Improve documentation, update workflows

Author: lorenzotomada

.github/workflows/docs.yml

@@ -4,40 +4,35 @@ on:
   push:
     branches:
       - main
-      - gpu_branch
       - final_project
 
   pull_request:
     branches:
       - main
       - final_project
-      - gpu_branch
 
 jobs:
   docs:
     name: Documentation
     runs-on: ubuntu-latest
-    container:
-      image: cupy/cupy:v13.4.0
 
     steps:
     - uses: actions/checkout@v3
 
     - name: Clean previous builds
       run: rm -rf build dist *.egg-info
 
-    - name: Set up git
-      run: apt-get update && apt-get install git -y
-
     - name: Install system dependencies
       run: |
-        apt-get update && apt-get install -y python3-venv python3-pip
+        sudo apt-get update
+        sudo apt-get install -y python3.12 python3.12-venv python3-pip git
 
-    - name: Install additional dependencies
+    - name: Create virtual environment and install package
       run: |
-        python3.10 -m venv venv
+        python3.12 -m venv venv
         source venv/bin/activate
-        python3.10 -m pip install --no-cache-dir .
+        python3.12 -m pip install --upgrade pip
+        python3.12 -m pip install --no-cache-dir .
       shell: bash -e {0}
 
     - name: Generate documentation
@@ -46,7 +41,7 @@ jobs:
         cd docs
         make html
       shell: bash -e {0}
-    
+
     - name: Deploy
       if: success()
       uses: peaceiris/actions-gh-pages@v3

.github/workflows/tests.yml

@@ -16,35 +16,44 @@ on:
 
 jobs:
   test:
-    name: Testing using pytest
+    name: Testing on Python ${{ matrix.python-version }}
     runs-on: ubuntu-latest
-    container:
-      image: cupy/cupy:v13.4.0
+
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.10', '3.11', '3.12']
 
     steps:
     - uses: actions/checkout@v3
 
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
     - name: Clean previous builds
       run: rm -rf build dist *.egg-info
 
     - name: Install system dependencies
       run: |
-        apt-get update && apt-get install -y python3.10-venv python3-pip cmake
+        sudo apt-get update
+        sudo apt-get install -y cmake
 
-    - name: Install additional dependencies
+    - name: Install Python dependencies
       run: |
-        python3.10 -m venv venv
+        python -m venv venv
         source venv/bin/activate
-        python3.10 -m pip install --no-cache-dir .
-      shell: bash -e {0}
+        python -m pip install --upgrade pip
+        pip install pybind11
+        pip install --no-cache-dir .
+      shell: bash
 
-    - name: Test with pytest
+    - name: Run tests with pytest
       run: |
         source venv/bin/activate
         mkdir -p build
         cmake -B build -S .
-        cd build
-        make
-        cd ..
-        python3.10 -m pytest
-      shell: bash -e {0}
+        cmake --build build
+        pytest
+      shell: bash

CMakeLists.txt

@@ -17,7 +17,16 @@ execute_process(
     OUTPUT_STRIP_TRAILING_WHITESPACE
 )
 set(CMAKE_PREFIX_PATH ${PYBIND11_CMAKE_DIR})
-find_package(pybind11 REQUIRED)
+
+
+execute_process(
+  COMMAND "${PYTHON_EXECUTABLE}" -m pybind11 --cmakedir
+  OUTPUT_VARIABLE PYBIND11_CMAKE_DIR
+  OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+
+list(APPEND CMAKE_PREFIX_PATH "${PYBIND11_CMAKE_DIR}")
+find_package(pybind11 REQUIRED CONFIG)
 
 # Needed for compilation (again, Ulysses... :/ )
 set(CMAKE_CXX_STANDARD 17)
@@ -30,4 +39,4 @@ pybind11_add_module(QR_cpp ${CMAKE_SOURCE_DIR}/src/pyclassify/QR_bindings.cpp)
 set_target_properties(QR_cpp PROPERTIES LIBRARY_OUTPUT_DIRECTORY ${CMAKE_LIBRARY_OUTPUT_DIRECTORY})
 
 target_compile_features(QR_cpp PUBLIC cxx_std_17)
-install(TARGETS QR_cpp LIBRARY DESTINATION ${CMAKE_SOURCE_DIR}/src/pyclassify)
+install(TARGETS QR_cpp LIBRARY DESTINATION ${CMAKE_SOURCE_DIR}/src/pyclassify)

