Fix broken links + update pyproject for poetry 2 (#332)

* closes #331

* closes #333

* use poetry 1.8 for python 3.8 tests

* update pyproject to work with poetry 1.8

* fix installation line in google collab

* fix pyproject.toml and README instructions for poetry

* clean notebooks

* fix author string for poetry 1.8

.github/workflows/pydna_test_and_coverage_workflow.yml

@@ -51,7 +51,7 @@ jobs:
         uses: snok/install-poetry@v1
         with:
           virtualenvs.prefer-active-python: true
-
+          version: ${{ matrix.python-version == '3.8' && '1.8.2' || 'latest' }}
       - name: 🔩 list Poetry settings
         run: poetry config --list
 

README.md

@@ -1,8 +1,8 @@
 # ![icon](docs/_static/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://github.com/BjornFJohansson/pydna/actions/workflows/publish-docs.yml/badge.svg)](https://github.com/BjornFJohansson/pydna/actions/workflows/publish-docs.yml)                                                      | [![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/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)          |
+| ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | -------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------- |
+| [![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)                    | [![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/pydna-group/pydna/stargazers) |
 
 <!-- docs/index.rst-start -->
 
@@ -42,7 +42,7 @@ Pereira, F., Azevedo, F., Carvalho, Â., Ribeiro, G. F., Budde, M. W., & Johanss
 
 ## Documentation and usage 📚
 
-Full documentation of all modules and classes can be found at [https://bjornfjohansson.github.io/pydna](https://bjornfjohansson.github.io/pydna).
+Full documentation of all modules and classes can be found at [https://pydna-group.github.io/pydna](https://pydna-group.github.io/pydna).
 
 To get started, we recommend you to have a look at the [example notebooks](docs/notebooks). Start by having a look at [Dseq](docs/notebooks/Dseq.ipynb), [Dseq_Features](docs/notebooks/Dseq_Features.ipynb) and [Importing_Seqs](docs/notebooks/Importing_Seqs.ipynb), which cover the basics of working with sequences. The rest of the notebooks cover how to use pydna for different cloning strategies, such as Gibson assembly, Restriction-Ligation, etc.
 
@@ -435,7 +435,10 @@ poetry config virtualenvs.in-project true
 # Install dependencies (extras are required for tests to pass)
 poetry install --all-extras
 
-# Activate virtual environment
+# Activate virtual environment (poetry version 2)
+poetry env activate
+
+# Activate virtual environment (poetry version 1)
 poetry shell
 
 # Install pre-commit hooks
@@ -487,7 +490,7 @@ 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/BjornFJohansson/pydna/actions/workflows/publish-docs.yml).
+using a GitHub [action](https://github.com/pydna-group/pydna/actions/workflows/publish-docs.yml).
 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.
@@ -505,7 +508,7 @@ More info about how to contribute to the documentation can be found [here](docs/
 
 ## Release process 🚀
 
-See the [releases](https://github.com/BjornFJohansson/pydna/releases) for changes and releases.
+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.
 
@@ -535,4 +538,4 @@ In Cold Spring Harbor Laboratory (p. 2021.01.17.427048). [DOI](https://doi.org/1
 
 [An Automated Protein Synthesis Pipeline with Transcriptic and Snakemake](http://blog.booleanbiotech.com/transcriptic_protein_synthesis_pipeline.html)
 
-and other projects on [github](https://github.com/BjornFJohansson/pydna/network/dependents?package_id=UGFja2FnZS01MjQ2MjYzNQ%3D%3D)
+and other projects on [github](https://github.com/pydna-group/pydna/network/dependents?package_id=UGFja2FnZS01MjQ2MjYzNQ%3D%3D)

docs/README.md

@@ -1,7 +1,7 @@
 # Documentation
 
 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/BjornFJohansson/pydna/actions/workflows/publish-docs.yml).
+using a GitHub [action](https://github.com/pydna-group/pydna/actions/workflows/publish-docs.yml).
 The [numpy](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.

docs/cookbook/cookbook.ipynb

@@ -21,7 +21,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "<a target=\"_blank\" href=\"https://colab.research.google.com/github/BjornFJohansson/pydna/blob/dev_bjorn/docs/cookbook/cookbook.ipynb\">\n",
+    "<a target=\"_blank\" href=\"https://colab.research.google.com/github/pydna-group/pydna/blob/master/docs/cookbook/cookbook.ipynb\">\n",
     "  <img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/>\n",
     "</a>"
    ]

docs/getting_started.md

@@ -2,7 +2,7 @@
 
 
 The best way to get started is to follow our tutorial notebooks, you can find them in the
-repository folder [docs/notebooks](https://github.com/BjornFJohansson/pydna/tree/main/docs/notebooks) and
+repository folder [docs/notebooks](https://github.com/pydna-group/pydna/tree/master/docs/notebooks) and
 are reproduced here so they can serve as documentation.
 
