Merge branch 'main' into ram

matthieutrs · matthieutrs · commit 64dfb69684a4 · 2025-07-18T09:06:09.000+02:00
diff --git a/.circleci/config.yml b/.circleci/config.yml
diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -3,6 +3,10 @@ Thank you for contributing to DeepInverse!
 
 Please refer to our [contributing guidelines](https://deepinv.github.io/deepinv/contributing.html) for full instructions on how to contribute, including writing tests, documentation and code style.
 
+Once the GitHub tests have been approved by a maintainer (only required for first-time contributors), and the `Build Docs` GitHub action
+has run successfully, you can download the documentation as a zip file from the [Actions page](https://github.com/deepinv/deepinv/actions/workflows/documentation.yml). Look for the workflow run corresponding to your pull request.
+
+
 ### Checks to be done before submitting your PR
 
 - [ ] `python3 -m pytest deepinv/tests` runs successfully.
diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
@@ -16,6 +16,7 @@ concurrency:
 
 permissions:
   contents: write
+  pull-requests: write  
 
 jobs:
   docs:
@@ -41,12 +42,15 @@ jobs:
           # Run doctest with sphinx, to get the extra IGNORE_OUTPUT primitive
           # using plot_gallery=0 to avoid building examples
           sphinx-build -M doctest docs/source/ docs/build/ -D plot_gallery=0 -v $_doctest_files
-      - name: Deploy
-        uses: peaceiris/actions-gh-pages@v3
-        if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
+      - name: Upload Documentation Artifact
+        id: upload-artifact
+        uses: actions/upload-artifact@v4
         with:
-          publish_branch: gh-pages
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: _build/
-          force_orphan: true
-          enable_jekyll: false
+          name: documentation
+          path: _build/
+
+      # Log artifact URL 
+      - name: Link to generated docs here
+        if: ${{ github.event_name == 'pull_request' && github.event.action != 'closed' }}
+        run: |
+          echo "Documentation artifact URL: ${{ steps.upload-artifact.outputs.artifact-url }}"
diff --git a/.github/workflows/expose_doc.yml b/.github/workflows/expose_doc.yml
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
@@ -15,9 +15,9 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: '3.9'
+          python-version: '3.10'   # minimum supported version 
       - uses: psf/black@stable
       - name: Install and run ruff
         run: |
           pip install ruff
-          ruff check --target-version "py39" --select "UP006"
+          ruff check --target-version "py310" --select "UP006"
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -50,7 +50,8 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.9'
+          python-version: '3.10'  # minimum supported version
+          cache: 'pip'  # caching pip dependencies
 
       - name: Install tools
         run: |
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -24,16 +24,32 @@ jobs:
     strategy:
       matrix:
         include:
-          # Test with all dependencies
+          # Ubuntu tests
           - os: ubuntu-latest
-            version_python: 3.9
+            version_python: "3.10"
             extra: dataset,denoisers,test
-            name: "ubuntu all dependencies"
-          # Test with all dependencies
+            name: "ubuntu py3.10 all dependencies"
+          - os: ubuntu-latest
+            version_python: "3.11"
+            extra: dataset,denoisers,test
+            name: "ubuntu py3.11 all dependencies"
+          - os: ubuntu-latest
+            version_python: "3.12"
+            extra: dataset,denoisers,test
+            name: "ubuntu py3.12 all dependencies"
+          # Windows tests
+          - os: windows-latest
+            version_python: "3.10"
+            extra: dataset,denoisers,test
+            name: "windows py3.10 all dependencies"
           - os: windows-latest
-            version_python: 3.9
+            version_python: "3.11"
             extra: dataset,denoisers,test
-            name: "windows all dependencies"
+            name: "windows py3.11 all dependencies"
+          - os: windows-latest
+            version_python: "3.12"
+            extra: dataset,denoisers,test
+            name: "windows py3.12 all dependencies"
     env:
       DEEPINV_MOCK_TESTS: "True"
     steps:
@@ -47,6 +63,17 @@ jobs:
         run: |
           pip install .[${{ matrix.extra }}]
 
+      # For debugging purposes
+      - name: Check Python version
+        run: python3 --version
+
+      - name: Check installed packages
+        run: pip list
+
+      - name: Test importing numpy
+        run: python3 -c "import numpy; print('NumPy version:', numpy.__version__)"
+      # ----------------------------
+
       - name: Test with pytest and generate coverage report
         run: |
           python3 -m pytest -n 2 --dist=loadgroup --cov=deepinv --junitxml=junit.xml -o junit_family=legacy -v
diff --git a/.github/workflows/upload_pypi.yml b/.github/workflows/upload_pypi.yml
@@ -18,7 +18,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.9'
+          python-version: '3.10'
 
