Merge branch 'develop'

Author: RKrahl

.github/workflows/rst-lint.yaml

@@ -14,7 +14,7 @@ jobs:
         with:
           fetch-depth: 0
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
       - name: Install dependencies
@@ -25,6 +25,6 @@ jobs:
           python setup.py build
           python doc/src/conf.py
       - name: doc8-check
-        uses: deep-entertainment/doc8-action@v4
+        uses: deep-entertainment/doc8-action@v5
         with:
           scanPaths: "doc/src"

CHANGES.rst

@@ -2,6 +2,35 @@ Changelog
 =========
 
 
+.. _changes-1_4_0:
+
+1.4.0 (2024-08-30)
+~~~~~~~~~~~~~~~~~~
+
+New features
+------------
+
++ `#155`_, `#156`_: Add an option to disable parsing of command line
+  arguments in :class:`icat.config.Config`.
+
+Bug fixes and minor changes
+---------------------------
+
++ `#152`_: Fix a documentation error
++ `#154`_: Fix a duplicate test name
+
+Misc
+----
+
++ `#157`_: :mod:`icat.ingest` now considered stable.
+
+.. _#152: https://github.com/icatproject/python-icat/pull/152
+.. _#154: https://github.com/icatproject/python-icat/pull/154
+.. _#155: https://github.com/icatproject/python-icat/issues/155
+.. _#156: https://github.com/icatproject/python-icat/pull/156
+.. _#157: https://github.com/icatproject/python-icat/pull/157
+
+
 .. _changes-1_3_0:
 
 1.3.0 (2024-03-21)

doc/examples/init-icat.py

@@ -126,8 +126,8 @@ def getUser(client, attrs):
 client.createRules("CRUD", uotables, uogroup)
 
 # Setup permissions for the data ingester.  They need read permission
-# on Investigation and Shift and create and create permission on
-# Dataset, Datafile, and the respective Parameter.
+# on Investigation and Shift and create permission on Dataset,
+# Datafile, and the respective Parameter.
 ingest = client.createUser("simple/dataingest", fullName="Data Ingester")
 ingestgroup = client.createGroup("ingest", [ ingest ])
 client.createRules("R", [ "Investigation", "Shift" ], ingestgroup)

doc/src/client.rst

@@ -48,8 +48,6 @@ manages the interaction with an ICAT service as a client.
 
         The :class:`ssl.SSLContext` instance that has been used to
         establish the HTTPS conection to the ICAT and IDS server.
-        This is :const:`None` for old Python versions that do not have
-        the :class:`ssl.SSLContext` class.
 
     .. attribute:: typemap
 

doc/src/ingest.rst

@@ -5,11 +5,6 @@
 
 .. versionadded:: 1.1.0
 
-.. note::
-   The status of this module in the current version is still
-   experimental.  There may be incompatible changes in the future
-   even in minor releases of python-icat.
-
 This module provides class :class:`icat.ingest.IngestReader` that
 reads :ref:`ICAT-ingest-files` to add them to ICAT.  It is designed
 for the use case of ingesting metadata for datasets created during

setup.py

@@ -175,6 +175,7 @@ def run(self):
         "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",
         "Programming Language :: Python :: 3.12",
+        "Programming Language :: Python :: 3.13",
         "Topic :: Software Development :: Libraries :: Python Modules",
     ],
     project_urls = dict(

src/icat/client.py

@@ -564,7 +564,7 @@ def searchChunked(self, query, skip=0, count=None, chunksize=100):
                 # This version works!
                 query = Query(client, "Dataset", includes="1", order=["id"])
                 for ds in client.searchChunked(query):
-                    if not ds.complete:
+                    if ds.complete:
                         continue
                     ds.complete = True
                     ds.update()

src/icat/config.py

@@ -271,6 +271,16 @@ def get(self, variable):
         raise NotImplementedError
 
 
+class ConfigSourceDisabled():
+    """A disabled configuration source.
+
+    Do nothing and return :const:`None` for each variable to signal
+    that this variable is not set in this source.
+    """
+    def get(self, variable):
+        return None
+
+
 class ConfigSourceCmdArgs(ConfigSource):
     """Get configuration from command line arguments.
     """
@@ -490,7 +500,7 @@ def add_variable(self, name, arg_opts=(), arg_kws=None,
         :type subst: :class:`bool`
         :return: the new configuration variable object.
         :rtype: :class:`icat.config.ConfigVariable`
-        :raise RuntimeError: if this objects already has subcommands
+        :raise RuntimeError: if this config object already has subcommands
             defined with :meth:`icat.config.BaseConfig.add_subcommands`.
         :raise ValueError: if the name is not valid.
         :see: the documentation of the :mod:`argparse` standard
@@ -502,6 +512,16 @@ def add_variable(self, name, arg_opts=(), arg_kws=None,
             raise ValueError("Config variable name '%s' is reserved." % name)
         if name in self.confvariable:
             raise ValueError("Config variable '%s' is already defined." % name)
+        if self.argparser:
+            self._add_argparser_argument(name, arg_opts, arg_kws, default, type)
+        if type == flag:
+            type = boolean
+        var = ConfigVariable(name, envvar, optional, default, type, subst)
+        self.confvariable[name] = var
+        self.confvariables.append(var)
+        return var
+
+    def _add_argparser_argument(self, name, arg_opts, arg_kws, default, type):
         if arg_kws is None:
             arg_kws = dict()
         else:
@@ -529,7 +549,6 @@ def add_variable(self, name, arg_opts=(), arg_kws=None,
                 arg_kws['const'] = False
                 arg_kws['help'] = argparse.SUPPRESS
                 self.argparser.add_argument("--no-"+arg, **arg_kws)
-            type = boolean
         elif arg_opts:
             prefix = self.argparser.prefix_chars
             if len(arg_opts) == 1 and arg_opts[0][0] not in prefix:
@@ -542,10 +561,6 @@ def add_variable(self, name, arg_opts=(), arg_kws=None,
                 # optional argument
                 arg_kws['dest'] = name
             self.argparser.add_argument(*arg_opts, **arg_kws)
-        var = ConfigVariable(name, envvar, optional, default, type, subst)
-        self.confvariable[name] = var
-        self.confvariables.append(var)
-        return var
 
