Update snapatac2 to 2.7.0 (#50349)

* Update snapatac2 to 2.7.0

* clean up recipe

* edit patch

* add c compiler back

---------

Co-authored-by: mencian <joshua.zhuang@yahoo.com>
Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>

recipes/snapatac2/build.sh

@@ -1,11 +1,5 @@
 #!/bin/bash -ex
 
-# Use a custom temporary directory as home on macOS.
-# (not sure why this is useful, but people use it in bioconda recipes)
-if [ `uname` == Darwin ]; then
-	export HOME=`mktemp -d`
-fi
-
 # build statically linked binary with Rust
 RUST_BACKTRACE=1
 # Build the package using maturin - should produce *.whl files.

recipes/snapatac2/meta.yaml

@@ -1,6 +1,6 @@
 {% set name = "snapatac2" %}
-{% set version = "2.6.4" %}
-{% set sha256 = "6ce80ae2c67f0ae05efed2b785b25e4d13fcc9d58697291b7d578a628b74bd05" %}
+{% set version = "2.7.0" %}
+{% set sha256 = "a37e86001da1e8f812d2e2dfda157ce131b8a0b54a44ae5bd72733c0171d4f1d" %}
 
 package:
   name: {{ name }}
@@ -11,9 +11,10 @@ source:
   sha256: {{ sha256 }}
   patches:
     - cargo.toml.patch
+    - pyproject.toml.patch
 
 build:
-  number: 1
+  number: 0
   skip: True  # [py < 39 or py > 312]
   run_exports:
     - {{ pin_subpackage('snapatac2', max_pin="x") }}
@@ -32,44 +33,42 @@ requirements:
   run:
     - python
     - anndata
-    - harmonypy >=0.0.9
     - python-igraph >=0.10.3
     - multiprocess
     - macs3
     - natsort
     - numpy >=1.16.0
     - pandas >=1.0,<2.1.2
-    - plotly >=5.6.0
-    - polars >=0.20.0
+    - plotly >=5.19.0
+    - polars >=1.0
     - pooch >=1.6.0
     - pyarrow
     - pyfaidx >=0.7.0,<0.8.0
     - python-kaleido
     - rustworkx
-    - scanorama >=1.7.3
-    - scanpy
     - scipy >=1.4
     - scikit-learn >=1.0
-    - scvi-tools >=1.0
     - tqdm >=4.62
     - typing_extensions
-    - umap-learn >=0.5.0
-    - xgboost >=1.4
 
 test:
   imports:
     - snapatac2
 
 about:
-  home: https://github.com/kaizhang/SnapATAC2
-  summary: "SnapATAC2: Single-cell epigenomics analysis pipeline"
+  home: "https://github.com/kaizhang/SnapATAC2"
+  summary: "SnapATAC2: Single-cell epigenomics analysis pipeline."
   license: MIT
   license_family: MIT
   license_file: LICENSE
-  doc_url: https://kzhang.org/SnapATAC2/
-  dev_url: https://github.com/kaizhang/SnapATAC2
+  doc_url: "https://kzhang.org/SnapATAC2"
+  dev_url: "https://github.com/kaizhang/SnapATAC2"
 
 extra:
   identifiers:
     - biotools:snapatac
     - doi:10.1038/s41592-023-02139-9
+    - usegalaxy-eu:snapatac2_preprocessing
+    - usegalaxy-eu:snapatac2_clustering
+    - usegalaxy-eu:snapatac2_peaks_and_motif
+    - usegalaxy-eu:snapatac2_plotting

recipes/snapatac2/pyproject.toml.patch

@@ -0,0 +1,14 @@
+diff --git a/pyproject.toml b/pyproject.toml
+index 0cc0ca0..eeb5899 100644
+--- a/pyproject.toml
++++ b/pyproject.toml
+@@ -7,6 +7,9 @@ features = ["pyo3/extension-module"]
+ python-source = "python"
+ module-name = "snapatac2._snapatac2"
+ manifest-path = "snapatac2-python/Cargo.toml"
++strip = true
++profile = "release"
++locked = true
+
+ [project]
+ name = "snapatac2"