       - name: Install tools
         run: |
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -30,6 +30,7 @@ Changed
 - Make autograd use the base linear operator for `deepinv.physics.adjoint_function` (:gh:`519` by `Jérémy Scanvic`_)
 - Parallelize the test suite making it 15% faster (:gh:`522` by `Jérémy Scanvic`_)
 - Adjust backward paths for tomography (:gh:`535` by `Johannes Hertrich`_)
+- Update python version to 3.10+ (:gh:`605` by `Minh Hai Nguyen`_)
 
 Fixed
 ^^^^^
diff --git a/CITATION.cff b/CITATION.cff
@@ -56,7 +56,7 @@ authors:
     given-names: "Romain"
   - family-names: "Weiss"
     given-names: "Pierre"
-version: "0.3.0"
+version: "0.3.2"
 doi: "https://doi.org/10.48550/arXiv.2505.20160"
 date-released: 2023-06-30
 repository-code: "https://github.com/deepinv/deepinv"
diff --git a/README.rst b/README.rst
@@ -42,6 +42,10 @@ To install the latest stable release of ``deepinv``, you can simply do:
 
     pip install deepinv
 
+    # or using uv for faster installation
+
+    uv pip install deepinv
+
 You can also install the latest version of ``deepinv`` directly from github:
 
 .. code-block:: bash
@@ -148,8 +152,8 @@ Star history
    :target: https://github.com/deepinv/deepinv/actions/workflows/test.yml
 .. |Docs Status| image:: https://github.com/deepinv/deepinv/actions/workflows/documentation.yml/badge.svg
    :target: https://github.com/deepinv/deepinv/actions/workflows/documentation.yml
-.. |Python Version| image:: https://img.shields.io/badge/python-3.9%2B-blue
-   :target: https://www.python.org/downloads/release/python-390/
+.. |Python Version| image:: https://img.shields.io/badge/python-3.10%2B-blue
+   :target: https://www.python.org/downloads/release/python-3100/
 .. |codecov| image:: https://codecov.io/gh/deepinv/deepinv/branch/main/graph/badge.svg?token=77JRvUhQzh
    :target: https://codecov.io/gh/deepinv/deepinv
 .. |pip install| image:: https://img.shields.io/pypi/dm/deepinv.svg?logo=pypi&label=pip%20install&color=fedcba
diff --git a/deepinv/__about__.py b/deepinv/__about__.py
@@ -7,3 +7,12 @@
 __author__ = metadata["Author"]
 __license__ = metadata["License"]
 __url__ = metadata["Project-URL"]
+
+__all__ = [
+    "__title__",
+    "__summary__",
+    "__version__",
+    "__author__",
+    "__license__",
+    "__url__",
+]
diff --git a/deepinv/models/GSPnP.py b/deepinv/models/GSPnP.py
@@ -97,7 +97,7 @@ def GSDRUNet(
     :param int in_channels: Number of input channels
     :param int out_channels: Number of output channels
     :param int nb: Number of blocks in the DRUNet
-    :param list nc: Number of channels in the DRUNet
+    :param list[int,int,int,int] nc: number of channels per convolutional layer in the DRUNet. The network has a fixed number of 4 scales with ``nb`` blocks per scale (default: ``[64,128,256,512]``).
     :param str act_mode: activation mode, "R" for ReLU, "L" for LeakyReLU "E" for ELU and "S" for Softplus.
     :param str downsample_mode: Downsampling mode, "avgpool" for average pooling, "maxpool" for max pooling, and
         "strideconv" for convolution with stride 2.
diff --git a/deepinv/models/diffunet.py b/deepinv/models/diffunet.py
@@ -26,11 +26,17 @@ class DiffUNet(Denoiser):
 
     The network can handle images of size :math:`2^{n_1}\times 2^{n_2}` with :math:`n_1,n_2 \geq 5`.
 
+    .. note::
+
+        The weights available for download are pretrained on 256x256 images,
+        thus generation is likely to fail for different image sizes
+        (see https://github.com/deepinv/deepinv/issues/602).
+
     .. warning::
 
         This model has 2 forward modes:
 
-        * ``forward_diffuse``: in the first mode, the model takes a noisy image and a timestep as input and estimates the noise map in the input image. This mode is consistent with the original implementation from the authors, i.e. it assumes the same image normalization.
+        * ``forward_diffusion``: in the first mode, the model takes a noisy image and a timestep as input and estimates the noise map in the input image. This mode is consistent with the original implementation from the authors, i.e. it assumes the same image normalization.
         * ``forward_denoise``: in the second mode, the model takes a noisy image and a noise level as input and estimates the noiseless underlying image in the input image. In this case, we assume that images have values in [0, 1] and a rescaling is performed under the hood.
 
