Change to Pyproject.toml installation and uv, remove python 3.8 support, add python 3.13 and 3.14 support

.github/workflows/main.yml

@@ -7,11 +7,11 @@ on:
     branches: [ master ]
 
 jobs:
-  test:
+  test-uv-pip-install:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13', '3.14']
     continue-on-error: true
 
     steps:
@@ -22,14 +22,43 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Install dependencies
+      - name: Install uv
         run: |
-          pip install --upgrade pip
-          pip install -r requirements.txt
-          pip install -e . --no-deps
+          pip install uv
+
+      - name: Create virtual environment
+        run: |
+          uv venv
+
+      - name: Install dependencies with uv
+        run: |
+          uv pip install ."[tests]"
 
       - name: Run tests
-        run: pytest
+        run: |
+          uv run pytest
+
+  test-pip-install:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.9', '3.14']
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies with pip
+        run: |
+          pip install ."[tests]"
+
+      - name: Run tests
+        run: |
+          pytest
 
   build-docs:
     if: github.event_name == 'push' && github.ref == 'refs/heads/master'
@@ -52,12 +81,17 @@ jobs:
         with:
           python-version: '3.9'
 
-      - name: Install dependencies
+      - name: Install uv
+        run: |
+          pip install uv
+
+      - name: Create virtual environment
+        run: |
+          uv venv
+
+      - name: Install dependencies with uv
         run: |
-          pip install --upgrade pip
-          pip install -r requirements.txt
-          pip install sphinx sphinx_rtd_theme sphinx-argparse
-          pip install -e . --no-deps
+          uv pip install ."[docs]"
 
       - name: Build docs
         working-directory: docs

.github/workflows/publish.yml

@@ -19,12 +19,19 @@ jobs:
       uses: actions/setup-python@v4
       with:
         python-version: "3.x"
-    - name: Install dependencies
+    - name: Install uv
       run: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel
-    - name: Build package (setup.py)
+        pip install uv
+
+    - name : Create virtual environment
       run: |
-        python setup.py sdist bdist_wheel
+        uv venv
+
+    - name: Install project with uv
+      run: |
+        uv pip install -e .
+    - name: Build package with uv
+      run: |
+        uv build
     - name: Publish package distributions to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1

README.md

@@ -26,14 +26,57 @@ model.compare(dataset) # See how the simulated and measured patterns compare
 plt.show()
 ```
 
+Further documentation is found [here](https://cdtools-developers.github.io/cdtools/).
+
+# Installation
+
+CDTools can be installed in several ways depending on your needs. For most users, installation from pypi is recommended. For developers or those who want the latest features, installation from source is available.
+
+## Installation from pypi
+
 CDTools can be installed via pip as the [cdtools-py](https://pypi.org/project/cdtools-py/) package on [PyPI](https://pypi.org/):
 
