2.4.11 bugfix release (#723)

* fix jktebop backend handling of mass-ratio and eccentricity for RVs. * bumps version requirements in pip for numpy, scipy, astropy. * allows sma@star and asini@star to flip to solve for q * fixes handling of spots on rotating single stars. * fixes constraint migration for 2.3 -> 2.4 --------- Co-authored-by: Jeppe Sinkbæk Thomsen <[email protected]> Co-authored-by: Michael Abdul-Masih <[email protected]> Co-authored-by: David Jones <[email protected]> Co-authored-by: Andrej Prsa <[email protected]>
phoebe-project · Jun 16, 2023 · 7bc4489 · 7bc4489
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Showing 20 changed files with 856 additions and 13 deletions.
diff --git a/.github/workflows/on_pr_test_python_31x.yml b/.github/workflows/on_pr_test_python_31x.yml
@@ -97,7 +97,23 @@ jobs:
     - name: Test photodynam install
       run: |
         python -c "import photodynam"
-  
+
+    - name: Setup GNU Fortran
+      uses: modflowpy/install-gfortran-action@v1
+
+    - name: Install jktebop
+      run: |
+        wget https://www.astro.keele.ac.uk/jkt/codes/jktebop-v43.tgz
+        tar -xvzf jktebop-v43.tgz
+        cd jktebop43
+        gfortran -o jktebop jktebop.f
+        echo $(pwd) >> $GITHUB_PATH
+        cd ..
+
+    - name: Test jktebop install
+      run: |
+        jktebop
+
     - name: Run tests
       run: |
         pytest --verbose --capture=no --full-trace tests/nosetests/
diff --git a/.github/workflows/on_pr_test_python_37.yml b/.github/workflows/on_pr_test_python_37.yml
@@ -88,6 +88,22 @@ jobs:
       run: |
         python -c "import photodynam"
 
+    - name: Setup GNU Fortran
+      uses: modflowpy/install-gfortran-action@v1
+
+    - name: Install jktebop
+      run: |
+        wget https://www.astro.keele.ac.uk/jkt/codes/jktebop-v43.tgz
+        tar -xvzf jktebop-v43.tgz
+        cd jktebop43
+        gfortran -o jktebop jktebop.f
+        echo $(pwd) >> $GITHUB_PATH
+        cd ..
+
+    - name: Test jktebop install
+      run: |
+        jktebop
+
     - name: Run tests
       run: |
         pytest --verbose --capture=no tests/nosetests/
diff --git a/.github/workflows/on_pr_test_python_38.yml b/.github/workflows/on_pr_test_python_38.yml
@@ -107,6 +107,22 @@ jobs:
       run: |
         python -c "import photodynam"
 
+    - name: Setup GNU Fortran
+      uses: modflowpy/install-gfortran-action@v1
+
+    - name: Install jktebop
+      run: |
+        wget https://www.astro.keele.ac.uk/jkt/codes/jktebop-v43.tgz
+        tar -xvzf jktebop-v43.tgz
+        cd jktebop43
+        gfortran -o jktebop jktebop.f
+        echo $(pwd) >> $GITHUB_PATH
+        cd ..
+
+    - name: Test jktebop install
+      run: |
+        jktebop
+
     - name: Run tests
       run: |
         pytest --verbose --capture=no tests/nosetests/
diff --git a/.github/workflows/on_pr_test_python_39.yml b/.github/workflows/on_pr_test_python_39.yml
@@ -88,6 +88,23 @@ jobs:
       run: |
         python -c "import photodynam"
 
