From b763708655d6a20a21ff7cad1467cc1ee5c2bc18 Mon Sep 17 00:00:00 2001 From: teald Date: Thu, 6 Mar 2025 11:18:43 -0800 Subject: [PATCH 01/18] fix(wcs): Log exception (debug), clarify error message --- astrodata/wcs.py | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/astrodata/wcs.py b/astrodata/wcs.py index 93bc54f..d04638f 100644 --- a/astrodata/wcs.py +++ b/astrodata/wcs.py @@ -657,7 +657,13 @@ def read_wcs_from_header(header): try: wcsaxes = header["WCSAXES"] - except KeyError: + except KeyError as err: + logging.debug( + "No WCSAXES in header; trying CTYPE/CD (exception: %s: %s)", + type(err), + err, + ) + wcsaxes = 0 for kw in header["CTYPE*"]: @@ -864,7 +870,7 @@ def make_fitswcs_transform(trans_input): Arguments --------- - header : `astropy.io.fits.Header` or dict + header : `astropy.io.fits.Header`, dict, or NDData FITS Header (or dict) with basic WCS information Raises @@ -889,7 +895,8 @@ def make_fitswcs_transform(trans_input): wcs_info = read_wcs_from_header(trans_input.meta["header"]) except AttributeError as err: - msg = "Expected a FITS Header, dict, or NDData object" + input_type = type(trans_input) + msg = f"Expected a FITS Header, dict, or NDData, not {input_type}" raise TypeError(msg) from err other = trans_input.meta["other"] From 43db4ef00fc3f1e783424355e90312c7e8ffab95 Mon Sep 17 00:00:00 2001 From: teald Date: Thu, 6 Mar 2025 11:35:06 -0800 Subject: [PATCH 02/18] fix(fits): Add info to error log --- astrodata/fits.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/astrodata/fits.py b/astrodata/fits.py index d07cd12..9a2d732 100644 --- a/astrodata/fits.py +++ b/astrodata/fits.py @@ -1170,7 +1170,7 @@ def wcs_to_asdftablehdu(wcs, extver=None): except jsonschema.exceptions.ValidationError as err: # (The original traceback also gets printed here) raise TypeError( - f"Cannot serialize model(s) for 'WCS' extension " f"{extver or ''}" + f"Cannot serialize model(s) for 'WCS' extension {extver or ''}" ) from err # ASDF can only dump YAML to a binary file object, so do that and read @@ -1277,8 +1277,9 @@ def asdftablehdu_to_wcs(hdu): except KeyError as err: LOGGER.warning( "Ignoring 'WCS' extension %s: missing " - "'wcs' dict entry. Error was %s", + "'wcs' dict entry. (got exception: %s: %s)", ver, + type(err), err, ) From d7860b20be9dbf974a3f6dd38aa9a6a4ddb0f2e7 Mon Sep 17 00:00:00 2001 From: teald Date: Mon, 17 Mar 2025 11:58:09 -0700 Subject: [PATCH 03/18] fix(dragons): Update nddata slicing Based on DRAGONS PR #483: https://github.com/GeminiDRSoftware/DRAGONS/pull/483 --- astrodata/nddata.py | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/astrodata/nddata.py b/astrodata/nddata.py index 05e4a76..295e747 100644 --- a/astrodata/nddata.py +++ b/astrodata/nddata.py @@ -154,15 +154,25 @@ def _slice_wcs(self, slices): if slice_.start: start = ( length + slice_.start - if slice_.start < 1 + if slice_.start < 0 else slice_.start ) if start > 0: model.append(models.Shift(start)) mapped_axes.append(max(mapped_axes) + 1 if mapped_axes else 0) + elif isinstance(slice_, INTEGER_TYPES): - model.append(models.Const1D(slice_)) + model.append( + models.Const1D((length + slice_) if slice_ < 0 else slice_) + ) mapped_axes.append(-1) + + # Equivalent to slice(None, None, None) + elif slice is None: + mapped_axes.append( + max(mapped_axes) + 1 if mapped_axes else None + ) + else: raise IndexError("Slice not an integer or range") if model: From 93c425fda45fdb573dbb09661642952b55a3a39e Mon Sep 17 00:00:00 2001 From: teald Date: Mon, 17 Mar 2025 12:01:50 -0700 Subject: [PATCH 04/18] fix(dragons): Update wcs indexing This is based on DRAGONS PR #483: https://github.com/GeminiDRSoftware/DRAGONS/pull/483 --- astrodata/wcs.py | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/astrodata/wcs.py b/astrodata/wcs.py index d04638f..b50d153 100644 --- a/astrodata/wcs.py +++ b/astrodata/wcs.py @@ -101,6 +101,8 @@ def fitswcs_to_gwcs(input_data, *, raise_errors: bool = False): err, ) + raise + return None raise @@ -306,7 +308,7 @@ def gwcs_to_fits(ndd, hdr=None): # Remove projection parts so we can calculate the CD matrix if projcode: nat2cel.name = "nat2cel" - transform_inverse = transform.inverse.copy() + transform_inverse = transform.inverse for m in transform_inverse: if isinstance(m, models.RotateCelestial2Native): @@ -607,25 +609,29 @@ def calculate_affine_matrices(func, shape, origin=None): if ndim > 1: transformed = list( - zip(*list(func(*point[:indim]) for point in points.T)) + zip(*list(func(*point[indim - 1 :: -1]) for point in points.T)) ) transformed = np.array(transformed).T else: transformed = np.array([func(*points)]).T + + # Matrix of wcs derivatives wrt input coordiantes in Python order matrix = np.array( [ [ 0.5 * (transformed[j + 1, i] - transformed[indim + j + 1, i]) / halfsize[j] - for j in range(indim) + for j in range(indim - 1, -1, -1) ] for i in range(ndim) ] ) - offset = transformed[0] - np.dot(matrix, halfsize) + + offset = transformed[0] - np.dot(matrix, halfsize[::-1]) + return AffineMatrices(matrix[::-1, ::-1], offset[::-1]) From 85dbd96490a774e405a22ac97763bcecb6e7d1f4 Mon Sep 17 00:00:00 2001 From: teald Date: Mon, 17 Mar 2025 12:03:05 -0700 Subject: [PATCH 05/18] chore: Formatting for astrodata/core.py --- astrodata/core.py | 16 ++++++---------- 1 file changed, 6 insertions(+), 10 deletions(-) diff --git a/astrodata/core.py b/astrodata/core.py index a61ea46..20a834e 100644 --- a/astrodata/core.py +++ b/astrodata/core.py @@ -859,13 +859,12 @@ def _my_attribute(attr): if attribute == DEFAULT_EXTENSION: raise AttributeError( - f"{attribute} extensions should be " - "appended with .append" + f"{attribute} extensions should be appended with .append" ) if attribute in {"DQ", "VAR"}: raise AttributeError( - f"{attribute} should be set on the " "nddata object" + f"{attribute} should be set on the nddata object" ) add_to = self.nddata if self.is_single else None @@ -898,7 +897,7 @@ def __delattr__(self, attribute): del self._tables[attribute] else: raise AttributeError( - f"'{attribute}' is not a global table " "for this instance" + f"'{attribute}' is not a global table for this instance" ) def __contains__(self, attribute): @@ -1381,8 +1380,7 @@ def _append_nddata(self, new_nddata, name, add_to): """ if add_to is not None: raise TypeError( - "You can only append NDData derived instances " - "at the top level" + "You can only append NDData derived instances at the top level" ) hd = new_nddata.meta["header"] @@ -1488,8 +1486,7 @@ def _append_astrodata(self, ad, name, header, add_to): if not ad.is_single: raise ValueError( - "Cannot append AstroData instances that are " - "not single slices" + "Cannot append AstroData instances that are not single slices" ) if add_to is not None: @@ -1564,8 +1561,7 @@ def append(self, ext, name=None, header=None): """ if self.is_sliced: raise