Fix urls

docs/cheaha/slurm/slurm_tutorial.md

@@ -294,7 +294,7 @@ for i in {1..5}; do
 done
 ```
 
-You can execute the `generate_input.sh` script as shown below. The first command `chmod` grants execute permission to the script so it can be run directly. The second command runs the script to generate the required input files. For more details on usage of bash scripting, refer to [Script Concepts](../../workflow_solutions/shell.md/#script-concepts)
+You can execute the `generate_input.sh` script as shown below. The first command `chmod` grants execute permission to the script so it can be run directly. The second command runs the script to generate the required input files. For more details on usage of bash scripting, refer to [Script Concepts](../../workflow_solutions/shell.md#script-concepts)
 
 ```bash
 chmod +x generate_input.sh

docs/cheaha/software/modules.md

@@ -225,7 +225,7 @@ Use of these software packages without authorization may be a violation of the [
 <!-- markdownlint-disable MD046 -->
 !!! danger
 
-    Versions of GSEA prior to `4.2.3` use a compromised version of log4j. Those versions are affected by a serious [remote code execution issue](https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2021-44832). Please transition your software to use versions of GSEA >= `4.2.3`.
+    Versions of GSEA prior to `4.2.3` use a compromised version of log4j. Those versions are affected by a serious [remote code execution issue](https://www.cve.org/CVERecord?id=CVE-2021-44832). Please transition your software to use versions of GSEA >= `4.2.3`.
 <!-- markdownlint-enable MD046 -->
 
 ### Rsync

docs/data_management/lts/index.md

@@ -33,7 +33,7 @@ When talking about S3 storage, some terms are different compared to a normal fil
     If you lose your access and secret keys, please submit a [support ticket](../../index.md#how-to-contact-us) to <support@listserv.uab.edu> to request your keys. Keys will only be given to an allocation owner as verified by RC staff.
 <!-- markdownlint-enable MD046 -->
 
-This documentation will use the standard file and path terms since those are more easily understood by most users. Just be aware that documentation such as [AWS CLI](https://awscli.amazonaws.com/v2/documentation/api/latest/index.html) will use terms prefix, object, and others that are not standard in a typical filesystem.
+This documentation will use the standard file and path terms since those are more easily understood by most users. Just be aware that documentation such as [AWS CLI](https://docs.aws.amazon.com/cli/latest/) will use terms prefix, object, and others that are not standard in a typical filesystem.
 
 ## Requesting an Allocation
 

docs/education/training_resources.md

@@ -34,10 +34,6 @@ The Carpentries is a 501(c)3 non-profit organization dedicated to educating rese
 
 - [Globus Events Calendar](https://www.globus.org/events/)
 
-### Data Science and Engineering
-
-- [Datapen.io Free Courses](https://www.datapen.io/resources/free-course-resources)
-
 ### Bioinformatics, Genetics, and Genomics
 
 - [Rosalind.info](https://rosalind.info/problems/locations/): A platform for learning bioinformatics and programming.

docs/index.md

@@ -72,4 +72,4 @@ For additional information please see our [Support Page](./help/support.md).
 
 Research Computing is developed and supported by UAB IT's Research Computing Group. We are developing a core set of applications to help you easily incorporate our services into your research processes and this documentation collection to help you leverage the resources already available. We follow the best practices of the Open Source community and develop our software in an open-source fashion.
 
-Research Computing is an out growth of the UABgrid pilot, launched in September 2007 which has focused on demonstrating the utility of unlimited analysis, storage, and application for research. RCS is built on the same technology foundations used by major cloud vendors and decades of distributed systems computing research, technology that powered the last ten years of large scale systems serving prominent national and international initiatives like the [Open Science Grid](https://osg-htc.org/), [XSEDE](https://www.xsede.org/), the [LHC Computing Grid](https://wlcg.web.cern.ch/), and [NCIP](https://datascience.cancer.gov/).
+Research Computing is an out growth of the UABgrid pilot, launched in September 2007 which has focused on demonstrating the utility of unlimited analysis, storage, and application for research. RCS is built on the same technology foundations used by major cloud vendors and decades of distributed systems computing research, technology that powered the last ten years of large scale systems serving prominent national and international initiatives like the [Open Science Grid](https://osg-htc.org/), [XSEDE](https://www.xsede.org/), the [LHC Computing Grid](https://wlcg.web.cern.ch/), and [NCI CBIIT](https://www.cancer.gov/about-nci/organization/cbiit).

