Update README installation instructions to be more user friendly #89 #91

rkstu · 2024-03-03T17:27:20Z

This is related to GeomScale/dingo issue #83

Instruction changes:

Make sure the Python version is 3.8 workflows
Install a specific version of poetry workflows

curl -sSL https://install.python-poetry.org | python3 - --version 1.3.2

Install the dependencies for the PySPQR library using

sudo apt-get update -y
sudo apt-get install -y libsuitesparse-dev

Installation Instructions in GitHub Codespaces added in readme file
For a quick and hassle-free Dingo project trial, reference on how to setup python version 3.8.x in GitHub Codespaces added, from where user can follow rest of the installation steps.

Tutorial for local environment added
A how to use dingo in local env file added in dingo/tutorials/dingo_walkthrough.ipynb. This is a smaller version of colab tutorial. User should be able to run all cells after complete installation.

Unit Tests
All unit tests passed without issues(OK status), except for the test tests/rounding.py, which returned an error.

output: tests/rounding.py

I followed these steps on my computer (Ubuntu 24.04) and GitHub Codespaces, and everything worked well for installing the Dingo project. If you have any suggestions or changes, please let me know.

vfisikop

Thanks! I would like to take some time to review the tutorial.

vfisikop · 2024-03-05T09:32:58Z

README.md

 You can have a look at our [Google Colab notebook](https://colab.research.google.com/github/GeomScale/dingo/blob/develop/tutorials/dingo_tutorial.ipynb)
 on how to use `dingo`.

+#### In local environment
+You can have a look at `dingo/tutorials/dingo_walkthrough.ipynb`. Now you should be able to run all cells.


It is easier if we include a link to the tutorial file

dingo/tutorials/dingo_walkthrough.ipynb is intended for tutorial purpose in local environment after complete installation.

Not sure about "include a link to the tutorial file", should I create a colab notebook or provide a link to the walkthrough file in GitHub?

I propose to minimize the review process and leave the tutorial as a separate PR. So this PR will only include the changes to README. Do you agree?

Also I am not convinced that we need a "local" version of the tutorial. Isn't the current tutorial enough to execute locally?

The current tutorial should be sufficient for local execution. My initial thought was to have a separate file specifically for the local project demo, but on second thought, the existing tutorial works perfectly. I've gone ahead and removed the "dingo_walkthrough" file to avoid any confusion.

Sure, Let's keep this PR focused on the README changes and submit the tutorial in a separate PR. This will help keep the review process streamlined.

