From bc1bc41255ad0ccda3e4a64eddc4a2042757bfc1 Mon Sep 17 00:00:00 2001
From: Ivan Ruiz Manuel <72193617+irm-codebase@users.noreply.github.com>
Date: Fri, 3 Jul 2026 12:40:05 +0200
Subject: [PATCH] Make export work on windows

---
 template/pixi.toml.jinja | 16 ++++++++++------
 tests/template_test.py   | 11 ++++++++++-
 2 files changed, 20 insertions(+), 7 deletions(-)

diff --git a/template/pixi.toml.jinja b/template/pixi.toml.jinja
index 80fdab3..64f4a12 100644
--- a/template/pixi.toml.jinja
+++ b/template/pixi.toml.jinja
@@ -44,10 +44,14 @@ cmd = "pixi workspace export conda-environment --environment '{{ env }}' '{{ out
 
 [tasks._export-snakemake-pin]
 description = "Export one Pixi environment/platform as a Snakemake-compatible pin file"
-args = ["env", "platform", { arg = "outdir", default = "workflow/envs" }]
-cmd = """
-set -e
-pixi workspace export conda-explicit-spec --environment '{{ env }}' --platform '{{ platform }}' '{{ outdir }}'
-mv '{{ outdir }}/{{ env }}_{{ platform }}_conda_spec.txt' '{{ outdir }}/{{ env }}.{{ platform }}.pin.txt'
-"""
+args = ["env", "platform", "outdir"]
+depends-on = [
+  { task = "_export-conda-explicit-spec", args = ["{{ env }}", "{{ platform }}", "{{ outdir }}"] },
+]
+cmd = "mv '{{ outdir }}/{{ env }}_{{ platform }}_conda_spec.txt' '{{ outdir }}/{{ env }}.{{ platform }}.pin.txt'"
+
+[tasks._export-conda-explicit-spec]
+description = "Export one Pixi environment/platform as an explicit conda spec file"
+args = ["env", "platform", "outdir"]
+cmd = "pixi workspace export conda-explicit-spec --environment '{{ env }}' --platform '{{ platform }}' '{{ outdir }}'"
 {% endraw %}
diff --git a/tests/template_test.py b/tests/template_test.py
index c499056..67b502b 100644
--- a/tests/template_test.py
+++ b/tests/template_test.py
@@ -45,12 +45,21 @@ def pixi_built(self, template_project):
         )
         return template_project
 
-    def test_pytest(self, pixi_built):
+    def test_task_test_integration(self, pixi_built):
         """The template's tests should pass by default."""
         assert subprocess.run(
             "pixi run test-integration", shell=True, check=True, cwd=pixi_built
         )
 
+    def test_task_export_snakemake_env(self, pixi_built):
+        """The template's export task should work as expected."""
+        assert subprocess.run(
+            "pixi run export-snakemake-env module",
+            shell=True,
+            check=True,
+            cwd=pixi_built,
+        )
+
     def test_linting(self, pixi_built):
         """The generated project should result in perfect snakemake linting."""
         assert subprocess.run(