Change example filename extension

alea/examples/configs/unbinned_wimp_running.yaml

@@ -14,7 +14,7 @@ computation_options:
     in_common:
       {
         hypotheses: ["free", "zero", "true"],
-        output_filename: "toymc_power_wimp_mass_{wimp_mass:d}_poi_expectation_{poi_expectation:.2f}.h5",
+        output_filename: "toymc_power_wimp_mass_{wimp_mass:d}_poi_expectation_{poi_expectation:.2f}.ii.h5",
         n_mc: 5000,
         n_batch: 40,
         toydata_mode: "generate",
@@ -30,7 +30,7 @@ computation_options:
     in_common:
       {
         hypotheses: ["free", "zero", "true"],
-        output_filename: "toymc_power_wimp_mass_{wimp_mass:d}_poi_expectation_{poi_expectation:.2f}.h5",
+        output_filename: "toymc_power_wimp_mass_{wimp_mass:d}_poi_expectation_{poi_expectation:.2f}.ii.h5",
         n_mc: 5000,
         n_batch: 40,
         limit_threshold: "thresholds.json",
@@ -44,14 +44,14 @@ computation_options:
         poi_expectation: 0.,
         wimp_mass: 50,
         hypotheses: ["free", "zero", "true"],
-        output_filename: "toymc_sensi_wimp_mass_{wimp_mass:d}_poi_expectation_{poi_expectation:.2f}.h5",
+        output_filename: "toymc_sensi_wimp_mass_{wimp_mass:d}_poi_expectation_{poi_expectation:.2f}.ii.h5",
         n_mc: 5000,
         n_batch: 40,
         compute_confidence_interval: True,
         limit_threshold: "thresholds.json",
         asymptotic_dof: 1,
         toydata_mode: "generate_and_store",
-        toydata_filename: "toyfile_wimp_mass_{wimp_mass:d}_poi_expectation_{poi_expectation:.2f}.h5",
+        toydata_filename: "toyfile_wimp_mass_{wimp_mass:d}_poi_expectation_{poi_expectation:.2f}.ii.h5",
       }
 
 slurm_configurations:

alea/examples/configs/unbinned_wimp_statistical_model.yaml

@@ -89,7 +89,7 @@ likelihood_config:
           - er_band_shift
         named_parameters:
           - er_band_shift
-        template_filename: er_template_{er_band_shift}.h5
+        template_filename: er_template_{er_band_shift}.ii.h5
         histogram_scale_factor: 1
 
       - name: wimp
@@ -100,7 +100,7 @@ likelihood_config:
           - signal_efficiency
         named_parameters:
           - wimp_mass
-        template_filename: wimp{wimp_mass:d}gev_template.h5
+        template_filename: wimp{wimp_mass:d}gev_template.ii.h5
         apply_efficiency: True
         efficiency_name: signal_efficiency
 
@@ -122,7 +122,7 @@ likelihood_config:
           - er_band_shift
         named_parameters:
           - er_band_shift
-        template_filename: er_template_{er_band_shift}.h5
+        template_filename: er_template_{er_band_shift}.ii.h5
         histogram_scale_factor: 2
 
       - name: wimp
@@ -133,6 +133,6 @@ likelihood_config:
           - signal_efficiency
         named_parameters:
           - wimp_mass
-        template_filename: wimp{wimp_mass:d}gev_template.h5
+        template_filename: wimp{wimp_mass:d}gev_template.ii.h5
         apply_efficiency: True
         efficiency_name: signal_efficiency

alea/examples/configs/unbinned_wimp_statistical_model_simple.yaml

@@ -68,11 +68,11 @@ likelihood_config:
           - er_band_shift
         named_parameters:
           - er_band_shift
-        template_filename: er_template_{er_band_shift}.h5
+        template_filename: er_template_{er_band_shift}.ii.h5
 
       - name: wimp
         histname: wimp_template
         parameters:
           - wimp_rate_multiplier
           - wimp_mass
-        template_filename: wimp50gev_template.h5
+        template_filename: wimp50gev_template.ii.h5

alea/examples/configs/unbinned_wimp_statistical_model_template_source_test.yaml

@@ -88,7 +88,7 @@ likelihood_config:
         fixed_weight: 0.2
         weight_names: [fixed_weight, er_band_shift]  # not meaningful, just an example
         histnames: [er_template, er_template, er_template]
-        template_filenames: [er_template_0.h5, er_template_1.h5, er_template_-1.h5]
+        template_filenames: [er_template_0.ii.h5, er_template_1.ii.h5, er_template_-1.ii.h5]
         histogram_scale_factor: 100  # absolute rate, /year
 
       - name: wimp
@@ -97,7 +97,7 @@ likelihood_config:
           - wimp_rate_multiplier
           - wimp_mass
           - signal_efficiency
-        template_filename: wimp50gev_template.h5
+        template_filename: wimp50gev_template.ii.h5
         apply_efficiency: True
         efficiency_name: signal_efficiency
 
@@ -121,7 +121,7 @@ likelihood_config:
           - er_band_shift
         named_parameters:
           - er_band_shift
-        template_filename: er_template_{er_band_shift}.h5
+        template_filename: er_template_{er_band_shift}.ii.h5
 
