From 03fa58ab81591e797cec3afcda399be3f36b4273 Mon Sep 17 00:00:00 2001 From: Garrett Wright Date: Wed, 9 Oct 2024 09:48:47 -0400 Subject: [PATCH 1/5] drop Python 3.8, require >=3.9 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 364ef107f0..a44033eccc 100644 --- a/pyproject.toml +++ b/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"} From 927caaad8be8268de4af12af5a86639bfec2bce5 Mon Sep 17 00:00:00 2001 From: Garrett Wright Date: Wed, 9 Oct 2024 09:51:24 -0400 Subject: [PATCH 2/5] Add Python 3.12, remove 3.8, move 3.8 jobs to 3.9 --- .github/workflows/workflow.yml | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/.github/workflows/workflow.yml b/.github/workflows/workflow.yml index 33a974b214..96ba8b4e51 100644 --- a/.github/workflows/workflow.yml +++ b/.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 From 2cbfdce0f27915f1b50508d3c03d7301323c17c0 Mon Sep 17 00:00:00 2001 From: Garrett Wright Date: Wed, 9 Oct 2024 09:55:26 -0400 Subject: [PATCH 3/5] move 3.8 conda envs to 3.9 --- environment-accelerate.yml | 2 +- environment-default.yml | 2 +- environment-intel.yml | 2 +- environment-openblas.yml | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/environment-accelerate.yml b/environment-accelerate.yml index cfe9631f3c..5248c3a953 100644 --- a/environment-accelerate.yml +++ b/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 diff --git a/environment-default.yml b/environment-default.yml index f5ff7ae893..f827ec55bc 100644 --- a/environment-default.yml +++ b/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 diff --git a/environment-intel.yml b/environment-intel.yml index 83250caeaf..840dd92f76 100644 --- a/environment-intel.yml +++ b/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 diff --git a/environment-openblas.yml b/environment-openblas.yml index ee2f665e6e..088035f88d 100644 --- a/environment-openblas.yml +++ b/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 From 3806c201ea773eca4ec49c9cb495484f12fef85a Mon Sep 17 00:00:00 2001 From: Garrett Wright Date: Wed, 9 Oct 2024 09:55:57 -0400 Subject: [PATCH 4/5] Tox add Python 3.12, remove 3.8, move 3.8 jobs to 3.9 --- tox.ini | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tox.ini b/tox.ini index 3970e6e317..f05f9896d4 100644 --- a/tox.ini +++ b/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 From b6514fb113f26d2c771607e7a52af430861cc63d Mon Sep 17 00:00:00 2001 From: Garrett Wright Date: Wed, 9 Oct 2024 09:57:57 -0400 Subject: [PATCH 5/5] Update documentation, drop 3.8 add 3.12 --- .github/ISSUE_TEMPLATE/bug_report.md | 2 +- README.md | 6 +++--- docs/source/installation.rst | 8 ++++---- 3 files changed, 8 insertions(+), 8 deletions(-) diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md index 106f10b040..41b94b3e7d 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.md +++ b/.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] diff --git a/README.md b/README.md index fd1b16c81f..f6a818247a 100644 --- a/README.md +++ b/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 diff --git a/docs/source/installation.rst b/docs/source/installation.rst index 1fca5a35dd..ad255bd19e 100644 --- a/docs/source/installation.rst +++ b/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