TypeError( - "Can't append objects to slices, use " - "'ext.NAME = obj' instead" + "Can't append objects to slices, use 'ext.NAME = obj' instead" ) # NOTE: Most probably, if we want to copy the input argument, we From 222c041cfa24d42824d1073dc782e22be103c9fa Mon Sep 17 00:00:00 2001 From: teald Date: Mon, 17 Mar 2025 12:03:46 -0700 Subject: [PATCH 06/18] fix(dragons): Add else to fits.py try/except This was a missing addition from a previous DRAGONS change. --- astrodata/fits.py | 29 +++++++++++++++-------------- 1 file changed, 15 insertions(+), 14 deletions(-) diff --git a/astrodata/fits.py b/astrodata/fits.py index 9a2d732..344466a 100644 --- a/astrodata/fits.py +++ b/astrodata/fits.py @@ -1270,20 +1270,21 @@ def asdftablehdu_to_wcs(hdu): return None - with af: - try: - wcs = af.tree["wcs"] - - except KeyError as err: - LOGGER.warning( - "Ignoring 'WCS' extension %s: missing " - "'wcs' dict entry. (got exception: %s: %s)", - ver, - type(err), - err, - ) - - return None + else: + with af: + try: + wcs = af.tree["wcs"] + + except KeyError as err: + LOGGER.warning( + "Ignoring 'WCS' extension %s: missing " + "'wcs' dict entry. (got exception: %s: %s)", + ver, + type(err), + err, + ) + + return None else: LOGGER.warning("Ignoring non-FITS-table 'WCS' extension %s", ver) From eaa6a707a9c0433bf2376a6816795ab1338bc79c Mon Sep 17 00:00:00 2001 From: teald Date: Mon, 17 Mar 2025 12:04:44 -0700 Subject: [PATCH 07/18] chore: Format astrodata/testing.py --- astrodata/testing.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/astrodata/testing.py b/astrodata/testing.py index b57409d..ee16de5 100644 --- a/astrodata/testing.py +++ b/astrodata/testing.py @@ -1037,7 +1037,7 @@ def compare_frames(frame1, frame2): except AssertionError: errorlist.compare( - f"Slice {i} {frame} differs: " f"{frame1} v {frame2}" + f"Slice {i} {frame} differs: {frame1} v {frame2}" ) corners = get_corners(ext1.shape) From 4167d2b94fed494aced7aa13e09eb693359fce14 Mon Sep 17 00:00:00 2001 From: teald Date: Thu, 20 Mar 2025 16:29:39 -0700 Subject: [PATCH 08/18] fix(wcs): Remove errant debug raise. --- astrodata/wcs.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/astrodata/wcs.py b/astrodata/wcs.py index b50d153..e26f9c1 100644 --- a/astrodata/wcs.py +++ b/astrodata/wcs.py @@ -101,8 +101,6 @@ def fitswcs_to_gwcs(input_data, *, raise_errors: bool = False): err, ) - raise - return None raise @@ -308,7 +306,7 @@ def gwcs_to_fits(ndd, hdr=None): # Remove projection parts so we can calculate the CD matrix if projcode: nat2cel.name = "nat2cel" - transform_inverse = transform.inverse + transform_inverse = transform.inverse.copy() for m in transform_inverse: if isinstance(m, models.RotateCelestial2Native): From 7f70714e323cb589b466220c6af8b2566f5f21a6 Mon Sep 17 00:00:00 2001 From: teald Date: Thu, 20 Mar 2025 16:30:13 -0700 Subject: [PATCH 09/18] fix(testing): Revert ADCompare change. --- astrodata/testing.py | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/astrodata/testing.py b/astrodata/testing.py index ee16de5..6e3ba5c 100644 --- a/astrodata/testing.py +++ b/astrodata/testing.py @@ -1083,13 +1083,9 @@ def ad_compare(ad1, ad2, **kwargs): ------- bool: are the two AD instances basically the same? """ - try: - ADCompare(ad1, ad2).run_comparison(**kwargs) - - except AssertionError: - return False + compare = ADCompare(ad1, ad2).run_comparison(**kwargs) - return True + return compare == {} _HDUL_LIKE_TYPE = fits.HDUList | list[fits.hdu.FitsHDU] From 002b798c3f8906a86bf65040c27732cdd9a83edd Mon Sep 17 00:00:00 2001 From: teald Date: Thu, 20 Mar 2025 16:40:46 -0700 Subject: [PATCH 10/18] fix(unit-tests): Update test to pass with exception. --- tests/unit/test_testing.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/tests/unit/test_testing.py b/tests/unit/test_testing.py index abcdd40..60f0298 100644 --- a/tests/unit/test_testing.py +++ b/tests/unit/test_testing.py @@ -990,7 +990,9 @@ def test_ADCompare_wcs(ad1, ad2): def test_ad_compare(ad1, ad2): assert testing.ad_compare(ad1, ad1) - assert not testing.ad_compare(ad1, ad2) + + with pytest.raises(AssertionError, match="Comparison between N20180304S0126.fits and N20180305S0001.fits"): + assert not testing.ad_compare(ad1, ad2) @pytest.fixture From f274909365bc589c685f241f73a6b6c73680724d Mon Sep 17 00:00:00 2001 From: teald Date: Tue, 25 Mar 2025 15:59:07 -0700 Subject: [PATCH 11/18] chore: Add issue reference to TODO comment. --- noxfile.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/noxfile.py b/noxfile.py index 598848b..11fb3bd 100644 --- a/noxfile.py +++ b/noxfile.py @@ -26,7 +26,7 @@ else: # Only for python 3.10 support, which wont' be maintained much longer. - # To be removed when we drop support for python 3.10 (see: ISSUE) + # To be removed when we drop support for python 3.10 (see: ISSUE #73) from pip._vendor import tomli tomllib = tomli From 0a573384fde80685b26eb42dd4f51d514ad0bb5c Mon Sep 17 00:00:00 2001 From: teald Date: Tue, 25 Mar 2025 16:00:22 -0700 Subject: [PATCH 12/18] fix(dragons): Add updates to testing functions from DRAGONS. --- astrodata/testing.py | 62 +++++++++++++++++++++++++++++++++++++++----- 1 file changed, 55 insertions(+), 7 deletions(-) diff --git a/astrodata/testing.py b/astrodata/testing.py index 6e3ba5c..06bf883 100644 --- a/astrodata/testing.py +++ b/astrodata/testing.py @@ -299,7 +299,7 @@ def assert_most_equal(actual, desired, max_miss, verbose=True): verbose : bool, optional If True, the conflicting values are appended to the error message. - Raises + Raiseqs ------ AssertionError If actual and desired are not equal. @@ -743,6 +743,9 @@ class ADCompare: ) fits_keys.update([f"CD{i}_{j}" for i in range(1, 6) for j in range(1, 6)]) + # Add PROCSVER and PROCSOFT (DRAGONS processing version/software kws) + fits_keys.update(["PROCSVER", "PROCSOFT"]) + def __init__(self, ad1, ad2): self.ad1 = ad1 self.ad2 = ad2 @@ -980,19 +983,64 @@ def attributes(self): return errorlist def _attributes(self, ext1, ext2): - """Check the attributes of two extensions.""" + """Check and compare attributes.""" errorlist = [] for attr in ["data", "mask", "variance", "OBJMASK", "OBJCAT"]: attr1 = getattr(ext1, attr, None) attr2 = getattr(ext2, attr, None) - if all(attr is None for attr in [attr1, attr2]): - continue + if hasattr(attr1, "shape") and hasattr(attr2, "shape"): + if attr1.shape != attr2.shape: + errorlist.append( + f"Attribute error for {attr}: " + f"Mismatching {attr}.shape values: {attr1} v {attr2}" + ) - if not np.array_equal(attr1, attr2): - errorlist.append(f"{attr} mismatch: {attr1} v {attr2}") - continue + continue + + if (attr1 is None) ^ (attr2 is None): + errorlist.append( + f"Attribute error for {attr}: " + f"{attr1 is not None} v {attr2 is not None}" + ) + elif attr1 is not None: + if isinstance(attr1, Table): + if len(attr1) != len(attr2): + errorlist.append( + f"attr