 ```bash
 $ pip install cdtools-py
 ```
 
-Further documentation is found [here](https://cdtools-developers.github.io/cdtools/).
+or using [uv](https://github.com/astral-sh/uv):
+
+```bash
+$ uv pip install cdtools-py
+```
+
+## Installation from Source
+
+For development or to access the latest features, CDTools can be installed directly from source:
+
+
+```bash
+$ git clone https://github.com/cdtools-developers/cdtools.git
+$ cd cdtools
+$ pip install -e .
+```
+
+
+or using [uv](https://github.com/astral-sh/uv):
+
+```bash
+$ git clone https://github.com/cdtools-developers/cdtools.git
+$ cd cdtools
+$ uv pip install -e .
+```
 
+## Installing for Contributors (with tests and docs dependencies)
+
+If you want to run the test suite or build the documentation, install with the extra dependencies:
+
+```bash
+$ pip install -e ."[tests,docs]"
+```
+or with uv:
+```bash
+$ uv pip install -e ."[tests,docs]"
+```
 
 CDTools was developed in the [photon scattering lab](https://scattering.mit.edu/) at MIT, and further development took place within the [computational x-ray imaging group](https://www.psi.ch/en/cxi) at PSI. The code is distributed under an MIT (a.k.a. Expat) license. If you would like to publish any work that uses CDTools, please contact [Abe Levitan](mailto:abraham.levitan@psi.ch).
 

docs/source/installation.rst

@@ -1,7 +1,7 @@
 Installation
 ============
 
-CDTools supports python >=3.8 and can be installed via pip as the the `cdtools-py`_ package on `PyPI`_. If you plan to contribute to the code or need a custom environment, installation from source is also possible.
+CDTools supports python >=3.9 and can be installed via pip as the the `cdtools-py`_ package on `PyPI`_. If you plan to contribute to the code or need a custom environment, installation from source is also possible.
 
 .. _`cdtools-py`: https://pypi.org/project/cdtools-py/
 .. _`PyPI`: https://pypi.org/
@@ -15,6 +15,14 @@ To install from `PyPI`_, run:
 
    $ pip install cdtools-py
 
+or you can use `uv`_ for a faster installation:
+
+.. _`uv`: https://github.com/astral-sh/uv
+
+.. code:: bash
+
+   $ uv pip install cdtools-py
+
 Pytorch, a major dependence of CDTools, often needs to be installed with a specific CUDA version for machine compatability. If you run into issues with pytorch, consider first installing pytorch into your environment using the instructions on `the pytorch site`_.
 
 .. _`the pytorch site`: https://pytorch.org/get-started/locally/
@@ -31,18 +39,51 @@ The source code for CDTools is hosted on `Github`_.
 .. _`Github`: https://github.com/cdtools-developers/cdtools
 
 
-Step 2: Install Dependencies
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+To download the source code, you can either clone the repository using git:
+
+.. code:: bash
+
+   $ git clone https://github.com/cdtools-developers/cdtools.git
+
+or you can download a zip file of the repository from the `releases page`_.
+
+.. _`releases page`: https://github.com/cdtools-developers/cdtools/releases
 
-The major dependency for CDTools is pytorch version 2.3.0 or greater. Because the details of the pytorch installation can vary depending on platform and GPU availability, it is recommended that you first install pytorch using the instructions on `the pytorch site`_. The remaining dependencies can be installed by running the following command from the top level directory of the git repository:
+
+Step 2: Install
+^^^^^^^^^^^^^^^
+
+Move to the directory where you downloaded the source code. It is recommended that you create a new python virtual environment to install CDTools into.
+
+Installation using pip and uv. Editable mode is recommended for development purposes and is added with the `-e` flag.
 
 .. code:: bash
-
-   $ pip install -r requirements.txt
 
-Note that several optional dependencies used for testing and documentation will also be installed. The full set of dependencies and minimum requirements are listed below. CDTools is reguarly tested with the latest versions of these packages and with python 3.8 through 3.12.
+   $ pip install -e .
+
+or using uv:
+
+.. code:: bash
+
+   $ uv pip install -e .
+
 
-Required dependencies:
+To install the required test and documentation dependencies as well, use:
+
+.. code:: bash
+
+   $ pip install -e ."[tests,docs]"
+
+or using uv:
+
+.. code:: bash
+
+   $ uv pip install -e ."[tests,docs]"
+
+CDTools is reguarly tested with the latest versions of these packages and with python 3.9 through 3.14.
+
+
+Required dependencies (see pyproject.toml for all details):
 
    * `numpy <http://www.numpy.org>`_ >= 1.0
    * `scipy <http://www.scipy.org>`_ >= 1.0
@@ -63,30 +104,13 @@ Optional dependencies for building docs:
    * `sphinx_rtd_theme <https://sphinx-rtd-theme.readthedocs.io/en/stable/>`_ >= 0.5.1
 
 
-Step 3: Install
-^^^^^^^^^^^^^^^
-
-To install CDTools, run the following command from the top level directory of the git repository:
-
-.. code:: bash
-
-   $ pip install -e . --no-deps
-
-
-This will install CDTools in developer mode, so that changes to the code will propagate to the installed version immediately. This is best if you plan to actively develop CDTools. If you simply need a custom environment, you can also install CDTools in standard mode using:
-
-.. code:: bash
-
-   $ pip install . --no-deps
-
-
-Step 4: Run The Tests
-^^^^^^^^^^^^^^^^^^^^^
+Optional step 4: Run The Tests
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 To ensure that the installation has worked correctly, it is recommended that you run the unit tests. Execute the following command from the top level directory of the git repository:
 
 .. code:: bash
 
-   $ pytest
+   $ python -m pytest
 
 If any tests fail, make sure that you have all the noted dependencies properly installed. If you do, and things still aren't working, `open an issue on the github page <https://github.com/cdtools-developers/cdtools/issues>`_ and we'll get to the bottom of it.

pyproject.toml

@@ -1,3 +1,53 @@
+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "cdtools-py"
+description = "Tools for coherent diffractive imaging and ptychography"
+readme = "README.md"
+requires-python = ">=3.9"
+license = { file = "LICENSE.txt" }
+authors = [
+	{ name = "Abe Levitan", email = "abraham.levitan@psi.ch" },
+	{ name = "Dayne Y. Sasaki" },
+	{ name = "Damian Guenzing" },
+	{ name = "Madelyn Cain" },
+	{ name = "Anastasiia Kutakh" }
+]
+maintainers = [
+	{ name = "Abe Levitan", email = "abraham.levitan@psi.ch" }
+]
+keywords = ["ptychography", "CDI", "imaging", "torch", "differentiable"]
+classifiers = [
+	"Programming Language :: Python :: 3",
+	"Operating System :: OS Independent",
+	"License :: OSI Approved :: MIT License"
+]
+urls = { "Homepage" = "https://github.com/cdtools-developers/cdtools", "Documentation" = "https://cdtools-developers.github.io/cdtools/" }
+dependencies = [
+	"numpy>=1.0",
+	"scipy>=1.0",
+	"matplotlib>=2.0",
+	"torch>=2.3.0",
+	"h5py>=2.1",
+	"python-dateutil",
+]
+dynamic = ["version"]
+
+[tool.setuptools.dynamic]
+version = {attr = "cdtools._version.__version__"}
+
+[project.optional-dependencies]
+tests = [
+	"pytest",
+	"pooch"
+]
+docs = [
+	"sphinx>=4.3.0",
+	"sphinx-argparse",
+	"sphinx_rtd_theme>=0.5.1"
+]
+
 [tool.ruff]
-# Decrease the maximum line length to 79 characters.
 line-length = 79