Merge pull request #1674 from braingram/update_3p0px

Update 3p0px

.github/workflows/ci.yml

@@ -108,6 +108,7 @@ jobs:
     needs: [core, asdf-schemas]
     uses: OpenAstronomy/github-actions-workflows/.github/workflows/publish_pure_python.yml@v1
     with:
+      python-version: "3.11"
       upload_to_pypi: false
       upload_to_anaconda: false
       test_extras: tests

.github/workflows/downstream.yml

@@ -41,6 +41,7 @@ jobs:
       default_python: '3.10'
       envs: |
         - linux: asdf-astropy
+        - linux: specutils
 
   stsci:
     uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@v1

.pre-commit-config.yaml

@@ -43,13 +43,13 @@ repos:
       exclude: "asdf/(extern||_jsonschema)/.*"
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: 'v0.0.292'
+  rev: 'v0.1.1'
   hooks:
     - id: ruff
       args: ["--fix"]
 
 - repo: https://github.com/psf/black
-  rev: 23.9.1
+  rev: 23.10.1
   hooks:
     - id: black
 
@@ -59,6 +59,6 @@ repos:
     - id: blacken-docs
 
 - repo: https://github.com/abravalheri/validate-pyproject
-  rev: "v0.14"
+  rev: "v0.15"
   hooks:
     - id: validate-pyproject

CHANGES.rst

@@ -1,10 +1,10 @@
-3.0.1 (unreleased)
+3.0.1 (2023-10-30)
 ------------------
 
 The ASDF Standard is at v1.6.0
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
--
+- Fix bug in ``asdftool diff`` for arrays within a list [#1672]
 
 3.0.0 (2023-10-16)
 ------------------

asdf/_tests/commands/tests/data/blocks.diff

@@ -10,4 +10,5 @@ tree:
       -
 >       9000
 <       10000
-    ndarrays at "foobar" differ by shape, datatype and contents
+>   ndarrays differ by shape, datatype and contents
+<   ndarrays differ by shape, datatype and contents

asdf/_tests/commands/tests/data/ndarray_in_list.diff

@@ -0,0 +1,9 @@
+< tree:
+< list:
+<   - a:
+<       offset:
+<         16
+<       strides:
+<         - -8
+>       ndarrays differ by contents
+<       ndarrays differ by contents

asdf/_tests/commands/tests/data/ndarrays.diff

@@ -1 +1,4 @@
-    ndarrays at "a" differ by contents
+tree:
+  a:
+>   ndarrays differ by contents
+<   ndarrays differ by contents

asdf/_tests/commands/tests/data/simple_inline_array.diff

@@ -1 +1,4 @@
-    ndarrays at "array" differ by contents
+tree:
+  array:
+>   ndarrays differ by contents
+<   ndarrays differ by contents

asdf/_tests/commands/tests/test_diff.py

@@ -54,6 +54,12 @@ def test_diff_ndarray():
     _assert_diffs_equal(filenames, result_file, minimal=False)
 
 
+def test_diff_ndarray_in_list():
+    filenames = ["ndarray_in_list0.asdf", "ndarray_in_list1.asdf"]
+    result_file = "ndarray_in_list.diff"
+    _assert_diffs_equal(filenames, result_file, minimal=False)
+
+
 def test_diff_block():
     filenames = ["block0.asdf", "block1.asdf"]
     result_file = "blocks.diff"

asdf/_tests/test_generic_io.py

@@ -112,7 +112,7 @@ def get_read_fd():
 
     with _roundtrip(tree, get_write_fd, get_read_fd) as ff:
         assert len(ff._blocks.blocks) == 2
-        assert isinstance(ff._blocks.blocks[0].cached_data, np.core.memmap)
+        assert isinstance(ff._blocks.blocks[0].cached_data, np.memmap)
 
 
 def test_open2(tree, tmp_path):
@@ -135,7 +135,7 @@ def get_read_fd():
 
     with _roundtrip(tree, get_write_fd, get_read_fd) as ff:
         assert len(ff._blocks.blocks) == 2
-        assert isinstance(ff._blocks.blocks[0].cached_data, np.core.memmap)
+        assert isinstance(ff._blocks.blocks[0].cached_data, np.memmap)
 
 
 @pytest.mark.parametrize("mode", ["r", "w", "rw"])
@@ -172,7 +172,7 @@ def get_read_fd():
 
     with _roundtrip(tree, get_write_fd, get_read_fd) as ff:
         assert len(ff._blocks.blocks) == 2
-        assert isinstance(ff._blocks.blocks[0].cached_data, np.core.memmap)
+        assert isinstance(ff._blocks.blocks[0].cached_data, np.memmap)
         ff.tree["science_data"][0] = 42
 
