringGroupCBMA/ypk-xylose-pathways#pereira-et-al-2016).
 
+See below for documentation.
 
 ![----]( http://bit.ly/coloredline)
 
@@ -80,11 +81,7 @@ DNA sequences are downloaded from Genbank by accession numbers that are guarante
     lin_vector = vector.linearize(EcoRV)
     rec_vec =  ( lin_vector + pcr_prod ).looped()
 
-Pydna can automate the simulation of [sub cloning](http://en.wikipedia.org/wiki/Subcloning) experiments using
-python. This is helpful to generate examples for teaching purposes.
-
-Read the documentation (below) or the [cookbook](https://github.com/BjornFJohansson/pydna/blob/master/docs/cookbook/cookbook.ipynb) with example files
-for further information.
+Another use case for pydna in the automatic generation of [sub cloning](http://en.wikipedia.org/wiki/Subcloning) examples for teaching purposes. These examples
 
 Feedback & suggestions are very welcome! Please post a message in the [google group](https://groups.google.com/d/forum/pydna) for pydna if you need help or have problems, questions or comments :sos:.
 
@@ -126,11 +123,10 @@ When using pydna.
 
 ![----]( http://bit.ly/coloredline)
 
-## Documentation
+## Documentation :page_with_curl:
 
 Documentation is built using [Sphinx](http://www.sphinx-doc.org/) from [docstrings](https://www.python.org/dev/peps/pep-0257/)
-in the code and displayed at readthedocs [![Documentation Status](https://readthedocs.org/projects/pydna/badge/?version=latest)](http://pydna.readthedocs.io/?badge=latest)
-
+in the code and displayed at readthedocs [![Documentation Status](https://readthedocs.org/projects/pydna/badge/?version=latest)](http://pydna.readthedocs.io/?badge=latest).
 The [numpy](www.numpy.org) [docstring format](https://github.com/numpy/numpy/blob/release/doc/HOWTO_DOCUMENT.rst.txt) is used.
 
 ![----]( http://bit.ly/coloredline)
@@ -150,7 +146,7 @@ or use the --pre switch to get the latest version of pydna.
 
 for optional functionality do:
 
-    pip install pydna[gel,download,express,gui]
+    pip install pydna[clipboard,download,express,gel]
 
 Remove options inside the square brackets as required, but be sure not to leave spaces as pip will not recognize the options. See below under "Optional dependencies".
 
@@ -178,32 +174,65 @@ I am happy to collaborate on new features or bugfixes.
 The list below is the minimal requirements for installing pydna.
 Biopython and pydivsufsort has c-extensions, but the other modules are pure python.
 
-- [Python 3.8, 3.9, 3.10 or 3.11](http://www.python.org)
+- [Python 3.8, 3.9, 3.10, 3.11 or 3.12](http://www.python.org)
 - [appdirs](https://pypi.python.org/pypi/appdirs)
 - [biopython](http://pypi.python.org/pypi/biopython)
 - [networkx](http://pypi.python.org/pypi/networkx)
 - [prettytable](https://pypi.python.org/pypi/PrettyTable)
 - [pydivsufsort](https://pypi.python.org/pypi/pydivsufsort)
+- [pyfiglet](https://pypi.python.org/pypi/pyfiglet)
 
-The above modules are installed as well as pyperclip and pyfiglet.
-Pydna is importable even without these two modules.
+Pydna is importable even without pyfiglet.
 
 ## Optional dependencies
 
-If the modules listed below in the first column are installed, they will provide the functionality listed in the second column.
+These can be installed `pip install pydna[clipboard,gel,download,express]`
+where `[clipboard,gel,download,express]` is the list of options available. Any
+combination of the words inside the square brackets are allowed, but no white space.
+
+
+### `clipboard`
+
+Enables the `pydna.dseqrecord.Dseqrecord.copy_gb_to_clipboard()` and `pydna.dseqrecord.Dseqrecord.copy_fasta_to_clipboard()`
+
+These methods will put a copy the sequence on the clipboard in either Genbank (gb) or fasta format.
+
 
 | Dependency                                          | Function in pydna                                      |
-|-----------------------------------------------------|--------------------------------------------------------|
-| [scipy](https://www.scipy.org)                      | gel simulation with pydna.gel                          |
-| [matplotlib](http://matplotlib.org)                 | “                                                      |
-| [pillow](https://github.com/python-pillow/Pillow)   | “                                                      |
-| [numpy](http://www.numpy.org)                       | "                                                      |
+| --------------------------------------------------- | ------------------------------------------------------ |
+| [pyperclip](https://pypi.python.org/pypi/pyperclip) | copy sequence to clipboard                             |
+
+### download
+
+Pyparsing enables the `pydna.genbankfixer.gbtext_clean()` function that can automatically
+correct malformed sequence files in Genbank format. These are often found online, so this option also installs requests to enable the  `pydna.genbankfixer.download.download_text()` function which can be used to get cleaned up text from a URL.
+
+
+| Dependency                                          | Function in pydna                                      |
+| --------------------------------------------------- | ------------------------------------------------------ |
 | [pyparsing](https://pypi.python.org/pypi/pyparsing) | fix corrupt Genbank files with pydna.genbankfixer      |
 | [requests](https://pypi.org/project/requests)       | download sequences with pydna.download                 |
+
+### express
+
+This option enables the `pydna.utils.cai()` function and the `cai()` method
+available from subclasses of `pydna.seqrecord.SeqRecord`, such as
+`pydna.dseqrecord.Dseqrecord`.
+
 | [cai2](https://pypi.python.org/pypi/cai2)           | codon adaptation index calculations in several modules |
-| [pyqt5](https://pypi.python.org/pypi/pyqt5)         | future plan for gui                                    |
-| [pyperclip](https://pypi.python.org/pypi/pyperclip) | copy sequence to clipboard                             |
-| [pyfiglet](https://pypi.python.org/pypi/pyfiglet)   | print nice logotype (pydna.logo()                      |
+
+### gel
+
+Scipy, matplotlib and pillow (PIL) enable the generation of gel images. Numpy is also
+needed, but usually installed as a dependency of biopython.
+
+
+| Dependency                                          | Function in pydna                                      |
+| --------------------------------------------------- | ------------------------------------------------------ |
+| [scipy](https://www.scipy.org)                      | gel simulation with pydna.gel                          |
+| [matplotlib](http://matplotlib.org)                 | “                                                      |
+| [pillow](https://github.com/python-pillow/Pillow)   | “                                                      |
+
 
 ## Requirements for running tests, coverage and profiling
 
@@ -217,7 +246,7 @@ If the modules listed below in the first column are installed, they will provide
 
 for instance by `pip install pytest pytest-cov pytest-doctestplus pytest-profiling coverage nbval requests-mock`
 
-Running the antire test suite also require:
+Running the entire test suite also require:
 
 - scipy
 - matplotlib
@@ -225,35 +254,64 @@ Running the antire test suite also require:
 - pyparsing
 - requests
 - cai2
-- pyqt5
 
-That can be installed by `pip install pydna[gel,gui,download,express]`
+That can be installed by `pip install pydna[clipboard,gel,download,express]`
 
-or by `pip install scipy matplotlib pillow pyparsing requests cai2 pyqt5`
+or by `pip install pyparsing requests cai2 scipy matplotlib pillow`
 
 
 ![----]( http://bit.ly/coloredline)
 
-## Releases
+## Contributing
 
-See the [releases](https://github.com/BjornFJohansson/pydna/releases) for changes and releases.
+Please direct pull requests towards the `develop` branch.
 
-![----]( http://bit.ly/coloredline)
+
+### Local development
+
+1. Use [Poetry](https://pypi.org/project/poetry) to install dependencies and activate virtual environment.
+
+    ```bash
+    # If you want the virtual environment to be created in this folder
+    poetry config virtualenvs.in-project true
+
+    # Install dependencies (extras are required for tests to pass)
+    poetry install --all-extras
+
+    # Activate virtual environment
+    poetry shell
+    ```
+
+2. Make your changes.
+3. Add the necessary tests in `tests/`.
+4. Run the tests from the root directory with `python run_test.py`.
+
+#### Building the documentation locally
+
+Below the commands to run a local sphinx server that auto-updated when files are changed.
+
+```
+# 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
+
+```
 
 ## Automatic testing & Release process
 
+See the [releases](https://github.com/BjornFJohansson/pydna/releases) for changes and releases.
+
 There are two github actions for this package:
 
