From 6d244d2f5ef55fc227f26640f27bc8d4ccc58d63 Mon Sep 17 00:00:00 2001
From: Pieter Moris <13552343+pmoris@users.noreply.github.com>
Date: Tue, 29 Oct 2024 11:25:08 +0100
Subject: [PATCH 1/3] Add linkify-py-it as explicit dependency

The bioconda version of nf-core tools produced errors
when running commands that launched the trogon TUI.
The reason was the missing package linkify,
which gets pulled in as a dependency of textual in the PyPi
build, but not in the conda-forge recipe.
See https://github.com/Textualize/textual/blob/22770300252deb28d266fe4ed4766d6e2a2f5dd2/pyproject.toml#L44,
https://github.com/conda-forge/textual-feedstock/blob/main/recipe/meta.yaml
and nf-core/tools#3257.
---
 requirements.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/requirements.txt b/requirements.txt
index b7f1c39ca..ade730348 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -20,6 +20,7 @@ rich-click==1.8.*
 rich>=13.3.1
 tabulate
 textual==0.71.0
+linkify-it-py
 trogon
 pdiff
 ruamel.yaml

From 71c004f711f43710a6f9291fe2b7063f51a2b8d1 Mon Sep 17 00:00:00 2001
From: Pieter Moris <13552343+pmoris@users.noreply.github.com>
Date: Tue, 29 Oct 2024 13:00:18 +0100
Subject: [PATCH 2/3] Pin linkify version

Code Rabbit AI suggestion:
The textual package version 0.71.0 depends on
markdown-it-py[linkify]>=2.1.0, which in turn
requires linkify-it-py>=2.0.0.

However, checking the actual dependencies of
markdown-it-py, it seems it wants linkify-it-py
to be >=1,<3.

See https://github.com/bioconda/bioconda-recipes/pull/51762
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index ade730348..432318d83 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -20,7 +20,7 @@ rich-click==1.8.*
 rich>=13.3.1
 tabulate
 textual==0.71.0
-linkify-it-py
+linkify-it-py>=1,<3
 trogon
 pdiff
 ruamel.yaml

From 3a80996664886e11d349e955ae46bd6376ab13c3 Mon Sep 17 00:00:00 2001
From: Pieter Moris <13552343+pmoris@users.noreply.github.com>
Date: Tue, 29 Oct 2024 13:07:48 +0100
Subject: [PATCH 3/3] Update changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index f2bf6fcae..69fe889a9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,7 @@
 - Fix Manifest DOI text ([#3224](https://github.com/nf-core/tools/pull/3224))
 - Do not assume pipeline name is url ([#3225](https://github.com/nf-core/tools/pull/3225))
 - fix worklfow_dispatch trigger and parse more review comments in awsfulltest ([#3235](https://github.com/nf-core/tools/pull/3235))
+- Add `linkify` as an explicit dependency, to avoid it from being absent in the bioconda build. ([#3260](https://github.com/nf-core/tools/pull/3260)).
 
 ### Download