search

tripal / tripal_doc

Official Documentation for the Tripal Platform
https://tripaldoc.readthedocs.io/en/latest/
GNU General Public License v3.0
2 stars 3 forks source link

Reference document and functions for tracking deprecations in Tripal v4 #85

Closed pdtouch closed 4 months ago

pdtouch commented 5 months ago

To keep track of deprecated functions in Tripal v4, a reference document is being created first and separate page for each of the different api sections listing the functions involved are created and including information on how to upgrade from it. Then, functions are deprecated after testing that it still works and alternate functions are written and tested.

laceysanderson commented 5 months ago

You ended up with a bunch on permission changes in this PR. To fix it, you will want to first change the permissions back on your local version (chmod -R 644 *), commit that change and push back up to github.

Then you can add set your local git to ignore these changes in the future by using git config core.fileMode false.

dsenalik commented 4 months ago

A couple of warnings when I build the docs. The tables need to be indented two spaces I think.

/tripal_doc/docs/dev_guide/deprecations/chado_cv_api.rst:13: WARNING: Content block expected for the "table" directive; none found.

.. table:: List of deprecated functions and corresponding new method

/tripal_doc/docs/dev_guide/deprecations/chado_db_api.rst:13: WARNING: Content block expected for the "table" directive; none found.

.. table:: List of deprecated functions and corresponding new method

/tripal_doc/docs/dev_guide/deprecations/chado_db_api.rst:28: WARNING: duplicate label tripal 4.x deprecations issue, other instance in /tripal_doc/docs/dev_guide/deprecations/chado_cv_api.rst

/tripal_doc/docs/dev_guide/deprecations/chado_query_api.rst:13: WARNING: Content block expected for the "table" directive; none found.

.. table:: List of deprecated functions and corresponding new method

/tripal_doc/docs/dev_guide/deprecations/chado_query_api.rst:54: WARNING: duplicate label tripal 4.x deprecations issue, other instance in /tripal_doc/docs/dev_guide/deprecations/chado_db_api.rst

/tripal_doc/docs/dev_guide/deprecations/chado_variables_api.rst:3: WARNING: Title underline too short.

dsenalik commented 4 months ago

Great, but I still get these errors

/tripal_doc/docs/dev_guide/deprecations/chado_db_api.rst:28: WARNING: duplicate label tripal 4.x deprecations issue, other instance in /tripal_doc/docs/dev_guide/deprecations/chado_cv_api.rst

/tripal_doc/docs/dev_guide/deprecations/chado_query_api.rst:54: WARNING: duplicate label tripal 4.x deprecations issue, other instance in /tripal_doc/docs/dev_guide/deprecations/chado_db_api.rst

/tripal_doc/docs/dev_guide/deprecations/chado_variables_api.rst:28: WARNING: duplicate label tripal 4.x deprecations issue, other instance in /tripal_doc/docs/dev_guide/deprecations/chado_query_api.rst

checking consistency... /tripal_doc/docs/dev_guide/deprecations.rst: WARNING: document isn't included in any toctree