-- `pydna_test_and_coverage_workflow.yml`
-- `pydna_pypi_build_workflow.yml`
+- `.github/workflows/pydna_test_and_coverage_workflow.yml`
+- `.github/workflows/pydna_pypi_build_workflow.yml`
 
-The `pydna_test_and_coverage_workflow.yml` is triggered on all pushed commits for all branches.
-This workflow run tests, doctests and a series of Jupyter notebooks using pytest on Linux, Windows and macOS and all
+The test_and_coverage workflow is triggered on all pushed commits for all branches except the `master` branch. This workflow run tests, doctests and a series of Jupyter notebooks using pytest on Linux, Windows and macOS with all
 supported python versions.
 
-The other workflow builds a PyPI packages using poetry on
-
-These are triggered by publishing a github release manually from the github interface.
+The build workflow builds a PyPI packages using poetry. This workflow is triggered by publishing a Github release manually from the Github web interface.
 
 ![----]( http://bit.ly/coloredline)
 
@@ -288,8 +346,6 @@ These are triggered by publishing a github release manually from the github inte
 
 Pydna was made public in 2012 on [Google code](https://code.google.com/archive/p/pydna).
 
-
 :microbe:
 
-
 :portugal:

{pydna-6.0.0a3 → pydna-6.0.0a15}/pyproject.toml

@@ -11,25 +11,25 @@ classifiers=["Development Status :: 4 - Beta",
              "Intended Audience :: Science/Research",
              "License :: OSI Approved :: BSD License",
              "Operating System :: OS Independent",
-             "Programming Language :: Python :: 3.7",
              "Programming Language :: Python :: 3.8",
              "Programming Language :: Python :: 3.9",
              "Programming Language :: Python :: 3.10",
              "Programming Language :: Python :: 3.11",
+             "Programming Language :: Python :: 3.12",
              "Topic :: Education",
              "Topic :: Scientific/Engineering :: Bio-Informatics", ]
-[project.urls]
-homepage = "https://github.com/BjornFJohansson/pydna#-pydna"
-documentation = "https://pydna.readthedocs.io/?badge=latest"
-repository = "https://github.com/BjornFJohansson/pydna/tree/dev_bjorn"
-changelog = "https://github.com/BjornFJohansson/pydna/blob/master/docs/CHANGELOG.md#changelog"
+[tool.poetry.urls]
+Changelog = "https://github.com/BjornFJohansson/pydna/blob/master/docs/CHANGELOG.md#changelog"
 [tool.poetry]
 name = "pydna"
-version = "6.0.0-a.3"
+version = "6.0.0-a.15"
 description = "Representing double stranded DNA and functions for simulating cloning and homologous recombination between DNA molecules."
 authors = ["BjornFJohansson <bjornjobb@gmail.com>"]
 license = "BSD"
 readme = "README.md"
+homepage = "https://github.com/BjornFJohansson/pydna#-pydna"
+documentation = "https://pydna.readthedocs.io/?badge=latest"
+repository = "https://github.com/BjornFJohansson/pydna/tree/dev_bjorn"
 [tool.poetry.dependencies]
 python = ">=3.8"
 appdirs = ">=1.4.4"
@@ -37,20 +37,18 @@ biopython = ">=1.80"
 networkx = ">=2.8.8"
 pydivsufsort = ">=0.0.11"
 prettytable = ">=3.5.0"
-pyfiglet = ">=0.8.post1"
+pyfiglet = "0.8.post1"
 pyperclip = { version = ">=1.8.2", optional = true }
-scipy = { version = ">=1.8.0", optional = true }
+scipy = { version = ">=1.9.3", optional = true }
 matplotlib = { version = ">=3.4.3", optional = true }
 pillow = { version = ">=8.4.0", optional = true }
 pyparsing = { version = ">=2.4.7", optional = true }
 requests = { version = ">=2.26.0", optional = true }
 cai2 = { version = ">=1.0.5", optional = true }
-pyqt5 = { version = ">=5.15.0", optional = true }
 [tool.poetry.extras]
 clipboard = ["pyperclip"]
 gel = ["scipy", "matplotlib", "pillow"]
 download = ["pyparsing", "requests"]
-gui = ["pyqt5"]
 express = ["cai2"]
 [build-system]
 requires = ["poetry-core",
@@ -73,6 +71,12 @@ pytest-profiling = ">=1.7.0"
 coverage = ">=7.1.0"
 nbval = ">=0.9.6"
 requests-mock = ">=1.10.0"
+
+[tool.poetry.group.docs.dependencies]
+sphinx-autobuild = "^2021.3.14"
+numpydoc = "^1.6.0"
+sphinx-rtd-theme = "^1.3.0"
+
 [tool.pytest.ini_options]
 minversion = "6.0.2"
 python_files = "test_*.py"

