removed 1_ and 0_ from into and getting started files

astro.config.mjs

@@ -20,8 +20,8 @@ export default defineConfig({
 				  label: 'User Guide',
 				  // introduce slurmtools and describe what it does
 				  items: [
-					{ label: 'Introduction', slug: 'guides/0_intro'},
-					{ label: 'Getting started', slug: 'guides/1_getting_started' },
+					{ label: 'Introduction', slug: 'guides/intro'},
+					{ label: 'Getting started', slug: 'guides/getting_started' },
 					// introduce submit functionality and how the tutorials work together
 					{
 						label: 'Submitting a job',

src/content/docs/blogs/nmm_template.mdx

@@ -14,13 +14,13 @@ This guide describes how to create a template file that uses [`nmm`](https://git
 </Steps>
 
 ## nmm template file
-Below is a simple template file that can be used to submit NONMEM jobs to slurm with [`nmm`](https://github.com/a2-ai/nonmem-monitor). 
+Below is a simple template file that can be used to submit NONMEM jobs to slurm with [`nmm`](https://github.com/a2-ai/nonmem-monitor)<span style={{ display: 'inline-block', verticalAlign: 'middle' }}><Icon name="external" /></span>. 
 
 import tmpl from '/src/code/nmm-template.tmpl?raw';
 
 <Code title='slurm-job.tmpl' lang='bash' code={tmpl}/>
 
-The template file uses the [whisker package](https://github.com/edwindj/whisker?tab=readme-ov-file)<span style={{ display: 'inline-block', verticalAlign: 'middle' }}><Icon name="external" /></span> to fill in variables according to the [Mustache templating standard](https://mustache.github.io). When `submit_slurm_job` is called, it reads the template file and injects both the [default values provided to the template](/reference/values_provided_to_template) and any values passed in via the [`slurm_template_opts` argument](/reference/submit_slurm_job_reference#using-the-slurm_template_opts-argument). Variables in the template file are denoted with double curly brackets, such as `{{ injected_variable }}`, and these placeholders are replaced with the respective values when submit_slurm_job runs.
+The template file uses the [whisker package](https://github.com/edwindj/whisker?tab=readme-ov-file)<span style={{ display: 'inline-block', verticalAlign: 'middle' }}><Icon name="external" /></span> to fill in variables according to the [Mustache templating standard](https://mustache.github.io)<span style={{ display: 'inline-block', verticalAlign: 'middle' }}><Icon name="external" /></span>. When `submit_slurm_job` is called, it reads the template file and injects both the [default values provided to the template](/reference/values_provided_to_template) and any values passed in via the [`slurm_template_opts` argument](/reference/submit_slurm_job_reference#using-the-slurm_template_opts-argument). Variables in the template file are denoted with double curly brackets, such as `{{ injected_variable }}`, and these placeholders are replaced with the respective values when submit_slurm_job runs.
 
 <Aside type="note"> 
 If a variable in the template file is not supplied to `submit_slurm_job`, it will remain blank in the final output. 

src/content/docs/blogs/simple_notifications.mdx

@@ -39,6 +39,6 @@ import submit from '/src/code/ntfy-submit.R?raw';
 <Code title='ntfy-submit.R' lang='r' code={submit}/>
 
 ## Job status alerts
-This sends off two messages to [ntfy.sh](https://ntfy.sh):
+This sends off two messages to [ntfy.sh](https://ntfy.sh)<span style={{ display: 'inline-block', verticalAlign: 'middle' }}><Icon name="external" /></span>:
 
 ![](/slurmtools-docs/ntfy_sh.png)

src/content/docs/guides/0_intro.mdx → src/content/docs/guides/intro.mdx

@@ -21,4 +21,4 @@ and a helper function:
 5. [generate_nmm_config](/slurmtools-docs/guides/generate_nmm_config) - which helps setup [nmm](https://github.com/a2-ai/nonmem-monitor) - a NONMEM monitor tool
 </Steps>
 
-Ready to dive into `slurmtools`? Head over to the [getting started guide](/slurmtools-docs/guides/1_getting_started) to get setup using `slurmtools` or check out our function-specific guides for detailed insights and advanced tips!
+Ready to dive into `slurmtools`? Head over to the [getting started guide](/slurmtools-docs/guides/getting_started) to get setup using `slurmtools` or check out our function-specific guides for detailed insights and advanced tips!

src/content/docs/guides/simple_template_file.mdx

@@ -6,7 +6,7 @@ pagefind: true
 
 import { Aside, Code, Icon } from '@astrojs/starlight/components';
 
-When calling `submit_slurm_job(mod)` the template file supplied through [`slurmtools` options](/slurmtools-docs/guides/1_getting_started#slurmtools-options), or the [`slurm_job_template_path` argument](/slurmtools-docs/reference/submit_slurm_job_reference#using-the-slurm_job_template_path-argument) is populated and submitted to slurm as a bash job. This setup offers extensive customization options through `slurmtools`, allowing you to adapt job configurations to suit your specific needs.
+When calling `submit_slurm_job(mod)` the template file supplied through [`slurmtools` options](/slurmtools-docs/guides/getting_started#slurmtools-options), or the [`slurm_job_template_path` argument](/slurmtools-docs/reference/submit_slurm_job_reference#using-the-slurm_job_template_path-argument) is populated and submitted to slurm as a bash job. This setup offers extensive customization options through `slurmtools`, allowing you to adapt job configurations to suit your specific needs.
 