lengths differ: {len(attr1)} v {len(attr2)}" + ) + else: # everything else is pixel-like + if attr1.dtype.name != attr2.dtype.name: + errorlist.append( + f"Datatype mismatch for {attr}: " + f"{attr1.dtype} v {attr2.dtype}" + ) + if attr1.shape != attr2.shape: + errorlist.append( + f"Shape mismatch for {attr}: {attr1.shape} " + f"v {attr2.shape}" + ) + if "int" in attr1.dtype.name: + try: + assert_most_equal( + attr1, attr2, max_miss=self.max_miss + ) + except AssertionError as e: + errorlist.append( + f"Inequality for {attr}: " + str(e) + ) + else: + try: + assert_most_close( + attr1, + attr2, + max_miss=self.max_miss, + rtol=self.rtol, + atol=self.atol, + ) + except AssertionError as e: + errorlist.append(f"Mismatch for {attr}: " + str(e)) return errorlist def wcs(self): From 5b2db1004c9ef7afd47a9c18e09502bad764a2f4 Mon Sep 17 00:00:00 2001 From: teald Date: Tue, 25 Mar 2025 16:13:47 -0700 Subject: [PATCH 13/18] fix(dragons): Add PROCMODE keyword to ignored comparison kws --- astrodata/testing.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/astrodata/testing.py b/astrodata/testing.py index 06bf883..caa32b5 100644 --- a/astrodata/testing.py +++ b/astrodata/testing.py @@ -744,7 +744,7 @@ class ADCompare: fits_keys.update([f"CD{i}_{j}" for i in range(1, 6) for j in range(1, 6)]) # Add PROCSVER and PROCSOFT (DRAGONS processing version/software kws) - fits_keys.update(["PROCSVER", "PROCSOFT"]) + fits_keys.update(["PROCSVER", "PROCSOFT", "PROCMODE"]) def __init__(self, ad1, ad2): self.ad1 = ad1 From 9406a7c140555fbdde9c191050b57fb0813c37a4 Mon Sep 17 00:00:00 2001 From: teald Date: Wed, 26 Mar 2025 11:06:01 -0700 Subject: [PATCH 14/18] fix: Indexing bug --- astrodata/nddata.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/astrodata/nddata.py b/astrodata/nddata.py index 295e747..367c485 100644 --- a/astrodata/nddata.py +++ b/astrodata/nddata.py @@ -138,9 +138,9 @@ def _slice_wcs(self, slices): "Only one ellipsis can be specified in a slice" ) - ell_index = slices.index(Ellipsis) + 1 + ell_index = slices.index(Ellipsis) slice_fill = [slice(None)] * (ndim - len(slices) + 1) - slices[ell_index:ell_index] = slice_fill + slices[ell_index : ell_index + 1] = slice_fill slices.extend([slice(None)] * (ndim - len(slices))) From a03c55b2bc3e80b0d95edafef5e6d0f742fe40cb Mon Sep 17 00:00:00 2001 From: teald Date: Wed, 26 Mar 2025 13:56:16 -0700 Subject: [PATCH 15/18] fix(dragons): Variable name without tailing _ --- astrodata/nddata.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/astrodata/nddata.py b/astrodata/nddata.py index 367c485..e9c420f 100644 --- a/astrodata/nddata.py +++ b/astrodata/nddata.py @@ -168,7 +168,7 @@ def _slice_wcs(self, slices): mapped_axes.append(-1) # Equivalent to slice(None, None, None) - elif slice is None: + elif slice_ is None: mapped_axes.append( max(mapped_axes) + 1 if mapped_axes else None ) From 97d50d3629fe576b69b82f948b186fab3a057ba4 Mon Sep 17 00:00:00 2001 From: teald Date: Tue, 1 Apr 2025 16:23:50 -0700 Subject: [PATCH 16/18] chore: Format files. --- astrodata/provenance.py | 24 +++--- astrodata/testing.py | 4 +- astrodata/wcs.py | 2 +- docs/manuals/conftest.py | 4 +- noxfile.py | 8 +- tests/integration/dragons/conftest.py | 4 +- .../integration/dragons/test_gmos_imaging.py | 12 +-- .../integration/dragons/test_niri_imaging.py | 12 +-- tests/script_tests/test_pyproject_scripts.py | 4 +- tests/test_data/generate_test_data.py | 8 +- tests/unit/conftest.py | 4 +- tests/unit/test_adfactory.py | 24 ++++-- tests/unit/test_core.py | 4 +- tests/unit/test_deprecated.py | 4 +- tests/unit/test_fits.py | 28 ++----- tests/unit/test_generic.py | 10 +-- tests/unit/test_nddata.py | 15 +--- tests/unit/test_object_construction.py | 18 +---- tests/unit/test_testing.py | 74 ++++++++++++++----- tests/unit/test_wcs.py | 25 ++++--- 20 files changed, 143 insertions(+), 145 deletions(-) diff --git a/astrodata/provenance.py b/astrodata/provenance.py index 385c595..7fca5a5 100644 --- a/astrodata/provenance.py +++ b/astrodata/provenance.py @@ -123,9 +123,11 @@ def add_history(ad, timestamp_start, timestamp_stop, primitive, args): if hasattr(ad, "HISTORY"): colsize = max( colsize, - (max(len(ph[args_col_idx]) for ph in ad.HISTORY) + 1) - if args_col_idx is not None - else 16, + ( + (max(len(ph[args_col_idx]) for ph in ad.HISTORY) + 1) + if args_col_idx is not None + else 16 + ), ) timestamp_start_arr = [ @@ -335,16 +337,16 @@ def provenance_summary(ad, provenance=True, history=True): # Titles retval += ( - f'{"Primitive":<{primitive_col_size}} ' - f'{"Args":<{args_col_size}} ' - f'{"Start":<{timestamp_start_col_size}} {"Stop"}\n' + f"{'Primitive':<{primitive_col_size}} " + f"{'Args':<{args_col_size}} " + f"{'Start':<{timestamp_start_col_size}} {'Stop'}\n" ) # now the lines retval += ( - f'{"":{"-"}<{primitive_col_size}} ' - f'{"":{"-"}<{args_col_size}} ' - f'{"":{"-"}<{timestamp_start_col_size}} ' - f'{"":{"-"}<{timestamp_stop_col_size}}\n' + f"{'':{'-'}<{primitive_col_size}} " + f"{'':{'-'}<{args_col_size}} " + f"{'':{'-'}<{timestamp_start_col_size}} " + f"{'':{'-'}<{timestamp_stop_col_size}}\n" ) # Rows, looping over args lines @@ -368,7 +370,7 @@ def provenance_summary(ad, provenance=True, history=True): ) else: - retval += f'{"":<{primitive_col_size}} {argrow}\n' + retval += f"{'':<{primitive_col_size}} {argrow}\n" # prep for additional arg rows without duplicating the # other values first = False diff --git a/astrodata/testing.py b/astrodata/testing.py index caa32b5..6423758 100644 --- a/astrodata/testing.py +++ b/astrodata/testing.py @@ -534,7 +534,7 @@ def download_multiple_files( "testing cache." ) - # This is cleaned up once the program finishes. + # This is does not persist the Python session finishes. os.environ[env_var] = str(path) if not os.path.isdir(path) and os.path.exists(path): @@ -621,7 +621,7 @@ def download_from_archive( warnings.warn( "sub_path is None, so the file will be saved to the root of the " "cache directory. To suppress this warning, set sub_path to a " - "valid path (e.g., empty string instead of None)." + "valid path (e.g., empty string/'.' instead of None)." ) # Check that the environment variable is a valid name. diff --git a/astrodata/wcs.py b/astrodata/wcs.py index e26f9c1..7236d4b 100644 --- a/astrodata/wcs.py +++ b/astrodata/wcs.py @@ -95,7 +95,7 @@ def fitswcs_to_gwcs(input_data, *, raise_errors: bool = False): except (IndexError, TypeError, ValueError) as err: if not raise_errors: - logging.warning( + logging.debug( "Could not create gWCS: %s: %s", err.__class__.__name__, err, diff --git a/docs/manuals/conftest.py b/docs/manuals/conftest.py index f62c17a..06f9604 100644 --- a/docs/manuals/conftest.py +++ b/docs/manuals/conftest.py @@ -122,9 +122,7 @@ def gain(self): return [1.5] * len(self) factory = doctest_namespace["astrodata"].factory - if not any( - DocTestAstroData.