Changelog

All notable changes to momapy will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Conventional Commits.

[0.6.1] - 2026-03-18

Added

Added a demo on map comparison
Added colinear case when reading reactions (celldesigner)

CI/CD

Bumped action versions

Changed

Hid wip celldesigner writer
Moved demos from demo to demos
Moved utils to root (demo)
Rearranged demo files
Removed unnecessary re-export of reader (celldesigner io)

Documentation

Moved demo to new paths and name

Fixed

Replaced with correct apt deps (binder)
Removed escaping brackets (binder)
Model elements such as modulations are now mapped to the full set of layout elements (sbgn io)
Removed >>> from examples
User manual files after refactor
Added skia extra dep to binder
Updated the demo with latest refactors (demo)
Fixed bug in coordinates of logic gate arcs (celldesigner)

Miscellaneous

Updated reactome analysis with maps display (demos)
Updated reactome analysis (demos)
Added apt packages required for skia-python
Simplified entries
Updated deps
Added jupyterlab dev dep
Wip implement celldesigner writer
Ruff formatting

Testing

Fixed new paths (demo)

[0.6.0] - 2026-03-10

Added

Added cache for font queries (fonts)
Added a helper function for creating a bbox around points and refactored to use it
Added group araound textlayout; made better svg element ids and classes
Replaced shapely and bezier geometry by custom analytical geometry

Changed

Replaced named tuple by dataclass (fonts)
Replaced matplotlib fonts finding by custom one
Renamed self_ methods to own_ methods
Replaced Bezier approximations with direct elliptical arc calculations (geometry)
Removed unnecessary helper functions (geometry)

Fixed

Set modifications to own_angle rather than angle (celldesigner)

Miscellaneous

Added support for python 3.13 and 3.14
Added TODO.txt to .gitignore

Testing

Updated test after refactor (geometry)
Added tests for union of bbox and making bbox around points

[0.5.0] - 2026-03-04

Added

Added optional dict cache to replace
Added singleton mapping for anchor layout element (layout model mapping)
Removed collection builders by mutable collections (builder)

CI/CD

Removed commit and made CHANGELOG.md directly from docs.yml (changelog)

Changed

Moved building builders outside of registering function
Complete split of model functions, with reader as an orchestrator
Complete split of layout and model functions, with reader as an orchestrator
Moved annotations and notes parsing to sbml
Replace model name from Model to SBMLModel
Removed duplicate modification and changed order
Complete refactor of celldesigner io
Arc flattening and associated refactor + writer cleaning
Complete refactor with code cleaning (sbgnml)
Complete refactor, separated parsing/model/layout (sbgnml)
Made subpackage and divided into modules (core)

Fixed

Active borders are now layout elements (fix #3)
Absence of modification is now treated as a modification with state='empty' (celldesigner)
Now hashable (builder)

Miscellaneous

Added instructions for debates/ and plans/ directories
Added debates/
Added CLAUDE.md and disallowed use of dangerouslyDisableSandbox
Added claude sandbox artifacts

Testing

Added tests for new active layout elements
Added tests for notes and annotations
Added tests for sbml
Added tests for sbgn.utils

[0.4.4] - 2026-02-24

Added

Added tidy option (cli)
Changed default font to Arial for macos and win and deja vu sans for linux
Added support for af compartment uoi
Added support for uoi for compartments and submap terminals in af
Added support for cardinality (a la newt)

CI/CD

Changed regex for version; made release conditional to testing; made docs independant of release

Fixed

Fixed label position for compartments; fixed rerouting equivalence arcs (tidy)
Activity is now a dataclass
Added uoi to ad compartment model element
Default font sizes are now closer to newt
Or nodes in af were stored and rendererd as and
Bug in shapely for bezier and elliptical curves
Bug in fraction for Arc
Accepts tag with no orientation

Miscellaneous

Added AGENTS.md for code agents
Cleaned useless function (sbgn.io.sbgnml)

Testing

Added tests for Arc fraction and

[0.4.3] - 2026-02-13

Documentation

Removed linenums for code snippets
Update example with new io and render_map api

Fixed

Changed stoichiometry type from int to float

Miscellaneous

Uv sync
Removed tracking of site/

[0.4.2] - 2026-02-12

Documentation

Changed order of sections
Added symlink to CHANGELOG.md from root to docs/

Fixed

Bug in point to fortranarray and in handling shapely polygons
Bug in invert of scaling

Miscellaneous

Added coverage files

Testing

Added new tests
Added coverage

[0.4.1] - 2026-02-10

Documentation

Added docs for cli and styling

[0.4.0] - 2026-02-10

Added

Added precommit linting (@conventional)
Added renderer and format autodetection (rendering)

CI/CD

Added automated changelog with git-cliff

Fixed

Distinguish scenario min and all for rendering images

Miscellaneous

Removed old testing file
Docs/plans->plans

Other

Added test for demo
Plugins.registry->plugins.core
Updated docs
Updated docs
Removed version; updated docs
_renderer_registry->renderer_registry
Added docs/plans and .tox
Rendering., io.: changed registering renderers/readers/writers to plugin system; plugins: new
Updated; rendering._cairo: rm
Update with renderer changes

Styling

Changed default fonts to DejaVu Sans

Testing

Update with new plugin api

[0.3.0] - 2026-02-03

Other

Fixed bug in argument names
Update
Init
Added entry point momapy
Changed 'formats' attributes to 'supported_formats'; added ValueError for unsupported formats

[0.2.8] - 2026-01-27

Fixed

Fixed python version to 3.13 for packaging

Other

Io.core; celldesigner.io.celldesigner: replaced ReaderResult's ids by FrozenSurjectionDict
Modified so it gets the latest tag on the main branch when triggering manually (Claude)
Add workflow_dispatch option to trigger manually

[0.2.7] - 2026-01-26

Other

Fixed id of layout element taking id of the cd element it comes from

[0.2.6] - 2026-01-21

Other

Fixed layout model mapping for subunits

[0.2.5] - 2026-01-14

Other

Merge branch 'develop' for release
Added layout model mapping for compartments

[0.2.4] - 2026-01-13

Other

Merge branch 'develop' for release
Fixed order of compartment aliases so they respect z-order

[0.2.3] - 2026-01-08

Other

Merge branch 'develop' for release
Added specific supported python 3 versions
Fixed bug in COPYING badge url
Fixed bug in COPYING badge url
Added badges
Merge branch 'develop'
Added binder link and how to run the demo locally
Removed useless demo extra; binder/requirements.txt: replaced demo extra by jupyter dep
Added demo extra and moved jupyter dep from dev to demo; binder/requirements.txt: added file for binder

[0.2.2] - 2026-01-07

Documentation

Update with new default rendering and reading modules
Removed copyright

Other

Merge branch 'develop'
Merge branch 'develop'

[0.2.1] - 2026-01-07

Other

Merge branch 'develop'
Fixed bug where rendering.skia was imported
Celldesigner.core, celldesigner.io.celldesigner: changed default font to Arial
Replaced celldesigner_pickle by celldesigner-pickle
Fixed bug momapy.io.WriterResult->momapy.io.core.WriterResult
Fixed type hint for .selectors attribute
Added tests (Claude)
Replaced pp by pyparsing
Added Not and Compound selectors
Update with new core for io and svg for rendering
Update explaining optional deps
Made true release conditional to TestPyPi release's success

[0.2.0] - 2026-01-06

Fixed

Fixed bug in checking files: added try in case the file is binary
Fixed bug where super was called in FrozenSurjectionDict init
Fixed test
Fixed import and extents bug
Fixed bug in class names for logical operators
Fixed bug: replaced ink_bbox by bbox
Fixed bug in value=='' for state variables
Fixed bugs in writing sbgnml
Fixed bug
Fixed bug where only macos would be tested
Fixed bug with group_transform in rendering; added transform if no group_transform
Fixed bug
Fixed bug: LogicArc->LogicArcLayout
Fixed bug in making LayoutModelMappingBuilder with new keys as frozendict
Fixed bug in filter vs filter_ and filter_.id vs filter_.id_
Fixed absent NoneValueType type hint for dahsarrays and others
Fixed bug in make_boolean_logic_gate

Other

Merge branch 'develop'
Made automatic github release
Updated tests to have frozendict notes and annotations
Changed type of notes and annotations to frozendict
One tox job per os
Adapted workflow to test all python versions on all os with tox
Added explicit utf-8 encoding when writing files to handle windows
Added tox.ini and python version
Typing.Self->typing_extensions.Self for 3.10 compat
Switched from pdm to uv; pdm-bachend to hatchling; made test dep group
Changed typing.Self to typing_extensions.Self for compat with 3.10
Added ModuleNotFoundError as potential source for not available renderer
Update
Added pytest tests to push on testing branch
Updated with new rendering tests
Merge branch 'develop'
Cleaned github actions
Removed comments and unnecessary asserts
Udpated tests
Removed all extras
Added insallation github action
Added pytest and tests generated by Claude
Update
Solved circular imports when registering; fixed bug in sbgn/io/sbgmml.py
Moved readers and writers registration to init of subpackage for sbml and celldesigner
Removed buged sbgnml-0.2 writer
Moved io to own subpackage; moved registering readers and writers to subpackage init
Moved registering svg-native renderer to base of subpackage
Changed default renderer to svg-native
Moved cairo and skia to extras
Added warning about installing extras
Added uharfbuzz and matplotlib
Replaced ink_bbox by bbox
Change default font to DejaVu Sans; replaced ink_bbox by bbox
Changed pango layout to harfbuzz and matplotlib (for fonts)
Merge branch 'develop' into freetype
Added freetype-py dep
Added test layout with freetype
Updated installation instructions
Updated dependencies
Added dependencies
Added frozen annotations
Added reading id
Added more layout model mappings
Added sbgn/io/pickle.py and rendering/cairo.py that were ai generated based on template files
Updated demo
Update
Update
Added print_source function
Update
Added participants of model elements to layout model mapping for: modulations, processes, logical operators
Added support for HAlignment in TextLayout; added HAligment.CENTER to all sbgn labels
Updated demo
Updated demo
Added NoneValue to edge_mode translation
Updated demo
Id->id_
Mod demo: added example; fixed bug in display where markers were transformed
_ReactionLayout->ReactionLayout
In Filter: id->id_
Made left/right_connector_fraction public attributes
Added function to set label font size
Updated packages

[0.1.3] - 2025-08-28

Fixed

Fixed link to doc

[0.1.2] - 2025-08-28

Other

Updated docs/index.md and README.md
Cleaned
Made version regex start with number after v
Publish to testpipy first

[0.1.1] - 2025-08-28

Other

Added module level doc
Build only if version
Only on version tags
Back to version as v.*
Added dynamic versioning
Added cd/ci for automatic release on tags
Moved to pdm build backend
Updated doc page

[0.1.0] - 2025-08-12

Changed

Refactored; fixed bugs; added truncation layout; id->id_
Refactored
Refactored reactions and taken into account transport
Refactored cairo renderer
Refactoring and bugs
Refactored code and fixed in set_arcs_to_borders; added tidy function
Refactored rendering; render multiple maps

Fixed

Fixed typo
Fixed merge
Fixed bugs and cleaned up
Fixed bug in to_top_left
Fixed return type of fit function
Fixed bug in biology-qualifiers: isValue->is
Fix #8
Fixed bug outputing wrong map element types depending on mode
Fixed typo
Fixed bug in intersection of line and shapely object; added rounding
Fixed bug type selector
Fixed bug no species in map
Fixed bug no reaction in map
Fixed bug in handling undefined state variables
Fixed bug in product from product link: was using Reactant
Fixed bug in processing annotations
Fixed bug in make_notes...: return [] rather than None
Fixed typo in _make_model_no_subelements...: layout->model
Fixed bug in finding correct module
Fixed bug: compartments and species templates were not added to the model
Fixed bug not taking into account subunits
Fixed bugs
Fixed bug: species_aliases includes subunits; removed subunits from those
Fixed bug: species_aliases includes subunits; removed subunits from those
Fixed bug in reading structural states
Fixed bug in start_arrowhead_base
Fixed bug biology-model->model-qualifiers
Fixed bug when no tagetLink in reaction modification
Fixed imports
Fixed module name after moving annotations to sbml
Fixed imports
Fixed bug: need to escape text values
Fixed import bug
Fixed childless functions: layout_elements=None->layout_elements=tuple([])
Fixed bug in arrowhead_border: is None->isnan
Fixed TransportLayout._end_arrowhead_border_drawing_elements: RIGTH->LEFT
Fixe bug intersection of line and segment
Fixed dimensions of layout
Fixed calls to new signature of momapy.positioning.fraction_of function
Fixed calls to new signature of momapy.positioning.fit function
Fixed bug self_children not implemented for arcs
Fixed bug in writer
Fixed bugs; took into account AF
Fixed variable names
Fixed border_->
Fixed bug with layout.fill being NoneValue
Fixed id->id_
Fixed bug in arrowhead_drawing_elements
Fixed id->id_
Fixed bug with file names
Fixed type hints
Fixed ) bug
Fixed type hint: self->Self
Fixed bugs with names
Fixed bug in Point: div to truediv
Fixed label_center
Fixed bug in product and reactant links
Fixed bugs in arrowhead_*
Fixed bug in call with wrong signature
Fixed bug in end and start arrowhead length
Fixed bug in grouplayout bbox
Fixed typo group drawing elements
Fixed bug in start_arrowhead for double_headed_arcs
Fixed bug shorten_bezier_curve, shorten_elliptical_arc: segment->bezier_curve, elliptical_arc
Fixed bug transform_elliptical_arc: self->elliptical_arc
Fixed bug: north_north_easr->north_north_east
Fixed bug setting dasharray to dashoffset
Fixed bug with doubleheadedarc
Fixed bugs
Fixed bugd in DoubleTriangle: momapy.nodes->momapy.meta.shapes, border_drawing_elements->drawing_elements
Fixed xsdata version to 23.8
Fixed bug position of layouts
Fixed bug RectangleCompartment
Fixed not right model element when already exists in set
Fixed bugs in shapes and receptor_layout
Fixed bug in multi_mixin
Fixed bug outside_model_element in make_and_add_compartment
Fixed bug in build function for frozendict: self->obj
Fixed bug with names of celldesignerspeciesreference and gene, rna, antisenserna
Fixed bug with name of protein that was a property: species already have a name (from SBML)
Fixed bug: did not take into account compartments
Fixed few bugs
Fixed bug: not taking into account compartment
Fixed names
Fixed bug
Fixed bug
Fixed type hint bug in association layout
Fixed bug type hint BQ
Fixed union bug
Fixed bug: color alpha int->float
Fixed bug: colors float->int
Fixed bug: product was made with Reactant cls
Fixed bug: uois added to svs
Fixed buggy inheritance of stimulation layout and equivalence arc layout
Fixed buggy inheritance of logic arc layout
Fixed builder for forward refs; added type | new_type in builder to allow non builders in builders
Fixed bug with colors: if colors not in list of color definitions, assumes its hex def
Fixed bug when no list_of_color_definitions or no list_of_styles
Fixed bug in split_line_coords
Fixed with new presentation attributes
Fixed type of transform from transformation to tuple[transformation]
Fixed bug: subunit attr can be None
Fixed typo
Fixed bug: no unset in simple value grammar
Fixed typo
Fixed font_color to new stroke/fill
Fixed typo
Fixed typing bug
Fixed imports
Fixed cairo import
Fixed bug render_curve_to
Fixed bug when saving state
Fixed bugs
Fixed import errors
Fixed kw_only in making skia renderer
Fixed fill and stroke for textlayouts
Fixed Close->ClosePath
Fixed bugs
Fixed bug font weight
Fixed transformed for text
Fixed new meta imports
Fixed bug on subunit presentation attributes
Fixed typo
Fixed typo
Fixed typos
Fixed typo
Fixed bug in bbox for shapely obj
Fixed bugs
Fixed typos
Fixed bug: two times slope1
Fixed Ellipse.to_path: now 4 elliptical arcs
Fixed bug: use arrohead_base for computing arrohead angle
Fixed bug: render_curve_to->add_curve_to
Fixed bug: to_cubic->to_curve_to
Fixed bug: fx->fX,fy->fY
Fixed bug
Fixed bugs
Fixed bugs
Fixed bug: n_segs not passed through for bezier curve to shapely
Fixed bug: no compartment
Fixed bug comparing points
Fixed multipages
Fixed bug: inverted is_sublayout relation
Fixed bug in compartment_ref
Fixed typo
Fixed bbox for whole map
Fixed bug when no state in sv
Fixed bug in hex output
Fixed bug: hex repr to 'x'
Fixed bug: hex on int not float
Fixed bug
Fixed bug in get_mapping
Fixed bug when no extension
Fixed reverse order for points of consumption
Fixed bugs
Fixed bug when color_str started with '#'
Fixed bugs with new layout_model_mapping
Fixed bug for ior: now like or and not dict.ior
Fixed bug
Fixed bug with or selector
Fixed bug in is_ovav: fields->dataclasses.fields
Fixed bug in shortened when self.length() == 0
Fixed bug in typing
Fixed typo in model: switched SpeciesReference and SimpleSpeciesReference
Fixed bug in coinsident lines
Fixed bug points to segments
Fixed bug: arc.x and arc.y
Fixed typo in angle
Fixed bug in crosspoint border drawing element
Fixed bug: TextLayoutElement -> TextLayout
Fixed label textlayout width and height
Fixed bug
Fixed bug in stylesheet list
Fixed bug in reading list of stylesheets
Fixed bug with returning results
Fixed bug when builders were used instead of built objects
Fixed unused imports
Fixed namespace error
Fixed tidy; set_arcs_to_borders does not do anything if no intersection is found
Fixed imports
Fixed imports
Fixed import
Fixed bug
Fix + vanted.css
Fixed bug in frozendict ini
Fixed frozendict bug: initialization from dict rather than list
Fix bug
Fixed bugs
Fixed bug in set_arcs_to_borders
Fixed bug when last_segment.length() == 0 in arc anchors
Fixed bug: set_matrix -> transform in cairo renderer
Fixed bug in intersection of line and circle
Fixed bug in render_maps
Fixed bug in textlayoutelement
Fixed bugs
Fixed import bug
Fixed bugs and replaced nodelabel by textlayout
Fixed bugs in render_maps: calculation of min_x and min_y
Fixed bug with labels of compartments in set_compartments...
Fixed bug with PhantomLayoutElement
Fixed bugs with arrowhead bboxes
Fixed bug in copying in render_map with to_top_left==True
Fixed bugs
Fixed typo
Fixed make_builder: Builder is now always a base class, and connectable_attributes are well set
Fixed imports
Fixed rendering of text with new coord system
Fixed import
Fixed imports

