Open pdtouch opened 1 week ago
laceysanderson
commented
1 week 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
1 week 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
1 week 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
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.