From 3316a2a60773a43206997f9ad63f45c7cf50ce79 Mon Sep 17 00:00:00 2001
From: Moritz Kern <92092328+Moritz-Alexander-Kern@users.noreply.github.com>
Date: Tue, 10 Dec 2024 10:33:07 +0100
Subject: [PATCH 01/12] [MAIN] remove gh-action runner macOS12 The macOS-12
 environment is deprecated, consider switching to macOS-13, macOS-14
 (macos-latest) or macOS-15. For more details, see
 https://github.com/actions/runner-images/issues/10721

---
 .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 d01bba6be..0355ea69c 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -134,7 +134,7 @@ jobs:
       fail-fast: false
       matrix:
         # OS [ubuntu-latest, macos-latest, windows-latest]
-        os: [macos-12,macos-13]
+        os: [macos-13,macos-14]
         python-version: [3.11]
     steps:
       - name: Get current year-month

From bd8b55ab9965bcc1ff4443f0e127e9d5bc7cbcb9 Mon Sep 17 00:00:00 2001
From: Moritz Kern <92092328+Moritz-Alexander-Kern@users.noreply.github.com>
Date: Tue, 10 Dec 2024 10:34:52 +0100
Subject: [PATCH 02/12] remove defaults channel from conda

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

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 0355ea69c..cc344bb46 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -167,7 +167,7 @@ jobs:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
           mamba-version: "*"
-          channels: conda-forge,defaults
+          channels: conda-forge
           channel-priority: true
           activate-environment: elephant
           environment-file: requirements/environment-tests.yml
@@ -388,7 +388,7 @@ jobs:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
           mamba-version: "*"
-          channels: conda-forge,defaults
+          channels: conda-forge
           channel-priority: true
           activate-environment: elephant
           environment-file: requirements/environment-tests.yml

From aabd6ca28a9946c457e1827d0757d56bda0fcb2a Mon Sep 17 00:00:00 2001
From: Moritz Kern <92092328+Moritz-Alexander-Kern@users.noreply.github.com>
Date: Tue, 10 Dec 2024 10:39:56 +0100
Subject: [PATCH 03/12] update setup mini-conda

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

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index cc344bb46..e25f8167a 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -162,7 +162,7 @@ jobs:
           key: datasets-${{ steps.elephant-data.outputs.dataset_hash }}
           restore-keys: datasets-      
 
-      - uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # corresponds to v3.0.4
+      - uses: conda-incubator/setup-miniconda@d2e6a045a86077fb6cad6f5adf368e9076ddaa8d # corresponds to v3.1.0
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
@@ -383,7 +383,7 @@ jobs:
           restore-keys: datasets-
           enableCrossOsArchive: true 
 
-      - uses: conda-incubator/setup-miniconda@030178870c779d9e5e1b4e563269f3aa69b04081 # corresponds to v3.0.3
+      - uses: conda-incubator/setup-miniconda@d2e6a045a86077fb6cad6f5adf368e9076ddaa8d # corresponds to v3.1.0
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
@@ -455,7 +455,7 @@ jobs:
           key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements-docs.txt') }}-${{ hashFiles('**/requirements-tutorials.txt') }}-${{ hashFiles('**/environment-docs.yml') }}
            -${{ hashFiles('**/CI.yml') }}-${{ steps.date.outputs.date }}
 
-      - uses: conda-incubator/setup-miniconda@030178870c779d9e5e1b4e563269f3aa69b04081 # corresponds to v3.0.3
+      - uses: conda-incubator/setup-miniconda@d2e6a045a86077fb6cad6f5adf368e9076ddaa8d # corresponds to v3.1.0
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}

From 7096576a8d8b0f1b0e1ce76cde9950052baa0c4f Mon Sep 17 00:00:00 2001
From: Moritz Kern <92092328+Moritz-Alexander-Kern@users.noreply.github.com>
Date: Tue, 10 Dec 2024 10:42:13 +0100
Subject: [PATCH 04/12] set remove defaults channel to true

