Merge branch 'master' into ci/update-dependencies

SINTEF · Oct 11, 2023 · 4ded010 · 4ded010
2 parents 1f4b8e9 + c6b2adc
commit 4ded010
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diff --git a/.github/workflows/cd_release.yml b/.github/workflows/cd_release.yml
@@ -114,7 +114,23 @@ jobs:
           - os: windows-2019
             system_type: ["win", ""]
             arch: amd64
-            py_minors: 7,8,9,10,11
+            py_minors: '7'
+          - os: windows-2019
+            system_type: ["win", ""]
+            arch: amd64
+            py_minors: '8'
+          - os: windows-2019
+            system_type: ["win", ""]
+            arch: amd64
+            py_minors: '9'
+          - os: windows-2019
+            system_type: ["win", ""]
+            arch: amd64
+            py_minors: '10'
+          - os: windows-2019
+            system_type: ["win", ""]
+            arch: amd64
+            py_minors: '11'
 
           # See issue #221: https://github.com/SINTEF/dlite/issues/221
           # # 64-bit (Intel) macOS
@@ -139,7 +155,8 @@ jobs:
     - name: Set up Python 3
       uses: actions/setup-python@v4
       with:
-        python-version: '3.x'
+        python-version: "3.${{ contains(matrix.py_minors, ',') && 'x' || matrix.py_minors }}"
+        architecture: ${{ matrix.arch == '' && 'x86' || 'x64' }}
 
     - name: Login to GitHub Container Registry
       if: startsWith(matrix.os, 'ubuntu')
@@ -161,7 +178,7 @@ jobs:
         python -m cibuildwheel --print-build-identifiers python
         python -m cibuildwheel --output-dir wheelhouse python
       env:
-        CIBW_BUILD: cp3{${{ matrix.py_minors }}}-${{ matrix.system_type[0] }}${{ matrix.arch != '' && '_' || '' }}${{ matrix.arch }}
+        CIBW_BUILD: cp3${{ contains(matrix.py_minors, ',') && format('{{{0}}}', matrix.py_minors) || matrix.py_minors }}-${{ matrix.system_type[0] }}${{ matrix.arch != '' && '_' || '' }}${{ matrix.arch }}
         CIBW_MANYLINUX_X86_64_IMAGE: ${{ env.CONTAINER_REGISTRY }}/sintef/dlite-python-manylinux${{ matrix.system_type[1] }}_x86_64:latest
         CIBW_MANYLINUX_I686_IMAGE: ${{ env.CONTAINER_REGISTRY }}/sintef/dlite-python-manylinux${{ matrix.system_type[1] }}_i686:latest
         CIBW_MUSLLINUX_X86_64_IMAGE: ${{ env.CONTAINER_REGISTRY }}/sintef/dlite-python-musllinux_1_1_x86_64:latest

diff --git a/.github/workflows/ci_build_wheels.yml b/.github/workflows/ci_build_wheels.yml
@@ -59,7 +59,11 @@ jobs:
           - os: windows-2019
             system_type: ["win", ""]
             arch: amd64
-            py_minors: 7,11
+            py_minors: '7'
+          - os: windows-2019
+            system_type: ["win", ""]
+            arch: amd64
+            py_minors: '11'
 
           # See issue #221: https://github.com/SINTEF/dlite/issues/221
           # # 64-bit (Intel) macOS
@@ -74,7 +78,8 @@ jobs:
 
       - uses: actions/setup-python@v4
         with:
-          python-version: '3.x'
+          python-version: "3.${{ contains(matrix.py_minors, ',') && 'x' || matrix.py_minors }}"
+          architecture: ${{ matrix.arch == '' && 'x86' || 'x64' }}
 
