What could be keeping `conda pack` from picking up monkey patches to the packages?

Question

I am trying to monkey patch a Python package before using conda pack to package up all of the packages for deployment.

The script sets up conda:

conda install -y --channel conda-forge conda-pack
conda create -y --name venv python=3.7
conda install -y --name venv --file requirements.txt

Then it monkey patches the library:

sed --in-place \
  's/CFUNCTYPE(c_int)(lambda: None)/# CCCFUNCTYPE(c_int)(lambda: None)/g' \
  /opt/conda/envs/venv/lib/python3.7/ctypes/__init__.py

Then it packages everything up for deployment:

conda pack --name venv --output "$BUILD_DIR/runtime.tar.gz"

So the weird thing is that when I copy the file directly into the build folder:

cp /opt/conda/envs/venv/lib/python3.7/ctypes/__init__.py "$BUILD_DIR"

The monkey-patched file is there.

However, when I extract $BUILD_DIR/runtime.tar.gz, the file is in its original form.

The other weird behavior is that when I manually run these steps, the monkey patched file is in $BUILD_DIR/runtime.tar.gz.

There's quite a bit of containers around, so I thought that maybe conda is using some catched tarball instead so I tried to add this into the script:

conda clean --tarballs

But that still didn't fix the problem.

I also tried to use conda pack's explicit path option, but it didn't work either:

conda pack --prefix /opt/conda/envs/venv --output "$BUILD_DIR/runtime.explicit.tar.gz"

Does conda pack pull the files from another location aside from: /opt/conda/envs/venv/lib/python3.7/site-packages

This doesn't explain why doing things manually would work, but maybe it'll point me to a new rock to look under.

Thank you for your time 🙏

Here is the entire script:

#!/usr/bin/env bash
#
# Bundle this project into a Rapid Deployment Archive (RDA)

set -ex

###########################
# Pre-reqs and pre-checks #
###########################

if [ ! -x "$(command -v conda)" ]; then
    echo "conda is required to run this script" >&2
    exit 1
fi

if [ -n "$CI_PROJECT_DIR" ]; then
    DIR="$CI_PROJECT_DIR"
else
    DIR="$(cd "$(dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd)/.."
fi

DIST_DIR="$DIR/dist"
rm -rvf "$DIST_DIR"/*.zip
BUILD_DIR="$(mktemp -d)"

#####################################
# Build client Angular UI component #
#####################################

CLIENT_DIR="$DIR/client"
mkdir -pv "$BUILD_DIR/client"
pushd "$CLIENT_DIR" || exit 1
npm install
npm run build:default
cp -R "$CLIENT_DIR/dist/template-angular-ts-master/"* "$BUILD_DIR/client"
popd

#######################################
# Build server Python/flask component #
#######################################

# Packages are installed to /opt/conda/envs/$VENV_NAME/lib/python$PYTHON_VERSION/site-packages
if [ -n "$SSL_NO_VERIFY" ]; then
    conda config --set ssl_verify false
fi
conda install -y --channel conda-forge conda-pack
conda create -y --name venv python=3.7
# Conda does not support -r spec or --file within a file
cp requirements/prod.txt requirements/prod.txt.noflag
sed -i '/^-r/d' requirements/prod.txt.noflag
conda install -y --name venv --file requirements/_base.txt --file requirements/prod.txt.noflag
sed --in-place \
  's/CFUNCTYPE(c_int)(lambda: None)/# CCCFUNCTYPE(c_int)(lambda: None)/g' \
  /opt/conda/envs/venv/lib/python3.7/ctypes/__init__.py
rm -f requirements/prod.txt.noflag
conda clean --tarballs
conda pack --name venv --output "$BUILD_DIR/runtime.tar.gz"

# Junk within pyapp that might be present if not building in CI
if [ -z "$CI_PROJECT_DIR" ]; then
    find "$DIR" -name '*.pyc' -type f -delete
    find "$DIR" -name '.DS_Store' -type f -delete
    find "$DIR" -name '__pycache__' -type d -delete
fi

# Copy this project's stuff into build dir
cp -v -R "$DIR/config" "$DIR/pyapp" "$BUILD_DIR"
cp -v "$DIR"/rda/* "$BUILD_DIR"
cp -v setup.{py,cfg} pyproject.toml "$BUILD_DIR"
cp -v "$DIR"/scripts/{start-server.sh,wsgi.py} "$BUILD_DIR"

cp -v /opt/conda/envs/venv/lib/python3.7/ctypes/__init__.py "$BUILD_DIR"

# Try to extract the version and appKey if we have jq
if [ -x "$(command -v jq)" ]; then
    VERSION="-$(jq -j '.version' rda/rda.manifest)"
    appKey="$(jq -j .appKey rda/rda.manifest)"
else
    VERSION=''
    appKey="$(grep --color=never -oP 'appKey":\s+"\K[^"]+' rda/rda.manifest)"
fi
if [ -z "$appKey" ]; then
    appKey="my.webapp.ng-py"
fi

# Bundle into RDA ZIP
mkdir -pv "$DIST_DIR"
pushd "$BUILD_DIR"
zip -q -9 -r "$DIST_DIR/${appKey}${VERSION}.rda.zip" *
popd
rm -rf "$BUILD_DIR"
ls -1 -l -F "$DIST_DIR"/*.zip

conda clean -afy

Answer 1

I wasn't able to get the monkey patching to work, but I was able to figure out that ctypes is not part of numpy and rather is part of Python's standard library. So conda pack could very well treat Python standard libraries a bit differently.

So I gave up on monkey patching and found out that upgrading my Python version fixed the underlying issue.

Thanks 🙏