From 0b22ce346ddcec2b44b76889c9930e187599e01e Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Tue, 25 Jun 2024 10:26:53 -0700
Subject: [PATCH 01/42] bump actions versions

---
 .github/workflows/python_package.yaml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/python_package.yaml b/.github/workflows/python_package.yaml
index c230f408..da1aa724 100644
--- a/.github/workflows/python_package.yaml
+++ b/.github/workflows/python_package.yaml
@@ -13,9 +13,9 @@ jobs:
         os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
         
@@ -56,13 +56,13 @@ jobs:
 
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
     - name: Cache pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         # This path is specific to Ubuntu
         path: ~/.cache/pip

From 1306f4809e3286545c2d0b967c34444861e7b971 Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Tue, 25 Jun 2024 10:53:19 -0700
Subject: [PATCH 02/42] Update ossar-analysis.yml

---
 .github/workflows/ossar-analysis.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ossar-analysis.yml b/.github/workflows/ossar-analysis.yml
index 2e0dfae1..b3a84140 100644
--- a/.github/workflows/ossar-analysis.yml
+++ b/.github/workflows/ossar-analysis.yml
@@ -16,7 +16,7 @@ jobs:
     steps:
       # Checkout your code repository to scan
     - name: Checkout repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@main
       with:
         # We must fetch at least the immediate parents so that if this is
         # a pull request then we can checkout the head.
@@ -29,17 +29,17 @@ jobs:
 
       # Install dotnet, used by OSSAR
     - name: Install .NET
-      uses: actions/setup-dotnet@v1
+      uses: actions/setup-dotnet@main
       with:
         dotnet-version: '6.0.x'
 
       # Run open source static analysis tools
     - name: Run OSSAR
-      uses: github/ossar-action@v1
+      uses: github/ossar-action@main
       id: ossar
 
       # Upload results to the Security tab
     - name: Upload OSSAR results
-      uses: github/codeql-action/upload-sarif@v1
+      uses: github/codeql-action/upload-sarif@main
       with:
         sarif_file: ${{ steps.ossar.outputs.sarifFile }}

From 929a511454a62f39c8ab0f96d03726fd6138a414 Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Tue, 25 Jun 2024 10:55:57 -0700
Subject: [PATCH 03/42] Update python_package.yaml

---
 .github/workflows/python_package.yaml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/python_package.yaml b/.github/workflows/python_package.yaml
index da1aa724..da34ec7a 100644
--- a/.github/workflows/python_package.yaml
+++ b/.github/workflows/python_package.yaml
@@ -13,9 +13,9 @@ jobs:
         os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@main
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@main
       with:
         python-version: ${{ matrix.python-version }}
         
@@ -56,13 +56,13 @@ jobs:
 
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@main
     - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@main
       with:
         python-version: '3.x'
     - name: Cache pip
-      uses: actions/cache@v4
+      uses: actions/cache@main
       with:
         # This path is specific to Ubuntu
         path: ~/.cache/pip

From e9efd98e3a7a8b361465f460f4e1061306650ea9 Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Tue, 25 Jun 2024 11:05:18 -0700
Subject: [PATCH 04/42] make pluggy an explicit test dependency

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

diff --git a/.github/workflows/python_package.yaml b/.github/workflows/python_package.yaml
index da34ec7a..36d51ac9 100644
--- a/.github/workflows/python_package.yaml
+++ b/.github/workflows/python_package.yaml
@@ -29,7 +29,7 @@ jobs:
     - name: Install test dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install setuptools wheel
+        pip install setuptools wheel pluggy
         pip install flake8 pytest pytest-cov coveralls
     - name: Install package requirements
       run: pip install -r requirements.txt

From 599653fe132addb71d05c9144fda9e9f8c26dfba Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Mon, 30 Dec 2024 15:56:39 -0800
Subject: [PATCH 05/42] remove pluggy

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

diff --git a/.github/workflows/python_package.yaml b/.github/workflows/python_package.yaml
index 36d51ac9..da34ec7a 100644
--- a/.github/workflows/python_package.yaml
+++ b/.github/workflows/python_package.yaml
@@ -29,7 +29,7 @@ jobs:
     - name: Install test dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install setuptools wheel pluggy
+        pip install setuptools wheel
         pip install flake8 pytest pytest-cov coveralls
     - name: Install package requirements
       run: pip install -r requirements.txt