---
 .github/workflows/CI.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index e25f8167a..30de03a5f 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -171,6 +171,7 @@ jobs:
           channel-priority: true
           activate-environment: elephant
           environment-file: requirements/environment-tests.yml
+          conda-remove-defaults: true
 
       - name: Install dependencies
         shell: bash -l {0}
@@ -392,6 +393,7 @@ jobs:
           channel-priority: true
           activate-environment: elephant
           environment-file: requirements/environment-tests.yml
+          conda-remove-defaults: true
 
       - name: Install dependencies
         shell: bash -el {0}
@@ -462,6 +464,7 @@ jobs:
           mamba-version: "*"
           activate-environment: elephant
           environment-file: requirements/environment.yml
+          conda-remove-defaults: true
 
       - name: Install dependencies
         shell: bash -el {0} # enables conda incubator to activate environment

From 10673e487f563666a2434f0a00262ed27195dffa Mon Sep 17 00:00:00 2001
From: Moritz Kern <92092328+Moritz-Alexander-Kern@users.noreply.github.com>
Date: Tue, 10 Dec 2024 10:53:17 +0100
Subject: [PATCH 05/12] set conda forge as channel

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

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 30de03a5f..372d43983 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -399,8 +399,8 @@ jobs:
         shell: bash -el {0}
         run: |
           python --version
-          conda install mpi4py openmpi
-          mamba install pytest pytest-cov coveralls
+          conda install -c conda-forge mpi4py openmpi
+          mamba install -c conda-forge pytest pytest-cov coveralls
           pip install -e .
 
       - name: List packages

From d13287a7c552a326e16327b0b24ea4a356f508b2 Mon Sep 17 00:00:00 2001
From: Moritz Kern <92092328+Moritz-Alexander-Kern@users.noreply.github.com>
Date: Tue, 10 Dec 2024 14:30:39 +0100
Subject: [PATCH 06/12] update CI

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

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 372d43983..69046a15e 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -399,8 +399,8 @@ jobs:
         shell: bash -el {0}
         run: |
           python --version
-          conda install -c conda-forge mpi4py openmpi
-          mamba install -c conda-forge pytest pytest-cov coveralls
+          # conda install mpi4py openmpi
+          mamba install -c conda-forge pytest pytest-cov coveralls mpi4py openmpi
           pip install -e .
 
       - name: List packages
@@ -472,7 +472,7 @@ jobs:
           sudo apt-get update
           sudo apt install -y libopenmpi-dev openmpi-bin
           
-          conda install -c conda-forge openmpi pandoc libstdcxx-ng # fix libstdc++.so.6: version for new scipy versions > 1.9.1
+          mamba install -c conda-forge openmpi pandoc libstdcxx-ng # fix libstdc++.so.6: version for new scipy versions > 1.9.1
           mamba env update --file requirements/environment-docs.yml --name elephant
           python -m pip install --upgrade pip
           pip install -e .[extras,tutorials,docs]

From 527b1dbdea8e1dfc9a1afce694daf726f42c680b Mon Sep 17 00:00:00 2001
From: Moritz Kern <92092328+Moritz-Alexander-Kern@users.noreply.github.com>
Date: Tue, 10 Dec 2024 14:41:47 +0100
Subject: [PATCH 07/12] remove comment

---
 .github/workflows/CI.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 69046a15e..9802605bd 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -399,7 +399,6 @@ jobs:
         shell: bash -el {0}
         run: |
           python --version
-          # conda install mpi4py openmpi
           mamba install -c conda-forge pytest pytest-cov coveralls mpi4py openmpi
           pip install -e .
 

