Update GHA actions in CI pipeline

.github/workflows/ci.yaml

@@ -3,8 +3,6 @@ name: CI
 
 on:
   push:
-    branches:
-      - "master"
   pull_request:
     branches:
       - "master"
@@ -21,6 +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 }}
@@ -30,38 +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/
 
@@ -76,6 +74,9 @@ jobs:
   #############
   lint-format:
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -el {0}
     env:
       CI_OS: ubuntu-latest
       PACKAGE: "opencadd"
@@ -85,27 +86,26 @@ 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
-        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/

.gitignore

@@ -103,4 +103,10 @@ ENV/
 .mypy_cache/
 
 # VSCode
-.vscode/
+.vscode/
+
+# PyCharm
+.idea/
+
+# MacOS
+.DS_Store