From 4628dea625cfca4aa016a4ba29340e30939fc96e Mon Sep 17 00:00:00 2001 From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com> Date: Mon, 9 Dec 2024 14:20:00 +1100 Subject: [PATCH 01/11] Add default flavour and varnish names This ensures the website is built with the default UoM flavour and that it uses the MB varnish branch --- config.yaml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/config.yaml b/config.yaml index b49991e9..3d1dac74 100644 --- a/config.yaml +++ b/config.yaml @@ -12,7 +12,7 @@ # This option supports custom types so lessons can be branded # and themed with your own logo and alt-text (see `carpentry_description`) # See https://carpentries.github.io/sandpaper-docs/editing.html#adding-a-custom-logo -carpentry: 'incubator' +carpentry: 'uom' # Alt-text description of the lesson. carpentry_description: 'Lesson Description' @@ -82,4 +82,7 @@ profiles: # This space below is where custom yaml items (e.g. pinning # sandpaper and varnish versions) should live +# This is the MB varnish, which is a custom version of the Carpentries varnish +varnish: 'melbournebionformatics/mb-varnish@main' +url: 'melbournebioinformatics.github.io/mb-varnish' From 5c357eb05b01be5186003a496a6e14efb58f63a4 Mon Sep 17 00:00:00 2001 From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com> Date: Mon, 9 Dec 2024 14:37:10 +1100 Subject: [PATCH 02/11] Fix value in key 'varnish' Fix typo. --- config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config.yaml b/config.yaml index 3d1dac74..937a3828 100644 --- a/config.yaml +++ b/config.yaml @@ -83,6 +83,6 @@ profiles: # sandpaper and varnish versions) should live # This is the MB varnish, which is a custom version of the Carpentries varnish -varnish: 'melbournebionformatics/mb-varnish@main' +varnish: 'melbournebioinformatics/mb-varnish@main' url: 'melbournebioinformatics.github.io/mb-varnish' From 500882f6d076d7ece7ac99baa9a299d02ce127c8 Mon Sep 17 00:00:00 2001 From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com> Date: Mon, 9 Dec 2024 15:49:40 +1100 Subject: [PATCH 03/11] Replace config values with UoM Use these rather than Carpentries values. --- config.yaml | 21 ++++++++------------- 1 file changed, 8 insertions(+), 13 deletions(-) diff --git a/config.yaml b/config.yaml index 937a3828..1ae7ebf1 100644 --- a/config.yaml +++ b/config.yaml @@ -2,16 +2,11 @@ # Values for this lesson. #------------------------------------------------------------ -# Which carpentry is this (swc, dc, lc, or cp)? -# swc: Software Carpentry -# dc: Data Carpentry -# lc: Library Carpentry -# cp: Carpentries (to use for instructor training for instance) -# incubator: The Carpentries Incubator -# -# This option supports custom types so lessons can be branded -# and themed with your own logo and alt-text (see `carpentry_description`) -# See https://carpentries.github.io/sandpaper-docs/editing.html#adding-a-custom-logo +# Which carpentry is this (swc, dc, lc, or cp)? < REPLACED with UNIMELB institutes > +# uom: University of Melbourne +# mb: Melbourne Bioinformatics +# mig: Melbourne Integrative Genomics +# wehi: Walter and Eliza Hall Institute carpentry: 'uom' # Alt-text description of the lesson. @@ -24,7 +19,7 @@ title: 'Lesson Title' # FIXME created: ~ # FIXME # Comma-separated list of keywords for the lesson -keywords: 'software, data, lesson, The Carpentries' # FIXME +keywords: 'software, data, lesson' # FIXME # Life cycle stage of the lesson # possible values: pre-alpha, alpha, beta, stable @@ -34,13 +29,13 @@ life_cycle: 'pre-alpha' # FIXME license: 'CC-BY 4.0' # Link to the source repository for this lesson -source: 'https://github.com/carpentries/workbench-template-md' # FIXME +source: 'https://github.com/melbournebioinformatics/workbench-template-md' # FIXME # Default branch of your lesson branch: 'main' # Who to contact if there are any issues -contact: 'team@carpentries.org' # FIXME +contact: 'fixme@fixme.org' # FIXME # Navigation ------------------------------------------------ # From 40603509fdf3eb54115777172a73215e37b7847e Mon Sep 17 00:00:00 2001 From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com> Date: Wed, 29 Jan 2025 15:32:38 +1100 Subject: [PATCH 04/11] Rename mb-varnish to uom-varnish --- config.