From aeb558ce3c6a403e846781c1a3ce1f06c6041f4a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Thu, 21 Nov 2024 13:24:13 +0100 Subject: [PATCH] =?UTF-8?q?Genome=20portal=20kit=20=F0=9F=8E=81?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- hugo/{config/_default/hugo.yaml => config.yaml} | 8 +++----- hugo/config/production/hugo.yaml | 1 - hugo/themes/genome-portal-kit/README.md | 8 ++++++++ .../genome-portal-kit}/archetypes/species/_index.md | 0 .../archetypes/species/assembly/assembly.yaml | 0 .../archetypes/species/assembly/contrib.md | 0 .../archetypes/species/assembly/index.md | 0 .../archetypes/species/download/data_tracks.json | 0 .../archetypes/species/download/index.md | 0 .../archetypes/species/lineage.default.yaml | 0 .../archetypes/species/placeholder.png | Bin .../genome-portal-kit/config/_default/hugo.yaml | 3 +++ .../genome-portal-kit}/config/_default/params.yaml | 0 .../layouts/partials/species_bundle/GetGbifKey.html | 0 .../layouts/partials/species_bundle/GetTaxId.html | 0 .../partials/species_bundle/LineageConfig.html | 0 .../partials/species_bundle/TaxonomyRanks.html | 0 .../species_bundle/assembly_description.html | 0 .../partials/species_bundle/assembly_stats.html | 0 .../partials/species_bundle/download_table.html | 0 .../partials/species_bundle/get-remote-data.html | 0 .../layouts/partials/species_bundle/lineage.html | 0 .../layouts/species_bundle/assembly.html | 0 .../layouts/species_bundle/download.html | 0 .../layouts/species_bundle/intro.html | 0 25 files changed, 14 insertions(+), 6 deletions(-) rename hugo/{config/_default/hugo.yaml => config.yaml} (92%) delete mode 100644 hugo/config/production/hugo.yaml create mode 100644 hugo/themes/genome-portal-kit/README.md rename hugo/{ => themes/genome-portal-kit}/archetypes/species/_index.md (100%) rename hugo/{ => themes/genome-portal-kit}/archetypes/species/assembly/assembly.yaml (100%) rename hugo/{ => themes/genome-portal-kit}/archetypes/species/assembly/contrib.md (100%) rename hugo/{ => themes/genome-portal-kit}/archetypes/species/assembly/index.md (100%) rename hugo/{ => themes/genome-portal-kit}/archetypes/species/download/data_tracks.json (100%) rename hugo/{ => themes/genome-portal-kit}/archetypes/species/download/index.md (100%) rename hugo/{ => themes/genome-portal-kit}/archetypes/species/lineage.default.yaml (100%) rename hugo/{ => themes/genome-portal-kit}/archetypes/species/placeholder.png (100%) create mode 100644 hugo/themes/genome-portal-kit/config/_default/hugo.yaml rename hugo/{ => themes/genome-portal-kit}/config/_default/params.yaml (100%) rename hugo/{ => themes/genome-portal-kit}/layouts/partials/species_bundle/GetGbifKey.html (100%) rename hugo/{ => themes/genome-portal-kit}/layouts/partials/species_bundle/GetTaxId.html (100%) rename hugo/{ => themes/genome-portal-kit}/layouts/partials/species_bundle/LineageConfig.html (100%) rename hugo/{ => themes/genome-portal-kit}/layouts/partials/species_bundle/TaxonomyRanks.html (100%) rename hugo/{ => themes/genome-portal-kit}/layouts/partials/species_bundle/assembly_description.html (100%) rename hugo/{ => themes/genome-portal-kit}/layouts/partials/species_bundle/assembly_stats.html (100%) rename hugo/{ => themes/genome-portal-kit}/layouts/partials/species_bundle/download_table.html (100%) rename hugo/{ => themes/genome-portal-kit}/layouts/partials/species_bundle/get-remote-data.html (100%) rename hugo/{ => themes/genome-portal-kit}/layouts/partials/species_bundle/lineage.html (100%) rename hugo/{ => themes/genome-portal-kit}/layouts/species_bundle/assembly.html (100%) rename hugo/{ => themes/genome-portal-kit}/layouts/species_bundle/download.html (100%) rename hugo/{ => themes/genome-portal-kit}/layouts/species_bundle/intro.html (100%) diff --git a/hugo/config/_default/hugo.yaml