Improve infrastructure (docker, requirements, coverage, gitignore)

.dockerignore

@@ -0,0 +1,153 @@
+# Tests output
+test/pocr_data/**/actual_*
+
+# Temp pytest-cov config
+.temp_coveragerc
+
+# Temp RAM usage file
+temp_ram_usage.txt
+
+# Local files
+.playground
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+#IDE
+.idea/

.gitignore

@@ -4,6 +4,13 @@ test/pocr_data/**/actual_*
 # Temp pytest-cov config
 .temp_coveragerc
 
+# Temp RAM usage file
+temp_ram_usage.txt
+
+# Local files
+.playground/**
+data
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

Dockerfile

@@ -1,13 +1,23 @@
-FROM graphblas/pygraphblas-minimal:v4.2.2
+FROM python:3.9-slim as builder
 
-ADD . /CFPQ_PyAlgo
+# Avoid prompts from apt
+ENV DEBIAN_FRONTEND=noninteractive
 
-WORKDIR /CFPQ_PyAlgo
-RUN git submodule init
-RUN git submodule update
+WORKDIR /app
 
-WORKDIR /CFPQ_PyAlgo/deps/CFPQ_Data
-RUN python3 setup.py install
+COPY requirements.txt /app/
+COPY deps/CFPQ_Data /app/deps/CFPQ_Data
 
-WORKDIR /CFPQ_PyAlgo
+RUN pip3 install pygraphblas==5.1.8.0
 RUN pip3 install -r requirements.txt
+RUN cd deps/CFPQ_Data && python3 setup.py install
+
+FROM python:3.9-slim
+
+RUN apt update
+RUN apt install time
+
+COPY --from=builder /usr/local /usr/local
+
+WORKDIR /app
+COPY . /app

Dockerfile-all-tools

@@ -0,0 +1,77 @@
+# Download base image here: https://figshare.com/ndownloader/files/42214812
+FROM pearl-ase23:v1
+ENV PEARL_DIR=/root/eval
+
+# Common utilities
+RUN apt-get update && apt-get install -y git sed time bsdmainutils vim
+
+# POCR dependencies
+RUN apt-get update && apt-get install -y \
+    cmake \
+    gcc \
+    g++ \
+    libtinfo-dev \
+    libz-dev \
+    zip \
+    wget \
+    npm
+
+# Gigascale dependencies
+RUN apt-get update && apt-get install -y openjdk-17-jdk ant python2
+
+# Graspan dependencies
+RUN apt-get update && apt-get install -y \
+    build-essential \
+    wget \
+    make \
+    g++ \
+    libboost-all-dev \
+    git
+RUN wget -qO- https://sourceforge.net/projects/boost/files/boost/1.62.0/boost_1_62_0.tar.gz | tar xvz -C /usr/local
+ENV BOOST_ROOT=/usr/local/boost_1_62_0
+ENV LD_LIBRARY_PATH=$BOOST_ROOT/stage/lib:$LD_LIBRARY_PATH
+
+## POCR dependency, that needs to be built from sources
+RUN git clone https://github.com/kisslune/SVF.git /SVF \
+    && cd /SVF \
+    && /bin/bash -c "source ./build.sh" \
+    && echo 'pushd /SVF > /dev/null && source setup.sh && popd > /dev/null' >> /root/.bashrc
+ENV SVF_DIR=/SVF
+
+# POCR (general-purpose CFL-r tool)
+RUN git clone https://github.com/kisslune/POCR.git /POCR \
+    && cd /POCR \
+    && /bin/bash -c "source ./../SVF/setup.sh && source ./build.sh" \
+    && echo 'pushd /POCR > /dev/null && source setup.sh && popd > /dev/null' >> /root/.bashrc
+ENV POCR_DIR=/POCR
+
+# Gigascale (specialized CFL-r tools)
+RUN git clone https://bitbucket.org/jensdietrich/gigascale-pointsto-oopsla2015.git /gigascale
+RUN sed -i 's/python /python2 /g' /gigascale/run.sh
+RUN sed -i 's/-d64 //g' /gigascale/run.sh
+ENV JAVA_TOOL_OPTIONS="-Dfile.encoding=UTF8"
+ENV GIGASCALE_DIR=/gigascale
+
+# Graspan (general-purpose CFL-r tool)
+RUN git clone https://github.com/Graspan/Graspan-C.git /graspan
+RUN sed -i 's|/home/aftab/Downloads/boost_1_62_installed|'$BOOST_ROOT'|g' /graspan/src/makefile
+RUN sed -i 's|/home/aftab/Downloads/boost_1_62_installed|'$BOOST_ROOT'|g' /graspan/src/run
+RUN cd /graspan/src && make
+ENV GRASPAN_DIR=/graspan
+
+# CFPQ_PyAlgo dependencies
+RUN apt-get update && apt-get install -y \
+    software-properties-common \
+    && add-apt-repository ppa:deadsnakes/ppa \
+    && apt-get update \
+    && apt-get install -y python3.9 python3.9-distutils python3.9-dev python3-pip
+RUN update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.9 1
+RUN python3 -m pip install --upgrade pip
+
+# CFPQ_PyAlgo (this tool)
+COPY requirements.txt /py_algo/requirements.txt
+COPY deps/CFPQ_Data /py_algo/deps/CFPQ_Data
+RUN pip3 install pygraphblas==5.1.8.0
+RUN cd /py_algo && pip3 install -r requirements.txt
+RUN cd /py_algo/deps/CFPQ_Data && python3 setup.py install
+COPY . /py_algo

collect_diff_coverage.sh

@@ -16,7 +16,7 @@ echo "Collecting coverage for files modified after commit:"
 git --no-pager log -n 1 $MERGE_BASE_COMMIT
 
 echo
-MODIFIED_FILES=$(git diff --name-only $MERGE_BASE_COMMIT | grep '.py$' | grep -v '^test')
+MODIFIED_FILES=$(git diff --name-only $MERGE_BASE_COMMIT | grep '.py$' | grep '^src')
 echo "Changed Python files:"
 echo $MODIFIED_FILES
 

requirements.txt

@@ -1,5 +1,5 @@
-tqdm
-pytest
+tqdm==4.62.2
+pytest==8.0.1
 pytest-benchmark
 pytest-cov
 cfpq_data==1.0.2