fix requirements to specific versions

.vscode/settings.json

@@ -36,7 +36,7 @@
   "editor.formatOnSave": true,
   "[python]": {
     "editor.codeActionsOnSave": {
-      "source.organizeImports": true
+      "source.organizeImports": "explicit"
     },
     "editor.defaultFormatter": "ms-python.python"
   },

Dockerfile

@@ -0,0 +1,94 @@
+# Base image
+FROM pytorch/pytorch:1.9.0-cuda10.2-cudnn7-runtime
+
+# Ensure noninteractive apt installs and use bash for RUN so conda works later
+ARG DEBIAN_FRONTEND=noninteractive
+SHELL ["/bin/bash", "-lc"]
+
+# Copy files (Singularity %files)
+COPY cli.sh /cli.sh
+
+COPY old_requirements.txt /requirements.txt
+
+# Environment (Singularity %environment)
+ENV SINGULARITY=true \
+PATH="$PATH:/GloVe/build"
+
+# Make CLI executable (part of %post)
+RUN chmod u+x /cli.sh
+
+# Update & base packages
+RUN apt-get update && \
+apt-get install -y --no-install-recommends \
+wget curl git build-essential cmake \
+graphviz zip unzip vim libexpat1-dev \
+gnupg bash sudo && \
+rm -rf /var/lib/apt/lists/*
+
+RUN pip install --no-cache-dir dgl-cu102 -f https://data.dgl.ai/wheels/repo.html 
+RUN pip install --no-cache-dir -r /requirements.txt
+
+
+# Install GloVe (from source)
+RUN cd / && \
+    git clone https://github.com/stanfordnlp/GloVe.git && \
+    cd GloVe && make
+
+# Build & install cppcheck 2.5 from source
+RUN cd / && \
+    curl -L https://github.com/danmar/cppcheck/archive/refs/tags/2.5.tar.gz -o cppcheck2.5.tar.gz && \
+    mkdir -p /cppcheck && mv cppcheck2.5.tar.gz /cppcheck && \
+    cd /cppcheck && tar -xzf cppcheck2.5.tar.gz && \
+    cd cppcheck-2.5 && mkdir build && cd build && \
+    cmake .. && cmake --build . && make install && \
+    rm -rf /cppcheck
+
+# Install Joern (non-interactive script drive similar to %post)
+# Note: Running as root in Docker, so no sudo needed.
+RUN apt-get update && apt-get install -y --no-install-recommends openjdk-8-jdk && \
+    rm -rf /var/lib/apt/lists/* && \
+    cd / && \
+    wget https://github.com/ShiftLeftSecurity/joern/releases/latest/download/joern-install.sh && \
+    chmod +x ./joern-install.sh && \
+    printf 'Y\n/bin/joern\ny\n/usr/local/bin\n\n' | ./joern-install.sh --interactive && \
+    rm -f /joern-install.sh
+
+# Install Miniconda (silent) and put it on PATH
+ENV CONDA_DIR=/root/miniconda3
+ENV PATH=$CONDA_DIR/bin:$PATH
+RUN cd / && \
+    wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
+    bash Miniconda3-latest-Linux-x86_64.sh -b -p "$CONDA_DIR" && \
+    rm -f Miniconda3-latest-Linux-x86_64.sh && \
+    conda clean -y --all
+
+# Install RATS (from archived tarball)
+RUN cd / && \
+    curl -L https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/rough-auditing-tool-for-security/rats-2.4.tgz -o rats-2.4.tgz && \
+    tar -xzf rats-2.4.tgz && \
+    cd rats-2.4 && ./configure && make && make install && \
+    cd / && rm -rf rats-2.4 rats-2.4.tgz
+
+# Python tools & dependencies
+# - flawfinder via pip
+# - requirements (kept same name mapping as Singularity)
+# - DGL CUDA 10.2 wheel
+# - pygraphviz via conda (conda-forge for reliability)
+# - NLTK + punkt
+RUN pip install --no-cache-dir flawfinder
+# RUN conda install -y -c conda-forge pygraphviz 
+RUN pip install --no-cache-dir nltk
+
+RUN python -c 'import nltk; nltk.download("punkt")' && \
+    conda clean -y --all && \
+    rm -rf /root/.cache/pip
+
+# Default working directory
+RUN mkdir -p linevd
+WORKDIR /linevd
+
+# Run script (Singularity %runscript)
+# ENTRYPOINT ["/bin/bash", "/cli.sh"]
+# ENTRYPOINT ["bash"]
+# If you prefer to allow overriding while still defaulting, you could use:
+# CMD []