b/hugo/config.yaml similarity index 92% rename from hugo/config/_default/hugo.yaml rename to hugo/config.yaml index 277d04c8..bf7af38b 100644 --- a/hugo/config/_default/hugo.yaml +++ b/hugo/config.yaml @@ -12,11 +12,9 @@ markup: endLevel: 4 ordered: false -permalinks: - section: - species: /:sections[1:] - page: - species: /:sections[1:]/:slug +module: + imports: + - path: genome-portal-kit menus: main: diff --git a/hugo/config/production/hugo.yaml b/hugo/config/production/hugo.yaml deleted file mode 100644 index 94144a66..00000000 --- a/hugo/config/production/hugo.yaml +++ /dev/null @@ -1 +0,0 @@ -panicOnWarning: true diff --git a/hugo/themes/genome-portal-kit/README.md b/hugo/themes/genome-portal-kit/README.md new file mode 100644 index 00000000..252a4636 --- /dev/null +++ b/hugo/themes/genome-portal-kit/README.md @@ -0,0 +1,8 @@ +# Genome portal +A Hugo theme for a genome portal embedding the JBrowse2 genome browser. + +## Features + +## Installation + +## Configuration diff --git a/hugo/archetypes/species/_index.md b/hugo/themes/genome-portal-kit/archetypes/species/_index.md similarity index 100% rename from hugo/archetypes/species/_index.md rename to hugo/themes/genome-portal-kit/archetypes/species/_index.md diff --git a/hugo/archetypes/species/assembly/assembly.yaml b/hugo/themes/genome-portal-kit/archetypes/species/assembly/assembly.yaml similarity index 100% rename from hugo/archetypes/species/assembly/assembly.yaml rename to hugo/themes/genome-portal-kit/archetypes/species/assembly/assembly.yaml diff --git a/hugo/archetypes/species/assembly/contrib.md b/hugo/themes/genome-portal-kit/archetypes/species/assembly/contrib.md similarity index 100% rename from hugo/archetypes/species/assembly/contrib.md rename to hugo/themes/genome-portal-kit/archetypes/species/assembly/contrib.md diff --git a/hugo/archetypes/species/assembly/index.md b/hugo/themes/genome-portal-kit/archetypes/species/assembly/index.md similarity index 100% rename from hugo/archetypes/species/assembly/index.md rename to hugo/themes/genome-portal-kit/archetypes/species/assembly/index.md diff --git a/hugo/archetypes/species/download/data_tracks.json b/hugo/themes/genome-portal-kit/archetypes/species/download/data_tracks.json similarity index 100% rename from hugo/archetypes/species/download/data_tracks.json rename to hugo/themes/genome-portal-kit/archetypes/species/download/data_tracks.json diff --git a/hugo/archetypes/species/download/index.md b/hugo/themes/genome-portal-kit/archetypes/species/download/index.md similarity index 100% rename from hugo/archetypes/species/download/index.md rename to hugo/themes/genome-portal-kit/archetypes/species/download/index.md diff --git a/hugo/archetypes/species/lineage.default.yaml b/hugo/themes/genome-portal-kit/archetypes/species/lineage.default.yaml similarity index 100% rename from hugo/archetypes/species/lineage.default.yaml rename to hugo/themes/genome-portal-kit/archetypes/species/lineage.default.yaml diff --git a/hugo/archetypes/species/placeholder.png b/hugo/themes/genome-portal-kit/archetypes/species/placeholder.png similarity index 100% rename from hugo/archetypes/species/placeholder.png rename to hugo/themes/genome-portal-kit/archetypes/species/placeholder.png diff --git a/hugo/themes/genome-portal-kit/config/_default/hugo.yaml b/hugo/themes/genome-portal-kit/config/_default/hugo.yaml new file mode 100644 index 00000000..231d7231 --- /dev/null +++ b/hugo/themes/genome-portal-kit/config/_default/hugo.yaml @@ -0,0 +1,3 @@ +permalinks: + page: + species_bundle: /:sections[1:]/:slug diff --git a/hugo/config/_default/params.yaml b/hugo/themes/genome-portal-kit/config/_default/params.yaml similarity index 100% rename from hugo/config/_default/params.yaml rename to hugo/themes/genome-portal-kit/config/_default/params.yaml diff --git a/hugo/layouts/partials/species_bundle/GetGbifKey.html b/hugo/themes/genome-portal-kit/layouts/partials/species_bundle/GetGbifKey.html similarity index 100% rename from hugo/layouts/partials/species_bundle/GetGbifKey.html rename to hugo/themes/genome-portal-kit/layouts/partials/species_bundle/GetGbifKey.html diff --git a/hugo/layouts/partials/species_bundle/GetTaxId.html b/hugo/themes/genome-portal-kit/layouts/partials/species_bundle/GetTaxId.html similarity index 100% rename from hugo/layouts/partials/species_bundle/GetTaxId.html rename to hugo/themes/genome-portal-kit/layouts/partials/species_bundle/GetTaxId.html diff --git a/hugo/layouts/partials/species_bundle/LineageConfig.html b/hugo/themes/genome-portal-kit/layouts/partials/species_bundle/LineageConfig.html similarity index 100% rename from hugo/layouts/partials/species_bundle/LineageConfig.html rename to hugo/themes/genome-portal-kit/layouts/partials/species_bundle/LineageConfig.html diff --git a/hugo/layouts/partials/species_bundle/TaxonomyRanks.html b/hugo/themes/genome-portal-kit/layouts/partials/species_bundle/TaxonomyRanks.html similarity index 100% rename from hugo/layouts/partials/species_bundle/TaxonomyRanks.html rename to hugo/themes/genome-portal-kit/layouts/partials/species_bundle/TaxonomyRanks.html diff --git a/hugo/layouts/partials/species_bundle/assembly_description.html b/hugo/themes/genome-portal-kit/layouts/partials/species_bundle/assembly_description.html similarity index 100% rename from hugo/layouts/partials/species_bundle/assembly_description.html rename to hugo/themes/genome-portal-kit/layouts/partials/species_bundle/assembly_description.html diff --git a/hugo/layouts/partials/species_bundle/assembly_stats.html b/hugo/themes/genome-portal-kit/layouts/partials/species_bundle/assembly_stats.html similarity index 100% rename from hugo/layouts/partials/species_bundle/assembly_stats.html rename to hugo/themes/genome-portal-kit/layouts/partials/species_bundle/assembly_stats.html diff --git a/hugo/layouts/partials/species_bundle/download_table.html b/hugo/themes/genome-portal-kit/layouts/partials/species_bundle/download_table.html similarity index 100% rename from hugo/layouts/partials/species_bundle/download_table.html rename to hugo/themes/genome-portal-kit/layouts/partials/species_bundle/download_table.html diff --git a/hugo/layouts/partials/species_bundle/get-remote-data.html b/hugo/themes/genome-portal-kit/layouts/partials/species_bundle/get-remote-data.html similarity index 100% rename from hugo/layouts/partials/species_bundle/get-remote-data.html rename to hugo/themes/genome-portal-kit/layouts/partials/species_bundle/get-remote-data.html diff --git a/hugo/layouts/partials/species_bundle/lineage.html b/hugo/themes/genome-portal-kit/layouts/partials/species_bundle/lineage.html similarity index 100% rename from hugo/layouts/partials/species_bundle/lineage.html rename to hugo/themes/genome-portal-kit/layouts/partials/species_bundle/lineage.html diff --git a/hugo/layouts/species_bundle/assembly.html b/hugo/themes/genome-portal-kit/layouts/species_bundle/assembly.html similarity index 100% rename from hugo/layouts/species_bundle/assembly.html rename to hugo/themes/genome-portal-kit/layouts/species_bundle/assembly.html diff --git a/hugo/layouts/species_bundle/download.html b/hugo/themes/genome-portal-kit/layouts/species_bundle/download.html similarity index 100% rename from hugo/layouts/species_bundle/download.html rename to hugo/themes/genome-portal-kit/layouts/species_bundle/download.html diff --git a/hugo/layouts/species_bundle/intro.html b/hugo/themes/genome-portal-kit/layouts/species_bundle/intro.html similarity index 100% rename from hugo/layouts/species_bundle/intro.html rename to hugo/themes/genome-portal-kit/layouts/species_bundle/intro.html