       - name: Login to GitHub Container Registry
         if: startsWith(matrix.os, 'ubuntu')
@@ -96,7 +101,7 @@ jobs:
           python -m cibuildwheel --print-build-identifiers python
           python -m cibuildwheel --output-dir wheelhouse python
         env:
-          CIBW_BUILD: cp3{${{ matrix.py_minors }}}-${{ matrix.system_type[0] }}${{ matrix.arch != '' && '_' || '' }}${{ matrix.arch }}
+          CIBW_BUILD: cp3${{ contains(matrix.py_minors, ',') && format('{{{0}}}', matrix.py_minors) || matrix.py_minors }}-${{ matrix.system_type[0] }}${{ matrix.arch != '' && '_' || '' }}${{ matrix.arch }}
           CIBW_MANYLINUX_X86_64_IMAGE: ${{ env.container_registry }}/sintef/dlite-python-manylinux${{ matrix.system_type[1] }}_x86_64:latest
           CIBW_MANYLINUX_I686_IMAGE: ${{ env.container_registry }}/sintef/dlite-python-manylinux${{ matrix.system_type[1] }}_i686:latest
           CIBW_MUSLLINUX_X86_64_IMAGE: ${{ env.container_registry }}/sintef/dlite-python-musllinux_1_1_x86_64:latest

diff --git a/.github/workflows/ci_tests.yml b/.github/workflows/ci_tests.yml
@@ -26,15 +26,15 @@ jobs:
 
     - name: Install Python dependencies
       run: |
+        which python3
+        python3 --version
+        python3 -m pip --version
         python3 -m pip install --upgrade pip
         python3 -m pip install -U setuptools wheel
         python3 -m pip install -r requirements.txt -r requirements_full.txt -r requirements_dev.txt -r requirements_doc.txt
 
     - name: Check numpy
       run: |
-        which python3
-        python3 --version
-        python3 -m pip --version
         python3 -c 'import numpy as np; print(np.get_include())'
 
     - name: Workaround - install CMake 3.25.2 since 3.26.0 doesn't work

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -3,7 +3,7 @@
 cmake_minimum_required(VERSION 3.14)
 
 project(dlite
-  VERSION 0.4.0
+  VERSION 0.4.1
   DESCRIPTION "Lightweight data-centric framework for semantic interoperability"
   HOMEPAGE_URL "https://github.com/SINTEF/dlite"
   LANGUAGES C

diff --git a/bindings/python/dlite-misc-python.i b/bindings/python/dlite-misc-python.i
@@ -4,29 +4,57 @@
 
 %pythoncode %{
 
-class err():
-    """Context manager for temporary turning off or redirecting errors.
-
-    By default errors are skipped within the err context. But if
-    `filename` is provided, the error messages are written to that file.
-    Special file names includes:
-
-    - "None" or empty: No output is written.
-    - "<stderr>": Write errors to stderr (default).
-    - "<stdout>": Write errors to stdout.
+class errctl():
+    """Context manager for temporary disabling specific DLite error
+    messages or redirecting them.
+
+    Arguments:
+        hide: Sequence of DLiteException subclasses or exception names
+            corresponding to error messages to hide.  A single class or
+            name is also allowed.
+        show: Sequence of DLiteException subclasses or exception names
+            corresponding to error messages to show.  A single class or
+            name is also allowed.
+        filename: Filename to redirect errors to.  The following values
+            are handled specially:
+              - "None" or empty: No output is written.
+              - "<stderr>": Write errors to stderr (default).
+              - "<stdout>": Write errors to stdout.
 
     """
-    def __init__(self, filename=None):
+    def __init__(self, hide=(), show=(), filename="<stderr>"):
+        self.hide = self._as_codes(hide)
+        self.show = self._as_codes(show)
         self.filename = filename
 
     def __enter__(self):
+        self.mask = _dlite._err_mask_get()
+        for code in self.hide:
+            _dlite._err_ignore_set(code, 1)
+        for code in self.show:
+            _dlite._err_ignore_set(code, 0)
         self.f = _dlite.err_get_stream()
         _dlite.err_set_file(self.filename)
-        return self.f
 
