zincware / ZnH5MD / 9952591135

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ZnH5MD v0.3 (#93)

* znh5md v0.3 redesign draft

* momenta

* forces

* add inline TODOs

* support observables

* first version of extend

* append / extend to existing dataset

* append testing

* test more datasets

* bugfix arrays, info, calc shape

* support changes in pbc

* the simplest dataset

* fix numpy pow and add mda tests

* test against MDAnalysis

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* update CI setup

* remove `calc data`

* fix momenta / velocities confusion

* a bit more testing

* bugfix energy shape

* add coverage to test deps

* update Readme

* fix `particle_group`

* add `particle_group` to README

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* set lower bound to Python 3.10

* first pre-release

* update README

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* inherit from `MutableSequence` and raise NotImplementedErrors

* code review

* code review

* update read, iread, write

* make linter pass

* test against pyh5md reference

* account for box in reference code testing

* typos

* check external file handle

* fix PBC bug

* add benchmark script

* exclude all ipynb files

* shorten line

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* update benchmark script

* move method to utils

* acces H5MD info

* remove in-code TODOs

* Update io.py

* bugfix "velocity" which is not stored in ASE

* ASE `calc.results` fix (#95)

* rename `info / arrays` to `observables/particles`

* do not handle position special case

* clean up velocities / positions

* clean up atomic_numbers

* clean up atomic_numbers, positions, velocities

* introduce "ASE_CALCULATOR_RESULT"

* tes... (continued)

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