From b24cd7c8de335095278502eae002b7f46ef7c758 Mon Sep 17 00:00:00 2001
From: Francisco Merino-Casallo
 <469246+fmerinocasallo@users.noreply.github.com>
Date: Fri, 20 Feb 2026 07:56:11 +0100
Subject: [PATCH] Update conda environment specs

Replace pip dependencies with conda equivalents for simplicity
---
 SQANTI3.conda_env.yml | 35 +++++++++++++++++------------------
 1 file changed, 17 insertions(+), 18 deletions(-)

diff --git a/SQANTI3.conda_env.yml b/SQANTI3.conda_env.yml
index f380d074..6149f406 100755
--- a/SQANTI3.conda_env.yml
+++ b/SQANTI3.conda_env.yml
@@ -67,21 +67,20 @@ dependencies:
   - seaborn=0.13.2
   - scikit-learn=1.5.2
   - pytest=7.4.4
-  - pip:
-    - argh==0.31.3
-    - dill==0.3.9
-    - edlib==1.3.9.post1
-    - gffutils==0.13
-    - gtfparse==2.5.0
-    - importlib-metadata==8.5.0
-    - intervaltree==3.1.0
-    - parasail==1.3.4
-    - pdf2image==1.17.0
-    - polars==0.20.31
-    - pyarrow==14.0.2
-    - pyfaidx==0.8.1.3
-    - simplejson==3.19.3
-    - sortedcontainers==2.4.0
-    - ultra-bioinformatics==0.1
-    - zipp==3.21.0
-    - TD2==1.0.6
+  - argh>=0.31
+  - dill>=0.3.9
+  - python-edlib>=1.3.9
+  - gffutils>=0.13
+  - gtfparse>=2.5
+  - importlib-metadata>=8.5
+  - intervaltree>=3.1
+  - parasail>=1.3
+  - pdf2image>=1.17
+  - polars>=0.20,<0.21
+  - pyarrow>=14.0,<15.0
+  - pyfaidx>=0.8
+  - simplejson>=3.19
+  - sortedcontainers>=2.4
+  - ultra_bioinformatics>=0.1
+  - zipp>=3.21
+  - td2>=1.0