Update

dadi_cli/__main__.py

@@ -1,7 +1,17 @@
 import argparse
 from dadi_cli.parsers.generate_fs_parsers import add_generate_fs_parsers
 from dadi_cli.parsers.generate_cache_parsers import add_generate_cache_parsers
+from dadi_cli.parsers.simulate_dm_parsers import add_simulate_dm_parsers
+from dadi_cli.parsers.simulate_dfe_parsers import add_simulate_dfe_parsers
+from dadi_cli.parsers.simulate_demes_parsers import add_simulate_demes_parsers
 from dadi_cli.parsers.infer_dm_parsers import add_infer_dm_parsers
+from dadi_cli.parsers.infer_dfe_parsers import add_infer_dfe_parsers
+from dadi_cli.parsers.plot_parsers import add_plot_parsers
+from dadi_cli.parsers.stat_dm_parsers import add_stat_dm_parsers
+from dadi_cli.parsers.stat_dfe_parsers import add_stat_dfe_parsers
+from dadi_cli.parsers.bestfit_parsers import add_bestfit_parsers
+from dadi_cli.parsers.model_parsers import add_model_parsers
+from dadi_cli.parsers.pdf_parsers import add_pdf_parsers
 
 
 def _set_sigpipe_handler() -> None:
@@ -18,7 +28,7 @@ def _set_sigpipe_handler() -> None:
 def _dadi_cli_parser() -> argparse.ArgumentParser:
     """
     Initializes and configures the command-line interface parser
-    for gita.
+    for dadi-cli.
 
     Returns
     -------
@@ -31,7 +41,17 @@ def _dadi_cli_parser() -> argparse.ArgumentParser:
     subparsers.required = True
     add_generate_fs_parsers(subparsers)
     add_generate_cache_parsers(subparsers)
+    add_simulate_dm_parsers(subparsers)
+    add_simulate_dfe_parsers(subparsers)
+    add_simulate_demes_parsers(subparsers)
     add_infer_dm_parsers(subparsers)
+    add_infer_dfe_parsers(subparsers)
+    add_plot_parsers(subparsers)
+    add_stat_dm_parsers(subparsers)
+    add_stat_dfe_parsers(subparsers)
+    add_bestfit_parsers(subparsers)
+    add_model_parsers(subparsers)
+    add_pdf_parsers(subparsers)
 
