Major feature release

Major feature release adding many new species and models, as well as support
for simulating selection via SLiM.

Bug fixes:

• Parameters in the HomSap/Zigzag_1S14 model now match those in Schiffels &
  Durbin (2014) (@grahamgower, #750).

• Recombination rate for DroMel chr4 changed to 0
  (@izabelcavassim, #1092).

• Per-chromosome mean recombination rates for HomSap were incorrectly
  calculated (@nspope, #1345).

Breaking changes:

• Removed GeneticMap class from public API (@jeromekelleher, #713).

• Samples are now specified via population/individual pairs, using
  species/chromosome ploidy. The old API for specifying haploid samples via
  population index has been retained, but is deprecated and will be
  removed at some point (@nspope, #1361).

New species:

• Aedes aegypti (@manolofperez, #871).
  QC'd by @petrelharp, #893.

• Anas platyrhynchos (@petrelharp, #826).
  QC'd by @igronau, #1070.

• Anolis carolinensis (@Vcaudill, #874).
  QC'd by @andrewkern, #896.

• Anopheles gambiae (@andrewkern, #856).
  QC'd by @petrelharp, #906.

• Apis mellifera (@janaobsteter, #1025).
  QC'd by @manolofperez, #1268.

• Bos taurus (@grahamgower, #600).
  QC'd by @gtsambos, #1269.

• Caenorhabditis elegans (@attrna, #910).
  QC'd by @chriscrsmith, #1265.

• Chlamydomonas reinhardtii (@aays, #863).
  QC'd by @izabelcavassim, #1067.

• Drosophila sechellia (@jradrion, #872).
  QC'd by @vitorpavinato, #1264.

• Gasterosteus aculeatus (@vitorpavinato, #1105).
  QC'd by @manolofperez, #1253.

• Helianthus annuus (@chriscrsmith, #1218).
  QC'd by @xin-huang, #1250.

• Heliconius melpomene (@percyfal, #870).
  QC'd by @noscode, #1165.

• Pan troglodytes (@xin-huang, #1215).
  QC'd by @janaobsteter, #1291.

• Papio anubis (@saurabhbelsare, #1216).
  QC'd by @mufernando, #1263.

• Streptococcus agalactiae (@jeanrjc, #854).
  QC'd by @vitorpavinato, #1251.

New models:

• AnaPla/MallardBlackDuck_2L19 (@petrelharp, #883).
  QC'd by @igronau, #1021.

• AnoGam/GabonAg1000G_1A17 (@andrewkern, #856).
  QC'd by @petrelharp, #1279.

• BosTau/HolsteinFriesian_1M13 (@grahamgower, #600).
  QC'd by @igronau, #1272.

• HomSap/OutOfAfricaExtendedNeandertalAdmixturePulse_3I21
  (@leonardolasi, #1066).
  QC'd by @awohns, #1259.

• HomSap/OutOfAfrica_4J17 (@rwaples, #726).
  QC'd by @jeffspence, #1246.

• HomSap/Africa_1B08 (@izabelcavassim, #993).
  QC'd by @petrelharp, #995.

• HomSap/AncientEurope_4A21 (@AliPearson, #941).
  QC'd by @mufernando, #1256.

• PanTro/BonoboGhost_4K19 (@xin-huang, #1215).
  QC'd by @kuhlwilm, #1370.

• PapAnu/SinglePopSMCpp_1W22 (@saurabhbelsare, #1216).
  QC'd by @attrna, #1261.

New genetic maps:

• CaeEle/RockmanRIAIL_ce11 (@attrna, #910).

• DroMel/ComeronCrossoverV2_dm6 liftover (@grahamgower, #592).

• HomSap/HapMapII_GRCh38 liftover (@saurabhbelsare, #1301).

• HomSap/DeCodeSexAveraged_GRCh38 liftover (@saurabhbelsare, #1301).

