Merge branch 'develop'

.gitignore

@@ -1,14 +1,9 @@
-*.pyc
-*~
 __pycache__/
-/.version
-/.vscode
 /MANIFEST
+/_meta.py
 /build/
 /dist/
-/icat.cfg
 /icat/__init__.py
-/tests/.cache/
 /tests/data/example_data.yaml
 /tests/data/icat.cfg
 /tests/data/icatdump-*.xml

CHANGES.rst

@@ -2,6 +2,98 @@ Changelog
 =========
 
 
+1.0.0 (2022-12-21)
+~~~~~~~~~~~~~~~~~~
+
+New features
+------------
+
++ `#73`_, `#106`_: Add support for the ICAT schema 5.0 extensions.
+
++ `#102`_, `#104`_: Make the `obj` argument to
+  :meth:`icat.client.Client.new` case insensitive.
+
++ `#77`_, `#103`_: Add a keyword argument `preset` to allow directly
+  passing configuration values to the constructor of class
+  :class:`icat.config.Config`.
+
++ `#66`_, `#75`_: Add pathlib support: methods that take a file name
+  argument also accept a :class:`pathlib.Path` object.  Internal
+  representation of file system paths are changed to use
+  :class:`pathlib.Path` where appropriate.  The predefined
+  configuarion variable `configFile` now supports tilde expansion.
+  Note incompatible changes below.
+
++ `#74`_: :class:`icat.ids.DataSelection` also accepts
+  `DataCollection` as argument.
+
+Incompatible changes and deprecations
+-------------------------------------
+
++ The order and arrangement of data objects in the dump file created
+  by :ref:`icatdump` has been changed.  In some cases, older versions
+  of :ref:`icatingest` will fail to read dump files written by new
+  versions of :ref:`icatdump`.
+
++ As a consequence of switching to pathlib for file system paths some
+  return values and variables are now :class:`pathlib.Path` objects
+  rather then :class:`str`.  This affects:
+
+  - the return value of :func:`icat.config.cfgpath`,
+  - the predefined configuarion variable `configFile`,
+  - the module variable :data:`icat.config.cfgdirs`.
+
++ Drop support for Python 2 and Python 3.3.
+
++ Drop keyword argument `attribute` and method
+  :meth:`icat.query.Query.setAttribute` from class
+  :class:`icat.query.Query`, deprecated in 0.18.0.
+
++ Drop module :mod:`icat.cgi`, deprecated in 0.13.0.
+
++ Drop module :mod:`icat.icatcheck` and exception
+  :exc:`icat.exception.GenealogyError`, deprecated in 0.17.0.
+
++ Drop methods :meth:`icat.ids.IDSClient.resetPrepared`,
+  :meth:`icat.ids.IDSClient.getPreparedDatafileIds`,
+  :meth:`icat.ids.IDSClient.getPreparedData`,
+  :meth:`icat.ids.IDSClient.getPreparedDataUrl`,
+  :meth:`icat.client.Client.getPreparedData`, and
+  :meth:`icat.client.Client.getPreparedDataUrl`, deprecated in 0.17.0.
+
++ Drop the predefined configuration variable `configDir`, deprecated
+  in 0.13.0.
+
++ Drop helper function :func:`icat.exception.stripCause`, deprecated
+  in 0.14.0.
+
++ Deprecate :data:`icat.config.defaultsection`.  Use the new `preset`
+  keyword argument to :class:`icat.config.Config` instead.
+
+Bug fixes and minor changes
+---------------------------
+
++ `#98`_, `#105`_: Review build tool chain.  Add a helper class
+  :class:`icat.helper.Version`.
+
++ `#101`_: Fix tests failing with PyYAML 6.0.
+
++ Some (more) example scripts now require ICAT 4.4.0 or newer.
+
+.. _#66: https://github.com/icatproject/python-icat/issues/66
+.. _#73: https://github.com/icatproject/python-icat/issues/73
+.. _#74: https://github.com/icatproject/python-icat/issues/74
+.. _#75: https://github.com/icatproject/python-icat/pull/75
+.. _#77: https://github.com/icatproject/python-icat/issues/77
+.. _#98: https://github.com/icatproject/python-icat/issues/98
+.. _#101: https://github.com/icatproject/python-icat/pull/101
+.. _#102: https://github.com/icatproject/python-icat/issues/102
+.. _#103: https://github.com/icatproject/python-icat/pull/103
+.. _#104: https://github.com/icatproject/python-icat/pull/104
+.. _#105: https://github.com/icatproject/python-icat/pull/105
+.. _#106: https://github.com/icatproject/python-icat/pull/106
+
+
 0.21.0 (2022-01-28)
 ~~~~~~~~~~~~~~~~~~~
 
@@ -19,6 +111,7 @@ New features
 
 .. _#100: https://github.com/icatproject/python-icat/pull/100
 
+
 0.20.1 (2021-11-04)
 ~~~~~~~~~~~~~~~~~~~
 

CITATION.cff

@@ -0,0 +1,37 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: python-icat – Python interface to ICAT and IDS
+message: Please cite this software using these metadata.
+type: software
+authors:
+  - given-names: Rolf
+    family-names: Krahl
+    email: [email protected]
+    affiliation: >-
+      Helmholtz-Zentrum Berlin für Materialien und
+      Energie
+    orcid: 'https://orcid.org/0000-0002-1266-3819'
+  - name: "The ICAT project"
+    website: https://icatproject.org/
+repository-code: 'https://github.com/icatproject/python-icat'
+repository-artifact: 'https://pypi.org/project/python-icat/'
+abstract: >-
+  The ICAT server is a metadata catalogue to support
+  Large Facility experimental data, linking all
+  aspects of the research chain from proposal through
+  to publication. It provides SOAP and RESTful web
+  service interfaces to an underlying database.
+
+  python-icat is a Python package that provides a
+  collection of modules for writing programs that
+  access an ICAT service using the SOAP interface. It
+  is based on Suds and extends it with ICAT specific
+  features.
+keywords:
+  - python
+  - metadata
+  - scientific-data
+  - metadata-catalogue
+license: Apache-2.0

MANIFEST.in

@@ -1,8 +1,8 @@
-include .version
 include CHANGES.rst
 include LICENSE.txt
 include MANIFEST.in
 include README.rst
+include _meta.py
 include doc/examples/*.py
 include doc/examples/example_data.yaml
 include doc/examples/icat.cfg
@@ -13,6 +13,10 @@ include doc/icatdata*.xsd
 include doc/man/*
 include doc/tutorial/*.py
 include tests/conftest.py
+include tests/data/legacy-icatdump-*.xml
+include tests/data/legacy-icatdump-*.yaml
+include tests/data/ref-icatdump-*.xml
+include tests/data/ref-icatdump-*.yaml
 include tests/data/summary*
 include tests/pytest.ini
 include tests/test_*.py

Makefile

@@ -1,7 +1,5 @@
 PYTHON = python3
 
-BUILDLIB = $(abspath build/lib)
-
 
 build:
 	$(PYTHON) setup.py build
@@ -12,33 +10,28 @@ test:
 sdist: doc-man
 	$(PYTHON) setup.py sdist
 
-doc-html: build
-	$(MAKE) -C doc html PYTHONPATH=$(BUILDLIB)
-
-doc-man: build
-	$(MAKE) -C doc man PYTHONPATH=$(BUILDLIB)
+doc-html: meta
+	$(MAKE) -C doc html PYTHONPATH=$(CURDIR)
 
+doc-man: meta
+	$(MAKE) -C doc man PYTHONPATH=$(CURDIR)
 
 clean:
-	rm -f *~ icat/*~ tests/*~ doc/*~ doc/examples/*~
 	rm -rf build
+	rm -rf __pycache__
 	rm -rf tests/data/example_data.yaml
 	rm -rf tests/data/icatdump-* tests/data/ingest-*.xml
 	rm -rf tests/scripts
 
 distclean: clean
-	rm -rf tests/.cache
-	rm -f MANIFEST .version
-	rm -rf python_icat.egg-info
-	rm -f *.pyc icat/*.pyc tests/*.pyc
-	rm -rf __pycache__ icat/__pycache__ tests/__pycache__
+	rm -f MANIFEST _meta.py
 	rm -f icat/__init__.py
 	rm -rf dist
+	rm -rf tests/.pytest_cache
 	$(MAKE) -C doc distclean
 
-
-init_py:
-	$(PYTHON) setup.py init_py
+meta:
+	$(PYTHON) setup.py meta
 
 
-.PHONY: build test sdist doc-html clean distclean init_py
+.PHONY: build test sdist doc-html doc-man clean distclean meta