__name__ in cls.__name__ for cls in factory.registry - ): + if not any(DocTestAstroData.__name__ in cls.__name__ for cls in factory.registry): factory.add_class(DocTestAstroData) return DocTestAstroData diff --git a/noxfile.py b/noxfile.py index 11fb3bd..4eb5d48 100644 --- a/noxfile.py +++ b/noxfile.py @@ -283,7 +283,13 @@ def start_devpi_server(self): devpi_server_path = result.strip() self.server_process = subprocess.Popen( - [devpi_server_path, "--serverdir", tmp_dir, "--port", str(port)], # noqa: S603 + [ + devpi_server_path, + "--serverdir", + tmp_dir, + "--port", + str(port), + ], # noqa: S603 stdout=subprocess.PIPE, stderr=subprocess.PIPE, ) diff --git a/tests/integration/dragons/conftest.py b/tests/integration/dragons/conftest.py index f770359..e4254ef 100644 --- a/tests/integration/dragons/conftest.py +++ b/tests/integration/dragons/conftest.py @@ -84,9 +84,7 @@ def setup_logging(): @pytest.fixture -def calibration_service( - tmp_path: Path, monkeypatch: pytest.MonkeyPatch -) -> LocalDB: +def calibration_service(tmp_path: Path, monkeypatch: pytest.MonkeyPatch) -> LocalDB: """Fixture to set up the calibration service.""" # 1) Create a dragonsrc file and assign it to the session environment. dragonsrc = tmp_path / ".dragonsrc" diff --git a/tests/integration/dragons/test_gmos_imaging.py b/tests/integration/dragons/test_gmos_imaging.py index 6d7a72b..6aa65a1 100644 --- a/tests/integration/dragons/test_gmos_imaging.py +++ b/tests/integration/dragons/test_gmos_imaging.py @@ -56,9 +56,7 @@ def _downloaded_gmos_imaging_data_star_field( @pytest.fixture -def gmos_imaging_data_star_field( - tmp_path, _downloaded_gmos_imaging_data_star_field -): +def gmos_imaging_data_star_field(tmp_path, _downloaded_gmos_imaging_data_star_field): """This copies files from another fixture (_downloaded_gmos_imaging_data_star_field), and copies those into a path for the current test. @@ -112,9 +110,7 @@ def test_gmos_imaging_tutorial_star_field( # Import required modules # ruff: noqa: F841 gemini_instruments = importlib.import_module("gemini_instruments") - Reduce = importlib.import_module( - "recipe_system.reduction.coreReduce" - ).Reduce + Reduce = importlib.import_module("recipe_system.reduction.coreReduce").Reduce dataselect = importlib.import_module("gempy.adlibrary.dataselect") cal_service = importlib.import_module("recipe_system.cal_service") @@ -140,9 +136,7 @@ def test_gmos_imaging_tutorial_star_field( all_files, [], ["CAL"], - dataselect.expr_parser( - '(observation_class=="science" and filter_name=="i")' - ), + dataselect.expr_parser('(observation_class=="science" and filter_name=="i")'), ) # Initialize calibration service diff --git a/tests/integration/dragons/test_niri_imaging.py b/tests/integration/dragons/test_niri_imaging.py index 35a8357..30e2f98 100644 --- a/tests/integration/dragons/test_niri_imaging.py +++ b/tests/integration/dragons/test_niri_imaging.py @@ -58,9 +58,7 @@ def _downloaded_niri_imaging_data_star_field( @pytest.fixture -def niri_imaging_data_star_field( - tmp_path, _downloaded_niri_imaging_data_star_field -): +def niri_imaging_data_star_field(tmp_path, _downloaded_niri_imaging_data_star_field): """This copies files from another fixture (_downloaded_niri_imaging_data_star_field), and copies those into a path for the current test. @@ -244,9 +242,7 @@ def test_niri_imaging_tutorial_star_field( processed_std_image = glob.glob("*image*") assert len(processed_std_image) == 1, "Multiple standard star images." - assert ( - "crash" not in processed_std_image[0] - ), "Standard star reduction failed." + assert "crash" not in processed_std_image[0], "Standard star reduction failed." # Science reduce_target = Reduce() @@ -260,6 +256,4 @@ def test_niri_imaging_tutorial_star_field( ] assert len(processed_target_image) == 1, "Multiple science images created." - assert ( - "crash" not in processed_target_image[0] - ), "Science reduction failed." + assert "crash" not in processed_target_image[0], "Science reduction failed." diff --git a/tests/script_tests/test_pyproject_scripts.py b/tests/script_tests/test_pyproject_scripts.py index 6e479f2..3546e13 100644 --- a/tests/script_tests/test_pyproject_scripts.py +++ b/tests/script_tests/test_pyproject_scripts.py @@ -56,7 +56,9 @@ def create_rst_extract_command(script: str, options: str | list[str]) -> str: @pytest.mark.parametrize("script, options", tuple(scripts().items())) -def test_script_executes(script: str, options: str, tmp_path: Path, monkeypatch: pytest.MonkeyPatch) -> None: +def test_script_executes( + script: str, options: str, tmp_path: Path, monkeypatch: pytest.MonkeyPatch +) -> None: """Test the script.""" # Use temporary directory as the working directory command = create_rst_extract_command(script, options) diff --git a/tests/test_data/generate_test_data.py b/tests/test_data/generate_test_data.py index 49daea7..d33021e 100644 --- a/tests/test_data/generate_test_data.py +++ b/tests/test_data/generate_test_data.py @@ -296,9 +296,7 @@ def create_random_files( # This is dumb, should probably just make an ID at the front or # something. while not filename or cls.check_if_file_exists(filename, path): - filename = cls.generate_random_file_name( - max_length, fixed_length - ) + filename = cls.generate_random_file_name(max_length, fixed_length) data = cls.generate_random_data() @@ -310,9 +308,7 @@ def create_random_files( @classmethod @contextmanager - def temp_files_context( - cls, count, max_length=50, fixed_length=-1, path="." - ): + def temp_files_context(cls, count, max_length=50, fixed_length=-1, path="."): """Creates temporary files using a context manager, and cleans up those files once the run is finished. diff --git a/tests/unit/conftest.py b/tests/unit/conftest.py index cf98972..ec74737 100644 --- a/tests/unit/conftest.py +++ b/tests/unit/conftest.py @@ -21,9 +21,7 @@ def assign_test_cache(tmp_path_factory): tmpdir = tmp_path_factory.mktemp(".testing_cache") if not (result := os.environ.get("ASTRODATA_TEST")): - os.environ["ASTRODATA_TEST"] = os.path.join( - tmpdir, "archive_downloads" - ) + os.environ["ASTRODATA_TEST"] = os.path.join(tmpdir, "archive_downloads") yield diff --git a/tests/unit/test_adfactory.py b/tests/unit/test_adfactory.py index 8d3a8b2..457d758 100644 --- a/tests/unit/test_adfactory.py +++ b/tests/unit/test_adfactory.py @@ -76,7 +76,11 @@ def test__open_file_file_not_found(nonexistent_file, example_dir): with factory._open_file(example_dir) as _: pass -def test_report_all_exceptions_on_failure_get_astro_data(example_fits_file, monkeypatch,): + +def test_report_all_exceptions_on_failure_get_astro_data( + example_fits_file, + monkeypatch, +): """Tests that all exceptions are reported if file fails to open. This test tries to capture errors that were previously discarded. It does @@ -91,18 +95,21 @@ def test_report_all_exceptions_on_failure_get_astro_data(example_fits_file, monk class AD1(AstroData): _message = "This_is_exception_1" + @staticmethod def _matches_data(source): raise ValueError(AD1._message) class AD2(AstroData): _message = "This_is_exception_2" + @staticmethod def _matches_data(source): raise IndexError(AD2._message) class AD3(AstroData): _message = "This_is_exception_3" + @staticmethod def _matches_data(source): raise Exception(AD3._message) @@ -115,7 +122,6 @@ def _matches_data(source): with pytest.raises(astrodata.AstroDataError) as exception_info: astrodata.from_file(example_fits_file) - caught_err = exception_info.value assert str(caught_err) assert "No class matches this dataset" in str(caught_err) @@ -123,7 +129,11 @@ def _matches_data(source): for message in (_cls._message for _cls in classes): assert message in str(caught_err), str(caught_err) -def test_report_all_exceptions_on_failure__open_file(example_fits_file, monkeypatch, ): + +def test_report_all_exceptions_on_failure__open_file( + example_fits_file, + monkeypatch, +): """Tests that all exceptions are reported if file fails to open. This test tries to capture errors that were previously discarded. It does @@ -152,17 +162,17 @@ def _matches_data(source): return True monkeypatch.setattr(astrodata, "factory", factory) - monkeypatch.setattr(astrodata.adfactory.AstroDataFactory, "_file_openers", factory._file_openers) - + monkeypatch.setattr( + astrodata.adfactory.AstroDataFactory, "_file_openers", factory._file_openers + ) with pytest.raises(astrodata.AstroDataError) as exception_info: astrodata.from_file(example_fits_file) - caught_err = exception_info.value assert str(caught_err) assert "No access, or not supported format for: " in str(caught_err) n_openers = len(factory._file_openers) - for message in (f"Exception_{i}" for i in range(1, n_openers+1)): + for message in (f"Exception_{i}" for i in range(1, n_openers + 1)): assert message in str(caught_err) diff --git a/tests/unit/test_core.py b/tests/unit/test_core.py index a79d31e..49ffe6e 100644 --- a/tests/unit/test_core.py +++ b/tests/unit/test_core.py @@ -213,9 +213,7 @@ def test_write_and_read(tmp_path, capsys): tbl = Table([np.zeros(10), np.ones(10)], names=("a", "b")) - with pytest.raises( - ValueError, match="Tables should be set directly as attribute" - ): + with pytest.raises(ValueError, match="Tables should be set directly as attribute"): ad.append(tbl, name="BOB") ad.BOB = tbl diff --git a/tests/unit/test_deprecated.py b/tests/unit/test_deprecated.py index 3df9767..0004256 100644 --- a/tests/unit/test_deprecated.py +++ b/tests/unit/test_deprecated.py @@ -69,8 +69,6 @@ def test_deprecated_astrodatafactory_getAstroData(example_fits_file): astrodata.factory.getAstroData(example_fits_file) -def test_deprecated_astrodatafactory_createFromScratch( - example_phu, example_extensions -): +def test_deprecated_astrodatafactory_createFromScratch(example_phu, example_extensions): with pytest.warns(AstroDataDeprecationWarning): astrodata.factory.createFromScratch(example_phu, example_extensions) diff --git a/tests/unit/test_fits.py b/tests/unit/test_fits.py index 4bdde7e..1264441 100644 --- a/tests/unit/test_fits.py +++ b/tests/unit/test_fits.py @@ -289,9 +289,7 @@ def test_slice_multiple(GMOSN_SPECT): with pytest.raises(TypeError, match=match): slc.FOO = 1 - with pytest.raises( - TypeError, match="Can't delete attributes on non-single slices" - ): + with pytest.raises(TypeError, match="Can't delete attributes on non-single slices"): del slc.FOO ext.bar = 1 @@ -305,9 +303,7 @@ def test_slice_data(GMOSN_SPECT): ad = astrodata.from_file(GMOSN_SPECT) slc = ad[1, 2] - match = ( - "Trying to assign to an AstroData object that is not a single slice" - ) + match = "Trying to assign to an AstroData object that is not a single slice" with pytest.raises(ValueError, match=match): slc.data = 1 with pytest.raises(ValueError, match=match): @@ -450,9 +446,7 @@ def test_from_hdulist2(): ] ) - with pytest.warns( - UserWarning, match="Skip HDU .* because it has no EXTNAME" - ): + with pytest.warns(UserWarning, match="Skip HDU .* because it has no EXTNAME"): ad = astrodata.from_file(hdul) assert len(ad) == 1 @@ -508,9 +502,7 @@ def test_can_append_table_and_access_data(capsys, tmp_path): phu = fits.PrimaryHDU() ad = astrodata.create(phu) - with pytest.raises( - ValueError, match="Tables should be set directly as attribute" - ): + with pytest.raises(ValueError, match="Tables should be set directly as attribute"): ad.append(tbl, name="BOB") ad.BOB = tbl @@ -556,9 +548,7 @@ def test_attributes(GSAOI_DARK): assert all(isinstance(nd, NDAstroData) for nd in ad.nddata) assert [nd.shape for nd in ad.nddata] == [(2048, 2048)] * 4 - match = ( - "Trying to assign to an AstroData object that is not a single slice" - ) + match = "Trying to assign to an AstroData object that is not a single slice" with pytest.raises(ValueError, match=match): ad.data = 1 with pytest.raises(ValueError, match=match): @@ -752,9 +742,7 @@ def test_header_collection(GMOSN_SPECT): assert ad.hdr.get_comment("DATATYPE") == ["Hello!"] * 12 ad.hdr["RDNOISE"] = (2.0, "New comment") assert ad.hdr.get_comment("RDNOISE") == ["New comment"] * 12 - with pytest.raises( - KeyError, match="Keyword 'FOO' not available at header 0" - ): + with pytest.raises(KeyError, match="Keyword 'FOO' not available at header 0"): ad.hdr.set_comment("FOO", "A comment") ad = astrodata.from_file(GMOSN_SPECT) @@ -811,9 +799,7 @@ def test_add_var_and_dq(): ): ad.append(np.zeros(shape), name="FOO") - with pytest.raises( - ValueError, match="'VAR' need to be associated to a 'SCI' one" - ): + with pytest.raises(ValueError, match="'VAR' need to be associated to a 'SCI' one"): ad.append(np.ones(shape), name="VAR") with pytest.raises( diff --git a/tests/unit/test_generic.py b/tests/unit/test_generic.py index 8e3ebf9..d3975ce 100644 --- a/tests/unit/test_generic.py +++ b/tests/unit/test_generic.py @@ -180,10 +180,7 @@ class TestClass(astrodata.AstroData): @staticmethod def _matches_data(source): - return ( - source[0].header.get("INSTRUME", "").upper() - == "TEST_INSTRUMENT" - ) + return source[0].header.get("INSTRUME", "").upper() == "TEST_INSTRUMENT" @astro_data_tag def tag1(self): @@ -229,10 +226,7 @@ class TestClass(astrodata.AstroData): @staticmethod def _matches_data(source): - return ( - source[0].header.get("INSTRUME", "").upper() - == "TEST_INSTRUMENT" - ) + return source[0].header.get("INSTRUME", "").upper() == "TEST_INSTRUMENT" @astro_data_descriptor def descriptor1(self): diff --git a/tests/unit/test_nddata.py b/tests/unit/test_nddata.py index d44fcbc..44bef49 100644 --- a/tests/unit/test_nddata.py +++ b/tests/unit/test_nddata.py @@ -103,9 +103,7 @@ def stack(arrays): result = windowed_operation(stack, [testnd, nd2], kernel=(3, 3)) with pytest.raises(AssertionError, match=r"Incompatible shape.*"): - result = windowed_operation( - stack, [testnd, testnd], kernel=[3], shape=(5, 5) - ) + result = windowed_operation(stack, [testnd, testnd], kernel=[3], shape=(5, 5)) @pytest.mark.skip( @@ -126,9 +124,7 @@ def test_transpose(testnd): def test_set_section(testnd): - sec = NDData( - np.zeros((2, 2)), uncertainty=VarianceUncertainty(np.ones((2, 2))) - ) + sec = NDData(np.zeros((2, 2)), uncertainty=VarianceUncertainty(np.ones((2, 2)))) testnd.set_section((slice(0, 2), slice(1, 3)), sec) assert_array_equal(testnd[:2, 1:3].data, 0) assert_array_equal(testnd[:2, 1:3].variance, 1) @@ -253,9 +249,7 @@ class TestClass(AstroDataMixin): assert isinstance(testclass_testnd.uncertainty, ADVarianceUncertainty) - assert_array_equal( - testclass_testnd.uncertainty.array, testclass_testnd.variance - ) + assert_array_equal(testclass_testnd.uncertainty.array, testclass_testnd.variance) # Test setting the variance testclass_testnd.variance = 2 @@ -375,6 +369,7 @@ def gen_lazy(): assert isinstance(result, ADVarianceUncertainty) assert_array_equal(result.array, testnd.variance[:2, 0]) + # Basically the same test as above but using slicing. def test_access_to_other_planes_when_sliced(testnd): ndwindow = testnd[1:, 1:] @@ -386,7 +381,5 @@ def test_access_to_other_planes_when_sliced(testnd): assert len(ndwindow.OBJCAT) == 3 - - if __name__ == "__main__": pytest.main() diff --git a/tests/unit/test_object_construction.py b/tests/unit/test_object_construction.py index d955c97..e119a30 100644 --- a/tests/unit/test_object_construction.py +++ b/tests/unit/test_object_construction.py @@ -111,9 +111,7 @@ def test_append_image_hdu(): def test_append_lowercase_name(): ad = astrodata.create({}) - with pytest.warns( - UserWarning, match="extension name 'sci' should be uppercase" - ): + with pytest.warns(UserWarning, match="extension name 'sci' should be uppercase"): ad.append(NDData(np.zeros((4, 5))), name="sci") @@ -131,10 +129,7 @@ def test_append_arrays(tmp_path): with pytest.raises(AttributeError): ad[0].DQ = np.arange(5) - match = ( - "Arbitrary image extensions can only be added in association " - "to a 'SCI'" - ) + match = "Arbitrary image extensions can only be added in association " "to a 'SCI'" with pytest.raises(ValueError, match=match): ad.append(np.zeros(10), name="FOO") @@ -283,10 +278,7 @@ def test_append_table_to_extensions(tmp_path): assert ad[2].hdr["FOO"] == "BAR" - match = ( - "Cannot append table 'TABLE1' because it would hide an " - "extension table" - ) + match = "Cannot append table 'TABLE1' because it would hide an " "extension table" with pytest.raises(ValueError, match=match): ad.TABLE1 = Table([[1]]) @@ -401,9 +393,7 @@ def test_append_slice_to_extension(testfile1, testfile2): @pytest.mark.dragons_remote_data def test_delete_named_associated_extension(testfile2): ad = astrodata.from_file(testfile2) - ad[0].MYTABLE = Table( - ([1, 2, 3], [4, 5, 6], [7, 8, 9]), names=("a", "b", "c") - ) + ad[0].MYTABLE = Table(([1, 2, 3], [4, 5, 6], [7, 8, 9]), names=("a", "b", "c")) assert "MYTABLE" in ad[0] del ad[0].MYTABLE assert "MYTABLE" not in ad[0] diff --git a/tests/unit/test_testing.py b/tests/unit/test_testing.py index 60f0298..93b15bd 100644 --- a/tests/unit/test_testing.py +++ b/tests/unit/test_testing.py @@ -1,6 +1,7 @@ """Tests for the `astrodata.testing` module.""" import copy +import gc import io import itertools import os @@ -8,9 +9,11 @@ import warnings import numpy as np +import objgraph import pytest import unittest from hypothesis import given, strategies as st +from pathlib import Path import astrodata import astrodata.testing as testing @@ -85,6 +88,48 @@ def mock_download(remote_url, **kwargs): os.remove(fname) +@pytest.mark.parametrize( + "filename", + [ + "test.fits", + "bpm_20220601_ghost_blue_11_full_4amp.fits", + ], +) +def test_download_memory_leaks(tmp_path, monkeypatch, filename): + """Test for memory leaks when downloading data and not saving to an ad.""" + path = tmp_path + sub_path = "." + monkeypatch.setenv("ASTRODATA_TEST", str(path.absolute())) + + initial_ndad = len(objgraph.by_type("NDAstroData")) + + assert initial_ndad == 0 + + path_to_data = download_from_archive(filename, path, sub_path) + + final_ndad = len(objgraph.by_type("NDAstroData")) + + assert Path(path_to_data).exists() + assert final_ndad == initial_ndad + + # Open the file and then remove ad refs and garbage collect. + n_pre_open_ndad = len(objgraph.by_type("NDAstroData")) + + ad = astrodata.from_file(path_to_data) + + del ad + gc.collect() + + post_objects = objgraph.by_type("NDAstroData") + + all_referrers = [ + ref for ref in itertools.chain(gc.get_referrers(o) for o in post_objects) if ref is not post_objects + ] + + + assert n_pre_open_ndad == len(post_objects) + + @pytest.mark.skipif(os.name == "nt", reason="Test only works on unix/osx") @skip_if_download_none @pytest.mark.dragons_remote_data @@ -128,9 +173,7 @@ def mock_download(remote_url, **kwargs): assert result is None with pytest.raises(IOError): - download_from_archive( - "N20180304S0126.fits", cache=False, fail_on_error=True - ) + download_from_archive("N20180304S0126.fits", cache=False, fail_on_error=True) testing.DownloadState().invalidate_cache() @@ -504,9 +547,7 @@ def test_warning_if_no_cache_path(monkeypatch): with warnings.catch_warnings(record=True) as w: warnings.simplefilter("always") - testing.download_from_archive( - "N20180304S0126.fits", env_var="ASTRODATA_TEST" - ) + testing.download_from_archive("N20180304S0126.fits", env_var="ASTRODATA_TEST") assert len(w) == 1 assert issubclass(w[-1].category, UserWarning) @@ -553,9 +594,7 @@ def test_download_file_path_subpath( ) else: - file_path = download_from_archive( - test_file_archive, path=path, cache=False - ) + file_path = download_from_archive(test_file_archive, path=path, cache=False) assert file_path == os.path.join(tmpdir, expected_path, test_file_archive) @@ -620,9 +659,7 @@ def test_download_raise_error_on_fail(tmpdir, bad_filename): @pytest.mark.skip(reason="See: https://github.com/GeminiDRSoftware/astrodata/issues/62") def test_get_associated_calibrations(tmpdir, test_file_archive): - associated_calibrations = testing.get_associated_calibrations( - test_file_archive - ) + associated_calibrations = testing.get_associated_calibrations(test_file_archive) results = associated_calibrations @@ -702,9 +739,7 @@ def test_ADCompare_run_comparison(ad1, ad2): compare.run_comparison() # Check that ad1 and ad3 are equal when ignoring keywords. - keywords = {key for key in ad1.phu.keys()} | { - key for key in ad3.phu.keys() - } + keywords = {key for key in ad1.phu.keys()} | {key for key in ad3.phu.keys()} compare.run_comparison(ignore_kw=list(keywords)) # Check that ad1 and ad2 are not equal. @@ -773,6 +808,7 @@ def resize_ext(ad, n): assert not compare.numext() + def