docs/workflow_solutions/getting_containers.md

@@ -64,7 +64,7 @@ Both the `Pascalnodes` and `Amperenodes` partitions use NVIDIA GPUs. Therefore,
 singularity run --nv [other-run-flags] <image.sif> [image-software-flags]
 ```
 
-The `--nv` tells Singularity to bind the NVIDIA driver libraries and GPU devices into the container. This ensures your containerized application can access the GPU as if it were running on the host. An example tutorial demonstrating how to run Parabricks software with GPU support using the `--nv` flag can be found in our [Parabricks Case Study](../education/case_studies.md/#parabricks-testing-on-amperenodes-on-cheaha). For more details on usage of `--nv` flag refer to the [Singulairty Official Documentation](https://docs.sylabs.io/guides/3.5/user-guide/gpu.html).
+The `--nv` tells Singularity to bind the NVIDIA driver libraries and GPU devices into the container. This ensures your containerized application can access the GPU as if it were running on the host. An example tutorial demonstrating how to run Parabricks software with GPU support using the `--nv` flag can be found in our [Parabricks Case Study](../education/case_studies.md#parabricks-testing-on-amperenodes-on-cheaha). For more details on usage of `--nv` flag refer to the [Singulairty Official Documentation](https://docs.sylabs.io/guides/3.5/user-guide/gpu.html).
 
 ### Singularity Paths
 

docs/workflow_solutions/git_collaboration.md

@@ -57,7 +57,7 @@ GitHub and GitLab can both be used for software project management, and have hel
 
 Both services use organizations to manage projects across a team of people: [GitHub docs page](https://docs.github.com/en/organizations), [GitLab docs page](https://docs.gitlab.com/topics/set_up_organization/). Within a GitHub organization, people and repositories can be arranged into [teams](https://docs.github.com/en/organizations/organizing-members-into-teams/about-teams). GitLab allows arrangement of people and repositories with [projects](https://docs.gitlab.com/user/project/).
 
-An important feature, used extensively for this documentation's GitHub repository, is the issue tracker. Both [GitHub](https://docs.github.com/en/issues/tracking-your-work-with-issues/about-issues) and [GitLab](https://docs.gitlab.com/user/project/issues/) have per-repository issue trackers. Collaborators can create and manage issues, label them, and resolve them.
+An important feature, used extensively for this documentation's GitHub repository, is the issue tracker. Both [GitHub](https://docs.github.com/en/issues/tracking-your-work-with-issues/learning-about-issues/about-issues) and [GitLab](https://docs.gitlab.com/user/project/issues/) have per-repository issue trackers. Collaborators can create and manage issues, label them, and resolve them.
 
 ### How Do I Choose Between GitHub and GitLab?
 
@@ -113,7 +113,7 @@ Sometimes merging will be blocked because of a merge conflict. One programmer ma
 
 ### Effective Issue Tracking
 
-Effective use of issue tracking can greatly reduce cognitive load and simplify code management. It gives a central location where users and maintainers can report bugs, make feature requests, and ask for clarifications on usage and documentation. These issues are tracked over time, can be labeled and organized, and closed and reopened. [GitHub](https://docs.github.com/en/issues/tracking-your-work-with-issues/about-issues), [GitLab](https://docs.gitlab.com/user/project/issues/)
+Effective use of issue tracking can greatly reduce cognitive load and simplify code management. It gives a central location where users and maintainers can report bugs, make feature requests, and ask for clarifications on usage and documentation. These issues are tracked over time, can be labeled and organized, and closed and reopened. [GitHub](https://docs.github.com/en/issues/tracking-your-work-with-issues/learning-about-issues/about-issues), [GitLab](https://docs.gitlab.com/user/project/issues/)
 
 The typical issue lifecycle, at a high level, is something like below.
 

verification_scripts/linkchecker.py

@@ -8,6 +8,7 @@
 from pathlib import Path, PurePath
 
 import pandas as pd
+import yaml
 
 """
 How to use:
@@ -24,6 +25,7 @@
 LINKCHECKER_LOG = OUTPUT / "linkchecker.log"
 LINKCHECKER_RAW_CSV = OUTPUT / "linkchecker-raw.csv"
 LINKCHECKER_OUT_CSV = OUTPUT / "linkchecker-out.csv"
+LINKCHECKER_OUT_YAML = OUTPUT / "linkchecker-out.yml"
 
 # COLUMNS
 ## ORIGINAL
@@ -206,3 +208,7 @@ def _get_linkchecker_path() -> PurePath:
 
     # output
     linkchecker_results.to_csv(LINKCHECKER_OUT_CSV, index=False)
+
+    records = linkchecker_results.to_dict(orient="records")
+    with Path(LINKCHECKER_OUT_YAML).open("w") as f:
+        yaml.safe_dump(records, f, sort_keys=False)