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compatibility with python on longleaf. To remove ?
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@jcblemai
jcblemai committed Sep 27, 2024
1 parent b5409a7 commit 7e2a061
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2 changes: 1 addition & 1 deletion flepimop/gempyor_pkg/src/gempyor/file_paths.py
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Expand Up @@ -9,7 +9,7 @@
- run_id: Generates a run ID based on the current or provided timestamp.
- create_dir_name: Creates a directory name based on given parameters.
"""

from __future__ import annotations
from datetime import datetime
import os
from pathlib import Path
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2 changes: 1 addition & 1 deletion flepimop/gempyor_pkg/src/gempyor/utils.py
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@@ -1,3 +1,4 @@
from __future__ import annotations
import datetime
import functools
import logging
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from gempyor import file_paths


logger = logging.getLogger(__name__)

config = confuse.Configuration("flepiMoP", read=False)
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5 comments on commit 7e2a061

@TimothyWillard
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I generally don't comment on commits outside of PRs, but since this was referenced in GH-280 this caught my eye. This is not resolved by upgrading from python 3.10 to 3.11, future annotations are still in place (in fact I don't think it made it into 3.13 either even). However, I'm confused why this is required here? I don't see any circular type hints between these two files which is typically what this is meant to fix. I was able to check out the branch and run the unit tests successfully without the from __future__ import annotations lines in either file.

@jcblemai
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no, you are right to comment here, I wanted to bring that to your attention. There are still some python3.9 env

(base) ➜  ~ python
Python 3.9.7 (default, Sep 16 2021, 13:09:58)
[GCC 7.5.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.

and without this we get as error

Traceback (most recent call last):
  File "/nas/longleaf/home/chadi/.local/bin/flepimop-calibrate", line 33, in <module>
    sys.exit(load_entry_point('gempyor', 'console_scripts', 'flepimop-calibrate')())
  File "/nas/longleaf/home/chadi/.local/bin/flepimop-calibrate", line 25, in importlib_load_entry_point
    return next(matches).load()
  File "/nas/longleaf/rhel8/apps/anaconda/2021.11/lib/python3.9/importlib/metadata.py", line 77, in load
    module = import_module(match.group('module'))
  File "/nas/longleaf/rhel8/apps/anaconda/2021.11/lib/python3.9/importlib/__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1030, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
  File "<frozen importlib._bootstrap>", line 972, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
  File "<frozen importlib._bootstrap>", line 1030, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
  File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 680, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 850, in exec_module
  File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
  File "/work/users/c/h/chadi/flepiMoP_Notebooks/flepiMoP/flepimop/gempyor_pkg/src/gempyor/__init__.py", line 3, in <module>
    from .inference import *
  File "/work/users/c/h/chadi/flepiMoP_Notebooks/flepiMoP/flepimop/gempyor_pkg/src/gempyor/inference.py", line 12, in <module>
    from . import seir, model_info
  File "/work/users/c/h/chadi/flepiMoP_Notebooks/flepiMoP/flepimop/gempyor_pkg/src/gempyor/seir.py", line 9, in <module>
    from . import NPI, model_info, steps_rk4
  File "/work/users/c/h/chadi/flepiMoP_Notebooks/flepiMoP/flepimop/gempyor_pkg/src/gempyor/model_info.py", line 3, in <module>
    from . import seeding, subpopulation_structure, parameters, compartments, file_paths, initial_conditions
  File "/work/users/c/h/chadi/flepiMoP_Notebooks/flepiMoP/flepimop/gempyor_pkg/src/gempyor/seeding.py", line 8, in <module>
    from . import utils
  File "/work/users/c/h/chadi/flepiMoP_Notebooks/flepiMoP/flepimop/gempyor_pkg/src/gempyor/utils.py", line 22, in <module>
    from gempyor import file_paths
  File "/work/users/c/h/chadi/flepiMoP_Notebooks/flepiMoP/flepimop/gempyor_pkg/src/gempyor/file_paths.py", line 21, in <module>
    index: str | int,
TypeError: unsupported operand type(s) for |: 'type' and 'type'

@jcblemai
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@jcblemai jcblemai commented on 7e2a061 Oct 18, 2024 •
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straightforward fix is to update the environement, but constantly things running at the moment. I think we'll remove that in the PR.

@TimothyWillard
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Oh, I see. This is because of the str | int syntax, for python 3.9 need to use Union[str, int]. Although that would be quite the change to support 3.9 in the mainstream gempyor. Yeah, I think this is the right approach for the moment, hopefully the HPC install script PR makes it easy to correct this soon.

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yes, can't wait to try this after the current rush.

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