From e9f71731c619ddd294a26ace6a0d942a5f4f8aac Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 22 Dec 2025 20:15:28 +0000
Subject: [PATCH 1/3] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.14.9 → v0.14.10](https://github.com/astral-sh/ruff-pre-commit/compare/v0.14.9...v0.14.10)
---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index d3998e1..7e708a8 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -17,7 +17,7 @@ repos:
       - id: trailing-whitespace
         exclude: "tests/cis_tests/.*"
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.9
+    rev: v0.14.10
     hooks:
       - id: ruff-check
         args: [--fix, --exit-non-zero-on-fix]

From 12ea3ce7d21ca57a382668699aeadb05acd76a0a Mon Sep 17 00:00:00 2001
From: Chen Zhang <zhangc@ornl.gov>
Date: Mon, 22 Dec 2025 15:32:48 -0500
Subject: [PATCH 2/3] Update pixi version and dependencies to address
 vulnerabilities

---
 .github/workflows/test_and_deploy.yaml |  8 ++---
 pixi.lock                              | 45 ++++++++++++--------------
 pyproject.toml                         |  5 +--
 3 files changed, 28 insertions(+), 30 deletions(-)

diff --git a/.github/workflows/test_and_deploy.yaml b/.github/workflows/test_and_deploy.yaml
index dffcf5c..632b33f 100644
--- a/.github/workflows/test_and_deploy.yaml
+++ b/.github/workflows/test_and_deploy.yaml
@@ -25,7 +25,7 @@ jobs:
       - name: Setup pixi
         uses: prefix-dev/setup-pixi@v0.9.3
         with:
-          pixi-version: v0.50.2
+          pixi-version: v0.62.2
           manifest-path: pyproject.toml
 
       - name: Run unit tests
@@ -54,7 +54,7 @@ jobs:
       - name: Setup pixi
         uses: prefix-dev/setup-pixi@v0.9.3
         with:
-          pixi-version: v0.50.2
+          pixi-version: v0.62.2
           manifest-path: pyproject.toml
 
       - name: Build conda package
@@ -91,7 +91,7 @@ jobs:
       - name: Setup Pixi
         uses: prefix-dev/setup-pixi@v0.9.3
         with:
-          pixi-version: v0.50.2
+          pixi-version: v0.62.2
           manifest-path: pyproject.toml
 
       - name: Download conda package artifact
@@ -127,7 +127,7 @@ jobs:
       - name: Setup pixi
         uses: prefix-dev/setup-pixi@v0.9.3
         with:
-          pixi-version: v0.50.2
+          pixi-version: v0.62.2
           manifest-path: pyproject.toml
 