 
@@ -208,7 +208,7 @@ def get_read_fd():
 
     with _roundtrip(tree, get_write_fd, get_read_fd) as ff:
         assert len(ff._blocks.blocks) == 2
-        assert not isinstance(ff._blocks.blocks[0].cached_data, np.core.memmap)
+        assert not isinstance(ff._blocks.blocks[0].cached_data, np.memmap)
         ff.tree["science_data"][0] = 42
 
 
@@ -224,7 +224,7 @@ def get_read_fd():
 
     with _roundtrip(tree, get_write_fd, get_read_fd) as ff:
         assert len(ff._blocks.blocks) == 2
-        assert not isinstance(ff._blocks.blocks[0].cached_data, np.core.memmap)
+        assert not isinstance(ff._blocks.blocks[0].cached_data, np.memmap)
         ff.tree["science_data"][0] = 42
 
 
@@ -252,7 +252,7 @@ def get_read_fd():
 
     with _roundtrip(tree, get_write_fd, get_read_fd) as ff:
         assert len(ff._blocks.blocks) == 2
-        assert not isinstance(ff._blocks.blocks[0].cached_data, np.core.memmap)
+        assert not isinstance(ff._blocks.blocks[0].cached_data, np.memmap)
 
 
 @pytest.mark.remote_data()

asdf/commands/diff.py

@@ -104,8 +104,9 @@ class ArrayNode:
     of but not necessarily display. This allows the diff output to be
     cleaner."""
 
-    def __init__(self, name):
+    def __init__(self, name, index):
         self.name = name
+        self.index = index
 
     def __hash__(self):
         return hash(self.name)
@@ -191,7 +192,7 @@ def print_in_tree(diff_ctx, node_list, thing, other, use_marker=False, last_was_
     # If tree element is list, recursively print list contents
     if isinstance(thing, list):
         for i, subthing in enumerate(thing):
-            key = ArrayNode(f"{node_list[-1]}_{i}")
+            key = ArrayNode(f"{node_list[-1]}_{i}", i)
             last_was_list = print_in_tree(
                 diff_ctx,
                 [*node_list, key],
@@ -277,9 +278,9 @@ def compare_ndarrays(diff_ctx, array0, array1, keys):
         differences.append("contents")
 
     if differences:
-        prefix = "  " * (len(keys) + 1)
-        msg = f"ndarrays at \"{'.'.join(keys)}\" differ by {human_list(differences)}"
-        diff_ctx.iostream.write(prefix + RED + msg + RESET_NEWLINE)
+        msg = f"ndarrays differ by {human_list(differences)}"
+        print_in_tree(diff_ctx, keys, msg, False, ignore_lwl=True)
+        print_in_tree(diff_ctx, keys, msg, True, ignore_lwl=True)
 
 
 def both_are_ndarrays(tree0, tree1):
@@ -321,7 +322,7 @@ def compare_trees(diff_ctx, tree0, tree1, keys=None):
         compare_dicts(diff_ctx, tree0, tree1, keys)
     elif isinstance(tree0, list) and isinstance(tree1, list):
         for i, (obj0, obj1) in enumerate(zip(tree0, tree1)):
-            key = ArrayNode(f"item_{i}")
+            key = ArrayNode(f"item_{i}", i)
             compare_trees(diff_ctx, obj0, obj1, [*keys, key])
     else:
         compare_objects(diff_ctx, tree0, tree1, keys)

asdf/generic_io.py

@@ -637,7 +637,7 @@ def clear(self, nbytes):
 
     def memmap_array(self, offset, size):
         """
-        Memmap a chunk of the file into a `np.core.memmap` object.
+        Memmap a chunk of the file into a `np.memmap` object.
 
         Parameters
         ----------
@@ -649,7 +649,7 @@ def memmap_array(self, offset, size):
 
         Returns
         -------
-        array : np.core.memmap
+        array : np.memmap
         """
         msg = f"memmapping is not implemented for {self.__class__.__name__}"
         raise NotImplementedError(msg)
@@ -680,7 +680,7 @@ def read_into_array(self, size):
 
         Returns
         -------
-        array : np.core.memmap
+        array : np.memmap
         """
         buff = self.read(size)
         return np.frombuffer(buff, np.uint8, size, 0)

tox.ini

@@ -2,8 +2,7 @@
 env_list =
     compatibility
     coverage
-    devdep{,-parallel}
-    py{39,310,311,312}{,-compatibility,-coverage,-jsonschema}{,-parallel}
+    py{39,310,311,312}{,-compatibility,-coverage,-jsonschema}{,-devdeps}{,-parallel}
     asdf{-standard,-transform-schemas,-unit-schemas,-wcs-schemas,-coordinates-schemas,-astropy}
     gwcs
     jwst