 
@@ -385,7 +391,10 @@ def forward_diffusion(self, x, timesteps, y=None):
         :param x: an [N x C x ...] Tensor of inputs.
         :param timesteps: a 1-D batch of timesteps.
         :param y: an [N] Tensor of labels, if class-conditional. Default=None.
-        :return: an `(N, C, ...)` Tensor of outputs.
+        :return: an `(N, 2*C, ...)` Tensor of outputs, where the first C
+            channels are the noise estimates and the remaining C are the per-pixel
+            variances, as in the original implementation:
+            https://github.com/openai/guided-diffusion/blob/main/guided_diffusion/gaussian_diffusion.py#L263
         """
         assert (y is not None) == (
             self.num_classes is not None
diff --git a/deepinv/models/drunet.py b/deepinv/models/drunet.py
@@ -23,9 +23,8 @@ class DRUNet(Denoiser):
 
     :param int in_channels: number of channels of the input.
     :param int out_channels: number of channels of the output.
-    :param list nc: number of convolutional layers.
+    :param list[int,int,int,int] nc: number of channels per convolutional layer, the network has a fixed number of 4 scales with ``nb`` blocks per scale (default: ``[64,128,256,512]``).
     :param int nb: number of convolutional blocks per layer.
-    :param int nf: number of channels per convolutional layer.
     :param str act_mode: activation mode, "R" for ReLU, "L" for LeakyReLU "E" for ELU and "s" for Softplus.
     :param str downsample_mode: Downsampling mode, "avgpool" for average pooling, "maxpool" for max pooling, and
         "strideconv" for convolution with stride 2.
diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst
@@ -44,7 +44,13 @@ check the following points:
   After making the desired changes, check the documentation by installing
   ``sphinx`` and building the docs by running one of the commands in the table below in the ``docs`` directory.
   Note that if the build process fails, supplementary additional libraries may need to be manually installed
-  (e.g. ``sphinx-gallery``): please follow instructions in the log.
+  (e.g. ``sphinx-gallery``): please follow instructions in the log. 
+
+.. tip::
+
+  Once the GitHub tests have been approved by a maintainer (only required for first-time contributors), and the `Build Docs` GitHub action
+  has run successfully, you can download the documentation as a zip file from the `Actions page <https://github.com/deepinv/deepinv/actions/workflows/documentation.yml>`_. Look for the workflow run corresponding to your pull request.
+
 
 .. list-table::
    :widths: 40 50
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -78,8 +78,8 @@ If you use DeepInverse in your research, please cite the following paper (availa
    :target: https://github.com/deepinv/deepinv/actions/workflows/test.yml
 .. |Docs Status| image:: https://github.com/deepinv/deepinv/actions/workflows/documentation.yml/badge.svg
    :target: https://github.com/deepinv/deepinv/actions/workflows/documentation.yml
-.. |Python Version| image:: https://img.shields.io/badge/python-3.9%2B-blue
-   :target: https://www.python.org/downloads/release/python-390/
+.. |Python Version| image:: https://img.shields.io/badge/python-3.10%2B-blue
+   :target: https://www.python.org/downloads/release/python-3100/
 .. |codecov| image:: https://codecov.io/gh/deepinv/deepinv/branch/main/graph/badge.svg?token=77JRvUhQzh
    :target: https://codecov.io/gh/deepinv/deepinv
 .. |pip install| image:: https://img.shields.io/pypi/dm/deepinv.svg?logo=pypi&label=pip%20install&color=fedcba
diff --git a/examples/self-supervised-learning/demo_n2n_denoising.py b/examples/self-supervised-learning/demo_n2n_denoising.py
@@ -51,7 +51,7 @@
 # In this example, we use the MNIST dataset as the base image dataset.
 #
 
-operation = "denoising"
+operation = "denoising_n2n"
 train_dataset_name = "MNIST"
 
 transform = transforms.Compose([transforms.ToTensor()])
diff --git a/pyproject.toml b/pyproject.toml
@@ -14,18 +14,21 @@ classifiers = [
     "License :: OSI Approved :: BSD License",
     "Operating System :: OS Independent",
     "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "Topic :: Utilities",
     "Topic :: Scientific/Engineering",
     "Topic :: Software Development :: Libraries",
 ]
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 version = "0.3.2"
 dependencies = [
     "numpy",
     "matplotlib",
     "hdf5storage",
     "tqdm",
-    "torch<2.7",
+    "torch>=2.2.0", 
     "torchvision",
     "torchmetrics",
     "einops",
