Handle old functions and update examples

.gitignore

@@ -265,3 +265,4 @@ package.json
 # Repo specific
 examples/using_sunkit_magex_pfss/aia_map.fits
 docs/sg_execution_times.rst
+aia_map.fits

CHANGELOG.rst

@@ -0,0 +1,22 @@
+1.0.0 (2024-05-31)
+==================
+
+This is the first release and aims to keep the API the same from `pfsspy` to
+`sunkit_magex`.  The main difference is that you will need to replace the
+import like so:
+
+  .. code-block:: python
+
+    # Before
+    import pfsspy
+    from pfsspy import tracing
+
+    # After
+    from sunkit_magex import pfss as pfsspy
+    from sunkit_magex.pfss import tracing
+
+The main changes from the previous release of `pfsspy` are as follows:
+
+* The ``GongSynopticMap`` class has moved into `sunpy`, note that the new
+  class in ``sunpy`` is slightly different in that it does not modify the
+  header.

changelog/63.breaking.1.rst

@@ -0,0 +1 @@
+Made streamtracer a hard dependency of sunkit-magex.

changelog/63.breaking.2.rst

@@ -0,0 +1,6 @@
+Deprecated the following pfss utils:
+
+- pfss.utils.fix_hmi_meta
+- pfss.utils.load_adapt
+
+These functions are no longer needed and will be removed.

changelog/63.breaking.rst

@@ -0,0 +1 @@
+Increased the minimum required version of ``sunpy``  to v6.0.0.

changelog/README.rst

@@ -0,0 +1,34 @@
+=========
+Changelog
+=========
+
+.. note::
+
+    This README was adapted from the pytest changelog readme under the terms of the MIT licence.
+
+This directory contains "news fragments" which are short files that contain a small **ReST**-formatted text that will be added to the next ``CHANGELOG``.
+
+The ``CHANGELOG`` will be read by users, so this description should be aimed at SunPy users instead of describing internal changes which are only relevant to the developers.
+
+Make sure to use full sentences with correct case and punctuation, for example::
+
+    Add support for Helioprojective coordinates in `sunpy.coordinates.frames`.
+
+Please try to use Sphinx intersphinx using backticks.
+
+Each file should be named like ``<PULL REQUEST>.<TYPE>[.<COUNTER>].rst``, where ``<PULL REQUEST>`` is a pull request number, ``COUNTER`` is an optional number if a PR needs multiple entries with the same type and ``<TYPE>`` is one of:
+
+* ``breaking``: A change which requires users to change code and is not backwards compatible. (Not to be used for removal of deprecated features.)
+* ``feature``: New user facing features and any new behavior.
+* ``bugfix``: Fixes a reported bug.
+* ``doc``: Documentation addition or improvement, like rewording an entire session or adding missing docs.
+* ``deprecation``: Feature deprecation
+* ``removal``: Feature removal.
+* ``trivial``: A change which has no user facing effect or is tiny change.
+
+So for example: ``123.feature.rst``, ``456.bugfix.rst``.
+
+If you are unsure what pull request type to use, don't hesitate to ask in your PR.
+
+Note that the ``towncrier`` tool will automatically reflow your text, so it will work best if you stick to a single paragraph, but multiple sentences and links are OK and encouraged.
+You can install ``towncrier`` and then run ``towncrier --draft`` if you want to get a preview of how your change will look in the final release notes.

docs/changelog.rst

@@ -4,25 +4,7 @@
 Full Changelog
 **************
 
-1.0.0 (2024-05-31)
-==================
-
-This is the first release and aims to keep the API the same from `pfsspy` to
-`sunkit_magex`.  The main difference is that you will need to replace the
-import like so:
-
-  .. code-block:: python
-
-    # Before
-    import pfsspy
-    from pfsspy import tracing
-
-    # After
-    from sunkit_magex import pfss as pfsspy
-    from sunkit_magex.pfss import tracing
-
-The main changes from the previous release of `pfsspy` are as follows:
-
-* The ``GongSynopticMap`` class has moved into `sunpy`, note that the new
-  class in ``sunpy`` is slightly different in that it does not modify the
-  header.
+.. changelog::
+   :towncrier: ../
+   :towncrier-skip-if-empty:
+   :changelog_file: ../CHANGELOG.rst

docs/conf.py

@@ -35,6 +35,7 @@
     "sphinx_automodapi.automodapi",
     "sphinx_automodapi.smart_resolver",
     'sphinx_gallery.gen_gallery',
+    'sphinx_changelog',
 ]
 
 # Add any paths that contain templates here, relative to this directory.

docs/installing.rst

@@ -17,8 +17,8 @@ Alternatively ``sunkit-magex`` can be installed from PyPI using:
     pip install sunkit-magex
 
 This will install sunkit_magex and all of its dependencies.
-In addition to the core dependencies, there are optional dependencies (numba, streamtracer) that can improve code performance.
-These can be installed with
+In addition to the core dependencies, numba is an optional dependency that can improve code performance.
+This can be installed with:
 
 .. code:: shell
 

docs/performance.rst

@@ -11,9 +11,8 @@ To enable this simply `install numba`_  and use `sunkit_magex.pfss` as normal.
 Streamline tracing
 ==================
 
-`sunkit_magex.pfss` has two streamline tracers: a pure python `sunkit_magex.pfss.tracing.PythonTracer` and a complied tracer `sunkit_magex.pfss.tracing.FortranTracer`.
-The compiled version is significantly faster, using the `streamtracer`_ package.
+`sunkit_magex.pfss` uses a complied tracer `sunkit_magex.pfss.tracing.PerformanceTracer` using the `streamtracer`_ package.
 
 .. _numba: https://numba.pydata.org
 .. _install numba: http://numba.pydata.org/numba-doc/latest/user/installing.html
-.. _streamtracer: https://github.com/sunpy/streamtracer
+.. _streamtracer: https://docs.sunpy.org/projects/streamtracer/en/stable/

examples/internals/tracer_performance.py

@@ -1,8 +1,8 @@
 """
-Tracer performance
+Tracer Performance
 ==================
 
-Comparing the performance of Python and Rust tracers.
+Comparing the performance of the Python and Compiled tracers.
 """
 import timeit
 
@@ -19,72 +19,69 @@
 ###############################################################################
 # Create a dipole map.
 
+def dipole_Br(r, theta):
+    return 2 * np.sin(theta) / r**3
+
+
 ntheta = 180
 nphi = 360
 nr = 50
 rss = 2.5
-
 phi = np.linspace(0, 2 * np.pi, nphi)
 theta = np.linspace(-np.pi / 2, np.pi / 2, ntheta)
 theta, phi = np.meshgrid(theta, phi)
-
-def dipole_Br(r, theta):
-    return 2 * np.sin(theta) / r**3
-
-
 br = dipole_Br(1, theta)
 br = sunpy.map.Map(br.T, pfss.utils.carr_cea_wcs_header('2010-01-01', br.shape))
 pfss_input = pfss.Input(br, nr, rss)
 pfss_output = pfss.pfss(pfss_input)
-print('Computed PFSS solution')
 
 ###############################################################################
 # Trace some field lines.
 
 seed0 = np.atleast_2d(np.array([1, 1, 0]))
-tracers = [pfss.tracing.PythonTracer(),
-           pfss.tracing.FortranTracer()]
+tracers = [
+    pfss.tracing.PythonTracer(),
+    pfss.tracing.PerformanceTracer(),
+]
 nseeds = 2**np.arange(14)
-times = [[], []]
+times = [[] for _ in tracers]
 
 for nseed in nseeds:
-    print(nseed)
     seeds = np.repeat(seed0, nseed, axis=0)
     r, lat, lon = pfss.coords.cart2sph(seeds[:, 0], seeds[:, 1], seeds[:, 2])
     r = r * astropy.constants.R_sun
     lat = (lat - np.pi / 2) * u.rad
     lon = lon * u.rad
     seeds = astropy.coordinates.SkyCoord(lon, lat, r, frame=pfss_output.coordinate_frame)
-
     for i, tracer in enumerate(tracers):
+        # Skip the Python tracer for large numbers of seeds.
+        # It is too slow.
         if nseed > 64 and i == 0:
             continue
-
         t = timeit.timeit(lambda: tracer.trace(seeds, pfss_output), number=1)
         times[i].append(t)
 
 ###############################################################################
 # Plot the results.
 
 fig, ax = plt.subplots()
-ax.scatter(nseeds[1:len(times[0])], times[0][1:], label='python')
-ax.scatter(nseeds[1:], times[1][1:], label='compiled')
 