From 7ab846e850ba24bc2ad331d656aa2c313274f975 Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Mon, 30 Dec 2024 16:00:04 -0800
Subject: [PATCH 06/42] revert previous

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

diff --git a/.github/workflows/python_package.yaml b/.github/workflows/python_package.yaml
index da34ec7a..36d51ac9 100644
--- a/.github/workflows/python_package.yaml
+++ b/.github/workflows/python_package.yaml
@@ -29,7 +29,7 @@ jobs:
     - name: Install test dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install setuptools wheel
+        pip install setuptools wheel pluggy
         pip install flake8 pytest pytest-cov coveralls
     - name: Install package requirements
       run: pip install -r requirements.txt

From d883070a56c74832d929361c2e439257691958fb Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Mon, 30 Dec 2024 16:03:18 -0800
Subject: [PATCH 07/42] update pytest call

following https://stackoverflow.com/a/75768202
---
 .github/workflows/python_package.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/python_package.yaml b/.github/workflows/python_package.yaml
index 36d51ac9..3e7cde65 100644
--- a/.github/workflows/python_package.yaml
+++ b/.github/workflows/python_package.yaml
@@ -43,7 +43,7 @@ jobs:
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 src tests setup.py --exclude=__init__.py --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
-      run: pytest --cov=src tests/
+      run: python -m pytest --cov=src tests/
       
     - name: Coveralls
       env:

From 943cdaf6ac9f903be1ad3db74917c57e3003b24e Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Mon, 30 Dec 2024 16:10:48 -0800
Subject: [PATCH 08/42] add pytest-metadata

per https://stackoverflow.com/a/47921369
---
 .github/workflows/python_package.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/python_package.yaml b/.github/workflows/python_package.yaml
index 3e7cde65..da903bd6 100644
--- a/.github/workflows/python_package.yaml
+++ b/.github/workflows/python_package.yaml
@@ -30,7 +30,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install setuptools wheel pluggy
-        pip install flake8 pytest pytest-cov coveralls
+        pip install flake8 pytest pytest-metadata pytest-cov coveralls
     - name: Install package requirements
       run: pip install -r requirements.txt
     - name: Install package

From cfaf2ec59048bbed403a4335c6fae7fc652f115c Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Mon, 30 Dec 2024 16:13:51 -0800
Subject: [PATCH 09/42] add pythonpath echo

---
 .github/workflows/python_package.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/python_package.yaml b/.github/workflows/python_package.yaml
index da903bd6..db92c118 100644
--- a/.github/workflows/python_package.yaml
+++ b/.github/workflows/python_package.yaml
@@ -31,6 +31,7 @@ jobs:
         python -m pip install --upgrade pip
         pip install setuptools wheel pluggy
         pip install flake8 pytest pytest-metadata pytest-cov coveralls
+        echo "PYTHONPATH=$PYTHONPATH" >> $GITHUB_ENV
     - name: Install package requirements
       run: pip install -r requirements.txt
     - name: Install package

From 9b624884483c27d6b56382db8d69dc488fbea4d0 Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Mon, 30 Dec 2024 16:17:21 -0800
Subject: [PATCH 10/42] force upgrade pluggy

---
 .github/workflows/python_package.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/python_package.yaml b/.github/workflows/python_package.yaml
index db92c118..f93963e4 100644
--- a/.github/workflows/python_package.yaml
+++ b/.github/workflows/python_package.yaml
@@ -29,9 +29,9 @@ jobs:
     - name: Install test dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install setuptools wheel pluggy
+        pip install setuptools wheel
         pip install flake8 pytest pytest-metadata pytest-cov coveralls
-        echo "PYTHONPATH=$PYTHONPATH" >> $GITHUB_ENV
+        pip install --upgrade pluggy
     - name: Install package requirements
       run: pip install -r requirements.txt
     - name: Install package

From 46d8b4a9421f043981e07203fe9a31f578428ecf Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Mon, 30 Dec 2024 16:22:46 -0800
Subject: [PATCH 11/42] downgrade pytest

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

diff --git a/.github/workflows/python_package.yaml b/.github/workflows/python_package.yaml
index f93963e4..d822406b 100644
--- a/.github/workflows/python_package.yaml
+++ b/.github/workflows/python_package.yaml
@@ -30,7 +30,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install setuptools wheel
-        pip install flake8 pytest pytest-metadata pytest-cov coveralls
+        pip install flake8 pytest==3.2.5 pytest-cov coveralls
         pip install --upgrade pluggy
     - name: Install package requirements
       run: pip install -r requirements.txt

