__file__ always points to __init__.py

[TristynAlxander]

Describe the bug

__file__ variable in python scipts is pointing to __init__.py instead of the respective script file.

To Reproduce

Steps to reproduce the behavior:

1. Make file 'temp_0.py'

print("__file__")
print(__file__)

2. run file through pymol __init__.py. I uses a short described below to simply run pymol temp_0.py Equivalently, you can run python /path/to/pymol/__init__.py temp_0.py

Expected behavior

Currently __file__ points to __init__.py, not temp_0.py. __file__ in temp_0.py should point totemp_0.py

I'm not exactly sure where the exec() function is in the pymol code, but essentially when you convert the temp_0.py file to a string and pass it to exec you need to modify the namespace you pass to the exec function such that __file__ points to the path of whatever you're converting to a string.

Something like this, but be careful of whether you feed it to globals or locals and it'll probably modifying the __file__ in some pre-existing namespace. Not sure about the details...

path = "/home/user/documents/folder/temp_0.py"
path = fix_path(path)
exec_str = file_to_str(path)
namespace = {"__file__": path,}
exec(exec_str, namespace)

Environment

• PyMOL Version: 3.1.0a0
• PyMOL Source: compiled from this repo
• Operating System: Linux Mint
• If you are using a conda environment, please supply your conda list:

# packages in environment at /opt/.miniconda/envs/protein_pymol:
#
# Name                       Version          Build                Channel
_libgcc_mutex                0.1              conda_forge          conda-forge
_openmp_mutex                4.5              2_gnu                conda-forge
brotli                       1.1.0            hb9d3cd8_2           conda-forge
brotli-bin                   1.1.0            hb9d3cd8_2           conda-forge
brotli-python                1.1.0            py313h46c70d0_2      conda-forge
bzip2                        1.0.8            h4bc722e_7           conda-forge
ca-certificates              2024.12.14       hbcca054_0           conda-forge
cairo                        1.18.2           h3394656_1           conda-forge
cctbx-base                   2024.12          pypi_0               pypi
certifi                      2024.12.14       pyhd8ed1ab_0         conda-forge
cffi                         1.17.1           py313hfab6e84_0      conda-forge
chardet                      5.2.0            py313h78bf25f_2      conda-forge
charset-normalizer           3.4.1            pyhd8ed1ab_0         conda-forge
cmake                        3.31.4           pypi_0               pypi
contourpy                    1.3.1            py313h33d0bda_0      conda-forge
cycler                       0.12.1           pyhd8ed1ab_1         conda-forge
font-ttf-dejavu-sans-mono    2.37             hab24e00_0           conda-forge
font-ttf-inconsolata         3.000            h77eed37_0           conda-forge
font-ttf-source-code-pro     2.038            h77eed37_0           conda-forge
font-ttf-ubuntu              0.83             h77eed37_3           conda-forge
fontconfig                   2.15.0           h7e30c49_1           conda-forge
fonts-conda-ecosystem        1                0                    conda-forge
fonts-conda-forge            1                0                    conda-forge
fonttools                    4.55.3           py313h8060acc_1      conda-forge
freetype                     2.12.1           h267a509_2           conda-forge
freetype-py                  2.3.0            pyhd8ed1ab_0         conda-forge
future                       1.0.0            pyhd8ed1ab_1         conda-forge
h2                           4.1.0            pyhd8ed1ab_1         conda-forge
hpack                        4.0.0            pyhd8ed1ab_1         conda-forge
hyperframe                   6.0.1            pyhd8ed1ab_1         conda-forge
icu                          75.1             he02047a_0           conda-forge
idna                         3.10             pyhd8ed1ab_1         conda-forge
kiwisolver                   1.4.7            py313h33d0bda_0      conda-forge
lcms2                        2.16             hb7c19ff_0           conda-forge
ld_impl_linux-64             2.43             h712a8e2_2           conda-forge
lerc                         4.0.0            h27087fc_0           conda-forge
libblas                      3.9.0            26_linux64_openblas  conda-forge
libboost                     1.86.0           h6c02f8c_3           conda-forge
libboost-python              1.86.0           py313hf0ab243_3      conda-forge
libbrotlicommon              1.1.0            hb9d3cd8_2           conda-forge
libbrotlidec                 1.1.0            hb9d3cd8_2           conda-forge
libbrotlienc                 1.1.0            hb9d3cd8_2           conda-forge
libcblas                     3.9.0            26_linux64_openblas  conda-forge
libdeflate                   1.23             h4ddbbb0_0           conda-forge
libdrm                       2.4.124          hb9d3cd8_0           conda-forge
libegl                       1.7.0            ha4b6fd6_2           conda-forge
libexpat                     2.6.4            h5888daf_0           conda-forge
libffi                       3.4.2            h7f98852_5           conda-forge
libgcc                       14.2.0           h77fa898_1           conda-forge
libgcc-ng                    14.2.0           h69a702a_1           conda-forge
libgfortran                  14.2.0           h69a702a_1           conda-forge
libgfortran5                 14.2.0           hd5240d6_1           conda-forge
libgl                        1.7.0            ha4b6fd6_2           conda-forge
libglib                      2.82.2           h2ff4ddf_1           conda-forge
libglu                       9.0.3            h03adeef_0           conda-forge
libglvnd                     1.7.0            ha4b6fd6_2           conda-forge
libglx                       1.7.0            ha4b6fd6_2           conda-forge
libgomp                      14.2.0           h77fa898_1           conda-forge
libiconv                     1.17             hd590300_2           conda-forge
libjpeg-turbo                3.0.0            hd590300_1           conda-forge
liblapack                    3.9.0            26_linux64_openblas  conda-forge
liblzma                      5.6.3            hb9d3cd8_1           conda-forge
libmpdec                     4.0.0            h4bc722e_0           conda-forge
libopenblas                  0.3.28           pthreads_h94d23a6_1  conda-forge
libpciaccess                 0.18             hd590300_0           conda-forge
libpng                       1.6.45           h943b412_0           conda-forge
libsqlite                    3.48.0           hee588c1_0           conda-forge
libstdcxx                    14.2.0           hc0a3c3a_1           conda-forge
libstdcxx-ng                 14.2.0           h4852527_1           conda-forge
libsvm                       335              h5888daf_1           conda-forge
libtiff                      4.7.0            hd9ff511_3           conda-forge
libuuid                      2.38.1           h0b41bf4_0           conda-forge
libwebp-base                 1.5.0            h851e524_0           conda-forge
libxcb                       1.17.0           h8a09558_0           conda-forge
libzlib                      1.3.1            hb9d3cd8_2           conda-forge
matplotlib-base              3.10.0           py313h129903b_0      conda-forge
mrcfile                      1.5.3            pyhd8ed1ab_1         conda-forge
munkres                      1.1.4            pyh9f0ad1d_0         conda-forge
ncurses                      6.5              h2d0b736_2           conda-forge
numpy                        2.2.2            py313h17eae1a_0      conda-forge
openjpeg                     2.5.3            h5fbd93e_0           conda-forge
openssl                      3.4.0            h7b32b05_1           conda-forge
packaging                    24.2             pyhd8ed1ab_2         conda-forge
pandas                       2.2.3            pypi_0               pypi
pcre2                        10.44            hba22ea6_2           conda-forge
pillow                       11.1.0           py313h8db990d_0      conda-forge
pip                          24.3.1           pyh145f28c_2         conda-forge
pixman                       0.44.2           h29eaf8c_0           conda-forge
psutil                       6.1.1            py313h536fd9c_0      conda-forge
pthread-stubs                0.4              hb9d3cd8_1002        conda-forge
pycairo                      1.27.0           py313h112314f_0      conda-forge
pycparser                    2.22             pyh29332c3_1         conda-forge
pymol                        3.1.0a0          pypi_0               pypi
pyparsing                    3.2.1            pyhd8ed1ab_0         conda-forge
pyqt5                        5.15.11          pypi_0               pypi
pyqt5-qt5                    5.15.16          pypi_0               pypi
pyqt5-sip                    12.16.1          pypi_0               pypi
pysocks                      1.7.1            pyha55dd90_7         conda-forge
python                       3.13.1           ha99a958_105_cp313   conda-forge
python-dateutil              2.9.0.post0      pyhff2d567_1         conda-forge
python_abi                   3.13             5_cp313              conda-forge
pytz                         2024.2           pypi_0               pypi
qhull                        2020.2           h434a139_5           conda-forge
readline                     8.2              h8228510_1           conda-forge
reportlab                    4.2.5            py313h536fd9c_0      conda-forge
requests                     2.32.3           pyhd8ed1ab_1         conda-forge
rlpycairo                    0.2.0            pyhd8ed1ab_0         conda-forge
scipy                        1.15.1           py313h750cbce_0      conda-forge
setuptools                   75.8.0           pypi_0               pypi
six                          1.17.0           pyhd8ed1ab_0         conda-forge
tk                           8.6.13           noxft_h4845f30_101   conda-forge
tzdata                       2025.1           pypi_0               pypi
unitment                     0.0.9            pypi_0               pypi
urllib3                      2.3.0            pyhd8ed1ab_0         conda-forge
xorg-libice                  1.1.2            hb9d3cd8_0           conda-forge
xorg-libsm                   1.2.5            he73a12e_0           conda-forge
xorg-libx11                  1.8.10           h4f16b4b_1           conda-forge
xorg-libxau                  1.0.12           hb9d3cd8_0           conda-forge
xorg-libxdamage              1.1.6            hb9d3cd8_0           conda-forge
xorg-libxdmcp                1.1.5            hb9d3cd8_0           conda-forge
xorg-libxext                 1.3.6            hb9d3cd8_0           conda-forge
xorg-libxfixes               6.0.1            hb9d3cd8_0           conda-forge
xorg-libxrender              0.9.12           hb9d3cd8_0           conda-forge
xorg-libxxf86vm              1.1.6            hb9d3cd8_0           conda-forge
zstandard                    0.23.0           py313h80202fe_1      conda-forge
zstd                         1.5.6            ha6fb4c9_0           conda-forge