       - name: Build pypi package
diff --git a/pixi.lock b/pixi.lock
index 9426b24..137854d 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -54,7 +54,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/editables-0.5-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/exceptiongroup-1.3.1-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/execnet-2.1.2-pyhd8ed1ab_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.20.0-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.20.1-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2
@@ -316,7 +316,7 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/19/47/034be51bc2b40279fd1417397d3f330b73906774bd6eaecd26ed93c1491f/bm4d-4.2.5-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/b8/14/bab308fc2c1b5228c3224ec2bf928ce2e4d21d8046c161e44a2012b5203e/greenlet-3.3.0-cp314-cp314-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl
       - pypi: https://files.pythonhosted.org/packages/31/b4/b9b800c45527aadd64d5b442f9b932b00648617eb5d63d2c7a6587b7cafc/jmespath-1.0.1-py3-none-any.whl
-      - pypi: https://files.pythonhosted.org/packages/e4/76/6d409e37e82cdd5dda3df1ab958130ae32b46e42458bd4fc93d7eb8749cb/playwright-1.56.0-py3-none-manylinux1_x86_64.whl
+      - pypi: https://files.pythonhosted.org/packages/56/61/3a803cb5ae0321715bfd5247ea871d25b32c8f372aeb70550a90c5f586df/playwright-1.57.0-py3-none-manylinux1_x86_64.whl
       - pypi: https://files.pythonhosted.org/packages/9b/4d/b9add7c84060d4c1906abe9a7e5359f2a60f7a9a4f67268b2766673427d8/pyee-13.0.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/98/1c/b00940ab9eb8ede7897443b771987f2f4a76f06be02f1b3f01eb7567e24a/pytest_base_url-2.1.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/76/61/4d333d8354ea2bea2c2f01bad0a4aa3c1262de20e1241f78e73360e9b620/pytest_playwright-0.7.2-py3-none-any.whl
@@ -365,7 +365,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/editables-0.5-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/exceptiongroup-1.3.1-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/execnet-2.1.2-pyhd8ed1ab_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.20.0-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.20.1-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/osx-arm64/giflib-5.2.2-h93a5062_0.conda
       - conda: https://conda.anaconda.org/conda-forge/osx-arm64/glib-2.86.2-h7ee6e74_1.conda
       - conda: https://conda.anaconda.org/conda-forge/osx-arm64/glib-tools-2.86.2-hb9d6e3a_1.conda
@@ -568,7 +568,7 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/19/47/034be51bc2b40279fd1417397d3f330b73906774bd6eaecd26ed93c1491f/bm4d-4.2.5-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/d7/7c/f0a6d0ede2c7bf092d00bc83ad5bafb7e6ec9b4aab2fbdfa6f134dc73327/greenlet-3.3.0-cp314-cp314-macosx_11_0_universal2.whl
       - pypi: https://files.pythonhosted.org/packages/31/b4/b9b800c45527aadd64d5b442f9b932b00648617eb5d63d2c7a6587b7cafc/jmespath-1.0.1-py3-none-any.whl
-      - pypi: https://files.pythonhosted.org/packages/ef/95/347eef596d8778fb53590dc326c344d427fa19ba3d42b646fce2a4572eb3/playwright-1.56.0-py3-none-macosx_11_0_arm64.whl
+      - pypi: https://files.pythonhosted.org/packages/8b/04/ef95b67e1ff59c080b2effd1a9a96984d6953f667c91dfe9d77c838fc956/playwright-1.57.0-py3-none-macosx_11_0_arm64.whl
       - pypi: https://files.pythonhosted.org/packages/9b/4d/b9add7c84060d4c1906abe9a7e5359f2a60f7a9a4f67268b2766673427d8/pyee-13.0.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/98/1c/b00940ab9eb8ede7897443b771987f2f4a76f06be02f1b3f01eb7567e24a/pytest_base_url-2.1.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/76/61/4d333d8354ea2bea2c2f01bad0a4aa3c1262de20e1241f78e73360e9b620/pytest_playwright-0.7.2-py3-none-any.whl
@@ -633,7 +633,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/distlib-0.4.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/exceptiongroup-1.3.1-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/executing-2.2.1-pyhd8ed1ab_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.20.0-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.20.1-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2
@@ -899,7 +899,7 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/19/47/034be51bc2b40279fd1417397d3f330b73906774bd6eaecd26ed93c1491f/bm4d-4.2.5-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/b8/14/bab308fc2c1b5228c3224ec2bf928ce2e4d21d8046c161e44a2012b5203e/greenlet-3.3.0-cp314-cp314-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl
       - pypi: https://files.pythonhosted.org/packages/cb/b1/3846dd7f199d53cb17f49cba7e651e9ce294d8497c8c150530ed11865bb8/iniconfig-2.3.0-py3-none-any.whl
-      - pypi: https://files.pythonhosted.org/packages/e4/76/6d409e37e82cdd5dda3df1ab958130ae32b46e42458bd4fc93d7eb8749cb/playwright-1.56.0-py3-none-manylinux1_x86_64.whl
+      - pypi: https://files.pythonhosted.org/packages/56/61/3a803cb5ae0321715bfd5247ea871d25b32c8f372aeb70550a90c5f586df/playwright-1.57.0-py3-none-manylinux1_x86_64.whl
       - pypi: https://files.pythonhosted.org/packages/54/20/4d324d65cc6d9205fabedc306948156824eb9f0ee1633355a8f7ec5c66bf/pluggy-1.6.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/9b/4d/b9add7c84060d4c1906abe9a7e5359f2a60f7a9a4f67268b2766673427d8/pyee-13.0.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/3b/ab/b3226f0bd7cdcf710fbede2b3548584366da3b19b5021e74f5bde2a8fa3f/pytest-9.0.2-py3-none-any.whl