{pydna-6.0.0a3 → pydna-6.0.0a15}/src/pydna/__init__.py

@@ -149,7 +149,7 @@ __license__ = "BSD"
 __maintainer__ = "Björn Johansson"
 __email__ = "bjorn_johansson@bio.uminho.pt"
 __status__ = "Development"  # "Production" #"Prototype"
-__version__ = "6.0.0-a.3"
+__version__ = "6.0.0-a.15"
 
 # create config directory
 _os.environ["pydna_config_dir"] = _os.getenv("pydna_config_dir", _appdirs.user_config_dir("pydna"))
@@ -230,30 +230,30 @@ _logger.info(
 _Path(_os.environ["pydna_data_dir"]).mkdir(parents=True, exist_ok=True)
 
 # find out if optional dependecies for gel module are in place
-
-
-def _missing_modules_for_gel():
-    import importlib
-    from importlib import util
-
-    _missing = []
-    for _optm in ["scipy", "PIL", "numpy", "pyparsing", "requests"]:
-        _missing.extend([_optm] if not util.find_spec(_optm) else [])
-    del importlib
-    del util
-    return _missing
-
-
-_missing = _missing_modules_for_gel()
-
-if _missing:
-    _logger.warning(
-        "gel simulation will NOT be available." " Missing modules: %s",
-        ", ".join(_missing),
-    )
-else:
-    _logger.info("gel simulation is available," " optional dependencies were found.")
-
+#
+#
+# def _missing_modules_for_gel():
+#    import importlib
+#    from importlib import util
+#
+#    _missing = []
+#    for _optm in ["scipy", "PIL", "numpy", "pyparsing", "requests"]:
+#        _missing.extend([_optm] if not util.find_spec(_optm) else [])
+#    del importlib
+#    del util
+#    return _missing
+#
+#
+# _missing = _missing_modules_for_gel()
+#
+# if _missing:
+#    _logger.warning(
+#        "gel simulation will NOT be available." " Missing modules: %s",
+#        ", ".join(_missing),
+#    )
+# else:
+#    _logger.info("gel simulation is available," " optional dependencies were found.")
+#
 
 _logger.info("__version__ = %s", __version__)
 

{pydna-6.0.0a3 → pydna-6.0.0a15}/src/pydna/design.py

@@ -700,7 +700,7 @@ def circular_assembly_fragments(f, overlap=35, maxlink=40):
     fragments = assembly_fragments(f + f[0:1], overlap=overlap, maxlink=maxlink)
 
     if hasattr(fragments[0], "template"):
-        fragments[0] = _pcr((fragments[-1].forward_primer, fragments[0].reverse_primer), fragments[0])
+        fragments[0] = _pcr((fragments[-1].forward_primer, fragments[0].reverse_primer), fragments[0].template)
     return fragments[:-1]
 
 

{pydna-6.0.0a3 → pydna-6.0.0a15}/src/pydna/download.py

@@ -4,10 +4,10 @@
 # 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.
-"""Provides a function for downloading online text files"""
+"""Provides a function for downloading online text files."""
 
 import textwrap as _textwrap
-import requests as _requests
+
 import os as _os
 from pydna._pretty import pretty_str as _pretty_str
 from pydna.utils import memorize as _memorize
@@ -18,9 +18,12 @@ _module_logger = _logging.getLogger("pydna." + __name__)
 
 @_memorize("pydna.download.download_text")
 def download_text(url):
+    """docstring."""
+    import requests
+
     _module_logger.info("#### DOWNLOAD TEXT ####")
     _module_logger.info("url = %s", url)
-    req = _requests.get(url)
+    req = requests.get(url)
     _module_logger.info("url = %s", str(req))
     result = _textwrap.dedent(req.text).strip()
     result = result.replace("\r\n", "\n").replace("\r", "\n")

{pydna-6.0.0a3 → pydna-6.0.0a15}/src/pydna/dseq.py

@@ -74,7 +74,8 @@ class Dseq(_Seq):
     The most common usage is probably to create a Dseq object as a
     part of a Dseqrecord object (see :class:`pydna.dseqrecord.Dseqrecord`).
 
