Matchmaps

Important changes

* `matchmaps` now supports both `phenix 1.20` (and earlier, though I'm not sure how far back it goes) and the new `phenix 1.21` syntax. `matchmaps` will attempt to automatically detect the user's phenix version based on the output from `phenix.version`, but the user can override this if it is wrong for some reason (e.g. multiple phenixes are present or something).
* Previously, when `CCP4` or `phenix` subprocesses failed, and the program was not being run in verbose mode, these failures were totally silent to the user. The failure then manifested as an unhelpful `FileNotFoundError`. Now, the user is specifically informed of which subprocess has failed, and is instructed to use verbose mode for more information.

Abbreviated Changelog
* Add support for phenix 1.21 by dennisbrookner in https://github.com/rs-station/matchmaps/pull/53
* Refactor argument parsers to avoid duplication by dennisbrookner in https://github.com/rs-station/matchmaps/pull/55
* clarify that phenix 1.21 is supported by dennisbrookner in https://github.com/rs-station/matchmaps/pull/56
* Helpful error detection from sub-processes by dennisbrookner in https://github.com/rs-station/matchmaps/pull/58


**Full Changelog**: https://github.com/rs-station/matchmaps/compare/v0.6.4...v0.6.5

What's Changed

* Drop support for python 3.8 by dennisbrookner in https://github.com/rs-station/matchmaps/pull/52

Documentation changes
* Add troubleshooting / advanced usage page to website by dennisbrookner in https://github.com/rs-station/matchmaps/pull/49
* link to paper rather than preprint by dennisbrookner in https://github.com/rs-station/matchmaps/pull/50

**Full Changelog**: https://github.com/rs-station/matchmaps/compare/v0.6.3...v0.6.4

What's Changed
* ci(dependabot): bump styfle/cancel-workflow-action from 0.12.0 to 0.12.1 by dependabot in https://github.com/rs-station/matchmaps/pull/40
* Expanding the "about the algorithm" page by dennisbrookner in https://github.com/rs-station/matchmaps/pull/41
* ci(dependabot): bump codecov/codecov-action from 3 to 4 by dependabot in https://github.com/rs-station/matchmaps/pull/42
* Suppress error where scaleit fails on non-isomorphous inputs by dennisbrookner in https://github.com/rs-station/matchmaps/pull/44
* ci(dependabot): bump softprops/action-gh-release from 1 to 2 by dependabot in https://github.com/rs-station/matchmaps/pull/45
* Make explicit that phenix 1.21 is not currently supported by dennisbrookner in https://github.com/rs-station/matchmaps/pull/47
* bump rs-booster dependency to version 0.1.2 by dennisbrookner in https://github.com/rs-station/matchmaps/pull/48


**Full Changelog**: https://github.com/rs-station/matchmaps/compare/v0.6.2...v0.6.3

This version adds support for error-weighting to `matchmaps` and `matchmaps.mr`. Various bug fixes are also included and are described below.

What's Changed
* Fix bug: unmasked_radius was parsed but ignored by dennisbrookner in https://github.com/rs-station/matchmaps/pull/34
* fast-forward `weights` branch with bug fix from `main` by dennisbrookner in https://github.com/rs-station/matchmaps/pull/35
* Weights by dennisbrookner in https://github.com/rs-station/matchmaps/pull/36
* ci(dependabot): bump actions/setup-python from 4 to 5 by dependabot in https://github.com/rs-station/matchmaps/pull/33
* Create new visualization.md page by dennisbrookner in https://github.com/rs-station/matchmaps/pull/37
* Fix crash when `--input-dir` and `--output-dir` match by dennisbrookner in https://github.com/rs-station/matchmaps/pull/39


**Full Changelog**: https://github.com/rs-station/matchmaps/compare/v0.6.1...v0.6.2

This PR doesn't include any material change to the outputs of matchmaps. The inclusion of FoFc coefficients in phenix outputs is purely for comparative analysis and does not affect the matchmaps difference map. Changes in map normalization lead to changes in contour levels, but not in the appearance of maps themselves when viewed at appropriate contour.

What's Changed
* Phenix outputs include FoFc map coefficients by dennisbrookner in https://github.com/rs-station/matchmaps/pull/30
* Implement proper map normalization by dennisbrookner in https://github.com/rs-station/matchmaps/pull/31


**Full Changelog**: https://github.com/rs-station/matchmaps/compare/v0.6.0...v0.6.1

Changes to solvent-region behavior

This release includes two PRs, 27 and 28 , which enhance the ability of `matchmaps` to show difference density far away from the protein model.

27 adds an `--unmasked-radius` parameter which changes the behavior of the `XXX_unmasked.map` output difference map. This map now incudes voxels up to `--unmasked-radius` Angstroms away from the protein model. **The default radius for the unmasked difference map was also increased from 3 A to 5 A; this is a semi-breaking change.** If you would like your unmasked map to look the same as it did in `matchmaps < 0.6`, set `--unmasked-radius 3`. The regular, "masked" difference map continues to be masked at 2 A away from the protein model. This PR does not introduce the ability to change this.

28 introduces the `--no-bss` flag, which allows the user to turn off bulk-solvent scaling in `phenix.refine`. For reverse compatibility, the default (no flag) continues to be that bulk-solvent scaling **is** included. This flag takes no argument, so simply add the flag to turn off BSS. The rationale for this feature is that signal for an unmodeled ligand or protein conformation may be altered by bulk-solvent scaling when this unmodeled signal lies in the solvent region. Turning off BSS can be thought of as a sort of "lazy polder map."

Two other minor changes described below:
- Reflection files may now be supplies using `.cif` files as an alternative to `.mtz` files. This makes `matchmaps` fully compatible with both mmCIF and sfCIF file types.
- `matchmaps` now writes out a shell script which can be used to re-run the same command (and of course, which can also be edited to run a slightly different command). This file is called `run_matchmaps.sh` by default; this name can be changed via the new `--script` flag. The script is written out to the ***current working directory*** to ensure compatibility with the input and output paths provided.

Auto-generated summary of changes
* ci(dependabot): bump actions/checkout from 3 to 4 by dependabot in https://github.com/rs-station/matchmaps/pull/22
* ci(dependabot): bump styfle/cancel-workflow-action from 0.11.0 to 0.12.0 by dependabot in https://github.com/rs-station/matchmaps/pull/25
* Support sfCIF files as alternatives to MTZs by dennisbrookner in https://github.com/rs-station/matchmaps/pull/26
* Add `--unmasked-radius` parameter to change the behavior of the unmasked difference map by dennisbrookner in https://github.com/rs-station/matchmaps/pull/27
* Add `--no-bss` flag to optionally turn off bulk-solvent scaling in phenix.refine by dennisbrookner in https://github.com/rs-station/matchmaps/pull/28
* Write out `.sh` file for reproducing command by dennisbrookner in https://github.com/rs-station/matchmaps/pull/29

New Contributors
* dependabot made their first contribution in https://github.com/rs-station/matchmaps/pull/22

**Full Changelog**: https://github.com/rs-station/matchmaps/compare/v0.5.0...v0.6.0