 You can run the notebooks locally, but also on the browser using Google Colab, simply click in the badge of

docs/notebooks/CRISPR.ipynb

@@ -6,7 +6,7 @@
    "source": [
     "# How to Model CRISPR-Cas9 Experiments in pydna\n",
     "\n",
-    "> Visit the full library documentation [here](https://bjornfjohansson.github.io/pydna/)\n",
+    "> Visit the full library documentation [here](https://pydna-group.github.io/pydna/)\n",
     "\n",
     "The pydna package can simulate CRISPR-Cas9 editing, which allows one to cut DNA sequences at specific sites using guide RNAs (gRNAs) that direct the Cas9 protein. This page will guide you through the process of using the `pydna.crispr` module to model a CRISPR-Cas9 cut on a DNA sequence.\n",
     "\n",
@@ -17,7 +17,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "<a target=\"_blank\" href=\"https://colab.research.google.com/github/BjornFJohansson/pydna/blob/dev_bjorn/docs/notebooks/CRISPR.ipynb\">\n",
+    "<a target=\"_blank\" href=\"https://colab.research.google.com/github/pydna-group/pydna/blob/master/docs/notebooks/CRISPR.ipynb\">\n",
     "  <img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/>\n",
     "</a>"
    ]
@@ -28,14 +28,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "%%capture\n",
     "# Install pydna (only when running on Colab)\n",
     "import sys\n",
     "if 'google.colab' in sys.modules:\n",
-    "    %%capture\n",
-    "    # Install the current development version of pydna (comment to install pip version)\n",
-    "    !pip install git+https://github.com/BjornFJohansson/pydna@dev_bjorn\n",
-    "    # Install pip version instead (uncomment to install)\n",
-    "    # !pip install pydna\n"
+    "    %pip install pydna\n"
    ]
   },
   {

docs/notebooks/Dseq.ipynb

@@ -5,14 +5,14 @@
    "metadata": {},
    "source": [
     "# Representing sequences in pydna\n",
-    "> Visit the full library documentation [here](https://bjornfjohansson.github.io/pydna/)"
+    "> Visit the full library documentation [here](https://pydna-group.github.io/pydna/)"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "<a target=\"_blank\" href=\"https://colab.research.google.com/github/BjornFJohansson/pydna/blob/dev_bjorn/docs/notebooks/Dseq.ipynb\">\n",
+    "<a target=\"_blank\" href=\"https://colab.research.google.com/github/pydna-group/pydna/blob/master/docs/notebooks/Dseq.ipynb\">\n",
     "  <img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/>\n",
     "</a>"
    ]
@@ -23,14 +23,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "%%capture\n",
     "# Install pydna (only when running on Colab)\n",
     "import sys\n",
     "if 'google.colab' in sys.modules:\n",
-    "    %%capture\n",
-    "    # Install the current development version of pydna (comment to install pip version)\n",
-    "    !pip install git+https://github.com/BjornFJohansson/pydna@dev_bjorn\n",
-    "    # Install pip version instead (uncomment to install)\n",
-    "    # !pip install pydna\n"
+    "    %pip install pydna\n"
    ]
   },
   {

docs/notebooks/Dseq_Features.ipynb

@@ -8,7 +8,7 @@
     "\n",
     "> Before working with features, check how to import sequences from files in the [Importing_Seqs notebook](./Importing_Seqs.ipynb).\n",
     ">\n",
-    "> For full library documentation, visit [here](https://bjornfjohansson.github.io/pydna/).\n",
+    "> For full library documentation, visit [here](https://pydna-group.github.io/pydna/).\n",
     "\n",
     "Some sequence file formats (like Genbank) include features, describing key biological properties of sequence regions. In Genbank, features \"include genes, gene products, as well as regions of biological significance reported in the sequence.\" (See [here](https://www.ncbi.nlm.nih.gov/genbank/samplerecord/) for a description of a Genbank file and associated terminologies/annotations) Examples include coding sequences (CDS), introns, promoters, etc.\n",
     "\n",
@@ -19,7 +19,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "<a target=\"_blank\" href=\"https://colab.research.google.com/github/BjornFJohansson/pydna/blob/dev_bjorn/docs/notebooks/Dseq_Features.ipynb\">\n",
+    "<a target=\"_blank\" href=\"https://colab.research.google.com/github/pydna-group/pydna/blob/master/docs/notebooks/Dseq_Features.ipynb\">\n",
     "  <img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/>\n",
     "</a>"
    ]
@@ -30,14 +30,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "%%capture\n",
     "# Install pydna (only when running on Colab)\n",
     "import sys\n",
     "if 'google.colab' in sys.modules:\n",
-    "    %%capture\n",
-    "    # Install the current development version of pydna (comment to install pip version)\n",
-    "    !pip install git+https://github.com/BjornFJohansson/pydna@dev_bjorn\n",
-    "    # Install pip version instead (uncomment to install)\n",
-    "    # !pip install pydna\n"
+    "    %pip install pydna"
    ]
   },
   {