-    There are three ways of creating a Dseq object directly:
+    There are three ways of creating a Dseq object directly listed below, but you can also
+    use the function Dseq.from_full_sequence_and_overhangs() to create a Dseq:
 
     Only one argument (string):
 
@@ -109,22 +110,22 @@ class Dseq(_Seq):
 
     The ovhg parameter controls the stagger at the five prime end::
 
-        dsDNA    ovhg
+        dsDNA       overhang
 
-          XXX    2
-        XXXXX
+          nnn...    2
+        nnnnn...
 
-         XXXX    1
-        XXXXX
+         nnnn...    1
+        nnnnn...
 
-        XXXXX    0
-        XXXXX
+        nnnnn...    0
+        nnnnn...
 
-        XXXXX   -1
-         XXXX
+        nnnnn...   -1
+         nnnn...
 
-        XXXXX   -2
-          XXX
+        nnnnn...   -2
+          nnn...
 
     Example of creating Dseq objects with different amounts of stagger:
 
@@ -428,6 +429,69 @@ class Dseq(_Seq):
         obj._data = _rc(cb[-max(0, ovhg) or len(cb) :]) + wb + _rc(cb[: max(0, len(cb) - ovhg - len(wb))])
         return obj
 
+    @classmethod
+    def from_full_sequence_and_overhangs(cls, full_sequence: str, crick_ovhg: int, watson_ovhg: int):
+        """Create a linear Dseq object from a full sequence and the 3' overhangs of each strand.
+
+        The order of the parameters is like this because the 3' overhang of the crick strand is the one
+        on the left side of the sequence.
+
+
+        Parameters
+        ----------
+        full_sequence: str
+            The full sequence of the Dseq object.
+
+        crick_ovhg: int
+            The overhang of the crick strand in the 3' end. Equivalent to Dseq.ovhg.
+
+        watson_ovhg: int
+            The overhang of the watson strand in the 5' end.
+
+        Returns
+        -------
+        Dseq
+            A Dseq object.
+
+        Examples
+        --------
+
+        >>> Dseq.from_full_sequence_and_overhangs('AAAAAA', crick_ovhg=2, watson_ovhg=2)
+        Dseq(-6)
+          AAAA
+        TTTT
+        >>> Dseq.from_full_sequence_and_overhangs('AAAAAA', crick_ovhg=-2, watson_ovhg=2)
+        Dseq(-6)
+        AAAAAA
+          TT
+        >>> Dseq.from_full_sequence_and_overhangs('AAAAAA', crick_ovhg=2, watson_ovhg=-2)
+        Dseq(-6)
+          AA
+        TTTTTT
+        >>> Dseq.from_full_sequence_and_overhangs('AAAAAA', crick_ovhg=-2, watson_ovhg=-2)
+        Dseq(-6)
+        AAAA
+          TTTT
+
+        """
+        full_sequence_rev = str(Dseq(full_sequence).reverse_complement())
+        watson = full_sequence
+        crick = full_sequence_rev
+
+        # If necessary, we trim the left side
+        if crick_ovhg < 0:
+            crick = crick[:crick_ovhg]
+        elif crick_ovhg > 0:
+            watson = watson[crick_ovhg:]
+
+        # If necessary, we trim the right side
+        if watson_ovhg < 0:
+            watson = watson[:watson_ovhg]
+        elif watson_ovhg > 0:
+            crick = crick[watson_ovhg:]
+
+        return Dseq(watson, crick=crick, ovhg=crick_ovhg)
+
     # @property
     # def ovhg(self):
     #     """The ovhg property. This cannot be set directly, but is a
@@ -942,6 +1006,10 @@ class Dseq(_Seq):
             type_ = "blunt"
         return type_, sticky
 
+    def watson_ovhg(self):
+        """Returns the overhang of the watson strand at the three prime."""
+        return len(self.watson) - len(self.crick) + self.ovhg
+
     def __add__(self, other):
         """Simulates ligation between two DNA fragments.
 
