tools & software rework

Author: s-sajid-ali

docs/hpc/06_tools_and_software/04_python_packages_with_virtual_environments.mdx

@@ -30,58 +30,42 @@ Thus you can consider the following options:
 :::
 ::::
 
-Thus you can consider the following options
-
--   Reinstall your packages if some of the files get deleted
-    -   You can do this manually 
-    -   You can also do this automatically. For example, within a workflow of pipeline software like [Nextflow](https://www.nextflow.io/)
--   Pay for "Research Project Space" - see details on the [Research Project Space](../03_storage/05_research_project_space.mdx) page.
--   Use Singularity and install packages within a corresponding overlay file - See instructions on our [Singularity with Conda](../07_containers/03_singularity_with_conda.md) page.
-
 ## Create virtual environment
-It is advisable to create private environment inside the project directory. This boosts reproducibility and does not use space in `/home/$USER`
-
-### virtualenv
-[virtualenv](https://virtualenv.pypa.io/en/latest/) is a tool to create isolated Python environments
-
-Since Python 3.3, a subset of it has been integrated into the standard library under the venv module.
-
-You can create new virtual environment in two ways:
-
--   empty
--   inherit all packages from those installed on HPC already (and available in PATH after you load python module)
-
+It is advisable to create private environment inside the project directory. This boosts reproducibility and does not use space in `/home/$USER`:
 ```sh
 ## created directory for your project and cd there
 mkdir /scratch/$USER/my_project
 cd /scratch/$USER/my_project
+```
 
+### `virtualenv`
+[`virtualenv`](https://virtualenv.pypa.io/en/latest/) is a tool to create isolated Python environments. Since Python 3.3, a subset of it has been integrated into the standard library under the venv module. You can create new virtual environment in two ways:
+-   empty
+```sh
 ## Create an EMPTY virtual environment
 virtualenv venv
-
+```
+-   inherit all packages from those installed on HPC already (and available in PATH after you load python module)
+```sh
 ## Create an virtual environment that inherits system packages
 virtualenv venv --system-site-packages
 ```
 
-### venv
-[venv](https://docs.python.org/3/library/venv.html) is package shipped with Python. It provides subset of options available in virtualenv tool ([link](https://virtualenv.pypa.io/en/latest/)).
+### `venv`
+[`venv`](https://docs.python.org/3/library/venv.html) is package shipped with Python. It provides subset of options available in virtualenv tool ([link](https://virtualenv.pypa.io/en/latest/)).
 ```sh
 python -m venv venv
 ```
 
-Create new virtual environment in current directory
-
+Create new virtual environment in current directory:
 -   empty
--   inherit all packages from those installed on HPC already (and available in PATH after you load python module)
 ```sh
-## created directory for your project and cd there
-mkdir /scratch/$USER/my_project
-cd /scratch/$USER/my_project
-##EMPTY
 ## (use venv command to create environment called "venv")
 
 python -m venv venv
-
+```
+-   inherit all packages from those installed on HPC already (and available in PATH after you load python module)
+```sh
 ## Inhering all packages
 python -m venv venv --system-site-packages
 ```

docs/hpc/06_tools_and_software/06_conda_environments.mdx

@@ -1,5 +1,10 @@
 # Conda Environments (Python, R)
 
+:::tip
+This page describes how you can create conda environments without containers in `$SCRATCH`/`/home/$USER`. We strongly encourage you to create conda enviroments within Overlay files attached to Apptainer containers [as decribed in this section](../07_containers/03_singularity_with_conda.md). Please note that creating both kinds of conda environments is strongly discouraged as it leads to packages from one environment being accidentally used in another.
+:::
+
+
 ## What is Conda?
 Package, dependency and environment management for any language—Python, R, Ruby, Lua, Scala, Java, JavaScript, C/ C++, FORTRAN, and more. Please find more information at [the official documentation page](https://docs.conda.io/en/latest/)