From f9f7335a7491b1574d0d1395db1fb1c43d26a07c Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Mon, 30 Dec 2024 16:26:45 -0800
Subject: [PATCH 12/42] set pytest to 7.1.3

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

diff --git a/.github/workflows/python_package.yaml b/.github/workflows/python_package.yaml
index d822406b..e6fab376 100644
--- a/.github/workflows/python_package.yaml
+++ b/.github/workflows/python_package.yaml
@@ -30,7 +30,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install setuptools wheel
-        pip install flake8 pytest==3.2.5 pytest-cov coveralls
+        pip install flake8 pytest==7.1.3 pytest-cov coveralls
         pip install --upgrade pluggy
     - name: Install package requirements
       run: pip install -r requirements.txt

From aba74d26d46b216ffdaa73ca6cf6a033a74b6ce3 Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Mon, 30 Dec 2024 16:33:23 -0800
Subject: [PATCH 13/42] downgrade pytest to 6.2.5

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

diff --git a/.github/workflows/python_package.yaml b/.github/workflows/python_package.yaml
index e6fab376..6b17f42e 100644
--- a/.github/workflows/python_package.yaml
+++ b/.github/workflows/python_package.yaml
@@ -30,7 +30,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install setuptools wheel
-        pip install flake8 pytest==7.1.3 pytest-cov coveralls
+        pip install flake8 pytest==6.2.5 pytest-cov coveralls
         pip install --upgrade pluggy
     - name: Install package requirements
       run: pip install -r requirements.txt

From c55afeac06141426b3d97453c1b5b09c5827d8f4 Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Mon, 30 Dec 2024 16:47:20 -0800
Subject: [PATCH 14/42] use fixed numpy version

---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 8235f94a..351932d1 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -3,7 +3,7 @@ matplotlib>=3.7.3
 pybind11==2.4.3
 pygmsh==7.1.17
 MeshPy==2022.1.3
-numpy>=1.24.4
+numpy==1.24.4
 pyquaternion==0.9.5
 pyvoro-mmalahe==1.3.4
 scipy>=1.10.1

From 8c08d2baf659e0d5ddb7e5b025d199c2216f6fec Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Mon, 30 Dec 2024 16:49:33 -0800
Subject: [PATCH 15/42] avoid numpy 2.0

---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 351932d1..901c77c0 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -3,7 +3,7 @@ matplotlib>=3.7.3
 pybind11==2.4.3
 pygmsh==7.1.17
 MeshPy==2022.1.3
-numpy==1.24.4
+numpy>=1.24.4,<2.0
 pyquaternion==0.9.5
 pyvoro-mmalahe==1.3.4
 scipy>=1.10.1

From 5baa492ef9c8ed7d6b44a117a951a71c17c87fac Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Mon, 30 Dec 2024 16:53:49 -0800
Subject: [PATCH 16/42] revert other attempts to fix

---
 .github/workflows/python_package.yaml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/python_package.yaml b/.github/workflows/python_package.yaml
index 6b17f42e..da34ec7a 100644
--- a/.github/workflows/python_package.yaml
+++ b/.github/workflows/python_package.yaml
@@ -30,8 +30,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install setuptools wheel
-        pip install flake8 pytest==6.2.5 pytest-cov coveralls
-        pip install --upgrade pluggy
+        pip install flake8 pytest pytest-cov coveralls
     - name: Install package requirements
       run: pip install -r requirements.txt
     - name: Install package
@@ -44,7 +43,7 @@ jobs:
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 src tests setup.py --exclude=__init__.py --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
-      run: python -m pytest --cov=src tests/
+      run: pytest --cov=src tests/
       
     - name: Coveralls
       env:

From c7329ee25a3edc288cc31bad57524212b2624743 Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Mon, 30 Dec 2024 16:55:46 -0800
Subject: [PATCH 17/42] added python -m back

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

diff --git a/.github/workflows/python_package.yaml b/.github/workflows/python_package.yaml
index da34ec7a..e9323757 100644
--- a/.github/workflows/python_package.yaml
+++ b/.github/workflows/python_package.yaml
@@ -43,7 +43,7 @@ jobs:
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 src tests setup.py --exclude=__init__.py --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
-      run: pytest --cov=src tests/
+      run: python -m pytest --cov=src tests/
       