Other

Updated docs
Added workflow for building docs
Updated doc
Updated demo
Rm unused import
Updated with proper display for layout elements with transformations
Bbox now takes into account ink_bbox of text
Ruff
Merge branch 'develop' into shapely_transform
Merge branch 'demo' into develop
Updated demo; fixed bug in utils
Added transform
Made transform a tuple of transformation
Udpated docs
Added ruff, pygments
Rm red layout stroke
Removed config from param for creating a skia renderer
Updated doc
Updated packages and removed sphinx related and black deps
Updated doc
Updated layout_model_mapping
Update
Merged
Updated doc
Updated documentation
Updated documentation
Merge branch 'develop' into docs_mkdocs
Updated documentation
Update
Added reading sbml skeleton
Updated demo
Added EMPTY_SET key; fixed bug in writing compartmentRef attribute
Updated functions to new layout_model_mapping
Added replace=True to add_mappings
Added replace option in add_mapping
Support for annotations, compartment_refs
Merge branch 'develop' into write_sbgnml
Replaced call to Pango.extents_to_pixels by pos / Pango.SCALE to avoid new bug with function
Merge branch 'develop' into write_sbgnml
Added pdm-readiness
Added cross_hv_of; cross_vh_of; set_mid_of; set_cross_hv_of; set_cross_vh_of functions
Added support in CellDesignerModel for Regions
Added mid_of function
Closes #19
Closes #18
Closes #14: replace is not NoneValue by != NoneValue
Closes #13: fixed bug in Color.to_rgba; fixed range to float in skia fill and stroke
Closes #10
Closes #9
Updated dependencies
Cleaned dependencies
Added id and class in rendering
Added structural state layout
Added post_init to pointbuilder
Replaced is momapy.drawing.NoneValue by ==
For notes, annotations, ids: frozendict to dict
Added hash and eq methods for NoneValue singleton
Added handling non text file exception in read
Added celldesigner pickle read and write
Removed reduduntant exceptions from WriterResult
Added _active to ids of active species
Added support for dasharray in SingleNode
Added support for stroke_dasharray
Mappings are now frozendicts
Merge branch 'develop' into cd_layout_model_mapping
Rounded for shapely
Rm unused import
Replaced typing for source and target of arc to LayoutElement
Added layout model mapping for reactions and modulations
Added layout_model_mapping for species
Changed require-python to >=3.10
Added SurjectionDict
Merge branch 'develop' into write_sbgnml
Modification residues are now sorted following their angle (ascending)
Taken into account undefined names for modification residues with an order attribute
Added order to modification residue
Update with new sbgnml export
Updated writing sbgnml
Changed function to make notes; added support for map/model notes and annotations
Added support for notes and annotations on the map itself
Rm annotations to frozendict
Added notes support for elements
Added notes for compartments
Added export of notes
Updated to python 3.12
Rm transformation of annotations and notes into frozen sets
Changed python
Start of new writer
Added support for af unit of informations
Added specific function for making activities
Removed unnecessary _sbgnml_parser*
Added support for labels in submaps
Added new support for reading af without xsdata
Added ids to map_element_to_ids
Added ids to ReaderResult
Removed print
Merge branch 'develop' into cd_ids
Merged sbgn_revamp
Added model layout mapping
Continued revamping
Removed annotations and notes
Added biomodel qualifiers
Rvamped
Removed old unused parse file
Added map_element_to_ids mapping
Removed useless dict transform of model_element_to_layout_element
Removed unused parser file
Annotations is now frozen
Sbml.Annotation->sbml.RDFAnnotation
List->set
Added ids for reactants and products
Stoichiometry can be None
Finished model maker
Added Palmytoylated
Added PALMITOYLATED
DON'T CARE->DON_T_CARE
Removed unused re import
AntisenseRNA->AntisenseRNA
Optional listOfModification in reaction
Added annotations
Removed map_element_to_annotations from CellDesignerMap
Added boolean logic gates for modulations
Added logic gates
Added class for logic arc layouts
Changed size and font of logic gates
Added gate layouts
Continued revamping
Removed useless newline
Removed useless print
Continued revamping
Udpated
Updated with_model/with_layout options
Read/write_file->read/write; added os.PathLike type annotation
More new methods
In Writer: write()->write_file()
Beginning of refactoring celldesigner reading
Update
Added annotations for included species
First fix read_file
New way of parsing: model, layout, map; annotations are outside of objects
Udpate with doc
Added undoc-members
Changed conf.py location for new org
Update docs/ organization
Mv .readthedocs.yaml to root
Added files for readthedocs
Mv sphinx_docs->docs
Removed ipykernel dependency
Udpated demo
Added dist/
Udpate with classifiers and urls
Updated package description
Update
Update
Remove intersection of line with drawing and layout elements
Added docs
Updated demo
Updated demo
Moved demo to /; cleaned up
Added documentation
Udpated docs
Udpated doc
Updated doc
Update doc
New_builder->new_builder_object; added type hints
New_builder->new_builder_object
Added full input of SBGN AF maps
Update
Updated demo
Updated type hints and methods
Added from_top_left option
Removed unused import
Update demo
Update with new attr names
Added center to border and angle functions
Update with new attr names
Fill of layout set to NoneValue
Changed qualified attrs to unqualified attrs (default)
Added notebook
Added docs"
Added init.py
Added init.py
To python 3.12
Added documentation
Updated
Added particular anchors for celldesigner shapes
Moved labels of modifications
Taken into account active; fixed bug in position of compartments
Added some anchor points
Added support for modulations
Taken into account catalysis
Put labels in right place
Added replacement of text by character
Added functions to find angle and border of shapely_object and collection of drawing elements
Update with dissociation
Replaced fit layout by the size of the layout
Added super_or_builder method
Added todos
Remade taking into account edit points with center or link anchor
Added anchor_point method to layout element
Added comment
Add get_transformation_for_frame_function
Partially fixed bug when no link anchor
Taken into account omitted transition, unknown transition, transcription, translation
Taken into account start node in base reactant layout
Refacrtored state_transition_layout and add heterodimer_association_layout
Took into account base reactants and edit points for association
Added layout for state transition, with reactants and products
Begined adding layout for reactions
Added with_layout option to prevent from making the layout
Added intermediate cardinal points
Added state transition layout prototype
Added compartment layouts; refactored code
Add_or_replace_element_in_set now returns the element that is in the set at the end
Code layout
In _Modifier: species->referred_species
Replaced .species by .referred_species in SpeciesReferences; replaced CellDesignerSpeciesReference by SpeciesTemplate
Added reading of empty state variable
Readded Annotation
Removed notes and annotations from sbase
Support for parsing sbml annotations inside notes
Added support for reduced boolean logic gates
Added listOfGateMember to reaction
Rm make layout and model_layout_mapping for celldesigner
Added None to model, layout and layout_model_mapping
Added annotations
Map_element_to_annotation->map_element_to_annotations
Added rdf annotations for species
Added function to make annotations
Qdded attributeFormDefault='qualified' for rdf
Added map_element_to_annotation to Map
Added attributes of annotations
Added empty state which arises sometimes
Changed to using aliases instead of species
Added acetylated modification
Updated schemas and changed location
Now transforming aliases rather than species
Added hypothetical for species
Taken into account: outside for complexed; modifiers with gates
Modification->modificationType
Homodimer->homomultimer
Adapted to minerva bug on type for rna, gene and anitsenserna references
Added # abstract
Removed momapy-model from ids for model elements
Removed metaid, notes and annotations of comparison for species
Udpated the celldesigner schema with reduced notation
Update
Cleaned model
Cleaned the model
Update
Cleaned modulations in CellDesignerModel
Cleaned modulations and modifiers
Cleaned modifier and added comment
Modulators->modifiers
No printing of base types or objects evaluating to False (e.g., empty collections)
Removed structuralstatevalue: now always str
Checks for subclass rather than exact type matching in exclude_cls
Cleaned make parser for celldesigner
Merge branch 'develop' into celldesigner
Updated python version to >3.10 and <3.11
Added AuxiliaryUnit concept
Redid tpying.union for forwardref
Replaced referes_to attribute by reference attribute
Got rid of typing.Union
Made the ids of model elements deterministic
Cleaned
Added add_or_replace_elemement_in_set function
Merge branch 'fix_builder' into celldesigner
Removed UndefinedVariable class; use order instead
Added annotations reading for macromolecules
Added superclass BiomodelQualifier for BQModel and BQBiol
Added module for forwardref of logicaloperator
Moved make_pango to new _pango module; forced ids to str
Cleaned up
Applying stylesheet to objects; to builder becomes _ function
Update
Shortening a segment of length 0 now returns a copy of the segment
Update
Updated code
Update with new way: build objects
Exluded Point from collections in pretty_print function
Added class exclusion feature in pretty print; changed color:black->green
Simplified names of mappings
Added make_union option to the transform_type
Removed add_element method
Builder transform type: now returns type_ | new_type
Bug fix: stopped transforming default factory functions
Changed variable names: field_->field, mappings to more conventional names
Antisens->Antisense
Merge branch 'develop' into celldesigner
Can perform functions on map
Changed check_file methods: no use of parser anymore
Render extension: made attributes qualified
Cleaned up; moved schemas and make_parser outside of src
Added parser for sbgnml_0_2 and _0_3
Updated the README with link to demo
Udpated the demo
Update
Added License
Added text to README
Merge branch 'develop' into celldesigner
Removed tests from git
Readded celldesigner/
Readded sbml/core.py
Deleted sbml/ and celldesigner/ to move them to branches
Pipenv->pdm; cleaned up
Changed rectangle compartment
Merge branch 'develop' into celldesigner
Added script for making a css template file from a module
Updated and added styles with @import
Updated demo
Changed defaults for subunits attributes
Updated with new presentation attributes
Changed defaults for presentation attributes
LogicArc->LogicArcLayout;EquivalenceArc->EquivalenceArcLayout
Added | None to types for stroke_width
Path_shorten->shorten; added start_shorten to Arc
Now built with @import cs_black_and_white and newt_no_cs
Added chdir for relative css @import
Added import statement feature inside css
StyleSheet read_file->StyleSheet.from_file; join_style_sheets->combine_style_sheets;read_string->from_string; added from_files classmethod
Update
Pseudo-fixed bug with unset
Update
Added script to make a css template
Harmonize initial values
Layout is now a Node
Added unset css value, that is transformed to Python's None
Added default values for presentation attrs of SBGNNode
Changed list_colors to print_colors; list_colors now list all pairs (color_name, color) of the module
Cleaned up code: new SBGNSingle/DoubleHeadedArc; arrowhead_drawing elements coded for arcs instead of subclassing; cleaned attributes order
Updated layouts with new shapes
Cleaned typing
File creation
Added make_node and make_arc functions
Changed default values for presentation attritubutes in TextLayout; use of make_pango_layout from utils in textLayout
Added get-initial_value method; fixed bug font weight mapping
Added get_initial_value method
Added FONT_WEIGHT_VALUE_MAPPING
Moved testing functions to testing; added make_pango_layout to utils; removed print_classes from utils
Added transformation of elliptical arc to bezier curves; cleaning
Cleaning
Cleaned up
Added sbmlutils
Continued coding drawing_elements methods
Update
Font family and size become mandatory on text layouts
Filter on all drawing elements
Added new StatefulRenderer
Added fill to textlayout
To python 3.11
Normalized presentation attributes; support in svg-native renderer
Update with new drawing elements
Added new classes following the spec
Added import for svg_native renderer
Added styling: fill, stroke, font
Added support for font style and weight; added support for text-anchor (not skia)
Added fill rule
Merge branch 'develop' into sbml_layout
Removed childless method from GroupLayout
NodeLayout->Node; ArcLayout->Arc
Update
Shorten->path_shorten
Added defaults for nodes and arcs; cleaned up
Removed nodes width and height in render function
Changed defaults of metas
Taken into account new shape buisness
Simple and Multi mixins return shapes instead of nodes
Cleaned up
Moved Shape to core
Shapes, nodes and arcs to meta dir
Revamped to shapely for elliptical arc function
Revamped _split_line_string function
Removed translated method from layout_element since not used anywhere
Updated nodes
Finished nodes and added all arcs
Removed arrowhead_fill from defaults
Reverted width for Bar: should only be arrowhead_stroke_width
Added width for Bar
Added rendering_testing for arcs; changed rendering nodes on grid to rendering_layout_elements
Finished rendering function
Cleaned up
Renamed geometry functions; added some new functions
Added rendering utility functions
Revamped intersection function
Changed defaults and attributes' order
Revamped nodes
New styling attributes for connectors
Revamped sbgn nodes
Cleaned defaults
Increased error tolerance for elliptical_arc to shapely
Added new arcs
Cleaned code and fixed bug with arrowhead_length==0
Shapes->nodes
Now SingleHeaded and DoubleHeaded arcs
Shapes->nodes
Started to change to new border style
New start and end arrowheads in arc; new border in node
New and updated functions for segments, elliptical arcs and bezier curves
Cleaned up
Added beginning of layout and render
First commit
Added x and y attribute to Layout
MapLayout->Layout
Added anchors for MapLayout
Width cannot be < to height
Removed arrowhead_bbox from arcs
Removed addition in path; Close->ClosePath action
Update
Vanted->sbgned
Cleaned up
Updated demo
Updated demo
Added pretty print function
Added apply_style_sheet to map
Removed return map from write
Added compartments to entities
Model and layout are now non optional
Added support for notes
Update
Changed notes parsing to strict
Added listOfBackgroundImages
Added annotations to map, notes to map, model, model_element
Cleaned up
Added option for reading and writing annotations
Support for writing annotations
Added annotations to sbgnmodel
Specified annotation class
Added support for sbml miriam annotation
Package name from momapy.about
Added package name
Added option for render_information
Added support for more glyphs
Added init.py
Remade parser
Added render information attributes
Added writing render information
Added about with version and author
Added leading # to to_hex and to_hexa return string
Added to_hex and to_hexa methods
Update sbgnml writer
Update
Udpate
Updated tidy function and nodes fit labels function
Udpated set_arcs_to_borders
Update
Updated newt.css
Added reversibility of processes; left-to-right of processes and operators
Added get_mapping to mapbuilder
Added upack option to get_mapping: unpacks the frozenset(frozenset) result; added get_mapping to map
Added left_to_right attribute to layout with connectors
Removed source and target from children in ArcLayout
Added reversibility for processes
New set_arcs_to_borders function
Added monitoring
Changed default renderer to skia
Update
Cleaned up
New subpackage
Cleaned up
Changed to reader class
Staticmethod->classmethod
Staticmethod->classmethod
Added new reader class
Changed parser file name
Updated read function; added perturbation unit of informaion to schema
Take into account map bbox
New read write functions
Added additional error: class where add_element is called
Base_left/right_connector->left/right_connector_base/g
Added two new anchors: left_connector_tip and right_connector_tip
Update
Update
Added utils module with a new str func
Added new layout_model_mapping
To python 3.11
Added pyparsing to setup
Cleaned
ObjectBoundingBox->ObjectBoundingBox
Writes to file only if output_file is defined in config
Added reactant and product edit points
Changed default width and height of reaction node
New nodes taken into account
Update
Fixed bug in copying dict for joining two stylesheets
Removed geometry import
Update
State variable set to '' is now considered to be None
Child can now be None and
Added default width and height to Arrow
More shapes taken into account
Added CellDesigner shapes and layout elements
Update
Added SBGNPD/AFLayout
Update
Cleaned up
Update
Build methods and from_object methods now take a mapping as parameter which avoids rebuilding identical object
Remove colors object: momapy.coloring.colors. -> momapy.coloring.; rgb, rgba, hex, hexa functions->from_rgb, from_rgba,... methods of Color
Update
Model_layout_mapping -> layout_model_mapping
Updated dependencies
Kw_only and new defaults
Updated to python 3.10; added Pipfile*
- in css is now possible; replace _ by - in css of sbgn
Updated notebook
Revert "updated notebook and cleaned up"

This reverts commit c115e10923928ebf55f116931bfbf39504451429. - Updated notebook and cleaned up - Changed defaults for af units of information - Made style for logic arc - Redeveloped svg native renderer - Changed arguments order in SkiaRenderer - Bug in renderer ini and added antialiasing to imagefilter painting - Added new reaction types - Added reactions and reactionmofication - Added PHYSICAL_STIMULATION to reaction types - Preserves init from being overwritten by xsdata - Trigger-> triggering + typo - Updated CellDesigner schema - Added Compartment - Other gates; complexes; compartments - Typo - Added Modulator and changed modifiers ontology - Added rest of modifier types - Updated read_file - Modulators -> modifiers - Modulator to Modifier - Added boolean logic gates - Added return value for read_file - Update - Cleaned - Added white colorscheme - Added classselector; simplified typeselector code - Update - Added rendering methods for all filter effects - Fixed bug;added enums for filter effects - Added with_alpha method - Added notebook - Added is_submapping for ModelLayoutMapping; cleaned is_sublayout - Position of text in TextMixin is now label_center() rather than position - Updated - Cleaned up - Added dasharray property - Svg implementation of get_region_filter - Updated newt style - Updated demo - Added get_filter_region method to drawing element - Bug in shapely method of elleptical arc - Implemented drop shadow filter - Replaced path in stadium by rectangle - Updated demo - Cleaned up - Cleaned up - Updated to_shapely method for elliptical arc - Changed sweep flag of stadium shape - Udpated demo - Added to_polygons option to to_shapely method - Fit nodes to labels: to logical bbox - Reverted Direction back to momapy.core - Anchors no longer abstractmethods, but implemented in parent nodelayout class - Moved Direction to sbgn.core - Added file - Updated gitignore - Updated dependencies - Fraction moved to core - New intersection method with shapely - Intersection function: new name - Updated demo - Added demo as subpackage - Cleaned; added general intersection function - Added shapely geometry - Added shapely dependency - Cleaned up and added div for point(builder) - Take into account bezier curves - Rearranged fraction function for bezier curve - Added bezier curve; core/arc: changed points to segments - Changed to python 3.9; added bezier module - Reworked transformed method for elliptical arc - Arrowhead now used transformed method instead of svg-style transform attribute - Typo - Removed arc drawing element - Removed arc drawing element - Added transformed methods - Updated rendereres - Bug skia renderer no dataclass decorator - Updated demo - Added fraction method to arclayout - Cleaned up - Updated demo - Added default width and height to SBGN glyphs - Cleaned up - Updated demo - Update - Added anchors to textlayout; fixed bugs in angles - Added anchors for crosspoint - Merged - Updated demo - Ignore demo/*.svg - Added demo - Moved is_sublayout method from LayoutElement to MapLayout - Updated vanted and newt styles with filter: none - Ink_bbox() -> bbox() - Updated vanted and newt styles with filter: none - Updated newt style sheet - Updated stylesheet - Descendants->ancestors in apply_style_sheet function - Added newt stylesheet - Cleaned up - Added submap, submodel and sublayout methods; added translated method - Added crosspoint - Updated demo - Anchors are computed automatically; shapes are computed using joints - Added demo and cleaned up - Updated celldesigner model and io - Merge branch 'cd' into developpment - Cd model elements now inherit from sbml core elements - Merge skia - Updated with skia - Added skia renderer - X/ysep for nodes set to 5 - Updated with required package skia-python - New filter effects and new svg-native-compat renderer - Implemented af model, layout and rendering - Merge remote-tracking branch 'origin/cd_dev' into cd - New model elements - Merge branch 'main_dev' into cd_dev - New celldesigner model - Added connectors stroke width - Added CardinalityLayout - Added support for cardinality and stoichiometry - Added package data - Import sbgn stylesheets - Upadted setup.py - New terminal layout - Shadows for subunits - Added filter for subunits in sbgn shape - Added none possibility for filters - Clean up - Color for subunits of macromolecule multimer layout - Added list value type - New fit submaps to content function - New styles for sumap and tag layout - Added new directions - Added submap and tag layouts - Set position of layout to position of label with anchor label_center - Added inverted hexagon shape and perturbing agent layout - Updated to new SBGNShape style - Updated with beginning of metaclass - Cleaned up - Is_ovav method - Clean up - Clean up code - Updated style sheets - Changed default filter units to object bounding box - Translation->translate in svg-native renderer - +import momapy.drawing - Impl copy and deepcopy for NoneValue singleton - Update - Added set_complexes_to_fit_content utils function - Fill of consumption to none - Removed shadows for arcs - Emptyset must