Update tests for change to subcommands (besides GenerateCache) that t…

…ake popt file
xin-huang · Aug 14, 2024 · d26b853 · d26b853
1 parent ded71d1
commit d26b853
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Showing 4 changed files with 3 additions and 29 deletions.
diff --git a/tests/test_Plot.py b/tests/test_Plot.py
@@ -126,7 +126,6 @@ def test_plot_fitted_demography(files):
         func=dadi.Demographics1D.two_epoch,
         popt=pytest.fs1d_demo_popt,
         projections=[8],
-        nomisid=True,
         cov_args=[],
         cov_inbreeding=[],
         output="tests/test_results/plot_plot_fitted_demography_1d_w_proj.png",
@@ -139,7 +138,6 @@ def test_plot_fitted_demography(files):
         func=dadi.Demographics2D.split_mig,
         popt=pytest.fs2d_demo_popt,
         projections=[8, 8],
-        nomisid=True,
         cov_args=[],
         cov_inbreeding=[],
         output="tests/test_results/plot_plot_fitted_demography_2d_w_proj.png",
@@ -152,7 +150,6 @@ def test_plot_fitted_demography(files):
         func=dadi.Demographics1D.two_epoch,
         popt=pytest.fs1d_demo_popt,
         projections=None,
-        nomisid=True,
         cov_args=[],
         cov_inbreeding=[],
         output="tests/test_results/plot_plot_fitted_demography_1d_no_proj.png",
@@ -165,7 +162,6 @@ def test_plot_fitted_demography(files):
         func=dadi.Demographics2D.split_mig,
         popt=pytest.fs2d_demo_popt,
         projections=None,
-        nomisid=True,
         cov_args=[],
         cov_inbreeding=[],
         output="tests/test_results/plot_plot_fitted_demography_2d_no_proj.png",
@@ -178,7 +174,6 @@ def test_plot_fitted_demography(files):
         func=dadi.Demographics3D.out_of_africa,
         popt=pytest.fs3d_popt,
         projections=None,
-        nomisid=False,
         cov_args=[],
         cov_inbreeding=[],
         output="tests/test_results/plot_plot_fitted_demography_3d_no_proj.png",
@@ -192,7 +187,6 @@ def test_plot_fitted_demography(files):
         func=dadi.Demographics2D.split_mig,
         popt=pytest.fs2d_demo_popt,
         projections=None,
-        nomisid=True,
         cov_args=[pickle.load(open("./tests/example_data/LowPass-files/cov.fs.coverage.pickle", 'rb')), 20, 20],
         cov_inbreeding=[],
         output="tests/test_results/plot_plot_low-pass_demography.png",
@@ -212,7 +206,6 @@ def test_plot_fitted_dfe(files):
         projections=[8, 8],
         pdf="lognormal",
         pdf2="biv_lognormal",
-        nomisid=True,
         cov_args=[],
         cov_inbreeding=[],
         output="tests/test_results/plot_fitted_dfe_mixture_w_proj.png",
@@ -229,7 +222,6 @@ def test_plot_fitted_dfe(files):
         projections=[8, 8],
         pdf="lognormal",
         pdf2="biv_lognormal",
-        nomisid=True,
         cov_args=[pickle.load(open("./tests/example_data/LowPass-files/cov.fs.coverage.pickle", 'rb')), 20, 20],
         cov_inbreeding=[],
         output="tests/test_results/plot_fitted_dfe_mixture_w_proj.png",

diff --git a/tests/test_Stat.py b/tests/test_Stat.py
@@ -24,7 +24,6 @@ def test_StatDM_code():
     bootstrap_dir = "./tests/example_data/split_mig_bootstrap_syn/"
     demo_popt = "tests/example_data/example.split_mig.demo.params.InferDM.bestfits"
     fixed_params = -1
-    nomisid = True
     logscale = False
     eps = [0.1]
     godambe_stat_demograpy(
@@ -35,7 +34,6 @@ def test_StatDM_code():
         bootstrap_dir,
         demo_popt,
         fixed_params,
-        nomisid,
         logscale,
         eps,
     )
@@ -51,7 +49,6 @@ def test_StatDM_fix_code():
     bootstrap_dir = "./tests/example_data/split_mig_bootstrap_syn/"
     demo_popt = "tests/example_data/example.split_mig.demo.params.with.misid.InferDM.bestfits"
     fixed_params = [-1, -1, 0.00984767, -1, -1]
-    nomisid = False
     logscale = True
     eps = [0.01, 0.1]
     godambe_stat_demograpy(
@@ -62,7 +59,6 @@ def test_StatDM_fix_code():
         bootstrap_dir,
         demo_popt,
         fixed_params,
-        nomisid,
         logscale,
         eps,
     )
@@ -79,7 +75,6 @@ def test_StatDFE_code_mix_lognormal():
     bootstrap_non_dir = "tests/example_data/split_mig_bootstrap_non/bootstrap_non_mix/"
     dfe_popt = "tests/example_data/example.split_mig.dfe.lognormal_mixture.params.with.misid.InferDFE.bestfits"
     fixed_params = [-1, -1, 0, -1, -1]
-    nomisid = False
     logscale = False
     eps = [0.01]
     godambe_stat_dfe(
@@ -93,7 +88,6 @@ def test_StatDFE_code_mix_lognormal():
         bootstrap_non_dir,
         dfe_popt,
         fixed_params,
-        nomisid,
         logscale,
         eps,
     )
@@ -112,7 +106,6 @@ def test_StatDFE_code_1d_lognormal():
         "tests/example_data/example.split_mig.dfe.1D_lognormal.params.with.misid.InferDFE.bestfits"
     )
     fixed_params = -1
-    nomisid = False
     logscale = True
     eps = [0.01]
     godambe_stat_dfe(
@@ -126,7 +119,6 @@ def test_StatDFE_code_1d_lognormal():
         bootstrap_non_dir,
         dfe_popt,
         fixed_params,
-        nomisid,
         logscale,
         eps,
     )
@@ -145,7 +137,6 @@ def test_StatDFE_code_2d_lognormal():
         "tests/example_data/example.split_mig.dfe.2D_lognormal.params.InferDFE.bestfits"
     )
     fixed_params = -1
-    nomisid = True
     logscale = False
     eps = [0.01]
     godambe_stat_dfe(
@@ -159,7 +150,6 @@ def test_StatDFE_code_2d_lognormal():
         bootstrap_non_dir,
         dfe_popt,
         fixed_params,
-        nomisid,
         logscale,
         eps,
     )
@@ -178,7 +168,7 @@ def test_StatDFE_terminal_1d_lognormal():
     )
     eps = " 0.1 "
     subprocess.run(
-        "dadi-cli StatDFE --nomisid"
+        "dadi-cli StatDFE"
         + " --fs "
         + fs
         + " --dfe-popt "
@@ -212,10 +202,9 @@ def test_StatDFE_terminal_2d_lognormal():
     dfe_popt = (
         "tests/example_data/example.split_mig.dfe.2D_lognormal.params.InferDFE.bestfits"
     )
-    nomisid = True
     logscale = False
     subprocess.run(
-        "dadi-cli StatDFE --nomisid"
+        "dadi-cli StatDFE"
         + " --fs "
         + fs
         + " --dfe-popt "
@@ -247,7 +236,7 @@ def test_StatDFE_terminal_mix_lognormal():
     dfe_popt = "tests/example_data/example.split_mig.dfe.lognormal_mixture.params.InferDFE.bestfits"
     constants = "-1 -1 0 -1"
     subprocess.run(
-        "dadi-cli StatDFE --nomisid"
+        "dadi-cli StatDFE"
         + " --fs "
         + fs
         + " --dfe-popt "

diff --git a/tests/test_cli.py b/tests/test_cli.py
@@ -467,7 +467,6 @@ def test_plot_args():
     cache2d = "tests/example_data/cache_split_mig_2d.bpkl"
     pdf1d = "lognormal"
     pdf2d = "biv_lognormal"
-    nomisid = True
     output = "tests/test_results/plot_cli_test.png"
     projections = [10, 10]
     resid_range = 3
@@ -495,7 +494,6 @@ def test_plot_args():
             pdf1d,
             "--pdf2d",
             pdf2d,
-            "--nomisid",
             "--output",
             output,
             "--projections",
@@ -518,7 +516,6 @@ def test_plot_args():
     assert args.cache2d == cache2d
     assert args.pdf1d == pdf1d
     assert args.pdf2d == pdf2d
-    assert args.nomisid == nomisid
     assert args.output == output
     assert args.projections == projections
     assert args.resid_range == resid_range
@@ -532,7 +529,6 @@ def test_stat_dm_args():
     fs = "tests/example_data/split_mig_syn.fs"
     model = "split_mig"
     grids = [60, 80, 100]
-    nomisid = False
     output = "tests/test_results/example.cli.split_mig.demo.params.ci"
     constants = -1
     demo_popt = "tests/example_data/example.split_mig.demo.params.InferDM.bestfits"
@@ -562,7 +558,6 @@ def test_stat_dm_args():
     assert args.fs == fs
     assert args.model == model
     assert args.grids == grids
-    assert args.nomisid == nomisid
     assert args.output == output
     assert args.constants == constants
     assert args.demo_popt == demo_popt
@@ -584,7 +579,6 @@ def test_stat_dfe_args():
     bootstrapping_nonsynonymous_dir = "tests/example_data/split_mig_bootstrap_non/bootstrap_non_mix/"
     dfe_popt = "tests/example_data/example.split_mig.dfe.lognormal_mixture.params.with.misid.InferDFE.bestfits"
     constants = [-1, -1, 0, -1, -1]
-    nomisid = False
     logscale = False
 
     args = parser.parse_args(

diff --git a/tests/test_main.py b/tests/test_main.py
@@ -629,7 +629,6 @@ def plot_args():
     pytest.dfe_popt = "tests/example_data/example.split_mig.dfe.lognormal_mixture.params.InferDFE.bestfits"
     pytest.cache1d = "tests/example_data/cache_split_mig_1d.bpkl"
     pytest.cache2d = "tests/example_data/cache_split_mig_2d.bpkl"
-    pytest.nomisid = True
     pytest.vmin = 1e-3
     pytest.resid_range = 10
     pytest.projections = None