     - name: Coveralls
       env:

From 7ac7d46ae1aaafe7f54c1b20badbd05fb096c1bb Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Mon, 30 Dec 2024 16:57:34 -0800
Subject: [PATCH 18/42] add pluggy upgrade

---
 .github/workflows/python_package.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/python_package.yaml b/.github/workflows/python_package.yaml
index e9323757..915b0cee 100644
--- a/.github/workflows/python_package.yaml
+++ b/.github/workflows/python_package.yaml
@@ -31,6 +31,7 @@ jobs:
         python -m pip install --upgrade pip
         pip install setuptools wheel
         pip install flake8 pytest pytest-cov coveralls
+        pip install --upgrade pluggy
     - name: Install package requirements
       run: pip install -r requirements.txt
     - name: Install package

From 15d1b3265788ad33683baed880e97ff4b5a72c54 Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Mon, 30 Dec 2024 16:59:25 -0800
Subject: [PATCH 19/42] specify pytest version

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

diff --git a/.github/workflows/python_package.yaml b/.github/workflows/python_package.yaml
index 915b0cee..6b17f42e 100644
--- a/.github/workflows/python_package.yaml
+++ b/.github/workflows/python_package.yaml
@@ -30,7 +30,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install setuptools wheel
-        pip install flake8 pytest pytest-cov coveralls
+        pip install flake8 pytest==6.2.5 pytest-cov coveralls
         pip install --upgrade pluggy
     - name: Install package requirements
       run: pip install -r requirements.txt

From 07a88329ad9ff4bfce7b4bd6be6ffd918c0fa80c Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Mon, 30 Dec 2024 17:02:15 -0800
Subject: [PATCH 20/42] remove pluggy upgrade

---
 .github/workflows/python_package.yaml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/python_package.yaml b/.github/workflows/python_package.yaml
index 6b17f42e..4849d845 100644
--- a/.github/workflows/python_package.yaml
+++ b/.github/workflows/python_package.yaml
@@ -31,7 +31,6 @@ jobs:
         python -m pip install --upgrade pip
         pip install setuptools wheel
         pip install flake8 pytest==6.2.5 pytest-cov coveralls
-        pip install --upgrade pluggy
     - name: Install package requirements
       run: pip install -r requirements.txt
     - name: Install package

From 7281aebf2832a22ad2793c778acaa8c7a6631b65 Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Mon, 30 Dec 2024 17:05:59 -0800
Subject: [PATCH 21/42] remove python -m from pytest call

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

diff --git a/.github/workflows/python_package.yaml b/.github/workflows/python_package.yaml
index 4849d845..af2f042b 100644
--- a/.github/workflows/python_package.yaml
+++ b/.github/workflows/python_package.yaml
@@ -43,7 +43,7 @@ jobs:
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 src tests setup.py --exclude=__init__.py --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
-      run: python -m pytest --cov=src tests/
+      run: pytest --cov=src tests/
       
     - name: Coveralls
       env:

From e70a935891d63c3e5201a2be6772138819818d06 Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Mon, 30 Dec 2024 17:09:04 -0800
Subject: [PATCH 22/42] try later pytest versions

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

diff --git a/.github/workflows/python_package.yaml b/.github/workflows/python_package.yaml
index af2f042b..4face8fd 100644
--- a/.github/workflows/python_package.yaml
+++ b/.github/workflows/python_package.yaml
@@ -30,7 +30,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install setuptools wheel
-        pip install flake8 pytest==6.2.5 pytest-cov coveralls
+        pip install flake8 pytest<8.0 pytest-cov coveralls
     - name: Install package requirements
       run: pip install -r requirements.txt
     - name: Install package

From cbc7d645e6abcb75e5b7610211b069c0e3a4c014 Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Mon, 30 Dec 2024 17:10:16 -0800
Subject: [PATCH 23/42] try <7 for pytest version

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

diff --git a/.github/workflows/python_package.yaml b/.github/workflows/python_package.yaml
index 4face8fd..8499619d 100644
--- a/.github/workflows/python_package.yaml
+++ b/.github/workflows/python_package.yaml
@@ -30,7 +30,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install setuptools wheel
-        pip install flake8 pytest<8.0 pytest-cov coveralls
+        pip install flake8 pytest<7.0 pytest-cov coveralls
     - name: Install package requirements
       run: pip install -r requirements.txt
     - name: Install package

From 2336ce67954b228ad49f6480357c25a2890101f2 Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Mon, 30 Dec 2024 17:14:21 -0800
Subject: [PATCH 24/42] lock down pytest version

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

diff --git a/.github/workflows/python_package.yaml b/.github/workflows/python_package.yaml
index 8499619d..af2f042b 100644
--- a/.github/workflows/python_package.yaml
+++ b/.github/workflows/python_package.yaml
@@ -30,7 +30,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install setuptools wheel
-        pip install flake8 pytest<7.0 pytest-cov coveralls
+        pip install flake8 pytest==6.2.5 pytest-cov coveralls
     - name: Install package requirements
       run: pip install -r requirements.txt
     - name: Install package

From bca22cba06246c394f6b1df815d7bd1c87a0d665 Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Mon, 30 Dec 2024 17:17:37 -0800
Subject: [PATCH 25/42] update python versions

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

diff --git a/.github/workflows/python_package.yaml b/.github/workflows/python_package.yaml
index af2f042b..deca8fdc 100644
--- a/.github/workflows/python_package.yaml
+++ b/.github/workflows/python_package.yaml
@@ -9,7 +9,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: [3.8, 3.9, '3.10', '3.11', '3.12']
+        python-version: [3.9, '3.10', '3.11', '3.12', '3.13']
         os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
 
     steps:

From 786ecd2fb4adec091fe3e2cbed782bc5173cf6e7 Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Mon, 30 Dec 2024 17:22:42 -0800
Subject: [PATCH 26/42] remove 3.13 due to pyvoro build fail

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

diff --git a/.github/workflows/python_package.yaml b/.github/workflows/python_package.yaml
index deca8fdc..b29b8bf6 100644
--- a/.github/workflows/python_package.yaml
+++ b/.github/workflows/python_package.yaml
@@ -9,7 +9,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: [3.9, '3.10', '3.11', '3.12', '3.13']
+        python-version: [3.9, '3.10', '3.11', '3.12']
         os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
 
     steps:

From 3cc40273952f0b14180602ea5a7707752d923455 Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Mon, 30 Dec 2024 17:24:20 -0800
Subject: [PATCH 27/42] remove 3.8 from supported versions

---
 setup.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/setup.py b/setup.py
index e6fcec9a..2aa562c0 100644
--- a/setup.py
+++ b/setup.py
@@ -57,7 +57,6 @@ def find_version(*fname):
         'Operating System :: MacOS :: MacOS X',
         'Operating System :: Microsoft :: Windows',
         'Operating System :: POSIX :: Linux',
-        'Programming Language :: Python :: 3.8',
         'Programming Language :: Python :: 3.9',
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',

From 2bd767f6fdcfd69e9e7511ca5af6112f476dd0c4 Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Mon, 30 Dec 2024 17:46:30 -0800
Subject: [PATCH 28/42] setuptools version snyk recommendation

---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 901c77c0..8fa8e4e1 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -7,7 +7,7 @@ numpy>=1.24.4,<2.0
 pyquaternion==0.9.5
 pyvoro-mmalahe==1.3.4
 scipy>=1.10.1
-setuptools>=65.5.1 
+setuptools>=70.0.0 
 xmltodict==0.12.0
 tox==3.14.0
 lsq-ellipse==2.0.1

From 0eb10f8810d23742cb484d843e36f8e0cd9fe86d Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Mon, 30 Dec 2024 17:49:57 -0800
Subject: [PATCH 29/42] add zipp from snyk

---
 requirements.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/requirements.txt b/requirements.txt
index 8fa8e4e1..8298e352 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -11,3 +11,4 @@ setuptools>=70.0.0
 xmltodict==0.12.0
 tox==3.14.0
 lsq-ellipse==2.0.1
+zipp>=3.19.1 # not directly required, pinned by Snyk to avoid a vulnerability

From ef7287ae64c6f4e842de33d2f455802e4a919107 Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Mon, 30 Dec 2024 18:03:34 -0800
Subject: [PATCH 30/42] update sphinx version

---
 docs/requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/requirements.txt b/docs/requirements.txt
index b701f490..56302ad8 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -3,5 +3,5 @@ matplotlib>=3.7.3
 numpy>=1.24.4
 pybind11==2.4.3
 setuptools>=65.5.1 
-sphinx==4.2.0
+sphinx>=5.0
 sphinx-gallery==0.8.1