@@ -1244,8 +1312,7 @@ class Dseq(_Seq):
         return self.n_cutters(n=2, batch=batch)
 
     def n_cutters(self, n=3, batch: _RestrictionBatch = None):
-        """Returns the enzymes in a RestrictionBatch that cut the sequence
-        n times."""
+        """Enzymes in a RestrictionBatch cutting n times."""
         if not batch:
             batch = CommOnly
         ana = batch.search(self)

{pydna-6.0.0a3 → pydna-6.0.0a15}/src/pydna/gel.py

@@ -9,17 +9,15 @@
 
 """docstring."""
 
-from PIL import Image as _Image
-from PIL import ImageDraw as _ImageDraw
-import numpy as _np
 import math as _math
-from scipy.interpolate import CubicSpline as _CubicSpline
 from pydna.ladders import GeneRuler_1kb_plus as _mwstd
 
 
 def interpolator(mwstd):
     """docstring."""
-    interpolator = _CubicSpline(
+    from scipy.interpolate import CubicSpline
+
+    interpolator = CubicSpline(
         [len(fr) for fr in mwstd[::-1]],
         [fr.rf for fr in mwstd[::-1]],
         bc_type="natural",
@@ -30,6 +28,10 @@ def interpolator(mwstd):
 
 
 def gel(samples=None, gel_length=600, margin=50, interpolator=interpolator(mwstd=_mwstd)):
+    import numpy as np
+    from PIL import Image as Image
+    from PIL import ImageDraw as ImageDraw
+
     """docstring."""
     max_intensity = 256
     lane_width = 50
@@ -37,9 +39,9 @@ def gel(samples=None, gel_length=600, margin=50, interpolator=interpolator(mwstd
     start = 10
     samples = samples or [interpolator.mwstd]
     width = int(60 + (lane_width + lanesep) * len(samples))
-    lanes = _np.zeros((len(samples), gel_length), dtype=int)
-    image = _Image.new("RGB", (width, gel_length), "#ddd")
-    draw = _ImageDraw.Draw(image)
+    lanes = np.zeros((len(samples), gel_length), dtype=int)
+    image = Image.new("RGB", (width, gel_length), "#ddd")
+    draw = ImageDraw.Draw(image)
     draw.rectangle((0, 0, (width, gel_length)), fill=(0, 0, 0))
     scale = (gel_length - margin) / interpolator(min(interpolator.x))
 
@@ -72,10 +74,10 @@ def gel(samples=None, gel_length=600, margin=50, interpolator=interpolator(mwstd
                         pass
 
     for i, lane in enumerate(lanes):
-        max_intensity = _np.amax(lanes[i])
+        max_intensity = np.amax(lanes[i])
         if max_intensity > 256:
-            lanes[i] = _np.multiply(lanes[i], 256)
-            lanes[i] = _np.divide(lanes[i], max_intensity)
+            lanes[i] = np.multiply(lanes[i], 256)
+            lanes[i] = np.divide(lanes[i], max_intensity)
 
     for i, lane in enumerate(lanes):
         x1 = 50 + i * (lane_width + lanesep)

{pydna-6.0.0a3 → pydna-6.0.0a15}/src/pydna/parsers.py

@@ -24,6 +24,7 @@ import xml.etree.ElementTree as _et
 def embl_gb_fasta(raw, ds, path=None):
     # regex = r"^>.+?^(?=$|LOCUS|ID|>|\#)|^(?:LOCUS|ID).+?^//"
     regex = r"(?:>.+\n^(?:^[^>]+?)(?=\n\n|>|" r"LOCUS|ID))|(?:(?:LOCUS|ID)(?:(?:.|\n)+?)^//)"
+    "(?:^>.+\n^(?:^[^>]+?)(?=\n\n|>|^LOCUS|ID))|(?:(?:^LOCUS|ID)(?:(?:.|\n)+?)^//)"
 
     result_list = []
 

{pydna-6.0.0a3 → pydna-6.0.0a15}/src/pydna/utils.py

@@ -129,7 +129,7 @@ def smallest_rotation(s):
     """
     from pydivsufsort import min_rotation
 
-    k = min_rotation(s)
+    k = min_rotation(bytes(s, "ascii"))
     return s[k:] + s[:k]