CHANGES
=======

v1.0.1
------

* Apply suggestions from code review
* account for bond order operators at the start of branches
* fix accidental docstring mistake
* fix issue 61 by doint the hcount adjustment in the end
* add test case from issue 61
* implement branch expansion in fragments correclty and test
* fix test parameters
* Add isomerisation/squash test case
* keep hcounts for squash connectors
* keep isomerisation class when squashing atoms
* Fragment colors now cycle over the defined ones
* Expanded squashing logic to check for element/name compatibility
* Overall fixes to the drawing logic of shared atoms

v1.0.0
------

* Update deploy.yml
* Update deploy.yml
* address review comments
* add deploy workflow
* use token authentication
* test vermouth workflow
* remove pysmiles git referenc
* More robust drawing tutorial
* Update README.rst (refine text)
* Fix citation (use .rst instead of \`\`\`) in main README.rst
* Fix typos and add JCIM citation to main readme
* Add matplotli plotting to drawing tutorial
* Update resolve.py
* set sphinx version
* quickfix rdkit docstring
* quickfix rdkit docstring
* quickfix rdkit docstring
* fix docstring typo
* add rdkit to dosc requr
* add test utils
* add rdkit as required
* update tests
* update docs
* test coordinates
* test rdkit conversion functions
* add coordinate generation
* Update resolve.py
* Create LICENSE
* change CGSmiles to CGsmiles
* add images
* fix resolve docstring
* have tutorials
* update docs
* change name to CGsmiles
* change name to CGsmiles
* update installation
* update doc confs
* fix docstrings
* remove nit
* remove nit
* fix docs ref
* fix docs ref
* change name of README in config
* add docs to test workflow
* add read the docs yml
* update requirements
* add missing version variable in \_\_init\_\_
* add doc
* fix multi squash
* remove README.md und add README.rst
* Update cgsmiles/drawing.py
* update docstirng
* assing alignment by keyword based on dict
* Apply suggestions from code review
* allow flexible axis rotation
* have default drawing method
* fix docstring
* remove duplicate function
* fix docstring
* fix docstring
* raise scale error
* remove import from \_init\_
* Update cgsmiles/graph\_layout\_utils.py
* Apply suggestions from code review
* address comments
* add scipy to dep list
* add mpl to dep list
* bug fix
* expose drawing
* add linalg functions
* fix default labels and provide example
* validate input
* update dependency
* address comments
* fix cis trans test
* take care of align api
* CIS trans aware drawing
* implement correct cis trans drawing
* set some defaults
* refactor graph layout
* refactor drawing utils
* refactor drawing
* adjust and add tests
* remove bits related to old chiral atom processingt
* remove bits related to old chiral atom processingt
* remove bits related to old chiral atom processingt
* add explicit type and make sure that None values are removed
* Update cgsmiles/dialects.py
* fix merge add test
* add test
* remove leftovers
* tests and account for bond order
* remove double atomname assignment in resolve
* set atomnames also for meta-graph if one is provided
* adjust hcount by bonding op number if required
* add tests for multiple bonding descriptors each having a bond order different from 1
* clear bond orders correclty
* add tests
* allow bonding after branch
* return positions
* change c to q and use fullnames for weight and charge
* enable explicit hatoms
* rename base dialect to default dialect
* test more verbose errors
* fix bugs regarding kwargs; raise more verbose errors
* merge master
* address some comments
* remove prints
* bug fix cis trans
* implement dialects and annotations
* implement dialects and annotations
* add more verbose error
* updated hydrogen accounting and aromaticity
* have hydrogen weights reconstructed
* take care of case where h comes first
* tests for hydrogen weights
* have hydrogen weights
* updated drawing
* updated drawing
* drawing utils
* patch tests
* have cg charges
* add error message and tests
* Update cgsmiles/read\_cgsmiles.py
* patch bug when string ends before we check a character
* add bond orders in combination with branches, expansion operators, and branch expansion
* equalize %01 1
* address comments
* add tests
* update tests
* implement weight annotation
* implement bond order syntax for CG
* Update cgsmiles/tests/test\_write\_cgsmiles.py
* remove print
* bug fix
* update tests
* update tests
* allow higher order rings
* address comments
* address comments
* address comments
* clean and add some wrappers
* address comment
* update writer
* fix bug
* overhaul write cgsmiles
* fix dep
* have rings taken into account when dealing with chirality; account correctly for implicit hydrogens
* draft
* address some comments
* Update cgsmiles/sample.py
* update tests and remove print
* update tests
* typo sphinx link
* Apply suggestions from code review
* fix doscstrings and spelling
* fix doscstrings
* fix doscstrings
* implement isomerism bug fixes plus tests
* update docstring
* address comments
* update docstring
* change naming in sampler and update doc strings
* change meaning of bonding operators and fix in test
* update sampler and change meaning of bonding operators
* keep proper track of fragid when adding terminals
* expose sampler
* install pysmiles master
* update sampler
* finalize tests for init function
* update handling of terminal addition
* add more tests
* refactor sample
* update function call set\_atom\_names\_atomistic according to new args
* the fragid for cgsmiles fragments should be 0 in agreement with the convention used in cgsmiles
* when annontating atomnames make meta\_graph optional; otherwise go off fragid
* adjust open bonds function to optionally take target nodes
* address style comments
* refactor random seed
* add seeds
* patch latest pysmiles version
* address comments and refactor slightly
* update docstrings
* make deepcopy when merging
* init draft for sampler
* Apply suggestions from code review
* rebase continue
* simplify and clean up writer
* doc strings
* get connections from full resolution molecule
* get connections from full resolution molecule
* implement cgsmiles writer for fragments
* implement cgsmiles writer for resgraphs
* first draft write cgsmiles
* adjust doc strings and add error message
* fix typo
* Apply suggestions from code review
* refactor new API using constructors
* read all fragments during init
* add tests for resolve and fix bugs in workflow
* refactor and include comments
* Apply suggestions from code review
* fix handling of fragments
* fix typo set\_atom\_names\_atomistic
* add a resolve all
* Apply suggestions from code review
* set atomnames according to all-atom MD convetion if resolution is AA
* add test for layering
* implement layered resolutions
* small bug fix; when the multiplication operator is used in fragments it is possible that it is the last character
* put change of supported python versions in setup.cfg
* increase python version requirement to 3.8
* install pysmiles from GH
* fix hydrogen count
* utalize latest pysmiles valance assignment
* utalize latest pysmiles valance assignment
* annotate aromatic edges before rebuilding hydrogen
* fix annotation of bond order in bonding descriptor
* fix count of hydrogen
* fix multiletter atoms
* refactor according to walrus
* adjust name of generate\_edge in test
* rename generate edge to better reflect what it does
* rebase and integrate with new pysmiles
* properly rebase branch
* add new iterator
* use \_valence function to get valences
* add hcounts
* allow bond orders based on SMILES syntax for bonding descrip
* Apply suggestions from code review
* add test for node with two additional cycle edges
* fix multiple cycles bug; add tests
* fix multiple cycles
* improve bonding function by making deepcopy of bonding list in first place
* make squash function even easier
* add test where squash and conect are used on same atom
* adjust test
* clean up squash function
* clean up squash function
* clean up resolve part I
* move rebuilding of hydrogen atoms to pysmiles utils and do after connecting molecule
* remove rebuilding of hydrogen atoms from fragment reader
* update tests with new ordering; assert equivl. based on graph isomorphism
* implement new sorting function; attatch graph\_frag as node attribute in annotate fragments
* implement squash operator
* make fragid a list to allow a single atom to belong to more than one fragment
* implement squash operator
* add CI
* rename files
* implement test for resolving molecules
* fix counting bug
* replace resname for fragname
* add tests for cgsmile parsing
* update setup
* add package details
* add tests
* add high level API
* add molecule resolver
* add reader for fragments
* add reader for cgsmiles
* add function for annotating fragments
* leightweight utilities for graphs
* Update README.md
* Initial commit