From b4f090740e896df8b3a4c5c333935ccb58bf2be1 Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Mon, 30 Dec 2024 18:09:01 -0800
Subject: [PATCH 31/42] pin to last v5 of sphinx

---
 docs/requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/requirements.txt b/docs/requirements.txt
index 56302ad8..f81c7d0e 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -3,5 +3,5 @@ matplotlib>=3.7.3
 numpy>=1.24.4
 pybind11==2.4.3
 setuptools>=65.5.1 
-sphinx>=5.0
+sphinx==5.3.0
 sphinx-gallery==0.8.1

From 6c7cc1161ba620b8d1093f1f838e337730ea7a24 Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Mon, 30 Dec 2024 18:22:04 -0800
Subject: [PATCH 32/42] synk fix for docs with zipp

---
 docs/requirements.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/requirements.txt b/docs/requirements.txt
index f81c7d0e..3b462f62 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -5,3 +5,4 @@ pybind11==2.4.3
 setuptools>=65.5.1 
 sphinx==5.3.0
 sphinx-gallery==0.8.1
+zipp==3.19.1

From a9042fcc064372ab002d58da940abfc6e4b89bdc Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Mon, 30 Dec 2024 18:25:49 -0800
Subject: [PATCH 33/42] or higher on zipp

---
 docs/requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/requirements.txt b/docs/requirements.txt
index 3b462f62..03b06e71 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -5,4 +5,4 @@ pybind11==2.4.3
 setuptools>=65.5.1 
 sphinx==5.3.0
 sphinx-gallery==0.8.1
-zipp==3.19.1
+zipp>=3.19.1 # not directly required, pinned by Snyk to avoid a vulnerability

From 0a17500dade3bbdf898164b40ffb064a269d3444 Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Mon, 30 Dec 2024 18:27:47 -0800
Subject: [PATCH 34/42] snyk setuptools version bump

---
 docs/requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/requirements.txt b/docs/requirements.txt
index 03b06e71..81fd030e 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -2,7 +2,7 @@ gmsh==4.11.1
 matplotlib>=3.7.3
 numpy>=1.24.4
 pybind11==2.4.3
-setuptools>=65.5.1 
+setuptools>=70.0.0
 sphinx==5.3.0
 sphinx-gallery==0.8.1
 zipp>=3.19.1 # not directly required, pinned by Snyk to avoid a vulnerability

From be31ce3ccef386b165cb184fa2e754e357dff66a Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Mon, 30 Dec 2024 18:37:03 -0800
Subject: [PATCH 35/42] add urllib to docs requirements per snyk

---
 docs/requirements.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/requirements.txt b/docs/requirements.txt
index 81fd030e..6d8c9db9 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -5,4 +5,5 @@ pybind11==2.4.3
 setuptools>=70.0.0
 sphinx==5.3.0
 sphinx-gallery==0.8.1
+urllib3>=2.2.2 # not directly required, pinned by Snyk to avoid a vulnerability
 zipp>=3.19.1 # not directly required, pinned by Snyk to avoid a vulnerability

From f54ff0e8cfaff1ab9bb739a3e3e254bec2fbd90d Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Mon, 30 Dec 2024 18:52:44 -0800
Subject: [PATCH 36/42] use latest versions for actions

---
 .github/workflows/documentation.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/documentation.yaml b/.github/workflows/documentation.yaml
index 75145c71..4b3deebb 100644
--- a/.github/workflows/documentation.yaml
+++ b/.github/workflows/documentation.yaml
@@ -13,9 +13,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Checkout
-      uses: actions/checkout@v3
+      uses: actions/checkout@main
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@main
       with:
         python-version: '3.10'
     - name: Setup Linux Environment
@@ -59,7 +59,7 @@ jobs:
         cd -
         
     - name: Upload artifact
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@main
       with:
         name: microstructpy_${{ matrix.doc-type }}_documentation
         path: ${{ env.art_path }} 

From 81acde2ad55f4cfe49e3f95e41b606c8fd24f8c2 Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Mon, 30 Dec 2024 19:09:27 -0800
Subject: [PATCH 37/42] rename cumtrapz

