Bump to v0.1.12

.github/workflows/test.yml

@@ -15,7 +15,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ["3.9", "3.10", "3.11"]  
+        python-version: ["3.9", "3.10", "3.11", "3.12"]  
 
     steps:
     - uses: actions/checkout@v4

.gitignore

@@ -1,26 +1,22 @@
-<<<<<<< HEAD
 pyaing/clocks
 pyaging_data/
 example_data/
-testing.ipynb
-=======
 pyaging/clocks/
 clocks/weights/
 *.pt
 *.json
 pyaging_data/
 example_data/
 testing.ipynb
-pyaging_manuscript.ipynb
 .ipynb_checkpoints/
 *.pyc
 .DS_Store
 pyaging.egg-info/
-update_pipeline_steps.txt
-update_package.sh
 dist/
 build/
 docs/_build
 docs/_templates
 *.RData
->>>>>>> fd1440b (first commit)
+.ruff_cache/
+.pytest_cache/
+

.pre-commit-config.yaml

@@ -0,0 +1,9 @@
+repos:
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.11
+    hooks:
+    -   id: ruff
+        args: [ --fix, --ignore=E501,E722,B904,E902 ]
+        stages: [manual]
+    -   id: ruff-format
+        stages: [manual]

docs/environment.yml

@@ -3,7 +3,7 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - python=3.9
+  - python=3.12
   - pip>=22.3
   - pip:
       - sphinx>=7.2.6
@@ -15,15 +15,15 @@ dependencies:
       - sphinx-design>=0.5.0
       - scanpydoc>=0.10.0
       - myst-parser>=2.0.0
-      - ipykernel>=5.5.6
+      - ipykernel>=6.29.0
       - nbsphinx>=0.8.12
       - pygments>=2.17.2
       - pytest>=7.4.4
       - nbmake>=1.4.6
       - scikit-learn>=1.4.0
       - pandas>=2.2.0
-      - torch>=2.1.2
-      - numpy>=1.26.3
-      - pyBigWig>=0.3.22
+      - torch>=2.2.0
+      - numpy>=2.0.0
+      - pyBigWig>=0.3.23
       - anndata>=0.10.4
 

docs/source/installation.rst

@@ -1,7 +1,7 @@
 Installation
 ============
 
-*Please note that pyaging is only supported by python versions 3.9, 3.10, and 3.11.**
+*Please note that pyaging is supported by python versions 3.9, 3.10, 3.11, and 3.12.**
 
 pyaging now has been released to PyPi and can easily be installed via:
 

pyaging/__init__.py

@@ -4,4 +4,4 @@
 from . import predict as pred
 from . import preprocess as pp
 
-__version__ = "0.1.11"
+__version__ = "0.1.12"

pyaging/predict/_pred_utils.py

@@ -91,7 +91,7 @@ def load_clock(clock_name: str, device: str, dir: str, logger, indent_level: int
     weights_path = os.path.join(dir, f"{clock_name}.pt")
 
     # Load the clock from the file
-    clock = torch.load(weights_path)
+    clock = torch.load(weights_path, weights_only=False)
 
     # Prepare clock for inference
     clock.to(torch.float64)

pyaging/utils/_utils.py

@@ -59,7 +59,7 @@ def decorator(func):
         @wraps(func)
         def wrapper(*args, **kwargs):
             # Extract indent_level from kwargs, default to 1 if not provided
-            indent_level = kwargs["indent_level"] if "indent_level" in kwargs.keys() else 1
+            indent_level = kwargs["indent_level"] if "indent_level" in kwargs else 1
 
             logger = args[-1]  # Assumes logger is the last positional argument
             logger.start_progress(f"{message} started", indent_level=indent_level)

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pyaging"
-version = "v0.1.11"
+version = "v0.1.12"
 description = "A Python-based compendium of GPU-optimized aging clocks."
 authors = ["Lucas Paulo de Lima Camillo <[email protected]>"]
 license = "BSD"
@@ -11,12 +11,14 @@ homepage = "https://github.com/rsinghlab/pyaging"
 repository = "https://github.com/rsinghlab/pyaging"
 
 [tool.poetry.dependencies]
-python = ">=3.9,<3.12"
+python = ">=3.9,<3.13"
 scikit-learn = "^1.3.2"
-pandas = "^2.1.3"
-torch = "^2.1.1"
-numpy = "^1.26.2"
+pandas = ">=2.2.0"
+torch = ">=2.2.0"
+numpy = ">=2.0.0"
 anndata = "^0.10.3"
+ipykernel = "^6.29.0"
+pybigwig = "^0.3.23"
 
 [tool.poetry.dev-dependencies]
 sphinx = "^7.1.2"
@@ -28,12 +30,11 @@ sphinx-issues = "^3.0.1"
 sphinx-design = "^0.5.0"
 scanpydoc = "^0.10.0"
 myst-parser = "^2.0.0"
-ipykernel = "^5.1.0"
 nbsphinx = "^0.8.11"
 pygments = "^2.6.1"
 pytest = "^7.2.0"
 nbmake = "^1.4.6"
-pyBigWig = {version = "^0.3.22", optional = true}
+pyBigWig = {version = "^0.3.23", optional = true}
 