From f0e2c0647c0761072d8b22a2917b74a15bd916b2 Mon Sep 17 00:00:00 2001
From: Moritz Kern <92092328+Moritz-Alexander-Kern@users.noreply.github.com>
Date: Wed, 11 Dec 2024 10:29:51 +0100
Subject: [PATCH 08/12] update action chace to v4

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

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 9802605bd..ed10789f6 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -144,7 +144,7 @@ jobs:
       - uses: actions/checkout@v4.1.6
 
       - name: Cache conda
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/conda_pkgs_dir
           key: ${{ runner.os }}-conda-${{hashFiles('requirements/environment.yml') }}-${{ hashFiles('**/CI.yml') }}-${{ steps.date.outputs.date }}
@@ -364,7 +364,7 @@ jobs:
           echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
 
       - name: Cache pip
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ steps.pip-cache.outputs.dir }}
 
@@ -449,7 +449,7 @@ jobs:
           echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
 
       - name: Cache pip
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ steps.pip-cache.outputs.dir }}
           # Look to see if there is a cache hit for the corresponding requirements files
@@ -515,7 +515,7 @@ jobs:
           python-version: ${{ matrix.python-version }}
 
       - name: Cache test_env
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/test_env
           # Look to see if there is a cache hit for the corresponding requirements files

From 5d9f224a6013504ca6a289251ce7a7138889d5e8 Mon Sep 17 00:00:00 2001
From: Moritz Kern <92092328+Moritz-Alexander-Kern@users.noreply.github.com>
Date: Wed, 11 Dec 2024 10:50:19 +0100
Subject: [PATCH 09/12] update upload artifact action

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

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index b5dbea1f9..0a94c2fb6 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -41,6 +41,6 @@ jobs:
           CIBW_PROJECT_REQUIRES_PYTHON: ">=3.8"
           CIBW_ARCHS: "auto64"
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           path: ./wheelhouse/*.whl

From d7c09d671f77e742ecce532b4759b1e0de02739a Mon Sep 17 00:00:00 2001
From: Moritz Kern <92092328+Moritz-Alexander-Kern@users.noreply.github.com>
Date: Wed, 11 Dec 2024 11:05:50 +0100
Subject: [PATCH 10/12] merge wheels into one artifact

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

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index 0a94c2fb6..c55524e8d 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -44,3 +44,5 @@ jobs:
       - uses: actions/upload-artifact@v4
         with:
           path: ./wheelhouse/*.whl
+          pattern: *.whl
+          merge-multiple: true

From 1af433dabd23aada7c3c2414b781a3cc2611e4bf Mon Sep 17 00:00:00 2001
From: Moritz Kern <92092328+Moritz-Alexander-Kern@users.noreply.github.com>
Date: Wed, 11 Dec 2024 11:12:39 +0100
Subject: [PATCH 11/12] add step to merge artifacts

---
 .github/workflows/build_wheels.yml | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index c55524e8d..b5f5b1af2 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -43,6 +43,14 @@ jobs:
 
       - uses: actions/upload-artifact@v4
         with:
+          name: wheels-${{ matrix.os }}
           path: ./wheelhouse/*.whl
-          pattern: *.whl
-          merge-multiple: true
+  merge:
+    runs-on: ubuntu-latest
+    needs: build_wheels
+    steps:
+      - name: Merge Artifacts
+        uses: actions/upload-artifact/merge@v4
+        with:
+          name: all-wheels
+          pattern: wheels-*
\ No newline at end of file

From 1bcc8188af419f347c180f8d4bce764adb450ca0 Mon Sep 17 00:00:00 2001
From: Moritz Kern <92092328+Moritz-Alexander-Kern@users.noreply.github.com>
Date: Wed, 11 Dec 2024 11:21:18 +0100
Subject: [PATCH 12/12] update job name

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

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index b5f5b1af2..a456b2898 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -45,7 +45,7 @@ jobs:
         with:
           name: wheels-${{ matrix.os }}
           path: ./wheelhouse/*.whl
-  merge:
+  merge_wheels:
     runs-on: ubuntu-latest
     needs: build_wheels
     steps: