Clean up prior to 3.0.0

[khaeru]

• Packaging is modernized (same as Modernize packaging ixmp#319, Weird behavior - automatic sets generation ixmp#326).
• Lint code further to satisfy flake8.
• Avoid use of deprecated f"{foo!r}" (same as Replace f'{foo!r}' with f'{foo}'/repr(foo) ixmp#293).
• Simplify the Sphinx configuration file, in line with the basic version produced by current sphinx-quickstart.
• Add disclaimer for unresolved issues with MACRO.
• Add graphviz to installation instructions (h/t @OFR-IIASA @francescolovat)
• Mention GAMS 30 free license issues; suggest GAMS 29 in installation instructions (h/t @OFR-IIASA @francescolovat)
• Add plotnine to tutorial requirements Update installation instructions to explicitly include [tutorials] extra target, which already included plotnine (h/t @OFR-IIASA)
• Update pyam requirement to >= 0.6 (h/t @OFR-IIASA @danielhuppmann).
  • This in turn depends on that release being on conda-forge, which in turn depends on Package for conda-forge IAMconsortium/units#22 / Add recipe for iam-units conda-forge/staged-recipes#11824.
• Update ixmp requirement to >= 3.0.0 (h/t @OFR-IIASA)
• Move MESSAGE_master.{gms,prj} to desired location and add instructions on using git update-index --assume-unchanged to install from source docs (h/t @OFR-IIASA; also closes Issue locating MESSAGE_master.gms file #346)
• conda-forge still lacks JPype1 0.7.5: https://anaconda.org/conda-forge/jpype1; mention in the install instructions how to install using pip.
  • Resolved; @khaeru opened Bump version to v0.7.5 conda-forge/jpype1-feedstock#20 Bump version to v0.7.5 conda-forge/jpype1-feedstock#21, which was merged.

How to review

• Note that the CI checks all pass.

PR checklist

• Tests added. N/A
• Documentation added.
• Release notes updated.

[khaeru]

• conda-forge still lacks JPype1 0.7.5: https://anaconda.org/conda-forge/jpype1; mention in the install instructions how to install using pip.

Since I had to deal with conda packaging today for IAMconsortium/units#22, I took a stab at putting together conda-forge/jpype1-feedstock#20. Hopefully the maintainers accept it promptly; this would let us avoid adding this extra step to our install instructions.

[khaeru]

I took a stab at putting together conda-forge/jpype1-feedstock#20. Hopefully the maintainers accept it promptly…

Ended up reopening that as conda-forge/jpype1-feedstock#21, which was merged.

[khaeru]

All green!