add examples and move loggers after imports

.github/workflows/tests.yml

@@ -27,12 +27,10 @@ jobs:
           pip install tox tox-gh-actions
       - name: Test generator and physics output
         run: tox
-      - name: Upload Coverage to Codecov
-        uses: codecov/codecov-action@v2
-      # - name: Generate Report
-      #   run: |
-      #     pip install coverage
-      #     coverage run -m pytest
-      # - name: Setup tmate session
-      #   if: success() || failure()
-      #   uses: mxschmitt/action-tmate@v3
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4.2.0
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml  # Specify your coverage file location if needed
+          flags: unittests  # Optional: Helps to tag results for more detail
+          fail_ci_if_error: false  # Optional: Don't fail the CI if Codecov fails

examples/Example_0_start_here.ipynb

@@ -533,7 +533,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3.9.12 ('base')",
+   "display_name": "darknews",
    "language": "python",
    "name": "python3"
   },
@@ -547,12 +547,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.0"
-  },
-  "vscode": {
-   "interpreter": {
-    "hash": "3067ead486e059ec00ffe7555bdb889e6e264a24dc711bf108106cc7baee8d5d"
-   }
+   "version": "3.11.8"
   }
  },
  "nbformat": 4,

examples/Example_4_MB_analysis.ipynb → examples/FastBNB_example_1_MB_analysis.ipynb

@@ -6,7 +6,7 @@
    "id": "chinese-isaac",
    "metadata": {},
    "source": [
-    "# Example 4\n",
+    "# Example 1 (FastBNB)\n",
     "\n",
     "This notebook shows predictions for nueCCQE-like events at MiniBooNE using the \"fastbnb\" module -- installed separately from:\n",
     "\n",
@@ -17,18 +17,27 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 6,
    "id": "compact-danger",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "The autoreload extension is already loaded. To reload it, use:\n",
+      "  %reload_ext autoreload\n"
+     ]
+    }
+   ],
    "source": [
     "%load_ext autoreload\n",
     "%autoreload 2"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 7,
    "id": "professional-latitude",
    "metadata": {},
    "outputs": [],
@@ -50,7 +59,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 8,
    "id": "a54bb01c",
    "metadata": {},
    "outputs": [],
@@ -70,7 +79,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 9,
    "id": "5becc5d3",
    "metadata": {},
    "outputs": [],
@@ -80,7 +89,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 10,
    "id": "fc5e1894",
    "metadata": {},
    "outputs": [

junit.xml

@@ -0,0 +1 @@
+<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="1" tests="15" time="78.531" timestamp="2024-10-03T17:30:46.438716-05:00" hostname="matheuss-mbp-2.guest-network.net"><testcase classname="tests.test_inputs" name="test_ModelContainer_default" file="tests/test_inputs.py" line="12" time="0.023" /><testcase classname="tests.test_inputs" name="test_input_parameter_files" file="tests/test_inputs.py" line="27" time="0.036" /><testcase classname="tests.test_inputs" name="test_argparse" file="tests/test_inputs.py" line="35" time="0.075" /><testcase classname="tests.test_physics" name="test_MB_benchmarks" file="tests/test_physics.py" line="19" time="1.398" /><testcase classname="tests.test_physics" name="test_MB_SM" file="tests/test_physics.py" line="37" time="0.452" /><testcase classname="tests.test_physics" name="test_MB_other_final_states" file="tests/test_physics.py" line="43" time="1.841" /><testcase classname="tests.test_physics" name="test_MB_generic_model" file="tests/test_physics.py" line="73" time="10.180" /><testcase classname="tests.test_physics" name="test_MB_dirt" file="tests/test_physics.py" line="91" time="2.592" /><testcase classname="tests.test_physics" name="test_portal_vs_simplified" file="tests/test_physics.py" line="113" time="0.936" /><testcase classname="tests.test_physics" name="test_xsecs" file="tests/test_physics.py" line="122" time="3.096" /><testcase classname="tests.test_physics" name="test_geometries" file="tests/test_physics.py" line="219" time="0.487" /><testcase classname="tests.test_readoutputs" name="test_output" file="tests/test_readoutputs.py" line="11" time="21.431" /><testcase classname="tests.test_scripts" name="test_dn_gen" file="tests/test_scripts.py" line="9" time="29.702" /><testcase classname="tests.test_scripts" name="test_python_call_to_dngen" file="tests/test_scripts.py" line="28" time="6.217" /><testcase classname="tests.test_scripts" name="test_examples_download" file="tests/test_scripts.py" line="33" time="0.003"><skipped type="pytest.skip" message="Still need to find a way to set up git for venvs">/Users/mhostert/Repos/DarkNews-generator/tests/test_scripts.py:34: Still need to find a way to set up git for venvs</skipped></testcase></testsuite></testsuites>