     return top_parser
 

dadi_cli/parsers/common_arguments.py

@@ -0,0 +1,305 @@
+import argparse
+
+
+def add_output_argument(parser):
+    parser.add_argument(
+        "--output", type=str, required=True, help="Name of the output file."
+    )
+
+
+def add_bounds_argument(parser):
+    # Check that the model is not a standard neutral model
+    if 'snm_1d' not in sys.argv and 'snm_2d' not in sys.argv:
+        boundary_req = True
+    else:
+        if '--nomisid' in sys.argv:
+            boundary_req = False
+        else:
+            boundary_req = True
+    parser.add_argument(
+        "--lbounds",
+        type=float,
+        nargs="+",
+        required=boundary_req,
+        help="Lower bounds of the optimized parameters.",
+    )
+    parser.add_argument(
+        "--ubounds",
+        type=float,
+        nargs="+",
+        required=boundary_req,
+        help="Upper bounds of the optimized parameters.",
+    )
+
+
+def add_demo_popt_argument(parser):
+    # Check that the model is not a standard neutral model
+    bestfit_req = False
+    if 'equil' not in sys.argv:
+        bestfit_req = True
+    parser.add_argument(
+        "--demo-popt",
+        type=str,
+        required=bestfit_req,
+        help="File containing the bestfit parameters for the demographic model.",
+        dest="demo_popt",
+    )
+
+
+def add_grids_argument(parser):
+    parser.add_argument(
+        "--grids",
+        type=_check_positive_int,
+        nargs=3,
+        help="Sizes of grids. Default is based on sample size.",
+    )
+
+
+def add_misid_argument(parser):
+    # Note that the code previously had a --misid function that did the opposite, but this ia more sensible default.
+    parser.add_argument(
+        "--nomisid",
+        default=False,
+        action="store_true",
+        help="Enable to *not* include a parameter modeling ancestral state misidentification when data are polarized.",
+    )
+
+
+def add_model_argument(parser):
+    # Because most of the functions for Plot
+    # do not require a model, we make it
+    # conditionally required.
+    req_model_arg = True
+    if 'Plot' in sys.argv:
+        req_model_arg = False
+    parser.add_argument(
+        "--model",
+        type=str,
+        required=req_model_arg,
+        help="Name of the demographic model. To check available demographic models, please use `dadi-cli Model`.",
+    )
+    parser.add_argument(
+        "--model-file",
+        type=str,
+        required=False,
+        dest="model_file",
+        help="Name of python module file (not including .py) that contains custom models to use. Can be an HTML link. Default: None.",
+    )
+
+
+def add_fs_argument(parser):
+    parser.add_argument(
+        "--fs",
+        type=str,
+        required=True,
+        help="Frequency spectrum of mutations used for inference. To generate the frequency spectrum, please use `dadi-cli GenerateFs`. Can be an HTML link.",
+    )
+
+
+def add_seed_argument(parser):
+    parser.add_argument("--seed", type=_check_positive_int, help="Random seed.")
+
+
+def add_constant_argument(parser):
+    parser.add_argument(
+        "--constants",
+        default=-1,
+        type=float,
+        nargs="+",
+        help="Fixed parameters during the inference or using Godambe analysis. Use -1 to indicate a parameter is NOT fixed. Default: None.",
+    )
+
+
+def add_delta_ll_argument(parser):
+    parser.add_argument(
+        "--delta-ll",
+        type=_check_positive_num,
+        required=False,
+        dest="delta_ll",
+        default=0.0001,
+        help="When using --check-convergence argument in InferDM or InferDFE modules or the BestFits module, set the max percentage difference for log-likliehoods compared to the best optimization log-likliehood to be consider convergent (with 1 being 100%% difference to the best optimization's log-likelihood). Default: 0.0001.",
+    )
+
+
+def add_sample_sizes_argument(parser):
+    parser.add_argument(
+        "--sample-sizes",
+        type=_check_positive_int,
+        nargs="+",
+        required=True,
+        help="Sample sizes of populations.",
+        dest="sample_sizes",
+    )
+
+
+def add_eps_argument(parser):
+    parser.add_argument(
+        "--eps",
+        default=[0.1, 0.01, 0.001],
+        type=_check_nonnegative_float,
+        nargs="+",
+        required=False,
+        help="Step sizes to try for Godambe analysis. Default: [0.1, 0.01, 0.001]",
+    )
+
+
+def add_popt_argument(parser):
+    parser.add_argument(
+        "--demo-popt",
+        type=str,
+        dest="demo_popt",
+        help="File containing the bestfit demographic parameters, generated by `dadi-cli BestFit`.",
+    )
+    parser.add_argument(
+        "--dfe-popt",
+        type=str,
+        dest="dfe_popt",
+        help="File containing the bestfit DFE parameters, generated by `dadi-cli BestFit`.",
+    )
+
+
+def add_dfe_argument(parser):
+    parser.add_argument(
+        "--cache1d",
+        type=str,
+        help="File name of the 1D DFE cache. To generate the cache, please use `dadi-cli GenerateCache`.",
