From 42a7eb6172f1df06571960173c841c2bebec6260 Mon Sep 17 00:00:00 2001
From: sfmig <33267254+sfmig@users.noreply.github.com>
Date: Tue, 17 Dec 2024 16:34:05 +0000
Subject: [PATCH] Fix pooch retrieval of file registry (#260)

* Fix pooch retrieval of file registry

We need to specify a filename in `pooch.retrieve` for the file to be correctly overwritten everytime.

If filename is None, it is set as <hash-of-the-url> + <last-part-of-url>. So if the URL stays the same, the file won't be updated, even if the contents are changed

Signed-off-by: sfmig <33267254+sfmig@users.noreply.github.com>

* Fix precommits and add wheel as dependency to check-manifest (py3.12)

* Force file registry to download every time

---------

Signed-off-by: sfmig <33267254+sfmig@users.noreply.github.com>
---
 .pre-commit-config.yaml       |  2 +-
 tests/fixtures/integration.py | 16 +++++++++++++---
 2 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index ed19f3ed..157827fc 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -50,7 +50,7 @@ repos:
       hooks:
           - id: check-manifest
             args: [--no-build-isolation]
-            additional_dependencies: [setuptools-scm]
+            additional_dependencies: [setuptools-scm, wheel]
     # - repo: https://github.com/codespell-project/codespell
     #   # Configuration for codespell is in pyproject.toml
     #   rev: v2.3.0
diff --git a/tests/fixtures/integration.py b/tests/fixtures/integration.py
index 393928c3..98439557 100644
--- a/tests/fixtures/integration.py
+++ b/tests/fixtures/integration.py
@@ -21,18 +21,28 @@ def pooch_registry() -> dict:
         URL and hash of the GIN repository with the test data
 
     """
+    # Cache the test data in the user's home directory
+    test_data_dir = Path.home() / ".crabs-exploration-test-data"
+
+    # Remove the file registry if it exists
+    # otherwise the registry is not downloaded everytime
+    file_registry_path = test_data_dir / "files-registry.txt"
+    if file_registry_path.is_file():
+        Path(file_registry_path).unlink()
+
     # Initialise pooch registry
     registry = pooch.create(
-        Path.home() / ".crabs-exploration-test-data",
+        test_data_dir,
         base_url=f"{GIN_TEST_DATA_REPO}/raw/master/test_data",
     )
 
     # Download only the registry file from GIN
-    # if known_hash = None, the file is always downloaded.
+    # (this file should always be downloaded fresh from GIN)
     file_registry = pooch.retrieve(
         url=f"{GIN_TEST_DATA_REPO}/raw/master/files-registry.txt",
         known_hash=None,
-        path=Path.home() / ".crabs-exploration-test-data",
+        fname=file_registry_path.name,
+        path=file_registry_path.parent,
     )
 
     # Load registry file onto pooch registry