Fix trailing spaces found by style CI

.github/workflows/burn_cell_primordial_chem.yml

@@ -47,7 +47,7 @@ jobs:
             value2=$(awk 'NR=='"$line_number"' {match($0, /[+-]?[0-9]+([.][0-9]+)?[eE]?[+-]?[0-9]+/); if (RSTART) print substr($0, RSTART, RLENGTH)}' reference_solution.out)
 
             difference=$(awk -v val1="$value1" -v val2="$value2" 'BEGIN { printf "%.2f", (val1 - val2) / val2 }')
-            
+
             if (( $(echo "$difference > $threshold" | bc -l) )); then
               echo "Line number: $line_number"
               echo "Value in test.out: $value1"

.github/workflows/create_release.yml

@@ -2,8 +2,8 @@ on:
   push:
     # Sequence of patterns matched against refs/tags
     tags:
-      - '[0-9][0-9].[0-9][0-9]' 
-  
+      - '[0-9][0-9].[0-9][0-9]'
+
 name: Create Release
 
 jobs:

.github/workflows/find_changed_files.py

@@ -28,7 +28,7 @@ def find_files(SHAs=None):
     if stderr is not None:
         raise Exception('git diff encountered an error')
 
-    files = [f for f in stdout.decode('utf-8').strip().split('\n') 
+    files = [f for f in stdout.decode('utf-8').strip().split('\n')
              if f.startswith('networks/')]
     print(files)
 

.github/workflows/get_release_txt.py

@@ -26,9 +26,9 @@
                     txt = txt[m.end():].strip()
             else:
                 txt = ""
-                    
-            # we now need to substitute characters in the string so that 
-            # the action can deal with line breaks 
+
+            # we now need to substitute characters in the string so that
+            # the action can deal with line breaks
             txt = txt.replace('%', '%25')
             txt = txt.replace('\n', '%0A')
             txt = txt.replace('\r', '%0D')

CMakeLists.txt

@@ -32,13 +32,13 @@ function(setup_target_for_microphysics_compilation network_name output_dir)
     set(networkdir "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/general_null/")
     set(networkheadertemplatefile "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/general_null/network_header.template")
 
-    set (gamma_law_dirs ${CMAKE_BINARY_DIR} ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/util ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/util/gcem/include 
+    set (gamma_law_dirs ${CMAKE_BINARY_DIR} ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/util ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/util/gcem/include
                              ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/interfaces
                              ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/EOS ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/EOS/gamma_law
-                             ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/general_null  
+                             ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/general_null
                              ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/constants PARENT_SCOPE)
 
-    execute_process(COMMAND python3 "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/util/build_scripts/write_probin.py" --pa "${EOSparamfile} ${networkparamfile} 
+    execute_process(COMMAND python3 "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/util/build_scripts/write_probin.py" --pa "${EOSparamfile} ${networkparamfile}
                     ${VODEparamfile} ${integrationparamfile}" --use_namespace WORKING_DIRECTORY ${output_dir}/)
 
     set(gamma_law_sources ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/interfaces/eos_data.cpp
@@ -57,12 +57,12 @@ function(setup_target_for_microphysics_compilation network_name output_dir)
     set(networkheadertemplatefile "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/general_null/network_header.template")
 
     #DO NOT change the order of the directories below!
-    set (primordial_chem_dirs ${CMAKE_BINARY_DIR} ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/util ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/util/gcem/include 
-                             ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/integration/VODE ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/integration/utils 
+    set (primordial_chem_dirs ${CMAKE_BINARY_DIR} ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/util ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/util/gcem/include
+                             ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/integration/VODE ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/integration/utils
                              ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/integration ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/interfaces
                              ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/EOS ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/EOS/primordial_chem
-                             ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/primordial_chem ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks 
-                             ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/constants 
+                             ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/primordial_chem ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks
+                             ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/constants
                              PARENT_SCOPE)
 
     #we need to have extern_parameters.cpp be available at configure time
@@ -72,11 +72,11 @@ function(setup_target_for_microphysics_compilation network_name output_dir)
     #to generate updated header files
 
     if(BUILD_UNIT_TEST)
-      execute_process(COMMAND python3 "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/util/build_scripts/write_probin.py" --pa "${paramfile} ${EOSparamfile} 
+      execute_process(COMMAND python3 "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/util/build_scripts/write_probin.py" --pa "${paramfile} ${EOSparamfile}
                       ${networkpcparamfile} ${networkparamfile} ${VODEparamfile} ${integrationparamfile} ${unittestparamfile}" --use_namespace WORKING_DIRECTORY ${output_dir}/)
     else()
       #do not need paramfile and unittestparamfile
-      execute_process(COMMAND python3 "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/util/build_scripts/write_probin.py" --pa "${EOSparamfile} ${networkpcparamfile} 
+      execute_process(COMMAND python3 "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/util/build_scripts/write_probin.py" --pa "${EOSparamfile} ${networkpcparamfile}
                       ${networkparamfile} ${VODEparamfile} ${integrationparamfile} " --use_namespace WORKING_DIRECTORY ${output_dir}/)
     endif()
 

deploy_docs_action.sh

@@ -9,10 +9,10 @@ TARGET_BRANCH="gh-pages"
 
 mkdir out
 
-# if on the dev branch, use the dev_layout.html template to get the 
+# if on the dev branch, use the dev_layout.html template to get the
 # links correct
 if [ "$GITHUB_BRANCH" = "$DEV_BRANCH" ]; then
-    mv sphinx_docs/source/_templates/dev_layout.html sphinx_docs/source/_templates/layout.html 
+    mv sphinx_docs/source/_templates/dev_layout.html sphinx_docs/source/_templates/layout.html
 fi
 
 # Build the Sphinx documentation
@@ -24,7 +24,7 @@ mkdir -p out/docs/
 if [ "$GITHUB_BRANCH" = "$MAIN_BRANCH" ]; then
     mkdir -p out/docs
     mv sphinx_docs/build/html/* out/docs
-else 
+else
     mkdir -p out/docs/dev/
     mv sphinx_docs/build/html/* out/docs/dev
 fi

networks/ase/ase.py

@@ -56,14 +56,14 @@ def get_library():
         print("removing: ", r)
         _r = subch.get_rate_by_name(r)
         subch.remove_rate(_r)
-        
+
     # additional neutron rates to remove
     for r in subch.get_rates():
         if (r == subch.get_rate_by_name("mg24(n,a)ne21") or r == subch.get_rate_by_name("ne21(a,n)mg24")
             or r == subch.get_rate_by_name("na22(n,g)na23") or r == subch.get_rate_by_name("na23(g,n)na22")
             or r == subch.get_rate_by_name("ne21(g,n)ne20") or r == subch.get_rate_by_name("ne20(n,g)ne21")):
             continue
-    
+
         if pyna.Nucleus("n") in r.reactants or pyna.Nucleus("n") in r.products:
             print("removing neutron rates: ", r)
             subch.remove_rate(r)

networks/ignition_chamulak/notes.txt

@@ -38,12 +38,12 @@ Basic idea:
                         ---            ---
 
      this means that 60% of the time, we will create Ne20 + O16 and
-     40% of the time we will create Na23 + C13.  
+     40% of the time we will create Na23 + C13.
 
      So the number of nuclei made from consuming 6 C12 is
      ~ 1.2 Ne20, 1.2 O16, 0.8 Na23, 0.8 C13.
 
-     
+
      Doing this, the ash has an A = 18 and a Z = 8.8
 
      We also note that since we are operating in a high temperature
@@ -61,4 +61,4 @@ Basic idea:
      release per C12 consumed), as a function of density.
 
 
-     
+

networks/rprox/reaclib/make_rates_module.py

@@ -50,7 +50,7 @@ def modulePreamble():
 def tFactorData():
     """Add  a routine to initialize the tfactors given the temperature.
     Return this text."""
-    
+
     text="""
 
 contains
@@ -74,7 +74,7 @@ def tFactorData():
 
 def buildRateRoutine(name,aFactors):
     """Given a reaction name and the list of aFactors from the ReacLib rate
-       file, build the appropriate structure for the reaction rate as a 
+       file, build the appropriate structure for the reaction rate as a
        subroutine.  Return this text."""
     text= """
   subroutine %s(tfactors,rate,dratedt)
@@ -142,7 +142,7 @@ def buildRateRoutine(name,aFactors):
         if not aFactors[start+4] == 0.0:
             str += "         +ct9 &\n"
         if not aFactors[start+5] == 0.0:
-            str += "         +FIVE3RD*ct953 &\n" 
+            str += "         +FIVE3RD*ct953 &\n"
         if not aFactors[start+6] == 0.0:
             str += "         +(%sd0))" % (aFactors[start+6])
         else:
@@ -177,7 +177,7 @@ def buildRateRoutine(name,aFactors):
     return text
 
 def numReactantsProducts(chapter):
-    """Return the number of reactants and products (in particles) for a 
+    """Return the number of reactants and products (in particles) for a
     reaction of ReacLib Chapter type chapter."""
     r,p = 1,1
     if chapter in [2,5,9,10]: p+= 1
@@ -190,11 +190,11 @@ def numReactantsProducts(chapter):
     return r,p
 
 def parseRateFile(file):
-    """Given a ReacLib v 1 rate file, file, parse it and determine an 
+    """Given a ReacLib v 1 rate file, file, parse it and determine an
     appropriate name and the "a" factors that build the rate.  Return the
     name as a string and the "a" factors as a list."""
 
-    try: 
+    try:
         fh = open(file,'r')
     except IOError:
         print "Couldn't open file %f for reading" % file
@@ -207,7 +207,7 @@ def parseRateFile(file):
 
     foundLabels = False
     rateString = "rate"
-    
+
     aFactors = []
 
     for line in data[numHeaderLines:]:
@@ -226,7 +226,7 @@ def parseRateFile(file):
             for term in range(nterms):
                 start = term*lengthEntry
                 stop = start + lengthEntry
-                
+
                 aFactors.append(float(line[start:stop]))
 
     if len(aFactors) % numTerms is not 0:
@@ -261,8 +261,8 @@ def weakRate(name,factor):
     return textParameter, textSubroutine
 
 def make_rates_module(rateFiles):
-    """Build the F90 module containing the subroutines for the reactions 
-    given in the list of ReacLib rate files, rateFiles, along with the helper 
+    """Build the F90 module containing the subroutines for the reactions
+    given in the list of ReacLib rate files, rateFiles, along with the helper
     routine to set the common temperature factors.  Return all this as a string
     for easy piping."""
 

sphinx_docs/notes.txt

@@ -6,10 +6,10 @@
 
    https://stackoverflow.com/questions/11347505/what-are-some-approaches-to-outputting-a-python-data-structure-to-restructuredte
 
-   
+
 
 ** index:
 
-  use 
+  use
 
 ..index:: burn_t

sphinx_docs/source/basics.rst

@@ -38,7 +38,7 @@ This will create an executable called ``main3d.gnu.ex``.  Then you can run it as
    ./main3d.gnu.ex inputs_aprox21
 
 By default, the test is built with the 21-isotope ``aprox21`` network.
-Here ``inputs_aprox21`` is the inputs file that sets options. 
+Here ``inputs_aprox21`` is the inputs file that sets options.
 
 
 

sphinx_docs/source/integrators.rst

@@ -22,7 +22,7 @@ The equations we integrate to do a nuclear burn are:
 
 Here, :math:`X_k` is the mass fraction of species :math:`k`, :math:`e` is the specific
 nuclear energy created through reactions. Also needed are density :math:`\rho`,
-temperature :math:`T`, and the specific heat. The function :math:`f` provides the energy release from reactions and can often be expressed in terms of the 
+temperature :math:`T`, and the specific heat. The function :math:`f` provides the energy release from reactions and can often be expressed in terms of the
 instantaneous reaction terms, :math:`\dot{X}_k`. As noted in the previous
 section, this is implemented in a network-specific manner.
 
@@ -70,7 +70,7 @@ routine (at the moment this can be ``VODE``, ``BackwardEuler``, ``ForwardEuler``
     AMREX_GPU_HOST_DEVICE AMREX_FORCE_INLINE
     void burner (burn_t& state, Real dt)
 
-The input is a ``burn_t``.  
+The input is a ``burn_t``.
 
 .. note::
 
@@ -369,7 +369,7 @@ the allowed options are:
 
   The spectral radius is estimated by default using the power method,
   built into RKC.  Alternately, by setting ``integrator.use_circle_theorem=1``,
-  the `Gershgorin circle theorem <https://en.wikipedia.org/wiki/Gershgorin_circle_theorem>`_ 
+  the `Gershgorin circle theorem <https://en.wikipedia.org/wiki/Gershgorin_circle_theorem>`_
   is used instead.
 
 * ``VODE``: the VODE :cite:`vode` integration package.  We ported this
@@ -383,7 +383,7 @@ robust.
 .. important::
 
    The integrator will not abort if it encounters trouble.  Instead it will
-   set ``burn_t burn_state.success = false`` on exit.  It is up to the 
+   set ``burn_t burn_state.success = false`` on exit.  It is up to the
    application code to handle the failure.
 
 .. note::

sphinx_docs/source/networks-overview.rst

@@ -42,7 +42,7 @@ for the ability to swap integrators as desired. We discuss the
 integrators in a later section.
 
 A network is defined by a ``.net`` file which provides a list of species
-and some data about each species (its name and some isotopic data). 
+and some data about each species (its name and some isotopic data).
 
