Eac/colors (#23)

* added better colors to tomo plots

* fix typo & arguement order

* coverage

src/rail/plotting/nz_data_extractor.py

@@ -107,7 +107,7 @@ def generate_dataset_dict(
         project_block = dict(
             Project=dict(
                 name=project_name,
-                yaml_file="dummy",
+                yaml_file=project_file,
             )
         )
 
@@ -158,7 +158,7 @@ def generate_dataset_dict(
                             classifier=classifier_,
                         )
 
-                        if not nz_true_paths:
+                        if not nz_true_paths:  # pragma: no cover
                             continue
 
                         for summarizer_ in summarizers:
@@ -171,7 +171,7 @@ def generate_dataset_dict(
                                 summarizer=summarizer_,
                             )
 
-                            if not nz_paths:
+                            if not nz_paths:  # pragma: no cover
                                 continue
 
                             dataset_name = f"{selection_}_{key}_{algo_}_{classifier_}_{summarizer_}"

src/rail/plotting/nz_plotters.py

@@ -7,6 +7,7 @@
 import qp
 from ceci.config import StageParameter
 from matplotlib import pyplot as plt
+import matplotlib as mpl
 
 from .dataset_holder import RailDatasetHolder
 from .plot_holder import RailPlotHolder
@@ -43,9 +44,13 @@ def _make_plot(
         nz_vals = nz_estimates.pdf(bin_edges)
         n_pdf = truth.npdf
 
+        cmap = mpl.colormaps['plasma']
+        colors = cmap(np.linspace(0, 1, n_pdf))
+
         for i in range(n_pdf):
-            axes.plot(bin_edges, truth_vals[i], "-")
-            axes.plot(bin_edges, nz_vals[i])
+            color=colors[i]
+            axes.plot(bin_edges, truth_vals[i], "-", color=color)
+            axes.plot(bin_edges, nz_vals[i], "--", color=color)
         plt.xlabel("z")
         plt.ylabel("n(z)")
         plot_name = self._make_full_plot_name(prefix, "")

src/rail/projects/pipeline_holder.py

@@ -504,7 +504,7 @@ def build(
 
         pipeline_kwargs = self.config.kwargs.copy()
 
-        if self.config.pipeline_overrides:
+        if self.config.pipeline_overrides:  # pragma: no cover
             copy_overrides = self.config.pipeline_overrides.copy()
 
             stages_config = os.path.join(

src/rail/projects/project.py

@@ -705,7 +705,7 @@ def add_flavor(self, name: str, **kwargs: Any) -> RailFlavor:
         """Add a new flavor to the Project"""
         if self._flavors is None:  # pragma: no cover
             self.get_flavors()
-
+        assert self._flavors is not None
         if name in self._flavors:
             raise KeyError(f"Flavor {name} already in RailProject {self.name}")
         flavor_params = self.config.Baseline.copy()

tests/cli/plot/test_plot_cli.py

@@ -35,7 +35,35 @@ def test_cli_inspect(setup_project_area: int) -> None:
     check_result(result)
 
 
-def test_cli_extract_datasets(setup_project_area: int) -> None:
+def test_cli_extract_nz_datasets(setup_project_area: int) -> None:
+    assert setup_project_area == 0
+    runner = CliRunner()
+
+    # run with split by flavor
+    result = runner.invoke(
+        plot_cli,
+        "extract-datasets "
+        "--extractor_class rail.plotting.nz_data_extractor.NZTomoBinDataExtractor "
+        "--flavor all "
+        "--split_by_flavor "
+        "--output_yaml tests/temp_data/dataset_nz_out.yaml "
+        "tests/ci_project.yaml",
+    )
+    check_result(result)
+
+    # run without split by flavor
+    result = runner.invoke(
+        plot_cli,
+        "extract-datasets "
+        "--extractor_class rail.plotting.nz_data_extractor.NZTomoBinDataExtractor "
+        "--flavor all "
+        "--output_yaml tests/temp_data/dataset_nz_out.yaml "
+        "tests/ci_project.yaml",
+    )
+    check_result(result)
+
+
+def test_cli_extract_pz_datasets(setup_project_area: int) -> None:
     assert setup_project_area == 0
     runner = CliRunner()
 
