diff --git a/doc/_config.yml b/doc/_config.yml index 071b29f4e..2e96ab6c2 100644 --- a/doc/_config.yml +++ b/doc/_config.yml @@ -9,6 +9,7 @@ author: Kevin Thornton # See https://jupyterbook.org/content/execute.html execute: execute_notebooks: force + stderr_output: error # Add a bibtex file so that we can create citations bibtex_bibfiles: diff --git a/doc/long_vignettes/gss_vignette.md b/doc/long_vignettes/gss_vignette.md index 77c4f352d..bd0c3bb82 100644 --- a/doc/long_vignettes/gss_vignette.md +++ b/doc/long_vignettes/gss_vignette.md @@ -68,12 +68,12 @@ p = { "rates": (0.0, 1e-3, None), # Keep mutations at frequency 1 in the pop if they affect fitness. "prune_selected": False, - "demography": None, + "demography": fwdpy11.ForwardDemesGraph.tubes([pop.N], burnin=10*pop.N, burnin_is_exact=True), "simlen": 10 * pop.N, } params = fwdpy11.ModelParams(**p) -r = Recorder(start=10 * pop.N) +r = Recorder(start=10 * pop.N - 200) fwdpy11.evolvets(rng, pop, params, 100, recorder=r, suppress_table_indexing=True) ``` diff --git a/doc/long_vignettes/pyfreqtracker.md b/doc/long_vignettes/pyfreqtracker.md index a1101f772..de1c2423f 100644 --- a/doc/long_vignettes/pyfreqtracker.md +++ b/doc/long_vignettes/pyfreqtracker.md @@ -71,6 +71,7 @@ pdict = { "sregions": [fwdpy11.ExpS(beg=0, end=1, weight=1, mean=0.2)], "recregions": [fwdpy11.PoissonInterval(0, 1, 1e-2)], "gvalue": [fwdpy11.Multiplicative(2.0)], + "demography": fwdpy11.ForwardDemesGraph.tubes([100], burnin=100, burnin_is_exact=True), "rates": (0.0, 1e-3, None), "simlen": 100, } @@ -190,6 +191,7 @@ pdict = { "sregions": [fwdpy11.ExpS(beg=0, end=1, weight=1, mean=0.2)], "recregions": [fwdpy11.PoissonInterval(0, 1, 1e-2)], "gvalue": [fwdpy11.Multiplicative(2.0)], + "demography": fwdpy11.ForwardDemesGraph.tubes([100], burnin=100, burnin_is_exact=True), # Add a mutation rate for neutral mutations: "rates": (5e-3, 1e-3, None), "simlen": 100, diff --git a/doc/long_vignettes/pyfreqtracker_sqlite.md b/doc/long_vignettes/pyfreqtracker_sqlite.md index 5b0ac72c4..c439c4757 100644 --- a/doc/long_vignettes/pyfreqtracker_sqlite.md +++ b/doc/long_vignettes/pyfreqtracker_sqlite.md @@ -324,6 +324,7 @@ pdict = { "sregions": [fwdpy11.ExpS(beg=0, end=1, weight=1, mean=0.2)], "recregions": [fwdpy11.PoissonInterval(0, 1, 1e-2)], "gvalue": [fwdpy11.Multiplicative(2.0)], + "demography": fwdpy11.ForwardDemesGraph.tubes([100], burnin=100, burnin_is_exact=True), # Add a mutation rate for neutral mutations: "rates": (5e-3, 1e-3, None), "simlen": 100, diff --git a/doc/pages/advancedtopics.md b/doc/pages/advancedtopics.md index 950785f99..c02ee5b30 100644 --- a/doc/pages/advancedtopics.md +++ b/doc/pages/advancedtopics.md @@ -129,6 +129,7 @@ pdict = { "rates": (0.0, 1e-3, None), "gvalue": gvalue, "prune_selected": False, + "demography": fwdpy11.ForwardDemesGraph.tubes([N], burnin=150, burnin_is_exact=True), "simlen": 150, } params = fwdpy11.ModelParams(**pdict) diff --git a/doc/short_vignettes/evolvets_vignette.md b/doc/short_vignettes/evolvets_vignette.md index bb07c6985..db31b4a6c 100644 --- a/doc/short_vignettes/evolvets_vignette.md +++ b/doc/short_vignettes/evolvets_vignette.md @@ -54,7 +54,7 @@ p = { "recregions": [fwdpy11.PoissonInterval(0, 1., rho / float(4 * pop.N))], "rates": (0.0, 1e-3, None), "prune_selected": False, - "demography": None, + "demography": fwdpy11.ForwardDemesGraph.tubes([pop.N], burnin=10), "simlen": 10 * pop.N, } params = fwdpy11.ModelParams(**p) diff --git a/doc/short_vignettes/mutationdominance_vignette.md b/doc/short_vignettes/mutationdominance_vignette.md index 76cbe3ecf..cefad7de0 100644 --- a/doc/short_vignettes/mutationdominance_vignette.md +++ b/doc/short_vignettes/mutationdominance_vignette.md @@ -64,7 +64,7 @@ p = { "recregions": [fwdpy11.PoissonInterval(0, 1., rho / float(4 * pop.N))], "rates": (0.0, 1e-3, None), "prune_selected": False, - "demography": None, + "demography": fwdpy11.ForwardDemesGraph.tubes([pop.N], burnin=10), "simlen": 10 * pop.N, } params = fwdpy11.ModelParams(**p) diff --git a/doc/short_vignettes/neutralmutsafter_vignette.md b/doc/short_vignettes/neutralmutsafter_vignette.md index 6735cd6df..e411fa0dd 100644 --- a/doc/short_vignettes/neutralmutsafter_vignette.md +++ b/doc/short_vignettes/neutralmutsafter_vignette.md @@ -42,7 +42,7 @@ p = { "recregions": [fwdpy11.PoissonInterval(0, 1., rho / float(4 * pop.N))], "rates": (0.0, 1e-3, None), "prune_selected": False, - "demography": None, + "demography": fwdpy11.ForwardDemesGraph.tubes([pop.N], burnin=10), "simlen": 10 * pop.N, } params = fwdpy11.ModelParams(**p) diff --git a/doc/short_vignettes/poptour_vignette.md b/doc/short_vignettes/poptour_vignette.md index 00f890f72..4b7030113 100644 --- a/doc/short_vignettes/poptour_vignette.md +++ b/doc/short_vignettes/poptour_vignette.md @@ -46,7 +46,7 @@ p = { "recregions": [fwdpy11.PoissonInterval(0, 1., rho / float(4 * pop.N))], "rates": (0.0, 1e-3, None), "prune_selected": False, - "demography": None, + "demography": fwdpy11.ForwardDemesGraph.tubes([pop.N], burnin=10), "simlen": 10 * pop.N, } params = fwdpy11.ModelParams(**p) diff --git a/doc/short_vignettes/recapitation.md b/doc/short_vignettes/recapitation.md index 2cc6fd3f7..032ea6ac8 100644 --- a/doc/short_vignettes/recapitation.md +++ b/doc/short_vignettes/recapitation.md @@ -30,6 +30,7 @@ pop = fwdpy11.DiploidPopulation(100, 1000.0) pdict = {"rates": (0.0, 0.0, 0.0), "gvalue": fwdpy11.Multiplicative(2.), "simlen": 10, + "demography": fwdpy11.ForwardDemesGraph.tubes([100], burnin=10, burnin_is_exact=True), } params = fwdpy11.ModelParams(**pdict) rng = fwdpy11.GSLrng(54321) diff --git a/doc/short_vignettes/recorders_vignette.md b/doc/short_vignettes/recorders_vignette.md index bccab5212..c41584a3e 100644 --- a/doc/short_vignettes/recorders_vignette.md +++ b/doc/short_vignettes/recorders_vignette.md @@ -110,7 +110,7 @@ p = { "recregions": [fwdpy11.PoissonInterval(0, 1., rho / float(4 * pop.N))], "rates": (0.0, 1e-3, None), "prune_selected": False, - "demography": None, + "demography": fwdpy11.ForwardDemesGraph.tubes([pop.N], burnin=1), "simlen": pop.N, } params = fwdpy11.ModelParams(**p)