Numba formal integral (#1549)

* Readded the numba formal integral changes

* Update base.py to match main

* Reverted formal integral instantiation to be more similar to the original C version for consistency

* Moved numba implimentation to the montecarlo_numba folder since this is a numba implementation

* Removed extra ravel

* Added back old formal integral for testing

* Added test for function in the numba formal integral

* Changed the way the shell size is computed, should be correct now

* nevermind

* Moved numba formal integral tests so that paths work out for testing framework

* Moved pointer incrementation to the end of the loop

* Fixed typo

* Switched tests to use numba models

* numba models instantiate with proper data types now

* Fixed numba_formal_integral tests to instantiate numba models with numba compatable types

* Added a couple docstrings with some notes about future improvements

* Streamlined the interface slightly to better catch bugs

* Added some debug statements to watch array sizes in tests

* Changed way size_line and size_shell are created using tau_sobolevs

* Changed the most inner for-loop to be more similar to the C code and updated the njit dict to no longer use fastmath

* Added back in the check for interpolate shells

* Added back in old code for interpolate shells and now computes over the interpolated shells

* Fixed interpolate shells function and made sure dataframes are properly returned when computing the intergral

* Fixed bug in counter for Jred_lu pointer

* More explicit about typing.  the value for SIGMA_THOMSON now comes from the numba config (which is should have in the past).  Should now match C code within test criteria

* Finished tests for the numba formal integral helper functions

* Added some docstrings and removed some commented out code

* Removed old import of C formal integral

* Removed deprecated formal integral import

* Changed test to generate a new numba model as to not interfere with other tests

* removed old C interface

* Updated tests and environment to exclude compilers and Cython

* Reformatted conftest so black doesn't complain

* Removed commented out lines, made cleaner

* Added back montecarlo tests since it apepars some r_packet tests are at least set up here.  Also, readded the setup_package.py file

* Removed commented out packages from the environment file

* Slight optimization and readability improvements

* Further optimization, now pre-computes indices of next resonance point

* Removed old binary search, made formatting fixed

Co-authored-by: Andrew Fullard <andrewgfullard@gmail.com>
Co-authored-by: Wolfgang Kerzendorf <wkerzendorf@gmail.com>

tardis/conftest.py

@@ -91,11 +91,9 @@
     PYTEST_HEADER_MODULES["Pandas"] = "pandas"
     PYTEST_HEADER_MODULES["Astropy"] = "astropy"
     PYTEST_HEADER_MODULES["Yaml"] = "yaml"
-    PYTEST_HEADER_MODULES["Cython"] = "cython"
     PYTEST_HEADER_MODULES["h5py"] = "h5py"
     PYTEST_HEADER_MODULES["Matplotlib"] = "matplotlib"
     PYTEST_HEADER_MODULES["Ipython"] = "IPython"
-#     del PYTEST_HEADER_MODULES['h5py']
 except (NameError, KeyError):  # NameError is needed to support Astropy < 1.0
     pass
 

tardis/montecarlo/base.py

@@ -12,7 +12,7 @@
 from tardis.util.base import quantity_linspace
 from tardis.io.util import HDFWriterMixin
 from tardis.montecarlo import packet_source as source
-from tardis.montecarlo.formal_integral import FormalIntegrator
+from tardis.montecarlo.montecarlo_numba.formal_integral import FormalIntegrator
 from tardis.montecarlo import montecarlo_configuration as mc_config_module
 
 
@@ -283,7 +283,6 @@ def run(
 
         set_num_threads(nthreads)
 
-        self._integrator = FormalIntegrator(model, plasma, self)
         self.time_of_simulation = self.calculate_time_of_simulation(model)
         self.volume = model.volume
 
@@ -296,6 +295,7 @@ def run(
 
         configuration_initialize(self, no_of_virtual_packets)
         montecarlo_radial1d(model, plasma, self)
+        self._integrator = FormalIntegrator(model, plasma, self)
         # montecarlo.montecarlo_radial1d(
         #    model, plasma, self,
         #    virtual_packet_flag=no_of_virtual_packets,
@@ -546,7 +546,9 @@ def calculate_f_lambda(self, wavelength):
         pass
 
     @classmethod
-    def from_config(cls, config, packet_source=None, virtual_packet_logging=False):
+    def from_config(
+        cls, config, packet_source=None, virtual_packet_logging=False
+    ):
         """
         Create a new MontecarloRunner instance from a Configuration object.
 
@@ -597,5 +599,8 @@ def from_config(cls, config, packet_source=None, virtual_packet_logging=False):
             debug_packets=config.montecarlo.debug_packets,
             logger_buffer=config.montecarlo.logger_buffer,
             single_packet_seed=config.montecarlo.single_packet_seed,
-            virtual_packet_logging=(config.spectrum.virtual.virtual_packet_logging | virtual_packet_logging),
+            virtual_packet_logging=(
+                config.spectrum.virtual.virtual_packet_logging
+                | virtual_packet_logging
+            ),
         )