v3.4.2: Added flip operator (^), fixed MacOs build using brew GCC

ibarrond · Sep 20, 2023 · a0ce75f · a0ce75f
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Showing 7 changed files with 71 additions and 42 deletions.
diff --git a/.github/workflows/pytest-coverage.yml b/.github/workflows/pytest-coverage.yml
@@ -1,4 +1,6 @@
 # This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For MacOs builds, GNU GCC is installed via Homebrew, and the CC/CXX environment variables are set to use it.
+# The echo "CC=..." >> $GITHUB_ENV syntax is used to set environment variables for the next steps in the workflow.
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
 name: CI
@@ -25,40 +27,60 @@ jobs:
         os: [ubuntu-latest, windows-latest, macos-latest]
     runs-on: ${{ matrix.os }}
     steps:
+
     - name: Checkout repo
       uses: actions/checkout@v3
       with:
         submodules: recursive
-    # brew install --with-toolchain llvm libomp ?
-    - name: (MAcOs only) Install GNU GCC
+
+    - name: (MacOs only) Install GNU GCC.
       if: matrix.os == 'macos-latest'
       run: |
         brew install gcc libomp
-    - name: (MacOs only) Set gcc/gxx environment variables 
+
+    - name: (MacOs only) Set CC/CXX environment variables to GNU GCC 
       if: matrix.os == 'macos-latest'
       run: |
-        echo "gcc=/usr/local/bin/$(ls /usr/local/bin | grep ^gcc-[0-9] | sort -V -r | head -n 1)"  >> $GITHUB_ENV
-        echo "gxx=/usr/local/bin/$(ls /usr/local/bin | grep ^g++-[0-9] | sort -V -r | head -n 1)"  >> $GITHUB_ENV
+
+        # Check GCC installation path. Brew installs GCC in /opt/homebrew/bin on Apple Silicon and /usr/local/bin on Intel.
+        if [[ $(uname -m) = "arm64" ]]; then BREW_GCC_PATH="/opt/homebrew/bin"; else BREW_GCC_PATH="/usr/local/bin"; fi
+        echo "GCC installed at $BREW_GCC_PATH"
+
+        # Set CC/CXX environment variables to GNU GCC
+        echo "CC=$BREW_GCC_PATH/$(ls $BREW_GCC_PATH | grep ^gcc-[0-9] | sort -V -r | head -n 1)" >> $GITHUB_ENV
+        echo "CXX=$BREW_GCC_PATH/$(ls $BREW_GCC_PATH | grep ^g++-[0-9] | sort -V -r | head -n 1)" >> $GITHUB_ENV
+        echo "CC=${{ env.CC }}"
+        echo "CXX=${{ env.CXX }}"
+        
+        # Set MACOSX_DEPLOYMENT_TARGET to avoid version mismatch warnings
+        echo "MACOSX_DEPLOYMENT_TARGET=$(sw_vers -productVersion)" >> $GITHUB_ENV
+        echo "MACOSX_DEPLOYMENT_TARGET=${{ env.MACOSX_DEPLOYMENT_TARGET }}"
+
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Update pip
-      run: |
-        python -m pip install --upgrade pip
-    # Run interactive debugging session for debug_enabled manually
-    - name: Setup tmate session
+        cache: 'pip' # caching pip dependencies
+
+    - name: (Manual) Setup tmate session for interactive debugging via SSH
       uses: mxschmitt/action-tmate@v3
       if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled }}
-    - name: Install package in test mode
+
+    - name: Update pip
+      run: python -m pip install --upgrade pip
+
+    - name: Install package verbosely
       run: |
-        touch .cov
+
+        touch .cov # Create a .cov file to trigger Cython compilation with coverage support 
         ls
-        python -m pip install .[test]
+        python -m pip install -v -v -v .
+
     - name: Test with pytest
       run: |
-        python -m pip install cython==3.0.0a11 pytest-cov
+        python -m pip install cython==3.0.2 pytest-cov
         pytest --cov .
+
     - name: Upload report to Codecov
       uses: codecov/codecov-action@v3.1.0
       with:

diff --git a/Pyfhel/backend/palisade b/Pyfhel/backend/palisade
diff --git a/Pyfhel/test/test_PyCtxt.py b/Pyfhel/test/test_PyCtxt.py
@@ -198,8 +198,8 @@ def test_PyCtxt_rotate(self, HE):
         assert np.round(HE.decrypt(c1)[0])==1
         # flip
         if c1._pyfhel.scheme == Scheme_t.bfv:
-            c1 |= 1
-            c1 |= 1
+            c1 ^= 1
+            c1 ^= 1
             assert np.round(HE.decrypt(c1)[0])==1
 
     def test_PyCtxt_io(self, HE):

diff --git a/README.md b/README.md
@@ -1,20 +1,20 @@
 <img width="70%" align="left"  src="/docs/static/logo_title.png"><img width="17%" height="17%" align="right"  src="/docs/static/logo.png">
 
-[![iCodecov](https://codecov.io/gh/ibarrond/Pyfhel/branch/dev/graph/badge.svg?token=S8J8Jlp1Fc)](https://codecov.io/gh/ibarrond/Pyfhel)
+[![iCodecov](https://codecov.io/gh/ibarrond/Pyfhel/branch/master/graph/badge.svg?token=S8J8Jlp1Fc)](https://codecov.io/gh/ibarrond/Pyfhel)
 [![Documentation Status](https://readthedocs.org/projects/pyfhel/badge/?version=latest)](https://pyfhel.readthedocs.io/en/latest/?badge=latest)
 [![PyPI version](https://badge.fury.io/py/Pyfhel.svg)](https://badge.fury.io/py/Pyfhel)
 [![Maintenance](https://img.shields.io/badge/Maintained%3F-yes-brightgreen.svg)](https://github.com/ibarrond/Pyfhel/graphs/commit-activity)
 [![GitHub issues](https://img.shields.io/github/issues/ibarrond/Pyfhel.svg)](https://github.com/ibarrond/Pyfhel/issues)
 [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 
 
-Python library for ADDITION, SUBSTRACTION, MULTIPLICATION and SCALAR PRODUCT over encrypted integers (BFV) and approximated floating point values (CKKS). This library acts as an optimized Python API for C++ Homomorphic Encryption libraries.
+Python library for Addition, Subtraction, Multiplication and Scalar Product over *encrypted* integers (BFV/BGV schemes) and approximated floating point values (CKKS scheme). This library acts as an optimized Python API for C++ Homomorphic Encryption libraries.
 
 |                                            |                                                                                            |
 |--------------------------------------------|--------------------------------------------------------------------------------------------|
 | :flags: **Language**                       | Python (3.7+), with Cython and C++ (:warning: _requires a [C++17 compiler][3]_ :warning:.) |
 | :computer: **OS**                          | Linux, Windows & MacOS.                                                                    |
-| :1234: **Version**                         | 3.4.1 (stable)                                                                             |
+| :1234: **Version** | 3.4.2 (stable)                                                                                                     |
 | :books: **Docs**                           | In [readthedocs][1]!                                                                       |
 | :pencil2: **Demos/Examples**               | [In the docs][4] with the outputs, sources in the [`examples`][2] folder.                  |
 | :electric_plug: **Backends**               | [SEAL][5], [OpenFHE (WIP)][6]. Shipped alongside Pyfhel.                                   |
@@ -56,28 +56,36 @@ If you wish to cite Pyfhel in your derived work, please use the following BibTeX
 ## Install & Uninstall
 To install `Pyfhel` from [PyPI](https://pypi.org/project/Pyfhel/), run (*WARNING! it takes several minutes to compile and install, be patient!*):
 ```bash
-> pip install Pyfhel
+pip install Pyfhel
 ```
 
 To install the latest version, you can clone this repository with [all the submodules](https://stackoverflow.com/questions/3796927/how-to-git-clone-including-submodules) and install it by running:
 ```bash
-> git clone --recursive https://github.com/ibarrond/Pyfhel.git
-> pip install .
+git clone --recursive https://github.com/ibarrond/Pyfhel.git
+pip install .
 ```
 
 To uninstall, just run:
 ```bash
-> pip uninstall Pyfhel
+pip uninstall Pyfhel
 ```
 
