Add pycoverm (#52941)

* Add `pycoverm`

* Move build command to script

* Add `cmake` build depedency

* Require `cxx` compiler

* Add `make` as a build requirement

* Remove `linux-aarch64` build

* Bump to 0.6.2

* Update sha256sum

* Remove `test.py` from the list of test files

* Remove cross-compilation

recipes/pycoverm/build.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+
+set -ex
+
+export CARGO_TARGET_X86_64_UNKNOWN_LINUX_GNU_LINKER="$CC"
+export CARGO_TARGET_AARCH64_UNKNOWN_LINUX_GNU_LINKER="$CC"
+export PYO3_USE_ABI3_FORWARD_COMPATIBILITY=1
+
+$PYTHON -m pip install . -vv --no-deps --no-build-isolation
+cargo-bundle-licenses --format yaml --output THIRDPARTY.yml

recipes/pycoverm/meta.yaml

@@ -0,0 +1,58 @@
+{% set name = "pycoverm" %}
+{% set version = "0.6.2" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
+  sha256: e5e96e55ee2756d0cbd1db383e136cd2c1e232204f25b015ce956b7a6f4ddee2
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('pycoverm', max_pin="x.x") }}
+
+requirements:
+  build:
+    - {{ compiler("c") }}
+    - {{ compiler("cxx") }}
+    - {{ compiler("rust") }}
+    - {{ stdlib("c") }}
+    - python
+    - maturin >=1.7,<2
+    - make
+    - cmake
+    - cargo-bundle-licenses
+  host:
+    - pip
+    - maturin >=1.7,<2
+    - python
+  run:
+    - python
+    - numpy >=1.16,<3
+
+test:
+  files:
+    - test.bam
+  imports:
+    - pycoverm
+  commands:
+    - pip check
+  requires:
+    - pip
+
+about:
+  home: /~https://github.com/apcamargo/pycoverm
+  license: GPL-3.0
+  license_file:
+    - LICENSE
+    - THIRDPARTY.yml
+  summary: Python bindings for CoverM
+
+extra:
+  additional-platforms:
+    - osx-arm64
+  skip-lints:
+    - version_constraints_missing_whitespace  # see /~https://github.com/bioconda/bioconda-recipes/issues/51185

recipes/pycoverm/run_test.py

@@ -0,0 +1,25 @@
+#!/usr/bin/env python
+
+import unittest
+
+import numpy as np
+import pycoverm
+
+
+class TestPycoverm(unittest.TestCase):
+    def setUp(self):
+        self.bam_file = "test.bam"
+
+    def test_is_bam_sorted(self):
+        result = pycoverm.is_bam_sorted(self.bam_file)
+        self.assertIsInstance(result, bool)
+
+    def test_get_coverages_from_bam(self):
+        result = pycoverm.get_coverages_from_bam([self.bam_file])
+        self.assertIsInstance(result[0], list)
+        self.assertIsInstance(result[1], np.ndarray)
+        self.assertAlmostEqual(result[1].sum(), 30.173173904418945)
+
+
+if __name__ == "__main__":
+    unittest.main()