Merge pull request #31 from popsim-consortium/petrelharp-patch-1

missing `import numpy as np` and other things

intro_stdpopsim_SMBE2024/Intro_stdpopsim.ipynb

@@ -370,6 +370,32 @@
     "ts = engine.simulate(model, contig, samples, slim_scaling_factor=100, seed=1)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "We're getting a lot of warnings. Don't ignore these!\n",
+    "At least, don't ignore them until you figure out why they are happening.\n",
+    "Some of these are because we're using approximations to make the simulations go extra fast;\n",
+    "the warnings are telling us that the approximations are approximate - so: beware!\n",
+    "If you're just using these for development (like us) then no worries.\n",
+    "But, if you use them for production, make sure to evaluate whether the approximations\n",
+    "are affecting your results!\n",
+    "\n",
+    "This will turn off these warnings below:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import warnings\n",
+    "warnings.simplefilter(\"ignore\", category=stdpopsim.SLiMScalingFactorWarning)\n",
+    "warnings.simplefilter(\"ignore\", category=stdpopsim.UnspecifiedSLiMWarning)"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -533,6 +559,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "import numpy as np\n",
     "contig = species.get_contig(\"chr6\", left=0, right=100000)\n",
     "# make the DFE apply to the entire contig \n",
     "contig.add_dfe(intervals=np.array([[0, int(contig.length)]]), DFE=dfe)\n",
@@ -667,7 +694,7 @@
     "samples =  #fill me!\n",
     "\n",
     "\n",
-    "contig = species.get_contig(\"\", length_multiplier=0.1) #fill me!\n",
+    "contig = species.get_contig(\"\", length_multiplier=0.001) #fill me!\n",
     "dfe = species.get_dfe(\"\") #fill me!\n",
     "exons = species.get_annotations(\"\") #fill me!\n",
     "exon_intervals = exons.get_chromosome_annotations(\"\") #fill me!\n",
@@ -1101,7 +1128,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "now we're ready to do PCA. we'll do the decomposition and then plot, note that allel requires a flattened version of the genotype array above that codes individual genotypes as 0/1/2 according to the number of reference alleles"
+    "now we're ready to do PCA. we'll do the decomposition and then plot, note that allel requires a flattened version of the genotype array above that codes individual genotypes as 0/1/2 according to the number of reference alleles\n",
+    "\n",
+    "note: if you get an error here, you may need to re-run the simulation and try again"
    ]
   },
   {
@@ -1148,6 +1177,8 @@
     "import stdpopsim\n",
     "from progressbar import ProgressBar #This is just to get a progress bar\n",
     "\n",
+    "import warnings\n",
+    "\n",
     "species = stdpopsim.get_species(\"HomSap\")\n",
     "model = species.get_demographic_model('OutOfAfrica_3G09')\n",
     "samples = {\"YRI\": 10, \"CHB\": 10, \"CEU\": 10}\n",
@@ -1164,7 +1195,11 @@
     "pi_list = []\n",
     "pbar = ProgressBar() #This is just to get a progress bar\n",
     "for i in pbar(range(n)):\n",
-    "    ts = engine.simulate(model, contig, samples, slim_scaling_factor=20, slim_burn_in=10)\n",
+    "    with warnings.catch_warnings():\n",
+    "        warnings.simplefilter(\"ignore\", category=stdpopsim.SLiMScalingFactorWarning)\n",
+    "        warnings.simplefilter(\"ignore\", category=stdpopsim.UnspecifiedSLiMWarning)\n",
+    "        warnings.simplefilter(\"ignore\", category=UserWarning)\n",
+    "        ts = engine.simulate(model, contig, samples, slim_scaling_factor=20, slim_burn_in=10)\n",
     "    sample_list = make_sample_list(ts)\n",
     "    pi_list.append(ts.diversity(sample_sets=sample_list))\n",
     "print('Done simulating {} replicates!'.format(n))\n",
@@ -1358,7 +1393,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.14"
+   "version": "3.12.4"
   }
  },
  "nbformat": 4,