Help and FAQ ============ This page provides help if you run into problems with ``refineGEMs``. Help ---- Known Issues and Bugs --------------------- .. hint:: For bug reports please write issues on the `GitHub page `__ or open a discussion `here `__. Pydantic ^^^^^^^^ Pydantic warning `underscore_attrs_are_private has been removed` has not - yet - caused any issues. However, the core of the problem (= what causes the warning) has yet to be identified. FAQ --- This site addresses frequently asked questions not addressed in other pages of the ``refineGEMs`` documentation. How do I install ``refineGEMs``? ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Please see :ref:`Installation`. How do I install ``refineGEMs`` as a developer? ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Please see :ref:`Installation for developers`. How do I cite ``refineGEMs``? ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Please see :ref:`How to cite`. After restarting my device (MacOS) my conda set-up has the wrong python version. What can I do? ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1. Deactivate all environments including the base environment 2. Activate your environment for ``refinegems`` again I cannot access ``python`` from within my conda environment in my VSCode terminal. What can I do? ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Please refer to the solution for :ref:`After restarting my device (MacOS) my conda set-up has the wrong python version. What can I do?` My ``pipenv`` is not locking after f.ex. moving the repository. What can I do? ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Try uninstalling ``pipenv`` and reinstalling it via pip. Then run ``pipenv install`` and it should work again. How to solve errors caused by ``pandoc`` (Development)? ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | `Here `__ is an answer that might help. | If you install pandoc with conda use: .. code:: console :class: copyable conda install -c conda-forge pandoc How to solve errors caused by ``jinja2`` (Development)? ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Try to switch to version 3.0.3: .. code:: console :class: copyable pip install jinja2==3.0.3 When do I use ``lab_strain=True``? ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ If the parameter ``lab_strain`` is set to ``True`` it is assumed that the input model was created for a strain of an organism for which so far no data is available in any database. To get sufficient information for the knowledge-base stored within the model of the strain the ``PGAB`` pipeline described in ``SPECIMEN`` should be used before model creation. The resulting FASTA from the ``PGAB`` pipeline can then be used als input for CarveMe and is then also required as additional input for :py:mod:`~refinegems.curation.polish`. In this case the parameter ``lab_strain`` should be set to ``True``.