Digichem
--------


vtest-tag
________________________________


v7.2.1
________________________________


Bugfixes
============================

- 2025-12-03: better error reporting when specifying a non-existant job ID
- 2025-12-03: fixed calling resolve() on Gaussian root, which interfers with symlink spoofing
- 2025-12-03: added workaround for PySCF issue #3061

Miscellaneous
============================

- 2025-12-03: update last modified
- 2025-12-03: bumped to 7.2.1
- 2025-05-25: Bumped version to 6.8.1; first release of blender versions
- 2025-05-25: bumped to 6.8.1-pre.3 for build testing
- 2025-05-25: bumped to 6.8.0-pre.2 for build testing
- 2025-05-25: bumped version to 6.8.1-pre.1 for updated build testing
- 2025-05-21: prebuild 2 for upcoming blender versions
- 2025-05-21: bumped version to 6.8.0-pre.1 to test new blender build system

v7.2.0
________________________________


New features
============================

- 2025-11-13: added better description for the auto_path option
- 2025-11-13: added support for automatically determining the scratch location

Documentation changes
============================

- 2025-11-19: another attempt to fix github worklow for docs
- 2025-11-19: fixed workflow not fetching tags
- 2025-11-19: auto changelog now starts at v6
- 2025-11-19: auto changelog no longer cuts off beginning of non-semantic commits
- 2025-11-19: added changelog to docs (auto generated)

Miscellaneous
============================

- 2025-11-19: update last modified
- 2025-11-18: update last modified
- 2025-11-17: bumped to v7.2.0

v7.1.0
________________________________


New features
============================

- 2025-11-13: added links dir to store spoofed progam installs
- 2025-11-13: added initial support for non-standard Gaussian installs
- 2025-11-10: added some initial groundwork for one-day supporting native mongita queries
- 2025-11-10: database search commands now accept skip & limit keywords

Documentation changes
============================

- 2025-11-13: added documentation for logging on to Compute Canada

Testing updates
============================

- 2025-11-10: added test for database skipping and limiting

Miscellaneous
============================

- 2025-11-13: update last modified
- 2025-11-13: bumped version to 7.1.0

v7.0.3
________________________________


Bugfixes
============================

- 2025-11-04: updated to 7.0.3 to fix botched build for 7.0.2

Miscellaneous
============================

- 2025-11-04: update last modified
- 2025-05-25: Bumped version to 6.8.1; first release of blender versions
- 2025-05-25: bumped to 6.8.1-pre.3 for build testing
- 2025-05-25: bumped to 6.8.0-pre.2 for build testing
- 2025-05-25: bumped version to 6.8.1-pre.1 for updated build testing
- 2025-05-21: prebuild 2 for upcoming blender versions
- 2025-05-21: bumped version to 6.8.0-pre.1 to test new blender build system

v7.0.2
________________________________


Bugfixes
============================

- 2025-10-31: fixed unnecessary error when changing settings and no server is available
- 2025-10-30: fixed missing species-data file for PySCF Berny optimisations

Miscellaneous
============================

- 2025-10-31: update last modified
- 2025-10-30: bumped version to v7.0.2

v7.0.1
________________________________


Bugfixes
============================

- 2025-10-01: fixed a problem validating licenses when no config directory exists

Documentation changes
============================

- 2025-10-23: added pydata theme to workflow
- 2025-10-23: initial documentation for managing downloads
- 2025-10-08: added initial docs for viewing results
- 2025-10-08: added tutorial for managing runnin calcs
- 2025-10-08: added tutorial for submitting a calc in get started
- 2025-10-07: started updating getting started guide
- 2025-10-06: migrated docs to new layout

Miscellaneous
============================

- 2025-10-23: update last modified
- 2025-10-21: update last modified
- 2025-10-21: bumped to v7.0.1
- 2025-10-02: added cname back to docs workflow
- 2025-10-02: removed conditional in docs workflow
- 2025-10-02: update last modified
- 2025-10-02: updates to doc workflow
- 2025-10-01: update last modified

v7.0.0
________________________________


New features
============================

- 2025-09-25: added ttl to machine files
- 2025-09-24: the license set program now aquires a machine file immediately
- 2025-09-24: added support for offline license files for clusters that don't have outgoing internet connections
- 2025-09-23: added better error messages for when no license key is set
- 2025-09-23: added license checking to main progam
- 2025-09-23: added license set and license info commands
- 2025-09-23: expanded license functionality to include seperate functions to validate and activate, functions now return useful data
- 2025-09-23: added code to check license key
- 2025-08-20: added better error reporting when fetching a job that does not exist
- 2025-08-20: added support for preventing multithreading in newer starlette versions
- 2025-08-14: server start command now retuns more information about installation and upgrade potential
- 2025-08-14: added installation_dir() function to __init__
- 2025-08-13: added force option to discover endpoints
- 2025-08-11: added support for parsing binary and text molecule files
- 2025-08-08: added support for setting config options
- 2025-08-07: reimplemented auto server shutdown after a timeout
- 2025-08-07: updated set_config() function to support server reloading and over improvements
- 2025-08-06: added server --reload command
- 2025-08-06: added a proper process manager for launching multiple server workers
- 2025-08-06: added digichem.config.set_config() method for updating settings
- 2025-08-04: added new endpoints for getting server settings
- 2025-07-09: added end point to run separate discovery of queues and progs
- 2025-07-09: added code to allow a running server process to interact with itself
- 2025-07-08: enabled find in Discover by default
- 2025-07-08: added support for running server setup from web server
- 2025-06-26: removed http plain auth entirely
- 2025-06-26: disabled plain http auth as unnecessary now client auth is active
- 2025-06-26: server start now returns a fresh client cert at each invocation
- 2025-06-26: added ability for server to issue temp client certs
- 2025-06-26: added better messages when a downgrade is available
- 2025-06-26: added support for both build and build-testing branches on buildboy
- 2024-09-11: the program can now automatically check for new versions
- 2024-09-11: the build target is now stored internally at build time
- 2025-06-18: added dummy code for enabling client cert stuff
- 2025-05-09: added support for jobId in calc results
- 2025-05-09: added miniId index to job DB
- 2025-05-09: jobs now use a fullsize uuid, but also support queries based on the first 8 chars (miniID)
- 2025-05-05: switched to a different method of including spectroscopy results in database sync results without recomputing
- 2025-05-05: database sync now includes spectroscopy results
- 2025-05-02: result sets inserted into a DB now include spectroscopy results
- 2025-04-30: added an --all switch to the result program
- 2025-04-30: result filters now support an 'all' argument to pass to dump(); added get_default_filters() as a better version of default_filters()
- 2025-04-29: added first version of post_properties() method
- 2025-04-29: switched to new calculate() method instead of generate_for_dump()
- 2025-04-01: the client can now specify a limit for DB sync
- 2025-04-01: added 100 document limit to dbSync endpoint
- 2025-03-24: added new parse/si endpoint to convert SI files
- 2025-03-24: added ability to conver files to arb types
- 2025-03-21: calc date is now set from the current datetime if it is not available (useful for ORCA)
- 2025-03-07: added db indices for job DB
- 2025-03-07: Added new metadata.insert_date property to better keep track of database syncing
- 2025-03-06: database sync endpoint now uses proper mongita search indexes
- 2025-03-06: result database records now have a date assigned even if missing one; extra records (HOMO/LUMO energies etc) are now inserted into the DB directly (for easier queries)
- 2025-03-06: database_sync now returns more fields (HOMO/LUMO etc.)
- 2025-03-03: database sync now streams results
- 2025-03-03: added database sync end point
- 2024-11-19: jobs now return their report paths directly
- 2024-11-19: the stat endpoint now also returns the associated molecule and calculation folder names
- 2024-11-13: added file download endpoints to server
- 2024-11-08: added error handling for method end point
- 2024-09-11: switched to safer lockf locks
- 2024-09-09: decreased JobDB default size to 1000
- 2024-09-09: added better logging when cleaning up an over-large JobDB
- 2024-09-09: added code to switch to lockf (but not turned on yet)
- 2024-08-27: job queue program now offers filters to only show certain jobs
- 2024-08-19: added new method_class end point
- 2024-08-16: improved error messages for hold/release
- 2024-08-16: added release and hold commands
- 2024-08-16: Added ability to delete jobs and/or update status in server
- 2024-08-16: SLURM can now detect HELD jobs
- 2024-08-16: added hold() and release() methods for jobs
- 2024-08-15: changed format of directory and queue endpoints to lists not dicts
- 2024-08-15: added new forget function to remove jobs from the DB without deleting files
- 2024-08-15: added better job deletion logic that also removes directories
- 2024-08-15: added new digichem metadata file to each calc dir to better identify them
- 2024-08-14: added delete method to jobs
- 2024-08-14: added job delete program to clear our the job database
- 2024-07-24: removed server slow-downg
- 2024-07-23: added artificial delay to stream for testing
- 2024-07-23: experiment with streaming JSON responses
- 2024-07-23: added SANs to server certs
- 2024-07-23: added TLS support for web-server
- 2024-07-23: the server will not automatically shutdown after a period of inactivity
- 2024-07-09: get_method() endpoint now accepts a path-like query variable
- 2024-07-09: the get_method() endpoint now returns indices
- 2024-07-08: updates to library endpoint
- 2024-07-08: updates to library endpoint
- 2024-07-06: added top-level method fetch end-point
- 2024-07-06: added option to skip NumForce grad check
- 2024-07-06: added support for calculating excited state freqs with Turbomole
- 2024-07-05: added initial endpoint for method library
- 2024-07-04: added initial endpoint for submitting new calcs
- 2024-07-04: added status property to submit Manager objects
- 2024-07-04: switched to using element_dic instead of formula string
- 2024-07-03: added support for retrieving a method from ID
- 2024-07-03: reversed ordering of jobs table
- 2024-07-02: added initial end-point for method parsing
- 2024-07-02: split parse_method_from_file() into two functions (one taking data from memory)
- 2024-05-28: Added new HELD status
- 2024-05-18: split old status endpoint into directories and queues
- 2024-05-18: changed performance settings for double-hybrid
- 2024-05-18: Added wPBEPP86 to Orca auto

