Update readme for the environment installation (#549)

* add tests for metrics calculation

* replace iou calculation with torchmetrics iou

* fix tests for init test tensors

* fix typo

* fix issue at inference without label

* fix raises for errored csv

* Update readme for the environment installation

* Update python version from 3.9 to 3.10 on readme

* doc changes

---------

Co-authored-by: Charles <authier1993@gmail.com>
Co-authored-by: Mathieu <mathieu.turgeon-pelchat@canada.ca>
Co-authored-by: mpelchat04 <38693210+mpelchat04@users.noreply.github.com>
Co-authored-by: Turgeon-Pelchat <mathieu.turgeon-pelchat@nrcan-rncan.gc.ca>
Co-authored-by: LucaRom <luca@l-she-A102425.nrn.nrcan.gc.ca>

README.md

@@ -10,20 +10,37 @@ In **Geo-Deep-Learning**, the learning process comprises two broad stages: tilin
 ## **Requirement**
 This project comprises a set of commands to be run at a shell command prompt.  Examples used here are for a bash shell in an Ubuntu GNU/Linux environment.
 
-- [Python 3.9](https://www.python.org/downloads/release/python-390/), see the full list of dependencies in [environment.yml](environment.yml)
+- [Python 3.10](https://www.python.org/downloads/release/python-3100/), see the full list of dependencies in [environment.yml](environment.yml)
 - [hydra](https://hydra.cc/docs/intro/)
 - [mlflow](https://mlflow.org/)
 - [miniconda](https://docs.conda.io/en/latest/miniconda.html) (highly recommended)
 - nvidia GPU (highly recommended)
 
 ## **Installation**
+Miniconda is suggested as the package manager for GDL. However, users are advised to [switch to libmamba](https://github.com/NRCan/geo-deep-learning#quickstart-with-conda) as conda's default solver or to __directly use mamba__ instead of conda if they are facing extended installation time or other issues. Additional problems are grouped in the [troubleshooting section](https://github.com/NRCan/geo-deep-learning#troubleshooting). If issues persist, users are encouraged to open a new issue for assistance.
+
+> Tested on Ubuntu 20.04, Windows 10 and WSL 2.
+
+### Quickstart with conda
 To execute scripts in this project, first create and activate your python environment with the following commands:  
 ```shell
 $ conda env create -f environment.yml
 $ conda activate geo_deep_env
 ```
-> Tested on Ubuntu 20.04 and Windows 10 using miniconda.
-> 
+
+### Change conda's default solver for faster install (__Optional__)
+```shell
+conda install -n base conda-libmamba-solver
+conda config --set solver libmamba
+```
+
+### Troubleshooting
+- *ImportError: /lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found*
+  - Export path to library or set it permenantly in your .bashrc file (example with conda) :
+    ```bash
+    export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CONDA_PREFIX/lib/
+    ```
+
 ## **How to use?**
 This is an example of how to run GDL with hydra in simple steps with the _**massachusetts buildings**_ dataset in the `tests/data/` folder, for segmentation on buildings: 
 

docs/source/quickstart.rst

@@ -21,6 +21,9 @@ Examples used here are for a bash shell in an Ubuntu GNU/Linux environment.
 
 Installation
 ------------
+Miniconda is suggested as the package manager for GDL. However, users are advised to `switch to libmamba <https://github.com/NRCan/geo-deep-learning#quickstart-with-conda>` as conda's default solver or to __directly use mamba__ instead of conda if they are facing extended installation time or other issues. Additional problems are grouped in the `troubleshooting section <https://github.com/NRCan/geo-deep-learning#troubleshooting>`. If issues persist, users are encouraged to open a new issue for assistance.
+
+Quickstart with conda
 
 To execute scripts in this project, first create and activate your 
 python environment with the following commands:
@@ -32,7 +35,26 @@ python environment with the following commands:
 
 .. note::
 
-   Tested on Ubuntu 20.04 and Windows 10 using miniconda.
+   Tested on Ubuntu 20.04, Windows 10 and WSL 2.
+
+Change conda's default solver for faster install (__Optional__)
+
+.. code-block:: console
+
+   $ conda install -n base conda-libmamba-solver
+   $ conda config --set solver libmamba
+
+.. _troubleshooting
+ Troubleshooting
+----------------
+
+ .. code-block:: console
+   $ *ImportError: /lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found*
+
+.. code-block:: console
+   $ # Export path to library or set it permenantly in your .bashrc file (example with conda) :
+   $ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CONDA_PREFIX/lib/
+
 
 .. _runninggdl: