remove wrong statement

[petrelharp]

This statement in the docs was wrong

as demonstrated by:

tables = tskit.TableCollection(sequence_length=10)
tables.populations.add_row()
tables.nodes.add_row(time=0, flags=1, population=0)
tables.nodes.add_row(time=0, flags=1, population=0)
tables.nodes.add_row(time=0, flags=1, population=0)
tables.nodes.add_row(time=1, flags=0, population=0)
tables.edges.add_row(left=1, right=5, parent=3, child=1)
tables.edges.add_row(left=1, right=5, parent=3, child=2)

ts.tables.tree_sequence()
print(ts.draw_text())

# 1.00┊       ┊    3  ┊       ┊ 
#     ┊       ┊   ┏┻┓ ┊       ┊ 
# 0.00┊ 0 1 2 ┊ 0 1 2 ┊ 0 1 2 ┊ 
#     0       1       5      10 

mts = msprime.sim_ancestry(initial_state=ts, population_size=1, random_seed=123)
print(mts.draw_text())

# 3.71┊   5   ┊   5   ┊   5   ┊ 
#     ┊  ┏┻━┓ ┊ ┏━┻┓  ┊  ┏┻━┓ ┊ 
# 1.00┊  ┃  ┃ ┊ ┃  3  ┊  ┃  ┃ ┊ 
#     ┊  ┃  ┃ ┊ ┃ ┏┻┓ ┊  ┃  ┃ ┊ 
# 0.79┊  4  ┃ ┊ ┃ ┃ ┃ ┊  4  ┃ ┊ 
#     ┊ ┏┻┓ ┃ ┊ ┃ ┃ ┃ ┊ ┏┻┓ ┃ ┊ 
# 0.00┊ 0 2 1 ┊ 0 1 2 ┊ 0 2 1 ┊ 
#     0       1       5      10 

Note that sim_ancestry has created a node at t=0.79, before the age of the oldest root (which is at 1.0).

However, doing mts = msprime.sim_ancestry(initial_state=ts, population_size=1, start_time=1.0 would start the simulation off at 1.0. We could add something to the docs saying this, but it's kinda a can of worms - for instance, the bit on recapitation says that "you must have all the input roots"; you might think it's okay to just specify start_time instead, but that's not right because you miss the recombinations that have happened to those root branches.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 90.93%. Comparing base (90c8ce1) to head (ba62bd0).
Report is 2 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #2332   +/-   ##
=======================================
  Coverage   90.93%   90.93%           
=======================================
  Files          20       20           
  Lines       12018    12018           
  Branches     2316     2316           
=======================================
  Hits        10929    10929           
  Misses        602      602           
  Partials      487      487           

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python	98.70% <ø> (ø)

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[benjeffery]

@Mergifyio rebase

[mergify]

rebase

✅ Branch has been successfully rebased

[benjeffery]

@Mergifyio refresh

[mergify]

refresh

✅ Pull request refreshed

[benjeffery]

@Mergifyio rebase

[mergify]

rebase

☑️ Nothing to do

• queue-position = -1 [📌 rebase requirement]
• any of:
  • #commits > 1 [📌 rebase requirement]
  • #commits-behind > 0 [📌 rebase requirement]
  • -linear-history [📌 rebase requirement]
• -closed [📌 rebase requirement]
• -conflict [📌 rebase requirement]