       - name: wimp
         class: alea.template_source.SpectrumTemplateSource
@@ -130,7 +130,7 @@ likelihood_config:
           - wimp_rate_multiplier
           - wimp_mass
           - signal_efficiency
-        template_filename: wimp50gev_template.h5
+        template_filename: wimp50gev_template.ii.h5
         spectrum_name: test_cs1_spectrum.json
         apply_efficiency: True
         efficiency_name: signal_efficiency

alea/runner.py

@@ -65,7 +65,7 @@ class Runner:
             toydata mode, choice from 'read', 'generate', 'generate_and_store', 'no_toydata'
         toydata_filename (str, optional (default=None)): toydata filename
         only_toydata (bool, optional (default=False)): whether only generate toydata
-        output_filename (str, optional (default='test_toymc.h5')): output filename
+        output_filename (str, optional (default='test_toymc.ii.h5')): output filename
         seed (int, optional (default=None)): random seed for runners before generating toydata
         metadata (dict, optional (default=None)): metadata to be saved in output file
 
@@ -88,9 +88,9 @@ def __init__(
         confidence_level: float = 0.9,
         confidence_interval_kind: str = "central",
         toydata_mode: str = "generate_and_store",
-        toydata_filename: str = "test_toydata_filename.h5",
+        toydata_filename: str = "test_toydata_filename.ii.h5",
         only_toydata: bool = False,
-        output_filename: str = "test_output_filename.h5",
+        output_filename: str = "test_output_filename.ii.h5",
         seed: Optional[int] = None,
         metadata: Optional[dict] = None,
     ):

docs/source/basics/runner.rst

@@ -2,4 +2,24 @@
 
 Runners
 =======
-**UNDER CONSTRUCTION**
+
+Data Format
+===========
+alea uses the
+`inference_interface <https://github.com/XENONnT/inference_interface>`_
+to handle storing fit results, toy data and to load _templates_
+-- histograms that define a PDF for e.g. the blueice_extended_model.
+inference_interface uses the pyhdf format, with specific fields for:
+* fit results: uses numpy_to_toyfile and toyfile_to_numpy to write
+and load best-fit values, upper/lower limits and other values from toy fits.
+* toy data: uses toydata_to_file and toydata_from_file to
+write and load toy data-- alea uses this format to read/write data.
+* templates: uses template_to_multihist and
+multihist_to_template, alternatively numpy_to_template,
+template_to_numpy (root version also exists but is not uses)
+
+To emphasize that we encourage this standard format for all
+alea
+read/writing,
+we use the file
+ending .ii.h5 for the files in these formats.

notebooks/3_sensitivity.ipynb

@@ -107,7 +107,7 @@
     "    generate_values={\"wimp_rate_multiplier\": 0.0},\n",
     "    compute_confidence_interval=True,\n",
     "    toydata_mode=\"generate\",\n",
-    "    output_filename=\"out.h5\",\n",
+    "    output_filename=\"out.ii.h5\",\n",
     "    **model_config\n",
     ")"
    ]
@@ -163,7 +163,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "results = toyfiles_to_numpy(\"out.h5\")\n",
+    "results = toyfiles_to_numpy(\"out.ii.h5\")\n",
     "uls = results[\"free\"][\"ul\"]"
    ]
   },

setup.cfg

@@ -3,6 +3,21 @@
 # Set maximum width of the line to 100
 max-line-length = 100
 
+# Excluding some directories:
+exclude =
+  .git
+  .github
+  docs*
+  notebooks*
+  *.yml
+  __pycache__
+  .venv
+  .eggs
+  *.egg
+  dist
+  *cfg
+
+
 # E203 whitespace before ':'
 # F401 imported but unused
 # F403 unable to detect undefined names

tests/test_blueice_extended_model.py

@@ -23,7 +23,7 @@ def setUp(cls):
         ]
         ns = [len(c["likelihood_config"]["likelihood_terms"]) for c in cls.configs]
         cls.n_likelihood_terms = ns
-        cls.toydata_filename = "simple_data.h5"
+        cls.toydata_filename = "simple_data.ii.h5"
         cls.set_new_models(cls)
 
     def set_new_models(self):

tests/test_gaussian_model.py

@@ -39,7 +39,7 @@ def test_data_generation(self):
 
     def test_data_storage(self):
         """Test storage of data to file and retrieval of data from file."""
-        toydata_filename = "simple_data.h5"
+        toydata_filename = "simple_data.ii.h5"
         self.model.data = self.model.generate_data(mu=0)
         self.model.store_data(toydata_filename, [self.model.data])
         stored_data = inference_interface.toydata_from_file(toydata_filename)

tests/test_runner.py

@@ -23,8 +23,8 @@ class TestRunner(TestCase):
     def setUp(cls):
         """Initialise the Runner instance."""
         cls.running_config = load_yaml("unbinned_wimp_running.yaml")
-        cls.toydata_filename = "simple_data.h5"
-        cls.output_filename = "test_toymc.h5"
+        cls.toydata_filename = "simple_data.ii.h5"
+        cls.output_filename = "test_toymc.ii.h5"
         cls.n_mc = 3
 
     def set_gaussian_runner(self, toydata_mode="generate_and_store"):