Singularity

@@ -3,7 +3,7 @@ From:pytorch/pytorch:1.9.0-cuda10.2-cudnn7-runtime
 
 %files
     cli.sh /cli.sh
-    requirements.txt /requirements.txt
+    old_requirements.txt /requirements.txt
 
 %environment
     export SINGULARITY=true

get_old_reqirements.py

@@ -0,0 +1,52 @@
+import requests
+from datetime import datetime, timezone
+
+def get_version_at_time(package_name, target_date):
+    """
+    Get the latest version of a package available on PyPI at a specific UTC date.
+    :param package_name: str, name of the package
+    :param target_date: datetime, UTC datetime to check
+    :return: str, version or None if not found
+    """
+    url = f"https://pypi.org/pypi/{package_name}/json"
+    resp = requests.get(url)
+    if resp.status_code != 200:
+        print(f"Package {package_name} not found on PyPI.")
+        return None
+
+    data = resp.json()
+    releases = data.get("releases", {})
+    latest_version = None
+    latest_time = None
+
+    for version, files in releases.items():
+        for file in files:
+            upload_time = file.get("upload_time_iso_8601")
+            if upload_time:
+                upload_dt = datetime.fromisoformat(upload_time.replace("Z", "+00:00"))
+                if upload_dt <= target_date:
+                    if (latest_time is None) or (upload_dt > latest_time):
+                        latest_time = upload_dt
+                        latest_version = version
+
+    return latest_version
+
+if __name__ == "__main__":
+    infile = "requirements.txt"
+    new_requirements = []
+    date_str = "2022-03-22"
+    target_dt = datetime.strptime(date_str, "%Y-%m-%d").replace(tzinfo=timezone.utc)
+
+    with open(infile, "r") as f:
+        packages = [line.strip() for line in f if line.strip() and not line.startswith("#")]
+        for package in packages:
+            if ">=" in package or "==" in package:
+              new_requirements.append(package)
+              continue
+            version = get_version_at_time(package, target_dt)
+            new_requirements.append(f"{package}=={version}" if version else package)
+
+    with open("old_requirements.txt", "w") as f:
+        for req in new_requirements:
+            f.write(req + "\n")
+    print("Old requirements saved to old_requirements.txt")

old_requirements.txt

@@ -0,0 +1,41 @@
+tqdm>=4.61.2
+numpy>=1.20.1
+jupyterlab==4.0.0a22
+gdown==4.4.0
+matplotlib==3.5.1
+gensim==4.1.2
+joblib==1.1.0
+lightgbm==3.3.2
+xgboost==1.5.2
+nltk==3.7
+seaborn==0.11.2
+pytest==7.1.1
+scikit-learn==1.0.2
+scipy==1.7.3
+pandas==1.3.5
+fastparquet==0.8.0
+spacy==3.2.3
+imbalanced-learn==0.9.0
+dgl==0.9.0
+networkx==2.6.3
+pydot==1.4.2
+graphviz==0.19.1
+python-Levenshtein==0.12.2
+tensorboard==2.8.0
+python-igraph==0.9.9
+unidiff==0.7.3
+fuzzywuzzy==0.18.0
+python-Levenshtein==0.12.2
+libclang==13.0.0
+pandarallel==1.6.1
+ipywidgets==7.7.0
+transformers==4.17.0
+torchtext==0.12.0
+torchsummary==1.5.1
+torchinfo==1.6.3
+tsne_torch==1.0.1
+pytorch-lightning==1.5.10
+torch_scatter==2.0.9
+ujson==5.1.0
+unidecode==1.3.4
+ray[tune]==2.0.0

setup_env.sh

@@ -0,0 +1,3 @@
+source /opt/conda/bin/activate
+pip uninstall -y dgl
+pip install dgl==0.9.0

start_container.sh

@@ -0,0 +1 @@
+docker run --shm-size=4gb --gpus=all --mount type=bind,src=.,dst=/linevd -it --entrypoint bash linevd:latest