tools & software rework

Author: s-sajid-ali

docs/hpc/06_tools_and_software/04_python_packages_with_virtual_environments.mdx

@@ -18,8 +18,11 @@ module load  python/intel/3.8.6
 ## Automatic deletion of your files
 This page describes the installation of packages on /scratch. One has to remember, though, that files stored in the HPC scratch file system are subject to the HPC Scratch old file purging policy: <br />
 
-::::warning[Automatic deletion of your files]
-Files on the /scratch file system that have not been accessed for 60 or more days will be purged (see [HPC Storage](../03_storage/01_intro_and_data_management.mdx) for details).
+<details>
+<summary>
+**Automatic deletion of your files**
+Files on the `/scratch` file system that have not been accessed for 60 or more days will be purged (see [HPC Storage](../03_storage/01_intro_and_data_management.mdx) for details). Click to see how you can work around this limitation.
+</summary>
 :::tip
 Thus you can consider the following options:
 
@@ -28,7 +31,7 @@ Thus you can consider the following options:
     -   You can do this automatically. For example, within a workflow of a pipeline software like [Nextflow](https://www.nextflow.io/)
 -   Pay for "Research Project Space" - for details see [Research Project Space](../03_storage/05_research_project_space.mdx)
 :::
-::::
+</details>
 
 ## 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`:

docs/hpc/06_tools_and_software/05_r_packages_with_renv.mdx

@@ -26,8 +26,11 @@ module load r/gcc/4.5.0
 R
 ```
 
-::::warning[Automatic deletion of your files]
-Files on the /scratch file system that have not been accessed for 60 or more days will be purged (see [HPC Storage](../03_storage/01_intro_and_data_management.mdx) for details).
+<details>
+<summary>
+**Automatic deletion of your files**
+Files on the `/scratch` file system that have not been accessed for 60 or more days will be purged (see [HPC Storage](../03_storage/01_intro_and_data_management.mdx) for details). Click to see how you can work around this limitation.
+</summary>
 :::tip
 Thus you can consider the following options:
 -   Reinstall your packages if some of the files get deleted
@@ -36,7 +39,8 @@ Thus you can consider the following options:
 -   Pay for "Research Project Space" - for details see [Research Project Space](../03_storage/05_research_project_space.mdx)
 -   Use Singularity and install packages within a corresponding overlay file - Details available at [Squash File System and Singularity](../07_containers/04_squash_file_system_and_singularity.md)
 :::
-::::
+</details>
+
 
 ### Cache directory setup
 By default, renv will cache package installation files to your home directory (most likely either in `~/.local/share/renv` or `~/.cache/R/renv/` or something similar). 

docs/hpc/06_tools_and_software/06_conda_environments.mdx

@@ -1,7 +1,7 @@
 # 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.
+This page describes how you can create conda environments without containers in `$SCRATCH`/`/home/$USER`. We strongly encourage you to create conda environments within Overlay files attached to Apptainer containers [as described 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.
 :::
 
 
@@ -30,21 +30,22 @@ However, Conda has a significantly larger number of pre-compiled packages.
 -   Conda does not take advantage of packages already installed in the system (while [virtualenv and venv](./04_python_packages_with_virtual_environments.mdx) do)
 -   As you will see below, you may need to do additional steps to keep track of all installed packages (including those installed by pip and/or install.packages)
 
-::::warning[Automatic deletion of your files]
-This page describes the installation of packages on `/scratch`. One has to remember, though, that files stored in the HPC scratch file system are subject to the HPC Scratch old file purging policy: <br />
-Files on the `/scratch` file system that have not been accessed for 60 or more days will be purged. <br />
-You can read more this in [Data Management](../03_storage/01_intro_and_data_management.mdx).
 
+<details>
+<summary>
+**Automatic deletion of your files**
+Files on the `/scratch` file system that have not been accessed for 60 or more days will be purged (see [HPC Storage](../03_storage/01_intro_and_data_management.mdx) for details). Click to see how you can work around this limitation.
+</summary>
 :::tip
 Thus you can consider the following options:
-
 -   Reinstall your packages if some of the files get deleted
     -   You can do this manually 
     -   You can do this automatically. For example, within a workflow of a pipeline software like [Nextflow](https://www.nextflow.io/)
 -   Pay for "Research Project Space" - for details see [Research Project Space](../03_storage/05_research_project_space.mdx)
--   Use Singularity and install packages within a corresponding overlay file - for details see [Singularity with Conda](../07_containers/03_singularity_with_conda.md)  
+-   Use Singularity and install packages within a corresponding overlay file - Details available at [Squash File System and Singularity](../07_containers/04_squash_file_system_and_singularity.md)
 :::
-::::
+</details>
+
 
 ## Initializing Conda
 Load anaconda module