From c59e164f0f3b82f010182ec67f44c8f743dd0e3b Mon Sep 17 00:00:00 2001
From: Thomas Cokelaer <cokelaer@gmail.com>
Date: Fri, 20 Mar 2026 22:27:06 +0100
Subject: [PATCH] pin version

---
 README.rst        |   2 +
 pyproject.toml    |  10 ++++-
 test/test_main.py | 112 +++++++++++++++++++++++-----------------------
 3 files changed, 66 insertions(+), 58 deletions(-)

diff --git a/README.rst b/README.rst
index e8b5873..985f9d3 100644
--- a/README.rst
+++ b/README.rst
@@ -135,6 +135,8 @@ Changelog
 ========= ======================================================================
 Version   Description
 ========= ======================================================================
+1.4.1     * update to use wrappers.shells and wrappers.snippets
+            drop wrappers usage
 1.4.0     * update wrappers to v24.8.29
           * update sequana_pipetools requirement to >=1.5
 1.3.1     * remove temp on BWA BAM file (more practical to keep them)
diff --git a/pyproject.toml b/pyproject.toml
index 13ba4c3..f82d027 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "sequana-mapper"
-version = "1.4.0"
+version = "1.4.1"
 description = "A multi-sample mapper to map reads onto a reference"
 authors = ["Sequana Team"]
 license = "BSD-3"
@@ -51,3 +51,11 @@ mock = "^5.1.0"
 pytest-mock = "^3.11.1"
 pytest-cov = "^4.1.0"
 
+[tool.pytest.ini_options]
+filterwarnings = [
+    "ignore::pytest.PytestDeprecationWarning",
+    "ignore::DeprecationWarning:click_completion",
+    "ignore::DeprecationWarning:importlib",
+]
+asyncio_mode = "auto"
+
diff --git a/test/test_main.py b/test/test_main.py
index b017880..65b9a89 100644
--- a/test/test_main.py
+++ b/test/test_main.py
@@ -13,72 +13,70 @@
 
 
 def test_standalone_subprocess():
-    directory = tempfile.TemporaryDirectory()
-    cmd = """sequana_mapper --input-directory {}
-            --working-directory {} --force""".format(
-        sharedir, directory.name
-    )
-    subprocess.call(cmd.split())
+    with tempfile.TemporaryDirectory() as directory:
+        cmd = """sequana_mapper --input-directory {}
+                --working-directory {} --force""".format(
+            sharedir, directory
+        )
+        subprocess.call(cmd.split())
 
 
 def test_standalone_script():
-    directory = tempfile.TemporaryDirectory()
-
-    runner = CliRunner()
-    results = runner.invoke(
-        main,
-        [
-            "--input-directory",
-            sharedir,
-            "--reference-file",
-            sharedir + "/measles.fa",
-            "--working-directory",
-            directory.name,
-            "--force",
-        ],
-    )
-    assert results.exit_code == 0
+    with tempfile.TemporaryDirectory() as directory:
+        runner = CliRunner()
+        results = runner.invoke(
+            main,
+            [
+                "--input-directory",
+                sharedir,
+                "--reference-file",
+                sharedir + "/measles.fa",
+                "--working-directory",
+                directory,
+                "--force",
+            ],
+        )
+        assert results.exit_code == 0
 
 
 def test_standalone_script_minimap2():
-    directory = tempfile.TemporaryDirectory()
-    runner = CliRunner()
-    results = runner.invoke(
-        main,
-        [
-            "--input-directory",
-            sharedir,
-            "--reference-file",
-            sharedir + "/measles.fa",
-            "--working-directory",
-            directory.name,
-            "--force",
-            "--aligner-choice",
-            "minimap2",
-        ],
-    )
-    assert results.exit_code == 0
+    with tempfile.TemporaryDirectory() as directory:
+        runner = CliRunner()
+        results = runner.invoke(
+            main,
+            [
+                "--input-directory",
+                sharedir,
+                "--reference-file",
+                sharedir + "/measles.fa",
+                "--working-directory",
+                directory,
+                "--force",
+                "--aligner-choice",
+                "minimap2",
+            ],
+        )
+        assert results.exit_code == 0
 
 
 def test_standalone_script_saf(tmpdir):
-    directory = tempfile.TemporaryDirectory()
-
-    runner = CliRunner()
-    results = runner.invoke(
-        main,
-        [
-            "--input-directory",
-            sharedir,
-            "--reference-file",
-            sharedir + "/measles.fa",
-            "--working-directory",
-            directory.name,
-            "--force",
-            "--capture-annotation-file",
-            sharedir + "/test.saf",
-        ],
-    )
-    assert results.exit_code == 0
+    with tempfile.TemporaryDirectory() as directory:
+        runner = CliRunner()
+        results = runner.invoke(
+            main,
+            [
+                "--input-directory",
+                sharedir,
+                "--reference-file",
+                sharedir + "/measles.fa",
+                "--working-directory",
+                directory,
+                "--force",
+                "--capture-annotation-file",
+                sharedir + "/test.saf",
+            ],
+        )
+        assert results.exit_code == 0
 
 
 def test_full():