ENH: Add conditional to adapt behaviour depending on astropy version and warn user

amical/mf_pipeline/bispect.py

@@ -14,12 +14,15 @@
 """
 import sys
 import time
+import warnings
 
+import astropy
 import numpy as np
 from astropy.io import fits
 from matplotlib import pyplot as plt
 from mpl_toolkits.axes_grid1 import make_axes_locatable
 from munch import munchify as dict2class
+from packaging.version import Version
 from scipy.optimize import minimize
 from termcolor import cprint
 from tqdm import tqdm
@@ -38,6 +41,9 @@
 from amical.tools import cov2cor
 
 
+ASTROPY_VERSION = Version(astropy.__version__)
+
+
 def _compute_complex_bs(
     ft_arr,
     index_mask,
@@ -985,19 +991,31 @@ def _add_infos_header(infos, hdr, mf, pa, filename, maskname, npix):
     infos["maskname"] = maskname
     infos["isz"] = npix
 
-    # HACK: astropy _HeaderCommentaryCards are registered as mappings,
-    # so munch tries to access their keys, leading to attribute error
-    # to prevent this, we remove commentary cards as a temporary fix.
-    # (As of June 23 2021, with astropy version 4.2.1)
-    # See:
-    # https://github.com/SydneyAstrophotonicInstrumentationLab/AMICAL/issues/31
-    # https://github.com/astropy/astropy/issues/11866
+    # Raise a warning that old astropy version drop commentary cards, but only if
+    # there are any in the original header
     hdr_commentary_keys = fits.Card._commentary_keywords
-    hdr = hdr.copy()
-    for key in hdr_commentary_keys:
-        hdr.remove(key, ignore_missing=True, remove_all=True)
+    if any(hck in hdr for hck in hdr_commentary_keys) and (
+        ASTROPY_VERSION < Version("5.0rc")
+    ):
+        warnings.warn(
+            "Commentary cards are removed from the header with astropy"
+            f" version < 5.0. Your astropy version is"
+            f" {ASTROPY_VERSION}",
+            RuntimeWarning,
+        )
+        # HACK: astropy _HeaderCommentaryCards are registered as mappings,
+        # so munch tries to access their keys, leading to attribute error
+        # to prevent this, we remove commentary cards as a temporary fix.
+        # (As of September 2 2021, with astropy version 4.3.1)
+        # See:
+        # https://github.com/SydneyAstrophotonicInstrumentationLab/AMICAL/issues/31
+        # https://github.com/astropy/astropy/issues/11866
+        # Resolved upstream with
+        # https://github.com/astropy/astropy/pull/11923
+        hdr = hdr.copy()
+        for key in hdr_commentary_keys:
+            hdr.remove(key, ignore_missing=True, remove_all=True)
 
-    # Now that header is compatible with munch, we add it to infos
     infos["hdr"] = hdr
 
     # Save keys of the original header (as needed):

amical/tests/test_extraction.py

@@ -1,9 +1,32 @@
+import astropy
 import munch
+import pytest
 from astropy.io import fits
+from packaging.version import Version
 
 from amical.mf_pipeline.bispect import _add_infos_header
 
 
+# Astropy versions for
+ASTROPY_VERSION = Version(astropy.__version__)
+
+
+@pytest.fixture()
+def commentary_infos():
+
+    # Add hdr to infos placeholders for everything but hdr
+    mf = munch.Munch(pixelSize=1.0)
+
+    # SimulatedData avoids requiring extra keys in infos
+    infos = munch.Munch(orig="SimulatedData", instrument="unknown")
+
+    # Create a fits header with commentary card
+    hdr = fits.Header()
+    hdr["HISTORY"] = "History is a commentary card"
+
+    return _add_infos_header(infos, hdr, mf, 1.0, "afilename", "amaskname", 1)
+
+
 def test_add_infos_simulated():
     # Ensure that keys are passed to infos for simulated data, but only when available
 
@@ -12,31 +35,56 @@ def test_add_infos_simulated():
     hdr["DATE-OBS"] = "2021-06-23"
     hdr["TELESCOP"] = "FAKE-TEL"
 
-    # This test is for simulated data only
+    # SimulatedData avoids requiring extra keys in infos
     infos = munch.Munch(orig="SimulatedData", instrument="unknown")
 
     # Add hdr to infos placeholders for everything but hdr
     mf = munch.Munch(pixelSize=1.0)
     infos = _add_infos_header(infos, hdr, mf, 1.0, "afilename", "amaskname", 1)
 
+    # Check that we kept required keys
     assert infos["date-obs"] == hdr["DATE-OBS"]
     assert infos["telescop"] == hdr["TELESCOP"]
-    assert "observer" not in infos  # Keys that are not in hdr should not be in infos
 
+    # Keys that are not in hdr should not be in infos or hdr
+    assert "observer" not in infos
+    assert "observer" not in infos.hdr
 
-def test_add_infos_header_commentary():
+
+@pytest.mark.filterwarnings("ignore: Commentary cards")
+def test_add_infos_header_commentary(commentary_infos):
     # Make sure that _add_infos_header handles _HeaderCommentaryCards from astropy
 
-    # Create a fits header with commentary card
-    hdr = fits.Header()
-    hdr["HISTORY"] = "History is a commentary card"
+    # Convert everything to munch object
+    munch.munchify(commentary_infos)
 
-    # SimulatedData avoids requiring extra keys in infos
-    infos = munch.Munch(orig="SimulatedData", instrument="unknown")
+
+@pytest.mark.xfail(
+    ASTROPY_VERSION < Version("5.0rc"),
+    reason="Munch cannot handle commentary cards for Astropy < 5.0",
+)
+def test_commentary_infos_keep(commentary_infos):
+    assert "HISTORY" in commentary_infos.hdr
+
+
+@pytest.mark.xfail(
+    ASTROPY_VERSION > Version("5.0rc"),
+    reason="Astropy > 5.0 should not raise a warning for commentary cards",
+)
+def test_no_commentary_warning_astropy_version():
 
     # Add hdr to infos placeholders for everything but hdr
     mf = munch.Munch(pixelSize=1.0)
-    infos = _add_infos_header(infos, hdr, mf, 1.0, "afilename", "amaskname", 1)
 
-    # Convert everything to munch object
-    munch.munchify(infos)
+    # SimulatedData avoids requiring extra keys in infos
+    infos = munch.Munch(orig="SimulatedData", instrument="unknown")
+
+    # Create a fits header with commentary card
+    hdr = fits.Header()
+    hdr["HISTORY"] = "History is a commentary card"
+
+    with pytest.warns(
+        RuntimeWarning,
+        match="Commentary cards are removed from the header with astropy",
+    ):
+        infos = _add_infos_header(infos, hdr, mf, 1.0, "afilename", "amaskname", 1)

setup.cfg

@@ -33,6 +33,7 @@ install_requires =
     matplotlib
     munch
     numpy
+    packaging>=21.0
     scipy
     termcolor
     tqdm