Polyply

New Features
* Using a `[ bending ]` directive in the build_file, polyply now allows sampling from an angle-dependent potential when doing the random walk. This allows tuning the rigidity of the polymer chain. 344
* Martini 3 IDPs are now officially implemented thanks to csbrasnett 331

Library Updates
* Add PTMA CGM3 IBI model to polyply library [10.1021/acs.macromol.3c00141] 279
* Add PTMA GBNO2 IBI model to polyply library [10.1021/acs.macromol.3c00141] 343
* Update citation of Martini 3 PTMA 348

Bug Fixes
* Checking of box coordinates caused an error when the box is supplied only via CLI. This is fixed now.

Library Updates:
* Switch to default OPLS atomtype names 317; OPLS itps can now be used with regular gromacs interaction table

Improvements
* Take box from starting coordinate if supplied or give warning or error 321
* Give a warning if meta-molecule coordinates exceed box 310
* `-name` flag becomes optional when generating coordinates (default is `polymer`) 312
* `-o` flag becomes optional when generating coordinates (default is `coords.gro`)
* Raise warning when no sequence is given in `gen_seq` 312

Dependency Updates
* Fix issue 305 when gen_params fails due to sequence resids not starting at 1 306
* Update CI; Codevoerage is now reported by GHA function 314
* Add scipy 1.11 patch 333
* Replace deprecated pkg_resources by importlib 347
* Change all paths in tests to proper Path objects 347

New Features
* Implement reading of the `error` directive 337
* Allow generation of double-stranded DNA itp files. 313

Other Changes
* Only parse files with known extensions in the force-field directory 253
* Ignore tests with coverage by fgrunewald in https://github.com/marrink-lab/polyply_1.0/pull/316

Library Updates:
- Martini3 PPE now prints warnings when termini are not applied
- Martini3 PDMS has been added to the library [10.1039/D2SM00939K](https://doi.org/10.1039/D2SM00939K)

Improvements
* Log entries for force-field data files are now available (292). This feature allows to print specific messages when specific blocks or links are applied
* Amino acid parsing via fasta files is now possible (303)

Dependency Updates
- vermouth dependency has been increased to version >= v0.9.1

Other Changes
- python 3.6 is dropped from CI

Library Updates:
- PTMA CG M3 model was added to the polyply library parameters are taken from [arXiv:2209.02072]
- A library table, i.e., list of models available in the polyply library was added to the README and LIBRARY.md file
- Carbohydrate parameters for Dextran were updated to the final released version, which for the time being disables branched Dextran.
- Cellulose parameters were added to polyply according to the latest parameter definitions https://pubs.acs.org/doi/10.1021/acs.jctc.2c00757

Bug Fixes:
- when reading the topology dihedral directives, where a single dihedral type in the itp file is matched to multiple definitions in the force-field file is now done correctly (i.e. all matches are generated).

Improvements
- Defining a name and output path for gen_params are now optional. By default the name polymer is given with the file called polymer.itp in the current working directory

**Full Changelog**: https://github.com/marrink-lab/polyply_1.0/compare/v1.4.0...v1.4.1

Library Updates:
- None

Bug Fixes:
- edges for constraints and angles were not created correctly in gen_coords; now only constraints create edges 243 242
- previously two itp files could not be directly connected with gen_params even if the residue graph was correctly supplied; this has been fixed allowing stitching together itp files arbitrarily 247
- links that affect bonded interactions within a residue were ignored; now they are taken into account 250

Improvements
- volumes used in the one-bead per residue random-walk can now be defined through an entry in the build_file 237 241
- templates for back mapping the one-bead per residue random-walk can now be defined through an entry in the build_file 235 236
- input argument of the top-level programs gen_coords, gen_params, gen_seq are exposed which makes them callable from within python scripts 42 229

Other Changes
- Create CONTRIBUTING.md 262
- Create issue templates 263 268