Merge pull request #222 from somexlab/v0.3.9

v0.3.9

.github/workflows/build_wheels.yml

@@ -14,6 +14,9 @@ on:
     branches:
       - main
 
+  # trigger on request
+  workflow_dispatch:
+
 jobs:
   build_sdist:
     name: Build source distribution
@@ -37,7 +40,7 @@ jobs:
           if-no-files-found: error
 
   build_wheels:
-    name: Build wheel for ${{ matrix.os }}, Python ${{ matrix.python-version }}
+    name: Build wheel for ${{ matrix.os }}, Python ${{ matrix.python-version[1] }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
@@ -48,6 +51,12 @@ jobs:
       - name: Checkout code
         uses: actions/checkout@v4
 
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+        if: runner.os == 'Windows'
+
       - name: Build wheels
         uses: pypa/cibuildwheel@v2.17.0
         env:
@@ -64,10 +73,15 @@ jobs:
           CIBW_ARCHS_WINDOWS: auto64
 
           # Configure environment variables
-          MACOSX_DEPLOYMENT_TARGET: "10.14"
+          MACOSX_DEPLOYMENT_TARGET: "10.9"
+
+          # verbosity
+          CIBW_BUILD_VERBOSITY: 1
 
           # Test the wheels
-          # TBD
+          #CIBW_TEST_REQUIRES: "pytest pytest-regtest"
+          #CIBW_TEST_COMMAND: "pytest -v {project}/tests"
+          #CIBW_TEST_SKIP: 
 
       - name: Upload wheel artifacts
         uses: actions/upload-artifact@v4

CHANGELOG.rst

@@ -5,6 +5,24 @@ Change Log
 v0.3
 ----
 
+v0.3.9 (2024-04-04)
+^^^^^^^^^^^^^^^^^^^
+
+*Added*
+
+* Instructions for installation via PyPI and on Google Colab
+
+*Changed*
+
+* Updated minimal example notebook
+
+*Fixed*
+
+* Windows' PyPI wheels
+
+.. *Deprecated*
+.. *Removed*
+
 v0.3.8 (2024-03-28)
 ^^^^^^^^^^^^^^^^^^^
 

docs/source/colab.rst

@@ -0,0 +1,100 @@
+.. Copyright (c) 2023-2023 University of Vienna, Enrico Lattuada, Fabian Krautgasser, and Roberto Cerbino.
+.. Part of FastDDM, released under the GNU GPL-3.0 License.
+
+Installing in Google Colab
+==========================
+
+**FastDDM** can be installed in `Google Colab <https://colab.research.google.com/>`_, also with GPU
+support. This allows to test the library without the need to install it locally on workstations.
+
+.. tip::
+
+    To better understand what the different options imply, see :ref:`build` and
+    :ref:`install_sdist`.
+
+Open a new notebook.
+If you wish to use the GPU provided by the host server, change the ``runtime type``.
+To do so, select from the toolbar ``Runtime > Change runtime type`` and select a GPU available from
+the ``Hardware accelerator`` list.
+As of today (3 April 2024), with the free plan, you should have access to the T4 GPU.
+Save and go back to your notebook.
+
+To check that the GPU is working, run the following command in a cell
+
+.. code-block:: python
+
+    !nvidia-smi
+
+From pip source distribution
+----------------------------
+
+To install the source distribution via ``pip``, run the command below
+
+.. code-block:: python
+
+    !pip3 install --no-binary fastddm fastddm
+
+From GitHub repository source code
+----------------------------------
+
+This is the preferred mode if you want to run the unit tests.
+Clone the source code from the GitHub repository
+
+.. code-block:: python
+
+    !git clone --depth 1 --branch <version_name> https://github.com/somexlab/fastddm.git
+
+For example, to clone the version ``v0.3.8``, run
+
+.. code-block:: python
+
+    !git clone --depth 1 --branch v0.3.8 https://github.com/somexlab/fastddm.git
+
+Change directory to the source code one
+
+.. code-block:: python
+
+    %cd fastddm
+
+If you want to install the library with C++ support, run the following command in a cell
+
+.. code-block:: python
+
+    %env ENABLE_CPP=ON
+
+If you want to install the library with GPU (CUDA) support, run the following command in a cell
+
+.. code-block:: python
+
+    %env ENABLE_CUDA=ON
+
+(This also enables the C++ support.)
+
+.. warning::
+
+    Due to the small amount of available RAM memory, we also warmly recommend to enable the single
+    precision calculation option::
+
+      %env SINGLE_PRECISION=ON
+
+Finally, install **FastDDM**
+
+.. code-block:: python
+
+    !python3 -m pip install .
+
+.. tip::
+
+    To run unit tests, you need some additional libraries. Run::
+
+      !python3 -m pip install pytest pytest-regtest
+
+    Then, run the tests with::
+
+      !pytest -v
+
+Now you can go back to your home directory and work with **FastDDM**!
+
+.. code-block:: python
+
+    %cd ..

docs/source/conf.py

@@ -12,7 +12,7 @@
 year = datetime.date.today().year
 copyright = f"2023-{year}, Enrico Lattuada, Fabian Krautgasser, Roberto Cerbino"
 author = "Enrico Lattuada, Fabian Krautgasser, Roberto Cerbino"
-version = "0.3.2"
+version = "0.3.9"
 release = version
 
 pygments_style = "friendly"

docs/source/getting-started.rst

@@ -11,3 +11,4 @@ Getting started
     build
     conda
     pypi
+    colab

docs/source/pypi.rst

@@ -4,6 +4,24 @@
 Installing from PyPI
 ====================
 
+Install precompiled wheels
+--------------------------
+
+Precompiled wheels are available through `PyPI <https://pypi.org/project/fastddm/>`_ with C++
+support for most OSs and Python versions.
+The command below will install **FastDDM**
+
+.. code-block:: bash
+
+    $ pip3 install fastddm
+
+.. warning::
+
+    If wheels are not available for your system, ``pip`` will fall back to the installation of the
+    source distribution. Refer to the :ref:`build` section for more information.
+
+.. _install_sdist:
+
 Install source distribution
 ---------------------------
 
@@ -14,4 +32,4 @@ Run the following line in your terminal:
 
 .. code-block:: bash
 
-    $ pip3 install --no-binary fastddm
+    $ pip3 install --no-binary fastddm fastddm

pyproject.toml

@@ -36,6 +36,7 @@ dynamic = [ "license", "version" ]
 keywords = [
     "cuda",
     "differential-dynamic-microscopy",
+    "digital-fourier-microscopy",
     "gpu",
     "image-analysis",
     "microscopy",

setup.py

@@ -175,7 +175,7 @@ def build_extension(self, ext):
 setup(
     name="fastddm",
     use_scm_version={
-        "fallback_version": "0.3.2",
+        "fallback_version": "0.3.9",
     },
     packages=find_packages(),
     setup_requires=[

src/python/make_install_setup.py

@@ -9,7 +9,7 @@
     name="fastddm",
     use_scm_version={
         "root": "${CMAKE_SOURCE_DIR}",
-        "fallback_version": "0.3.2",
+        "fallback_version": "0.3.9",
     },
     setup_requires=["setuptools_scm"],
     packages=["fastddm"],