@@ -951,7 +951,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/distlib-0.4.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/exceptiongroup-1.3.1-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/executing-2.2.1-pyhd8ed1ab_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.20.0-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.20.1-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/fonttools-4.61.0-pyh7db6752_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/fqdn-1.5.1-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/osx-arm64/freetype-2.14.1-hce30654_0.conda
@@ -1163,7 +1163,7 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/19/47/034be51bc2b40279fd1417397d3f330b73906774bd6eaecd26ed93c1491f/bm4d-4.2.5-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/d7/7c/f0a6d0ede2c7bf092d00bc83ad5bafb7e6ec9b4aab2fbdfa6f134dc73327/greenlet-3.3.0-cp314-cp314-macosx_11_0_universal2.whl
       - pypi: https://files.pythonhosted.org/packages/cb/b1/3846dd7f199d53cb17f49cba7e651e9ce294d8497c8c150530ed11865bb8/iniconfig-2.3.0-py3-none-any.whl
-      - pypi: https://files.pythonhosted.org/packages/ef/95/347eef596d8778fb53590dc326c344d427fa19ba3d42b646fce2a4572eb3/playwright-1.56.0-py3-none-macosx_11_0_arm64.whl
+      - pypi: https://files.pythonhosted.org/packages/8b/04/ef95b67e1ff59c080b2effd1a9a96984d6953f667c91dfe9d77c838fc956/playwright-1.57.0-py3-none-macosx_11_0_arm64.whl
       - pypi: https://files.pythonhosted.org/packages/54/20/4d324d65cc6d9205fabedc306948156824eb9f0ee1633355a8f7ec5c66bf/pluggy-1.6.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/9b/4d/b9add7c84060d4c1906abe9a7e5359f2a60f7a9a4f67268b2766673427d8/pyee-13.0.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/3b/ab/b3226f0bd7cdcf710fbede2b3548584366da3b19b5021e74f5bde2a8fa3f/pytest-9.0.2-py3-none-any.whl
@@ -2162,8 +2162,8 @@ packages:
   timestamp: 1733208220327
 - pypi: ./
   name: examplepyapp
-  version: 1.1.0.dev94
-  sha256: 5e219d8921bdf2fda28802d7a881420a1885e2d8bccdfbeddbae895acf0953ef
+  version: 0.2.0.dev290
+  sha256: aeb7e9da091e6d84cf074603a4dd5575ec7e698a72297ace72c1958ff9749e90
   requires_dist:
   - bm3d-streak-removal>=0.2.0,<0.3
   - numpy>=2.2,<3
@@ -2176,7 +2176,6 @@ packages:
   - sphinx-rtd-theme ; extra == 'docs'
   - versioningit ; extra == 'docs'
   requires_python: '>=3.10'
-  editable: true
 - conda: https://conda.anaconda.org/conda-forge/noarch/exceptiongroup-1.3.1-pyhd8ed1ab_0.conda
   sha256: ee6cf346d017d954255bbcbdb424cddea4d14e4ed7e9813e429db1d795d01144
   md5: 8e662bd460bda79b1ea39194e3c4c9ab
@@ -2210,16 +2209,14 @@ packages:
   - pkg:pypi/executing
   size: 30753
   timestamp: 1756729456476
-- conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.20.0-pyhd8ed1ab_0.conda
-  sha256: 19025a4078ff3940d97eb0da29983d5e0deac9c3e09b0eabf897daeaf9d1114e
-  md5: 66b8b26023b8efdf8fcb23bac4b6325d
+- conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.20.1-pyhd8ed1ab_0.conda
+  sha256: 8028582d956ab76424f6845fa1bdf5cb3e629477dd44157ca30d45e06d8a9c7c
+  md5: 81a651287d3000eb12f0860ade0a1b41
   depends:
   - python >=3.10
   license: Unlicense
-  purls:
-  - pkg:pypi/filelock
-  size: 17976
-  timestamp: 1759948208140
+  size: 18609
+  timestamp: 1765846639623
 - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2
   sha256: 58d7f40d2940dd0a8aa28651239adbf5613254df0f75789919c4e6762054403b
   md5: 0c96522c6bdaed4b1566d11387caaf45
@@ -5785,18 +5782,18 @@ packages:
   - pkg:pypi/platformdirs
   size: 23625
   timestamp: 1759953252315
-- pypi: https://files.pythonhosted.org/packages/e4/76/6d409e37e82cdd5dda3df1ab958130ae32b46e42458bd4fc93d7eb8749cb/playwright-1.56.0-py3-none-manylinux1_x86_64.whl
+- pypi: https://files.pythonhosted.org/packages/56/61/3a803cb5ae0321715bfd5247ea871d25b32c8f372aeb70550a90c5f586df/playwright-1.57.0-py3-none-manylinux1_x86_64.whl
   name: playwright
-  version: 1.56.0
-  sha256: 404be089b49d94bc4c1fe0dfb07664bda5ffe87789034a03bffb884489bdfb5c
+  version: 1.57.0
+  sha256: 284ed5a706b7c389a06caa431b2f0ba9ac4130113c3a779767dda758c2497bb1
   requires_dist:
   - pyee>=13,<14
   - greenlet>=3.1.1,<4.0.0
   requires_python: '>=3.9'
-- pypi: https://files.pythonhosted.org/packages/ef/95/347eef596d8778fb53590dc326c344d427fa19ba3d42b646fce2a4572eb3/playwright-1.56.0-py3-none-macosx_11_0_arm64.whl
+- pypi: https://files.pythonhosted.org/packages/8b/04/ef95b67e1ff59c080b2effd1a9a96984d6953f667c91dfe9d77c838fc956/playwright-1.57.0-py3-none-macosx_11_0_arm64.whl
   name: playwright
-  version: 1.56.0
-  sha256: b228b3395212b9472a4ee5f1afe40d376eef9568eb039fcb3e563de8f4f4657b
+  version: 1.57.0
+  sha256: a4a9d65027bce48eeba842408bcc1421502dfd7e41e28d207e94260fa93ca67e
   requires_dist:
   - pyee>=13,<14
   - greenlet>=3.1.1,<4.0.0
diff --git a/pyproject.toml b/pyproject.toml
index 62459e4..6e98728 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -108,9 +108,10 @@ qt = "*"
 qtpy = "*"
 pyqt = "*"
 # pip-audit
-h2 = ">=4.3.0"      # Known vulnerability in <4.3.0
+h2 = ">=4.3.0"        # Known vulnerability in <4.3.0
 brotli = ">=1.2.0"
-urllib3 = ">=2.6.0" # Known vulnerability in <2.6.0
+urllib3 = ">=2.6.0"   # Known vulnerability in <2.6.0
+filelock = ">=3.20.1" # Known vulnerability in <3.20.1
 
