From b9d18d51bce470a17fb766705d2f2c30150a5eb0 Mon Sep 17 00:00:00 2001 From: Wesley B <62723358+wesleyboar@users.noreply.github.com> Date: Wed, 7 Oct 2026 14:08:26 -0500 Subject: [PATCH 01/10] chore(deps): require mkdocs-tacc >=1.0.5 Bump after mkdocs-tacc release with admonition CDN fix; run poetry lock after 1.0.5 publishes. Co-authored-by: Cursor --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 3db45d45..4537c2be 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -19,7 +19,7 @@ maintainers = [ readme = "README.md" requires-python = ">=3.10,<3.13" dependencies = [ - "mkdocs-tacc[all] (>=1.0.4,<2.0.0)", + "mkdocs-tacc[all] (>=1.0.5,<2.0.0)", "mkdocs-exclude-search (>=0.6.6,<0.7.0)", "mkdocs-include-markdown-plugin (>=5.1.0,<6.0.0)", ] From c88164ddae2f4bac0f1bccd3c94469278aec3dd9 Mon Sep 17 00:00:00 2001 From: Wesley B <62723358+wesleyboar@users.noreply.github.com> Date: Wed, 7 Oct 2026 17:42:24 -0500 Subject: [PATCH 02/10] chore(deps): require mkdocs-tacc >=1.0.5rc1 Lock to the published RC with admonition CDN fixes ahead of 1.0.5 stable. Co-authored-by: Cursor --- poetry.lock | 10 +++++----- pyproject.toml | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/poetry.lock b/poetry.lock index e52b4913..2e608b1f 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 2.3.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.1.1 and should not be changed by hand. [[package]] name = "babel" @@ -266,14 +266,14 @@ cache = ["platformdirs"] [[package]] name = "mkdocs-tacc" -version = "1.0.4" +version = "1.0.5rc1" description = "TACC-specific MkDocs theme" optional = false python-versions = "<3.13,>=3.10" groups = ["main"] files = [ - {file = "mkdocs_tacc-1.0.4-py3-none-any.whl", hash = "sha256:1029eafd35b9996e19fb560aae9d1174d4262e1e3a3c3c5ed3518f7d5cd0a16a"}, - {file = "mkdocs_tacc-1.0.4.tar.gz", hash = "sha256:9945a00aeb67ca27609d7a15e63e6495fe4bc404af1ac8ac4731507a814470db"}, + {file = "mkdocs_tacc-1.0.5rc1-py3-none-any.whl", hash = "sha256:c104647554a345652f1d65cd283965087860546925395b14397a9082c99dacff"}, + {file = "mkdocs_tacc-1.0.5rc1.tar.gz", hash = "sha256:1ab71060e203d75cb89ad91189ca5bea4d0cf588117db443ba95e65f90819931"}, ] [package.dependencies] @@ -490,4 +490,4 @@ watchmedo = ["PyYAML (>=3.10)"] [metadata] lock-version = "2.1" python-versions = ">=3.10,<3.13" -content-hash = "2a74ac71807eeda0d921aa985de7c7e25ca34ff184fb34822adff68e04f8d8fa" +content-hash = "502432420b8c415603281ba1a3d3df01cabcaaf22d9af91d20e6eed341e270d8" diff --git a/pyproject.toml b/pyproject.toml index 4537c2be..825f7a17 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -19,7 +19,7 @@ maintainers = [ readme = "README.md" requires-python = ">=3.10,<3.13" dependencies = [ - "mkdocs-tacc[all] (>=1.0.5,<2.0.0)", + "mkdocs-tacc[all] (>=1.0.5rc1,<2.0.0)", "mkdocs-exclude-search (>=0.6.6,<0.7.0)", "mkdocs-include-markdown-plugin (>=5.1.0,<6.0.0)", ] From 2353b0b83321a85f9b7b66dcf93c58b4affc39de Mon Sep 17 00:00:00 2001 From: Wesley B <62723358+wesleyboar@users.noreply.github.com> Date: Wed, 7 Oct 2026 18:10:27 -0500 Subject: [PATCH 03/10] fix(docs): swap caution and warning admonitions Preserve on-screen severity after Core-Styles and mkdocs-tacc correct caution vs warning styling. Co-authored-by: Cursor --- user-guide/datadepotrepo/resources.md | 14 +++++++------- user-guide/deleted.md | 2 +- user-guide/redirect.md | 2 +- 3 files changed, 9 insertions(+), 9 deletions(-) diff --git a/user-guide/datadepotrepo/resources.md b/user-guide/datadepotrepo/resources.md index aab24f25..ede4f50a 100644 --- a/user-guide/datadepotrepo/resources.md +++ b/user-guide/datadepotrepo/resources.md @@ -1,11 +1,11 @@ # Resources for Users -!!! caution "Content Undecided" +!!! warning "Content Undecided" Much of this page is incomplete. We might not use this page. ## Frequently Asked Questions -!!! caution "Content Undefined" +!!! warning "Content Undefined" Should this introduce some F.A.Q. and/or link to it? ## Data Management Plan @@ -14,12 +14,12 @@ Depositing your data and other resources such as documentation and research soft ## Data and Intellectual Property -!!! caution "Content Undefined" +!!! warning "Content Undefined" What content belongs here? ## Support and Contact Information -!!! caution "Content Undefined" +!!! warning "Content Undefined" Should this introduce the Support and Contact Information and/or link to it? ## DesignSafe Office Hours @@ -37,19 +37,19 @@ CONVERGE has a series of [check sheets](https://converge.colorado.edu/resources/ In addition, we suggest that users look into the [Data Curation Primers](https://datacurationnetwork.org/outputs/data-curation-primers/) from the Data Curation Network, which are "peer-reviewed, living documents that detail a specific subject, disciplinary area or curation task, and that can be used as a guidelines to curate research data. The primers include curation practices for documenting data types that while not open or recommended, are very established in the academic fields surrounding Natural Hazards research such as Matlab and Microsoft Excel. -!!! caution "Needs Review" +!!! warning "Needs Review" How to introduce this random link? [https://www.copyright.gov/circs/circ33.pdf](https://www.copyright.gov/circs/circ33.pdf)  ## Exemplary Datasets -!!! caution "Needs Review" +!!! warning "Needs Review" "Need to review this list now." — M.E. Below are examples of good organization and description for different dataset types: -!!! caution "Formatting Uncertain" +!!! warning "Formatting Uncertain" Should this be a nested list, a table, sub-headings and lists? Is it supposed to be [the user guide dictionaries](/user-guide/dictionary/)? * Experimental diff --git a/user-guide/deleted.md b/user-guide/deleted.md index 700bde39..d1262f32 100644 --- a/user-guide/deleted.md +++ b/user-guide/deleted.md @@ -1,5 +1,5 @@ !!! attention "This page has been deleted." Please use navigation panel or links below to find other content. -!!! caution "Update bookmarks and links." +!!! warning "Update bookmarks and links." This page is now temporary, unmaintained, and will be deleted. diff --git a/user-guide/redirect.md b/user-guide/redirect.md index d3c0c13a..74dc2632 100644 --- a/user-guide/redirect.md +++ b/user-guide/redirect.md @@ -1,5 +1,5 @@ !!! attention "This page has moved." Please use navigation panel or any links below to find the content. -!!! caution "Update bookmarks and links." +!!! warning "Update bookmarks and links." This page is now temporary, unmaintained, and will be deleted. From f685ea77a0ea291ff06bfe6bc77c3e43b5d77ca3 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Wed, 7 Oct 2026 23:11:49 +0000 Subject: [PATCH 04/10] chore: auto-update requirements.txt [bot] --- requirements.txt | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/requirements.txt b/requirements.txt index b6fbf2e3..b43d66e5 100644 --- a/requirements.txt +++ b/requirements.txt @@ -115,9 +115,9 @@ mkdocs-exclude-search==0.6.6 ; python_version >= "3.10" and python_version < "3. mkdocs-include-markdown-plugin==5.1.0 ; python_version >= "3.10" and python_version < "3.13" \ --hash=sha256:4a1b8d79a0e1b6fd357ca8013a6d1701c755ada4acb74ee97b0642d1afe6756e \ --hash=sha256:e9ca188ab1d86f5fc4a6b96ce8c85acf6e25f114897868041056ec7945f29f65 -mkdocs-tacc==1.0.4 ; python_version >= "3.10" and python_version < "3.13" \ - --hash=sha256:1029eafd35b9996e19fb560aae9d1174d4262e1e3a3c3c5ed3518f7d5cd0a16a \ - --hash=sha256:9945a00aeb67ca27609d7a15e63e6495fe4bc404af1ac8ac4731507a814470db +mkdocs-tacc==1.0.5rc1 ; python_version >= "3.10" and python_version < "3.13" \ + --hash=sha256:1ab71060e203d75cb89ad91189ca5bea4d0cf588117db443ba95e65f90819931 \ + --hash=sha256:c104647554a345652f1d65cd283965087860546925395b14397a9082c99dacff