Update

.gitignore

@@ -15,3 +15,8 @@ ssh-key
 ssh-key.pub
 terraform.tfstate
 terraform.tfstate.backup
+bestfits_file.bestfits
+dadi_models.py
+demes_file.yml
+sfs.fs
+demo-popt.bestfits

dadi_cli/parsers/argument_validation.py

@@ -31,7 +31,37 @@ def positive_int(value: str) -> int:
     return ivalue
 
 
-def positive_number(value: str) -> float:
+def nonnegative_int(value: str) -> int:
+    """
+    Validates if the provided string represents a nonnegative integer.
+
+    Parameters
+    ----------
+    value : str
+        The value to validate.
+
+    Returns
+    -------
+    int
+        The validated nonnegative integer.
+
+    Raises
+    ------
+    argparse.ArgumentTypeError
+        If the value is not a valid integer or nonnegative integer.
+
+    """
+    if value is not None:
+        try:
+            ivalue = int(value)
+        except ValueError:
+            raise argparse.ArgumentTypeError(f"{value} is not a valid integer")
+        if ivalue < 0:
+            raise argparse.ArgumentTypeError(f"{value} is not a nonnegative integer")
+    return ivalue
+
+
+def positive_num(value: str) -> float:
     """
     Validates if the provided string represents a positive number.
 
@@ -61,6 +91,36 @@ def positive_number(value: str) -> float:
     return fvalue
 
 
+def nonnegative_num(value: str) -> float:
+    """
+    Validates if the provided string represents a nonnegative number.
+
+    Parameters
+    ----------
+    value : str
+        The value to validate.
+
+    Returns
+    -------
+    float
+        The validated nonnegative number.
+
+    Raises
+    ------
+    argparse.ArgumentTypeError
+        If the value is not a valid number or nonnegative number.
+
+    """
+    if value is not None:
+        try:
+            fvalue = float(value)
+        except ValueError:
+            raise argparse.ArgumentTypeError(f"{value} is not a valid number")
+        if fvalue < 0:
+            raise argparse.ArgumentTypeError(f"{value} is not a nonnegative number")
+    return fvalue
+
+
 def existed_file(value: str) -> str:
     """
     Validates if the provided string is a path to an existing file.

dadi_cli/parsers/common_arguments.py

@@ -1,4 +1,5 @@
-import argparse
+import argparse, multiprocessing, sys
+import numpy as np
 from dadi_cli.parsers.argument_validation import *
 
 
@@ -290,7 +291,7 @@ def add_inference_argument(parser) -> None:
 
     parser.add_argument(
         "--gpus",
-        type=positive_int,
+        type=nonnegative_int,
         default=0,
         help="Number of GPUs to use in multiprocessing. Default: 0.",
     )

dadi_cli/parsers/generate_cache_parsers.py

@@ -1,4 +1,4 @@
-import argparse
+import argparse, multiprocessing
 from dadi_cli.parsers.common_arguments import *
 from dadi_cli.parsers.argument_validation import *
 from dadi_cli.GenerateCache import *
@@ -88,7 +88,7 @@ def add_generate_cache_parsers(subparsers) -> None:
 
     parser.add_argument(
         "--gpus",
-        type=positive_int,
+        type=nonnegative_int,
         default=0,
         help="Number of GPUs to use in multiprocessing. Default: 0.",
     )

dadi_cli/parsers/infer_dm_parsers.py

@@ -1,11 +1,13 @@
-import argparse, inspect, nlopt, os, random, sys, time,
+import argparse, inspect, nlopt, os, random, sys, time
 import work_queue as wq
 from multiprocessing import Process, Queue
 from sys import exit
 from dadi_cli.parsers.common_arguments import *
 from dadi_cli.parsers.argument_validation import *
+from dadi_cli.InferDM import *
 from dadi_cli.utilities import *
-from dadi_cli.BestFit import get_bestfit_params
+from dadi_cli.BestFit import *
+from dadi_cli.Models import *
 
 
 def _run_infer_dm(args) -> None:
@@ -56,13 +58,13 @@ def _run_infer_dm(args) -> None:
     args.misid = not (fs.folded or args.nomisid)
 
     if not args.model_file and args.constants != -1:
-        args.constants = _check_params(
+        args.constants = check_params(
             args.constants, args.model, "--constant", args.misid
         )
     if not args.model_file and args.lbounds != -1:
-        args.lbounds = _check_params(args.lbounds, args.model, "--lbounds", args.misid)
+        args.lbounds = check_params(args.lbounds, args.model, "--lbounds", args.misid)
     if not args.model_file and args.ubounds != -1:
-        args.ubounds = _check_params(args.ubounds, args.model, "--ubounds", args.misid)
+        args.ubounds = check_params(args.ubounds, args.model, "--ubounds", args.misid)
 
