From 2df3d4c13acdcdea1153b594c83a2fedbfa3f8c0 Mon Sep 17 00:00:00 2001 From: Aprameyaraya <91876432+Aprameyaraya@users.noreply.github.com> Date: Mon, 31 Aug 2026 21:32:39 +0530 Subject: [PATCH 01/12] Refactor top_events to filter upcoming events Added Filtering: Added select { |e| e[:end] >= Time.now.to_date } to exclude past events based on their end date. Safe Slicing: Using .last(5) prevents potential nil errors if there are fewer than 5 upcoming events (compared to [-5..-1]). --- lib/helpers.rb | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/lib/helpers.rb b/lib/helpers.rb index cc79c50b..ecaae67d 100644 --- a/lib/helpers.rb +++ b/lib/helpers.rb @@ -450,12 +450,11 @@ def previous_events(events) end def top_events(events) - sorted = events.children.sort do |a, b| - a[:start] <=> b[:start] - end - toplist = sorted[-5..-1] - toplist.reverse -end + upcoming = events.children.select { |e| e[:end] >= Time.now.to_date } + sorted = upcoming.sort_by { |e| e[:start] } + + sorted.last(5).reverse +end def event_date(e) if (e[:start].month == e[:end].month) From 261299ec0ba28e5b287b5e654d01073295905ff2 Mon Sep 17 00:00:00 2001 From: Aprameyaraya <91876432+Aprameyaraya@users.noreply.github.com> Date: Mon, 31 Aug 2026 21:45:32 +0530 Subject: [PATCH 02/12] Modify header height and overflow styles Adjust header height and overflow properties for better responsiveness. --- assets/style/sections/header.css | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/assets/style/sections/header.css b/assets/style/sections/header.css index d8d7c0c4..8d43a1d2 100644 --- a/assets/style/sections/header.css +++ b/assets/style/sections/header.css @@ -171,14 +171,16 @@ input:focus::placeholder { transition: 0.3s; gap: 0; top: 100%; - height: 2px; + height: 0; overflow: hidden; opacity: 0; } .header-nav.active { opacity: 1; - height: 21rem; + height: auto; + max-height: 80vh; + overflow-y: auto; } .nav-mobile { From bdebe8f60dcf22e2f1bd473a085d110978f5e3b1 Mon Sep 17 00:00:00 2001 From: Aprameyaraya <91876432+Aprameyaraya@users.noreply.github.com> Date: Mon, 31 Aug 2026 22:14:48 +0530 Subject: [PATCH 03/12] Update typography.css --- assets/style/base/typography.css | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/assets/style/base/typography.css b/assets/style/base/typography.css index beed2b2f..8b1e9979 100644 --- a/assets/style/base/typography.css +++ b/assets/style/base/typography.css @@ -57,7 +57,12 @@ h6, } a { - color: black; + color: #1a0dab; /* Or use the site's standard brand/accent blue */ + text-decoration: underline; +} + +a:hover { + text-decoration: none; } @media (max-device-width: 768px),(width <= 768px){ From 6826101c573342d00a55ba2b2c9302606be1b25e Mon Sep 17 00:00:00 2001 From: Aprameyaraya <91876432+Aprameyaraya@users.noreply.github.com> Date: Mon, 31 Aug 2026 22:15:26 +0530 Subject: [PATCH 04/12] Add hover effect for footer links --- assets/style/sections/footer.css | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/assets/style/sections/footer.css b/assets/style/sections/footer.css index 2e89db5c..8ca8f7ad 100644 --- a/assets/style/sections/footer.css +++ b/assets/style/sections/footer.css @@ -13,8 +13,12 @@ footer { box-sizing: border-box; } -footer * { +footer a { color: #fff; + text-decoration: underline; +} + +footer a:hover { text-decoration: none; } From 77a46d0f92c398b24aabcc8eff2a98e8411073e6 Mon Sep 17 00:00:00 2001 From: Aprameyaraya <91876432+Aprameyaraya@users.noreply.github.com> Date: Mon, 31 Aug 2026 22:23:30 +0530 Subject: [PATCH 05/12] Clean up disallow rules in robots.txt Removed multiple package disallow rules from robots.txt to simplify access. --- assets/robots.txt | 45 --------------------------------------------- 1 file changed, 45 deletions(-) diff --git a/assets/robots.txt b/assets/robots.txt index 3396a0ab..86a3a6bc 100644 --- a/assets/robots.txt +++ b/assets/robots.txt @@ -3,50 +3,6 @@ Disallow: /packages/submitted/ Disallow: /packages/misc/ Disallow: /packages/lindsey/ Disallow: /packages/omegahat/ -Disallow: /packages/1.8/ -Disallow: /packages/1.9/ -Disallow: /packages/2.0/ -Disallow: /packages/2.1/ -Disallow: /packages/2.2/ -Disallow: /packages/2.3/ -Disallow: /packages/2.4/ -Disallow: /packages/2.5/ -Disallow: /packages/2.6/ -Disallow: /packages/2.7/ -Disallow: /packages/2.8/ -Disallow: /packages/2.9/ -Disallow: /packages/2.10/ -Disallow: /packages/2.11/ -Disallow: /packages/2.12/ -Disallow: /packages/2.13/ -Disallow: /packages/2.14/ -Disallow: /packages/3.0/ -Disallow: /packages/3.1/ -Disallow: /packages/3.2/ -Disallow: /packages/3.3/ -Disallow: /packages/3.4/ -Disallow: /packages/3.5/ -Disallow: /packages/3.6/ -Disallow: /packages/3.7/ -Disallow: /packages/3.8/ -Disallow: /packages/3.9/ -Disallow: /packages/3.10/ -Disallow: /packages/3.11/ -Disallow: /packages/3.12/ -Disallow: /packages/3.13/ -Disallow: /packages/3.14/ -Disallow: /packages/3.15/ -Disallow: /packages/3.16/ -Disallow: /packages/3.17/ -Disallow: /packages/3.18/ -Disallow: /packages/3.19/ -Disallow: /packages/3.20/ -Disallow: /packages/3.21/ -Disallow: /packages/3.22/ -Disallow: /packages/3.23/ -Disallow: /packages/3.24/ -Disallow: /packages/devel/ -Disallow: /packages/release/ Disallow: /packages/bioc/ Disallow: /packages/data/ Disallow: /repository/ @@ -54,7 +10,6 @@ Disallow: /checkResults/ Disallow: /data/ Disallow: /datafiles/ Disallow: /installScripts/ -Disallow: /biocViews/ Disallow: /stats/ Disallow: /dataann-stats/ Disallow: /dataexp-stats/ From e4dc93b98edc09b05d01f1a4d64a16b2a237bd1c Mon Sep 17 00:00:00 2001 From: Aprameyaraya <91876432+Aprameyaraya@users.noreply.github.com> Date: Tue, 1 Sep 2026 14:41:16 +0530 Subject: [PATCH 06/12] Update header navigation styles Change header navigation height and remove overflow properties. --- assets/style/sections/header.css | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/assets/style/sections/header.css b/assets/style/sections/header.css index 8d43a1d2..4bd6f496 100644 --- a/assets/style/sections/header.css +++ b/assets/style/sections/header.css @@ -178,9 +178,7 @@ input:focus::placeholder { .header-nav.active { opacity: 1; - height: auto; - max-height: 80vh; - overflow-y: auto; + height: 21rem; } .nav-mobile { From ec894d146ad360a517f83bac9fa1a689ce7a5c09 Mon Sep 17 00:00:00 2001 From: Aprameyaraya <91876432+Aprameyaraya@users.noreply.github.com> Date: Tue, 1 Sep 2026 14:41:58 +0530 Subject: [PATCH 07/12] Change header height from 0 to 2px --- assets/style/sections/header.css | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/assets/style/sections/header.css b/assets/style/sections/header.css index 4bd6f496..d8d7c0c4 100644 --- a/assets/style/sections/header.css +++ b/assets/style/sections/header.css @@ -171,7 +171,7 @@ input:focus::placeholder { transition: 0.3s; gap: 0; top: 100%; - height: 0; + height: 2px; overflow: hidden; opacity: 0; } From ed7cd40337c503f074e02f0603deeaff9f7d48ea Mon Sep 17 00:00:00 2001 From: Aprameyaraya <91876432+Aprameyaraya@users.noreply.github.com> Date: Tue, 1 Sep 2026 14:42:53 +0530 Subject: [PATCH 08/12] Update typography.css --- assets/style/base/typography.css | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/assets/style/base/typography.css b/assets/style/base/typography.css index 8b1e9979..3ee0baed 100644 --- a/assets/style/base/typography.css +++ b/assets/style/base/typography.css @@ -57,8 +57,7 @@ h6, } a { - color: #1a0dab; /* Or use the site's standard brand/accent blue */ - text-decoration: underline; + color: black } a:hover { From e0660c5e263321fdc1c0554471a9765bb753c051 Mon Sep 17 00:00:00 2001 From: Aprameyaraya <91876432+Aprameyaraya@users.noreply.github.com> Date: Tue, 1 Sep 2026 14:43:35 +0530 Subject: [PATCH 09/12] Update footer.css --- assets/style/sections/footer.css | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/assets/style/sections/footer.css b/assets/style/sections/footer.css index 8ca8f7ad..380f8587 100644 --- a/assets/style/sections/footer.css +++ b/assets/style/sections/footer.css @@ -13,9 +13,9 @@ footer { box-sizing: border-box; } -footer a { +footer * { color: #fff; - text-decoration: underline; + text-decoration: none; } footer a:hover { From 6d07294b5b0882f8c6cfba9dd6ae242e22f8efe6 Mon Sep 17 00:00:00 2001 From: Aprameyaraya <91876432+Aprameyaraya@users.noreply.github.com> Date: Tue, 1 Sep 2026 14:44:15 +0530 Subject: [PATCH 10/12] Update robots.txt to disallow additional packages --- assets/robots.txt | 45 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/assets/robots.txt b/assets/robots.txt index 86a3a6bc..3396a0ab 100644 --- a/assets/robots.txt +++ b/assets/robots.txt @@ -3,6 +3,50 @@ Disallow: /packages/submitted/ Disallow: /packages/misc/ Disallow: /packages/lindsey/ Disallow: /packages/omegahat/ +Disallow: /packages/1.8/ +Disallow: /packages/1.9/ +Disallow: /packages/2.0/ +Disallow: /packages/2.1/ +Disallow: /packages/2.2/ +Disallow: /packages/2.3/ +Disallow: /packages/2.4/ +Disallow: /packages/2.5/ +Disallow: /packages/2.6/ +Disallow: /packages/2.7/ +Disallow: /packages/2.8/ +Disallow: /packages/2.9/ +Disallow: /packages/2.10/ +Disallow: /packages/2.11/ +Disallow: /packages/2.12/ +Disallow: /packages/2.13/ +Disallow: /packages/2.14/ +Disallow: /packages/3.0/ +Disallow: /packages/3.1/ +Disallow: /packages/3.2/ +Disallow: /packages/3.3/ +Disallow: /packages/3.4/ +Disallow: /packages/3.5/ +Disallow: /packages/3.6/ +Disallow: /packages/3.7/ +Disallow: /packages/3.8/ +Disallow: /packages/3.9/ +Disallow: /packages/3.10/ +Disallow: /packages/3.11/ +Disallow: /packages/3.12/ +Disallow: /packages/3.13/ +Disallow: /packages/3.14/ +Disallow: /packages/3.15/ +Disallow: /packages/3.16/ +Disallow: /packages/3.17/ +Disallow: /packages/3.18/ +Disallow: /packages/3.19/ +Disallow: /packages/3.20/ +Disallow: /packages/3.21/ +Disallow: /packages/3.22/ +Disallow: /packages/3.23/ +Disallow: /packages/3.24/ +Disallow: /packages/devel/ +Disallow: /packages/release/ Disallow: /packages/bioc/ Disallow: /packages/data/ Disallow: /repository/ @@ -10,6 +54,7 @@ Disallow: /checkResults/ Disallow: /data/ Disallow: /datafiles/ Disallow: /installScripts/ +Disallow: /biocViews/ Disallow: /stats/ Disallow: /dataann-stats/ Disallow: /dataexp-stats/ From d65422af3af5276f332ab766b74d58d5c917ab50 Mon Sep 17 00:00:00 2001 From: Aprameyaraya <91876432+Aprameyaraya@users.noreply.github.com> Date: Wed, 2 Sep 2026 11:07:35 +0530 Subject: [PATCH 11/12] Refactor top_events method to simplify sorting --- lib/helpers.rb | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/lib/helpers.rb b/lib/helpers.rb index ecaae67d..96882132 100644 --- a/lib/helpers.rb +++ b/lib/helpers.rb @@ -450,10 +450,11 @@ def previous_events(events) end def top_events(events) - upcoming = events.children.select { |e| e[:end] >= Time.now.to_date } - sorted = upcoming.sort_by { |e| e[:start] } - - sorted.last(5).reverse + sorted = events.children.sort do |a, b| + a[:start] <=> b[:start] + end + toplist = sorted[-5..-1] + toplist.reverse end def event_date(e) From caf7c770451b2dd2e1a09d077af919917fa324c3 Mon Sep 17 00:00:00 2001 From: Aprameyaraya <91876432+Aprameyaraya@users.noreply.github.com> Date: Wed, 2 Sep 2026 11:17:50 +0530 Subject: [PATCH 12/12] Refactor package detail layout to include new fields Removed deprecated package information and added new fields for version, date, license, URL, and bug reports. --- layouts/_bioc_views_package_detail.html | 106 ++++++++++-------------- 1 file changed, 43 insertions(+), 63 deletions(-) diff --git a/layouts/_bioc_views_package_detail.html b/layouts/_bioc_views_package_detail.html index fa669400..29f27b25 100644 --- a/layouts/_bioc_views_package_detail.html +++ b/layouts/_bioc_views_package_detail.html @@ -1,70 +1,50 @@ -

<%=@package[:Package]%>

- -
- <% if @package.has_key? :PackageStatus and @package[:PackageStatus] == "Deprecated" %> - -

This package is deprecated. It will probably - be removed from Bioconductor. Please refer to - the - package end-of-life guidelines for more information. -

- + + <% if @package[:biocViews] %> + + + + <% end %> - <%= get_fragment(@package, @item, @item_rep) %> - - <%# package title - not to be confused with page title %> - -

<%= @package[:Title]%>

- - <%= render("/components/packages/badges/", :package => @package) %> -


- -
- -

- Bioconductor version: <%= verbose_bioc_version(@package) %> -

-

- <%= @package[:Description] %> -

-

- Author: <%= filter_emails(@package[:Author])%> -

-

- Maintainer: <%= filter_emails(@package[:Maintainer])%> -

- - + <% if @package[:Version] %> +
+ + + + <% end %> -
- Citation (from within R, enter citation("<%=@package[:Package]%>")): -
-
-
- Seminal Bioconductor project articles: -
-

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, - Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, - Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, - Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput - genomic analysis with Bioconductor." Nature Methods, 12(2), - 115–121. doi:10.1038/nmeth.3252.

-

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, - Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, - Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, - Zhang J (2004). "Bioconductor: open software development for computational biology and - bioinformatics." Genome Biology, 5(10), R80. - doi:10.1186/gb-2004-5-10-r80.

-
-
- + <% if @package[:Date] %> + + + + + <% end %> + <% if @package[:"In Bioconductor since"] %> + + + + + <% end %> + <% if @package[:License] %> + + + + + <% end %> - <%= render("/components/packages/installation/", :package => @package) %> - <%= render("/components/packages/documentation/", :package => @package) %> - <%= render("/components/packages/details/", :package => @package) %> - <%= render("/components/packages/archives/", :package => @package) %> - + <% if @package[:URL] %> + + + + + <% end %> + <% if @package[:BugReports] %> + + + + + <% end %> +
biocViews<%= @package[:biocViews] %>
Version<%= @package[:Version] %>
Date<%= @package[:Date] %>
In Bioconductor since<%= @package[:"In Bioconductor since"] %>
License<%= @package[:License] %>
URL<%= @package[:URL] %>
BugReports<%= @package[:BugReports] %>