From ed3706cf80ca74035e630ac3d385c7ab400fa11b Mon Sep 17 00:00:00 2001
From: "Corey R. Randall" <corey.r.randall@gmail.com>
Date: Mon, 23 Dec 2024 11:39:35 -0700
Subject: [PATCH 01/13] Add windows build/tests to test-sundials CI

---
 .github/workflows/test-sundials.yml | 58 +++++++++++++++++++++++++++++
 1 file changed, 58 insertions(+)

diff --git a/.github/workflows/test-sundials.yml b/.github/workflows/test-sundials.yml
index aa0b8ad..b6acae0 100644
--- a/.github/workflows/test-sundials.yml
+++ b/.github/workflows/test-sundials.yml
@@ -127,3 +127,61 @@ jobs:
         tox
       env:
         TOXENV: ${{ matrix.tox-env }}
+
+  test-windows:
+    name: (Test ${{ matrix.python-version }}, ${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      matrix:
+        os: [macos-latest, windows-latest]  # set more OS here, if desired
+        python-version: ["3.9", "3.13"]  # set more python versions here, if desired
+        
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Setup conda/python
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          miniconda-version: latest
+          activate-environment: odes
+          python-version: ${{ matrix.python-version }}
+
+      - name: Setup SUNDIALS
+        run: conda install sundials=7.1.1 -c conda-forge  # SUNDIALS version is set here
+
+      - name: Verify environment
+        run: |
+          conda info
+          conda list
+
+      - name: Set SUNDIALS installation path
+        run: |
+          if [[ "$RUNNER_OS" == "Windows" ]]; then
+            echo "SUNDIALS_INST=%CONDA_PREFIX%/Library" >> $GITHUB_ENV
+          else
+            echo "SUNDIALS_INST=$CONDA_PREFIX" >> $GITHUB_ENV
+          fi
+
+      - name: Install scikits-odes-sundials
+        working-directory: packages/scikits-odes-sundials
+        run: |
+          python -m pip install --upgrade pip
+          pip install .
+
+      - name: List info
+        run: |
+          conda info
+          conda list
+                
+      - name: Run tests
+        working-directory: packages/scikits-odes-sundials/src/scikits_odes_sundials
+        run: |
+          pip install pytest
+          pytest .

From 2891ddd078d47126e54e3f6e88e9c069699f3bf7 Mon Sep 17 00:00:00 2001
From: "Corey R. Randall" <corey.r.randall@gmail.com>
Date: Mon, 23 Dec 2024 12:25:06 -0700
Subject: [PATCH 02/13] Fix issue with SUNDIALS_INST path variables

---
 .github/workflows/test-sundials.yml | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/test-sundials.yml b/.github/workflows/test-sundials.yml
index b6acae0..ffd439a 100644
--- a/.github/workflows/test-sundials.yml
+++ b/.github/workflows/test-sundials.yml
@@ -129,13 +129,14 @@ jobs:
         TOXENV: ${{ matrix.tox-env }}
 
   test-windows:
-    name: (Test ${{ matrix.python-version }}, ${{ matrix.os }})
+    name: tests (${{ matrix.python-version }}, ${{matrix.sundials-version}}, ${{ matrix.os }}, double, 32)
     runs-on: ${{ matrix.os }}
 
     strategy:
       matrix:
         os: [macos-latest, windows-latest]  # set more OS here, if desired
         python-version: ["3.9", "3.13"]  # set more python versions here, if desired
+        sundials-version: ["7.1.1"]  # set more SUNDIALS version here, if desired
         
     defaults:
       run:
@@ -154,7 +155,7 @@ jobs:
           python-version: ${{ matrix.python-version }}
 
       - name: Setup SUNDIALS
-        run: conda install sundials=7.1.1 -c conda-forge  # SUNDIALS version is set here
+        run: conda install sundials=${{ matrix.sundials-version }} -c conda-forge
 
       - name: Verify environment
         run: |
@@ -164,11 +165,14 @@ jobs:
       - name: Set SUNDIALS installation path
         run: |
           if [[ "$RUNNER_OS" == "Windows" ]]; then
-            echo "SUNDIALS_INST=%CONDA_PREFIX%/Library" >> $GITHUB_ENV
+            SUNDIALS_INST="$CONDA_PREFIX\Library"
           else
-            echo "SUNDIALS_INST=$CONDA_PREFIX" >> $GITHUB_ENV
+            SUNDIALS_INST="$CONDA_PREFIX"
           fi
 
+          echo "SUNDIALS_INST is set to: $SUNDIALS_INST"
+          echo "SUNDIALS_INST=$SUNDIALS_INST" >> $GITHUB_ENV
+
       - name: Install scikits-odes-sundials
         working-directory: packages/scikits-odes-sundials
         run: |

From ecb57b79e87ade7817e034ca7459f794f63e20e3 Mon Sep 17 00:00:00 2001
From: "Corey R. Randall" <corey.r.randall@gmail.com>
Date: Mon, 23 Dec 2024 12:50:03 -0700
Subject: [PATCH 03/13] Rename new windows/mac tests job to include "mac"

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

diff --git a/.github/workflows/test-sundials.yml b/.github/workflows/test-sundials.yml
index ffd439a..75e61c9 100644
--- a/.github/workflows/test-sundials.yml
+++ b/.github/workflows/test-sundials.yml
@@ -128,7 +128,7 @@ jobs:
       env:
         TOXENV: ${{ matrix.tox-env }}
 
-  test-windows:
+  tests-win-mac:
     name: tests (${{ matrix.python-version }}, ${{matrix.sundials-version}}, ${{ matrix.os }}, double, 32)
     runs-on: ${{ matrix.os }}
 

From 8bda1c5d9284af9208dffe627c752606aca60388 Mon Sep 17 00:00:00 2001
From: "Corey R. Randall" <corey.r.randall@gmail.com>
Date: Tue, 31 Dec 2024 00:33:53 -0700
Subject: [PATCH 04/13] Move to using tox

---
 .github/workflows/test-sundials.yml    | 23 +++++++++++++----------
 packages/scikits-odes-sundials/tox.ini |  1 +
 2 files changed, 14 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/test-sundials.yml b/.github/workflows/test-sundials.yml
index 75e61c9..fcfb16f 100644
--- a/.github/workflows/test-sundials.yml
+++ b/.github/workflows/test-sundials.yml
@@ -134,9 +134,13 @@ jobs:
 
     strategy:
       matrix:
-        os: [macos-latest, windows-latest]  # set more OS here, if desired
-        python-version: ["3.9", "3.13"]  # set more python versions here, if desired
-        sundials-version: ["7.1.1"]  # set more SUNDIALS version here, if desired
+        os: [windows-latest, macos-latest, macos-13]
+        sundials-version: ["7.1.1"]
+        include:
+          - python-version: "3.9"
+            tox-env: py39
+          - python-version: "3.13"
+            tox-env: py313
         
     defaults:
       run:
@@ -173,11 +177,10 @@ jobs:
           echo "SUNDIALS_INST is set to: $SUNDIALS_INST"
           echo "SUNDIALS_INST=$SUNDIALS_INST" >> $GITHUB_ENV
 
-      - name: Install scikits-odes-sundials
-        working-directory: packages/scikits-odes-sundials
+      - name: Install python dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install .
+          python -m pip install --upgrade tox
 
       - name: List info
         run: |
@@ -185,7 +188,7 @@ jobs:
           conda list
                 
       - name: Run tests
-        working-directory: packages/scikits-odes-sundials/src/scikits_odes_sundials
-        run: |
-          pip install pytest
-          pytest .
+        working-directory: packages/scikits-odes-sundials
+        run: tox
+        env:
+          TOXENV: ${{ matrix.tox-env }}
diff --git a/packages/scikits-odes-sundials/tox.ini b/packages/scikits-odes-sundials/tox.ini
index 22853a3..d924136 100644
--- a/packages/scikits-odes-sundials/tox.ini
+++ b/packages/scikits-odes-sundials/tox.ini
@@ -4,6 +4,7 @@ setenv = LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8
 
 [testenv]
 passenv=
+    SUNDIALS_INST
     SUNDIALS_DIR
     SUNDIALS_LIBDIR
     SUNDIALS_INCLUDEDIR

