From b25f3cd2d12dc68e36262eb7ce67b36816a12cef Mon Sep 17 00:00:00 2001
From: Armin Ariamajd <armin.ariam@fu-berlin.de>
Date: Fri, 14 Mar 2025 14:10:02 +0100
Subject: [PATCH 1/4] Update ci.yaml

---
 .github/workflows/ci.yaml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index d3090038f..497faf867 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -3,8 +3,6 @@ name: CI
 
 on:
   push:
-    branches:
-      - "master"
   pull_request:
     branches:
       - "master"

From 85a30054028cdbbfef5b9726083cf311f7f93bab Mon Sep 17 00:00:00 2001
From: AAriam <80158628+AAriam@users.noreply.github.com>
Date: Fri, 14 Mar 2025 14:13:06 +0100
Subject: [PATCH 2/4] Update .gitignore

---
 .gitignore | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 8ae7018ef..34b4390c8 100644
--- a/.gitignore
+++ b/.gitignore
@@ -103,4 +103,10 @@ ENV/
 .mypy_cache/
 
 # VSCode
-.vscode/
\ No newline at end of file
+.vscode/
+
+# PyCharm
+.idea/
+
+# MacOS
+.DS_Store

From 0bac78a60008c42349f8a59087c02fdeae28cda4 Mon Sep 17 00:00:00 2001
From: AAriam <80158628+AAriam@users.noreply.github.com>
Date: Fri, 14 Mar 2025 14:23:22 +0100
Subject: [PATCH 3/4] Update ci.yaml

---
 .github/workflows/ci.yaml | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 497faf867..fbe879359 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -19,6 +19,9 @@ jobs:
       matrix:
         os: [macOS-latest, ubuntu-latest]
         python-version: [3.7, 3.8]
+    defaults:
+      run:
+        shell: bash -el {0}
     env:
       CI_OS: ${{ matrix.os }}
       PYVER: ${{ matrix.python-version }}
@@ -28,38 +31,35 @@ jobs:
       - uses: actions/checkout@v3
 
       - name: Additional info about the build
-        shell: bash
         run: |
           uname -a
           df -h
           ulimit -a
 
-      - uses: conda-incubator/setup-miniconda@v2
+      - name: Miniconda Setup
+        uses: conda-incubator/setup-miniconda@v3
         with:
-          python-version: ${{ matrix.python-version }}
-          miniforge-variant: Mambaforge
           miniforge-version: latest
-          activate-environment: test
-          environment-file: devtools/conda-envs/test_env.yaml
+          auto-update-conda: true
+          conda-build-version: '>=25.1'
           channels: conda-forge,defaults,bioconda
+          environment-file: devtools/conda-envs/test_env.yaml
+          python-version: ${{ matrix.python-version }}
+          activate-environment: test
 
       # TODO: Remove this step when patched theseus makes it to CF
       - name: Build patched mmligner
-        shell: bash -l {0}
         run: |
           conda activate base
-          conda install conda-build
           conda build devtools/conda-recipes/mmligner/
 
       - name: Install package
-        shell: bash -l {0}
         run: |
           conda install -c local mmligner pip
           python -m pip install . --no-deps
           conda list
 
       - name: Run tests
-        shell: bash -l {0}
         run: |
           pytest -v --cov=${PACKAGE} --cov-report=xml --color=yes ${PACKAGE}/tests/
 
@@ -74,6 +74,9 @@ jobs:
   #############
   lint-format:
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -el {0}
     env:
       CI_OS: ubuntu-latest
       PACKAGE: "opencadd"
@@ -93,17 +96,14 @@ jobs:
           channels: conda-forge,defaults,bioconda
 
       - name: Install linter and formatter
-        shell: bash -l {0}
         run: |
           conda install -y pylint black
 
       - name: Run pylint
-        shell: bash -l {0}
         run: |
           pylint $PACKAGE/
 
       - name: Run black check
-        shell: bash -l {0}
         if: always()
         run: |
           black --check -l 99 $PACKAGE/

From 85ed641ea8ac031d2c014d6077752fb99080f96a Mon Sep 17 00:00:00 2001
From: AAriam <80158628+AAriam@users.noreply.github.com>
Date: Fri, 14 Mar 2025 14:28:52 +0100
Subject: [PATCH 4/4] Update ci.yaml

---
 .github/workflows/ci.yaml | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index fbe879359..3e85dd56d 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -86,14 +86,16 @@ jobs:
       - name: Checkout the code
         uses: actions/checkout@v3
 
-      - uses: conda-incubator/setup-miniconda@v2
+      - name: Miniconda Setup
+        uses: conda-incubator/setup-miniconda@v3
         with:
-          python-version: "3.8"
-          miniforge-variant: Mambaforge
           miniforge-version: latest
-          activate-environment: test
-          environment-file: devtools/conda-envs/test_env.yaml
+          auto-update-conda: true
+          conda-build-version: '>=25.1'
           channels: conda-forge,defaults,bioconda
+          environment-file: devtools/conda-envs/test_env.yaml
+          python-version: 3.8
+          activate-environment: test
 
       - name: Install linter and formatter
         run: |