fix: conda python interpreter path on Windows

snakemake/script.py

@@ -532,13 +532,18 @@ def write_script(self, preamble, fd):
         fd.write(self.source.encode())
 
     def _is_python_env(self):
-        if self.conda_env is not None:
+        if self.conda_env is not None and ON_WINDOWS:
+            prefix = self.conda_env
+        elif self.conda_env is not None:
             prefix = os.path.join(self.conda_env, "bin")
         elif self.env_modules is not None:
             prefix = self._execute_cmd("echo $PATH", read=True).split(":")[0]
         else:
             raise NotImplementedError()
-        return os.path.exists(os.path.join(prefix, "python"))
+        if not ON_WINDOWS:
+            return os.path.exists(os.path.join(prefix, "python"))
+        else:
+            return os.path.exists(os.path.join(prefix, "python.exe"))
 
     def _get_python_version(self):
         out = self._execute_cmd(

tests/test_conda_python_script/Snakefile

@@ -0,0 +1,7 @@
+rule random_python_conda_script:
+	output:
+		"version.txt"
+	conda:
+		"test_python_env.yaml"
+	script:
+		"test_script.py"

tests/test_conda_python_script/expected-results/version.txt

@@ -0,0 +1 @@
+1.21.4

tests/test_conda_python_script/test_python_env.yaml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - numpy ==1.21.4
+  - python <3.10

tests/test_conda_python_script/test_script.py

@@ -0,0 +1,4 @@
+import numpy
+
+with open('version.txt', 'w') as f:
+    f.write(numpy.__version__)

tests/tests.py

@@ -1659,3 +1659,7 @@ def test_conda_pin_file():
 @skip_on_windows  # sufficient to test this on linux
 def test_github_issue1618():
     run(dpath("test_github_issue1618"), cores=5)
+
+
+def test_conda_python_script():
+    run(dpath("test_conda_python_script"), use_conda=True)