From 590fbd51d6c6cf7090ef59a8e809d678f8b68ad6 Mon Sep 17 00:00:00 2001
From: "Alicia A. Evans" <108547992+aliciaaevans@users.noreply.github.com>
Date: Tue, 10 Sep 2024 14:45:31 -0400
Subject: [PATCH] Bulk: Update MS2PIP version to 4.0.0 (#50609)

* Bump MS2PIP version from to 4.0.0

* Add ms2rescore_rs dependency

* dont't allow py312 since pandas <2 doesnt support

* try dropping pyopenms depenency, should be resolved via psm_utils

* add pyopenms again

---------

Co-authored-by: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com>
---
 recipes/ms2pip/meta.yaml | 26 ++++++++++++++------------
 1 file changed, 14 insertions(+), 12 deletions(-)

diff --git a/recipes/ms2pip/meta.yaml b/recipes/ms2pip/meta.yaml
index 095eb5313e4db..df283caa45a97 100644
--- a/recipes/ms2pip/meta.yaml
+++ b/recipes/ms2pip/meta.yaml
@@ -1,17 +1,18 @@
-{% set version = "4.0.0.dev8" %}
+{% set version = "4.0.0" %}
 {% set name = "ms2pip" %}
-{% set sha256 = "2a464e00135c875c12c98f6853a4487e193a0730b5bd94f82a44e8d5fb21a7bb" %}
+{% set sha256 = "b2329700e8c2af5c64d8fa0ef62dbc6ee52c60d7b18e5d860a4d9194c225ec29" %}
 
 package:
-  name: "ms2pip"
+  name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
-  url: https://pypi.io/packages/source/m/ms2pip/ms2pip-{{ version }}.tar.gz
+  url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
   sha256: {{ sha256 }}
 
 build:
-  number: 1
+  number: 0
+  skip: true # [py >= 312]
   run_exports:
     - {{ pin_subpackage(name, max_pin="x") }}
   entry_points:
@@ -34,21 +35,22 @@ requirements:
   run:
     - python >=3.8
     - {{ pin_compatible('numpy') }}
-    - pandas >=1.0
-    - pyteomics >=3.5
+    - pandas >=1.0,<2
+    - pyteomics >=3.5,<5
     - tqdm >=4
     - pytables >=3.4
-    - tomlkit >=0.5
-    - click >=7
-    - xgboost >=1.3
+    - tomlkit >=0.5,<1
+    - click >=7,<9
+    - xgboost >=1.3,<2
     - matplotlib-base >=3.0
     - lxml >=4
     - rich >=13
-    - pydantic >=1.10,<2
-    - psm-utils
+    - pydantic >=2
+    - psm-utils >=0.9
     - werkzeug >=2
     - pyarrow
     - pyopenms
+    - ms2rescore-rs
 
 test:
   imports: