adding sphinx-lint

MESAHub · Feb 13, 2025 · a5eda76 · a5eda76
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diff --git a/.github/workflows/static-analysis.yml b/.github/workflows/static-analysis.yml
@@ -33,4 +33,8 @@ jobs:
         run: |
           cd ${{ github.workspace }}
           black --check .
-        
+        
+      - name: Apply RST linter, sphinx-lint
+        run: |
+          cd ${{ github.workspace }}
+          sphinx-lint --ignore=gyre/gyre
diff --git a/.zenodo.json b/.zenodo.json
@@ -43,7 +43,7 @@
             "affiliation": "Trinity College Dublin",
             "name": "Farrell, Eoin",
             "orcid": "0000-0001-5631-5878"
-        },   
+        },
         {
             "affiliation": "Center for Computational Astrophysics",
             "name": "Jermyn, Adam",

diff --git a/README.rst b/README.rst
@@ -42,7 +42,7 @@ Modules for Experiments in Stellar Astrophysics (MESA)
 Overview
 ========
 
-MESA is a powerful and versatile open-source software suite built to 
+MESA is a powerful and versatile open-source software suite built to
 allow users to run experiments in stellar evolution.
 Stellar evolution calculations (i.e., stellar evolution tracks and
 detailed information about the evolution of internal and global
@@ -71,7 +71,7 @@ Links
 * `Landing page <https://mesastar.org/>`__ for links to all things MESA.
 * `Code repository <https://github.com/MESAHub/mesa>`__ on GitHub (this page).
 * `Documentation <https://docs.mesastar.org/>`__ for up-to-date information about installing and running MESA.
-* `MESA Marketplace <http://cococubed.com/mesa_market/>`__ for resources for published papers using MESA. 
+* `MESA Marketplace <http://cococubed.com/mesa_market/>`__ for resources for published papers using MESA.
 * `MESA Zenodo Community <https://zenodo.org/communities/mesa/records?q=&l=list&p=1&s=10>`__ for downloading official release versions, SDKs, and MESA project inlists.
 * `MESA Users Mailing List <https://lists.mesastar.org/mailman/listinfo/mesa-users>`__ for info about new releases, news items, and requests for help/bug reports.
 * `mesa_reader <https://github.com/wmwolf/py_mesa_reader>`__ to interact and plot data from MESA in Python.

diff --git a/astero/defaults/astero_pgstar.defaults b/astero/defaults/astero_pgstar.defaults
@@ -7,19 +7,19 @@
    ! PGSTAR echelle plot
    ! -------------------
    ! ::
-   
+
          echelle_win_flag = .false.
 
          echelle_win_width = 6
          echelle_win_aspect_ratio = 0.6 ! aspect_ratio = height/width
-         
+
          echelle_xleft = 0.15
          echelle_xright = 0.85
          echelle_ybot = 0.15
          echelle_ytop = 0.85
          echelle_txt_scale = 1.0
-         echelle_title = 'Echelle'      
-         
+         echelle_title = 'Echelle'
+
          echelle_delta_nu = 0 ! <= 0 means use seismic delta_nu from search inlist
 
          show_echelle_next_best_at_higher_frequency = .false.
@@ -29,7 +29,7 @@
          show_echelle_annotation1 = .false.
          show_echelle_annotation2 = .false.
          show_echelle_annotation3 = .false.
-         
+
 !          ! file output
 
          echelle_file_flag = .false.
@@ -47,19 +47,19 @@
    ! PGSTAR ratios plot
    ! ------------------
    ! ::
-   
+
          ratios_win_flag = .false.
 
          ratios_win_width = 6
          ratios_win_aspect_ratio = 1.2 ! aspect_ratio = height/width
-         
+
          ratios_xleft = 0.15
          ratios_xright = 0.85
          ratios_ybot = 0.15
          ratios_ytop = 0.85
          ratios_txt_scale = 1.0
-         ratios_title = 'Ratios'      
-         
+         ratios_title = 'Ratios'
+
          ratios_margin_sig_factor = 1 ! controls horizontal margin in units of max sigma
 
          show_ratios_annotation1 = .false.

diff --git a/binary/defaults/binary_controls.defaults b/binary/defaults/binary_controls.defaults
@@ -607,7 +607,7 @@
 
 ! Tolerance for which a solution is considered valid. For the Ritter and Kolb
 ! schemes if we call mdot the mass transfer rate used for the step, and mdot_end
-! the one computed at the end of it, a solution is valid if :: 
+! the one computed at the end of it, a solution is valid if ::
 
 !     abs((mdot-mdot_end)/mdot_end) < b% implicit_scheme_tolerance
 
@@ -1004,7 +1004,7 @@
 ! do_j_accretion
 ! ~~~~~~~~~~~~~~
 
-! If true, compute accretion of angular momentum following A.3.3 of 
+! If true, compute accretion of angular momentum following A.3.3 of
 ! de Mink et al. 2013, ApJ, 764, 166. Otherwise, incoming  material is
 ! assumed to have the specific angular momentum of the surface of the accretor.
 
@@ -1210,7 +1210,7 @@
 ! col_depth_for_eps_extra
 ! ~~~~~~~~~~~~~~~~~~~~~~~
 
-! Energy from irradiation will be deposited in the outer 
+! Energy from irradiation will be deposited in the outer
 ! ``4*Pi*R^2*col_depth_for_eps_extra`` grams of the star.
 
 ! ::

diff --git a/binary/test_suite/evolve_both_stars/README.rst b/binary/test_suite/evolve_both_stars/README.rst
@@ -90,12 +90,12 @@ pgstar commands used for the binary and star1 plots above:
 
   Text_Summary1_name(4,1) = 'Jdot'
   Text_Summary1_name(4,2) = 'jdot_gr'
-  Text_Summary1_name(4,3) = 'jdot_mb' 
+  Text_Summary1_name(4,3) = 'jdot_mb'
   Text_Summary1_name(4,4) = 'jdot_ls'
   Text_Summary1_name(4,5) = 'jdot_ml'
-  Text_Summary1_name(4,6) = '' 
-  Text_Summary1_name(4,7) = '' 
-  Text_Summary1_name(4,8) = '' 
+  Text_Summary1_name(4,6) = ''
+  Text_Summary1_name(4,7) = ''
+  Text_Summary1_name(4,8) = ''
 
   History_Track1_win_flag = .false.
   History_Track1_win_width = 12
@@ -228,8 +228,8 @@ pgstar commands used for the binary and star1 plots above:
   Grid1_file_dir = 'pgstar_out'
   Grid1_file_prefix = 'grid_'
   Grid1_file_interval = 10000
-  Grid1_file_width = -1      
-  Grid1_file_aspect_ratio = -1 
+  Grid1_file_width = -1
+  Grid1_file_aspect_ratio = -1
 
  / ! end of pgstar namelist
 

diff --git a/binary/test_suite/jdot_gr_check/README.rst b/binary/test_suite/jdot_gr_check/README.rst
@@ -4,7 +4,7 @@
 jdot_gr_check
 *************
 
-This test case verifies that the orbital evolution due to GW emission follows the 
+This test case verifies that the orbital evolution due to GW emission follows the
 analytical result of `Peters (1964) <https://ui.adsabs.harvard.edu/abs/1964PhRv..136.1224P>`_.
 
 This test case has 1 part. Click to see a larger version of a plot.
@@ -201,7 +201,7 @@ pgstar commands used for the plot above:
  Grid1_file_prefix = 'grid_'
  Grid1_file_interval = 10000
  Grid1_file_width = -1
- Grid1_file_aspect_ratio = -1         
+ Grid1_file_aspect_ratio = -1
  / ! end of pgstar namelist
 
 Last-Updated: 12Jul2021 (MESA 094ff71) by fxt.

diff --git a/binary/test_suite/jdot_ls_check/README.rst b/binary/test_suite/jdot_ls_check/README.rst
@@ -188,7 +188,7 @@ pgstar commands used for the plot above:
  Grid1_file_prefix = 'grid_'
  Grid1_file_interval = 10000
  Grid1_file_width = -1
- Grid1_file_aspect_ratio = -1         
+ Grid1_file_aspect_ratio = -1
 
  / ! end of pgstar namelist
 

diff --git a/binary/test_suite/jdot_ml_check/README.rst b/binary/test_suite/jdot_ml_check/README.rst
@@ -7,7 +7,7 @@ jdot_ml_check
 This test case checks the evolution of one star plus a point mass, including mass transfer to the point mass.
 Using pre-specified efficiency options, verifies that the binary evolution, including mass transfer to the point mass,
 follows the analytical result of `Tauris & van den Heuvel (2006)
-<https://ui.adsabs.harvard.edu/abs/2006csxs.book..623T>`_. 
+<https://ui.adsabs.harvard.edu/abs/2006csxs.book..623T>`_.
 
 This test case has 1 part. Click to see a larger version of a plot.
 
