Merge pull request #620 from drdavella/v2.3.x

Release candidate for v2.3.0

.travis.yml

@@ -22,64 +22,65 @@ env:
         # overidden underneath. They are defined here in order to save having
         # to repeat them for all configurations.
         - PYTHON_VERSION=3.6
-        - PYTEST_VERSION=3.7
+        - PYTEST_VERSION=3.10
         - ASTROPY_VERSION=stable
         - NUMPY_VERSION=stable
-        - PIP_DEPENDENCIES='pytest-faulthandler importlib_resources'
-        - CONDA_DEPENDENCIES='semantic_version jsonschema pyyaml six lz4 pytest-astropy'
+        - ALL_PIP_DEPENDENCIES='pytest-faulthandler importlib_resources'
+        - PIP_DEPENDENCIES="$ALL_PIP_DEPENDENCIES"
+        - ALL_CONDA_DEPENDENCIES='semantic_version jsonschema pyyaml six lz4 pytest-astropy'
+        - CONDA_DEPENDENCIES="$ALL_CONDA_DEPENDENCIES"
         - GWCS_GIT='git+git://github.com/spacetelescope/gwcs.git#egg=gwcs'
         - GWCS_PIP='gwcs'
-        - MAIN_CMD='python setup.py'
-        - SETUP_CMD='test --remote-data'
+        - RUN_CMD='pytest'
 
     matrix:
         # Make sure that installation does not fail
-        - SETUP_CMD='install'
+        - RUN_CMD='python setup.py install'
         # Make sure README will display properly on pypi
         - PIP_DEPENDENCIES='twine' TWINE_CHECK=1
-        - PYTHON_VERSION=3.5 SETUP_CMD='test'
-        - PYTHON_VERSION=3.6 SETUP_CMD='test'
-        - PYTHON_VERSION=3.7 PYTEST_VERSION=3.8 SETUP_CMD='test'
+        - PYTHON_VERSION=3.5
+        - PYTHON_VERSION=3.6 PYTEST_VERSION=3.8
+        - PYTHON_VERSION=3.7 PYTEST_VERSION=3.9
 
 matrix:
     fast_finish: true
     include:
 
         # Do a coverage test
-        - env: SETUP_CMD='test --coverage --open-files --remote-data'
+        - env: COVERAGE=1
+               PIP_DEPENDENCIES="$ALL_PIP_DEPENDENCIES coverage coveralls"
 
         # Check for sphinx doc build warnings - we do this first because it
         # may run for a long time
-        - env: SETUP_CMD='build_docs -w'
+        - env: RUN_CMD='python setup.py build_docs -w'
+               CONDA_DEPENDENCIES="$ALL_CONDA_DEPENDENCIES sphinx-astropy"
 
         # Do a code style check
-        - env: MAIN_CMD="flake8 asdf --count" SETUP_CMD=''
+        - env: RUN_CMD="flake8 asdf --count"
+               PIP_DEPENDENCIES="$ALL_PIP_DEPENDENCIES flake8"
 
         # try older numpy versions
-        - env: PYTHON_VERSION=3.5 NUMPY_VERSION=1.11 SETUP_CMD='test'
-        - env: NUMPY_VERSION=1.12 SETUP_CMD='test'
+        - env: PYTHON_VERSION=3.5 NUMPY_VERSION=1.11
+        - env: NUMPY_VERSION=1.12
 
-        # run a test using native pytest
         # also test against development version of Astropy
-        - env: MAIN_CMD='pytest' SETUP_CMD='' ASTROPY_VERSION=development
-               GWCS_PIP="$GWCS_GIT"
-               PYTEST_VERSION=3.8
+        - env: ASTROPY_VERSION=development GWCS_PIP="$GWCS_GIT"
 
         # latest stable versions
-        - env: NUMPY_VERSION=stable SETUP_CMD='test'
+        - env: NUMPY_VERSION=stable
 
         # Test against development version of numpy (this job can fail)
-        - env: NUMPY_VERSION=development SETUP_CMD='test'
+        - env: NUMPY_VERSION=development
 
         # Try a run on OSX
         - os: osx
-          env: NUMPY_VERSION=stable SETUP_CMD='test'
+          env: NUMPY_VERSION=stable
 
         # Test against latest version of jsonschema
         - env: PIP_DEPENDENCIES='jsonschema pytest-faulthandler importlib_resources'
 
     allow_failures:
-        - env: NUMPY_VERSION=development SETUP_CMD='test'
+        - env: NUMPY_VERSION=development
         - env: PIP_DEPENDENCIES='jsonschema pytest-faulthandler importlib_resources'
 
 install:
@@ -92,12 +93,15 @@ script:
     - if [[ $TWINE_CHECK ]]; then
         python setup.py build sdist;
         twine check dist/*;
+      elif [[ $COVERAGE ]]; then
+        coverage run --source=asdf -m pytest --remote-data --open-files;
+        coverage report -m;
       else
-        $MAIN_CMD $SETUP_CMD;
+        $RUN_CMD;
       fi
 
 after_success:
     # If coveralls.io is set up for this package, uncomment the line
     # below and replace "packagename" with the name of your package.
     # The coveragerc file may be customized as needed for your package.
-    - if [[ $SETUP_CMD == 'test --coverage --open-files --remote-data' ]]; then coveralls --rcfile='asdf/tests/coveragerc'; fi
+    - if [[ $COVERAGE ]]; then coveralls --rcfile='asdf/tests/coveragerc'; fi