     def __exit__(self, *exc):
-        _dlite.errclr()
+        ignored = _dlite._err_ignore_get(_dlite.errval())
+        _dlite._err_mask_set(self.mask)
         _dlite.err_set_stream(self.f)
-
-silent = err()
+        if ignored or self.filename is None:
+            _dlite.errclr()
+
+    @staticmethod
+    def _as_codes(seq):
+        """Return sequence of exceptions/exception names as a sequence of
+        DLite error coces.  `seq` may also be a single exception or name."""
+        sequence = [seq] if isinstance(seq, (str, type)) else seq
+        return [
+            _dlite._err_getcode(
+                exc.__name__ if isinstance(exc, type) else str(exc)
+            )
+            for exc in sequence
+        ]
+
+
+silent = errctl(filename="None")
 %}
diff --git a/bindings/python/dlite-misc.i b/bindings/python/dlite-misc.i
@@ -27,8 +27,14 @@
     return atob(str);
   }
 
+  int64_t _err_mask_get(void) {
+    return *_dlite_err_mask_get();
+  }
+
 %}
 
+%include <stdint.i>
+
 %feature("docstring", "\
 Returns the current version of DLite.
 ") dlite_get_version;
@@ -158,6 +164,29 @@ All other values are treated as a filename that will be opened in append mode.
 ") dlite_err_set_file;
 void dlite_err_set_file(const char *filename);
 
+%feature("docstring", "\
+Return DLite error code corresponding to `name`.  Unknown names will return
+`dliteUnknownError`.
+") dlite_errcode;
+%rename(_err_getcode) dlite_errcode;
+int dlite_errcode(const char *name);
+
+/* Private help functions */
+%feature("docstring", "\
+Set whether to ignore printing given error code.
+") dlite_err_ignored_set;
+%rename(_err_ignore_set) dlite_err_ignored_set;
+void dlite_err_ignored_set(int code, int value);
+
+%feature("docstring", "\
+Return whether printing is ignored for given error code.
+") dlite_err_ignored_get;
+%rename(_err_ignore_get) dlite_err_ignored_get;
+int dlite_err_ignored_get(int code);
+
+int64_t _err_mask_get(void);
+%rename(_err_mask_set) _dlite_err_mask_set;
+void _dlite_err_mask_set(int64_t mask);
 
 
 /* ------------------------------

diff --git a/bindings/python/dlite-storage-python.i b/bindings/python/dlite-storage-python.i
@@ -40,11 +40,6 @@
           "hold multiple instances, including both data and metadata."
       )
 
-      @classmethod
-      def from_url(cls, url):
-          """Create a new storage from `url`."""
-          return cls(url)
-
       @classmethod
       def load_plugins(cls):
           """Load all storage plugins."""
@@ -85,9 +80,28 @@
 
 %extend StorageIterator {
   %pythoncode %{
+
+      # Override default __init__()
+      def __init__(self, s, pattern=None):
+          """Iterates over instances in storage `s`.
+
+          If `pattern` is given, only instances whos metadata URI
+          matches glob pattern `pattern` are returned.
+          """
+          _dlite.StorageIterator_swiginit(
+              self, _dlite.new_StorageIterator(s, pattern))
+
+          # Keep a reference to self, such that it is not garbage-collected
+          # before end of iterations
+          if not hasattr(_dlite, "_storage_iters"):
+              _dlite._storage_iters = {}
+          _dlite._storage_iters[id(self.state)] = self
+
       def __next__(self):
           inst = self.next()
           if not inst:
+              # Delete reference to iterator object stored away in __init__()
+              _dlite._storage_iters.pop(id(self.this), None)
               raise StopIteration()
           return inst
   %}
@@ -97,20 +111,20 @@
   %pythoncode %{
       # Override default __init__()
       def __init__(self):
-          """Iterates over loaded storage plugins."""
+          """Iterator over loaded storage plugins."""
           _dlite.StoragePluginIter_swiginit(
               self, _dlite.new_StoragePluginIter())
           # Keep a reference to self, such that it is not garbage-collected
           # before end of iterations
-          if not hasattr(_dlite, "_storage_plugin_iters"):
-              _dlite._storage_plugin_iters = {}
-          _dlite._storage_plugin_iters[id(self.iter)] = self
+          if not hasattr(_dlite, "_storage_iters"):
+              _dlite._storage_iters = {}
+          _dlite._storage_iters[id(self.iter)] = self
 