src/DarkNews/const.py

@@ -36,6 +36,8 @@
 rad_to_deg = 180.0 / np.pi
 deg_to_rad = 1 / rad_to_deg
 
+s_in_year = 60 * 60 * 24 * 365.25
+
 invGeV_to_cm = hb * c_LIGHT  # hbar c = 197.3269804e-16 GeV.cm
 invGeV2_to_cm2 = invGeV_to_cm**2
 

src/DarkNews/model.py

@@ -1,16 +1,16 @@
 import numpy as np
 import math
 
-import logging
-
-logger = logging.getLogger("logger." + __name__)
-prettyprinter = logging.getLogger("prettyprinter." + __name__)
-
 from particle import literals as lp
 
 from DarkNews import const
 from DarkNews import pdg
 
+import logging
+
+logger = logging.getLogger("logger." + __name__)
+prettyprinter = logging.getLogger("prettyprinter." + __name__)
+
 
 class HNLModel:
     def __init__(self, model_file=None, **user_input):
@@ -413,35 +413,37 @@ def set_vertices(self):
         # self.tanof2beta = const.sw * self.sinof2chi / (entry_22)
 
         # Mass mixing and kinetic mixing
-        entry_11 = const.sw * self.sinof2chi + 2 * self.epsilonZ * np.sqrt(self.c2chi)
-        entry_22 = self.c2chi - const.s2w * self.s2chi - (self.mzprime / const.m_Z) ** 2 - 2 * self.epsilonZ * const.sw * np.sqrt(self.s2chi)
-        self.tanof2beta = entry_11 / entry_22
+        self._entry_11 = const.sw * self.sinof2chi + 2 * self.epsilonZ * np.sqrt(self.c2chi)
+        self._entry_22 = self.c2chi - const.s2w * self.s2chi - (self.mzprime / const.m_Z) ** 2 - 2 * self.epsilonZ * const.sw * np.sqrt(self.s2chi)
+        self.tanof2beta = self._entry_11 / self._entry_22
 
         # self.beta = const.sw * self.chi
-        self.sinof2beta = entry_11 / np.sqrt(entry_22**2 + entry_11**2)
-        self.cosof2beta = entry_22 / np.sqrt(entry_22**2 + entry_11**2)
+        self.sinof2beta = self._entry_11 / np.sqrt(self._entry_22**2 + self._entry_11**2)
+        self.cosof2beta = self._entry_22 / np.sqrt(self._entry_22**2 + self._entry_11**2)
 
         # #####################
         if self.tanof2beta != 0:
             self.tbeta = self.sinof2beta / (1 + self.cosof2beta)
+            self.cbeta = math.sqrt((1 + self.cosof2beta) / 2.0)  # FIX ME -- works only for |beta| < pi/2
+            self.sbeta = math.sqrt(1 - self.cbeta**2)  # FIX ME -- works only for |beta| < pi/2
         else:
             self.tbeta = 0.0
-
-        self.sbeta = math.sqrt((1 - self.cosof2beta) / 2.0) * np.sign(self.sinof2beta)  # FIX ME -- works only for |beta| < pi/2
-        self.cbeta = math.sqrt((1 + self.cosof2beta) / 2.0)  # FIX ME -- works only for |beta| < pi/2
+            self.cbeta = 1.0
+            self.sbeta = 0.0
 
         # some abbreviations
         self._weak_vertex = const.gweak / const.cw / 2.0
         self._gschi = self.gD * self.sbeta
+
         # dark couplings acquired by Z boson
         self._g_weak_correction = self.cbeta + self.tanchi * const.sw * self.sbeta
         self._g_dark_correction = self.cbeta * self.tanchi * const.sw - self.sbeta
 
         # Charged leptons
         self.ceV = self._weak_vertex * (self.cbeta * (2 * const.s2w - 0.5) + 3.0 / 2.0 * self.sbeta * const.sw * self.tanchi)
         self.ceA = self._weak_vertex * (-(self.cbeta + self.sbeta * const.sw * self.tanchi) / 2.0)
-        # self.ceV = weak_vertex*(const.gweak/(2*const.cw) * (2*const.s2w - 0.5))
-        # self.ceA = weak_vertex*(const.gweak/(2*const.cw) * (-1.0/2.0))
+        # self.ceV = self._weak_vertex * (const.gweak / (2 * const.cw) * (2 * const.s2w - 0.5))
+        # self.ceA = self._weak_vertex * (const.gweak / (2 * const.cw) * (-1.0 / 2.0))
 