Bugfixes
============================

- 2025-09-24: fixed returning slightly outdated meta info when just activating a license
- 2025-09-23: fixed handling license time expiry
- 2025-09-23: fixed crash when clicking on authorship info
- 2025-09-22: fixed line encoding problem when parsing molecules with the server
- 2025-08-26: fixed not wrapping temp dir in Path
- 2025-08-26: fixed image program potentially overwriting old temp dirs
- 2025-08-26: fixed pyscf not having date or jobID
- 2025-08-20: added threading lock to job db to help avoid race condition corruption
- 2025-08-19: fixed extra status information (path, distro etc) not being printed by digichem info
- 2025-08-14: fixed uvicorn using spawn method which is incompatible with frozen distributions
- 2025-08-14: implemented server startup timeouts to prevent hangs on error
- 2025-08-13: fixed restarting the server for config changes
- 2025-08-11: possible fix for data mangling in mol parsing
- 2025-08-11: fixed server having to write molecules to a temp dir to parse them
- 2025-08-11: fixed potentially closing all worker pipes
- 2025-08-11: fixed crash on increasing number of server procs
- 2025-08-11: fixed server dying when a worker closes
- 2025-08-08: fixed not returning anything from settings endpoint
- 2025-08-07: fixed overly verbose error in obtaining local destination data
- 2025-08-06: moved signal overriding behavior to resume progam only
- 2025-08-04: fixed not dumping all settings
- 2025-08-04: removed erroneous async endpoints (was there a reason for this?)
- 2025-07-29: fixed mongita errors in new installs
- 2025-07-09: fixed called server.stop() in the background
- 2025-07-09: fixed leftover debug code
- 2025-07-09: fixed duplicate end-point names
- 2025-07-09: fixed problems with trying to halt server
- 2025-07-09: fixed server program trying to dump info on both sides of the fork
- 2025-07-08: fixed catching wrong error in server stop code
- 2025-07-08: same again, but better
- 2025-07-08: fixed server crashing noisely when running server stop
- 2025-07-08: fixed Discover.__init__ not accepting unspecified output
- 2025-06-30: fixed passing wrong arguments to Pyscf parse
- 2025-06-30: _fork_and_monitor() no longer uses an internal function (which cannot be picked easily)
- 2025-06-30: set default multiprocessing spawn mode to fork
- 2025-06-26: fixed CA not being marked as a CA
- 2025-06-26: added missing hidden imports to build script
- 2025-05-05: database sync no longer regenerates each result; spectroscopy is now correctly included
- 2025-05-05: fixed spectroscopy results not being included in DB dump
- 2025-05-05: updated server program to new parser structure
- 2025-05-05: fixed new post_properties() function
- 2025-05-02: fixed not passing options to Json_parser constructor
- 2025-04-30: fixed calling calculate on nmr rather than the spectrum object
- 2025-04-01: still fighting with mongita sort
- 2025-04-01: fixed mongita sort nomenclature
- 2025-03-24: fixed pydantic typing errors
- 2025-03-24: fixed using async on non endpoint func in server app
- 2025-03-21: fixed not using current date in individual programs where necessary
- 2025-03-21: fixe get_method_part_generic() accidentally set a async
- 2025-03-21: fixed using unsupported multithreading in server program
- 2025-03-07: job inserts should also now use a naive datetime
- 2025-03-07: wip fix with naive vs aware job datetimes
- 2025-03-07: db sync will no longer choke on faulty records
- 2025-03-06: fixed database endpoint returning lists
- 2024-11-26: fixed missing typing import
- 2024-11-26: and now fixed for Python < 3.10
- 2024-11-26: fixed overly strict molecule type definition
- 2024-11-26: fixed trying to print exception as warning in job delete code
- 2024-11-21: replaced Path.is_relative_to() with custom implementation (not supported until 3.9)
- 2024-11-19: added missing commit for job.dump()
- 2024-11-19: fixed missing path attribute in job dump()
- 2024-11-13: added missing content-type for download end-point
- 2024-11-13: fixed incorrect locking open method for resume
- 2024-11-13: fixed missing parsing of coords following dodgy rebase
- 2024-11-05: fixed startup bugs in server program, greatly improved startup process
- 2024-10-29: fixed bug in job database submit()
- 2024-10-23: fixed merge problem after rebase in SLURM
- 2024-10-23: fixed manager progam using both done and self.status (just status is fine)
- 2024-09-09: increased default timeout for JobDB to 5 mins
- 2024-08-22: fixed a bug with SLURM returning too many reasons
- 2024-08-16: fixed incorect type comparisons for new job status
- 2024-08-16: made file not found error more specific
- 2024-08-16: fixed storing relative paths in job db
- 2024-08-16: added better detection for HELD status
- 2024-08-16: removed incorrectly assigned async defs
- 2024-08-15: fixed typo in defining flags folder
- 2024-08-14: fixed wrong comparison to enum
- 2024-08-14: added delete progam to available job programs
- 2024-07-23: fixed weird encoding errors with cert SANs
- 2024-07-09: fixed endpoint name collision between method and library
- 2024-07-09: fixed get_method endpoint
- 2024-07-08: fixed missing index
- 2024-07-08: added WIP fix for indexes sometimes being wrong
- 2024-07-08: fixed using loader directly instead of loader path
- 2024-07-08: moved method library end point logic to separate function to share between both endpoint types, fixed inconsistencies between them
- 2024-07-06: fixed hidden -> show_hidden
- 2024-07-06: fixed typo
- 2024-07-06: fixed wrap_unsafe_module no supporting working_directory
- 2024-07-06: fixed typo in turbomole
- 2024-07-06: fixed numforce -ex option
- 2024-07-06: Fixed library endpoint not accepting identifiers correctly
- 2024-07-04: reduced daemon umask to 077
- 2024-07-04: dir permissions on server run dir
- 2024-07-04: fixed accidentally including file extension in mol name
- 2024-07-04: Fixed not expanding server run path
- 2024-07-04: fixed not creating server submit dir
- 2024-07-04: fixed not yet supported formula
- 2024-07-04: fixed using pydantic objects directly in submit endpoint
- 2024-07-04: fixed using molecules as methods
- 2024-07-04: fixed not parsing data from client when trying to submit
- 2024-07-04: replaced list with correct List type
- 2024-07-04: fixed parse/molecule end-point not returning formula or setting file name
- 2024-07-04: fixed not triming dot from babel data type
- 2024-07-04: parse/molecule no longer expects a dict
- 2024-07-03: fixed accidentally using huge objects as keys in endpoint
- 2024-07-03: fixed tring to json encode entire method objects instead of dumped version
- 2024-07-03: fixed missing method_library param in server endpoint
- 2024-07-03: wrong order of args in parse_method() func
- 2024-07-01: job status also assuming a queue object is available
- 2024-07-01: wrong type conversion for DB ID for arrays
- 2024-07-01: Array destinations using wrong DB update func
- 2024-07-01: Array destinations not working because missing args/kwargs in init
- 2024-06-08: fixed install script not using v7 locations
- 2024-05-23: Updates to ORCA memory allocation to try and address over assignment
- 2024-10-23: re-added missing server files lost in rebase

Testing updates
============================

- 2025-07-10: fixed using yaml.load instead of yaml.safe_load in tests
- 2025-05-09: fixed test_insert_and_fetch trying to compare insert_date
- 2025-05-02: added test for inserting spectroscopy result into the DB
- 2025-04-30: added tests for the all option

Miscellaneous
============================

- 2025-09-30: removed license date from freeze code
- 2025-09-30: updated license terms to reflect new license keys
- 2025-09-30: update last modified
- 2025-09-30: first v7 release
- 2025-09-25: bumped pre-release to 26
- 2025-09-25: bumped pre-release to 25
- 2025-09-23: added requests to depends
- 2025-09-23: removed old 'license' code
- 2025-09-22: bumped pre-release to 24
- 2025-08-27: bumped to prerelease 23
- 2025-08-27: updated license end date to 30-09-2025
- 2025-08-26: bumped version to pre.22
- 2025-08-20: set pre-release to 21
- 2025-08-19: added more missing depends
- 2025-08-19: added missing pyopenssl depends
- 2025-08-19: removed some old imports
- 2025-08-15: bumped pre-release to 15
- 2025-08-07: cleaned up old code
- 2025-08-05: removed unused job_database:id_length param
- 2025-07-29: bumped to pre14
- 2025-07-10: added semver to environment.yml
- 2025-07-10: updated github tests to use v7.x of digichem-core
- 2025-07-09: bumped version to 7.0.0-pre.12
- 2025-07-09: automated tests are now also run against build branches
- 2025-07-09: refactored server code into separate server class
- 2025-06-30: bumped prerelease to 9
- 2025-06-30: bumped pre-release to 8
- 2025-06-30: bumped pre-release to 7
- 2025-06-26: bumped pre-release to 6
- 2025-06-26: removed double space
- 2025-06-26: set version to 7.0.0-pre.5
- 2025-06-26: automatic update checking is disabled by default for now
- 2025-06-26: added minor comment in update.py
- 2025-06-26: fixed indentation
- 2024-09-11: added semver as dependency
- 2025-02-25: Removed uuid from server run jobs
- 2024-11-05: updated dependencies for server
- 2024-09-09: bumped pre-release to 4
- 2024-08-19: rearranged server imports
- 2024-08-14: added future todo
- 2024-07-08: added debugging code for library endpoint
- 2024-07-03: Molecule parse endpoint can now guess file type based on file name
- 2024-07-03: Added initial endpoint for loading molecules
- 2024-07-01: bumped pre-release
- 2024-05-18: renames /queue -> /jobs and /status -> /queues
- 2024-05-16: Fixed trailing slash in queue endpoint
- 2024-05-16: Removed path style variables from queue endpoint
- 2024-05-06: Added todo:
- 2024-04-22: Removed debugging pass statement
- 2024-04-22: Used file space is now reported as part of server status info
- 2024-04-22: Added run_dir config option for servers
- 2024-04-22: Fixed incorrectly reusing pam auth object
- 2024-04-18: Fixed missing return command in status_data
- 2024-04-18: Fixed missing return command in status_data
- 2024-04-18: Fixed missing comma in sinfo command
- 2024-04-18: Fixed missing comma in sinfo command
- 2024-04-18: Changed queue_id endpoint to job_id
- 2024-04-18: Added timeline to job objects
- 2024-04-18: Changed default for server queue endpoint from active to all
- 2024-04-18: Added new status rest endpoint
- 2024-04-18: Added new status rest endpoint
- 2024-04-18: Added new get_sinfo() classmethod to SLURM for buffered access to sinfo
- 2024-04-18: Added new get_sinfo() classmethod to SLURM for buffered access to sinfo
- 2024-04-15: Added server endpoints for checking jobs
- 2024-04-15: Added server endpoints for checking jobs
- 2024-04-15: Minor updates to server program for digichem split
- 2024-04-15: Fixed accidentally parsing newline from sbatch command
- 2024-04-15: Fixed using wrong ID in SLURM squeue
- 2024-04-15: Fixed not decoding output from squeue
- 2024-04-15: Fixed wrong use of variable expansion in SLURM queue
- 2024-04-15: Fixed incorrect reference to slurm_executable
- 2024-04-15: Fixed not using tz aware datetime in SLURM
- 2024-04-15: Added a validate_now option to method_from_dump()
- 2024-04-15: Switched to faster formula_string in job queue program
- 2024-04-15: Added support for unlimited job db size
- 2024-04-15: Expanded help for db max_size
- 2024-04-15: Added support for job database size limit
- 2024-04-15: Performance Opt for parsing job records
- 2024-04-11: Added job cancel command
- 2024-04-11: Added cancel() method to local queue objects, and check for hostname
- 2024-04-11: Minor refactor
- 2024-04-11: Added a cancel() method to Jobs
- 2024-04-11: Made queue_date a required arg for from_method()
- 2024-04-11: Added smarter status detection for job records
- 2024-04-11: Reduced verbosity on DB messages
- 2024-04-11: Minor updates to job program
- 2024-04-11: Added better support for monitoring job progress for SLURM and local methods
- 2024-04-11: Updates to job program to better control printing of job queue
- 2024-04-11: Added config options for id_length an max_size
- 2024-04-10: Job records now use a mini UUID with configurable length
- 2024-04-10: Database insert() functions can now pass kwargs
- 2024-04-03: Added result ID to job program
- 2024-04-03: safe_insert() now returns the ID of any inserted doc
- 2024-04-03: The result ID is not inserted into the job DB
- 2024-04-03: Added option to control whether a job is inserted into the DB
- 2024-04-02: Added support for setting job status during calculation
- 2024-04-02: Added support for setting job status during calculation
- 2024-04-02: Fixed timezone issues in job records
- 2024-04-01: Various fixes to job db mechansim
- 2024-04-01: Fixed typos in setting job status
- 2024-04-01: The job command now only returns the short status name
- 2024-04-01: Fixed various problems with updating jobs based in ID
- 2024-04-01: Added program.set_status() function
- 2024-04-01: Job ID is now saved to each calculation object
- 2024-04-01: Tweaks to job program
- 2024-04-01: Fixed method_from_dump() not returning anything
- 2024-04-01: Fixed dumping of input file in job db
- 2024-04-01: Fixed molecule name being lost when inserted into job db
- 2024-04-01: Fixed typo in Job.from_dump()
- 2024-04-01: Changed 'id' to '_id' in Job constructor
- 2024-03-29: Initial implementation of inserting job records with calc submission
- 2024-03-29: Initial implementation of inserting job records with calc submission
- 2024-03-27: WIP interface to squeue and friends
- 2024-03-26: WIP job records
- 2024-04-15: Added server endpoints for checking jobs
- 2024-04-02: Added support for setting job status during calculation
- 2024-03-26: WIP job records
- 2024-03-21: Removed debug line
- 2024-03-21: Added support for native mongo datetime
- 2024-03-21: Fixed mongita not being able to create parents if its folder doesn't exist yet
- 2024-03-21: Fixed inconsitent support for expand_path in databases
- 2024-03-21: Added WIP job db submit
- 2024-03-21: Fixed version not set to 7
- 2024-03-21: Fixed version not set to 7
- 2024-03-21: More WIP job db bits
- 2024-03-19: WIP implementation of job DB
- 2024-03-19: Move code for safe_insert() to relevant class
- 2024-03-19: Added a default to the job DB
- 2024-03-19: Reordered database to distinguish between result and job DBs
- 2024-03-14: Added some help text to explain result and job DBs
- 2024-03-14: Work on an initial spec for job DB records
- 2024-03-14: Added some initial config files for working with job DBs

v6.9.3
________________________________


Bugfixes
============================

- 2025-07-29: fixed mongita errors in new installs

Miscellaneous
============================

- 2025-07-29: update last modified
- 2025-07-29: bumped version to 6.9.3

v6.9.2
________________________________


Bugfixes
============================

- 2025-07-10: fixed a typo in parsing CCSD(T) calcs with PySCF
- 2025-07-10: fixed unnecessary warning messages in cubegen_parallel
- 2025-07-10: greatly simplified fork_and_monitor() code so the main process runs the program, and the subprocess is used for monitoring. This also fixes a bug in PySCF resulting in deadlocks when running multiple calcs back-to-back

Testing updates
============================

- 2025-07-10: expanded tests for PySCF
- 2025-07-10: added opt tests for PySCF

Miscellaneous
============================

- 2025-07-10: update last modified
- 2025-07-10: updated github tests to use git version of cclib in both push and pull tests
- 2025-07-10: bumped version to 6.9.2

v6.9.1
________________________________


New features
============================

- 2025-07-08: if no hints are given to setup, various sensible defaults will be tried instead
- 2025-07-08: added option to disable find searching as well as locate searching in Discover
- 2025-07-01: added file locking to setup program
- 2025-07-01: also migrated locate/plocate code to async
- 2025-07-01: migrate discover code to asyncio
- 2025-07-01: initial work to moving discover functionality into separate module

Miscellaneous
============================

- 2025-07-08: bumped pre-release to 6.9.1
- 2025-07-08: moved locate and find code to separate functions

v6.9.0
________________________________


New features
============================

- 2025-06-26: scratch space usag is now activated by default
- 2025-06-25: added support for custom Orca keywords
- 2025-06-03: added ability to track scratch space file usage
- 2025-04-22: added default configs for PySCF
- 2025-04-22: reimplemented performance tracking for PySCF
- 2025-04-22: added support for dispersion correction for PySCF
- 2024-09-18: added support for 50-50 excited state calculations
- 2024-09-18: added support for saving intermediate results of SCF steps
- 2024-09-18: added better support for the two types of optimisers in PySCF
- 2024-08-28: added support for alpha/beta orbital rendering with PySCF
- 2024-08-28: added initial support for rendering PySCF images
- 2024-08-28: added support for running excited state optimisations with PySCF
- 2024-08-28: reduced table of singly excited configurations to only show significant contributions
- 2024-08-28: added support for saving intermediate optimisation steps with PySCF
- 2024-06-18: added initial checkfile saving for pyscf
- 2024-06-17: cleaned-up error reporting for failed calcs
- 2024-06-10: initial support for parsing results with pyscf
- 2024-06-10: pyscf methods are now saved properly, initial support for emp disp
- 2024-06-10: enabled post processing for pyscf
- 2024-06-03: added support for excited state opts with pyscf
- 2024-06-03: added gradient and solution options to pyscf calculation object
- 2024-06-02: added support for calculating frequencies with pyscf
- 2024-06-02: added support for calculating gradients with pyscf
- 2024-06-02: added support for excited states with pySCF
- 2024-06-02: added support for SCF solvents with PySCF
- 2024-06-02: added new monitor function for forked calc engines
- 2024-06-02: added initial support for pyscf

Bugfixes
============================

- 2025-06-30: fixed wrong dependenceis
- 2025-06-30: fixed missing pyscf libraries when freezing
- 2025-06-30: added data collection for pyscf (and removed hidden import for numpy.ctypes which did nothing)
- 2025-06-30: added numpy.ctypes as hidden import to build
- 2025-04-22: added fix for crash when parsing PySCF grad calcs
- 2024-09-18: fixed freq support
- 2024-09-18: some minor fixes
- 2024-09-11: fixed passing freq object as hessian method for pyscf
- 2024-08-28: now it works
- 2024-06-17: pyscf results not containing molecule name

Testing updates
============================

- 2025-06-30: added initial tests for PySCF
- 2025-06-30: removed old references to input files which are now included in the digichem-core repo
- 2025-06-30: added check for correct digichem core version

Miscellaneous
============================

- 2025-06-30: bumped version to 6.9.0
- 2025-06-30: tried to make github install work
- 2025-06-30: added github version of cclib to github dependencies
- 2025-06-30: added missing pyscf depends for github tests
- 2025-06-30: reduced demo license duration to 2 months
- 2025-06-30: update last modified
- 2025-06-30: added pyscf dependencies to freeze file
- 2025-06-30: removed leftover print commands
- 2025-06-30: updated dependencies to include pyscf
- 2025-06-27: update last modified
- 2025-06-26: update last modified
- 2025-04-22: added pyscf and pyscf-dispersion to depends
- 2024-06-18: wip: added image gen for pyscf
- 2024-06-17: wip: reenabled reports for pyscf
- 2024-06-10: wip: changes to fork_and_monitor to avoid trying to pickle large amounts of data
- 2024-06-10: removed unused imports
- 2024-06-10: bumped minor version
- 2024-06-02: added better comments for pyscf code
- 2024-06-02: fixed typo

v6.8.3
________________________________


New features
============================

- 2025-06-06: increased default define timeout to 5 min for BIG molecules

Bugfixes
============================

- 2025-06-09: missing symlinks for blender are now setup in install.sh
- 2025-06-09: fixed trying to check cubes that aren't available
- 2025-06-09: fixed distracting cleanup error when a report fails
- 2025-06-09: fixed cubegen pool sometimes making the same file twice
- 2025-06-06: fixed define timeout error log message being mangled

Miscellaneous
============================

- 2025-06-09: update last modified
- 2025-06-09: bumped to 6.8.3
- 2025-06-03: update last modified
- 2025-05-29: update last modified

v6.8.2
________________________________


New features
============================

- 2025-05-28: switched report_output to True by default following from further testing
- 2025-05-28: added a new scratch:report_output option to control writing the report to the scratch dir, and disabled by default (because performance gains were negligible?)
- 2025-05-28: added support for writing reports to scratch dir
- 2025-05-28: added image_hints argument to report objects to allow better prediction of which cubes to pre-generate
- 2025-05-27: added support for VMD and Batoms multithreading
- 2025-05-24: report objects now log how many CPUs they use to pre-generate cubes
- 2025-05-24: added dont_clean option to report.write() to keep intermediate files for later
- 2025-05-26: updated banner

Bugfixes
============================

- 2025-05-28: added possible fix for some report .html files no-longer being deleted automatically
- 2025-05-24: fixed report objects not inheriting num_cpu from calculations
- 2025-05-24: added fix for trying to generate cube precursor files that might not exist
- 2025-05-24: fixed using name rather than object in pre-generate
- 2025-05-24: fixed cube-precursor files sometimes being written multiple times when cubegen_parallel: pool
- 2025-04-30: fixed NMR spectra not being saved automatically at the end of each calculation

Documentation changes
============================

- 2025-05-29: download link now automatically updates
- 2025-05-29: updated copyright year to 2025
- 2024-12-18: added initial photonic examples
- 2024-12-13: swapped report multi examples
- 2024-12-09: Increased download link version to 6.6.3 (need to atuomate this)

