From 105edcb08df3a9906b5c9459befd2ce44460e7b8 Mon Sep 17 00:00:00 2001
From: Copilot <198982749+Copilot@users.noreply.github.com>
Date: Thu, 11 Sep 2025 09:42:22 -0700
Subject: [PATCH 1/3] Add .pre-commit-ci.yaml configuration for develop branch
 autoupdates (#681)

* Initial plan

* Add .pre-commit-ci.yaml configuration file for develop branch autoupdates

Co-authored-by: ktehranchi <83722342+ktehranchi@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: ktehranchi <83722342+ktehranchi@users.noreply.github.com>
---
 .pre-commit-ci.yaml | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 .pre-commit-ci.yaml

diff --git a/.pre-commit-ci.yaml b/.pre-commit-ci.yaml
new file mode 100644
index 00000000..eabac4bb
--- /dev/null
+++ b/.pre-commit-ci.yaml
@@ -0,0 +1 @@
+autoupdate_branch: develop
\ No newline at end of file

From 04a043923dac7a8d246bb2045ba2916c5ae09437 Mon Sep 17 00:00:00 2001
From: Will McNeil <wilsonhm18@gmail.com>
Date: Mon, 29 Sep 2025 16:39:42 -0700
Subject: [PATCH 2/3] Make rule runnable on windows; add zipfile-deflate64
 dependency

---
 pyproject.toml                           |  1 +
 workflow/scripts/retrieve_databundles.py | 26 ++++++++++++++++--------
 2 files changed, 18 insertions(+), 9 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 726fe0c3..10591538 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -60,6 +60,7 @@ dependencies = [
     "tsam>=2.3.6",
     "xarray==2024.9.0",
     "xlrd==2.0.1",
+    "zipfile-deflate64==0.2.0"
 ]
 
 
diff --git a/workflow/scripts/retrieve_databundles.py b/workflow/scripts/retrieve_databundles.py
index 95921ea3..458c78d0 100644
--- a/workflow/scripts/retrieve_databundles.py
+++ b/workflow/scripts/retrieve_databundles.py
@@ -6,6 +6,11 @@
 import zipfile
 from pathlib import Path
 
+import zipfile_deflate64 # For Windows OS, use zipfile-deflate64
+
+def is_wsl():
+    with open('/proc/version', 'r') as f:
+        return 'microsoft' in f.read().lower()
 from _helpers import configure_logging, progress_retrieve
 
 logger = logging.getLogger(__name__)
@@ -29,14 +34,17 @@ def download_repository(url, rootpath, repository):
     progress_retrieve(url, tarball_fn)
 
     logger.info(f"Extracting {repository} databundle.")
-    if (
-        repository == "EFS"
-    ):  # deflate64 compression not supported by zipFile, current subprocess command will only work on linux and mac
-        if platform.system() == "Windows":
-            cmd = ["tar", "-xf", tarball_fn, "-C", to_fn]
-        else:
-            cmd = ["unzip", tarball_fn, "-d", to_fn]
-        subprocess.run(cmd, check=True)
+    if repository == "EFS":
+        if platform.system() == "Windows" or is_wsl():  # Handle both Windows and WSL
+            try:
+                with zipfile_deflate64.ZipFile(tarball_fn, "r") as zip_ref:
+                    zip_ref.extractall(to_fn)
+            except Exception as e:
+                logger.error(f"Failed to extract zip file with zipfile_deflate64: {e}")
+                raise
+        else:  # Pure Linux environment
+            cmd = ["unzip", tarball_fn, "-d", str(to_fn)]
+            subprocess.run(cmd, check=True)
     else:
         with zipfile.ZipFile(tarball_fn, "r") as zip_ref:
             zip_ref.extractall(to_fn)
@@ -62,4 +70,4 @@ def download_repository(url, rootpath, repository):
     repositories = snakemake.params[0]
     for repository in repositories:
         url = repositories[repository]
-        download_repository(url, rootpath, repository)
+        download_repository(url, rootpath, repository)
\ No newline at end of file

From baf16cf720267ef5a3cb28b371b89a50634df1b7 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 29 Sep 2025 23:43:06 +0000
Subject: [PATCH 3/3] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .pre-commit-ci.yaml                      |  2 +-
 workflow/scripts/retrieve_databundles.py | 11 +++++++----
 2 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/.pre-commit-ci.yaml b/.pre-commit-ci.yaml
index eabac4bb..47258ede 100644
--- a/.pre-commit-ci.yaml
+++ b/.pre-commit-ci.yaml
@@ -1 +1 @@
-autoupdate_branch: develop
\ No newline at end of file
+autoupdate_branch: develop
diff --git a/workflow/scripts/retrieve_databundles.py b/workflow/scripts/retrieve_databundles.py
index 458c78d0..096f7456 100644
--- a/workflow/scripts/retrieve_databundles.py
+++ b/workflow/scripts/retrieve_databundles.py
@@ -6,11 +6,14 @@
 import zipfile
 from pathlib import Path
 
-import zipfile_deflate64 # For Windows OS, use zipfile-deflate64
+import zipfile_deflate64  # For Windows OS, use zipfile-deflate64
+
 
 def is_wsl():
-    with open('/proc/version', 'r') as f:
-        return 'microsoft' in f.read().lower()
+    with open("/proc/version") as f:
+        return "microsoft" in f.read().lower()
+
+
 from _helpers import configure_logging, progress_retrieve
 
 logger = logging.getLogger(__name__)
@@ -70,4 +73,4 @@ def download_repository(url, rootpath, repository):
     repositories = snakemake.params[0]
     for repository in repositories:
         url = repositories[repository]
-        download_repository(url, rootpath, repository)
\ No newline at end of file
+        download_repository(url, rootpath, repository)