From 1d8478f5ffdc04fd69c73105e39a1f6fa6202ccd Mon Sep 17 00:00:00 2001
From: "Corey R. Randall" <corey.r.randall@gmail.com>
Date: Tue, 31 Dec 2024 01:04:48 -0700
Subject: [PATCH 05/13] Fix matrix to include 3.9 again

---
 .github/workflows/test-sundials.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/test-sundials.yml b/.github/workflows/test-sundials.yml
index fcfb16f..7b55bd6 100644
--- a/.github/workflows/test-sundials.yml
+++ b/.github/workflows/test-sundials.yml
@@ -135,6 +135,7 @@ jobs:
     strategy:
       matrix:
         os: [windows-latest, macos-latest, macos-13]
+        python-version: ["3.9", "3.13"]
         sundials-version: ["7.1.1"]
         include:
           - python-version: "3.9"

From b643c9206cbcd38855e8b4d450afa6cd011a533c Mon Sep 17 00:00:00 2001
From: "Corey R. Randall" <corey.r.randall@gmail.com>
Date: Tue, 31 Dec 2024 01:13:15 -0700
Subject: [PATCH 06/13] Explicitly install setuptools before tox

---
 .github/workflows/test-sundials.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/test-sundials.yml b/.github/workflows/test-sundials.yml
index 7b55bd6..ca3fe08 100644
--- a/.github/workflows/test-sundials.yml
+++ b/.github/workflows/test-sundials.yml
@@ -133,6 +133,7 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     strategy:
+      fail-fast: false
       matrix:
         os: [windows-latest, macos-latest, macos-13]
         python-version: ["3.9", "3.13"]
@@ -181,6 +182,7 @@ jobs:
       - name: Install python dependencies
         run: |
           python -m pip install --upgrade pip
+          python -m pip install --upgrade setuptools
           python -m pip install --upgrade tox
 
       - name: List info

From 61c6f5de84b96085e69602db63c832d333b6b3ba Mon Sep 17 00:00:00 2001
From: "Corey R. Randall" <corey.r.randall@gmail.com>
Date: Tue, 31 Dec 2024 02:10:15 -0700
Subject: [PATCH 07/13] Try recreate on tox fails

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

diff --git a/.github/workflows/test-sundials.yml b/.github/workflows/test-sundials.yml
index ca3fe08..e6f4cd6 100644
--- a/.github/workflows/test-sundials.yml
+++ b/.github/workflows/test-sundials.yml
@@ -192,6 +192,6 @@ jobs:
                 
       - name: Run tests
         working-directory: packages/scikits-odes-sundials
-        run: tox
+        run: tox || tox --recreate
         env:
           TOXENV: ${{ matrix.tox-env }}

From 1fb7c9a4373f003e4fc0eabebc80f58034ba162c Mon Sep 17 00:00:00 2001
From: "Corey R. Randall" <corey.r.randall@gmail.com>
Date: Tue, 31 Dec 2024 02:18:38 -0700
Subject: [PATCH 08/13] Try tox from conda

---
 .github/workflows/test-sundials.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test-sundials.yml b/.github/workflows/test-sundials.yml
index e6f4cd6..a42fd43 100644
--- a/.github/workflows/test-sundials.yml
+++ b/.github/workflows/test-sundials.yml
@@ -183,7 +183,9 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           python -m pip install --upgrade setuptools
-          python -m pip install --upgrade tox
+
+      - name: Get tox
+        run: conda install tox
 
       - name: List info
         run: |
@@ -192,6 +194,6 @@ jobs:
                 
       - name: Run tests
         working-directory: packages/scikits-odes-sundials
-        run: tox || tox --recreate
+        run: tox
         env:
           TOXENV: ${{ matrix.tox-env }}

From 823de6b0cce5de4f1bcecd81e9955748371b6191 Mon Sep 17 00:00:00 2001
From: "Corey R. Randall" <corey.r.randall@gmail.com>
Date: Tue, 31 Dec 2024 02:27:31 -0700
Subject: [PATCH 09/13] Skip windows/py39 due to tox SSL error