Miscellaneous
============================

- 2025-05-29: debugging conda setup in workflow
- 2025-05-29: debugging conda setup in workflow
- 2025-05-29: added mako to build depends
- 2025-05-29: adjusted upload location
- 2025-05-29: trying different version
- 2025-05-29: set sftp_only to true
- 2025-05-29: added SFTP deploy to workflow
- 2025-05-29: fixed typo
- 2025-05-29: added sphinx-rtd-theme and sphinx_design to docs build depends
- 2025-05-29: added sphinx-argparse to docs build depends
- 2025-05-29: added sphinxcontrib-bibtex to depends for docs build
- 2025-05-29: fixed not setting pythonpath correctly
- 2025-05-29: added initial workflow to autobuild docs
- 2025-05-28: update last modified
- 2025-05-28: bumped version to 6.8.2
- 2025-05-26: dev version is now 6.9.0-pre.1
- 2025-05-26: version is now 6.8.1
- 2025-05-26: update last modified
- 2025-05-24: update last modified

v6.8.1
________________________________


Miscellaneous
============================

- 2025-05-25: Bumped version to 6.8.1; first release of blender versions
- 2025-05-25: bumped to 6.8.1-pre.3 for build testing
- 2025-05-25: bumped to 6.8.0-pre.2 for build testing
- 2025-05-25: bumped version to 6.8.1-pre.1 for updated build testing

v6.8.0
________________________________


New features
============================

- 2025-05-23: added ability to generate cube files in parallel
- 2025-05-23: updated freeze script to include batoms driver

Bugfixes
============================

- 2025-04-30: fixed NMR spectra not being saved automatically at the end of each calculation

Miscellaneous
============================

- 2025-05-23: bumped version to 6.8.0
- 2025-05-23: bumped min digichem-core version to 6.10.0
- 2025-05-23: update last modified
- 2025-05-21: prebuild 2 for upcoming blender versions
- 2025-05-21: bumped version to 6.8.0-pre.1 to test new blender build system

v6.7.1
________________________________


New features
============================

- 2025-04-28: added support for Orca 6 changes in orca plot commands
- 2025-04-28: added support for handling densitiesinfo info files when submitting
- 2025-04-28: added support for Orca 6 orcaplot

Bugfixes
============================

- 2025-04-29: fixed passing None density_info_file for Orca <= 5
- 2025-04-28: possible fix for .density .densities weirdness
- 2025-04-28: attempt to fix Orca's weird get_env() method
- 2025-04-28: fixed passing wrong class types for orca cubes
- 2025-04-28: added support for using the correct orca definition for generating cubes

Miscellaneous
============================

- 2025-04-29: update last modified
- 2025-04-29: bumped version to 6.7.1
- 2025-04-29: increased min version of digichem-chore to 6.7.0

v6.7.0
________________________________


New features
============================

- 2024-12-06: added full support for detecting Orca 6
- 2024-12-06: added new trigger file for discovering orca 6

Bugfixes
============================

- 2024-11-18: added better type detection for destination memory amounts

Miscellaneous
============================

- 2025-04-18: bumped version to 6.7.0
- 2025-04-01: update license copyright to 2025
- 2025-04-18: update last modified

v6.6.5
________________________________


Miscellaneous
============================

- 2025-03-25: update last modified
- 2025-03-25: refresh license

v6.6.4
________________________________


Miscellaneous
============================

- 2025-01-06: update last modified
- 2025-01-06: refreshed license

v6.6.3
________________________________


Bugfixes
============================

- 2024-10-31: added missing dispersion correction for Orca

Miscellaneous
============================

- 2024-11-08: update last modified
- 2024-10-31: bumped version to 6.6.3

v6.6.2
________________________________


New features
============================

- 2024-10-25: added slightly better error reporting for Gaussian discover
- 2024-10-25: moved main 'silico.yaml' file to 'digichem.yaml' for consistency (fixes #148)

Bugfixes
============================

- 2024-10-29: fix for generating orbitals from archive turbomole calc dirs
- 2024-10-25: fixed not supporting -o for setup program
- 2024-10-25: fixed setup program using -o rather than -O for output option
- 2024-10-25: fixed crash in Gaussian setup if missing minor version
- 2024-10-25: fixed the urwid palette not being part of the main config

Miscellaneous
============================

- 2024-10-29: update last modified
- 2024-10-28: bumped version to 6.6.2

v6.6.1
________________________________


New features
============================

- 2024-10-25: gaussian wrapper script now use shlex for quoting
- 2024-10-25: any leftover program output is now printed even if the calculation succeeded
- 2024-10-25: reduced length of post calculation folder names
- 2024-06-17: added validation for excluding bse for Orca

Bugfixes
============================

- 2024-10-25: added explicit .log suffix to output symlink to fix Gaussian
- 2024-10-25: fixed gaussian crash with long folder names
- 2024-10-23: fixed method library always reloading from file
- 2024-07-23: changed silico -> digichem in help message
- 2024-07-09: fixed typo in short_name option

Documentation changes
============================

- 2024-10-10: adde better documentation for image program input/output files
- 2024-10-10: added initial documentation for the image command
- 2024-10-09: expanded documentation for report settings
- 2024-10-09: expanded documentation for report density files
- 2024-10-08: WIP report documentation
- 2024-10-08: added extension to generate documentation from configurables (WIP)
- 2024-10-08: updated banner with aligned icon
- 2024-10-08: updated favicon with new docs icon
- 2024-10-08: updated favicon with non wonky variety
- 2024-10-07: added favicon
- 2024-10-07: fixed minor typo
- 2024-10-04: added initial documentation for report program
- 2024-10-04: fixed some typos
- 2024-10-03: split program documentation and command line references
- 2024-08-27: updated some links to 6.1.2
- 2024-08-07: updated link to latest download
- 2024-08-01: added monitor section to the quick start guide
- 2024-08-01: added fix for tables not supporting word-wrap
- 2024-08-01: wip updates to monitor walkthrough
- 2024-07-31: wip adding calc monitoring section to getting started
- 2024-07-17: added link to quick setup
- 2024-07-17: expanded documentation for setup process
- 2024-07-16: added quick-start guide to cover first calculation submission
- 2024-07-16: Added new quick-start documentation
- 2024-07-16: added link for full installation instructions
- 2024-07-16: fixed using wrong headers for program docs
- 2024-07-09: added reference for program options
- 2024-07-09: added links for Program setup and minor tweaks
- 2024-07-09: added documentation for post-processing options
- 2024-07-09: minor updates to calc method
- 2024-07-08: Added documentation for the structure options
- 2024-07-08: Added documentation for scratch options
- 2024-07-08: added COSX documentation
- 2024-07-08: minor tweaks to method docs
- 2024-06-17: minor fixes
- 2024-06-15: minor changes
- 2024-06-15: added section on RI
- 2024-06-15: ammended examples for electron occupations
- 2024-06-15: added documentation for electron occupation
- 2024-06-15: added documentation for solvents
- 2024-06-15: increased depth of method spec TOC
- 2024-06-15: added link to destination memory
- 2024-06-15: expanded excited states properties and added performance doc
- 2024-06-15: added section on opt + freq jobs
- 2024-06-15: fixed short underline
- 2024-06-14: expanded docs for turbomole excited states
- 2024-06-13: expanded properties doc to include freq, nmr, and initial es
- 2024-06-13: minor typo fixes and ammendments
- 2024-06-13: increase max depth of nav bar
- 2024-06-12: expanded documentation for basis sets and some initial properties
- 2024-06-12: fixed various minor typos
- 2024-06-11: expanded docs for SCF options
- 2024-06-11: added doc for scf method
- 2024-06-11: added sphinx_design as a dependency
- 2024-06-11: wip updates to SCF options
- 2024-06-07: expanded bibliography with emp dispersion and CC2 references
- 2024-06-07: fixed typo
- 2024-06-07: commented out unused section
- 2024-06-07: minor tweak to destination methods
- 2024-06-07: added initial documentation for calculation methods
- 2024-06-07: updates to destination documentation
- 2024-06-06: initial work on method spec
- 2024-06-06: minor fixes for sphinx
- 2024-06-06: added documentation for setting up external programs etc
- 2024-06-06: wip adding external programs doc
- 2024-06-06: moved setup out of installation
- 2024-06-06: added substitution for major digichem version