@@ -45,7 +73,6 @@ def test_cli_extract_datasets(setup_project_area: int) -> None:
         "extract-datasets "
         "--extractor_class rail.plotting.pz_data_extractor.PZPointEstimateDataExtractor "
         "--flavor all "
-        "--selection all "
         "--split_by_flavor "
         "--output_yaml tests/temp_data/dataset_out.yaml "
         "tests/ci_project.yaml",
@@ -58,13 +85,13 @@ def test_cli_extract_datasets(setup_project_area: int) -> None:
         "extract-datasets "
         "--extractor_class rail.plotting.pz_data_extractor.PZPointEstimateDataExtractor "
         "--flavor all "
-        "--selection all "
         "--output_yaml tests/temp_data/dataset_out.yaml "
         "tests/ci_project.yaml",
     )
     check_result(result)
 
 
+
 def test_cli_make_plot_groups(setup_project_area: int) -> None:
     assert setup_project_area == 0
     runner = CliRunner()
@@ -79,3 +106,19 @@ def test_cli_make_plot_groups(setup_project_area: int) -> None:
         "--dataset_list_name blend_baseline_all",
     )
     check_result(result)
+
+
+def test_cli_make_nz_plot_groups(setup_project_area: int) -> None:
+    assert setup_project_area == 0
+    runner = CliRunner()
+
+    result = runner.invoke(
+        plot_cli,
+        "make-plot-groups "
+        "--output_yaml tests/temp_data/check_nz_plot_group.yaml "
+        "--plotter_yaml_path tests/ci_plots.yaml "
+        "--dataset_yaml_path tests/ci_datasets.yaml "
+        "--plotter_list_name tomo_bins "
+        "--dataset_list_name blend_baseline_tomo_knn",
+    )
+    check_result(result)

tests/plotting/test_plot_group_factory.py

@@ -39,3 +39,25 @@ def test_load_yaml(setup_project_area: int) -> None:
 
     check_plot_group = RailPlotGroupFactory.get_plot_group("accuracy_v_ztrue")
     assert isinstance(check_plot_group, RailPlotGroup)
+
+
+
+def test_make_instance_yaml(setup_project_area: int):
+    assert setup_project_area == 0
+
+    RailPlotGroupFactory.make_yaml(
+        output_yaml='tests/temp_data/check_pz_plot_groups.yaml',
+        plotter_yaml_path='tests/ci_plots.yaml',
+        dataset_yaml_path='tests/ci_datasets.yaml',
+        plotter_list_name='zestimate_v_ztrue',
+        output_prefix="",
+        dataset_list_name='baseline_test',
+    )
+    RailPlotGroupFactory.make_yaml(
+        output_yaml='tests/temp_data/check_nz_plot_groups.yaml',
+        plotter_yaml_path='tests/ci_plots.yaml',
+        dataset_yaml_path='tests/ci_datasets.yaml',
+        plotter_list_name='tomo_bins',
+        output_prefix="",
+        dataset_list_name='blend_baseline_tomo_knn',
+    )

tests/projects/test_project.py

@@ -3,7 +3,7 @@
 
 import pytest
 
-from rail.projects.project import RailFlavor, RailProject
+from rail.projects.project import RailProject
 
 
 def check_get_func(func: Callable, check_dict: dict[str, Any]) -> None:
@@ -16,6 +16,12 @@ def check_get_func(func: Callable, check_dict: dict[str, Any]) -> None:
         func("does_not_exist")
 
 
+def test_project_doc() -> None:
+
+    RailProject.functionality_help()
+    RailProject.configuration_help()
+
+
 def test_project_class(setup_project_area: int) -> None:
     assert setup_project_area == 0