0.1.2 roadmap

[gfudenberg]

• [ ] rename branch master → main

• [x] add get_requirements to setup.py, move install instructions to readme

• [ ] change functions with camelCase → snake_case (note: seems many of these are from the pyx)

• [x] remove random things (e.g. Untitled.ipynb)

• [ ] finalize decision on ./cli/ (delete?)

• [x] create ./polychrom/visualization/

  • [x] migrate ./polychrom/pymol_show.py into this
  • [x] move ./utilities/ into this and installpymol.sh
  • [ ] longer term see below

• [x] delete simulation.show(), delete & deprecate rasol-dependent code in general

• [ ] legacy: clean up and rename into ./experimental/ namespace

• [ ] migrate 1D extrusion code out of library

  • [ ] keep the milker, in new ./polychrom/scheduler.py that can update bonds. Try to remain agnostic to how bond is generated & generalize the function.
  • [ ] Clarify that the scope of polychrom is doing polymer simulations, including those that can have non-equilibrium update rules (in readme/docs).

• [ ] extend examples

  • [ ] fix example.ipynb, currently breaks due to chain format (maybe default to CPU as well)
  • [ ] new notebooks using the polymer_analyses functions
  • [ ] extrusion 1D+3D example that relies on migrated extrusion scripts
  • [ ] add yeast interphase model to examples
  • [ ] replace storage_formats example with an ipynb that explains how to access & process saved data

• [x] rename hdf5_format.py module to storage.py

  • [ ] update examples etc to reflect this change (tests currently pass though)

• [x] refactor polymerutils: rotation matrix joins polymer_analyses, everything else to storage.py

further future:

• [ ] discuss where to put ndarray_groupby_aggregate/streaming_ndarray_agg
• [ ] develop visualization for polychrom, potentially based off of nglutils
• [ ] extend scheduler to manage non-bonded forces

[gfudenberg]

Qs:

• should we remove simulation.show?
• should we consider deprecating rasmol generally?
• should the try statement be removed & _polymer_math be assumed to work in polymer_analyses? https://github.com/gfudenberg/polychrom/blob/bdbd0687227ed7cbbf2fa2c088a5aeb0289da194/polychrom/polymer_analyses.py#L46

[mimakaev]

Yes on removing simulation.show and deprecating rasmol.

No about the try statement so far: it is for sphynx & readthedocs. Sphynx doesn't compile the module and imports it "as is" - which is why polymer math isn't there. There probably is a more graceful solution for this... but dealing with Sphynx always feels like some hardcore archeology... and I'm not ready.