Miscellaneous
============================

- 2024-10-25: update last modified
- 2024-10-25: bumped core min-version
- 2024-10-23: bumped version
- 2024-10-17: update last modified
- 2024-10-17: docs: minor updates to programs
- 2024-10-17: docs: updated download information
- 2024-10-16: docs: added info for status command
- 2024-10-16: docs: fixed missing whitespace in report doc
- 2024-10-16: docs: moved warning re. advanced queries
- 2024-10-16: docs: added initial documentation for 'complex' queries
- 2024-10-16: docs: moved db format and queries to end
- 2024-10-16: docs: added documentation for simple db queries
- 2024-10-16: docs: added documentation for delete --search option
- 2024-10-16: docs: added documentation for database search, count, and delete commands
- 2024-10-16: docs: fixed minor typos in database documentation
- 2024-10-16: docs: added initial documentation for database command and insert and slice sub-commands
- 2024-10-16: docs: split long line
- 2024-10-15: docs: added description of merged and multiple calcs for image command
- 2024-10-15: docs: added description of working directory for image command
- 2024-10-15: docs: added description of image --list command
- 2024-10-15: docs: expanded report program docs for output options
- 2024-10-15: docs: fixed short titles
- 2024-10-15: docs: expanded documentation for report program to include multiple reports
- 2024-10-08: moved configurables extension to Configurables package
- 2024-07-16: removed old introduction section ready for replacement
- 2024-06-17: minor typo fixes and todos

v6.6.0
________________________________


New features
============================

- 2024-10-16: added --structure search query for DBs
- 2024-10-15: image progam will now use a temp working dir if non is available
- 2024-10-15: increased mim digichem-core version to 6.1.0
- 2024-10-15: image program now reports rendering errors
- 2024-10-15: image program will no longer overwrite files it just wrote
- 2024-10-10: image program now correctly writes one image when writing to a specific location
- 2024-10-10: image command can now write image files outside of the report directory
- 2024-10-08: updated logos to non-wonky varients

Bugfixes
============================

- 2024-10-16: fixed database slice program not starting up
- 2024-10-16: image program can now write cube files to specific location
- 2024-10-14: added fix for method files not loading properly
- 2024-10-10: fixed some behaviour of the image command; images/cubes are now overwritten by default; the cleanup behaviour is now much improved

Testing updates
============================

- 2024-10-16: added skips for image program test
- 2024-10-16: added PATH to git auto tests
- 2024-10-16: fixed calling wrong program
- 2024-10-10: added tests for image program
- 2024-10-10: fixed report tests using local test data for some reason

Miscellaneous
============================

- 2024-10-16: update last modified
- 2024-10-16: added bin directory
- 2024-10-16: removed old code in db search command
- 2024-10-14: removed unused test data dir
- 2024-10-10: bumped version to 6.6.0

v6.5.1
________________________________


Bugfixes
============================

- 2024-10-13: re-build for CentOS Stream 8 to fix cclib; chore: bump to 6.5.1
- 2024-10-13: fixed broken error message when submitting from a method file

Miscellaneous
============================

- 2024-10-13: update last modified
- 2024-10-10: removed old explicit build target check with general check
- 2024-10-10: added Rocky-Linux-9 as build target

v6.5.0
________________________________


New features
============================

- 2024-10-07: added support for cleanup_time in SLURM

Miscellaneous
============================

- 2024-10-07: update last modified
- 2024-10-07: bumped version to 6.5.0

v6.4.0
________________________________


New features
============================

- 2024-10-03: The mail: events option now uses none_to_default
- 2024-10-02: increased number of log file lines to 100
- 2024-10-01: calculation manager objects now return a list of submitted calcs (rather than just the count)
- 2024-10-01: increased the number of lines from the log file included in error messages (addresses #131)
- 2024-09-30: fixed a few minor errors in program help string
- 2024-09-30: swapped versioning system to hatchling compatible
- 2024-09-27: scratch cleanup can now remove files as well as folders
- 2024-09-27: changed default scratch dir to /tmp
- 2024-09-27: added new loading bar to setup program
- 2024-09-27: added a new scratch: expiry calc option to clean up old files
- 2024-09-26: added a progress indicator to the setup program
- 2024-09-26: improved logging fo setup command
- 2024-09-26: Gaussian discover() now uses minor version is available in logging
- 2024-09-26: setup program now has better version detection and avoids duplicate definitions

Bugfixes
============================

- 2024-10-02: fixed series calcs referring to old defs
- 2024-10-01: fixed not resolving methods in library test
- 2024-10-01: fixed not expanding coord list in submit tests
- 2024-09-27: fixed bug in checking scratch expiry
- 2024-09-27: fixed setup program accidentally using only Turbomole calc definitions
- 2024-09-26: fixed setup program favouring old versions over recent ones
- 2024-09-26: fixed trying to reference non-existent setups
- 2024-09-26: fixed logging calls
- 2024-09-26: fixed not saving in done
- 2024-09-26: fixed another bug in setup
- 2024-09-26: fixed not using list over generator
- 2024-09-26: fixed not updating setup program to new return values of discover()

Testing updates
============================

- 2024-10-02: fixed broken test for NMR images
- 2024-10-02: fixed library test not referencing new unrestricted calcs
- 2024-10-01: updated test_library to support now method manager

Miscellaneous
============================

- 2024-10-03: update last modified
- 2024-10-03: mim version of digichem-core is now 6.0.3
- 2024-10-03: bumped v to 6.4.0
- 2024-10-03: increased min version of configurables to 1.2.0
- 2024-10-01: update last modified
- 2024-09-30: fixed ordering of Usage and Documentation in README
- 2024-09-30: minor updates to README
- 2024-09-30: updated README
- 2024-09-30: removed old pack_current script
- 2024-09-30: updated changelog (although this might not be staying around for long
- 2024-09-30: added project file
- 2024-09-30: removed server files which aren't needed until v7
- 2024-09-30: added LICENSE file (currently proprietary
- 2024-09-27: removed old files
- 2024-09-27: removed old logo folder
- 2024-09-26: added future todo

v6.3.0
________________________________


New features
============================

- 2024-09-23: added initial support for Orca frozen core
- 2024-09-23: added support for FC, Full and Window frozen core keywords in Gussian
- 2024-09-20: added initial support for frozen core for all calc programs

Bugfixes
============================

- 2024-09-24: fixed not understanding how FrozenCore -n works
- 2024-09-23: fixed using wrong FC keywords
- 2024-09-23: fixed orca specific freeze options located in the wrong place
- 2024-09-23: fixed not stringifying new Gaussian keywords
- 2024-09-23: fixed using number_virtual not virtual_number
- 2024-09-20: fixed a typo specifying freeze:threshold was in eV rather than H

Miscellaneous
============================

- 2024-09-25: update last modified
- 2024-09-25: bumped version to 6.3.0.

v6.2.0
________________________________


New features
============================

- 2024-09-19: added support for Turbomole's frozen core approximation

Bugfixes
============================

- 2024-09-19: fixed using sub-options as attributed not keys

Miscellaneous
============================

- 2024-09-19: update last modified
- 2024-09-19: bumped version to 6.2.0
- 2024-09-09: update last modified

v6.1.3
________________________________


Miscellaneous
============================

- 2024-09-09: fixed bundled pysoc not supporting rwfdump

v6.1.2
________________________________


New features
============================

- 2024-08-21: Gaussian programs will now try and correctly specify the relevant rwfdump path

Bugfixes
============================

- 2024-08-21: fixed another confusing messge if a program stops almost immediately
- 2024-08-21: fixed a confusing error message if a program stops immediately

Miscellaneous
============================

- 2024-08-21: update last modified
- 2024-08-21: bumped version to 6.1.2

v6.1.1
________________________________


Miscellaneous
============================

- 2024-08-01: update last modified
- 2024-08-01: update to new Digichem-core version 6.0.1

v6.1.0
________________________________


New features
============================

- 2024-07-15: setup program now sticks to supplied hints even when using 'locate'
- 2024-07-15: setup program can now find VMD installations at setup appropriately
- 2024-07-15: changed default scratch path to /tmp/$USER
- 2024-07-11: better naming for default server queues
- 2024-07-11: added better file sorting for setup program
- 2024-07-11: added sorting to discovered program names
- 2024-07-11: tweaked orca discover() logging
- 2024-07-11: improved version detection for Orca
- 2024-07-11: added alias for programs
- 2024-07-11: discovered queues now have capitalised names
- 2024-07-11: added support for both 'locate' and 'plocate'
- 2024-07-11: added support for using 'find' as a backup for 'locate' if the latter is unavailable
- 2024-07-11: tweaks to logging level of discover methods()
- 2024-07-10: improved logging of setup program
- 2024-07-10: setup program can now setup computational engines
- 2024-07-10: added discover() methods for Gaussian, Orca, and Turbomole
- 2024-07-10: setup script can now write configs for SLURM and PBS
- 2024-07-10: added discover() functions for both SLURM and PBS
- 2024-05-28: setup program will safely move old configs before overwriting
- 2024-05-17: install script now sets up skeleto dir
- 2024-05-17: Added example configs for programs and destinations in skeleton dir
- 2024-05-17: Added skeleton digichem.yaml file