 [tool.poetry.scripts]
 pyaging = "pyaging:main"

update_package.sh

@@ -0,0 +1,155 @@
+#!/bin/bash
+
+# Define the new version and commit/release messages
+new_version="v0.1.12" # Replace with the actual version number
+commit_message="Bump to $new_version" # Replace with the actual commit message
+release_message="Release $new_version" # Replace with the actual release message
+
+# Update version in pyproject.toml
+echo "Updating version in pyproject.toml to $new_version..."
+sed -i '' "s/^version = \".*\"/version = \"$new_version\"/" pyproject.toml
+if [ $? -ne 0 ]; then
+    echo "Error updating version in pyproject.toml"
+    exit 1
+fi
+
+# Update version in __init__.py
+echo "Updating version in __init__.py to $new_version..."
+sed -i '' "s/__version__ = \".*\"/__version__ = \"${new_version#v}\"/" pyaging/__init__.py
+if [ $? -ne 0 ]; then
+    echo "Error updating version in __init__.py"
+    exit 1
+fi
+
+# Run ruff for linting
+echo "Running ruff for linting..."
+ruff check pyaging --fix
+
+# Run black for code formatting
+echo "Running ruff for code formatting..."
+ruff format pyaging
+if [ $? -ne 0 ]; then
+    echo "ruff formatting failed"
+    exit 1
+fi
+
+# Run poetry update
+echo "Running poetry update..."
+poetry update
+if [ $? -ne 0 ]; then
+    echo "Poetry update failed"
+    exit 1
+fi
+
+# Build the package
+echo "Building the package..."
+poetry build
+if [ $? -ne 0 ]; then
+    echo "Poetry build failed"
+    exit 1
+fi
+
+# Install the package
+echo "Installing the package..."
+poetry install
+if [ $? -ne 0 ]; then
+    echo "Poetry install failed"
+    exit 1
+fi
+
+# Update clocks and notebooks in the 'clocks/notebooks' directory
+#echo "Updating clocks and notebooks..."
+#cd clocks/notebooks
+#total=$(ls *.ipynb | wc -l)
+#counter=1
+#for notebook in *.ipynb; do
+#    # Skip the file if it is 'template.ipynb'
+#    if [ "$notebook" = "template.ipynb" ]; then
+#        echo "Skipping template.ipynb"
+#        continue
+#    fi
+#
+#    echo "Processing clock notebook ($counter/$total): $notebook"
+#    #jupyter nbconvert --to notebook --execute "$notebook" #Change 
+#    jupyter nbconvert --execute --inplace "$notebook" # Execute in place
+#    if [ $? -ne 0 ]; then
+#        echo "Error processing $notebook"
+#        exit 1
+#    fi
+#    let counter=counter+1
+#done
+#cd ../..
+
+# Run the script to update all clocks
+#echo "Running script to update all clocks..."
+#cd clocks
+#python3 update_all_clocks.py $new_version
+#if [ $? -ne 0 ]; then
+#    echo "Updating clocks failed"
+#    exit 1
+#fi
+#cd ..
+#echo "Reminder: Upload all clocks and metadata to S3!"
+
+# Process tutorials
+#echo "Processing tutorials..."
+#cd tutorials
+#for notebook in *.ipynb; do
+#    echo "Processing tutorial notebook: $notebook"
+#    jupyter nbconvert --ExecutePreprocessor.timeout=600 --to notebook --execute --inplace "$notebook"
+#done
+#cd ..
+
+# Run gold standard tests
+echo "Running gold standard tests..."
+poetry run pytest
+if [ $? -ne 0 ]; then
+    echo "Gold standard tests failed"
+    exit 1
+fi
+
+# Run tutorial tests
+echo "Running tutorial tests..."
+poetry run pytest --nbmake tutorials/
+if [ $? -ne 0 ]; then
+    echo "Tutorial tests failed"
+    exit 1
+fi
+
+# Build documentation
+echo "Building documentation..."
+cp tutorials/*.ipynb docs/source/tutorials
+cp clocks/notebooks/*.ipynb docs/source/clock_notebooks
+cd docs
+make html
+if [ $? -ne 0 ]; then
+    echo "Documentation build failed"
+    exit 1
+fi
+cd ..
+
+# Commit and push changes
+echo "Committing and pushing changes..."
+git add .
+git commit -m "$commit_message"
+if [ $? -ne 0 ]; then
+    echo "Git commit failed"
+    exit 1
+fi
+
+git push
+if [ $? -ne 0 ]; then
+    echo "Git push failed"
+    exit 1
+fi
+
+# Create and push tag
+echo "Creating and pushing tag $new_version..."
+git tag -a "$new_version" -m "$release_message"
+git push origin "$new_version"
+if [ $? -ne 0 ]; then
+    echo "Git tag creation or push failed"
+    exit 1
+fi
+
+echo "Version update pipeline completed successfully."