update workflow

.github/workflows/style.yml

@@ -0,0 +1,44 @@
+name: Style
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  PYTHON_VERSION: "3.10"
+
+jobs:
+  linter-check:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Set up Python ${{ env.PYTHON_VERSION }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+          cache: pip
+
+      - name: Install Python deps
+        shell: bash
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install black ruff
+          python -m pip install -e .
+
+      - name: Black Check
+        shell: bash
+        run: black . --diff --color --check
+
+      # - name: ruff Check
+        # shell: bash
+        # run: ruff check src

.github/workflows/test-ci.yml

@@ -1,154 +1,54 @@
-name: CI
+name: CI-CD
 
 on:
   push:
     branches: [ "main" ]
   pull_request:
     branches: [ "main" ]
 
-  workflow_dispatch:
-
 jobs:
-  linter-check:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v3
-      - name: Set up Python "3.10"
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.10"
-      - name: Black setup
-        shell: bash
-        run: pip install black ruff mypy
-      - name: Black Check
-        shell: bash
-        run: black . --diff --color --check
-
-  test-cpu:
+  test:
     runs-on: ubuntu-latest
-    needs: linter-check
+
     strategy:
-      fail-fast: true
       matrix:
-        python-version: ["3.12", "3.10"]
+        python-version: [3.11, 3.12]  # Specify the desired Python versions
 
     steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Install Dependencies
-        shell: bash
-        run: |
-          python --version
-          python -m pip install --upgrade pip
-          python -m pip install .[test]
-      - name: Run Tests
-        shell: bash
-        run: |
-          export COVERAGE_FILE=coverage_${{ matrix.python-version }}
-          pytest -n auto --cov --disable-pytest-warnings --cov-branch --cov-report=term    
-      - name: Upload coverage
-        if: success()
-        uses: actions/upload-artifact@v4
-        with:
-          name: coverage_${{ matrix.python-version }}
-          path: coverage_${{ matrix.python-version }}
-
-  get-commit-message:
-    runs-on: ubuntu-latest
-    outputs:
-       message: ${{ steps.get_commit_message.outputs.message }}
-    steps:
-       - uses: actions/checkout@v3
-         with:
-           ref: ${{ github.event.pull_request.head.sha }}
-       - name: Get commit message
-         id: get_commit_message
-         run: |
-            COMMIT_MESSAGE=$(git log -1 --pretty=%B)
-            echo "Commit message $COMMIT_MESSAGE"
-            echo "::set-output name=message::$COMMIT_MESSAGE"
-    
-  coverage:
-    runs-on: ubuntu-latest
-    needs: [test-cpu, get-commit-message]
-    if: ${{ always() }}
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v3
-
-      - name: Collect Coverages
-        uses: actions/download-artifact@v4
-        with:
-          path: coverage_data
-          pattern: coverage_*
-          merge-multiple: true
-
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ env.PYTHON_VERSION }}
-
-      - name: add the coverage tool
-        shell: bash
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install coverage[toml]
-          python -m pip install -e .
-
-      - name: Combine coverage
-        run: |
-          export COVERAGE_FILE=coverage_combined
-          coverage combine -a coverage_data/*
+      - name: Checkout code
+        uses: actions/checkout@v4
 
-      - name: Upload Combined coverage
-        uses: actions/upload-artifact@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
         with:
-          name: coverage_combined
-          path: coverage_combined
-
-      - name: Reports
-        run: |
-          export COVERAGE_FILE=coverage_combined
-          coverage xml
-          coverage report
-          echo COVERAGE_PERC=$(coverage report | tail -n 1 | grep -oE [0-9\.]*?% | cut -d '%' -f1) >> $GITHUB_ENV
+          python-version: ${{ matrix.python-version }}
 
-      - name: Create a Coverage Badge
-        if: ${{github.event_name == 'push'}}
+      - name: Install dependencies
         run: |
-          wget https://img.shields.io/badge/coverage-${{env.COVERAGE_PERC}}%25-green -O coverage_badge.svg
+          pip install .[test]
 
-      - name: Upload badge as artifact
-        if: ${{github.event_name == 'push'}}
-        uses: actions/upload-artifact@v4
+      - name: Run tests
+        run: pytest --cov --cov-report=xml tests	
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v4.0.1
         with:
-          name: coverage_badge
-          path: coverage_badge.svg
+          token:  ${{ secrets.CODECOV_TOKEN }}
+          slug: INFN-MRI/torchsim
 
-  BuildDocs:
-    name: Build API Documentation
-    runs-on: ubuntu-latest
-    needs: get-commit-message
-    if: ${{ contains(needs.get-commit-message.outputs.message, '!docs_build') || github.ref == 'refs/heads/main' }}
+  docs:
+    runs-on: ubuntu-20.04
+    needs: test
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
-      - name: Get history and tags for SCM versioning to work
-        run: |
-          git fetch --prune --unshallow
-          git fetch --depth=1 origin +refs/tags/*:refs/tags/*
-
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.10"
 
-      - name: Restore cached ixi directory
+      - name: Restore cached IXI directory
         uses: actions/cache/restore@v4
         id: cache-restore
         with:
@@ -166,49 +66,22 @@ jobs:
         run: |
           python -m sphinx docs docs_build
       
-      - name: Display data
-        run: ls -R
-        working-directory: docs_build/_static
+      - name: Display structure of docs
+        run: ls -R docs_build/	 
 
-      - name: Cache ixi directory
+      - name: Cache IXI directory
         uses: actions/cache/save@v4
         if: ${{ steps.cache-restore.outputs.cache-hit != 'true' }}
         with:
           path: ~/.ixi
-          key: ${{ runner.os }}-ixi
-
-      - name: Upload artifact
-        id: artifact-upload-step
-        uses: actions/upload-artifact@v4
-        with:
-          # Upload the docs
-          name: docs
-          path: 'docs_build'
-          retention-days: 5
-
-  CompileDocs:
-    name: Compile the coverage badge in docs
-    runs-on: ubuntu-latest
-    if: ${{ github.ref == 'refs/heads/main' }}
-    needs: [BuildDocs, coverage]
-    steps:
-      - name: Get the docs_build artifact
-        uses: actions/download-artifact@v4
-        with:
-          name: docs
-          path: docs_build
-          overwrite: true
-
-      - name: Get the badge from CI
-        uses: actions/download-artifact@v4
-        with:
-          name: coverage_badge
-          path: docs_build/_static
-          github-token: ${{ secrets.GITHUB_TOKEN }}
+          key: ${{ runner.os }}-ixi 
 
-      - name: ReUpload artifacts
-        uses: actions/upload-artifact@v4
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v4
         with:
-          name: docs_final
-          retention-days: 20
-          path: docs_build
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./docs_build
+          destination_dir: .  # Ensure you deploy to the root of the gh-pages branch
+          publish_branch: gh-pages
+          keep_files: false
+

README.rst

@@ -5,13 +5,10 @@ TorchSim is a pure Pytorch-based MR simulator, including analytical and EPG mode
 
 |Coverage| |CI| |CD| |License| |Codefactor| |Sphinx| |PyPi| |Black| |PythonVersion|
 
-.. |Coverage| image:: https://infn-mri.github.io/torchsim/_static/coverage_badge.svg
-   :target: https://infn-mri.github.io/torchsim
-
-.. |CI| image:: https://github.com/INFN-MRI/torchsim/workflows/CI/badge.svg
-   :target: https://github.com/INFN-MRI/torchsim
+.. |Coverage| image:: https://codecov.io/gh/INFN-MRI/torchsim/graph/badge.svg?token=qtB53xANwI 
+   :target: https://codecov.io/gh/INFN-MRI/torchsim
 
-.. |CD| image:: https://github.com/INFN-MRI/torchsim/workflows/CD/badge.svg
+.. |CI/CD| image:: https://github.com/INFN-MRI/torchsim/workflows/CI-CD/badge.svg
    :target: https://github.com/INFN-MRI/torchsim
 
 .. |License| image:: https://img.shields.io/github/license/INFN-MRI/torchsim

docs/sg_execution_times.rst

@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**01:31.589** total execution time for 4 files **from all galleries**:
+**01:07.135** total execution time for 4 files **from all galleries**:
 
 .. container::
 
@@ -33,14 +33,14 @@ Computation times
      - Time
      - Mem (MB)
    * - :ref:`sphx_glr_generated_autoexamples_02-synth-data.py` (``../examples/02-synth-data.py``)
-     - 00:41.073
+     - 00:42.438
      - 0.0
    * - :ref:`sphx_glr_generated_autoexamples_03-fitting.py` (``../examples/03-fitting.py``)
-     - 00:24.580
-     - 0.0
-   * - :ref:`sphx_glr_generated_autoexamples_04-derivatives.py` (``../examples/04-derivatives.py``)
-     - 00:14.056
+     - 00:24.697
      - 0.0
    * - :ref:`sphx_glr_generated_autoexamples_01-simple-simulator.py` (``../examples/01-simple-simulator.py``)
-     - 00:11.881
+     - 00:00.000
+     - 0.0
+   * - :ref:`sphx_glr_generated_autoexamples_04-derivatives.py` (``../examples/04-derivatives.py``)
+     - 00:00.000
      - 0.0