 ## Simple template file
 

src/content/docs/guides/submit_slurm_job.mdx

@@ -5,7 +5,7 @@ pagefind: true
 ---
 import { Aside, Code, Steps, Icon } from '@astrojs/starlight/components';
 
-This guide describes how to submit a NONMEM job to slurm using the `submit_slurm_job` function. First, make sure you have loaded `slurmtools` and are familiar with the [needed options](/slurmtools-docs/guides/1_getting_started) to use slurmtools.
+This guide describes how to submit a NONMEM job to slurm using the `submit_slurm_job` function. First, make sure you have loaded `slurmtools` and are familiar with the [needed options](/slurmtools-docs/guides/getting_started) to use slurmtools.
 
 ## Prerequisites
 
@@ -21,7 +21,7 @@ To use `submit_slurm_job` you need a few things set before hand
 Once these are set, you're ready to roll with your Slurm submission! 
 
 ## Submitting a NONMEM job
-Here's the code you'll use to submit a job with `submit_slurm_job`, this uses default values for all arguments, many of which are determined via the `slurmtools` options discussed [here](/slurmtools-docs/guides/1_getting_started).
+Here's the code you'll use to submit a job with `submit_slurm_job`, this uses default values for all arguments, many of which are determined via the `slurmtools` options discussed [here](/slurmtools-docs/guides/getting_started).
 
 import submit_code from '/src/code/submit.R?raw';
 

src/content/docs/index.mdx

@@ -8,7 +8,7 @@ hero:
     file: ../../assets/slurmtools.png
   actions:
     - text: Slurmtools User Guide
-      link: guides/0_intro/
+      link: guides/intro/
       icon: right-arrow
     - text: Explore the slurmtools repository
       link: https://github.com/a2-ai/slurmtools/

src/content/docs/reference/submit_slurm_job_reference.mdx

@@ -67,14 +67,14 @@ $partition
 ```
 
 ### Using the `slurm_job_template_path` argument
-By default, `submit_slurm_job` uses `getOption('slurmtools.slurm_job_template_path')` for the path to the template file (see [Getting Started Guide](/slurmtools-docs/guides/1_getting_started) if you're unfamiliar with the `slurmtools` options). You can update this argument to use a different template file as needed.
+By default, `submit_slurm_job` uses `getOption('slurmtools.slurm_job_template_path')` for the path to the template file (see [Getting Started Guide](/slurmtools-docs/guides/getting_started) if you're unfamiliar with the `slurmtools` options). You can update this argument to use a different template file as needed.
 
 import submit_code_path from '/src/code/submit_path.R?raw';
 
 <Code title="submit_job.R" lang="r" code={submit_code_path}/>
 
 ### Using the `submission_root` argument
-This directory is used to track submission scripts and output. It will be populated with the shell scripts created from filling in the template file when calling `submit_slurm_job` and the stdout/stderr from the bash script. If you would like to set it and forget it use the `slurmtools` option `options('slurmtools.submission_root')` (see the [Getting Started Guide](/slurmtools-docs/guides/1_getting_started) if you are unfamiliar with this option). If you'd like to set this at runtime simply provide the path to the directory you'd like to save the output to. 
+This directory is used to track submission scripts and output. It will be populated with the shell scripts created from filling in the template file when calling `submit_slurm_job` and the stdout/stderr from the bash script. If you would like to set it and forget it use the `slurmtools` option `options('slurmtools.submission_root')` (see the [Getting Started Guide](/slurmtools-docs/guides/getting_started) if you are unfamiliar with this option). If you'd like to set this at runtime simply provide the path to the directory you'd like to save the output to. 
 
 import submit_code_root from '/src/code/submit_path.R?raw';
 
@@ -85,7 +85,7 @@ If the directory does not exists, `submit_slurm_job` will create it.
 </Aside>
 
 ### Using the `bbi_config_path` argument
-If you are using [`bbi`](https://github.com/metrumresearchgroup/bbi)<Icon name='external'/> to submit nonmem jobs this specifies the path to the bbi config file `bbi.yaml`. By default, `submit_slurm_job` uses the `slurmtools` option `options('slurmtools.bbi_config_path)` (see the [Getting Started Guide](/slurmtools-docs/guides/1_getting_started) if you are unfamiliar with this option). If you would like to use a different configuration for `bbi` you can specify the path to a new config file and use that.
+If you are using [`bbi`](https://github.com/metrumresearchgroup/bbi)<Icon name='external'/> to submit nonmem jobs this specifies the path to the bbi config file `bbi.yaml`. By default, `submit_slurm_job` uses the `slurmtools` option `options('slurmtools.bbi_config_path)` (see the [Getting Started Guide](/slurmtools-docs/guides/getting_started) if you are unfamiliar with this option). If you would like to use a different configuration for `bbi` you can specify the path to a new config file and use that.
 
 import submit_code_bbi from '/src/code/submit_bbi.R?raw';