From 33f96547f7b5720bb98334304417385f0f1b86da Mon Sep 17 00:00:00 2001
From: Pieter Moris <13552343+pmoris@users.noreply.github.com>
Date: Tue, 29 Oct 2024 11:14:13 +0100
Subject: [PATCH 1/4] Add missing linkify 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 https://github.com/nf-core/tools/issues/3257.
---
 recipes/nf-core/meta.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/recipes/nf-core/meta.yaml b/recipes/nf-core/meta.yaml
index b546fdafe2ee0..ec43b3f16c5ed 100644
--- a/recipes/nf-core/meta.yaml
+++ b/recipes/nf-core/meta.yaml
@@ -50,6 +50,7 @@ requirements:
     - ruamel.yaml
     - tabulate
     - textual ==0.71.0
+    - linkify-it-py
     - trogon
     - nextflow >=24.04.4
     - nf-test

From 633094e5358519c4813bcc72fdb9e7b97b381fe9 Mon Sep 17 00:00:00 2001
From: Pieter Moris <13552343+pmoris@users.noreply.github.com>
Date: Tue, 29 Oct 2024 11:48:38 +0100
Subject: [PATCH 2/4] 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.
---
 recipes/nf-core/meta.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/recipes/nf-core/meta.yaml b/recipes/nf-core/meta.yaml
index ec43b3f16c5ed..b95544e49a2e2 100644
--- a/recipes/nf-core/meta.yaml
+++ b/recipes/nf-core/meta.yaml
@@ -50,7 +50,7 @@ requirements:
     - ruamel.yaml
     - tabulate
     - textual ==0.71.0
-    - linkify-it-py
+    - linkify-it-py>=1,<3
     - trogon
     - nextflow >=24.04.4
     - nf-test

From caf6a23237efdd8945d6d04c8dbd37728afc8501 Mon Sep 17 00:00:00 2001
From: Pieter Moris <13552343+pmoris@users.noreply.github.com>
Date: Tue, 29 Oct 2024 12:58:28 +0100
Subject: [PATCH 3/4] Update build number

---
 recipes/nf-core/meta.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/recipes/nf-core/meta.yaml b/recipes/nf-core/meta.yaml
index b95544e49a2e2..cddd64fb05ecb 100644
--- a/recipes/nf-core/meta.yaml
+++ b/recipes/nf-core/meta.yaml
@@ -12,7 +12,7 @@ source:
 
 build:
   noarch: python
-  number: 0
+  number: 1
   script: "touch requirements.txt && {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
   entry_points:
     - nf-core=nf_core.__main__:run_nf_core

From ce2d8708939156aa62dfd2da48d35bcf8eed57e6 Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Tue, 29 Oct 2024 14:45:14 -0500
Subject: [PATCH 4/4] fix typo

---
 recipes/nf-core/meta.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/recipes/nf-core/meta.yaml b/recipes/nf-core/meta.yaml
index cddd64fb05ecb..c518daa0d9876 100644
--- a/recipes/nf-core/meta.yaml
+++ b/recipes/nf-core/meta.yaml
@@ -50,7 +50,7 @@ requirements:
     - ruamel.yaml
     - tabulate
     - textual ==0.71.0
-    - linkify-it-py>=1,<3
+    - linkify-it-py >=1,<3
     - trogon
     - nextflow >=24.04.4
     - nf-test