Merge branch 'master' into djs/new_operation_for_SP

deepanshs · Jun 27, 2024 · fe70c72 · fe70c72
2 parents 1f6a661 + d494e16
commit fe70c72
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diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -33,7 +33,7 @@ If applicable, add screenshots to help explain your problem.
 - For mac OS, please specify which BLAS library (OpenBLAS or Accelerate) you use to
   install the `mrsimulator` library. This point is only applicable if you installed
   the `mrsimulator` library from the source code.
-- Python version: [e.g. 3.7.1]
+- Python version: [e.g. 3.10.1]
 - `mrsimulator` version: [e.g. 0.3]
 
 **Additional context**

diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
@@ -26,11 +26,11 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v2
+      uses: github/codeql-action/init@v3
       with:
         languages: ${{ matrix.language }}
         # If you wish to specify custom queries, you can do so here or in a config file.
@@ -41,7 +41,7 @@ jobs:
     # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
     # If this step fails, then you should remove it and run the build manually (see below)
     - name: Autobuild
-      uses: github/codeql-action/autobuild@v2
+      uses: github/codeql-action/autobuild@v3
 
     # ℹ️ Command-line programs to run using the OS shell.
     # 📚 https://git.io/JvXDl
@@ -55,4 +55,4 @@ jobs:
     #   make release
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v2
+      uses: github/codeql-action/analyze@v3
diff --git a/.github/workflows/continuous-integration-pip.yml b/.github/workflows/continuous-integration-pip.yml
@@ -9,18 +9,22 @@ on:
   pull_request:
     branches: [master, 'v?.?*']
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   code_lint:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: ["3.10"]
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
@@ -36,36 +40,64 @@ jobs:
 
   testing_unix:
     needs: [code_lint]
+    runs-on: "ubuntu-latest"
     strategy:
       matrix:
-        os: ["ubuntu-latest", "macos-latest"]
-        python-version: [3.7, 3.8, 3.9, "3.10", "3.11"]
-    runs-on: ${{ matrix.os }}
+        python-version: [3.9, "3.10", "3.11", "3.12"]
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Install linux system dependencies
-        if: startsWith(matrix.os, 'ubuntu')
         run: |
           sudo apt-get install --yes libopenblas-dev libfftw3-dev
           gcc -v
 
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install setuptools
+          pip install -r requirements-dev.txt
+
+      - name: Build and install package from source
+        run: python setup.py develop
+
+      - name: Test with pytest
+        run: pytest --cov=./ --cov-report=xml
+
+      - name: Upload coverage
+        uses: codecov/codecov-action@v4.5.0
+
+  testing_mac_arm:
+    needs: [code_lint]
+    runs-on: "macos-latest"
+    strategy:
+      matrix:
+        python-version: [3.9, "3.10", "3.11", "3.12"]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
       - name: Install macos system dependencies
-        if: startsWith(matrix.os, 'mac')
         run: brew install openblas fftw
 
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install pytest cython setuptools pytest-cov sympy sybil
-          pip install -r requirements.txt
+          pip install setuptools
+          pip install -r requirements-dev.txt
 
       - name: Build and install package from source
         run: python setup.py develop
@@ -74,60 +106,54 @@ jobs:
         run: pytest --cov=./ --cov-report=xml
 
       - name: Upload coverage
-        uses: codecov/codecov-action@v3.1.4
-
-  # build_windows_test:
-  #   needs: [code_lint]
-  #   strategy:
-  #     matrix:
-  #       os: ["windows-latest"]
-  #       python-version: [3.6, 3.7]
-  #   runs-on: ${{ matrix.os }}
-
-  #   env:
-  #     LIB: "C:\\Miniconda\\Library\\lib"
-  #     INCLUDE: "C:\\Miniconda\\Library\\include;C:\\Miniconda\\Library\\include\\openblas"
-  #     MRSIM_LIB: "C:\\Miniconda\\Library\\lib"
-  #   steps:
-  #     - name: Checkout
-  #       uses: actions/checkout@v3
-
-  #     - name: Set up Python ${{ matrix.python-version }}
-  #       uses: actions/setup-python@v4
-  #       with:
-  #         python-version: ${{ matrix.python-version }}
-
-  #     - name: Install windows dependencies
-  #       run: |
-  #         C:\Miniconda\Scripts\conda install -c conda-forge openblas fftw
-
-  #     - name: Install package dependencies
-  #       run: |
-  #         python -m pip install --upgrade pip
-  #         pip install pytest cython setuptools pytest-cov sympy
-  #         pip install -r requirements.txt
-
-  #     - name: Build and install package from source
-  #       run: python setup.py develop
-
-  #     - name: Test with pytest
-  #       run: pytest --cov=./ --cov-report=xml
-
-  #     - name: Upload coverage
-  #       uses: codecov/codecov-action@v3.1.4
+        uses: codecov/codecov-action@v4.5.0
 
-  testing_windows:
+  testing_mac_intel:
     needs: [code_lint]
+    runs-on: "macos-13"
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9, "3.10", "3.11"]
+        python-version: ["3.12"]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install macos system dependencies
+        run: brew install openblas fftw
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install setuptools
+          pip install -r requirements-dev.txt
+
+      - name: Build and install package from source
+        run: python setup.py develop
+
+      - name: Test with pytest
+        run: pytest --cov=./ --cov-report=xml
+
+      - name: Upload coverage
+        uses: codecov/codecov-action@v4.5.0
+
+  testing_windows:
+    needs: [code_lint]
     runs-on: "windows-latest"
+    strategy:
+      matrix:
+        python-version: [3.9, "3.10", "3.11", "3.12"]
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         env:
           ACTIONS_ALLOW_UNSECURE_COMMANDS: "true"
         with:
@@ -150,4 +176,4 @@ jobs:
         shell: pwsh
         run: pytest --cov=./ --cov-report=xml
       - name: Upload coverage
-        uses: codecov/codecov-action@v3.1.4
+        uses: codecov/codecov-action@v4.5.0