 ### Installing a C/C++ Compiler
 `Pyfhel` requires a C/C++ compiler with C++17 support. We have tested:
 - *gcc6* to *gcc12* in Linux/MacOS/Windows WSL. To install:
    - Ubuntu: `sudo apt install gcc g++`
-   - MacOS: `brew install gcc`. MacOS users must set the environment variables `gcc` and `gxx` to the installed compilers, e.g.:
+   - MacOS: `brew install gcc`. MacOS users must also set several environment variables by running:
 ```bash
-      > export gcc=/usr/local/bin/gcc-12
-      > export gxx=/usr/local/bin/g++-12
+        # Brew installs GCC in /opt/homebrew/bin on Apple Silicon and /usr/local/bin on Intel.
+        if [[ $(uname -m) = "arm64" ]]; then BREW_GCC_PATH="/opt/homebrew/bin"; else BREW_GCC_PATH="/usr/local/bin"; fi
+
+        # Set CC/CXX environment variables to the most recent GNU GCC
+        export CC="$BREW_GCC_PATH/$(ls $BREW_GCC_PATH | grep ^gcc-[0-9] | sort -V -r | head -n 1)"
+        export CXX="$BREW_GCC_PATH/$(ls $BREW_GCC_PATH | grep ^g++-[0-9] | sort -V -r | head -n 1)"
+
+        # Set MACOSX_DEPLOYMENT_TARGET to avoid version mismatch warnings
+        echo "MACOSX_DEPLOYMENT_TARGET=$(sw_vers -productVersion)" >> $GITHUB_ENV
+        echo "MACOSX_DEPLOYMENT_TARGET=${{ env.MACOSX_DEPLOYMENT_TARGET }}"
 ```
 - *MSVC2017* and *MSVC2019* in Windows. To install:
    - Install Visual C++ Build tools (Download [here](https://learn.microsoft.com/en-US/cpp/windows/latest-supported-vc-redist?view=msvc-170), guide in [here](https://stackoverflow.com/questions/40504552))
@@ -98,7 +106,7 @@ This repository contains:
 This is the standard process to develop/contribute:
 1. _Code a new feature/fix a bug_. Using [Cython](https://cython.readthedocs.io/en/latest/) for the `.pyx` and `.pxd` extensions, C++ for `Afhel` or Python for examples/tests/other.
 
-2. _Build/Install Pyfhel locally_. Use either `pip install .` or `python3 setup.py build` (for verbose output and fine control. Run `python3 setup.py --help` for further options).
+2. _Build/Install Pyfhel locally_. Use `pip install -v -v -v .` for a verbose installation.
 
 3. _Test changes (requires installing `pytest`)_. Run the tests locally by executing `pytest .`  in the root directory, and make sure all tests pass. 
 

diff --git a/examples/Demo_2_Integer_BFV.py b/examples/Demo_2_Integer_BFV.py
@@ -98,9 +98,9 @@
                             #  to each of the rows!
 cRotL = ctxt1 << 2          # Calls HE.rotate(ctxt1, k=-2, in_new_ctxt=True)
                             #  `ctxt1 <<= 2` for inplace operation
-cFlip = ctxt1 | 1           # Calls HE.flip(ctxt1, k=1, in_new_ctxt=True)
+cFlip = ctxt1 ^ 1           # Calls HE.flip(ctxt1, k=1, in_new_ctxt=True)
                             #  `ctxt1 |= 1` for inplace operation
-cCuAdd = (+ctxt1)        # Calls HE.cumul_add(ctxt1, in_new_ctxt=True)
+cCuAdd = (+ctxt1)           # Calls HE.cumul_add(ctxt1, in_new_ctxt=True)
                             #  There is no equivalent for in-place operator, use
                             #  the above call with `in_new_ctxt=False` if required.
 
@@ -189,7 +189,7 @@
 print("   ->\tctxt1 >> 2    = cRotR --(decr)--> ", rcRotR)
 print("   ->\tctxt1 << 2    = cRotL --(decr)--> ", rcRotL)
 print("   ->\tctxt1 | 1     = cFlip --(decr)--> ", rcFlip)
-print("   ->\t(+cCuAdd)     = cCuAdd --(decr)--> ", cCuAdd)
+print("   ->\t(+tctxt1)     = cCuAdd -(decr)--> ", rcCuAdd)
 print(" Ciphertext-plaintext ops: ")
 print("   ->\tctxt1 + ptxt2 = cpSum --(decr)--> ", rcpSum)
 print("   ->\tctxt1 - ptxt2 = cpSub --(decr)--> ", rcpSub)