+    )
+    parser.add_argument(
+        "--cache2d",
+        type=str,
+        help="File name of the 2D DFE cache. To generate the cache, please use `dadi-cli GenerateCache`.",
+    )
+    parser.add_argument(
+        "--pdf1d",
+        type=str,
+        help="1D probability density function for the DFE inference. To check available probability density functions, please use `dadi-cli Pdf`.",
+    )
+    parser.add_argument(
+        "--pdf2d",
+        type=str,
+        help="2D probability density function for the joint DFE inference. To check available probability density functions, please use `dadi-cli Pdf`.",
+    )
+
+
+# Currently this command is only needed for param_names.
+def add_mix_pdf_argument(parser):
+    parser.add_argument(
+        "--mix-pdf",
+        dest="mix_pdf",
+        type=str,
+        default=None,
+        help="If you are using a model that is a mixture of probability density function for the joint DFE inference pass in the model name. To check available probability density functions, please use `dadi-cli Pdf`.",
+    )
+
+
+def add_inference_argument(parser):
+    parser.add_argument(
+        "--p0",
+        default=-1,
+        type=float,
+        nargs="+",
+        required=False,
+        help="Initial parameter values for inference.",
+    )
+    parser.add_argument(
+        "--output-prefix",
+        type=str,
+        required=True,
+        dest="output_prefix",
+        help="Prefix for output files, which will be named <output_prefix>.InferDM.opts.<N>, where N is an increasing integer (to avoid overwriting existing files).",
+    )
+    parser.add_argument(
+        "--optimizations",
+        default=100,
+        type=_check_positive_int,
+        help="Total number of optimizations to run. Default: 100.",
+    )
+    parser.add_argument(
+        "--check-convergence",
+        default=0,
+        type=_check_positive_int,
+        dest="check_convergence",
+        help="Start checking for convergence after a chosen number of optimizations. Optimization runs will stop early if convergence criteria are reached. BestFit results file will be call <output_prefix>.InferDM.bestfits. Convergence not checked by default.",
+    )
+    parser.add_argument(
+        "--force-convergence",
+        default=0,
+        type=_check_positive_int,
+        dest="force_convergence",
+        help="Start checking for convergence after a chosen number of optimizations. Optimization runs will continue until convergence criteria is reached (--optimizations flag will be ignored). BestFit results file will be call <output_prefix>.InferDM.bestfits. Convergence not checked by default.",
+    )
+    parser.add_argument(
+        "--work-queue",
+        nargs=2,
+        default=[],
+        action="store",
+        dest="work_queue",
+        help="Enable Work Queue. Additional arguments are the WorkQueue project name, the name of the password file.",
+    )
+    parser.add_argument(
+        "--port",
+        default=9123,
+        type=_check_positive_int,
+        dest="port",
+        help="Choose a specific port for Work Queue communication. Default 9123.",
+    )
+    parser.add_argument(
+        "--debug-wq",
+        default=False,
+        action="store_true",
+        dest="debug_wq",
+        help='Store debug information from WorkQueue to a file called "debug.log". Default: False.',
+    )
+    parser.add_argument(
+        "--maxeval",
+        type=_check_positive_int,
+        default=False,
+        help="Max number of parameter set evaluations tried for optimizing demography. Default: Number of parameters multiplied by 100.",
+    )
+    parser.add_argument(
+        "--maxtime",
+        type=_check_positive_int,
+        default=np.inf,
+        help="Max amount of time for optimizing demography. Default: infinite.",
+    )
+    parser.add_argument(
+        "--cpus",
+        type=_check_nonnegative_int,
+        default=multiprocessing.cpu_count(),
+        help="Number of CPUs to use in multiprocessing. Default: All available CPUs.",
+    )
+    parser.add_argument(
+        "--gpus",
+        type=_check_nonnegative_int,
+        default=0,
+        help="Number of GPUs to use in multiprocessing. Default: 0.",
+    )
+    parser.add_argument(
+        "--bestfit-p0-file", 
+        type=str, 
+        dest="bestfit_p0", 
+        help="Pass in a .bestfit or .opt.<N> file name to cycle --p0 between up to the top 10 best fits for each optimization."
+    )
+
+
+def add_p0_argument(parser):
+    p0_req = False
+    if 'snm_1d' not in sys.argv and 'snm_2d' not in sys.argv:
+        p0_req = True
+    else:
+        if '--nomisid' not in sys.argv:
+            p0_req = True
+
+    parser.add_argument(
+        "--p0",
+        type=float,
+        nargs="+",
+        required=p0_req,
+        help="Parameters for simulated demography or dfe.",
+    )
+
+
+def make_dir(path):
+    parent_dir = os.path.dirname(path)
+    if parent_dir != '':
+        os.makedirs(parent_dir, exist_ok=True)