Additional context

My pymol short cut does run through __init__.py

if [ ! -d ~/bin ]; then mkdir ~/bin; fi;
    echo '#!/bin/sh' > ~/bin/pymol
    echo exec \"/opt/.miniconda/envs/protein_pymol/bin/python\" \"$(( python -c "import site; print(site.getsitepackages()[0])" ) >&1)/pymol/__init__.py\" \"\$@\" >> ~/bin/pymol
    chmod 777 ~/bin/pymol

[JarrettSJohnson]

Does the run command with module argument suit your needs?
See:
https://pymol.org/dokuwiki/doku.php?id=command:run
or
https://pymolwiki.org/index.php/Run

Doing

run temp_0.py, module

Gives me:

__file__
temp_0.py

whereas what the default is (and what you observed) with

run temp_0.py

Gave me:

__file__
<path_to_pymol>/__init__.py

[TristynAlxander]

run temp_0.py, module produces the right output, but it's not great for running as a sub-script of a larger pipeline.

If change my pymol command to use a wrapper: exec "python" "/path/to/pymol/__init__.py" "/path/to/wrapper.py" "--" "$@"
then use wrapper.py as:

import sys, os
import pymol
pymol.finish_launching()

command = " ".join(sys.argv[1:])
pymol.cmd.do(f"run {command}, module")

It does work for simple scripts, but breaks down if there's additional arguments. So, at that stage I'm better off just using making an exec wrapper:

pymol file:

#!/usr/bin/env bash

OPTIONS=()
ARGS=()

for arg in "$@"; do
  if [[ "$arg" == -* ]]; then
    OPTIONS+=("$arg")
  else
    ARGS+=("$arg")
  fi
done

exec "/path/to/python" "/path/to/pymol/__init__.py" "${OPTIONS[@]}" "/path/to/wrapper.py" "--" "${ARGS[@]}"

Wrapper.py:

import sys, os

def file_to_str(path):
  path_file = open(path, 'r', encoding="utf8")
  file_str  = path_file.read()
  path_file.close()
  return file_str
def fix_path(path):
  path = os.path.expanduser(path)
  path = os.path.normpath(path)
  path = os.path.realpath(path)
  return path

sys.argv = sys.argv[1:] # This file is [0]
if len(sys.argv) and sys.argv[0].endswith(".py"):
  script_path = fix_path(sys.argv[0])
  script_args = sys.argv[1:]
  script_str  = file_to_str(script_path)
  script_complie = compile(script_str, script_path, "exec")
  script_namespace = {
    "__name__": "__main__",
    "__file__": script_path,
    }
  exec(script_complie,script_namespace)

This is kinda hacky, and really not "proper", but... it works for my purposes.

After reading the provided documentation it's not clear to me whether this is a pymol issue or a Pickle issue. It's definitely not a users make a wrapper issue, but the work around is appreciated. Not sure if the issue should be closed. If it's a pymol issue, it should be fixed because __file__ working is fundamental to python coding. If it's a Pickle issue, someone should reference this thread from a Pickle Issue.