vfisikop · 2024-03-05T09:33:31Z

README.md

 ```
-apt-get install libsuitesparse-dev
+
+To install the Python dependencies, [Poetry](https://python-poetry.org/). 


What happens with other poetry versions? Have you tried?

I have tried multiple combinations of Python and poetry versions and followed the same installation instructions, below is the output of the poetry install command

Python 3.10.13 and Poetry (version 1.8.2) [If installed using pip install poetry]

Python 3.8.18 and Poetry (version 1.8.2) [If installed using pip install poetry]

Python 3.10.13 and Poetry (version 1.3.2)

Python 3.8.18 and Poetry (version 1.3.2)

vfisikop · 2024-03-05T09:38:17Z

README.md

+
+**Note:** If you are using `GitHub Codespaces`. Start [here](https://docs.github.com/en/codespaces/setting-up-your-project-for-codespaces/adding-a-dev-container-configuration/setting-up-your-python-project-for-codespaces) to set the python version. Once your Python version is `3.8.x` you can start following the below instructions.
+
+Clone dino repository


dino --> dingo

Updated in readme file

vfisikop · 2024-03-05T09:38:39Z

README.md

 ## Installation

+**Note:** Python version should be 3.8.x. You can check this by running the following command in your terminal:


what happens with other Python versions?

I have tried multiple combinations of Python and poetry versions and followed the same installation instructions, below is the output of the poetry install command

Python 3.10.13 and Poetry (version 1.8.2) [If installed using pip install poetry]

Python 3.8.18 and Poetry (version 1.8.2) [If installed using pip install poetry]

Python 3.10.13 and Poetry (version 1.3.2)

Python 3.8.18 and Poetry (version 1.3.2)

great, could you please list all the possible choices and the possible solutions/workarounds in the README.
e.g. Python 3.8.18, Poetry 1.3.2 -- OK
Python 3.10.13, Poetry 1.3.2 -- fail

BTW why the second case above fails? Is there a workaround?

I tried with multiple other combinations of Python and Poetry versions, but only Python 3.8 with Poetry 1.3.2 seems to work consistently yet, while other combinations like Python 3.10.13 with Poetry 1.3.2 fails due to dependency compatibility issues. This is likely because some libraries haven't been updated for other python versions such as Python 3.10 yet. I tried workarounds like specifying broader version ranges (e.g., numpy==^1.20.1) in the pyproject.toml file, and this doesn't seems to help.

vfisikop · 2024-03-05T09:39:13Z

README.md

+```bash
+python --version
+```
+If you have a different version of Python installed, you'll need to install it or update-alternatives [start here](https://www.youtube.com/watch?v=w7v4CZt1po8).


I would prefer a Python site or blog and not a youtube link

I've revised the Readme file to include installation instruction blog posts similar to those found in the video.

Python installation: https://linuxize.com/post/how-to-install-python-3-8-on-ubuntu-18-04/
Update default Python version: https://linuxhint.com/update_alternatives_ubuntu/

If you have any suggestions or changes, please let me know.

vfisikop · 2024-03-05T09:39:51Z

tutorials/dingo_walkthrough.ipynb

+   "metadata": {},
+   "source": [
+    "Now, you can load a metabolic model. \n",
+    "Currently, `dingo` may get either a `.json` or a '.mat` model format."


.mat is not correctly rendered.

Updated in dingo_walkthrough.ipynb file

vfisikop · 2024-03-19T08:34:03Z

README.md

+
+**Note:** If you are using `GitHub Codespaces`. Start [here](https://docs.github.com/en/codespaces/setting-up-your-project-for-codespaces/adding-a-dev-container-configuration/setting-up-your-python-project-for-codespaces) to set the python version. Once your Python version is `3.8.x` you can start following the below instructions.
+
+Clone dingo repository


I propose to remove this step, cloning a repo is a straightforward command and I think not needed in installation instructions. Also there are variations of cloning not described here (https, ssh).

Removed cloning

vfisikop · 2024-03-19T08:36:33Z

README.md

 ## Installation

+**Note:** Python version should be 3.8.x. You can check this by running the following command in your terminal:


great, could you please list all the possible choices and the possible solutions/workarounds in the README.
e.g. Python 3.8.18, Poetry 1.3.2 -- OK
Python 3.10.13, Poetry 1.3.2 -- fail

BTW why the second case above fails? Is there a workaround?

vfisikop · 2024-03-19T08:39:30Z

README.md


-To install the Python dependencies, install [Poetry](https://python-poetry.org/). Then, run
+To install the Python dependencies, [Poetry](https://python-poetry.org/). 


Please rephrase. I propose to leave the phrasing as it was before and only change the installation command.

Understood. I've kept the original phrasing as much as possible, except for adding the installation guide for GitHub Codespaces.

vfisikop · 2024-03-19T08:40:55Z

README.md

 You can have a look at our [Google Colab notebook](https://colab.research.google.com/github/GeomScale/dingo/blob/develop/tutorials/dingo_tutorial.ipynb)
 on how to use `dingo`.

+#### In local environment
+You can have a look at `dingo/tutorials/dingo_walkthrough.ipynb`. Now you should be able to run all cells.


I propose to minimize the review process and leave the tutorial as a separate PR. So this PR will only include the changes to README. Do you agree?

vfisikop · 2024-03-19T08:43:21Z

README.md

 You can have a look at our [Google Colab notebook](https://colab.research.google.com/github/GeomScale/dingo/blob/develop/tutorials/dingo_tutorial.ipynb)
 on how to use `dingo`.

+#### In local environment
+You can have a look at `dingo/tutorials/dingo_walkthrough.ipynb`. Now you should be able to run all cells.


Also I am not convinced that we need a "local" version of the tutorial. Isn't the current tutorial enough to execute locally?

vfisikop

Thanks.

rkstu added 2 commits March 3, 2024 17:01

Update README installation instructions to be more user friendly #89

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Update README installation instructions to be more user friendly #89

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rkstu added 2 commits March 19, 2024 22:30

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vfisikop merged commit 3295932 into GeomScale:develop Mar 28, 2024

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Update README installation instructions to be more user friendly #89 #91

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		Note: If you are using `GitHub Codespaces`. Start [here](https://docs.github.com/en/codespaces/setting-up-your-project-for-codespaces/adding-a-dev-container-configuration/setting-up-your-python-project-for-codespaces) to set the python version. Once your Python version is `3.8.x` you can start following the below instructions.

		Clone dino repository

		## Installation

		Note: Python version should be 3.8.x. You can check this by running the following command in your terminal:


		Note: If you are using `GitHub Codespaces`. Start [here](https://docs.github.com/en/codespaces/setting-up-your-project-for-codespaces/adding-a-dev-container-configuration/setting-up-your-python-project-for-codespaces) to set the python version. Once your Python version is `3.8.x` you can start following the below instructions.

		Clone dingo repository


		To install the Python dependencies, install [Poetry](https://python-poetry.org/). Then, run
		To install the Python dependencies, [Poetry](https://python-poetry.org/).

Update README installation instructions to be more user friendly #89 #91

Update README installation instructions to be more user friendly #89 #91

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