before folding into GenomicsStandardsConsortium org

[turbomam]

• [ ] look for potential problems in log files from make all
  • maybe rerun in DEBUG mode, esp conversion.log?
  • conversion.log
  • generation.log
  • mkdocs.log
• [ ] problems with docs generation and publishing?
  • [ ] slow
  • [ ] poorly organized documentation-related Makefile rules
  • [ ] default docs home page broken? For now, use /mixs-source instead
• [ ] annotations don't appear in docs (previous appeared as comments)
• [ ] owl artifact looks funny in Protege... named individuals and object properties don't have labels

see also https://github.com/GenomicsStandardsConsortium/mixs/issues/329

generation.log

• ~ 800 lines of ERROR:root:Multiple slots with URI: https://w3id.org/mixs/terms/...
• ~ 22k lines of ERROR:root:No PK for quantity_value
  • Expected? From SQL DDL generation?

mkdocs.log

• ~ 20 lines like Documentation file 'ph.md' contains a link to 'water_ph.md' which is not found in the documentation files
  • from slot utilization mangling?

conversion.log

ERROR:root:No slot_uri for Environmental package                          food-food production facility
Structured comment name                                    prod_label_claims
Package item                                      production labeling claims
Definition                 Labeling claims containing descriptors such as...
Expected value                                                          text
Value syntax                                                          {text}
Example                                                           free range
Section                                                                     
Requirement                                                                X
Preferred unit                                                              
Occurrence                                                                 m
MIXS ID                                                                     
github ticket                                                   MIXS:0001337
Unnamed: 13                                                             #298
Name: 1431, dtype: object
ERROR:root:No slot_uri for Environmental package                                  food-farm environment
Structured comment name                                    prod_label_claims
Package item                                      production labeling claims
Definition                 Labeling claims containing descriptors such as...
Expected value                                                          text
Value syntax                                                          {text}
Example                                                           free range
Section                                                                     
Requirement                                                                X
Preferred unit                                                              
Occurrence                                                                 m
MIXS ID                                                                     
github ticket                                                   MIXS:0001337
Unnamed: 13                                                             #298
Name: 1541, dtype: object

[turbomam]

make sure rdf/owl artifacts good

[turbomam]

• make sure rdf/owl artifacts good
• don't cal the jinja templates folder templates
  • doc_templates
• clarify generated vs release
• packages as classes vs checklist as mixins and combinations
• integration with hunter's docs page @ ???
  • org-level gh pages should use canonical url
• symlink to readme for static portion of mkdocs
• add origin (core, checklist, package) to gen-docs pages
  • color code?
• display annotations
• consistent capitalization