+    - name: Setup GNU Fortran
+      uses: modflowpy/install-gfortran-action@v1
+
+    - name: Install jktebop
+      run: |
+        wget https://www.astro.keele.ac.uk/jkt/codes/jktebop-v43.tgz
+        tar -xvzf jktebop-v43.tgz
+        cd jktebop43
+        gfortran -o jktebop jktebop.f
+        echo $(pwd) >> $GITHUB_PATH
+        cd ..
+
+    - name: Test jktebop install
+      run: |
+        echo $PATH
+        jktebop
+
     - name: Run tests
       run: |
         pytest --verbose --capture=no --full-trace tests/nosetests/
diff --git a/.gitignore b/.gitignore
@@ -18,7 +18,8 @@ MANIFEST
 *.log
 *.txt
 *.png
+*.so
+*.egg-info
 .DS_Store
-libphoebe.so
 
 *.swp
diff --git a/README.md b/README.md
@@ -85,6 +85,14 @@ To understand how to use PHOEBE, please consult the [tutorials, scripts and manu
 CHANGELOG
 ----------
 
+### 2.4.11
+
+* fix jktebop backend handling of mass-ratio and eccentricity for RVs.
+* bumps version requirements in pip for numpy, scipy, astropy.
+* allows sma@star and asini@star to flip to solve for q
+* fixes handling of spots on rotating single stars.
+* fixes constraint migration for 2.3 -> 2.4 
+
 ### 2.4.10
 
 * fixes implementation of gravitational redshift.

diff --git a/phoebe/__init__.py b/phoebe/__init__.py
@@ -17,7 +17,7 @@
 
 """
 
-__version__ = '2.4.10'
+__version__ = '2.4.11'
 
 import os as _os
 import sys as _sys

diff --git a/phoebe/backend/backends.py b/phoebe/backend/backends.py
@@ -2145,8 +2145,11 @@ def _worker_setup(self, b, compute, infolist, **kwargs):
         rA = b.get_value(qualifier='requiv', component=starrefs[0], context='component', unit=u.solRad, **_skip_filter_checks)
         rB = b.get_value(qualifier='requiv', component=starrefs[1], context='component', unit=u.solRad, **_skip_filter_checks)
         sma = b.get_value(qualifier='sma', component=orbitref, context='component', unit=u.solRad, **_skip_filter_checks)
+        sma_A = b.get_value(qualifier='sma', component=starrefs[0], context='component', unit=u.solRad, **_skip_filter_checks)
+        sma_B = b.get_value(qualifier='sma', component=starrefs[1], context='component', unit=u.solRad, **_skip_filter_checks)
         incl = b.get_value(qualifier='incl', component=orbitref, context='component', unit=u.deg, **_skip_filter_checks)
         q = b.get_value(qualifier='q', component=orbitref, context='component', **_skip_filter_checks)
+        ecc = b.get_value(qualifier='ecc', component=orbitref, context='component', **_skip_filter_checks)
         ecosw = b.get_value(qualifier='ecosw', component=orbitref, context='component', **_skip_filter_checks)
         esinw = b.get_value(qualifier='esinw', component=orbitref, context='component', **_skip_filter_checks)
 
@@ -2167,7 +2170,11 @@ def _worker_setup(self, b, compute, infolist, **kwargs):
                     ecosw=ecosw, esinw=esinw,
                     gravbA=gravbA, gravbB=gravbB,
                     period=period, t0_supconj=t0_supconj,
-                    pblums=kwargs.get('pblums'))
+                    pblums=kwargs.get('pblums'),
+                    sma_A=sma_A,
+                    sma_B=sma_B,
+                    ecc=ecc
+                    )
 
     def _run_single_dataset(self, b, info, **kwargs):
         """
@@ -2183,12 +2190,15 @@ def _run_single_dataset(self, b, info, **kwargs):
         rA = kwargs.get('rA')
         rB = kwargs.get('rB')
         sma = kwargs.get('sma')
+        sma_A = kwargs.get('sma_A')
+        sma_B = kwargs.get('sma_B')
         incl = kwargs.get('incl')
         q = kwargs.get('q')
         if distortion_method == 'sphere':
             q *= -1
         ecosw = kwargs.get('ecosw')
         esinw = kwargs.get('esinw')
+        ecc = kwargs.get('ecc')
         gravbA = kwargs.get('gravbA')
         gravbB = kwargs.get('gravbB')
         period = kwargs.get('period')
@@ -2337,7 +2347,8 @@ def _run_single_dataset(self, b, info, **kwargs):
         #~ fi.write('rv2 llaqr-rv2.dat llaqr-rv2.out 55.0 -10.0 0 0\n')
         if info['kind'] == 'rv':
             # NOTE: we disable systemic velocity as it will be added in bundle.run_compute
-            K = np.pi * (sma*u.solRad).to(u.km).value * np.sin((incl*u.deg).to(u.rad).value) / (period*u.d).to(u.s).value
+            sma_ = sma_A if info['component'] == starrefs[0] else sma_B
+            K = np.pi * 2*(sma_*u.solRad).to(u.km).value * np.sin((incl*u.deg).to(u.rad).value) / ((period*u.d).to(u.s).value * np.sqrt(1-ecc**2))
             fi.write('{} {} {} {} {} 0 0\n'.format('rv1' if info['component'] == starrefs[0] else 'rv2', tmpfilenamervin, tmpfilenamervout, K, 0.0))
 
 

diff --git a/phoebe/backend/universe.py b/phoebe/backend/universe.py
@@ -2432,7 +2432,7 @@ def is_convex(self):
     def needs_recompute_instantaneous(self):
         # recompute instantaneous for asynchronous spots, even if meshing
         # doesn't need to be recomputed
-        return self.needs_remesh or (len(self.features) and self.F != 1.0)
+        return self.needs_remesh or (not self.is_single and len(self.features) and self.F != 1)
 
     @property
     def needs_remesh(self):

diff --git a/phoebe/frontend/bundle.py b/phoebe/frontend/bundle.py
@@ -989,9 +989,9 @@ def existing_value(param):
                 logger.warning("re-creating {} constraint".format(constraint.twig))
                 solved_for = constraint.get_constrained_parameter()
                 b.remove_constraint(uniqueid=constraint.uniqueid)
-                new_constraint = b.add_constraint(constraint.constraint_func, component=constraint.component)
+                new_constraint_ps = b.add_constraint(constraint.constraint_func, component=constraint.component)
                 if solved_for.qualifier != constraint.constraint_func:
-                    new_constraint.flip_for(solved_for.twig)
+                    new_constraint_ps.get_parameter().flip_for(solved_for.twig)
 
 
         if conf_interactive_checks:

diff --git a/phoebe/parameters/constraint.py b/phoebe/parameters/constraint.py
@@ -1778,7 +1778,7 @@ def mass(b, component, solve_for=None, **kwargs):
     #
     # return lhs, rhs, [esinw, ecosw, ecc, per0], {'orbit': orbit}
 
-_validsolvefor['comp_sma'] = ['sma@orbit', 'incl@orbit']
+_validsolvefor['comp_sma'] = ['sma@orbit', 'incl@orbit', 'q']
 def comp_sma(b, component, solve_for=None, **kwargs):
     """
     Create a constraint for the star's semi-major axes WITHIN its
@@ -1854,12 +1854,20 @@ def comp_sma(b, component, solve_for=None, **kwargs):
         lhs = sma
         rhs = compsma * qthing
 
+    elif solve_for == q:
+        if hier.get_primary_or_secondary(component)=='primary':
+            lhs = q
+            rhs = 1.0 / ((sma / compsma) - 1.0)
+        else:
+            lhs = q
+            rhs = (sma / compsma) - 1.0
+
     else:
         raise NotImplementedError
 
     return lhs, rhs, [], {'component': component}
 
-_validsolvefor['comp_asini'] = ['asini@star', 'sma@orbit']
+_validsolvefor['comp_asini'] = ['asini@star', 'sma@orbit', 'q']
 def comp_asini(b, component, solve_for=None, **kwargs):
     """
     Create a constraint for the star's projected semi-major axes WITHIN its
@@ -1934,6 +1942,13 @@ def comp_asini(b, component, solve_for=None, **kwargs):
         lhs = sma
         rhs = compasini / sin(incl) * qthing
 
+    elif solve_for == q:
+        if hier.get_primary_or_secondary(component)=='primary':
+            lhs = q
+            rhs = 1.0 / (((sma * sin(incl)) / compasini) - 1.0)
+        else:
+            lhs = q
+            rhs = ((sma * sin(incl)) / compasini) - 1.0
     else:
         raise NotImplementedError
 

diff --git a/phoebe/parameters/figure/common.py b/phoebe/parameters/figure/common.py
@@ -205,9 +205,9 @@ def _figure_style_nosources(b, cycler='default', **kwargs):
 
     params += [ChoiceParameter(qualifier='color', value=b._mplcolorcyclers.get(cycler).get(kwargs.get('color', None)), choices=_mplcolors, description='Default color when plotted via run_figure')]
 
-    params += [ChoiceParameter(qualifier='marker', value=b._mplmarkercyclers.get(cycler).get(kwargs.get('marker', None)) if kwargs.get('marker', None) is not "None" else "None", choices=["None"] + _mplmarkers, description='Default marker when plotted via run_figure')]
+    params += [ChoiceParameter(qualifier='marker', value=b._mplmarkercyclers.get(cycler).get(kwargs.get('marker', None)) if kwargs.get('marker', None) != "None" else "None", choices=["None"] + _mplmarkers, description='Default marker when plotted via run_figure')]
 
-    params += [ChoiceParameter(qualifier='linestyle', value=b._mpllinestylecyclers.get(cycler).get(kwargs.get('linestyle', None)) if kwargs.get('linestyle', None) is not "None" else "None", choices=["None"] + _mpllinestyles, description='Default linestyle when plotted via run_figure')]
+    params += [ChoiceParameter(qualifier='linestyle', value=b._mpllinestylecyclers.get(cycler).get(kwargs.get('linestyle', None)) if kwargs.get('linestyle', None) != "None" else "None", choices=["None"] + _mpllinestyles, description='Default linestyle when plotted via run_figure')]
 
     return params
 

diff --git a/setup.py b/setup.py
@@ -405,7 +405,7 @@ def _env_variable_bool(key, default):
     long_description = "\n".join(long_description_s[long_description_s.index("INTRODUCTION"):])
 
 setup (name = 'phoebe',
-       version = '2.4.10',
+       version = '2.4.11',
        description = 'PHOEBE 2.4',
        long_description=long_description,
        author = 'PHOEBE development team',

