Update readme and add tqdm

Author: cchlanger

README.md

@@ -1,50 +1,61 @@
 # Gerlich Jupyter
-**Gerlich Jupyter** This is the the Gerlich group base container for [JupyterHub](https://jupyterhub.vbc.ac.at/), with all internally used NGS and image analysis tools preinstalled.
+**Gerlich Jupyter** This is the Gerlich group base container for [JupyterHub](https://jupyterhub.vbc.ac.at/), with all internally used NGS and image analysis tools preinstalled.
 
 # Startup on VBC JupyterHub
 
-You can run use this container on [JupyterHub](https://jupyterhub.vbc.ac.at/).
-To set it up, use the following settings.
+You can use this container on [JupyterHub](https://jupyterhub.vbc.ac.at/).
+To set it up, use the following settings:
  - After authenticating on JupyterHub and clicking "Add New Server" on the hub homepage, select `JupyterLab based on custom Singularity image (EXPERIMENTAL)`
- - Type in the link to the image location, you can find a link in the [changelog](./changelog.md)
+ - Type in the link to the image location. You can find a link in the [changelog](./changelog.md).
  - **Attention:** You do not need to contact IT. We set everything up for you!
 
-
 ![JupyterHub Settings](images/settings.png)
 
-
-You change the version by changing the version identifier, which is the part of the image URL after the colon:
+You can change the version by modifying the version identifier, which is the part of the image URL after the colon:
 `.../gerlichlab/jupyter-gerlich:YOUR_FAVORITE_VERSION`
 
-or <span style="color:red">**copy and past the link from the version subsection below.**<span>
+or <span style="color:red">**copy and paste the link from the version subsection below.**<span>
 
-**Please for now use the cached location!**
-
-Once the server is started, do not choose a specific kernel. Rather, choose the basic Python3 kernel.
+**Please, for now, use the cached location!**
 
+Once the server is started, do not choose a specific kernel. Instead, choose the basic Python3 kernel.
 
 ![Python Kernel](images/kernel.png)
 
-
 It will contain everything installed in the container.
 
 # Running the notebook locally (OPTIONAL)
-For your convenience, you can then start a notebook server with all the necessary libraries installed with:
+For your convenience, you can start a notebook server with all the necessary libraries installed by running:
 `docker-compose up` from the command line in the directory of this repository.
-Then open up a browser and navigate to http://localhost:9999 or http://localhost:9999/lab for the jupyter lab interface. 
-This will prompt you for a password, which we disclosed in the python club lecture.
+Then open a browser and navigate to http://localhost:9999 or http://localhost:9999/lab for the JupyterLab interface. 
+This will prompt you for a password, which we disclosed in the Python Club lecture.
+
+If you use this setup more regularly, please change the password in the `jupyter_notebook_config.py`. 
+To do this, modify the following line in the configuration file:
+
+```python
+# The string should be of the form type:salt:hashed-password.
+c.NotebookApp.password = u'sha1:d1ed07fdae18:5423fffeca03b4b1c1d96f79317abe816a220a69'
+```
+
+To create a new hashed password, you can use the following Python code:
+
+```python
+from notebook.auth import passwd
+print(passwd())
+```
 
-If you use this setup more regularly, please change the password in the jupyter_notebook_config.py
+This will prompt you to enter a new password and generate a hashed password string. Replace the existing value of `c.NotebookApp.password` with the new hashed password string.
 
 # Connecting the local notebook to VSCode 
 A brief description by Michael can be found [here](https://github.com/gerlichlab/python_club_seq_formats_I).
 
 # How do I get a custom version?
 
-1. Fork the repository
-1. Create a new branch
-1. Modify the [gerlich_base.yml](./gerlich_base.yml) (e.g., add all your missing libraries or change the version of the libraries)
-1. Test your build by running: `docker-compose -f docker-dev.yml up`
-1. Test your notebook in the browser: `http://localhost:9999`
+1. Fork the repository.
+1. Create a new branch.
+1. Modify the [gerlich_base.yml](./gerlich_base.yml) (e.g., add all your missing libraries or change the version of the libraries).
+1. Test your build by running: `docker-compose -f docker-dev.yml up`.
+1. Test your notebook in the browser: `http://localhost:9999`.
 1. Pushing your branch will create a pull request. Add a description for your version, including what is different from the base version and why it was created. The description can be extended and modified on the GitHub homepage.
-1. Contact Christoph or Michael. We will give it a new version number and make it available on JupyterHub, at `jupyterhub.vbc.ac.at`
+1. Contact Christoph or Michael. We will give it a new version number and make it available on JupyterHub at `jupyterhub.vbc.ac.at`.

VERSION

@@ -1 +1 @@
-1.8
+1.9

changelog.md

@@ -1,6 +1,13 @@
 # Changelog
 
-## Verion 1.8
+## Version 1.9
+- Version for the Teloni et al. paper
+
+Cached Location:
+
+ `/groups/gerlich/labinfo/Methods/singularity_images/gerlich_jupyter_version-1.9.sif`
+
+## Version 1.8
 - Version 1.7 - lmfit and linescan tool, and removed legacy NGS packages
 
 Cached Location:
@@ -11,8 +18,7 @@ Singularity image URL:
 
 `https://singularity.vbc.ac.at/v1/imagefile/library/gerlichlab/jupyter-gerlich:version-1.8`
 
-
-## Verion 1.7
+## Version 1.7
 - Version 1.6 - updated bioframe to v0.6.2
 
 Cached Location:
@@ -23,21 +29,21 @@ Singularity image URL:
 
 `https://singularity.vbc.ac.at/v1/imagefile/library/gerlichlab/jupyter-gerlich:main`
 
-## Verion 1.6
+## Version 1.6
 - Version 1.5 - updated jupyterlab and batch spawner
 
-## Verion 1.5
+## Version 1.5
 - Version 1.4 + opencv, umap and shap
 
-Chached Location:
+Cached Location:
 
  `/groups/gerlich/labinfo/Methods/singularity_images/jupyter-gerlich:version-1.5`
 
 Singularity image URL:
 
 `https://singularity.vbc.ac.at/v1/imagefile/library/gerlichlab/jupyter-gerlich:version-1.5`
 
-## Verion 1.4
+## Version 1.4
 - Version that supports to read ROI files .zip or .roi generated with ImageJ
 
 Cached Location:
@@ -48,7 +54,7 @@ Singularity image URL:
 
 `https://singularity.vbc.ac.at/v1/imagefile/library/gerlichlab/jupyter-gerlich:version-1.4`
 
-## Verion 1.3
+## Version 1.3
 
 - Fixed bug in ngs package
 
@@ -60,7 +66,7 @@ Singularity image URL:
 
 `https://singularity.vbc.ac.at/v1/imagefile/library/gerlichlab/jupyter-gerlich:version-1.3`
 
-## Verion 1.2
+## Version 1.2
 
 - Version with sparse package installed for dask access of coolers
 
@@ -72,7 +78,7 @@ Singularity image URL:
 
 `https://singularity.vbc.ac.at/v1/imagefile/library/gerlichlab/jupyter-gerlich:version-1.2`
 
-## Verion 1.1
+## Version 1.1
 
 - Version with singularity terminal support
 

gerlich_base.yml

@@ -57,6 +57,7 @@ dependencies:
   - python-graphviz
   - umap-learn
   - lmfit
+  - tqdm
   #more ngs tools
   - pip
   - pip: