Fix admonitions; fix broken images link; improve readme

README.md

@@ -99,8 +99,38 @@ pandoc --wrap=none -f rst -t gfm input.rst -o output.md
 pandoc --wrap=none --from=rst --to=gfm-raw_html input.rst -o output.md
 ```
 
-Note: After conversion, you may need to manually adjust:
-- Table of contents (toctree directives)
-- Sphinx-specific roles and directives
-- Cross-references
-- Code block language specifications
+Note: After conversion, you will likely need to manually adjust the following elements:
+
+1. Sphinx-specific directives:
+   - `.. toctree::` directives (table of contents)
+   - `.. note::`, `.. warning::`, etc. (admonitions)
+   - `.. code-block::` with complex options
+   - Custom Sphinx directives
+
+2. Cross-references and links:
+   - `:ref:` references
+   - `:doc:` references
+   - Internal document links
+   - Custom role references
+
+3. Advanced formatting:
+   - Complex tables with merged cells
+   - Sidebar content
+   - Figure directives with options
+   - Math equations (may need reformatting)
+
+4. Code blocks:
+   - Language specifications
+   - Line highlighting
+   - Line number references
+   - Code block captions
+
+5. Extensions and custom roles:
+   - Domain-specific roles (e.g., `:py:class:`)
+   - Custom extension directives
+   - Substitutions and replacements
+
+6. Meta information:
+   - Document metadata
+   - Version information
+   - Copyright notices in special formats

docs/crc_infra/crc_uge_env.md

@@ -42,8 +42,8 @@ Common Parallel Environments include:
 
     * mpi-64 (multi [64 core per] machine processing in 64 core increments)
 
-> [!NOTE]
-> Increments (24,48,64) are mapped to total cores per server. A server with 24 cores will not accept mpi-32 requests.
+!!! note
+    Increments (24,48,64) are mapped to total cores per server. A server with 24 cores will not accept mpi-32 requests.
 
 PEs are specified in your submit script with the syntax:
 

docs/help/faq.md

@@ -38,8 +38,8 @@ If the form is not visible, it can be searched for in the search bar. This will
 
 ### How Can I Maintain My CRC Account After Graduating/Leaving Notre Dame?
 
-> [!NOTE]
-> The university disables staff accounts on the final day of employment, while graduating student accounts are disabled at the conclusion of the current semester.
+!!! note
+    The university disables staff accounts on the final day of employment, while graduating student accounts are disabled at the conclusion of the current semester.
 
 If you have research related to work here at Notre Dame and are able to justify continued access, you may request a faculty member sponsor your account as an external affiliate. These accounts are valid for up to one year, but may be renewed annualy. This process can be initiated by having your sponsor complete an `external account request <Request External Account>`. To avoid losing your CRC account and all associated data, please complete this process prior to your account being disabled.
 
@@ -114,8 +114,8 @@ Many software packages can be installed in your local home directory and we're h
 
 Software that is installed globally through our `modules` tool must undergo license review by the Notre Dame legal department. For this reason, all requests to add a new module must come from Notre Dame faculty. Please submit a [Software Request Form](https://docs.google.com/a/nd.edu/forms/d/e/1FAIpQLSdzy-F9X6wykK1KhRdsT-8QtlcPvs8nwPLid6fnGXD-QAjQCg/viewform) and review the attached CRC Software Policy. The software policy also contains information on licensing and cost sharing with CRC.
 
-> [!NOTE]
-> This process can take up to 7 business days from receipt of the software request. If you require an expedited service, please make that apparent on your request form.
+!!! note
+    This process can take up to 7 business days from receipt of the software request. If you require an expedited service, please make that apparent on your request form.
 
 ### Notes on sudo/root access
 
@@ -247,14 +247,14 @@ If an invalid resource request is identified by this validation procedure, your
 
 For example the mpi-8 machines (machines with 8 cores) are either faculty owned (restricted) or on a restricted access list for codes which require an Infiniband interconnect. Standard user scripts will fail when specifying mpi-8. In the case the user should use mpi-12 as the majority of systems available for general access are 12 core machines.
 
-> [!NOTE]
-> Scripts that contain the '''mem_free=''' resource request i.e.
->
-> > \#\$ -l mem_free=X
->
-> will unfortunately always fail the validation test (due to lack of memory information at the time the validation is undertaken). To overcome this situation, please disable the validation process in your submission script by adding the following line:
->
-> > \#\$ -w n
+!!! note
+    Scripts that contain the '''mem_free=''' resource request i.e.
+    
+    > \#\$ -l mem_free=X
+    
+    will unfortunately always fail the validation test (due to lack of memory information at the time the validation is undertaken). To overcome this situation, please disable the validation process in your submission script by adding the following line:
+    
+    > \#\$ -w n
 
 ### How Can I Monitor The Behavior Of My Running Jobs?
 

docs/modules/conda.md

@@ -4,10 +4,10 @@
 
 ## General Description
 
-Conda is a popular package management system used in machine learning and artificial intelligence research. It is built as a part of Anaconda distribution and provides a useful alternative for the pip package manager. Conda allows users to create many different environments containing different packages without there being any overlap or crossover that may occur when using pip. Each environment may be customized to a specific program’s needs and therefore allows for easy package management and access.
+Conda is a popular package management system used in machine learning and artificial intelligence research. It is built as a part of Anaconda distribution and provides a useful alternative for the pip package manager. Conda allows users to create many different environments containing different packages without there being any overlap or crossover that may occur when using pip. Each environment may be customized to a specific program's needs and therefore allows for easy package management and access.
 
-> !!! warning
-> In order to use `conda`, you must be using `bash` as your shell. If you have an account created after May of 2018, your default shell is bash. To check your shell, type: `echo $0`. If your shell is tcsh and you'd like it to be bash, email us at <[email protected]>.
+!!! warning
+    In order to use `conda`, you must be using `bash` as your shell. If you have an account created after May of 2018, your default shell is bash. To check your shell, type: `echo $0`. If your shell is tcsh and you'd like it to be bash, email us at <[email protected]>.
 
 ------------------------------------------------------------------------
 
@@ -118,8 +118,8 @@ Once you have found the name of the package you want to install you may install
 conda install -n ENVNAME PKGNAME 
 ```
 