Bugfixes
============================

- 2024-07-15: fixed resolving symlinks in setup
- 2024-07-15: fixed setup program not always using absolute paths
- 2024-07-11: fixed assigning wrong calc class to programs
- 2024-07-11: type conversion nonsense
- 2024-07-11: fixed name collisions in destinations
- 2024-07-11: fixed sort
- 2024-07-11: more of the same
- 2024-07-11: fixes to orca discover
- 2024-07-11: stopped overwriting nested MPI
- 2024-07-11: fixed broken log call
- 2024-07-11: fixed typo
- 2024-07-11: fixed not looking for symlinks (even tho mpirun is normally a symlink
- 2024-07-11: don't take parent twice
- 2024-07-11: tweaks to orca version detection code
- 2024-07-11: fixed typo
- 2024-07-11: fixed not casting to str
- 2024-07-11: fixed program definitions possible having overlapping names
- 2024-07-11: fixed path -> str conversion
- 2024-07-11: fixed order of path operations
- 2024-07-11: fixed gaussian discover
- 2024-07-11: removed left-over unknown mpi version
- 2024-07-11: fixed mangled log line
- 2024-07-11: added missing capture groups
- 2024-07-11: fixed wrong order in list comprehension
- 2024-07-11: fixed using wrong indices
- 2024-07-11: fixed taking too many parents for Orca discover
- 2024-07-11: fixed mixing up orca and MPI paths
- 2024-07-11: fixed not taking path parent in Orca discover
- 2024-07-11: removed multiple -types to find which are not supported on older versions
- 2024-07-11: no longer check return value of 'plocate' or 'locate'
- 2024-07-11: fixed bug in switching from plocate to locate
- 2024-07-11: fixed using wrong separator in SLURM discover
- 2024-05-28: Removed unused server program
- 2024-06-06: fixed config show command after change to library location
- 2024-06-02: fixe resumable submission not able to find digichem executable
- 2024-05-31: prevented openbabel imports in submodules
- 2024-05-28: old setup files are moved out of active dir
- 2024-05-28: Removed unused server program
- 2024-05-17: Changed SLURM max-nodes default to 1

Documentation changes
============================

- 2024-06-06: tweaked setup instructions for Orca
- 2024-06-06: added some additional comments re. installation folder structure
- 2024-06-06: removed WIP sections from doc index
- 2024-05-17: completed setup documentation
- 2024-05-17: started adding setup documentation
- 2024-05-17: Added main install documentation
- 2024-05-17: minor updates to main install doc
- 2024-05-17: minor updates to dependencies
- 2024-05-17: Updated version info for supported builds
- 2024-05-17: minor updates to install doc
- 2024-05-13: initial documentation for installation instructions etc
- 2024-05-13: Added version info to documentation
- 2024-05-13: changed theme to read-the-docs
- 2024-05-13: finished doc of result --auto
- 2024-05-12: updated dependencies

Testing updates
============================

- 2024-06-06: fixed missing destination definition
- 2024-06-06: prepared for new submission tests