mkdocs==1.4.3 ; python_version >= "3.10" and python_version < "3.13" \ --hash=sha256:5955093bbd4dd2e9403c5afaf57324ad8b04f16886512a3ee6ef828956481c57 \ --hash=sha256:6ee46d309bda331aac915cd24aab882c179a933bd9e77b80ce7d2eaaa3f689dd From 12b8bb2e585665af58cdb19e444c462c0f4335a3 Mon Sep 17 00:00:00 2001 From: Wesley B <62723358+wesleyboar@users.noreply.github.com> Date: Wed, 7 Oct 2026 21:40:34 -0500 Subject: [PATCH 05/10] chore(deps): require mkdocs-tacc >=1.0.5rc2 Refresh lock for RC with Core-Styles 2.59.2 heading fix. Co-authored-by: Cursor --- poetry.lock | 8 ++++---- pyproject.toml | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/poetry.lock b/poetry.lock index 2e608b1f..4dc94439 100644 --- a/poetry.lock +++ b/poetry.lock @@ -266,14 +266,14 @@ cache = ["platformdirs"] [[package]] name = "mkdocs-tacc" -version = "1.0.5rc1" +version = "1.0.5rc2" description = "TACC-specific MkDocs theme" optional = false python-versions = "<3.13,>=3.10" groups = ["main"] files = [ - {file = "mkdocs_tacc-1.0.5rc1-py3-none-any.whl", hash = "sha256:c104647554a345652f1d65cd283965087860546925395b14397a9082c99dacff"}, - {file = "mkdocs_tacc-1.0.5rc1.tar.gz", hash = "sha256:1ab71060e203d75cb89ad91189ca5bea4d0cf588117db443ba95e65f90819931"}, + {file = "mkdocs_tacc-1.0.5rc2-py3-none-any.whl", hash = "sha256:6e5555d0235c5489d2a61c26f771b9007d5ec67e9df2ef5e9db61538192b5f19"}, + {file = "mkdocs_tacc-1.0.5rc2.tar.gz", hash = "sha256:8aeb9d126402f9cae3b88a29d4096ad3685c904acab84615f0cf6da42c8ed8c3"}, ] [package.dependencies] @@ -490,4 +490,4 @@ watchmedo = ["PyYAML (>=3.10)"] [metadata] lock-version = "2.1" python-versions = ">=3.10,<3.13" -content-hash = "502432420b8c415603281ba1a3d3df01cabcaaf22d9af91d20e6eed341e270d8" +content-hash = "721e4490e199be94d14bb595e631c8080c0740607254ec9ff4b1b8d532e2282d" diff --git a/pyproject.toml b/pyproject.toml index 825f7a17..56dbb5af 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -19,7 +19,7 @@ maintainers = [ readme = "README.md" requires-python = ">=3.10,<3.13" dependencies = [ - "mkdocs-tacc[all] (>=1.0.5rc1,<2.0.0)", + "mkdocs-tacc[all] (>=1.0.5rc2,<2.0.0)", "mkdocs-exclude-search (>=0.6.6,<0.7.0)", "mkdocs-include-markdown-plugin (>=5.1.0,<6.0.0)", ] From 9ac97fafb5b8f614c52d3339ddd7f5d762f7aeb4 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Thu, 8 Oct 2026 02:41:39 +0000 Subject: [PATCH 06/10] chore: auto-update requirements.txt [bot] --- requirements.txt | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/requirements.txt b/requirements.txt index b43d66e5..8c2bc6a1 100644 --- a/requirements.txt +++ b/requirements.txt @@ -115,9 +115,9 @@ mkdocs-exclude-search==0.6.6 ; python_version >= "3.10" and python_version < "3. mkdocs-include-markdown-plugin==5.1.0 ; python_version >= "3.10" and python_version < "3.13" \ --hash=sha256:4a1b8d79a0e1b6fd357ca8013a6d1701c755ada4acb74ee97b0642d1afe6756e \ --hash=sha256:e9ca188ab1d86f5fc4a6b96ce8c85acf6e25f114897868041056ec7945f29f65 -mkdocs-tacc==1.0.5rc1 ; python_version >= "3.10" and python_version < "3.13" \ - --hash=sha256:1ab71060e203d75cb89ad91189ca5bea4d0cf588117db443ba95e65f90819931 \ - --hash=sha256:c104647554a345652f1d65cd283965087860546925395b14397a9082c99dacff +mkdocs-tacc==1.0.5rc2 ; python_version >= "3.10" and python_version < "3.13" \ + --hash=sha256:6e5555d0235c5489d2a61c26f771b9007d5ec67e9df2ef5e9db61538192b5f19 \ + --hash=sha256:8aeb9d126402f9cae3b88a29d4096ad3685c904acab84615f0cf6da42c8ed8c3 mkdocs==1.4.3 ; python_version >= "3.10" and python_version < "3.13" \ --hash=sha256:5955093bbd4dd2e9403c5afaf57324ad8b04f16886512a3ee6ef828956481c57 \ --hash=sha256:6ee46d309bda331aac915cd24aab882c179a933bd9e77b80ce7d2eaaa3f689dd From 81f8763ded0a3a7a531b48696afef895a69ea235 Mon Sep 17 00:00:00 2001 From: Wesley B <62723358+wesleyboar@users.noreply.github.com> Date: Wed, 7 Oct 2026 22:13:43 -0500 Subject: [PATCH 07/10] fix: better icon for deleted/redirect pages --- user-guide/deleted.md | 2 +- user-guide/redirect.