update verification

.gitignore

@@ -95,4 +95,7 @@ tmp__NOBACKUP__
 .DS_Store
 
 # vscode stuff
-.vscode
+.vscode
+
+# verfification files
+verification/*

Makefile

@@ -27,6 +27,10 @@ clang-format:
 tags:
 	ctags -f TAGS msprime/*.c lib/*.[c,h] msprime/*.py tests/*.py algorithms.py
 
+verification:
+	pip install -e ".[verification]"
+	$(MAKE) -C data
+	python verification.py -t 4 -d verification
 
 clean:
 	rm -fR build

data/Makefile

@@ -1,4 +1,4 @@
-all: scrm ms msHOT slim seq-gen msms msprime-0.7.4
+all: scrm ms msHOT slim seq-gen msms msprime-0.7.4 discoal
 
 seq-gen:
 	rm -fR seq-gen Seq-Gen* 1.3.4.tar.gz
@@ -9,12 +9,12 @@ seq-gen:
 
 slim:
 	rm -fR SLiM*
-	wget https://github.com/MesserLab/SLiM/archive/refs/tags/v3.7.1.tar.gz
-	tar -zxvf v3.7.1.tar.gz 
-	mkdir SLiM-3.7.1/build
+	wget https://github.com/MesserLab/SLiM/archive/refs/tags/v5.1.tar.gz
+	tar -zxvf v5.1.tar.gz
+	mkdir SLiM-5.1/build
 	# Arbitrarily using 4 threads to build here..
-	cd SLiM-3.7.1/build && cmake .. && make -j 4
-	cp SLiM-3.7.1/build/slim ./
+	cd SLiM-5.1/build && cmake .. && make -j 4
+	cp SLiM-5.1/build/slim ./
 
 scrm:
 	wget https://github.com/scrm/scrm/releases/download/v1.7.2/scrm-src.tar.gz

docs/development.md

@@ -760,6 +760,15 @@ directory.
 Please read the comments at the top of the `verification.py` script for details
 on how to write and run these tests.
 
+The make rule `verification` bundles the three steps in one command: installs the dependencies, 
+compiles customised versions of `ms` (and other tools), and runs all the tests sequentially. 
+
+To invoke this rule run the command:
+```
+$ make verification
+```
+The output should be in the directory: `/verification`
+
 ## Benchmarking
 
 Benchmarks to measure performance are in the `benchmarks` folder and are run using

verification.py

@@ -141,7 +141,7 @@ def write_slim_script(outfile, format_dict):
         initializeRecombinationRate({RHO});
     }}
     // create a population
-    1
+    1 early()
     {{
         {POP_STRS};
         sim.tag = 0;
@@ -151,11 +151,11 @@ def write_slim_script(outfile, format_dict):
     {{
         if (sim.tag == 0) {{
             if (sim.treeSeqCoalesced()) {{
-                sim.tag = sim.generation;
+                sim.tag = sim.cycle;
                 catn(sim.tag + ': COALESCED');
             }}
         }}
-        if (sim.generation == sim.tag * 10) {{
+        if (sim.cycle == sim.tag * 10) {{
             sim.simulationFinished();
             catn('Ran a further ' + sim.tag * 10 + ' generations');
             sim.treeSeqOutput('{OUTFILE}');
@@ -185,7 +185,7 @@ def write_sweep_slim_script(outfile, format_dict):
                     sim.simulationFinished();
         }}
 
-        1 {{
+        1 early(){{
             // save this run's identifier, used to save and restore
             defineConstant("simID", getSeed());
             sim.addSubpop("p1", {POPSIZE});
@@ -195,7 +195,7 @@ def write_sweep_slim_script(outfile, format_dict):
         2 late() {{
             // save the state of the simulation
             sim.treeSeqOutput("/tmp/slim_" + simID + ".trees");
-            target = sample(p1.genomes, 1);
+            target = sample(p1.haplosomes, 1);
             target.addNewDrawnMutation(m2, {SWEEPPOS});
         }}
         2:2000 late() {{
@@ -208,15 +208,15 @@ def write_sweep_slim_script(outfile, format_dict):
                 if (fixed)
                 {{
                     if (sim.getValue("flag") == 1){{
-                        sim.rescheduleScriptBlock(s1,
-                        start=sim.generation+{TAU}, end=sim.generation+{TAU});
+                        community.rescheduleScriptBlock(s1,
+                        start=sim.cycle+{TAU}, end=sim.cycle+{TAU});
                     }}
                 }}
                 else
                 {{
                     sim.readFromPopulationFile("/tmp/slim_" + simID + ".trees");
                     setSeed(rdunif(1, 0, asInteger(2^62) - 1));
-                    target = sample(p1.genomes, 1);
+                    target = sample(p1.haplosomes, 1);
                     target.addNewDrawnMutation(m2, {SWEEPPOS});
                 }}
             }}
@@ -946,9 +946,9 @@ def sample_recap_simplify(slim_ts, sample_size, Ne, r, mu):
             demography=demography,
             recombination_rate=r,
             # TODO is this needed now? Shouldn't be, right?
-            start_time=slim_ts.metadata["SLiM"]["generation"],
+            start_time=slim_ts.metadata["SLiM"]["cycle"],
         )
-    logging.debug(f"pyslim: slim generation:{slim_ts.metadata['SLiM']['generation']}")
+    logging.debug(f"pyslim: slim generation:{slim_ts.metadata['SLiM']['cycle']}")
     alive_inds = pyslim.individuals_alive_at(recap, 0)
     keep_indivs = np.random.choice(alive_inds, sample_size, replace=False)
     keep_nodes = []
@@ -3823,7 +3823,9 @@ def test_gc_correlation_between_trees(self):
         seq_length = 500
         # tests both Hudson as well as SMC K
         # by setting hull_offset to seq_length are essentially simulating Hudson
-        models = ["hudson", msprime.SmcKApproxCoalescent(hull_offset=seq_length)]
+        # models = ["hudson", msprime.SmcKApproxCoalescent(hull_offset=seq_length)]
+        # GC for smck is currently not supported
+        models = ["hudson"]
         predicted_prob = np.zeros([gc_length_rate_ratio.size, seq_length], dtype=float)
         empirical_prob_first = np.zeros(
             [2, gc_length_rate_ratio.size, seq_length], dtype=float
@@ -4949,6 +4951,8 @@ def test_smck_vs_smckapprox_multiple_bottleneck(self):
             sequence_length=5e7,
         )
 
+    '''
+    Commented as gc is not yet supported in SmcKApproxCoalescent
     def test_gc_tract_length_smc(self):
         """
         Runs the check for the mean length of gene conversion tracts.
@@ -5132,6 +5136,7 @@ def test_smc_k_num_trees_gc(self):
         pyplot.tight_layout()
         pyplot.savefig(self.output_dir / "breakpoints_boxplot.png")
         pyplot.close()
+    '''
 
     def test_out_of_africa_migration_model(self):
         s_no = 10