       def __next__(self):
           name = self.next()
           if not name:
               # Delete reference to iterator object stored away in __init__()
-              del _dlite._storage_plugin_iters[id(self.this)]
+              _dlite._storage_iters.pop(id(self.this), None)
               raise StopIteration()
           return name
   %}

diff --git a/bindings/python/dlite-storage.i b/bindings/python/dlite-storage.i
@@ -49,8 +49,12 @@ Returns next instance or None if exhausted.") next;
   %newobject next;
   struct _DLiteInstance *next(void) {
     char uuid[DLITE_UUID_LENGTH+1];
-    if (dlite_storage_iter_next($self->s, $self->state, uuid) == 0)
-      return dlite_instance_load($self->s, uuid);
+    if (dlite_storage_iter_next($self->s, $self->state, uuid) == 0) {
+      DLiteInstance *inst = dlite_instance_load($self->s, uuid);
+      // Why isn't the refcount already increased?
+      dlite_instance_incref(inst);
+      return inst;
+    }
     return NULL;
   }
 

diff --git a/bindings/python/mappings.py b/bindings/python/mappings.py
@@ -471,7 +471,10 @@ def get_values(
                 else value
             )
         elif isinstance(input_value, Value):
-            values[key] = quantity(input_value.value, input_value.unit)
+            if isinstance(input_value.value, str):
+                values[key] = input_value.value
+            else:
+                values[key] = quantity(input_value.value, input_value.unit)
         else:
             raise TypeError(
                 "Expected values in inputs to be either MappingStep or Value objects."
@@ -742,9 +745,12 @@ def instance_routes(
     for inst in instances:
         props = {prop.name: prop for prop in inst.meta["properties"]}
         for key, value in inst.properties.items():
-            sources[f"{inst.meta.uri}#{key}"] = quantity(
-                value, props[key].unit
-            )
+            if isinstance(value, str):
+                sources[f"{inst.meta.uri}#{key}"] = value
+            else:
+                sources[f"{inst.meta.uri}#{key}"] = quantity(
+                    value, props[key].unit
+                )
 
     routes = {}
     for prop in meta["properties"]:

diff --git a/bindings/python/scripts/CMakeLists.txt b/bindings/python/scripts/CMakeLists.txt
@@ -36,14 +36,14 @@ test_success(
 )
 test_success(
   dlite-validate-persons
-  dlite-validate -p ../tests/Person.json -i 51c0d700-9ab0-43ea-9183-6ea22012ebee
+  dlite-validate -p ../tests/Person.json -i a1d8d35f-723c-5ea1-abaf-8fc8f1d0982f
     ../tests/persons.json
 )
 test_success(
   dlite-validate-persons2
   dlite-validate
-    --storage-path=../tests/Person.json
-    --id=13c5007b-c665-4709-a11c-255919306547
+    --storage-path=../tests
+    --id=Ada
     --show
     ../tests/persons.json
   )

diff --git a/bindings/python/tests/.gitignore b/bindings/python/tests/.gitignore
@@ -11,5 +11,6 @@ xxx2.json
 yyy.json
 
 myentity.json
+persons2.json
 
 db.xml
diff --git a/bindings/python/tests/SimplePerson.json b/bindings/python/tests/SimplePerson.json
@@ -1,21 +1,17 @@
 {
-  "name": "SimplePerson",
-  "version": "0.1",
-  "namespace": "http://onto-ns.com/meta",
+  "uri": "http://onto-ns.com/meta/0.1/SimplePerson",
   "meta": "http://onto-ns.com/meta/0.3/EntitySchema",
   "description": "A simple person representation.",
-  "dimensions": [],
-  "properties": [
-    {
-      "name": "name",
+  "dimensions": {},
+  "properties": {
+    "name": {
       "type": "string",
       "description": "Full name."
     },
-    {
-      "name": "age",
+    "age": {
       "type": "float",
       "unit": "years",
       "description": "Age of person."
     }
-  ]
+  }
 }