Output YAML for the Graph __str__.

[grahamgower]

Closes #235.
Closes #291.

Sample output:

$ python
Python 3.9.3 (default, Apr  8 2021, 23:35:02)
[GCC 10.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import demes
>>> demes.load("examples/gutenkunst_ooa.yml")
description: The Gutenkunst et al. (2009) OOA model.
time_units: years
generation_time: 25
doi: ['https://doi.org/10.1371/journal.pgen.1000695']
demes:
- name: ancestral
  description: Equilibrium/root population
  epochs:
  - {end_time: 220000.0, start_size: 7300}
- name: AMH
  description: Anatomically modern humans
  ancestors: [ancestral]
  epochs:
  - {end_time: 140000.0, start_size: 12300}
- name: OOA
  description: Bottleneck out-of-Africa population
  ancestors: [AMH]
  epochs:
  - {end_time: 21200.0, start_size: 2100}
- name: YRI
  description: Yoruba in Ibadan, Nigeria
  ancestors: [AMH]
  epochs:
  - {end_time: 0, start_size: 12300}
- name: CEU
  description: Utah Residents (CEPH) with Northern and Western European Ancestry
  ancestors: [OOA]
  epochs:
  - {end_time: 0, start_size: 1000, end_size: 29725}
- name: CHB
  description: Han Chinese in Beijing, China
  ancestors: [OOA]
  epochs:
  - {end_time: 0, start_size: 510, end_size: 54090}
migrations:
- demes: [YRI, CEU]
  rate: 3e-05
- demes: [YRI, CHB]
  rate: 1.9e-05
- demes: [CEU, CHB]
  rate: 9.6e-05
- {source: YRI, dest: OOA, rate: 0.00025}
- {source: OOA, dest: YRI, end_time: 21200.0, rate: 0.00025}

[codecov]

Codecov Report

Merging #293 (3b12f32) into main (5620c5c) will increase coverage by 0.00%.
The diff coverage is 100.00%.

@@           Coverage Diff           @@
##             main     #293   +/-   ##
=======================================
  Coverage   98.14%   98.14%           
=======================================
  Files           7        7           
  Lines        1401     1403    +2     
=======================================
+ Hits         1375     1377    +2     
  Misses         26       26           

Impacted Files	Coverage Δ
demes/demes.py	100.00% <100.00%> (ø)
demes/load_dump.py	100.00% <100.00%> (ø)

---

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[jeromekelleher]

Looks great, but this should be the __str__ not the __repr__. str is for humans and repr is the concise machine readable version.

[grahamgower]

Thanks @jeromekelleher. You're right, of course. I'll take this as a reminder to always look up the docs for __repr__ and __str__ whenever I use them. :)

The output is now:

$ python
Python 3.9.3 (default, Apr  8 2021, 23:35:02)
[GCC 10.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import demes
>>> g = demes.load("examples/gutenkunst_ooa.yml")
>>> g
Graph(description='The Gutenkunst et al. (2009) OOA model.', time_units='years', generation_time=25, doi=['https://doi.org/10.1371/journal.pgen.1000695'], demes=[Deme(name='ancestral', description='Equilibrium/root population', start_time=inf, ancestors=[], proportions=[], epochs=[Epoch(start_time=inf, end_time=220000.0, start_size=7300, end_size=7300, size_function='constant', selfing_rate=0, cloning_rate=0)]), Deme(name='AMH', description='Anatomically modern humans', start_time=220000.0, ancestors=['ancestral'], proportions=[1.0], epochs=[Epoch(start_time=220000.0, end_time=140000.0, start_size=12300, end_size=12300, size_function='constant', selfing_rate=0, cloning_rate=0)]), Deme(name='OOA', description='Bottleneck out-of-Africa population', start_time=140000.0, ancestors=['AMH'], proportions=[1.0], epochs=[Epoch(start_time=140000.0, end_time=21200.0, start_size=2100, end_size=2100, size_function='constant', selfing_rate=0, cloning_rate=0)]), Deme(name='YRI', description='Yoruba in Ibadan, Nigeria', start_time=140000.0, ancestors=['AMH'], proportions=[1.0], epochs=[Epoch(start_time=140000.0, end_time=0, start_size=12300, end_size=12300, size_function='constant', selfing_rate=0, cloning_rate=0)]), Deme(name='CEU', description='Utah Residents (CEPH) with Northern and Western European Ancestry', start_time=21200.0, ancestors=['OOA'], proportions=[1.0], epochs=[Epoch(start_time=21200.0, end_time=0, start_size=1000, end_size=29725, size_function='exponential', selfing_rate=0, cloning_rate=0)]), Deme(name='CHB', description='Han Chinese in Beijing, China', start_time=21200.0, ancestors=['OOA'], proportions=[1.0], epochs=[Epoch(start_time=21200.0, end_time=0, start_size=510, end_size=54090, size_function='exponential', selfing_rate=0, cloning_rate=0)])], migrations=[AsymmetricMigration(source='YRI', dest='OOA', start_time=140000.0, end_time=21200.0, rate=0.00025), AsymmetricMigration(source='OOA', dest='YRI', start_time=140000.0, end_time=21200.0, rate=0.00025), AsymmetricMigration(source='YRI', dest='CEU', start_time=21200.0, end_time=0, rate=3e-05), AsymmetricMigration(source='CEU', dest='YRI', start_time=21200.0, end_time=0, rate=3e-05), AsymmetricMigration(source='YRI', dest='CHB', start_time=21200.0, end_time=0, rate=1.9e-05), AsymmetricMigration(source='CHB', dest='YRI', start_time=21200.0, end_time=0, rate=1.9e-05), AsymmetricMigration(source='CEU', dest='CHB', start_time=21200.0, end_time=0, rate=9.6e-05), AsymmetricMigration(source='CHB', dest='CEU', start_time=21200.0, end_time=0, rate=9.6e-05)], pulses=[])

>>> print(g)
description: The Gutenkunst et al. (2009) OOA model.
time_units: years
generation_time: 25
doi: ['https://doi.org/10.1371/journal.pgen.1000695']
demes:
- name: ancestral
  description: Equilibrium/root population
  epochs:
  - {end_time: 220000.0, start_size: 7300}
- name: AMH
  description: Anatomically modern humans
  ancestors: [ancestral]
  epochs:
  - {end_time: 140000.0, start_size: 12300}
- name: OOA
  description: Bottleneck out-of-Africa population
  ancestors: [AMH]
  epochs:
  - {end_time: 21200.0, start_size: 2100}
- name: YRI
  description: Yoruba in Ibadan, Nigeria
  ancestors: [AMH]
  epochs:
  - {end_time: 0, start_size: 12300}
- name: CEU
  description: Utah Residents (CEPH) with Northern and Western European Ancestry
  ancestors: [OOA]
  epochs:
  - {end_time: 0, start_size: 1000, end_size: 29725}
- name: CHB
  description: Han Chinese in Beijing, China
  ancestors: [OOA]
  epochs:
  - {end_time: 0, start_size: 510, end_size: 54090}
migrations:
- demes: [YRI, CEU]
  rate: 3e-05
- demes: [YRI, CHB]
  rate: 1.9e-05
- demes: [CEU, CHB]
  rate: 9.6e-05
- {source: YRI, dest: OOA, rate: 0.00025}
- {source: OOA, dest: YRI, end_time: 21200.0, rate: 0.00025}

[jeromekelleher]

Beautiful!