diff --git a/tests/nosetests/test_jktebop_agreement/jktebop1.rv1.out b/tests/nosetests/test_jktebop_agreement/jktebop1.rv1.out
@@ -0,0 +1,101 @@
+#     TIME       RV_STAR_A    ERROR      PHASE        MODEL      (O-C)
+      0.000000     1.00000  -1.000000   0.00000000    0.00000    1.00000
+      0.010101     1.00000  -1.000000   0.01010100   -8.50328    9.50328
+      0.020202     1.00000  -1.000000   0.02020200  -16.97233   17.97233
+      0.030303     1.00000  -1.000000   0.03030300  -25.37303   26.37303
+      0.040404     1.00000  -1.000000   0.04040400  -33.67156   34.67156
+      0.050505     1.00000  -1.000000   0.05050500  -41.83451   42.83451
+      0.060606     1.00000  -1.000000   0.06060600  -49.82901   50.82901
+      0.070707     1.00000  -1.000000   0.07070700  -57.62287   58.62287
+      0.080808     1.00000  -1.000000   0.08080800  -65.18470   66.18470
+      0.090909     1.00000  -1.000000   0.09090900  -72.48405   73.48405
+      0.101010     1.00000  -1.000000   0.10101000  -79.49154   80.49154
+      0.111111     1.00000  -1.000000   0.11111100  -86.17894   87.17894
+      0.121212     1.00000  -1.000000   0.12121200  -92.51933   93.51933
+      0.131313     1.00000  -1.000000   0.13131300  -98.48718   99.48718
+      0.141414     1.00000  -1.000000   0.14141400 -104.05845  105.05845
+      0.151515     1.00000  -1.000000   0.15151500 -109.21073  110.21073
+      0.161616     1.00000  -1.000000   0.16161600 -113.92324  114.92324
+      0.171717     1.00000  -1.000000   0.17171700 -118.17704  119.17704
+      0.181818     1.00000  -1.000000   0.18181800 -121.95497  122.95497
+      0.191919     1.00000  -1.000000   0.19191900 -125.24184  126.24184
+      0.202020     1.00000  -1.000000   0.20202000 -128.02440  129.02440
+      0.212121     1.00000  -1.000000   0.21212100 -130.29145  131.29145
+      0.222222     1.00000  -1.000000   0.22222200 -132.03387  133.03387
+      0.232323     1.00000  -1.000000   0.23232300 -133.24464  134.24464
+      0.242424     1.00000  -1.000000   0.24242400 -133.91887  134.91887
+      0.252525     1.00000  -1.000000   0.25252500 -134.05387  135.05387
+      0.262626     1.00000  -1.000000   0.26262600 -133.64907  134.64907
+      0.272727     1.00000  -1.000000   0.27272700 -132.70612  133.70612
+      0.282828     1.00000  -1.000000   0.28282800 -131.22882  132.22882
+      0.292929     1.00000  -1.000000   0.29292900 -129.22310  130.22310
+      0.303030     1.00000  -1.000000   0.30303000 -126.69704  127.69704
+      0.313131     1.00000  -1.000000   0.31313100 -123.66082  124.66082
+      0.323232     1.00000  -1.000000   0.32323200 -120.12667  121.12667
+      0.333333     1.00000  -1.000000   0.33333300 -116.10881  117.10881
+      0.343434     1.00000  -1.000000   0.34343400 -111.62342  112.62342
+      0.353535     1.00000  -1.000000   0.35353500 -106.68856  107.68856
+      0.363636     1.00000  -1.000000   0.36363600 -101.32410  102.32410
+      0.373737     1.00000  -1.000000   0.37373700  -95.55166   96.55166
+      0.383838     1.00000  -1.000000   0.38383800  -89.39445   90.39445
+      0.393939     1.00000  -1.000000   0.39393900  -82.87729   83.87729
+      0.404040     1.00000  -1.000000   0.40404000  -76.02642   77.02642
+      0.414141     1.00000  -1.000000   0.41414100  -68.86941   69.86941
+      0.424242     1.00000  -1.000000   0.42424200  -61.43509   62.43509
+      0.434343     1.00000  -1.000000   0.43434300  -53.75339   54.75339
+      0.444444     1.00000  -1.000000   0.44444400  -45.85525   46.85525
+      0.454545     1.00000  -1.000000   0.45454500  -37.77246   38.77246
+      0.464646     1.00000  -1.000000   0.46464600  -29.53758   30.53758
+      0.474747     1.00000  -1.000000   0.47474700  -21.18376   22.18376
+      0.484848     1.00000  -1.000000   0.48484800  -12.74464   13.74464