test_ADCompare_unequal_tags(tmp_path): ad1_file_path = tmp_path / "file_1.fits" ad2_file_path = tmp_path / "file_2.fits" @@ -784,7 +820,7 @@ def test_ADCompare_unequal_tags(tmp_path): ] for file_path in file_paths: - data = np.random.random((100,100)).astype(np.float32) + data = np.random.random((100, 100)).astype(np.float32) hdu = fits.PrimaryHDU() hdu.writeto(file_path) @@ -825,7 +861,6 @@ def _matches_data(source): return False - astrodata.factory.add_class(ADClass1) astrodata.factory.add_class(ADClass2) astrodata.factory.add_class(ADClass3) @@ -991,7 +1026,10 @@ def test_ADCompare_wcs(ad1, ad2): def test_ad_compare(ad1, ad2): assert testing.ad_compare(ad1, ad1) - with pytest.raises(AssertionError, match="Comparison between N20180304S0126.fits and N20180305S0001.fits"): + with pytest.raises( + AssertionError, + match="Comparison between N20180304S0126.fits and N20180305S0001.fits", + ): assert not testing.ad_compare(ad1, ad2) diff --git a/tests/unit/test_wcs.py b/tests/unit/test_wcs.py index 33095ab..6d56115 100644 --- a/tests/unit/test_wcs.py +++ b/tests/unit/test_wcs.py @@ -252,9 +252,7 @@ def test_loglinear_axis(NIRI_IMAGE, tmp_path, monkeypatch): new_output_frame = cf.CompositeFrame( [loglinear_frame, celestial_frame], name="world" ) - new_wcs = ( - models.Exponential1D(amplitude=1, tau=2) & ad[0].wcs.forward_transform - ) + new_wcs = models.Exponential1D(amplitude=1, tau=2) & ad[0].wcs.forward_transform ad[0].wcs = gWCS([(new_input_frame, new_wcs), (new_output_frame, None)]) new_coords = ad[0].wcs(2, 200, 300) assert_allclose(coords, new_coords[1:]) @@ -265,6 +263,7 @@ def test_loglinear_axis(NIRI_IMAGE, tmp_path, monkeypatch): ad2 = astrodata.from_file("test.fits") assert_allclose(ad2[0].wcs(2, 200, 300), new_coords) + @pytest.mark.skip(reason="Requires external test data.") def test_tabular1D_axis(tmp_path, monkeypatch): """Check a FITS file with a tabular 1D axis is read correctly and @@ -284,10 +283,12 @@ def test_tabular1D_axis(tmp_path, monkeypatch): assert ad2[0].wcs(0) == pytest.approx(3017.51065254) assert ad2[0].wcs(1021) == pytest.approx(4012.89510727) + # Coordinates of projection center and new projection center -@pytest.mark.parametrize("coords", ([(0, 0), (0.1, -0.1)], - [(120, -50), (119.5, -49.5)], - [(270, 89.9), (0, 89)])) +@pytest.mark.parametrize( + "coords", + ([(0, 0), (0.1, -0.1)], [(120, -50), (119.5, -49.5)], [(270, 89.9), (0, 89)]), +) @pytest.mark.parametrize("flip", (True, False)) def test_create_new_image_projection(flip, coords): shifts = (100, 200) @@ -298,13 +299,15 @@ def test_create_new_image_projection(flip, coords): if not flip: matrix[0] *= -1 lon, lat = coords[0] - projection = (models.AffineTransformation2D(matrix=matrix) | - models.Pix2Sky_Gnomonic() | - models.RotateNative2Celestial(lon=lon, lat=lat, lon_pole=180)) + projection = ( + models.AffineTransformation2D(matrix=matrix) + | models.Pix2Sky_Gnomonic() + | models.RotateNative2Celestial(lon=lon, lat=lat, lon_pole=180) + ) transform = shifts | projection new_transform = adwcs.create_new_image_projection(transform, coords[1]) for x in (0, 1000): for y in (0, 1000): - c1 = SkyCoord(*transform(x, y), unit='deg') - c2 = SkyCoord(*new_transform(x, y), unit='deg') + c1 = SkyCoord(*transform(x, y), unit="deg") + c2 = SkyCoord(*new_transform(x, y), unit="deg") assert c1.separation(c2).arcsec < 0.5 From ccf61591602562b8a60e9a3935c67b773b6a806c Mon Sep 17 00:00:00 2001 From: teald Date: Tue, 1 Apr 2025 16:24:22 -0700 Subject: [PATCH 17/18] test: Add objgraph dependency. --- poetry.lock | 945 ++++++++++++++++++++++++++----------------------- pyproject.toml | 1 + 2 files changed, 501 insertions(+), 445 deletions(-) diff --git a/poetry.lock b/poetry.lock index 8ad4a56..46d6318 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 2.0.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.1.2 and should not be changed by hand. [[package]] name = "alabaster" @@ -26,14 +26,14 @@ files = [ [[package]] name = "anyio" -version = "4.8.0" +version = "4.9.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" optional = false python-versions = ">=3.9" groups = ["build_test"] files = [ - {file = "anyio-4.8.0-py3-none-any.whl", hash = "sha256:b5011f270ab5eb0abf13385f851315585cc37ef330dd88e27ec3d34d651fd47a"}, - {file = "anyio-4.8.0.tar.gz", hash = "sha256:1d9fe889df5212298c0c0723fa20479d1b94883a2df44bd3897aa91083316f7a"}, + {file = "anyio-4.9.0-py3-none-any.whl", hash = "sha256:9f76d541cad6e36af7beb62e978876f3b41e3e04f2c1fbf0884604c0a9c4d93c"}, + {file = "anyio-4.9.0.tar.gz", hash = "sha256:673c0c244e15788651a4ff38710fea9675823028a6f08a5eda409e0c9840a028"}, ] [package.dependencies] @@ -43,20 +43,20 @@ sniffio = ">=1.1" typing_extensions = {version = ">=4.5", markers = "python_version < \"3.13\""} [package.extras] -doc = ["Sphinx (>=7.4,<8.0)", "packaging", 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= ">=3.10" groups = ["main"] files = [ - {file = "asdf_astropy-0.7.0-py3-none-any.whl", hash = "sha256:77ac1055c9439ae121b418b2fcc19117ee3f726e0fbd2d73ea8b173761788f0b"}, - {file = "asdf_astropy-0.7.0.tar.gz", hash = "sha256:c981754e10145439de3cc6808ffb3101ef055d0b3164742c72f44b0b2b5c0525"}, + {file = "asdf_astropy-0.7.1-py3-none-any.whl", hash = "sha256:003b6969e066b3bae07027c724fe3e6434c49c3ba9d09f889bfecdc587086ba0"}, + {file = "asdf_astropy-0.7.1.tar.gz", hash = "sha256:5aa5a448ee0945bd834a9ba8fb86cf43b39e85d24260e1339b734173ab6024c7"}, ] [package.dependencies] @@ -252,14 +252,14 @@ test = ["asdf (>=2.8.0)", "asdf-astropy", "pytest (>=4.6.0)"] [[package]] name = "astroid" -version = "3.3.8" +version = "3.3.9" description = "An abstract syntax tree for Python with inference support." optional = false python-versions = ">=3.9.0" groups = ["docs"] files = [ - {file = "astroid-3.3.8-py3-none-any.whl", hash = "sha256:187ccc0c248bfbba564826c26f070494f7bc964fd286b6d9fff4420e55de828c"}, - 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\"cygwin\"", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel (>=0.44.0)"] +type = ["importlib_metadata (>=7.0.2) ; python_version < \"3.10\"", "jaraco.develop (>=7.21) ; sys_platform != \"cygwin\"", "mypy (==1.14.