CHANGES.rst

@@ -1,3 +1,22 @@
+2.3.0 (unreleased)
+------------------
+
+- Storage of arbitrary precision integers is now provided by
+  ``asdf.IntegerType``.  Reading a file with integer literals that are too
+  large now causes only a warning instead of a validation error. This is to
+  provide backwards compatibility for files that were created with a buggy
+  version of ASDF (see #553 below). [#566]
+
+- Remove WCS tags. These are now provided by the `gwcs package
+  <https://github.com/spacetelescope/gwcs>`_. [#593]
+
+- Deprecate the ``asdf.asdftypes`` module in favor of ``asdf.types``. [#611]
+
+- Support use of ``pathlib.Path`` with ``asdf.open`` and ``AsdfFile.write_to``.
+  [#617]
+
+- Update ASDF Standard submodule to version 1.3.0.
+
 2.2.1 (2018-11-15)
 ------------------
 
@@ -31,6 +50,9 @@
   index before any others. This fixes a bug that was related to the way that
   subclass tags were overwritten by external extensions. [#598]
 
+- Remove WCS tags. These are now provided by the `gwcs package
+  <https://github.com/spacetelescope/gwcs>`_. [#593]
+
 2.1.1 (2018-11-01)
 ------------------
 

appveyor.yml

@@ -8,19 +8,19 @@ environment:
       PYTEST_VERSION: "3.7"
       MINICONDA_VERSION: "latest"
       CMD_IN_ENV: "cmd /E:ON /V:ON /C .\\ci-helpers\\appveyor\\windows_sdk.cmd"
-      SETUP_CMD: "test"
+      RUN_CMD: "pytest"
       NUMPY_VERSION: "stable"
       ASTROPY_VERSION: "stable"
       GWCS_GIT: "git+git://github.com/spacetelescope/gwcs.git#egg=gwcs"
       GWCS_PIP: "gwcs"
-      CONDA_DEPENDENCIES: "semantic_version jsonschema pyyaml six lz4 pytest=3.6 pytest-astropy"
+      CONDA_DEPENDENCIES: "semantic_version jsonschema pyyaml six lz4 pytest-astropy"
       PIP_DEPENDENCIES: "pytest-faulthandler importlib_resources"
       PYTHON_ARCH: "64"
 
   matrix:
       # Make sure that installation does not fail
       - PYTHON_VERSION: "3.6"
-        SETUP_CMD: "install"
+        RUN_CMD: "python setup.py install"
         platform: x64
 
       - PYTHON_VERSION: "3.5"
@@ -65,4 +65,4 @@ install:
 build: false
 
 test_script:
-  - "%CMD_IN_ENV% python setup.py %SETUP_CMD%"
+  - "%CMD_IN_ENV% %RUN_CMD%"

asdf/__init__.py

@@ -15,7 +15,7 @@
 
 __all__ = [
     'AsdfFile', 'CustomType', 'AsdfExtension', 'Stream', 'open', 'test',
-    'commands', 'ExternalArrayReference'
+    'commands', 'IntegerType', 'ExternalArrayReference'
 ]
 
 try:
@@ -34,10 +34,11 @@
     raise ImportError("asdf requires numpy")
 
 from .asdf import AsdfFile, open_asdf
-from .asdftypes import CustomType
+from .types import CustomType
 from .extension import AsdfExtension
 from .stream import Stream
 from . import commands
+from .tags.core import IntegerType
 from .tags.core.external_reference import ExternalArrayReference
 
 from jsonschema import ValidationError

asdf/asdf.py

@@ -67,7 +67,7 @@ def __init__(self, tree=None, uri=None, extensions=None, version=None,
 
         extensions : list of AsdfExtension
             A list of extensions to use when reading and writing ASDF files.
-            See `~asdf.asdftypes.AsdfExtension` for more information.
+            See `~asdf.types.AsdfExtension` for more information.
 
         version : str, optional
             The ASDF version to use when writing out.  If not
@@ -411,13 +411,14 @@ def comments(self):
         """
         return self._comments
 
-    def _validate(self, tree, custom=True):
+    def _validate(self, tree, custom=True, reading=False):
         tagged_tree = yamlutil.custom_tree_to_tagged_tree(
             tree, self)
-        schema.validate(tagged_tree, self)
+        schema.validate(tagged_tree, self, reading=reading)
         # Perform secondary validation pass if requested
         if custom and self._custom_schema:
-            schema.validate(tagged_tree, self, self._custom_schema)
+            schema.validate(tagged_tree, self, self._custom_schema,
+                            reading=reading)
 
     def validate(self):
         """
@@ -650,10 +651,10 @@ def _open_asdf(cls, self, fd, uri=None, mode='r',
 
         tree = reference.find_references(tree, self)
         if not do_not_fill_defaults:
-            schema.fill_defaults(tree, self)
+            schema.fill_defaults(tree, self, reading=True)
 
         try:
-            self._validate(tree)
+            self._validate(tree, reading=True)
         except ValidationError:
             self.close()
             raise
@@ -1275,7 +1276,7 @@ def open_asdf(fd, uri=None, mode=None, validate_checksums=False,
 
     extensions : list of AsdfExtension
         A list of extensions to use when reading and writing ASDF files.
-        See `~asdf.asdftypes.AsdfExtension` for more information.
+        See `~asdf.types.AsdfExtension` for more information.
 
     do_not_fill_defaults : bool, optional
         When `True`, do not fill in missing default values.