     def add_subcommands(self, name='subcmd', arg_kws=None, optional=False):
         """Defines a new configuration variable to select subcommands.
@@ -576,11 +591,16 @@ def add_subcommands(self, name='subcmd', arg_kws=None, optional=False):
         :type optional: :class:`bool`
         :return: the new subcommand object.
         :rtype: :class:`icat.config.ConfigSubCmd`
-        :raise RuntimeError: if this objects already has subcommands.
+        :raise RuntimeError: if parsing of command line arguments is
+            disabled in this config object or if it already has
+            subcommands.
         :raise ValueError: if the name is not valid.
         :see: the documentation of the :mod:`argparse` standard
             library module for details on `arg_kws`.
         """
+        if not self.argparser:
+            raise RuntimeError("Command line parsing is disabled "
+                               "in this config, cannot add subcommands.")
         if self._subcmds is not None:
             raise RuntimeError("This config already has subcommands.")
         if name in self.ReservedVariables or name[0] == '_':
@@ -618,12 +638,12 @@ def _getconfig(self, sources, config=None):
             if value is not None and var.subst:
                 value = value % config.as_dict()
             setattr(config, var.name, value)
+            if var.postprocess:
+                var.postprocess(self, config)
             if isinstance(var, ConfigSubCmds):
                 if value is not None:
                     value._getconfig(sources, config)
                 break
-            if var.postprocess:
-                var.postprocess(self, config)
         return config
 
 
@@ -662,21 +682,30 @@ class Config(BaseConfig):
         environment variables, and settings in the configuration files
         still take precedence over the preset values.
     :type preset: :class:`dict`
-    :param args: list of command line arguments or :const:`None`.  If
-        not set, the command line arguments will be taken from
-        :data:`sys.argv`.
-    :type args: :class:`list` of :class:`str`
+    :param args: list of command line arguments.  If set to the
+        special value :const:`False`, parsing of command line
+        arguments will be disabled.  The default, if :const:`None` is
+        to take the command line arguments from :data:`sys.argv`.
+    :type args: :class:`list` of :class:`str` or :class:`bool`
 
     .. versionchanged:: 1.0.0
         add the `preset` argument.
+
+    .. versionchanged:: 1.4.0
+        allow to disable parsing of command line arguments, setting
+        `args` to :const:`False`.
     """
 
     def __init__(self, defaultvars=True, needlogin=True, ids="optional", 
                  preset=None, args=None):
         """Initialize the object.
         """
-        super().__init__(argparse.ArgumentParser())
-        self.cmdargs = ConfigSourceCmdArgs(self.argparser)
+        if args is False:
+            super().__init__(None)
+            self.cmdargs = ConfigSourceDisabled()
+        else:
+            super().__init__(argparse.ArgumentParser())
+            self.cmdargs = ConfigSourceCmdArgs(self.argparser)
         self.environ = ConfigSourceEnvironment()
         defaultFiles = [str(d / cfgfile) for d in cfgdirs]
         self.conffile = ConfigSourceFile(defaultFiles)
@@ -731,7 +760,8 @@ def getconfig(self):
             configuration file, if an invalid value is given to a
             variable, or if a mandatory variable is not defined.
         """
-        self.cmdargs.parse_args(self.args)
+        if self.argparser:
+            self.cmdargs.parse_args(self.args)
         config = self._getconfig(self.sources)
 
         if self.needlogin:
@@ -841,9 +871,10 @@ def _setup_client(self):
         """Initialize the client.
         """
         try:
-            with _argparserDisableExit(self.argparser):
-                self.cmdargs.parse_args(self.args, partial=True)
-                config = self._getconfig(self.sources)
+            if self.argparser:
+                with _argparserDisableExit(self.argparser):
+                    self.cmdargs.parse_args(self.args, partial=True)
+            config = self._getconfig(self.sources)
         except ConfigError:
             return None, None
         client_kwargs = {}

src/icat/ingest.py

@@ -1,10 +1,5 @@
 """Ingest metadata into ICAT.
 
-.. note::
-   The status of this module in the current version is still
-   experimental.  There may be incompatible changes in the future
-   even in minor releases of python-icat.
-
 .. versionadded:: 1.1.0
 """