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CSV files with chemical_names as null or no value fail on molecule load #38

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PhillipDowney opened this issue Mar 22, 2024 · 0 comments

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read_csv in loading molecules loading 'nan' instead of string into cells causing naming algorithm to fail

PhillipDowney pushed a commit that referenced this issue Mar 22, 2024
PhillipDowney pushed a commit that referenced this issue Mar 22, 2024
PhillipDowney pushed a commit that referenced this issue Mar 22, 2024
PhillipDowney added a commit that referenced this issue Jun 14, 2024
* #38 addressed

* #38 problem addressed

* #38 addressed

* integration of models

* update with catalog services

* update with catalog services

* combined properties and generator

* grammar cleanup

* namespacing added

* addressed error checking, tab forward, Help and display formatting

* addressed error checking, tab forward, Help and display formatting

* model service api

* added model mgt services

* model service api updates

* bugfix services

* using inheritance

* working on bug fix for save

* servicer updates

* added skypilot

* phils changes

* download models

* pytest tests added

* new tests

* updated servicer

* change default port

* updated capabilities

* updated capabilities

* #42 addresses issue of canonical smiles being overwritten with 2D canonical from Pubchem

* testing and fixes

* bugs for launching services

* partially implemented context sensitive output

* temp feat gpu

* create config from service file

* remove unused grammer

* set default workdir

* version bump servicing

* print config specs

* try to remove service

* rename to cfg

* format config print

* fixes

* skip test until next servicing

* updated tests and servicing

* -c implementation for comand line raw

* implemented api

* implemented api

* reduce interval for spinner

* wait for service to ping

* add status

* cast vars

* bug fix

* updates for merge data

* fix cfg file types

* updated tests

* bug fix status

* scaffold for local service

* more fixes

* high speed merge of property output

* improvements to handling data only modes in api

* better status

* major services update

* spinner function hints

* more hints

* add remote service

* added grammar for remote service catalog

* fix Notetype error in returns

* start without gpu

* fixurl

* setup pre-commit

* chore format and lint

* added append and fixed messaging

* fixed adding or displaying molecule not on pubchem

* demonstration testing and new notebooks

* fix return_val parameter typo

* llm model update to latest granite

* llm model update to latest granite

* update on doco and demo

* update notebooks and for demonstration

* working remote service defs

* servicing version bump

* remote service working

* chore: linter

* fix logger

* notebook update

* notebook update

* better logging

* remove lower()

* one more log :-)

* change save

* expand user path

* remove sentence transformer

* fix remote fetch

* service grammar instant refresh

* save when necessary

* caching service definitions

* clean up and debug

* update service defs

* use python cache decorator

* reduce sleep

* fix tests

* timout on catalog query increase 1 - 3 seconds

* timout on catalog query increase 1 - 3 seconds

* increase linter line length

* fix lru cache update

* readme update

* temporary fix for url fetch

* updates

* readme updates

* readme updates

* linter

* corrected Readme and added plugin loader

* updated pnd files

* updated version

* merge

* merge

* merge

* merge

* llm ollama support

* tuning model output and changing embeddings

* finalise on llama3 for ollama and granite-chat for BAM

* readme update for ollama

* Feat auth api (#47)

* authentication grammer

* auth with api key

* chore: sort imports

* auth model inference

* rename headers

* file lock + optimize + api obfuscate

* working proxy

* add headers to proxy

* can add bearer token in USING quotes

---------

Co-authored-by: Brian Duenas <[email protected]>

* llm instructions

* chore: lint

* updated version

---------

Co-authored-by: Phil Downey <[email protected]>
Co-authored-by: Phil Downey <[email protected]>
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