*)", "pytest-mypy"] [[package]] name = "six" @@ -2774,24 +2813,24 @@ test = ["cython (>=3.0)", "defusedxml (>=0.7.1)", "pytest (>=8.0)", "setuptools [[package]] name = "sphinx-autoapi" -version = "3.4.0" +version = "3.6.0" description = "Sphinx API documentation generator" optional = false -python-versions = ">=3.8" +python-versions = ">=3.9" groups = ["docs"] files = [ - {file = "sphinx_autoapi-3.4.0-py3-none-any.whl", hash = "sha256:4027fef2875a22c5f2a57107c71641d82f6166bf55beb407a47aaf3ef14e7b92"}, - {file = "sphinx_autoapi-3.4.0.tar.gz", hash = "sha256:e6d5371f9411bbb9fca358c00a9e57aef3ac94cbfc5df4bab285946462f69e0c"}, + {file = "sphinx_autoapi-3.6.0-py3-none-any.whl", hash = "sha256:f3b66714493cab140b0e896d33ce7137654a16ac1edb6563edcbd47bf975f711"}, + {file = "sphinx_autoapi-3.6.0.tar.gz", hash = "sha256:c685f274e41d0842ae7e199460c322c4bd7fec816ccc2da8d806094b4f64af06"}, ] [package.dependencies] astroid = [ {version = ">=2.7", markers = "python_version < \"3.12\""}, - {version = ">=3.0.0a1", markers = "python_version >= \"3.12\""}, + {version = ">=3", markers = "python_version >= \"3.12\""}, ] Jinja2 = "*" PyYAML = "*" -sphinx = ">=6.1.0" +sphinx = ">=7.4.0" [[package]] name = "sphinx-automodapi" @@ -2810,7 +2849,7 @@ sphinx = ">=4" [package.extras] rtd = ["sphinx (<7)", "sphinx-rtd-theme"] -test = ["coverage", "cython", "pytest", "pytest-cov", "setuptools"] +test = ["coverage", "cython", "pytest", "pytest-cov", "setuptools ; python_version >= \"3.12\""] [[package]] name = "sphinx-rtd-theme" @@ -3021,6 +3060,7 @@ files = [ {file = "tomli-2.2.1-py3-none-any.whl", hash = "sha256:cb55c73c5f4408779d0cf3eef9f762b9c9f147a77de7b258bef0a5628adc85cc"}, {file = "tomli-2.2.1.tar.gz", hash = "sha256:cd45e1dc79c835ce60f7404ec8119f2eb06d38b1deba146f07ced3bbc44505ff"}, ] +markers = {build_test = "python_version < \"3.12\"", test = "python_version < \"3.12\""} [[package]] name = "tomlkit" @@ -3051,16 +3091,31 @@ docs = ["Sphinx (>=1.3.1)", "docutils", "pylons-sphinx-themes"] [[package]] name = "typing-extensions" -version = "4.12.2" +version = "4.13.0" description = "Backported and Experimental Type Hints for Python 3.8+" optional = false python-versions = ">=3.8" groups = ["main", "build_test", "docs", "test"] files = [ - {file = "typing_extensions-4.12.2-py3-none-any.whl", hash = "sha256:04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d"}, - {file = "typing_extensions-4.12.2.tar.gz", hash = "sha256:1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8"}, + {file = "typing_extensions-4.13.0-py3-none-any.whl", hash = "sha256:c8dd92cc0d6425a97c18fbb9d1954e5ff92c1ca881a309c45f06ebc0b79058e5"}, + {file = "typing_extensions-4.13.0.tar.gz", hash = "sha256:0a4ac55a5820789d87e297727d229866c9650f6521b64206413c4fbada24d95b"}, +] +markers = {main = "python_version <= \"3.12\"", docs = "python_version == \"3.10\""} + +[[package]] +name = "typing-inspection" +version = "0.4.0" +description = "Runtime typing introspection tools" +optional = false +python-versions = ">=3.9" +groups = ["test"] +files = [ + {file = "typing_inspection-0.4.0-py3-none-any.whl", hash = "sha256:50e72559fcd2a6367a19f7a7e610e6afcb9fac940c650290eed893d61386832f"}, + {file = "typing_inspection-0.4.0.tar.gz", hash = "sha256:9765c87de36671694a67904bf2c96e395be9c6439bb6c87b5142569dcdd65122"}, ] -markers = {main = "python_version < \"3.13\"", docs = "python_version < \"3.11\""} + +[package.dependencies] +typing-extensions = ">=4.12.0" [[package]] name = "urllib3" @@ -3075,7 +3130,7 @@ files = [ ] [package.extras] -brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"] +brotli = ["brotli (>=1.0.9) ; platform_python_implementation == \"CPython\"", "brotlicffi (>=0.8.0) ; platform_python_implementation != \"CPython\""] h2 = ["h2 (>=4,<5)"] socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"] zstd = ["zstandard (>=0.18.0)"] @@ -3098,14 +3153,14 @@ testing = ["coverage", "pytest", "pytest-cov"] [[package]] name = "virtualenv" -version = "20.29.1" +version = "20.30.0" description = "Virtual Python Environment builder" optional = false python-versions = ">=3.8" groups = ["dev", "test"] files = [ - {file = "virtualenv-20.29.1-py3-none-any.whl", hash = "sha256:4e4cb403c0b0da39e13b46b1b2476e505cb0046b25f242bee80f62bf990b2779"}, - {file = "virtualenv-20.29.1.tar.gz", hash = "sha256:b8b8970138d32fb606192cb97f6cd4bb644fa486be9308fb9b63f81091b5dc35"}, + {file = "virtualenv-20.30.0-py3-none-any.whl", hash = "sha256:e34302959180fca3af42d1800df014b35019490b119eba981af27f2fa486e5d6"}, + {file = "virtualenv-20.30.0.tar.gz", hash = "sha256:800863162bcaa5450a6e4d721049730e7f2dae07720e0902b0e4040bd6f9ada8"}, ] [package.dependencies] @@ -3115,7 +3170,7 @@ platformdirs = ">=3.9.1,<5" [package.extras] docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2,!=7.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"] -test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"] +test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8) ; platform_python_implementation == \"PyPy\" or platform_python_implementation == \"GraalVM\" or platform_python_implementation == \"CPython\" and sys_platform == \"win32\" and python_version >= \"3.13\"", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10) ; platform_python_implementation == \"CPython\""] [[package]] name = "waitress" @@ -3244,11 +3299,11 @@ files = [ markers = {main = "python_version <= \"3.11\"", build_test = "python_full_version < \"3.10.2\""} [package.extras] -check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"] +check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""] cover = ["pytest-cov"] doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] enabler = ["pytest-enabler (>=2.2)"] -test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] +test = ["big-O", "importlib-resources ; python_version < \"3.9\"", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] type = ["pytest-mypy"] [[package]] @@ -3328,4 +3383,4 @@ testing = ["coverage[toml]", "zope.event", "zope.testing"] [metadata] lock-version = "2.1" python-versions = "^3.10" -content-hash = "6205508f35c0a0c4fa89c94647b35211c91508c3d7141071d945d4a87d43d19e" +content-hash = "2d58aca218eeb6b190a536ff963d049f0149d6aad3640f4347a785def015300b" diff --git a/pyproject.toml b/pyproject.toml index 18e9c8b..8dbb93a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -51,6 +51,7 @@ hypothesis = "^6.99.13" nox = "^2024.4.15" watchdog = "^4.0.1" rst-extract = {git = "https://github.com/teald/rst_extract/"} +objgraph = "^3.6.2" [tool.poetry.group.build_test.dependencies] From fa53e8b4aad9f288681c902a3991e2dd74f438f7 Mon Sep 17 00:00:00 2001 From: teald Date: Wed, 2 Apr 2025 09:18:25 -0700 Subject: [PATCH 18/18] fix(test,script): Update tomli/tomllib handling. --- tests/script_tests/test_pyproject_scripts.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/tests/script_tests/test_pyproject_scripts.py b/tests/script_tests/test_pyproject_scripts.py index 3546e13..94b5cb1 100644 --- a/tests/script_tests/test_pyproject_scripts.py +++ b/tests/script_tests/test_pyproject_scripts.py @@ -11,7 +11,12 @@ from pathlib import Path import pytest -import tomli + +if int(sys.version_info[0]) == 3 and int(sys.version_info[1]) >= 12: + from tomllib import load as toml_load + +else: + from tomli import load as toml_load @functools.cache @@ -21,7 +26,7 @@ def scripts() -> dict[str, str]: root_dir = pyproject.parent with open(pyproject, "rb") as file: - data = tomli.load(file) + data = toml_load(file) scripts = data["tool"]["script_tests"]