docs/notebooks/Example_CRISPR.ipynb

@@ -15,6 +15,15 @@
     "https://academic.oup.com/femsyr/article/doi/10.1093/femsyr/foae026/7740463?login=false "
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "<a target=\"_blank\" href=\"https://colab.research.google.com/github/pydna-group/pydna/blob/master/docs/notebooks/Example_CRISPR.ipynb\">\n",
+    "  <img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/>\n",
+    "</a>"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -60,29 +69,17 @@
     "- Let's see how this can be implemented in pydna\n"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "<a target=\"_blank\" href=\"https://colab.research.google.com/github/BjornFJohansson/pydna/blob/dev_bjorn/docs/notebooks/Example_CRISPR.ipynb\">\n",
-    "  <img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/>\n",
-    "</a>"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
+    "%%capture\n",
     "# Install pydna (only when running on Colab)\n",
     "import sys\n",
     "if 'google.colab' in sys.modules:\n",
-    "    %%capture\n",
-    "    # Install the current development version of pydna (comment to install pip version)\n",
-    "    !pip install git+https://github.com/BjornFJohansson/pydna@dev_bjorn\n",
-    "    # Install pip version instead (uncomment to install)\n",
-    "    # !pip install pydna\n"
+    "    %pip install pydna\n"
    ]
   },
   {

docs/notebooks/Example_Gibson.ipynb

@@ -5,7 +5,7 @@
    "metadata": {},
    "source": [
     "# Example of a Gibson Assembly in pydna\n",
-    "> Visit the full library documentation [here](https://bjornfjohansson.github.io/pydna/)\n",
+    "> Visit the full library documentation [here](https://pydna-group.github.io/pydna/)\n",
     "\n",
     "This example showcases a workflow of modelling Gibson assembly to clone gene fragments into plasmids for synthetic biology. The biological example is sourced [here](https://www.nature.com/articles/nmeth.1318#MOESM319), from the original Gibson assembly paper. This example constructs a synthetic pCC1BAC plasmid by joining sequence fragments from Ruminiclostridium (Clostridium) cellulolyticum. The R. cellulolyticum fragments joined are termed F1, F2, and F3, as in the paper.\n",
     "\n",
@@ -16,7 +16,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "<a target=\"_blank\" href=\"https://colab.research.google.com/github/BjornFJohansson/pydna/blob/dev_bjorn/docs/notebooks/Example_Gibson.ipynb\">\n",
+    "<a target=\"_blank\" href=\"https://colab.research.google.com/github/pydna-group/pydna/blob/master/docs/notebooks/Example_Gibson.ipynb\">\n",
     "  <img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/>\n",
     "</a>"
    ]
@@ -27,14 +27,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "%%capture\n",
     "# Install pydna (only when running on Colab)\n",
     "import sys\n",
     "if 'google.colab' in sys.modules:\n",
-    "    %%capture\n",
-    "    # Install the current development version of pydna (comment to install pip version)\n",
-    "    !pip install git+https://github.com/BjornFJohansson/pydna@dev_bjorn\n",
-    "    # Install pip version instead (uncomment to install)\n",
-    "    # !pip install pydna\n"
+    "    %pip install pydna\n"
    ]
   },
   {

docs/notebooks/Example_Restriction.ipynb

@@ -5,7 +5,7 @@
    "metadata": {},
    "source": [
     "# Example of a Plasmid Restriction/Ligation Cloning\n",
-    "> Visit the full library documentation [here](https://bjornfjohansson.github.io/pydna/)\n",
+    "> Visit the full library documentation [here](https://pydna-group.github.io/pydna/)\n",
     "\n",
     "This example showcases a workflow of modelling molecular cloning with restriction enzymes, PCR, and ligases, to clone gene fragments into plasmids. This example constructs a synthetic plasmid by cloning the ase1 gene, which encodes a microtubule associated protein responsible for mitotic spindle assembly, into the pFA6a-kanMX6 cloning vector:\n",
     "\n",
@@ -20,7 +20,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "<a target=\"_blank\" href=\"https://colab.research.google.com/github/BjornFJohansson/pydna/blob/dev_bjorn/docs/notebooks/Example_Gibson.ipynb\">\n",
+    "<a target=\"_blank\" href=\"https://colab.research.google.com/github/pydna-group/pydna/blob/master/docs/notebooks/Example_Gibson.ipynb\">\n",
     "  <img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/>\n",
     "</a>"
    ]
@@ -31,14 +31,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "%%capture\n",
     "# Install pydna (only when running on Colab)\n",
     "import sys\n",
     "if 'google.colab' in sys.modules:\n",
-    "    %%capture\n",
-    "    # Install the current development version of pydna (comment to install pip version)\n",
-    "    !pip install git+https://github.com/BjornFJohansson/pydna@dev_bjorn\n",
-    "    # Install pip version instead (uncomment to install)\n",
-    "    # !pip install pydna\n"
+    "    %pip install pydna\n"
    ]
   },
   {