diff --git a/pyproject.toml b/pyproject.toml
@@ -59,7 +59,7 @@ repository = "https://github.com/ibarrond/github"
 requires = [
   "setuptools<=60.9",
   "wheel",
-  "cython==3.0.0b3",
+  "cython>=3.0.0",
   "numpy>=1.21",
   "cmake>=3.15",
   "toml>=0.10"
@@ -138,30 +138,32 @@ platforms = ["Linux", "Windows", "Darwin"]
   ]
   extra_compile_args = [
     {Windows = ["/O2","/std:c++17","/openmp"]},
-    {Darwin = ["-std=c++17","-O3","-fopenmp"]},
+    {Darwin = ["-std=c++17","-O3","-Xpreprocessor","-fopenmp"]},
     {Linux = ["-std=c++17","-O3","-fopenmp"]} ]
   extra_link_args = [
     {Windows = []},
-    {Darwin = ["-Wl,-rpath,@loader_path/.",  "-Wl,-no_compact_unwind", "-fopenmp"]},
+    {Darwin = ["-Wl,-rpath,@loader_path/.", "-fopenmp","-Wl,-no_compact_unwind"]},
     {Linux = ["-Wl,-rpath=$ORIGIN/.", "-fopenmp"]} ]
   libraries = ['SEAL']
 
 
 #----------------------------- CYTHON EXTENSIONS -------------------------------
 [extensions.config]   # Common compilation config for all extensions
-include_dirs = []
+include_dirs = [
+    {Darwin = ["/usr/local/include"]},
+]
 define_macros = [
   ["NPY_NO_DEPRECATED_API", "NPY_1_7_API_VERSION"],
   ["__PYX_ENUM_CLASS_DECL", "enum"], # Support enums in cython
 ]
 extra_compile_args = [
   {Windows = ["/O2","/openmp","/std:c++17"]},
-  {Darwin = ["-std=c++17","-O3","-fopenmp"]},
+  {Darwin = ["-std=c++17","-O3","-Xpreprocessor","-fopenmp","-Wno-unreachable-code","-Wno-unqualified-std-cast-call"]},
   {Linux = ["-std=c++17","-O3","-fopenmp"]},
 ]
 extra_link_args = [
   {Windows = []},
-  {Darwin = ["-Wl,-rpath,@loader_path/.", "-Wl,-no_compact_unwind", "-fopenmp"]},
+  {Darwin = ["-Wl,-rpath,@loader_path/.", "-fopenmp","-Wl,-no_compact_unwind"]},
   {Linux = ["-Wl,-rpath=$ORIGIN/.", "-fopenmp"]},
 ]
 libraries = []  # libraries to link with, cpplibraries above are added by default

diff --git a/setup.py b/setup.py
@@ -28,9 +28,6 @@
 
 # Get platform system
 platform_system = platform.system()
-if platform_system == 'Darwin':
-        vars = sysconfig.get_config_vars()
-        vars["LDSHARED"] = (vars["LDSHARED"]+" -Wl,-no_fixup_chains,-x -undefined dynamic_lookup ").replace('-bundle', '-dynamiclib')
 
 # Read config file
 config = toml.load("pyproject.toml")
@@ -55,7 +52,7 @@ def re_sub_file(regex: str, replace: str, filename: str):
         sub_file.write(re.sub(regex, '{}'.format(replace), file_string))
 
 # Writing version in __init__.py and README.md
-V_README_REGEX = r'(?<=\* \*\*_Version_\*\*: )[0-9]+\.[0-9]+\.[0-9a-z]+'
+V_README_REGEX = r'(?<=\*\*Version\*\* \| )[0-9]+\.[0-9]+\.[0-9a-z]+'
 V_INIT_REGEX = r'(?<=__version__ = \")[0-9]+\.[0-9]+\.[0-9a-z]+(?=\")'
 re_sub_file(regex=V_README_REGEX, replace=VERSION, filename='README.md')
 re_sub_file(regex=V_INIT_REGEX, replace=VERSION, filename='Pyfhel/__init__.py')
@@ -404,6 +401,7 @@ def build_shared_lib(self, lib_name, build_info):
 
         if platform_system == 'Darwin':
             build_info['extra_link_args'].append(f"-Wl,-install_name,@loader_path/{lib_file}")
+            self.compiler.linker_so = ['-dynamiclib' if val=='-bundle' else val for val in self.compiler.linker_so]
         self.compiler.link_shared_object(
             objects,                     
             lib_file,