     if args.p0 == -1:
         args.p0 = _calc_p0_from_bounds(args.lbounds, args.ubounds)
@@ -191,13 +193,13 @@ def _run_infer_dm(args) -> None:
                 # Create workers
                 workers = [
                     Process(
-                        target=_worker_func,
+                        target=worker_func,
                         args=(infer_global_opt, in_queue, out_queue, worker_args)
                     )
                     for ii in range(args.cpus)
                 ]
                 workers.extend([
-                    Process(target=_worker_func,
+                    Process(target=worker_func,
                         args=(infer_global_opt, in_queue, out_queue, worker_args, True))
                     for ii in range(args.gpus)
                 ])
@@ -312,13 +314,13 @@ def _run_infer_dm(args) -> None:
             # Create workers
             workers = [
                 Process(
-                    target=_worker_func,
+                    target=worker_func,
                     args=(infer_demography, in_queue, out_queue, worker_args)
                 )
                 for ii in range(args.cpus)
             ]
             workers.extend([
-                Process(target=_worker_func,
+                Process(target=worker_func,
                     args=(infer_demography, in_queue, out_queue, worker_args, True))
                 for ii in range(args.gpus)
             ])

dadi_cli/parsers/pdf_parsers.py

@@ -4,7 +4,7 @@
 from dadi_cli.Pdfs import *
 
 
-def run_pdf(args) -> None:
+def _run_pdf(args) -> None:
     """
     """
     if args.names is None:

dadi_cli/parsers/stat_dfe_parsers.py

@@ -4,7 +4,7 @@
 from dadi_cli.Stat import godambe_stat_dfe
 
 
-def run_stat_dfe(args) -> None:
+def _run_stat_dfe(args) -> None:
     """
     """
     # # Code kept just in case user requests functionality if the future

dadi_cli/parsers/stat_dm_parsers.py

@@ -5,7 +5,7 @@
 from dadi_cli.Stat import godambe_stat_demograpy
 
 
-def run_stat_demography(args) -> None:
+def _run_stat_demography(args) -> None:
     """
     """
     # # Code kept just in case user requests functionality if the future

setup.py

@@ -1,5 +1,5 @@
 import os.path
-from setuptools import setup
+from setuptools import setup, find_packages
 
 # The directory containing this file
 HERE = os.path.abspath(os.path.dirname(__file__))
@@ -11,6 +11,7 @@
 # This call to setup() does all the work
 setup(
     name="dadi-cli",
+    python_requires='>=3.9',
     version="0.9.4b",
     description="A command line interface for dadi",
     long_description=README,
@@ -24,7 +25,7 @@
         "Programming Language :: Python",
         "Programming Language :: Python :: 3.9",
     ],
-    packages=["dadi_cli"],
+    packages=find_packages(),
     include_package_data=True,
     # install_requires=[
     #    "dadi"

tests/test_cli.py

@@ -2,6 +2,7 @@
 import dadi_cli.__main__ as cli
 import os
 
+
 try:
     if not os.path.exists("./tests/test_results"):
         os.makedirs("./tests/test_results")
@@ -10,10 +11,10 @@
 
 
 def test_generate_fs_args():
-    parser = cli.dadi_cli_parser()
+    parser = cli._dadi_cli_parser()
     cmd = "GenerateFs"
-    vcf = "test.vcf"
-    pop_infos = "test.info"
+    vcf = "tests/example_data/1KG.YRI.CEU.biallelic.synonymous.snps.withanc.strict.short.vcf"
+    pop_infos = "tests/example_data/four.popfile.txt"
     output = "test.output"
     args = parser.parse_args(
         [
@@ -38,10 +39,10 @@ def test_generate_fs_args():
 
 
 def test_generate_cache_args():
-    parser = cli.dadi_cli_parser()
+    parser = cli._dadi_cli_parser()
     cmd = "GenerateCache"
     model = "split_mig_fix_T_one_s"
-    model_file = "tests/example_data/example_models"
+    model_file = "tests/example_data/example_models.py"
     grids = [20, 40, 60]
     demo_popt = "tests/example_data/example.split_mig_fix_T.demo.params.InferDM.bestfits"
     gamma_bounds = [1e-4, 10.0]
@@ -93,8 +94,9 @@ def test_generate_cache_args():
     assert args.demo_popt == demo_popt
     assert args.additional_gammas == additional_gammas
 
+
 def test_simulate_dm_args():
-    parser = cli.dadi_cli_parser()
+    parser = cli._dadi_cli_parser()
     cmd = "SimulateDM"
     model = "two_epoch"
     model_file = None
@@ -132,8 +134,9 @@ def test_simulate_dm_args():
     assert args.output == output
     assert args.inference_file == inference_file
 
+
 def test_simulate_dfe_args():
-    parser = cli.dadi_cli_parser()
+    parser = cli._dadi_cli_parser()
     cmd = "SimulateDFE"
     cache1d = "tests/example_data/cache_split_mig_1d.bpkl"
     cache2d = "tests/example_data/cache_split_mig_2d.bpkl"
@@ -173,15 +176,17 @@ def test_simulate_dfe_args():
     assert args.nomisid == nomisid
     assert args.output == output
 
+
 try:
     import demes
     skip = False
 except:
     skip = True
 
+
 @pytest.mark.skipif(skip, reason="Could not load Demes")
 def test_simulate_demes_args():
-    parser = cli.dadi_cli_parser()
+    parser = cli._dadi_cli_parser()
     cmd = "SimulateDemes"
     demes_file = "examples/data/gutenkunst_ooa.yml"
     sample_sizes = [10, 10, 10]
@@ -213,13 +218,13 @@ def test_simulate_demes_args():
 
 
 @pytest.mark.parametrize("model, model_file, nomisid",
-                        [
-                        ("split_mig_fix_T", "tests/example_data/example_models", False),
-                        ("snm_1d", None, True)
-                         ]
-                         )
+    [
+        ("split_mig_fix_T", "tests/example_data/example_models.py", False),
+        ("snm_1d", None, True)
+    ]
+)
 def test_infer_dm_args(model, model_file, nomisid):
-    parser = cli.dadi_cli_parser()
+    parser = cli._dadi_cli_parser()
     cmd = "InferDM"
     fs = "tests/example_data/two_epoch_syn.fs"
     p0 = [1, 1, 0.01, 1, 0.05]
@@ -300,7 +305,8 @@ def test_infer_dm_args(model, model_file, nomisid):
     assert args.delta_ll == delta_ll
     assert args.gpus == gpus
     assert args.model == model
-    assert args.model_file == str(model_file)
+    #assert args.model_file == str(model_file)
+    assert args.model_file == model_file
     assert args.grids == grids
     assert args.nomisid == False
     assert args.constants == -1
@@ -311,7 +317,7 @@ def test_infer_dm_args(model, model_file, nomisid):
 
 
 def test_infer_dfe_args():
-    parser = cli.dadi_cli_parser()
+    parser = cli._dadi_cli_parser()
     cmd = "InferDFE"
     fs_mix = "tests/example_data/split_mig_non_mix.fs"
     fs_1d_lognorm = "tests/example_data/split_mig_non_1d.fs"
@@ -425,8 +431,9 @@ def test_infer_dfe_args():
     assert args.pdf_file == None
     assert args.bestfit_p0 == None
 
+
 def test_bestfit_args():
-    parser = cli.dadi_cli_parser()
+    parser = cli._dadi_cli_parser()
     cmd = "BestFit"
     input_prefix = "tests/example_data/example.split_mig.demo.params.InferDM"
     args = parser.parse_args(
@@ -449,7 +456,7 @@ def test_bestfit_args():
 
 
 def test_plot_args():
-    parser = cli.dadi_cli_parser()
+    parser = cli._dadi_cli_parser()
     cmd = "Plot"
     fs = "tests/example_data/split_mig_non_1d.fs"
     fs2 = "tests/example_data/split_mig_non_2d.fs"
@@ -519,9 +526,8 @@ def test_plot_args():
     assert args.ratio == ratio
 
 
-
 def test_stat_dm_args():
-    parser = cli.dadi_cli_parser()
+    parser = cli._dadi_cli_parser()
     cmd = "StatDM"
     fs = "tests/example_data/split_mig_syn.fs"
     model = "split_mig"
@@ -564,8 +570,9 @@ def test_stat_dm_args():
     assert args.bootstrapping_dir == bootstrapping_dir
     assert args.logscale == logscale
 
+
 def test_stat_dfe_args():
-    parser = cli.dadi_cli_parser()
+    parser = cli._dadi_cli_parser()
     cmd = "StatDFE"
     fs = "tests/example_data/split_mig_non_mix.fs"
     cache1d = "tests/example_data/cache_split_mig_1d.bpkl"
@@ -618,8 +625,9 @@ def test_stat_dfe_args():
     assert args.bootstrapping_non_dir == bootstrapping_nonsynonymous_dir
     assert args.logscale == logscale
 
+
 def test_model_args():
-    parser = cli.dadi_cli_parser()
+    parser = cli._dadi_cli_parser()
     cmd = "Model"
     args = parser.parse_args([cmd, "--names", "two_epoch"])
     assert args.names == "two_epoch"