From 8e9bbf1bee848b8912590cc85c265a4599f6b62e Mon Sep 17 00:00:00 2001
From: ym3141 <yitongma7@gmail.com>
Date: Tue, 20 May 2025 23:43:47 -0700
Subject: [PATCH 1/4] relax the requirement of onnxruntime to <=1.16.3, making
 it compatible with CentOS 7

---
 pyproject.toml   | 2 +-
 requirements.txt | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 7d37db1..b66f4ba 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -18,7 +18,7 @@ python = "^3.9"
 biopython = "^1.83"
 ipywidgets = "^7.0.0"
 numpy = "<2.0.0"
-onnxruntime = "^1.17.3"
+onnxruntime = "^1.16.3"
 pandas = "^2.0.0"
 python_codon_tables = "^0.1.12"
 pytorch_lightning = "^2.2.1"
diff --git a/requirements.txt b/requirements.txt
index efabc68..3130661 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -2,7 +2,7 @@ biopython>=1.83,<2.0
 CAI-PyPI>=2.0.1,<3.0
 ipywidgets>=7.0.0,<10.0
 numpy>=1.26.4,<2.0
-onnxruntime>=1.17.3,<3.0
+onnxruntime>=1.16.3,<3.0
 pandas>=2.0.0,<3.0
 python_codon_tables>=0.1.12,<1.0
 pytorch_lightning>=2.2.1,<3.0

From dccbf1eb2cb537981d2814d0bbe3f6ba997a5ded Mon Sep 17 00:00:00 2001
From: Adibvafa Fallahpour <90617686+Adibvafa@users.noreply.github.com>
Date: Wed, 21 May 2025 16:31:47 -0400
Subject: [PATCH 2/4] Update pyproject.toml

---
 pyproject.toml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index b66f4ba..9346183 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -51,3 +51,9 @@ quote-style = "double"
 indent-style = "space"
 skip-magic-trailing-comma = false
 line-ending = "auto"
+
+[tool.coverage.run]
+omit = [
+    # omit pytorch-generated files in /tmp
+    "/tmp/*",
+]

From 8cc8d49621bc70f524cc64e6e27e2215f9db8231 Mon Sep 17 00:00:00 2001
From: Adibvafa Fallahpour <90617686+Adibvafa@users.noreply.github.com>
Date: Wed, 21 May 2025 16:38:05 -0400
Subject: [PATCH 3/4] Update pyproject.toml

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 9346183..9b5a2f3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -31,7 +31,7 @@ transformers = "^4.40.0"
 CAI-PyPI = "^2.0.1"
 
 [tool.poetry.dev-dependencies]
-coverage = "^7.0"
+coverage = {version = "^7.0", extras = ["toml"]}
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]

From 44e65b7092b7ebc6666c766556873a9ff8f75037 Mon Sep 17 00:00:00 2001
From: Adibvafa Fallahpour <90617686+Adibvafa@users.noreply.github.com>
Date: Wed, 21 May 2025 16:47:19 -0400
Subject: [PATCH 4/4] Update ci.yml

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 26201c6..6b6ea1d 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -21,7 +21,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install -r requirements.txt
-        pip install coverage
+        pip install "coverage[toml]"
 
     - name: Run tests with coverage
       run: |