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/config.yaml b/config.yaml index 1ae7ebf1..c22efced 100644 --- a/config.yaml +++ b/config.yaml @@ -77,7 +77,7 @@ profiles: # This space below is where custom yaml items (e.g. pinning # sandpaper and varnish versions) should live -# This is the MB varnish, which is a custom version of the Carpentries varnish -varnish: 'melbournebioinformatics/mb-varnish@main' -url: 'melbournebioinformatics.github.io/mb-varnish' +# This is the UoM varnish, which is a custom version of the Carpentries varnish +varnish: 'melbournebioinformatics/uom-varnish@main' +url: 'melbournebioinformatics.github.io/uom-varnish' From 32a496024059986a87949734676a1c2cb386ea6f Mon Sep 17 00:00:00 2001 From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com> Date: Tue, 25 Feb 2025 12:44:30 +1100 Subject: [PATCH 05/11] Testing CI --- .github/workflows/sandpaper-main.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/sandpaper-main.yaml b/.github/workflows/sandpaper-main.yaml index b3d1de8c..86cef1fc 100644 --- a/.github/workflows/sandpaper-main.yaml +++ b/.github/workflows/sandpaper-main.yaml @@ -60,5 +60,5 @@ jobs: run: | reset <- "${{ github.event.inputs.reset }}" == "true" sandpaper::package_cache_trigger(TRUE) - sandpaper:::ci_deploy(reset = reset) + sandpaper:::ci_deploy(reset = "false") shell: Rscript {0} From fb030c6bc2ffb48fec9a9510e21329a5de21642e Mon Sep 17 00:00:00 2001 From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com> Date: Tue, 25 Feb 2025 12:46:53 +1100 Subject: [PATCH 06/11] Undo last commit --- .github/workflows/sandpaper-main.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/sandpaper-main.yaml b/.github/workflows/sandpaper-main.yaml index 86cef1fc..b3d1de8c 100644 --- a/.github/workflows/sandpaper-main.yaml +++ b/.github/workflows/sandpaper-main.yaml @@ -60,5 +60,5 @@ jobs: run: | reset <- "${{ github.event.inputs.reset }}" == "true" sandpaper::package_cache_trigger(TRUE) - sandpaper:::ci_deploy(reset = "false") + sandpaper:::ci_deploy(reset = reset) shell: Rscript {0} From 50f8fe2dc6eb1a1f1e83b94763faa1645b143b22 Mon Sep 17 00:00:00 2001 From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com> Date: Tue, 25 Feb 2025 12:44:30 +1100 Subject: [PATCH 07/11] Testing CI --- .github/workflows/sandpaper-main.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/sandpaper-main.yaml b/.github/workflows/sandpaper-main.yaml index b3d1de8c..86cef1fc 100644 --- a/.github/workflows/sandpaper-main.yaml +++ b/.github/workflows/sandpaper-main.yaml @@ -60,5 +60,5 @@ jobs: run: | reset <- "${{ github.event.inputs.reset }}" == "true" sandpaper::package_cache_trigger(TRUE) - sandpaper:::ci_deploy(reset = reset) + sandpaper:::ci_deploy(reset = "false") shell: Rscript {0} From 0dddc2ae16be92aa8ee7bb02dc88e4297770c226 Mon Sep 17 00:00:00 2001 From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com> Date: Tue, 25 Feb 2025 12:46:53 +1100 Subject: [PATCH 08/11] Undo last commit --- .github/workflows/sandpaper-main.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/sandpaper-main.yaml b/.github/workflows/sandpaper-main.yaml index 86cef1fc..b3d1de8c 100644 --- a/.github/workflows/sandpaper-main.yaml +++ b/.github/workflows/sandpaper-main.yaml @@ -60,5 +60,5 @@ jobs: run: | reset <- "${{ github.event.inputs.reset }}" == "true" sandpaper::package_cache_trigger(TRUE) - sandpaper:::ci_deploy(reset = "false") + sandpaper:::ci_deploy(reset = reset) shell: Rscript {0} From 44c1031298093f65364c078f324b7ad0a45f5f07 Mon Sep 17 00:00:00 2001 From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com> Date: Mon, 14 Jul 2025 14:20:29 +1000 Subject: [PATCH 09/11] Add renv to .gitignore --- .gitignore | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.gitignore b/.gitignore index bd874548..481aa290 100644 --- a/.gitignore +++ b/.gitignore @@ -49,3 +49,5 @@ docs/ # translation temp files po/*~ +# Custom +renv/ From 4e48746de82fa77f74f85dc56a6aa66a42433169 Mon Sep 17 00:00:00 2001 From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com> Date: Mon, 27 Oct 2025 16:15:37 +1100 Subject: [PATCH 10/11] UoM template updates --- CODE_OF_CONDUCT.md | 2 ++ config.yaml | 8 ++++---- index.md | 6 +++++- 3 files changed, 11 insertions(+), 5 deletions(-) diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index 4153dd42..db14a936 100644 --- a/CODE_OF_CONDUCT.md +++ b/CODE_OF_CONDUCT.md @@ -2,6 +2,8 @@ title: "Contributor Code of Conduct" --- +Although this is Melbourne Bioinformatics content, we abide by the same Carpentries Code of Conduct explicited below: + As contributors and maintainers of this project, we pledge to follow the [The Carpentries Code of Conduct][coc]. diff --git a/config.yaml b/config.yaml index c22efced..b6d52847 100644 --- a/config.yaml +++ b/config.yaml @@ -10,15 +10,15 @@ carpentry: 'uom' # Alt-text description of the lesson. -carpentry_description: 'Lesson Description' +carpentry_description: 'Lesson Description' # FIXME # Overall title for pages. title: 'Lesson Title' # FIXME -# Date the lesson was created (YYYY-MM-DD, this is empty by default) +# Date the lesson was created ('YYYY-MM-DD', this is empty by default) created: ~ # FIXME -# Comma-separated list of keywords for the lesson +# Comma-separated list of keywords for the lesson. Avoid words in the title. keywords: 'software, data, lesson' # FIXME # Life cycle stage of the lesson @@ -29,7 +29,7 @@ life_cycle: 'pre-alpha' # FIXME license: 'CC-BY 4.0' # Link to the source repository for this lesson -source: 'https://github.com/melbournebioinformatics/workbench-template-md' # FIXME +source: 'https://github.com/melbournebioinformatics/workbench-template-rmd' # FIXME # Default branch of your lesson branch: 'main' diff --git a/index.md b/index.md index af662764..0ab24315 100644 --- a/index.md +++ b/index.md @@ -2,8 +2,12 @@ site: sandpaper::sandpaper_site --- -This is a new lesson built with [The Carpentries Workbench][workbench]. +This is a new lesson built with the [Melbourne Bioinformatics fork](https://github.com/melbournebioinformatics/workbench-template-md) of the [Carpentries Workbench](workbench). +For more information on Melbourne Bioinformatics, please see our [official page](mb-uom-page) and our [tutorial collection](mb-tutorials). If you would like to attend one of our workshops, please follow our [Eventbrite page](https://www.eventbrite.com.au/d/australia--melbourne/melbourne-bioinformatics/), where you can get notifications and register for upcoming workshops. +[mb-uom-page]: https://mdhs.unimelb.edu.au/melbournebioinformatics +[mb-tutorials]: https://melbournebioinformatics.github.io/MelBioInf_docs/ +[mb-eventbrite]: https://www.eventbrite.com.au/d/australia--melbourne/melbourne-bioinformatics/ [workbench]: https://carpentries.github.io/sandpaper-docs From a80f1343395448560be41b12bc396b1ff1d70f98 Mon Sep 17 00:00:00 2001 From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com> Date: Mon, 27 Oct 2025 16:22:04 +1100 Subject: [PATCH 11/11] Fix link --- index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/index.md b/index.md index 0ab24315..420573c6 100644 --- a/index.md +++ b/index.md @@ -4,7 +4,7 @@ site: sandpaper::sandpaper_site This is a new lesson built with the [Melbourne Bioinformatics fork](https://github.com/melbournebioinformatics/workbench-template-md) of the [Carpentries Workbench](workbench). -For more information on Melbourne Bioinformatics, please see our [official page](mb-uom-page) and our [tutorial collection](mb-tutorials). If you would like to attend one of our workshops, please follow our [Eventbrite page](https://www.eventbrite.com.au/d/australia--melbourne/melbourne-bioinformatics/), where you can get notifications and register for upcoming workshops. +For more information on Melbourne Bioinformatics, please see our [official page](mb-uom-page) and our [tutorial collection](mb-tutorials). If you would like to attend one of our workshops, please follow our [Eventbrite page](mb-eventbrite), where you can get notifications and register for upcoming workshops. [mb-uom-page]: https://mdhs.unimelb.edu.au/melbournebioinformatics [mb-tutorials]: https://melbournebioinformatics.github.io/MelBioInf_docs/