 An example is ``Microphysics/networks/iso7/iso7.net``:
 

sphinx_docs/source/networks.rst

@@ -158,7 +158,7 @@ X_a / (A_a m_u)`, our rate equation is
 
    \begin{align}
     \frac{dX_f}{dt} &= - \frac{r_0}{m_u} \rho X_f^2 \frac{1}{A_f} \left (\frac{T}{T_0}\right)^\nu \equiv \omegadot_f  \\
-    \frac{dX_a}{dt} &= \frac{1}{2}\frac{r_0}{m_u} \rho X_f^2 \frac{A_a}{A_f^2} \left (\frac{T}{T_0}\right)^\nu = \frac{r_0}{m_u} \rho X_f^2 \frac{1}{A_f} \left (\frac{T}{T_0}\right)^\nu 
+    \frac{dX_a}{dt} &= \frac{1}{2}\frac{r_0}{m_u} \rho X_f^2 \frac{A_a}{A_f^2} \left (\frac{T}{T_0}\right)^\nu = \frac{r_0}{m_u} \rho X_f^2 \frac{1}{A_f} \left (\frac{T}{T_0}\right)^\nu
    \end{align}
 
 We define a new rate constant, :math:`\rt` with units of :math:`[\mathrm{s^{-1}}]` as
@@ -287,6 +287,6 @@ to disable rates:
   :math:`\isotm{N}{13}(\alpha,p)\isotm{O}{16}` and its inverse are
   disabled.
 
-Together, these parameters allow us to turn off the sequence 
+Together, these parameters allow us to turn off the sequence
 :math:`\isotm{C}{12}(p,\gamma)\isotm{N}{13}(\alpha, p)\isotm{O}{16}` that
 acts as a bypass for :math:`\isotm{C}{12}(\alpha, \gamma)\isotm{O}{16}`.

sphinx_docs/source/nse.rst

@@ -254,7 +254,7 @@ There are 3 main criteria discussed in the :cite:`Kushnir_2020`.
   An example of such reaction cycle would be:
 
   .. math::
-     
+
      \isotm{S}{32} (\gamma, p)(\gamma, p)(\gamma, n)(\gamma, n) \isotm{Si}{28}
      (\alpha, \gamma) \isotm{S}{32}
 
@@ -265,11 +265,11 @@ There are 3 main criteria discussed in the :cite:`Kushnir_2020`.
   If there are no isotope present in the network that would form a closed-cycle,
   we move on to the next nuclei. We break out of the iteration once we found
   a fast reaction cycle.
-    
+
 * If the previous two check pass, we proceed to nuclei grouping. Initially,
   :math:`p`, :math:`n`, and :math:`\alpha` are grouped into a single group called
   the light-isotope-group, or LIG. Other isotopes belong to their own group,
-  which only contains themselves. During each iteration, we find all valid reaction, 
+  which only contains themselves. During each iteration, we find all valid reaction,
   :math:`k`, that has the fastest time-scale,
   :math:`t_{i,k} = \tilde{Y}_i/\textbf{min}(b_f(k), b_r(k))`, for :math:`i` to be the isotope
   involved with the reaction that is different from :math:`p`, :math:`n`, and :math:`\alpha`.
@@ -283,13 +283,13 @@ There are 3 main criteria discussed in the :cite:`Kushnir_2020`.
     .. math::
 
        t_{i,k} < \epsilon t_s
-       
+
   *
 
     .. math::
 
       2|b_f(k) - b_r(k)|/(b_f(k) + b_r(k) < \epsilon
-    
+
   Here we only consider two cases of reactions:
 
   * There are exactly two isotopes involved in reaction, :math:`k`, that are not in the
@@ -307,7 +307,7 @@ There are 3 main criteria discussed in the :cite:`Kushnir_2020`.
   * Reactions that involve more than 2 reactants and products
 
   * Reactions that have more than 2 non-light-isotope-group.
-    
+
   * The nuclei that participate in the reaction is either in LIG or in another group.
     This means that the non-LIG nuclei have already merged.
 
@@ -320,8 +320,8 @@ There are 3 main criteria discussed in the :cite:`Kushnir_2020`.
   a single group due to the missing neutron rates. Therefore, there is an alternative
   criteria of defining a "single group" when neutron is not present in the network:
   for isotopes, :math:`Z >= 14`, isotopes with odd and even :math:`N` form two
-  distinct groups. 
-  
+  distinct groups.
+
 
 Additional Options
 ------------------

sphinx_docs/source/sdc.rst

@@ -53,9 +53,9 @@ The reactions don’t modify the total density, :math:`\rho`, or momentum,
 
 .. math::
 
-   \frac{d}{dt}\left ( 
-      \begin{array}{c} \rho X_k \\ \rho e \end{array} 
-   \right ) = 
+   \frac{d}{dt}\left (
+      \begin{array}{c} \rho X_k \\ \rho e \end{array}
+   \right ) =
    \left ( \begin{array}{c}
       \Adv{\rho X_k}^{n+1/2} \\ \Adv{\rho e}^{n+1/2} \\
    \end{array} \right ) +