closes #333

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 -->
 
@@ -487,7 +487,7 @@ 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 +505,7 @@ 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 +535,4 @@ 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

@@ -33,7 +33,7 @@
                 "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",
+                "    !pip install git+https://github.com/pydna-group/pydna@dev_bjorn\n",
                 "    # Install pip version instead (uncomment to install)\n",
                 "    # !pip install pydna\n"
             ]

docs/notebooks/Dseq.ipynb

@@ -28,7 +28,7 @@
                 "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",
+                "    !pip install git+https://github.com/pydna-group/pydna@dev_bjorn\n",
                 "    # Install pip version instead (uncomment to install)\n",
                 "    # !pip install pydna\n"
             ]

docs/notebooks/Dseq_Features.ipynb

@@ -35,7 +35,7 @@
                 "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",
+                "    !pip install git+https://github.com/pydna-group/pydna@dev_bjorn\n",
                 "    # Install pip version instead (uncomment to install)\n",
                 "    # !pip install pydna\n"
             ]