-> [!NOTE]
-> If you omit the “-n ENVNAME” portion of code the package will be installed in your current environment. All installs must be executed in a specific conda environment, not the base environment. This means that (ENVNAME) must appear to the left of your \[username\]. This ensures that no base packages are uninstalled, for example pip or python.''
+!!! note
+    If you omit the "-n ENVNAME" portion of code the package will be installed in your current environment. All installs must be executed in a specific conda environment, not the base environment. This means that (ENVNAME) must appear to the left of your [username]. This ensures that no base packages are uninstalled, for example pip or python.
 
 When you need to update one of your packages you may use the following update command.
 
@@ -174,7 +174,7 @@ conda config --add channels bioconda
 conda config --set channel_priority strict 
 ```
 
-When adding this channel using the “add” command we are telling Conda to add the channel at the top, or highest priority of the channels accessible to our manager. The order of channels in your Conda matters due to the potential of channel collisions. To circumvent this issue and ensure that we do not encounter any channel collisions from duplicate packages we use the second line of code above. This ensures that all of the dependencies come from the bioconda channel as opposed to the default channel.
+When adding this channel using the "add" command we are telling Conda to add the channel at the top, or highest priority of the channels accessible to our manager. The order of channels in your Conda matters due to the potential of channel collisions. To circumvent this issue and ensure that we do not encounter any channel collisions from duplicate packages we use the second line of code above. This ensures that all of the dependencies come from the bioconda channel as opposed to the default channel.
 
 If we wanted to set the priority back to our default channel we would have to edit the ~/.condarc file so that defaults is the first channel shown. The ~/.condarc file is only created upon creation of a new channel.
 
@@ -211,12 +211,12 @@ conda install bioconda::PKGNAME
 
 ## Job Submission Using Conda Environments
 
-Since your environments are saved in a unique file path on your node all of the packages will already be installed in the referenced environment, allowing you to customize your environment before submitting your job. Once the job is submitted it will be referencing the packages in your environment, meaning that you don’t need to redo any of your previous installations.
+Since your environments are saved in a unique file path on your node all of the packages will already be installed in the referenced environment, allowing you to customize your environment before submitting your job. Once the job is submitted it will be referencing the packages in your environment, meaning that you don't need to redo any of your previous installations.
 
 To load your environment use the following code, keeping in mind that the first three lines are example job submission code. Everything after those initial three lines will be as if you are running the same code in your node.
 
-> [!NOTE]
-> Unlike many software packages at the CRC, you generally should never load the conda module in your job scripts or configuration files after the initial configuration is complete.
+!!! note
+    Unlike many software packages at the CRC, you generally should never load the conda module in your job scripts or configuration files after the initial configuration is complete.
 
 ``` shell
 #!/bin/bash

docs/modules/python.md

@@ -1,11 +1,11 @@
 # Python
 
-![image](images/python-logo-master-v3-TM.png)
+![image](../images/python-logo-master-v3-TM.png)
 
 Python is an interpreted, interactive, object-oriented programming language. It incorporates modules, exceptions, dynamic typing, very high level dynamic data types, and classes. Python combines remarkable power with very clear syntax. It has interfaces to many system calls and libraries, as well as to various window systems, and is extensible in C or C++. It is also usable as an extension language for applications that need a programmable interface. Finally, Python is portable: it runs on many Unix variants, on the Mac, and on PCs under MS-DOS, Windows, Windows NT, and OS/2.
 
