Switch dxtbx to unified dependency system

[ndevenish]

This is an attempt to consolidate the requirements for specifying dxtbx dependencies for development, testing, conda-forge, mac, linux, windows, prebuilt-cctbx and bootstrap. It is intended to encompass DIALS also, but dxtbx being handled is a prerequisite for updating DIALS, and using just for CI here seemed like a reasonable stepping point.

All dependencies are declared in a single dependencies.yaml in the dxtbx root. They are now split up into categories matching the conda-build definitions:

• build is for build tooling only required when you build the packages (the user would not install these)
• host is.. slightly harder to pin down. It's effectively the binary packages that you need present at build time, to e.g. link against.
• run is any dependencies only required to actually run dxtbx, separate from building it
• test is any dependencies used for running tests (e.g. dials-data, pytest...)

Platform/target selection of dependencies is handled with selectors. This is a very small subset of the concept used by conda-build. Effectively, you can mark lines as only included when a condition is met. For example:

  - pycbf #[prebuilt_cctbx]
  - scipy
  - wxpython >=4.2.0 #[not osx]
  - wxpython >=4.2.0=*_5 #[osx]
  - pytest
  - pytest-nunit # [win]

• pycbf will only be included when using prebuilt (e.g. from conda-forge) cctbx. scipy and pytest will always be included, wxpython will have different constraints depending on whether you are running on macOS or not, and pytest-nunit will only be included on windows.

Valid selector combinations are currently specified in the header of dependencies.yaml.

The driver for this is continually having to update dependencies in several places whenever something needs to be changed. As well as separate dependency lists for mac, linux and windows, we have some custom heuristics for removing unnecessary packages from release bundles, we have the dependencies entirely separately specified as part of the conda-forge package, and it's otherwise pretty difficult to work out what is needed for build vs runtime (which lets us deliberately include less in the bundles).

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Although this is a somewhat complex change, it isn't really adding complexity that isn't present across the system anyway.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 41.54%. Comparing base (38c95db) to head (64d11d9).
Report is 4 commits behind head on main.

Additional details and impacted files

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