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conda installation doesn't work out of the box - ModuleNotFoundError psycopg2 #1552

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ligerzero-ai opened this issue Jul 24, 2024 · 2 comments · May be fixed by #1553
Open

conda installation doesn't work out of the box - ModuleNotFoundError psycopg2 #1552

ligerzero-ai opened this issue Jul 24, 2024 · 2 comments · May be fixed by #1553
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@ligerzero-ai
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mamba install -c conda-forge pyiron_workflow pyiron_atomistics pyiron_base

Attempting to import

from pyiron_atomistics.vasp.output import parse_vasp_output as pvo

results in:

Traceback (most recent call last):
  File "/cmmc/ptmp/hmai/mambaforge/envs/pyiron_workflow/lib/python3.12/site-packages/pyiron_base/database/generic.py", line 198, in __init__
    self._engine = create_engine(
                   ^^^^^^^^^^^^^^
  File "<string>", line 2, in create_engine
  File "/cmmc/ptmp/hmai/mambaforge/envs/pyiron_workflow/lib/python3.12/site-packages/sqlalchemy/util/deprecations.py", line 281, in warned
    return fn(*args, **kwargs)  # type: ignore[no-any-return]
           ^^^^^^^^^^^^^^^^^^^
  File "/cmmc/ptmp/hmai/mambaforge/envs/pyiron_workflow/lib/python3.12/site-packages/sqlalchemy/engine/create.py", line 599, in create_engine
    dbapi = dbapi_meth(**dbapi_args)
            ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/cmmc/ptmp/hmai/mambaforge/envs/pyiron_workflow/lib/python3.12/site-packages/sqlalchemy/dialects/postgresql/psycopg2.py", line 690, in import_dbapi
    import psycopg2
ModuleNotFoundError: No module named 'psycopg2'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/cmmc/u/hmai/github_dev_pyiron/pyiron_vasp_nodes/min_example.py", line 7, in <module>
    from pyiron_atomistics.vasp.output import parse_vasp_output as pvo
  File "/cmmc/ptmp/hmai/mambaforge/envs/pyiron_workflow/lib/python3.12/site-packages/pyiron_atomistics/__init__.py", line 1, in <module>
    from pyiron_base import JOB_CLASS_DICT, Notebook, install_dialog
  File "/cmmc/ptmp/hmai/mambaforge/envs/pyiron_workflow/lib/python3.12/site-packages/pyiron_base/__init__.py", line 5, in <module>
    from pyiron_base.state import state
  File "/cmmc/ptmp/hmai/mambaforge/envs/pyiron_workflow/lib/python3.12/site-packages/pyiron_base/state/__init__.py", line 17, in <module>
    from pyiron_base.database.manager import database as _database
  File "/cmmc/ptmp/hmai/mambaforge/envs/pyiron_workflow/lib/python3.12/site-packages/pyiron_base/database/manager.py", line 255, in <module>
    database = DatabaseManager()
               ^^^^^^^^^^^^^^^^^
  File "/cmmc/ptmp/hmai/mambaforge/envs/pyiron_workflow/lib/python3.12/site-packages/pyiron_snippets/singleton.py", line 21, in __call__
    cls._instances[cls] = super(Singleton, cls).__call__(*args, **kwargs)
                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/cmmc/ptmp/hmai/mambaforge/envs/pyiron_workflow/lib/python3.12/site-packages/pyiron_base/database/manager.py", line 31, in __init__
    self.open_connection()
  File "/cmmc/ptmp/hmai/mambaforge/envs/pyiron_workflow/lib/python3.12/site-packages/pyiron_base/database/manager.py", line 126, in open_connection
    self._database = DatabaseAccess(
                     ^^^^^^^^^^^^^^^
  File "/cmmc/ptmp/hmai/mambaforge/envs/pyiron_workflow/lib/python3.12/site-packages/pyiron_base/database/generic.py", line 212, in __init__
    raise ValueError("Connection to database failed: " + str(except_msg))
ValueError: Connection to database failed: No module named 'psycopg2'
Exception ignored in: <function DatabaseAccess.__del__ at 0x154009dac220>
Traceback (most recent call last):
  File "/cmmc/ptmp/hmai/mambaforge/envs/pyiron_workflow/lib/python3.12/site-packages/pyiron_base/database/generic.py", line 371, in __del__
    self.conn.close()
    ^^^^^^^^^
AttributeError: 'DatabaseAccess' object has no attribute 'conn'
@ligerzero-ai ligerzero-ai added the bug Something isn't working label Jul 24, 2024
@jan-janssen
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This depends on your ~/.pyiron file. By default pyiron uses SQLite, on the Cluster we use PostgreSQL, but using PostgreSQL comes with the additional requirement to install psycopg2.

@jan-janssen jan-janssen transferred this issue from pyiron/pyiron Jul 25, 2024
@pmrv
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pmrv commented Jul 25, 2024

We should still wrap this in an ImportAlarm somehwere.

@jan-janssen jan-janssen linked a pull request Jul 25, 2024 that will close this issue
Add psycopg2 as optional dependency #1553
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Add psycopg2 as optional dependency pyiron/pyiron_base
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@pmrv @jan-janssen @ligerzero-ai