-pydt = (times[0][4] - times[0][3]) / (nseeds[4] - nseeds[3])
-ax.plot([1, 1e5], [pydt, 1e5 * pydt])
-
-fort0 = times[1][1]
-fordt = (times[1][-1] - times[1][-2]) / (nseeds[-1] - nseeds[-2])
-ax.plot(np.logspace(0, 5, 100), fort0 + fordt * np.logspace(0, 5, 100))
+for i, tracer in enumerate(tracers):
+    if i == 0:
+        ax.scatter(nseeds[1:len(times[i])], times[i][1:], label=tracer.__class__.__name__)
+        pydt = (times[0][4] - times[0][3]) / (nseeds[4] - nseeds[3])
+        ax.plot([1, 1e5], [pydt, 1e5 * pydt])
+    else:
+        ax.scatter(nseeds[1:], times[i][1:], label=tracer.__class__.__name__)
+        t0 = times[i][1]
+        dt = (times[i][-1] - times[i][-2]) / (nseeds[-1] - nseeds[-2])
+        ax.plot(np.logspace(0, 5, 100), t0 + dt * np.logspace(0, 5, 100))
 
 ax.set_xscale('log')
 ax.set_yscale('log')
-
 ax.set_xlabel('Number of seeds')
 ax.set_ylabel('Seconds')
-
 ax.axvline(180 * 360, color='k', linestyle='--', label='180x360 seed points')
-
 ax.legend()
 
 plt.show()

examples/testing/plot_error_map.py

@@ -48,7 +48,7 @@
 dthetas = []
 print(f'Tracing {step_size}...')
 # Trace
-tracer = pfss.tracing.FortranTracer(step_size=step_size)
+tracer = pfss.tracing.PerformanceTracer(step_size=step_size)
 flines = tracer.trace(seeds, pfss_out)
 # Set a mask of open field lines
 mask = flines.connectivities.astype(bool).reshape(theta.shape)
@@ -85,10 +85,10 @@ def plot_map(field, ax, label, title):
 
 
 plot_map(dtheta.to_value(u.deg), axs[0],
-         r'$\theta_{sunkit_magex.pfss} - \theta_{analytic}$ (deg)',
+         r'$\theta_{pfss} - \theta_{analytic}$ (deg)',
          'Error in latitude')
 plot_map(dphi.to_value(u.deg), axs[1],
-         r'$\phi_{sunkit_magex.pfss} - \phi_{analytic}$ (deg)',
+         r'$\phi_{pfss} - \phi_{analytic}$ (deg)',
          'Error in longitude')
 
 ax = axs[1]

examples/testing/plot_open_flux_harmonics.py

@@ -35,7 +35,7 @@
 
 cbar = axs.fig.colorbar(cm.ScalarMappable(norm=norm, cmap=cmap),
                         ax=axs.all_axs)
-cbar.ax.set_ylabel(r'$\frac{\Phi_{sunkit_magex.pfss}}{\Phi_{analytic}}$', rotation=0,
+cbar.ax.set_ylabel(r'$\frac{\Phi_{pfss}}{\Phi_{analytic}}$', rotation=0,
                    size=18, labelpad=27, va='center')
 
 plt.show()

examples/testing/plot_open_flux_nr.py

@@ -41,7 +41,7 @@
 
         ax.yaxis.set_ticks([1, 1.05, 1.1])
         ax.yaxis.tick_right()
-        ax.set_ylabel(r'$\frac{\Phi_{sunkit_magex.pfss}}{\Phi_{analytic}}$',
+        ax.set_ylabel(r'$\frac{\Phi_{pfss}}{\Phi_{analytic}}$',
                       rotation=0, labelpad=30, fontsize=16, loc='center')
         ax.yaxis.set_label_position('right')
         ax.yaxis.set_major_formatter(mticker.ScalarFormatter())

examples/testing/tracer_step_size.py

@@ -45,7 +45,7 @@
 for step_size in step_sizes:
     print(f'Tracing {step_size}...')
     # Trace
-    tracer = tracing.FortranTracer(step_size=step_size)
+    tracer = tracing.PerformanceTracer(step_size=step_size)
     flines = tracer.trace(seeds, pfss_out)
     # Set a mask of open field lines
     mask = flines.connectivities.astype(bool).reshape(theta.shape)