---
 .github/workflows/test-sundials.yml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/test-sundials.yml b/.github/workflows/test-sundials.yml
index a42fd43..49d1432 100644
--- a/.github/workflows/test-sundials.yml
+++ b/.github/workflows/test-sundials.yml
@@ -143,6 +143,9 @@ jobs:
             tox-env: py39
           - python-version: "3.13"
             tox-env: py313
+        exclude:
+          - os: windows-latest  # Issue with tox venv, cannot access openssl
+            python-version: "3.9"
         
     defaults:
       run:
@@ -183,9 +186,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           python -m pip install --upgrade setuptools
-
-      - name: Get tox
-        run: conda install tox
+          python -m pip install --upgrade tox
 
       - name: List info
         run: |

From 7476b725061c219e58b577d082a022df3142b2d4 Mon Sep 17 00:00:00 2001
From: "Corey R. Randall" <corey.r.randall@gmail.com>
Date: Thu, 2 Jan 2025 14:27:46 -0700
Subject: [PATCH 10/13] Try adding SSL_CERT_FILE to passenv

---
 .github/workflows/test-sundials.yml    | 6 +++---
 packages/scikits-odes-sundials/tox.ini | 1 +
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/test-sundials.yml b/.github/workflows/test-sundials.yml
index 49d1432..e17f3b1 100644
--- a/.github/workflows/test-sundials.yml
+++ b/.github/workflows/test-sundials.yml
@@ -143,9 +143,9 @@ jobs:
             tox-env: py39
           - python-version: "3.13"
             tox-env: py313
-        exclude:
-          - os: windows-latest  # Issue with tox venv, cannot access openssl
-            python-version: "3.9"
+        # exclude:
+        #   - os: windows-latest  # Issue with tox venv, pip has no ssl access
+        #     python-version: "3.9"
         
     defaults:
       run:
diff --git a/packages/scikits-odes-sundials/tox.ini b/packages/scikits-odes-sundials/tox.ini
index d924136..06968e9 100644
--- a/packages/scikits-odes-sundials/tox.ini
+++ b/packages/scikits-odes-sundials/tox.ini
@@ -13,6 +13,7 @@ passenv=
     CPATH
     PIP_VERBOSE
     PYTHONFAULTHANDLER
+    SSL_CERT_FILE
 deps =
     pytest
     -r local-requirements.txt

From 6b83d5ef0f43cf9acc3fab3d5d9c8f0eba2152df Mon Sep 17 00:00:00 2001
From: "Corey R. Randall" <corey.r.randall@gmail.com>
Date: Thu, 2 Jan 2025 14:36:25 -0700
Subject: [PATCH 11/13] Add SSL_CERT_FILE to GITHUB_ENV

---
 .github/workflows/test-sundials.yml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test-sundials.yml b/.github/workflows/test-sundials.yml
index e17f3b1..2b5cef8 100644
--- a/.github/workflows/test-sundials.yml
+++ b/.github/workflows/test-sundials.yml
@@ -171,7 +171,7 @@ jobs:
           conda info
           conda list
 
-      - name: Set SUNDIALS installation path
+      - name: Set SUNDIALS and SSL paths
         run: |
           if [[ "$RUNNER_OS" == "Windows" ]]; then
             SUNDIALS_INST="$CONDA_PREFIX\Library"
@@ -182,6 +182,9 @@ jobs:
           echo "SUNDIALS_INST is set to: $SUNDIALS_INST"
           echo "SUNDIALS_INST=$SUNDIALS_INST" >> $GITHUB_ENV
 
+          echo "SSL_CERT_FILE is at: $SSL_CERT_FILE"
+          echo "SSL_CERT_FILE=$SSL_CERT_FILE" >> $GITHUB_ENV
+
       - name: Install python dependencies
         run: |
           python -m pip install --upgrade pip

From f7db0dc02adc77ea6c6b64fa5c71224f0c06f6cc Mon Sep 17 00:00:00 2001
From: "Corey R. Randall" <corey.r.randall@gmail.com>
Date: Thu, 2 Jan 2025 14:43:45 -0700
Subject: [PATCH 12/13] SSL_CERT_FILE didn't work, exclude win-py39 again