@@ -207,7 +207,7 @@ pgstar commands used for the binary and star1 plots above:
  Grid1_file_prefix = 'grid_'
  Grid1_file_interval = 10000
  Grid1_file_width = -1
- Grid1_file_aspect_ratio = -1         
+ Grid1_file_aspect_ratio = -1
 
 
   Profile_Panels2_win_flag = .true.

diff --git a/binary/test_suite/star_plus_point_mass/README.rst b/binary/test_suite/star_plus_point_mass/README.rst
@@ -97,7 +97,7 @@ pgstar commands used for the plots above:
   History_Track2_file_interval = 100
   History_Track2_file_width = -1
   History_Track2_file_aspect_ratio = -1
-         
+
 
   Kipp_win_flag = .true.
   Kipp_win_width = 12

diff --git a/binary/test_suite/star_plus_point_mass_explicit_mdot/README.rst b/binary/test_suite/star_plus_point_mass_explicit_mdot/README.rst
@@ -96,7 +96,7 @@ pgstar commands used for the plots above:
   History_Track2_file_interval = 100
   History_Track2_file_width = -1
   History_Track2_file_aspect_ratio = -1
-         
+
 
   Kipp_win_flag = .true.
   Kipp_win_width = 12

diff --git a/docs/source/atm/mapping.rst b/docs/source/atm/mapping.rst
@@ -32,7 +32,7 @@ to the new one described here, the mapping is as follows:
 
    * - ``which_atm_option == 'grey_irradiated'``
      - | ``atm_option == 'irradiated_grey'``
-       | ``atm_irradiated_opacity == 'fixed | varying'`` 
+       | ``atm_irradiated_opacity == 'fixed | varying'``
 
 .. note::
    If MESA is run using one of the old options, it will print out the

diff --git a/docs/source/atm/t-tau.rst b/docs/source/atm/t-tau.rst
@@ -8,7 +8,7 @@ relation, as follows:
 
 .. list-table:: The ``atm_T_tau_relation`` control
    :widths: 25 75
-	    
+
    * - Value
      - Meaning
 
@@ -24,7 +24,7 @@ relation, as follows:
    * - ``'Krishna_Swamy'``
      - Use the approximate Hopf function given by Krishna-Swamy
        (1966, ApJ, 145, 174).
-    
+
 For the selected :math:`T(\tau)` relation, the pressure structure of
 the atmosphere is obtained by integrating the equation of hydrostatic
 equilibrium

diff --git a/docs/source/atm/table.rst b/docs/source/atm/table.rst
@@ -30,15 +30,15 @@ the boundary conditions. The interpolations are performed using
    * - ``'tau_10'``
      - Same as ``'tau_100'``, except that surface optical depth is
        :math:`\tau_{\rm surf} = 10`.
-  
+
    * - ``'tau_1'``
      - Same as ``'tau_100'``, except that surface optical depth is
        :math:`\tau_{\rm surf} = 1`.
-  
+
    * - ``'tau_1m1'``
      - Same as ``'tau_100'``, except that surface optical depth is
        :math:`\tau_{\rm surf} = 0.1`.
-  
+
    * - ``'WD_tau_25'``
      - Use model atmospheres for cool white dwarfs, via Rohrmann et
        al. (2011, MNRAS, 411, 781) treatment. Surface optical depth

diff --git a/docs/source/auto_diff/example.rst b/docs/source/auto_diff/example.rst
@@ -71,7 +71,7 @@ Instead, we could use ``auto_diff``::
 
  type(auto_diff_real_4var_order1) :: L, lnR, lnM, lnkap, M, R, kap, g, lnT, lnP
  real(dp) :: g
- 
+
  ! Set up auto_diff base variables.
  ! Note that the ordering of which variable goes in which d1val slot doesn't matter.
  ! We just need to use the same ordering when reading the results out.

diff --git a/docs/source/auto_diff/more_detail.rst b/docs/source/auto_diff/more_detail.rst
@@ -81,7 +81,7 @@ Behind the scenes are ludicrously large Fortran files, which begin like:
          use utils_lib
          use support_functions
          use math_lib
-      
+
          implicit none
          private
       public :: auto_diff_real_1var_order1, &
@@ -200,7 +200,7 @@ Two functions I want to highlight are ``make_unop`` and ``make_binop``:
          unary%val = z_val
          unary%d1val1 = x%d1val1*z_d1x
       end function make_unary_operator
-      
+
       function make_binary_operator(x, y, z_val, z_d1x, z_d1y) result(binary)
          type(auto_diff_real_1var_order1), intent(in) :: x
          type(auto_diff_real_1var_order1), intent(in) :: y