-> [!WARNING]
-> Starting in May, 2019, the CRC Python module defaults to `Python 3`. If you are using code based on `Python 2`, we highly recommend moving to the 3.X branch of Python. Python 2 stopped being maintained in January of 2020 and have been completely removed from RHEL8.
+!!! warning
+    Starting in May, 2019, the CRC Python module defaults to `Python 3`. If you are using code based on `Python 2`, we highly recommend moving to the 3.X branch of Python. Python 2 stopped being maintained in January of 2020 and have been completely removed from RHEL8.
 
 ------------------------------------------------------------------------
 
@@ -105,8 +105,8 @@ Next, install the virtualenv package into your user space:
 pip3 install --user virtualenv
 ```
 
-> [!NOTE]
-> The virtualenv executable will not be automatically added to your path.
+!!! note
+    The virtualenv executable will not be automatically added to your path.
 
 Next, you will need to create a folder named whatever you like and move into it:
 

docs/new_user/connecting_to_crc.md

@@ -4,8 +4,8 @@ All activity performed on the CRC infrastructure occurs on remote servers, this
 
 For more information on the Public head nodes see the `front_end_workflow` page.
 
-> [!NOTE]
-> For users connecting from off campus, please review the section `off-campus-connect` first.
+!!! note
+    For users connecting from off campus, please review the section `off-campus-connect` first.
 
 ------------------------------------------------------------------------
 
@@ -49,8 +49,8 @@ Once `XQuartz` is installed, you can use the `-Y` flag to `ssh` within a termina
 ssh -Y [email protected]
 ```
 
-> [!NOTE]
-> Development of `XQuartz` has lagged quite behind macOS. A number of issues with it has been reported to us. It may be easier to use `fastx` for Mac users.
+!!! note
+    Development of `XQuartz` has lagged quite behind macOS. A number of issues with it has been reported to us. It may be easier to use `fastx` for Mac users.
 
 ------------------------------------------------------------------------
 

docs/new_user/modules.md

@@ -62,10 +62,10 @@ There are different categories in which the Modules are organized:
 - general_software
 - development_tools_and_libraries.
 
-> [!IMPORTANT]
-> Modules within the restricted_software category cannot be used without first receiving permission to access those pieces of software.
->
-> The deprecated category contains modules which are out of date or no longer being supported after the next biannual outage. The date of the next biannual outage can be found on the [main page](../index.html) . These modules can still be used, however it is recommended to move your application to a newer version of the deprecated module.
+!!! important
+    Modules within the restricted_software category cannot be used without first receiving permission to access those pieces of software.
+    
+    The deprecated category contains modules which are out of date or no longer being supported after the next biannual outage. The date of the next biannual outage can be found on the [main page](../index.md) . These modules can still be used, however it is recommended to move your application to a newer version of the deprecated module.
 
 ------------------------------------------------------------------------
 
@@ -127,8 +127,8 @@ module help matlab
 
 There are some cases where a module is desired for software which is installed into local user space. Local modules can coexist with CRC modules and being user space installed software, these modules will not become deprecated and removed over time by CRC administrators. Creating a local or private module can be straightforward once a piece of software is installed into user space.
 
-> [!NOTE]
-> For the rest of these instructions, it is assumed the software a module is intended for is already installed.
+!!! note
+    For the rest of these instructions, it is assumed the software a module is intended for is already installed.
 
 For more information on the module command itself, see `Module Command`.
 

docs/new_user/obtain_account.md

@@ -7,5 +7,5 @@ To apply for an account with the CRC, complete the steps below:
 - You must be signed into your *Notre Dame affliated email account*, for example <[email protected]>. If you are not already signed in, open a new tab within your browser and sign into your ND account.
 - Once logged in, you can fill out all entries within the [new user form](https://docs.google.com/a/nd.edu/forms/d/e/1FAIpQLSeeGPVf09NQAzwzQa-RcrDm2X3GeCufq1ObhdzVfLftbUGNsA/viewform) and a CRC account will be created for you. You will be notified via email.
 
-> [!NOTE]
-> Email is the official line of communication for your CRC account. Be sure you are checking your ND affiliated email account often for any news, updates, or direct communication from CRC staff related to your jobs and account usage.
+!!! note
+    Email is the official line of communication for your CRC account. Be sure you are checking your ND affiliated email account often for any news, updates, or direct communication from CRC staff related to your jobs and account usage.