Remove deprecated API use from manual (#1233)

* Add stderr_output: error to doc/config.yml Closes #1231
molpopgen · Nov 11, 2023 · 078cd99 · 078cd99
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Showing 11 changed files with 13 additions and 7 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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)