• HomSap/PyrhoXXX_GRCh38 (@jeffspence, #572` and #575),
  for XXX in ACB, ASW, BEB, CDX, CEU, CHB, CHS, CLM, ESN, FIN, GBR, GIH, GWD,
  IBS, ITU, JPT, KHV, LWK, MSL, MXL, PEL, PJL, PUR, STU, TSI, and YRI.

• PapAnu/Pyrho_PAnubis1_0 (@saurabhbelsare, #1216)

New features:

• Distributions of fitness effects ("DFEs") defined over genomic intervals
  (@mufernando, #644; @izabelcavassim, #1002;
  plus numerous others).

• DFE simulation via SLiM
  (@mufernando, #930; plus numerous others).

• Metadata for tree sequences produced by SLiM
  (@mufernando, #1152).

• Per-generation fitness statistics for SLiM simulations
  (@petrelharp, #1200).

• Selective sweep simulation and allele frequency conditioning via SLiM
  (@grahamgower, #462; @nspope, #1341).

• Gene conversion simulation via msprime and SLiM
  (@fbaumdicker, #1106; @petrelharp, #1355).

• Genome annotation tracks
  (@andrewkern, #560` and #960).

• Masking intervals in simulated data
  (@apragsdale, #664).

• Method to get generic contig of arbitrary length for a species
  (@apragsdale, #664).

• Method to get contig from a segment of a named chromosome
  (@nspope, #1348).

• Pass keyworded arguments from simulation engine to msprime
  (@awohns, #736).

• Use msprime 1.0 for simulation from msprime engine
  (@jeromekelleher, #764).

• Use SLiM 4.0 for simulation from SLiM engine
  (@petrelharp, #1326).

• Mutation rates can be stored in catalog models
  (@apragsdale, #839).

• Ploidy is a species and chromosome attribute
  (@nspope, #1361).

• Mutations from SLiM simulations converted to nucleotides
  (@nspope, #1356).

• Various improvements and fixes to the documentation and error messaging.

Additions to CLI:

• Sample specification has switched from positional and haploid (e.g. stdpopsim HomSap -d OutOfAfrica_3G09 6 0 10) to named with species-specific ploidy (equivalent to stdpopsim HomSap -d OutOfAfrica_3G09 YRI:3 CEU:0 CHB:5). Positional sample specification is still supported but will raise a deprecation warning.

• Arguments --dfe, --dfe-interval, --dfe-bed-file, --help-dfe
  for specifying DFEs (@izabelcavassim, #1052).

• Arguments --help-annotations, --dfe-annotation for associating annotation
  tracks with DFEs (@andrewkern, #1117).

• Argument --length for simulating from a generic contig
  (@apragsdale, #664).

• Arguments --inclusion-mask, --exclusion-mask for masking simulated sequences
  (@apragsdale, #664).

• Arguments --left and --right for simulating an interval on a named chromosome
  (@nspope, #1348)

• Argument --keep-mutation-ids-as-alleles retains SLiM mutation IDs for
  allele codes instead of converting these to nucleotides (@nspope, #1356).

Catalog maintenance infrastructure:

• Quality control infrastructure for DFEs
  (@xin-huang, #1292).

• Pull species information from NCBI
  (@andrewkern, #875).

• Automated species addition to catalog
  (@jeromekelleher, #790).

• Github issue template for requesting addition of species
  (@petrelharp, #772).

• Tools for assembly liftover
  (@jradrion, #574).

• Pull genome data from Ensembl
  (@jeromekelleher, #563).

New annotations:

• AraTha/araport_11 (@andrewkern, #1327).

• DroMel/FlyBase_BDGP6.32.51 (@andrewkern, #1042).

• HomSap/ensembl_havana_104 (@andrewkern, #960).

New DFEs:

• DroMel/Gamma_H17 (@izabelcavassim, #1046).

• DroMel/LognormalPlusPositive_R16 (@apragsdale, #1178).

• HomSap/Gamma_K17 (@izabelcavassim, #1002).

• HomSap/Gamma_H17 (@chriscrsmith, #1099).