README.md

@@ -12,3 +12,5 @@ TO DO:
 4) Accuracy vs efficiency
 5) Script to run on Ulysses
 6) Add missing tests
+7) Possibly delete eigenvalues\_np and so on, which I inserted because I thought it was not going to be necessary to compute the eigenvectors, making these wrappers useless
+8) Write missing documentation

docs/index.rst

@@ -7,11 +7,10 @@ final_project documentation
 ===========================
 
 Welcome to the documentation for the final project of the course in Development Tools for Scientific Computing.
-We are currently working on the project and on the documentation.
-Stay tuned!
+Our goal is to compute an efficient solver for eigenvalue problems.
 
-Recall that the documentation is written following
-`reStructuredText <https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html>`_
+For theoretical details, please check the file docs/Documentation.ipynb
+To install the package, please read the README.md file.
 
 
 Table of Contents
@@ -30,4 +29,4 @@ Module Documentation
    :members:
    :undoc-members:
    :show-inheritance:
-   :noindex:
+   :noindex:

docs/pyclassify.rst

@@ -17,4 +17,13 @@ Submodule: utils
 .. automodule:: pyclassify.utils
    :members:
    :undoc-members:
-   :show-inheritance:
+   :show-inheritance:
+
+Submodule: helpers_secular
+================
+
+.. automodule:: pyclassify.helpers_secular
+   :members:
+   :undoc-members:
+   :show-inheritance:
+

setup.py

@@ -1,6 +1,7 @@
 import os
 import sys
 import shutil
+import glob
 from setuptools import setup, find_packages, Extension
 from setuptools.command.build_ext import build_ext
 
@@ -21,22 +22,19 @@ def build_extension(self, ext):
         self.spawn(["cmake", ext.sourcedir, "-B", build_temp])
         self.spawn(["cmake", "--build", build_temp, "--target", "QR_cpp"])
 
-        python_version = sys.version_info
-        so_filename = (
-            f"QR_cpp.cpython-{python_version[0]}{python_version[1]}-x86_64-linux-gnu.so"
-        )
-
-        src_lib = os.path.join(build_temp, f"../../src/pyclassify/{so_filename}")
-        dst_lib = os.path.join(build_lib, f"pyclassify/{so_filename}")
-
-        if os.path.exists(src_lib):
-            os.makedirs(os.path.dirname(dst_lib), exist_ok=True)
-            shutil.copy(src_lib, dst_lib)
-        else:
+        # Dynamically find the compiled shared library
+        matches = glob.glob(os.path.join(build_temp, "../../src/pyclassify/QR_cpp*.so"))
+        if not matches:
             raise RuntimeError(
-                f"Could not find compiled QR_cpp shared library at {src_lib}!"
+                "Could not find compiled QR_cpp shared library in expected location."
             )
 
+        src_lib = os.path.abspath(matches[0])
+        dst_lib = os.path.join(build_lib, "pyclassify", os.path.basename(src_lib))
+
+        os.makedirs(os.path.dirname(dst_lib), exist_ok=True)
+        shutil.copy(src_lib, dst_lib)
+
 
 setup(
     name="pyclassify",
@@ -48,7 +46,7 @@ def build_extension(self, ext):
     ext_modules=[CMakeExtension("pyclassify.QR_cpp")],
     packages=find_packages(where="src/"),
     package_dir={"": "src/"},
-    package_data={"pyclassify": ["QR_cpp.cpython-312-x86_64-linux-gnu.so"]},
+    package_data={"pyclassify": ["QR_cpp*.so"]},
     include_package_data=True,
     cmdclass={"build_ext": CMakeBuild},
     zip_safe=False,