TODO list for JOSS manuscript

[alchem0x2A]

A few TODO lists before initial submission for JOSS manuscript

** JOSS manuscript preparation (in JOSS branch)

• Check affl., ORCID, acknowledgment
• typos in references
• check joss submission guidelines
• pin sparc-x-api release version in joss branch
• Frozen code dump of dev_SPARC to include? Public SPARC but cherry-picking MLFF/Socket compatibility?
• merge dev_SPARC socket --> main
• [] Few parameters in SPARC LaTeX doc

** Current bugs

• [] Incorrect reinitialization of mesh spacing #55 Mesh re-init for non-orthogonal cell (related to the SPARC C-code)
• [] Segmentation fault when running socket in run mode b with OFDFT. #50 OFDFT bug, related to previous issue
• [] Incremental reading of static files in socket calculation #51 Need lazy-loading / delayed read of static files (medium priority)
• [] Track total SCF calls across restarts #52 Compatibility with restart file
• Pass initial magnetic moments from ASE atoms object to SPARC #54 Init magmom as input (high priority, to fulfill ASE compatibility)
• [] Migration to ASE 3.23 #48 ASE 3.23 various changes
• Fix CI workflow with latest SPARC doc parsing

** JSON Schema

• Check current warnings in Schema generation (low priority)
• Split CI workflow with i/o and docparsing for public SPARC branch as separate task
• More detailed SPARC JSON schema version (major - date version, e.g. version 2.0 - 2024.06.24)
• Add schema check in public SPARC repo as well?

** Examples

• [] Clearer listing of examples (maybe try choosing examples from SPARC paper?)
• [] Remove cluster details in active learning / mlff-socket examples

** Doc
Current readme may be good, but we may want to have several separated md files for specific topics:

• @alchem0x2A restructure doc for standard ASE / socket
• @ltimmerman3 restructure doc for MLFF MD

** Improvements

• Doc to maintainance guidance (esp. how to update actions / conda-forge package)
• Check current package coverage