have a stroke color - Set stroke to none - Bug _render_filters - Typo - Typo - Typo - Typo - Added shadows.css stylsheet - Added drop-shadow in styling css - Added filter with drop shadow effect - Typo - Layout fill to white - Changed font sizes in shapes with text - Aux units font - Font to Cantarell - Font to cantarell - Text drawing element: font_color replaced by fill and stroke - Rgba to rgb and opacity - Layout fill: none; textlayout: font_color - Default sbgn style: fill of layout set to none - Styling none returns NoneValue - Default fill value to black - Set_size->set_absolute_size in pango font description - String to output file - Set_size->set_absolute_size for pango font description - Merge branch 'arc_to_elliptical' into native_svg - Changed arc to elliptical arc in shapes - More methods for native svg renderer - First class and methods for nativesvgrenderer - Int to float - Multiple style sheets; join style sheets - Update - Added default_colorscheme.css - +width and height - Added default stylesheet for sbgn - Added strict option to applying collection of styles - Removed _ from color names to be consistent with css - Added none value that does not work - Added has_color method to colors - Added none value in style_sheets - Added set_auilliary_units_to_borders function - Added self_border and self_angle functions - Splited fontdescription into fontsize and fontfamily - +pyparsing - Added parser for stylesheets - Clean up - In node layout: removed foreground_path; renamed background_path to border_drawing_element - Render_maps(): changed bbox to self_bbox to compute surface width and height - Changed drawing path of Layout: bbox() -> self_bbox() - Cleanup - Added ancestor and parent selectors;type selector->class selector; now ancestors in select method - Added children mehtod to layouts - Added tidy and stylesheet options to read_file - Can now supply a mapbuilder to apply_style_sheet - Added set_arcs_to_borders function - Cleaning - Addition of point to point builder - Added automatic border functions and related changes - New function for intersection of line and ellipse - Removed y_from_x methods (not much sense) - New geometry shapes: Arc, Circle; new intersection functions - Recodes parallel lines; added slope and intercept to line; recoded intersection of lines - Added set_layout_to_fit_content function - Added set_nodes_to_fit_labels - Label_center taken into account and bold text in shapes - Added label_center anchor - Added vertical alignment for textlayoutelement - Bugs and replaces text by new text and textlayout - Changed nodelabel to textlayoutelement - New text drawing element and textlayoutelement - Added style_sheets from styling to render_map(s) - Added position to sbgn maps when reading sbgn-ml file - Added position to layout - Removed optional from transform attribute of drawing element (default is tuple) - Dfault for transform attribute is set to tuple - Merge branch 'main_dev' into sbgn_dev - Fit now return position, width, height and not bbox: fixed related bugs in self.bbox() functions - Bug in set_compartments_to_fit_content - Merge branch 'main_dev' into sbgn_dev - Bug in set_fit function - New set_compartments_to_fit_content function - Merge branch 'main_dev' into sbgn_dev - Fit returns position, width and height rather than a bbox; implemented set_fit function - Added new sbgn shapes - Added EmptySetLayout to emptyset and source and sink - New styling feature - Completed fraction function - Recoded arcs with anchors - Cleaned code - Maj - Bug restore after stroke and fill; factored _stroke_and_fill - Added height and width in _make_renderer_for_render_function - Typo in parameter name - Added a function to render a collection of drawing elements and factored make_renderer_for_render_function - Added ellipse to drawing and rendering - Added arcs to drawing and rendering - Typo - Added origin point for rotation - Experimental update with updated_object - Revamped relative_point to updated_object - Removed prints - New animating module - Bug fix - Bug fix in Color.or - Bug fix in Color.or - Added png rendering - Updated Pipfile - Cleanup - Cleanup - Cleanup - Cleaned imports - Added alpha modification to Color - Mod essai.py - Cleanup - Reference->phantomlayoutelement, fixed bugs, fixed positioning with new coord sys - Added self_bbox to grouplayout and to nodelayout - Mod bbox to follow new coord system - Mod essai.py - Inverted y axis to mimick svg and sbgnml - Cleaned rendering and drawing code - Updated gitignore - Updated grouplayoutelement - Cleanup - Renderer to rendering - Renderer.py to rendering.py - Cleanup - Removed position.py.save - Added folder momapy/ - Removed submodule momapy - Updated gitignore - Updated pipfile - Initial commit

Styling

Styles to/from render_information: border>group attrs for nodes, arrowhead>path>group attrs for arcs
Stylesheet is now unfrozen so it can be easily modified
Styles in grouplayoutelement applied to the top group element; arcs have styles for arrowhead
Style_sheets from files and multiple style_sheets
Stylesheet applied to layout instead of map