 [tool.pixi.pypi-dependencies]
 # PyPI dependencies, including this package to allow local editable installs

From a407075e9c0d12c000b4429db91d1efe8ca83f8e Mon Sep 17 00:00:00 2001
From: Chen Zhang <zhangc@ornl.gov>
Date: Mon, 22 Dec 2025 15:38:16 -0500
Subject: [PATCH 3/3] Update examplepyapp version and adjust pixi build backend
 version constraint

---
 pixi.lock      | 4 ++--
 pyproject.toml | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/pixi.lock b/pixi.lock
index 137854d..e6f023d 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -2162,8 +2162,8 @@ packages:
   timestamp: 1733208220327
 - pypi: ./
   name: examplepyapp
-  version: 0.2.0.dev290
-  sha256: aeb7e9da091e6d84cf074603a4dd5575ec7e698a72297ace72c1958ff9749e90
+  version: 0.2.0.dev291
+  sha256: c489a6c027608695b0f8e3f54996b76e046b775b65aa6db2c502b1925c17a13a
   requires_dist:
   - bm3d-streak-removal>=0.2.0,<0.3
   - numpy>=2.2,<3
diff --git a/pyproject.toml b/pyproject.toml
index 6e98728..ee39e8e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -135,7 +135,7 @@ name = "examplepyapp"
 version = "0.0.0"     # placeholder, overwritten by sync-version
 
 [tool.pixi.package.build]
-backend = { name = "pixi-build-python", version = "0.1.*" }
+backend = { name = "pixi-build-python", version = "*" }
 
 # Environments and Features