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/user-guide/deleted.md b/user-guide/deleted.md index 700bde39..ed2ec745 100644 --- a/user-guide/deleted.md +++ b/user-guide/deleted.md @@ -1,5 +1,5 @@ !!! attention "This page has been deleted." Please use navigation panel or links below to find other content. -!!! caution "Update bookmarks and links." +!!! danger "Update bookmarks and links." This page is now temporary, unmaintained, and will be deleted. diff --git a/user-guide/redirect.md b/user-guide/redirect.md index d3c0c13a..c9987e40 100644 --- a/user-guide/redirect.md +++ b/user-guide/redirect.md @@ -1,5 +1,5 @@ !!! attention "This page has moved." Please use navigation panel or any links below to find the content. -!!! caution "Update bookmarks and links." +!!! danger "Update bookmarks and links." This page is now temporary, unmaintained, and will be deleted. From 59522a30e95086880f24485f7ebd14f21ec734aa Mon Sep 17 00:00:00 2001 From: Wesley B <62723358+wesleyboar@users.noreply.github.com> Date: Wed, 7 Oct 2026 22:40:23 -0500 Subject: [PATCH 08/10] fix(docs): use danger for deleted/redirect bookmark callouts Special case: not part of caution/warning swap. Co-authored-by: Cursor --- user-guide/deleted.md | 2 +- user-guide/redirect.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/user-guide/deleted.md b/user-guide/deleted.md index d1262f32..ed2ec745 100644 --- a/user-guide/deleted.md +++ b/user-guide/deleted.md @@ -1,5 +1,5 @@ !!! attention "This page has been deleted." Please use navigation panel or links below to find other content. -!!! warning "Update bookmarks and links." +!!! danger "Update bookmarks and links." This page is now temporary, unmaintained, and will be deleted. diff --git a/user-guide/redirect.md b/user-guide/redirect.md index 74dc2632..c9987e40 100644 --- a/user-guide/redirect.md +++ b/user-guide/redirect.md @@ -1,5 +1,5 @@ !!! attention "This page has moved." Please use navigation panel or any links below to find the content. -!!! warning "Update bookmarks and links." +!!! danger "Update bookmarks and links." This page is now temporary, unmaintained, and will be deleted. From a6198ef81545c7f27453637640a2f9722fa1c078 Mon Sep 17 00:00:00 2001 From: Wesley B <62723358+wesleyboar@users.noreply.github.com> Date: Wed, 7 Oct 2026 22:50:51 -0500 Subject: [PATCH 09/10] fix(css): uppercase sidebar nav name after Core-Styles bump Co-authored-by: Cursor --- user-guide/css/tacc/mkdocs-tacc.css | 1 + 1 file changed, 1 insertion(+) diff --git a/user-guide/css/tacc/mkdocs-tacc.css b/user-guide/css/tacc/mkdocs-tacc.css index 3a76ac31..aefd010f 100644 --- a/user-guide/css/tacc/mkdocs-tacc.css +++ b/user-guide/css/tacc/mkdocs-tacc.css @@ -11,6 +11,7 @@ .wy-side-nav-search .nav-name { font-weight: var(--medium); color: #565656; + text-transform: uppercase; } /* To give logo more horizontal space */ .wy-side-nav-search > a { From 3880a4858aa4d666cb939ee2e60e7a4e06a5a6f6 Mon Sep 17 00:00:00 2001 From: Wesley B <62723358+wesleyboar@users.noreply.github.com> Date: Thu, 8 Oct 2026 10:25:48 -0500 Subject: [PATCH 10/10] fix: use / for internal links, not http(s):// --- user-guide/account-help.md | 2 +- user-guide/curating/guides.md | 2 +- user-guide/how-to-cite.md | 2 +- user-guide/tools/advanced/dsfaq.md | 2 +- user-guide/usecases/README.md | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/user-guide/account-help.md b/user-guide/account-help.md index bc68aea9..0342267b 100644 --- a/user-guide/account-help.md +++ b/user-guide/account-help.md @@ -19,7 +19,7 @@ There are multiple reasons you would either want to or be required to [update yo 3. Your citizenship changes. 