---
 src/microstructpy/examples/grain_neighborhoods.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/microstructpy/examples/grain_neighborhoods.py b/src/microstructpy/examples/grain_neighborhoods.py
index 9c2ccfa3..b84d26c5 100644
--- a/src/microstructpy/examples/grain_neighborhoods.py
+++ b/src/microstructpy/examples/grain_neighborhoods.py
@@ -44,7 +44,7 @@
 dx = np.insert(np.diff(x_perim), 0, 0)
 dy = np.insert(np.diff(y_perim), 0, 0)
 ds = np.sqrt(dx * dx + dy * dy)
-arc_len = scipy.integrate.cumtrapz(ds, x=t_perim, initial=0)
+arc_len = scipy.integrate.cumulative_trapezoid(ds, x=t_perim, initial=0)
 eq_spaced = arc_len[-1] * np.arange(n) / n
 x_pts = np.interp(eq_spaced, arc_len, x_perim)
 y_pts = np.interp(eq_spaced, arc_len, y_perim)

From 1863b44ee345c9db0456836c246e426b8e84de82 Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Mon, 30 Dec 2024 19:11:23 -0800
Subject: [PATCH 38/42] Update requirements.txt for scipy cumtrapz name change

---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 8298e352..72cd2004 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -6,7 +6,7 @@ MeshPy==2022.1.3
 numpy>=1.24.4,<2.0
 pyquaternion==0.9.5
 pyvoro-mmalahe==1.3.4
-scipy>=1.10.1
+scipy>=1.15.0
 setuptools>=70.0.0 
 xmltodict==0.12.0
 tox==3.14.0

From d191fd555112966e5904c57e2f80a9570fdadd72 Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Mon, 30 Dec 2024 19:16:14 -0800
Subject: [PATCH 39/42] revert previous

---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 72cd2004..8298e352 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -6,7 +6,7 @@ MeshPy==2022.1.3
 numpy>=1.24.4,<2.0
 pyquaternion==0.9.5
 pyvoro-mmalahe==1.3.4
-scipy>=1.15.0
+scipy>=1.10.1
 setuptools>=70.0.0 
 xmltodict==0.12.0
 tox==3.14.0

From 82003dbba6fe7b34ee87fd001776db5ca5fbc575 Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Tue, 31 Dec 2024 09:18:45 -0800
Subject: [PATCH 40/42] try to fix missing reference warning

---
 src/microstructpy/geometry/ellipse.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/microstructpy/geometry/ellipse.py b/src/microstructpy/geometry/ellipse.py
index 364d9c70..05013765 100644
--- a/src/microstructpy/geometry/ellipse.py
+++ b/src/microstructpy/geometry/ellipse.py
@@ -182,7 +182,7 @@ def best_fit(self, points):
             points (list or numpy.ndarray): An Nx2 list of points to fit.
 
         Returns:
-            .Ellipse: An instance of the class that best fits the points.
+            Ellipse: An instance of the class that best fits the points.
 
         .. _`least-squares-ellipse-fitting`: https://github.com/bdhammel/least-squares-ellipse-fitting
 

From 5ff337e9f6bbfc4cc50e79904f8b620d19a69636 Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Tue, 31 Dec 2024 09:38:20 -0800
Subject: [PATCH 41/42] add requests to docs reqs per snyk

---
 docs/requirements.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/requirements.txt b/docs/requirements.txt
index 6d8c9db9..86459fa1 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -2,6 +2,7 @@ gmsh==4.11.1
 matplotlib>=3.7.3
 numpy>=1.24.4
 pybind11==2.4.3
+requests>=2.32.0 # not directly required, pinned by Snyk to avoid a vulnerability
 setuptools>=70.0.0
 sphinx==5.3.0
 sphinx-gallery==0.8.1

From 7a0a377767c9da31292dc669b584df374ad0d19a Mon Sep 17 00:00:00 2001
From: Kip Hart <41959581+kip-hart@users.noreply.github.com>
Date: Tue, 31 Dec 2024 09:50:17 -0800
Subject: [PATCH 42/42] fix TOC depth for API

---
 docs/source/api/index.rst | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/source/api/index.rst b/docs/source/api/index.rst
index 69018f94..71989d83 100644
--- a/docs/source/api/index.rst
+++ b/docs/source/api/index.rst
@@ -4,6 +4,7 @@ API
 ===
 
 .. toctree::
+    :maxdepth: 2
 
     cli
     geometry/index