         # quarks
         self.cuV = self._weak_vertex * (self.cbeta * (0.5 - 4 * const.s2w / 3.0) - 5.0 / 6.0 * self.sbeta * const.sw * self.tanchi)

src/DarkNews/processes.py

@@ -1,11 +1,6 @@
 import numpy as np
 import vegas as vg
 import json
-import os
-
-import logging
-
-logger = logging.getLogger("logger." + __name__)
 
 from DarkNews import const
 from DarkNews import pdg
@@ -18,6 +13,10 @@
 
 from . import Cfourvec as Cfv
 
+import logging
+
+logger = logging.getLogger("logger." + __name__)
+
 
 class UpscatteringProcess:
     def __init__(self, nu_projectile, nu_upscattered, nuclear_target, scattering_regime, TheoryModel, helicity):
@@ -270,14 +269,14 @@ def __init__(self, nu_parent, nu_daughter, final_lepton1, final_lepton2, TheoryM
         else:
             self.CC_mixing1 = 0
             self.CC_mixing2 = 0
-        ## Minus sign important for interference!
+        # Minus sign important for interference!
         self.CC_mixing2 *= -1
 
         if self.m_parent - self.m_daughter - self.mm - self.mp < 0:
             logger.error(f"Error! Final states are above the mass of parent particle: mass excess = {self.m_parent - self.m_daughter - self.mm - self.mp}.")
             raise ValueError("Energy not conserved.")
 
-        ## Is the mediator on shell?
+        # Is the mediator on shell?
         self.vector_on_shell = (
             (TheoryModel.mzprime is not None) and (self.m_parent - self.m_daughter > TheoryModel.mzprime) and (TheoryModel.mzprime > self.mm + self.mp)
         )
@@ -288,7 +287,7 @@ def __init__(self, nu_parent, nu_daughter, final_lepton1, final_lepton2, TheoryM
         )
         self.scalar_off_shell = not self.scalar_on_shell
 
-        ## does it have transition magnetic moment?
+        # does it have transition magnetic moment?
         self.TMM = TheoryModel.has_TMM
 
     def SamplePS(
@@ -336,13 +335,11 @@ def total_width(self, NINT=MC.NINT, NEVAL=MC.NEVAL, NINT_warmup=MC.NINT_warmup,
             logger.error("Vector and scalar simultaneously on shell is not implemented.")
             raise NotImplementedError("Feature not implemented.")
         elif self.vector_on_shell and self.scalar_off_shell:
-            return dr.gamma_Ni_to_Nj_V(vertex_ij=self.Dih, mi=self.m_parent, mj=self.m_daughter, mV=self.mzprime, HNLtype=self.HNLtype) * dr.gamma_V_to_ell_ell(
-                vertex=self.TheoryModel.deV, mV=self.mzprime, m_ell=self.mm
-            )
+            return dr.gamma_Ni_to_Nj_V(vertex_ij=self.Dih, mi=self.m_parent, mj=self.m_daughter, mV=self.mzprime, HNLtype=self.HNLtype)
+        # * dr.gamma_V_to_ell_ell(vertex=self.TheoryModel.deV, mV=self.mzprime, m_ell=self.mm)
         elif self.vector_off_shell and self.scalar_on_shell:
-            return dr.gamma_Ni_to_Nj_S(vertex_ij=self.Sih, mi=self.m_parent, mj=self.m_daughter, mS=self.mhprime, HNLtype=self.HNLtype) * dr.gamma_S_to_ell_ell(
-                vertex=self.TheoryModel.deS, mS=self.mhprime, m_ell=self.mm
-            )
+            return dr.gamma_Ni_to_Nj_S(vertex_ij=self.Sih, mi=self.m_parent, mj=self.m_daughter, mS=self.mhprime, HNLtype=self.HNLtype)
+            # * dr.gamma_S_to_ell_ell(vertex=self.TheoryModel.deS, mS=self.mhprime, m_ell=self.mm)
         elif self.vector_off_shell and self.scalar_off_shell:
 
             # We need to integraate the differential cross section

tox.ini

@@ -23,13 +23,11 @@ setenv =
     PYTHONHASHSEED = 0
 
 commands =
-    pytest
-    # pytest --basetemp={envtmpdir} --cov={envtmpdir} --cov-append --cov-report=xml
+    pytest --basetemp={envtmpdir} --cov={envtmpdir} --cov-append --cov-report=xml --cov --junitxml=junit.xml -o junit_family=legacy
 depends =
     {py38,py39,py310,py311,py312}: clean
     report: py38,py39,py310,py311,py312
 
-
 [testenv:report]
 deps = coverage
 skip_install = true