From bee8c870ed42aadb9d61dbcf44250bb9336d641c Mon Sep 17 00:00:00 2001
From: Bob Myhill <myhill.bob@gmail.com>
Date: Sun, 6 Oct 2024 17:37:22 +0100
Subject: [PATCH 1/2] replace deprecated/modified functions

---
 burnman/classes/material.py | 3 ++-
 burnman/classes/solution.py | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/burnman/classes/material.py b/burnman/classes/material.py
index 3e7c36ac..462ea7de 100644
--- a/burnman/classes/material.py
+++ b/burnman/classes/material.py
@@ -293,9 +293,10 @@ def evaluate(self, vars_list, pressures, temperatures, molar_fractions=None):
 
         assert pressures.shape == temperatures.shape
 
+        first_index = list(np.ndenumerate(temperatures))[0][0]
         if molar_fractions is not None:
             molar_fractions = np.array(molar_fractions)
-            self.set_composition(molar_fractions[0])
+            self.set_composition(molar_fractions[first_index])
             assert temperatures.shape == molar_fractions.shape[:-1]
 
         # First, check the output types of all the requested variables:
diff --git a/burnman/classes/solution.py b/burnman/classes/solution.py
index 4ad6d100..b96731a8 100644
--- a/burnman/classes/solution.py
+++ b/burnman/classes/solution.py
@@ -679,7 +679,8 @@ def compositional_null_basis(self):
         null_basis = np.array([v[:] for v in null])
 
         M = null_basis[:, self.dependent_element_indices]
-        assert (M.shape[0] == M.shape[1]) and (M == np.eye(M.shape[0])).all()
+        assert (M.shape[0] == M.shape[1])
+        assert (np.abs(M - np.eye(M.shape[0])) < 1.e-20).all()
 
         return null_basis
 

From 7c780aae359edcf3e3c45a999aea7263a097d2b2 Mon Sep 17 00:00:00 2001
From: Bob Myhill <myhill.bob@gmail.com>
Date: Sun, 6 Oct 2024 17:38:04 +0100
Subject: [PATCH 2/2] update installation and test.sh

---
 .github/workflows/main.yml           | 12 ++++++------
 .github/workflows/python-publish.yml |  2 +-
 burnman/classes/seismic.py           |  2 +-
 burnman/classes/solution.py          |  4 ++--
 test.sh                              |  2 +-
 5 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 6325917d..67cd544b 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -13,9 +13,9 @@ jobs:
         python-versions: ['3.12']
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-versions }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-versions }}
     - name: make indent
@@ -24,7 +24,7 @@ jobs:
         ./contrib/utilities/indent
         git diff > changes-astyle.diff
     - name: archive indent results
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v4
       with:
         name: changes-astyle.diff
         path: changes-astyle.diff
@@ -41,9 +41,9 @@ jobs:
         python-versions: ['3.9', '3.10', '3.11', '3.12']
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-versions }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-versions }}
     - name: setup
@@ -55,7 +55,7 @@ jobs:
          texlive \
          texlive-latex-extra
         python -m pip install --upgrade pip
-        pip install pycddlib # this is optional
+        pip install pycddlib==2.1.7 # this is optional
         pip install autograd # this is optional
         python --version
     - name: test
diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml
index b7a704be..f1ce1159 100644
--- a/.github/workflows/python-publish.yml
+++ b/.github/workflows/python-publish.yml
@@ -23,7 +23,7 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: '3.x'
     - name: Install dependencies
diff --git a/burnman/classes/seismic.py b/burnman/classes/seismic.py
index 4fa833fc..08cc8704 100644
--- a/burnman/classes/seismic.py
+++ b/burnman/classes/seismic.py
@@ -333,7 +333,7 @@ def _compute_pressure(self):
         # convert radii to depths
         depth = self.earth_radius - radii
         pressure = scipy.integrate.cumulative_trapezoid(
-            gravity * density, x=depth, initial=0.0
+            gravity * density, x=depth, initial=0
         )
 
         self.table_pressure = pressure
diff --git a/burnman/classes/solution.py b/burnman/classes/solution.py
index b96731a8..31cdcf9c 100644
--- a/burnman/classes/solution.py
+++ b/burnman/classes/solution.py
@@ -679,8 +679,8 @@ def compositional_null_basis(self):
         null_basis = np.array([v[:] for v in null])
 
         M = null_basis[:, self.dependent_element_indices]
-        assert (M.shape[0] == M.shape[1])
-        assert (np.abs(M - np.eye(M.shape[0])) < 1.e-20).all()
+        assert M.shape[0] == M.shape[1]
+        assert (np.abs(M - np.eye(M.shape[0])) < 1.0e-20).all()
 
         return null_basis
 
diff --git a/test.sh b/test.sh
index e2b93841..b2d06e34 100755
--- a/test.sh
+++ b/test.sh
@@ -30,7 +30,7 @@ echo ""
 
 # Quietly install optional modules after burnman
 echo "Installing optional cvxpy, pycddlib, autograd and jupyter modules ..."
-$PYTHON -m pip install -q cvxpy pycddlib autograd jupyter
+$PYTHON -m pip install -q cvxpy pycddlib==2.1.7 autograd jupyter
 echo ""
 
 function testit {