+      0.494949     1.00000  -1.000000   0.49494900   -4.25420    5.25420
+      0.505051     1.00000  -1.000000   0.50505100    4.25420   -3.25420
+      0.515152     1.00000  -1.000000   0.51515200   12.74464  -11.74464
+      0.525253     1.00000  -1.000000   0.52525300   21.18376  -20.18376
+      0.535354     1.00000  -1.000000   0.53535400   29.53758  -28.53758
+      0.545455     1.00000  -1.000000   0.54545500   37.77246  -36.77246
+      0.555556     1.00000  -1.000000   0.55555600   45.85525  -44.85525
+      0.565657     1.00000  -1.000000   0.56565700   53.75339  -52.75339
+      0.575758     1.00000  -1.000000   0.57575800   61.43509  -60.43509
+      0.585859     1.00000  -1.000000   0.58585900   68.86941  -67.86941
+      0.595960     1.00000  -1.000000   0.59596000   76.02642  -75.02642
+      0.606061     1.00000  -1.000000   0.60606100   82.87729  -81.87729
+      0.616162     1.00000  -1.000000   0.61616200   89.39445  -88.39445
+      0.626263     1.00000  -1.000000   0.62626300   95.55166  -94.55166
+      0.636364     1.00000  -1.000000   0.63636400  101.32410 -100.32410
+      0.646465     1.00000  -1.000000   0.64646500  106.68856 -105.68856
+      0.656566     1.00000  -1.000000   0.65656600  111.62342 -110.62342
+      0.666667     1.00000  -1.000000   0.66666700  116.10881 -115.10881
+      0.676768     1.00000  -1.000000   0.67676800  120.12667 -119.12667
+      0.686869     1.00000  -1.000000   0.68686900  123.66082 -122.66082
+      0.696970     1.00000  -1.000000   0.69697000  126.69704 -125.69704
+      0.707071     1.00000  -1.000000   0.70707100  129.22310 -128.22310
+      0.717172     1.00000  -1.000000   0.71717200  131.22882 -130.22882
+      0.727273     1.00000  -1.000000   0.72727300  132.70612 -131.70612
+      0.737374     1.00000  -1.000000   0.73737400  133.64907 -132.64907
+      0.747475     1.00000  -1.000000   0.74747500  134.05387 -133.05387
+      0.757576     1.00000  -1.000000   0.75757600  133.91887 -132.91887
+      0.767677     1.00000  -1.000000   0.76767700  133.24464 -132.24464
+      0.777778     1.00000  -1.000000   0.77777800  132.03387 -131.03387
+      0.787879     1.00000  -1.000000   0.78787900  130.29145 -129.29145
+      0.797980     1.00000  -1.000000   0.79798000  128.02440 -127.02440
+      0.808081     1.00000  -1.000000   0.80808100  125.24184 -124.24184
+      0.818182     1.00000  -1.000000   0.81818200  121.95497 -120.95497
+      0.828283     1.00000  -1.000000   0.82828300  118.17704 -117.17704
+      0.838384     1.00000  -1.000000   0.83838400  113.92324 -112.92324
+      0.848485     1.00000  -1.000000   0.84848500  109.21073 -108.21073
+      0.858586     1.00000  -1.000000   0.85858600  104.05845 -103.05845
+      0.868687     1.00000  -1.000000   0.86868700   98.48718  -97.48718
+      0.878788     1.00000  -1.000000   0.87878800   92.51933  -91.51933
+      0.888889     1.00000  -1.000000   0.88888900   86.17894  -85.17894
+      0.898990     1.00000  -1.000000   0.89899000   79.49154  -78.49154
+      0.909091     1.00000  -1.000000   0.90909100   72.48405  -71.48405
+      0.919192     1.00000  -1.000000   0.91919200   65.18470  -64.18470
+      0.929293     1.00000  -1.000000   0.92929300   57.62287  -56.62287
+      0.939394     1.00000  -1.000000   0.93939400   49.82901  -48.82901
+      0.949495     1.00000  -1.000000   0.94949500   41.83451  -40.83451
+      0.959596     1.00000  -1.000000   0.95959600   33.67156  -32.67156
+      0.969697     1.00000  -1.000000   0.96969700   25.37303  -24.37303
+      0.979798     1.00000  -1.000000   0.97979800   16.97233  -15.97233
+      0.989899     1.00000  -1.000000   0.98989900    8.50328   -7.50328
+      1.000000     1.00000  -1.000000   0.00000000    0.00000    1.00000