4. You receive an email from TACC requiring an annual profile update. -It's possible the policies regarding email domains and Institutions have changed since the last time you either created your account or updated your profile, so you may want to review the [User Account Registration guide](https://designsafe-ci.org/user-guide/#user-account-registration) for the current guidance. +It's possible the policies regarding email domains and Institutions have changed since the last time you either created your account or updated your profile, so you may want to review the [User Account Registration guide](/user-guide/#user-account-registration) for the current guidance. ## Additional Account Resources diff --git a/user-guide/curating/guides.md b/user-guide/curating/guides.md index e5bba5ae..ac49f2d8 100644 --- a/user-guide/curating/guides.md +++ b/user-guide/curating/guides.md @@ -493,7 +493,7 @@ In addition, the release must include a README file with detailed instructions o Failure to adequately describe your software with these files may result in removal of your publication. -[Read about best practices for creating CodeMeta and README files.](https://www.designsafe-ci.org/user-guide/curating/bestpractices/#research-software) +[Read about best practices for creating CodeMeta and README files.](/user-guide/curating/bestpractices/#research-software) After adding these files, create a new release. diff --git a/user-guide/how-to-cite.md b/user-guide/how-to-cite.md index 2aa332d7..dffcb273 100644 --- a/user-guide/how-to-cite.md +++ b/user-guide/how-to-cite.md @@ -8,7 +8,7 @@ Rathje, E., Dawson, C. Padgett, J.E., Pinelli, J.-P., Stanzione, D., Adair, A., ## Additional Citation Information -If you receive HPC allocations for use in your computational research, in addition to citing DesignSafe per the marker paper please use the following acknowledgement. We also encourage you to curate and publish simulation data results using the [Simulation Data Model](https://www.designsafe-ci.org/user-guide/curating/guides/#simulation). +If you receive HPC allocations for use in your computational research, in addition to citing DesignSafe per the marker paper please use the following acknowledgement. We also encourage you to curate and publish simulation data results using the [Simulation Data Model](/user-guide/curating/guides/#simulation). The authors acknowledge the Texas Advanced Computing Center (TACC) at The University of Texas at Austin for providing computational resources that have contributed to the research results reported within this paper. URL: http://www.tacc.utexas.edu diff --git a/user-guide/tools/advanced/dsfaq.md b/user-guide/tools/advanced/dsfaq.md index 36c1a34f..8baca4e4 100644 --- a/user-guide/tools/advanced/dsfaq.md +++ b/user-guide/tools/advanced/dsfaq.md @@ -166,7 +166,7 @@ The Jupyter Notebook is a web application that allows you to create and share do /// /// details | What do people do with Jupyter? -Many people use Jupyter in a similar fashion as they use MATLAB to analyze and plot their data. We will be sharing example Jupyter Notebooks soon that you can copy into your My Data and customize for your research. We also provide [Jupyter training](https://designsafe-ci.org/user-guide/tools/jupyterhub/). +Many people use Jupyter in a similar fashion as they use MATLAB to analyze and plot their data. We will be sharing example Jupyter Notebooks soon that you can copy into your My Data and customize for your research. We also provide [Jupyter training](/user-guide/tools/jupyterhub/). /// diff --git a/user-guide/usecases/README.md b/user-guide/usecases/README.md index 8b4f9753..ee2ec5ea 100644 --- a/user-guide/usecases/README.md +++ b/user-guide/usecases/README.md @@ -1,6 +1,6 @@ # DesignSafe Use Cases -How to contribute to [DesignSafe Use Cases](https://designsafe-ci.org/user-guide/usecases/overview/). +How to contribute to [DesignSafe Use Cases](/user-guide/usecases/overview/). ## A Guide to Adding Your Use Case Project