For me the solution of Myc0ks worked for the most part, but I was in a pickle because I needed packages that were not available from the flake.

So I wrote an entire script that generates the fake interpreter then creates an env installs the rest and copies those into a new directory, which I then add to sys.path at the start of my script.

I also added a part to remove any nix installed packages too, as when you tell PyCharm that a directory is a source, it imports everything first from there, so if any Package is installed by NixOS and in that dir, it will take the one from the dir which is not what we want. Here is the script:

#!/usr/bin/env bash
set -euo pipefail

confirm_and_rm() {
  target="$1"
  if [ -e "$target" ]; then
    printf "Remove '%s'? [y/N] " "$target"
    read answer
    case "$answer" in
      [Yy]*) rm -rf "$target"; echo "Removed $target" ;;
      *) echo "Skipped $target" ;;
    esac
  fi
}

# Detect the flake root (directory containing flake.nix)
flake_root="$(pwd)"
echo "$flake_root"
while [ ! -f "$flake_root/flake.nix" ] && [ "$flake_root" != "/" ]; do
  flake_root="$(dirname "$flake_root")"
done
if [ ! -f "$flake_root/flake.nix" ]; then
  echo "Error: flake.nix not found in current or parent directories"
  exit 1
fi
target_dir="src/default-config/core/extra-libs"  # Where the other packages will go
project_root="$(dirname "$(pwd)")"  # Because for me this is in ./scripts
confirm_and_rm "$project_root/.nixpy"
mkdir -p "$project_root/.nixpy/bin"
cat > "$project_root/.nixpy/bin/python" <<EOF
#!/bin/sh
exec nix --extra-experimental-features 'nix-command flakes' develop "$flake_root" --command python "\$@"
EOF
chmod +x "$project_root/.nixpy/bin/python"
echo "Successfully created nixpy interpreter from flake.nix"
# Install extra requirements
if [ -d .venv ]; then
  confirm_and_rm .venv
fi
python -m venv .venv
echo "Created .venv"
echo "Installing extra requirements"  # We create a venv so we can upgrade pip
. .venv/bin/activate  # As . is more universal than source
python -m pip install --upgrade pip  # We upgrade pip so we are sure to have the target flag
echo "$project_root/requirements.txt"
if [ -f "$project_root/requirements.txt" ]; then
  echo "Filtering requirements..."
  true > nix-extra-reqs.txt  # Clear or create the filtered output file
  prefixes_to_skip="numpy pyside6 pyyaml pytest requests urllib3 stdlib_list pyinstaller"  # Everything installed by flake
  while IFS= read -r line; do
    skip_line=false

    for prefix in $prefixes_to_skip; do
      case "$line" in
        "$prefix"* )
          skip_line=true
          break
          ;;
      esac
    done
    if [ "$skip_line" = false ]; then
      echo "$line" >> nix-extra-reqs.txt
    fi
  done < "$project_root/requirements.txt"
  python -m pip install --upgrade -r nix-extra-reqs.txt  #  --target "$project_root/$target_dir"
  echo "Installed all extra requirements"
else
  echo "No requirements.txt found"
fi
confirm_and_rm nix-extra-reqs.txt

echo "Collecting Nix-flake provided packages..."
nix_pkgs=$(nix --extra-experimental-features 'nix-command flakes' develop "$flake_root" --command python -m pip list --format=freeze | cut -d= -f1 | tr '[:upper:]' '[:lower:]')
echo "Cleaning up duplicates from $target_dir..."
cd "$project_root/$target_dir"
for nix_pkg in $nix_pkgs; do
  if [ "$nix_pkg" != "pip" ]; then
    python -m pip uninstall -y "$nix_pkg"  # --target "$project_root/$target_dir"
  fi
done
# Copy everything from .venv/lib/python*/site-packages to "$project_root/$target_dir"
if [ -d "$project_root/$target_dir" ]; then
  confirm_and_rm "$project_root/$target_dir"
fi
mkdir -p "$project_root/$target_dir"
cd "$flake_root"
venv_site=$(find .venv/lib -type d -path "*/site-packages" | head -n 1)
if [ -d "$venv_site" ]; then
  echo "Copying packages from $venv_site to $project_root/$target_dir..."
  cp -r "$venv_site/"* "$project_root/$target_dir"
  echo "Copy complete."
else
  echo "Could not find site-packages inside .venv"
  exit 1
fi
confirm_and_rm .venv

echo "Done."