Add Python 3.12, drop 3.8

.github/ISSUE_TEMPLATE/bug_report.md

@@ -18,7 +18,7 @@ A clear and concise description of what you expected to happen.
 
 **Environment (please complete the following information):**
  - OS: [e.g. RHEL 8, OSX 13.4.1]
- - Python: [e.g. Python 3.8]
+ - Python: [e.g. Python 3.12]
  - ASPIRE Version: [e.g. 12.0, `develop`]
  - CPU Type: [e.g. Intel I9-9980HK, Apple M2 Pro]
  - GPU Extensions: [yes/no]

.github/workflows/workflow.yml

@@ -14,7 +14,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: '3.8'
+        python-version: '3.9'
     - name: Install dependencies
       run: |
         pip install tox tox-gh-actions
@@ -28,15 +28,15 @@ jobs:
     if: ${{ github.event_name == 'push' || github.event.pull_request.draft == false }}    
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
         pyenv: [pip]
         exclude:
-          # Exclude 3.8-pip so we can add pre/post tasks to that environment.
-          - python-version: '3.8'
+          # Exclude 3.9-pip so we can add pre/post tasks to that environment.
+          - python-version: '3.9'
             pyenv: pip
         include:
-          # Re-include 3.8 with additional tox tasks.
-          - python-version: '3.8'
+          # Re-include 3.9 with additional tox tasks.
+          - python-version: '3.9'
             pyenv: pip,docs
 
 
@@ -70,7 +70,7 @@ jobs:
       matrix:
         os: [ubuntu-latest, ubuntu-20.04, macOS-latest, macOS-13]
         backend: [default, openblas]
-        python-version: ['3.8']
+        python-version: ['3.9']
         include:
           - os: ubuntu-latest
             backend: intel
@@ -112,7 +112,7 @@ jobs:
     - name: Setup Python
       uses: actions/setup-python@v5
       with:
-        python-version: '3.8'
+        python-version: '3.9'
     - name: Install Dependencies
       run: |
         pip install -e ".[dev]"
@@ -176,11 +176,11 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.8'
+          python-version: '3.9'
       - name: Install Dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -e ".[dev]"	  
+          pip install -e ".[dev]"
       - name: Create Cache
         uses: actions/cache@v4
         with:
@@ -200,7 +200,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.8'
+          python-version: '3.9'
       - name: Install Dependencies
         run: |
           python -m pip install --upgrade pip
@@ -232,7 +232,7 @@ jobs:
     - uses: actions/checkout@v4
     - uses: actions/setup-python@v5
       with:
-        python-version: '3.11'
+        python-version: '3.12'
     - name: Complete Install and Log Environment
       run: |
         python --version

README.md

@@ -30,7 +30,7 @@ Getting Started - Installation
 ------------------------------
 
 ASPIRE is a pip-installable package for Linux/Mac/Windows, and
-requires Python 3.8-3.11. The recommended method of installation for
+requires Python 3.9-3.12. The recommended method of installation for
 getting started is to use Anaconda (64-bit) for your platform to
 install Python. Python's package manager `pip` can then be used to
 install `aspire` safely in that environment.
@@ -49,7 +49,7 @@ git clone https://github.com/ComputationalCryoEM/ASPIRE-Python.git
 cd ASPIRE-Python
 
 # Create a fresh environment
-conda create --name aspire python=3.8 pip
+conda create --name aspire python=3.9 pip
 
 # Enable the environment
 conda activate aspire
@@ -59,7 +59,7 @@ conda activate aspire
 pip install -e ".[dev]"
 ```
 
-If you prefer not to use Anaconda, or have other preferences for managing environments, you should be able to directly use `pip` with Python >= 3.8 from the local checkout or via PyPI.
+If you prefer not to use Anaconda, or have other preferences for managing environments, you should be able to directly use `pip` with Python >= 3.9 from the local checkout or via PyPI.
 Please see the full documentation for details and advanced instructions.
 
 ### Installation Testing

docs/source/installation.rst

@@ -37,8 +37,8 @@ to view Conda's installation instructions.
 Getting Started - Installation
 ************************************
 
-Python 3.8 is used as an example, but the same procedure should work
-for any of our supported Python versions 3.8-3.11. Below we pip install
+Python 3.9 is used as an example, but the same procedure should work
+for any of our supported Python versions 3.9-3.12. Below we pip install
 the ``aspire`` package using the ``-e`` flag to install the project in
 editable mode. The ``".[dev]"`` command installs ``aspire`` from the local
 path with additional development tools such as pytest and Jupyter Notebook.
@@ -53,7 +53,7 @@ for more details on using pip install.
    cd ASPIRE-Python
 
    # Create a fresh environment
-   conda create --name aspire python=3.8 pip
+   conda create --name aspire python=3.9 pip
 
    # Enable the environment
    conda activate aspire
@@ -62,7 +62,7 @@ for more details on using pip install.
    # with the additional ``dev`` extension.
    pip install -e ".[dev]"
 
-.. note:: Required dependent packages supporting Python 3.11 are currently only supported on Linux.
+.. note:: Required dependent packages supporting the latest Python may only be supported on Linux.
 
 
 Test the package

environment-accelerate.yml

@@ -6,7 +6,7 @@ channels:
 
 dependencies:
   - pip
-  - python=3.8
+  - python=3.9
   - numpy=1.24.1
   - scipy=1.10.1
   - scikit-learn

environment-default.yml

@@ -6,7 +6,7 @@ channels:
 
 dependencies:
   - pip
-  - python=3.8
+  - python=3.9
   - numpy=1.23.5
   - scipy=1.9.3
   - scikit-learn

environment-intel.yml

@@ -6,7 +6,7 @@ channels:
 
 dependencies:
   - pip
-  - python=3.8
+  - python=3.9
   - numpy=1.23.5
   - scipy=1.9.3
   - scikit-learn

environment-openblas.yml

@@ -6,7 +6,7 @@ channels:
 
 dependencies:
   - pip
-  - python=3.8
+  - python=3.9
   - numpy=1.23.5
   - scipy=1.9.3
   - scikit-learn

pyproject.toml

@@ -3,7 +3,7 @@ name = "aspire"
 version = "0.13.0"
 description = "Algorithms for Single Particle Reconstruction"
 readme = "README.md" # Optional
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 license = {file = "LICENSE"}
 maintainers = [
   {name = "ASPIRE Developers", email = "ASPIRE-DEVS@princeton.edu"}

tox.ini

@@ -4,7 +4,7 @@ envlist =
     clean
     check
     docs
-    py{3.8,3.9,3.10,3.11}-{pip}
+    py{3.9,3.10,3.11,3.12}-{pip}
 minversion = 3.8.0
 
 [testenv]
@@ -101,10 +101,10 @@ addopts = -m "not expensive"
 
 [gh-actions]
 python =
-    3.8: py3.8
     3.9: py3.9
     3.10: py3.10
     3.11: py3.11
+    3.12: py3.12
 
 [coverage:run]
 relative_files = True