Miscellaneous
============================

- 2024-07-16: update last modified
- 2024-07-16: removed pre-release
- 2024-07-15: updated version to 6.1.0
- 2024-07-15: update last modified
- 2024-07-15: minor tweaks to setup program
- 2024-06-11: update last modified
- 2024-06-11: fixed adding wrong dir in workflow
- 2024-06-11: update push workflwo
- 2024-06-11: added digichem test data
- 2024-06-11: added obabel workaround for workflow
- 2024-06-11: relaxed obabel version requirements
- 2024-06-11: updated depends for workflow tests
- 2024-06-11: added workflows for testing and last modified string
- 2024-06-07: bump pre
- 2024-06-07: bumped pre-release
- 2024-06-03: bumped pre-release
- 2024-06-02: bumped pre-release
- 2024-05-31: bumped version
- 2024-05-31: bumped version, update depends
- 2024-05-31: bumped version number; new cclib hotfix
- 2024-05-28: wip: added barebones discover_partitions function
- 2024-05-28: wip: added barebones setup program
- 2024-05-18: Added chain of spheres for wPBEPP86
- 2024-05-17: minor updates to skeleton directory
- 2024-05-17: Moved skeleton folder into data
- 2024-05-17: bumped pre-release
- 2024-05-17: Removed old and unused freeze dirs
- 2024-05-17: Removed some lingering configs in preparation for new skeleton dir
- 2024-05-17: Changed the location of some server locations
- 2024-05-17: updated freeze script to not include version numbers in unpacked digichem dir
- 2024-05-14: Bumped pre-release
- 2024-05-13: Updated install script to match new build style
- 2024-05-12: Another version bump for build test
- 2024-05-12: bumped version for build-test
- 2024-05-12: Updated pre-release
- 2024-05-10: Build test
- 2024-05-10: Added CentOS Stream 8
- 2024-05-09: Removed license warnings
- 2024-05-09: Bumped pre-release
- 2024-05-09: Openprattle is now bundled into its own folder
- 2024-05-09: Fixed looking for wrong spec file
- 2024-05-09: Moved general build files
- 2024-05-09: Added missing spec file
- 2024-05-09: Added general build script
- 2024-05-09: Fixes to build scripts
- 2024-05-09: Replaced tabs with whitespace
- 2024-05-09: Updates to 7.9 build script
- 2024-05-09: Updated to install script
- 2024-05-09: Minor fixes to CentOS8.5 script
- 2024-05-09: Fixed accidentally removing libinchi
- 2024-05-09: Removed obabel code
- 2024-05-09: Moved collect licenses
- 2024-05-09: Moved license code to own module
- 2024-05-09: Added pyphen to source modules
- 2024-05-09: Fixed old references to LICENSE.md
- 2024-05-09: Added chardet to src modules
- 2024-05-09: Added support for adding license for non-compiled python libs
- 2024-05-09: Changed LICENSE.md to LICENSE
- 2024-05-09: Copy main license into dist
- 2024-05-09: Added better placement of licenses for digichem and silico
- 2024-05-09: Fixed accidentally deleting license template
- 2024-05-09: Reduced with of license template to 80 chars
- 2024-05-08: Fixed not finding licenses for binaries
- 2024-05-08: Fixed adding empty license
- 2024-05-08: Fixed typo
- 2024-05-08: Removed inefficient double loop
- 2024-05-08: Added detection of share/licenses
- 2024-05-08: Also look for binary licenses
- 2024-05-08: Fixed 'extensions' over 'suffixes'
- 2024-05-08: Added all .so to conda licenses
- 2024-05-08: Added warning for missing binary licenses
- 2024-05-08: Also look for binary files in conda metadata
- 2024-05-08: Fixed crash
- 2024-05-08: Fixed CONDA_ENV not CONDA_PREFIX
- 2024-05-08: More conda special boy code
- 2024-05-08: Fix
- 2024-05-08: Fixe thinking this was JS
- 2024-05-08: WIP adding smarter conda license searching
- 2024-05-08: Added fix for some conda licenses being nested
- 2024-05-08: Fixed not opening json file before parsing
- 2024-05-08: Fixed bug in new conda license finder
- 2024-05-08: Added detection of conda licenses
- 2024-05-08: Source code licenses are now only found for top-level modules
- 2024-05-08: Added more license detection logic for local source code
- 2024-05-08: Fixed trying to add licenses folder as data object
- 2024-05-08: Added detection of 'licenses' folders
- 2024-05-08: Fixed issuing license warning for non-top level modules
- 2024-05-08: Fixed some bugs
- 2024-05-08: Fixed missing Path()
- 2024-05-08: Fixed continue instead of return
- 2024-05-08: Added code to actually collect licenses
- 2024-05-08: Added detection of COPYING files in addition to LICENSE
- 2024-05-08: Slowly massaging license code to something worthwhile
- 2024-05-08: Troubleshooting for license finder
- 2024-05-08: More license experiments
- 2024-05-08: Added better license detection
- 2024-05-08: Expanded license find test
- 2024-05-08: Added test for detecting licenses
- 2024-05-08: Added explicit non-package modules
- 2024-05-08: Removed weird ls import
- 2024-05-08: Added test for collection mode
- 2024-05-08: Removed test data from build
- 2024-05-08: Added WIP script to collect licenses during build
- 2024-05-08: Added excludes for tkinter and qt5
- 2024-05-08: Exluded PyQt
- 2024-05-08: More experiments with excludes
- 2024-05-08: Set matplotlib backend to Agg
- 2024-05-08: Added PYTHONOPTIMISE to CentOS7.9 too
- 2024-05-08: Moved PYTHONOPTIMISE code out of spec file (because python has already started; it is too late here
- 2024-05-08: Experimenting with excludes
- 2024-05-07: Updated hidden imports for CentOS7.9
- 2024-05-07: Added PYTHONOPTIMIZE to build script
- 2024-05-07: Removed inspect from hidden imports (it's not hidden
- 2024-05-07: Added missing hidden import 'inspect'
- 2024-05-07: Fixed missing comma in hiden imports
- 2024-05-07: Updated some more outdated hidden imports
- 2024-05-07: Fixed some old hidden imports not updated to digichem
- 2024-05-07: Changed digichem data collection
- 2024-05-07: Added missing digichem data files
- 2024-05-07: Added missing spec for 8.5
- 2024-05-07: Removed .spec from gitignore
- 2024-05-07: Added build scripts for 8.5
- 2024-05-07: Fixed using old silico.version
- 2024-05-07: Added license template
- 2024-05-07: Added license checker code
- 2024-05-07: Testing build server
- 2024-05-07: Set pre-release flag
- 2024-05-07: Added ability to specify oprattle location when freezing
- 2024-05-07: WIP updates to result --auto
- 2024-05-07: Added code to freeze script to insert license stuff
- 2024-05-07: Removed old demo license code
- 2024-05-07: Testing build server
- 2024-05-07: Set pre-release flag
- 2024-05-07: Added ability to specify oprattle location when freezing
- 2024-04-30: Added workaround for missing whitespace in page counter
- 2024-04-15: Fixed weird whitespace in method library loader
- 2024-04-11: A computational engine's child processes are now correctly murdered
- 2024-04-03: Fixed saving config options to the wrong location
- 2024-04-02: Fixed silico using weird config locations
- 2024-04-01: Moved functions in program.base to match their order of execution
- 2024-03-21: Fixed default option for gen3D all over the place
- 2024-03-14: Fixed a long-standing bug with SLURM submission not using the SLURM_ID for scratch dirs #92
- 2024-03-13: Removed debug line
- 2024-05-06: Updates to documentation
- 2024-04-26: Updated old 'silico' branding to 'digichem' in calc report
- 2024-04-01: Fixed resume program not using file locking correctly
- 2024-03-21: Fixed wrong import of Gaussian_input_parser
- 2024-03-21: Fixed using wrong config location for master library files
- 2024-03-20: Fixed float -> int conversion bug
- 2024-03-20: Fixed a string conversion error in Orca
- 2024-03-20: Added support for setting maxdim and scspar in orca calcs
- 2024-03-17: Bumped version
- 2024-03-17: Added support for PBS job arrays
- 2024-03-15: Fixed slurm arrays not submitting when not packed
- 2024-03-15: Removed extra directory in slurm array output paths
- 2024-03-15: Fixed symlinks for SLURM arrays being immediately deleted
- 2024-03-15: Fixed a bug setting stdout location when submitting a job array of size 1
- 2024-03-15: Fixed bug in slurm array
- 2024-03-15: The symdir is now shared between all packed methods
- 2024-03-15: Added support for array log files in slurm templates
- 2024-03-15: Added comment
- 2024-03-15: SLURM arrays now setup symlinks for log files
- 2024-03-15: Added cleanup function for SLURM array
- 2024-03-14: Added cleanup() function for destinations
- 2024-03-14: Added initial support for SLURM job arrays
- 2024-03-14: Added new submission tests
- 2024-03-14: Parallel local destination objects now store the popen object
- 2024-03-14: Added new Manager class for running calculations
- 2024-03-14: Added default destination and program configs
- 2024-03-14: Fixed accidentally overwriting global environmental variables in blender render
- 2024-03-13: Added setters for location attributes of Gaussian, Orca and Turbomole
- 2024-03-13: Orca and Turbomole now support expand_path()
- 2024-03-13: Updated location of expand_path()
- 2024-03-11: Fixed typo
- 2024-03-11: Fixed wrong imports in result program
- 2024-03-11: Fixed wrong import in convert program
- 2024-03-11: Added some missing imports to silico.log
- 2024-03-11: Configurables with 'path' as their type now use a better setedit class
- 2024-03-11: Fixed default of lock_file option not being a path
- 2024-03-08: Added missing digichem_options fixture
- 2024-03-08: Updated old references to silico.result
- 2024-03-08: Replaced tabs with whitespace
- 2024-03-08: Added get_config() function to silico.config
- 2024-03-08: Updated incorrect references to either digichem or silico
- 2024-03-08: Removed tests that have moved to digichem; updated necessary imports to digichem
- 2024-03-07: Upated NTO and cube to reference digichem
- 2024-03-07: Removed image makers, file makers, and other code that has been migrated to digichem. Other migration updates
- 2024-03-05: Migrated config/ to config.py
- 2024-03-02: Moved file.gaussian module to digichem
- 2024-03-02: Moved exceptions package to digichem-core
- 2024-03-02: Moved misc package to digichem-core
- 2024-03-02: Fixed weird import
- 2024-03-01: Removed Dynamic_parent, defres and other misc code which no belongs in the configurables library
- 2024-03-01: Errors raised during config reading are now shown with full stack trace
- 2024-02-28: Updated imports to new configurables library
- 2024-02-28: Moved configurables to own library

v6.0.0
________________________________


Miscellaneous
============================

- 2024-02-27: Bumped to v6
- 2024-02-13: Fixed title underline too short
- 2024-02-12: Updates to doc
- 2024-02-11: Updates to result program documentation
- 2024-02-11: Remove some unused obabel formats
- 2024-02-10: Added --writable --readable and --json options to convert program
- 2024-02-09: Tweaked reference to obabel in report
- 2024-02-09: Updated to API documentation
- 2024-02-09: Removed GPL pybel and openbabel library calls
- 2024-02-08: Updates to submit program help
- 2024-02-06: Updated to digichem submit command
- 2024-02-06: Fixed missing formatting on errors and warnings in interactive interface
- 2024-02-05: Updated to doc
- 2024-02-05: Updated dependencies
- 2024-02-05: Added option to include message time in logged messages
- 2024-02-05: Silico resume now uses file locking
- 2024-02-02: Fixed typo in server response
- 2024-02-02: Server now saves its silico version to port file
- 2024-02-02: Remove whitespace
- 2024-02-02: Fixed server start command not actually dumping JSON
- 2024-02-01: Fixed server startup problems
- 2024-02-01: Adde better error handling for early server crashes
- 2024-02-01: Added restart option to server start
- 2024-02-01: Added PAM auth to server
- 2024-02-01: Added server info program
- 2024-02-01: Moved some imports, explained how the sever lock files work
- 2024-02-01: Added functional -p option to server start to control port
- 2024-02-01: Refactored server code, fixed a minor race condition in server startup, added server stop command
- 2024-01-31: Split server program into subprograms, fixed race condition in server startup code
- 2024-01-31: Added intial code for server
- 2024-01-31: Added option to write silico logs to log file
- 2024-01-31: Added log and lock file locations to server config