---
 .github/workflows/test-sundials.yml    | 11 ++++-------
 packages/scikits-odes-sundials/tox.ini |  1 -
 2 files changed, 4 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/test-sundials.yml b/.github/workflows/test-sundials.yml
index 2b5cef8..f2285c4 100644
--- a/.github/workflows/test-sundials.yml
+++ b/.github/workflows/test-sundials.yml
@@ -143,9 +143,9 @@ jobs:
             tox-env: py39
           - python-version: "3.13"
             tox-env: py313
-        # exclude:
-        #   - os: windows-latest  # Issue with tox venv, pip has no ssl access
-        #     python-version: "3.9"
+        exclude:
+          - os: windows-latest  # Issue with tox venv, pip has no ssl access
+            python-version: "3.9"
         
     defaults:
       run:
@@ -171,7 +171,7 @@ jobs:
           conda info
           conda list
 
-      - name: Set SUNDIALS and SSL paths
+      - name: Set SUNDIALS path
         run: |
           if [[ "$RUNNER_OS" == "Windows" ]]; then
             SUNDIALS_INST="$CONDA_PREFIX\Library"
@@ -182,9 +182,6 @@ jobs:
           echo "SUNDIALS_INST is set to: $SUNDIALS_INST"
           echo "SUNDIALS_INST=$SUNDIALS_INST" >> $GITHUB_ENV
 
-          echo "SSL_CERT_FILE is at: $SSL_CERT_FILE"
-          echo "SSL_CERT_FILE=$SSL_CERT_FILE" >> $GITHUB_ENV
-
       - name: Install python dependencies
         run: |
           python -m pip install --upgrade pip
diff --git a/packages/scikits-odes-sundials/tox.ini b/packages/scikits-odes-sundials/tox.ini
index 06968e9..d924136 100644
--- a/packages/scikits-odes-sundials/tox.ini
+++ b/packages/scikits-odes-sundials/tox.ini
@@ -13,7 +13,6 @@ passenv=
     CPATH
     PIP_VERBOSE
     PYTHONFAULTHANDLER
-    SSL_CERT_FILE
 deps =
     pytest
     -r local-requirements.txt

From 755b666d0453daad57de140080d654af03717857 Mon Sep 17 00:00:00 2001
From: "Corey R. Randall" <corey.r.randall@gmail.com>
Date: Sat, 11 Jan 2025 19:59:05 -0700
Subject: [PATCH 13/13] move conda setup action from miniconda to micromamba

---
 .github/workflows/test-sundials.yml | 29 +++++++++++++----------------
 1 file changed, 13 insertions(+), 16 deletions(-)

diff --git a/.github/workflows/test-sundials.yml b/.github/workflows/test-sundials.yml
index f2285c4..0a1982d 100644
--- a/.github/workflows/test-sundials.yml
+++ b/.github/workflows/test-sundials.yml
@@ -143,9 +143,6 @@ jobs:
             tox-env: py39
           - python-version: "3.13"
             tox-env: py313
-        exclude:
-          - os: windows-latest  # Issue with tox venv, pip has no ssl access
-            python-version: "3.9"
         
     defaults:
       run:
@@ -155,21 +152,21 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v4
 
-      - name: Setup conda/python
-        uses: conda-incubator/setup-miniconda@v3
+      - name: Setup Python and SUNDIALS
+        uses: mamba-org/setup-micromamba@v2
         with:
-          auto-update-conda: true
-          miniconda-version: latest
-          activate-environment: odes
-          python-version: ${{ matrix.python-version }}
-
-      - name: Setup SUNDIALS
-        run: conda install sundials=${{ matrix.sundials-version }} -c conda-forge
+          environment-name: odes
+          create-args: >-
+            python=${{ matrix.python-version }}
+            sundials=${{ matrix.sundials-version }}
+          condarc: |
+            channels:
+              - conda-forge
 
       - name: Verify environment
         run: |
-          conda info
-          conda list
+          micromamba info
+          micromamba list
 
       - name: Set SUNDIALS path
         run: |
@@ -190,8 +187,8 @@ jobs:
 
       - name: List info
         run: |
-          conda info
-          conda list
+          micromamba info
+          micromamba list
                 
       - name: Run tests
         working-directory: packages/scikits-odes-sundials