doc updates

matthiasprobst · Dec 17, 2023 · 7964052 · 7964052
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diff --git a/docs/api.rst b/docs/api.rst
@@ -27,12 +27,8 @@ Layouts
 .. autosummary::
     :toctree: generated/
 
-    h5rdmtoolbox.conventions.layout.core.Layout
-    h5rdmtoolbox.conventions.layout.validators.Equal
-    h5rdmtoolbox.conventions.layout.validators.Regex
-    h5rdmtoolbox.conventions.layout.validators.Any
-    h5rdmtoolbox.conventions.layout.validators.ExistIn
-    h5rdmtoolbox.conventions.layout.validators.In
+    h5rdmtoolbox.layout.core.LayoutSpecification
+    h5rdmtoolbox.layout.core.Layout
 
 
 
@@ -42,19 +38,19 @@ Standard attributes
 .. autosummary::
    :toctree: generated/
 
-   h5rdmtoolbox.conventions.StandardAttribute
-   h5rdmtoolbox.conventions.StandardAttribute.get
-   h5rdmtoolbox.conventions.StandardAttribute.set
+   h5rdmtoolbox.convention.StandardAttribute
+   h5rdmtoolbox.convention.StandardAttribute.get
+   h5rdmtoolbox.convention.StandardAttribute.set
 
 Standard names and tables
 -------------------------
 
 .. autosummary::
    :toctree: generated/
 
-   h5rdmtoolbox.conventions.standard_names.name.StandardName
-   h5rdmtoolbox.conventions.standard_names.table.StandardNameTable
-   h5rdmtoolbox.conventions.standard_names.table.StandardNameTable.from_web
-   h5rdmtoolbox.conventions.standard_names.table.StandardNameTable.from_yaml
-   h5rdmtoolbox.conventions.standard_names.table.StandardNameTable.from_xml
-   h5rdmtoolbox.conventions.standard_names.table.StandardNameTable.from_zenodo
+   h5rdmtoolbox.convention.standard_names.name.StandardName
+   h5rdmtoolbox.convention.standard_names.table.StandardNameTable
+   h5rdmtoolbox.convention.standard_names.table.StandardNameTable.from_web
+   h5rdmtoolbox.convention.standard_names.table.StandardNameTable.from_yaml
+   h5rdmtoolbox.convention.standard_names.table.StandardNameTable.from_xml
+   h5rdmtoolbox.convention.standard_names.table.StandardNameTable.from_zenodo
diff --git a/docs/colab/quickstart.ipynb b/docs/colab/quickstart.ipynb
@@ -33,7 +33,7 @@
     "import h5rdmtoolbox as h5tbx\n",
     "\n",
     "# Assume we published a convention here: https://zenodo.org/record/8281285\n",
-    "cv = h5tbx.conventions.from_zenodo(doi='10156750')"
+    "cv = h5tbx.convention.from_zenodo(doi='10156750')"
    ]
   },
   {

diff --git a/docs/conventions/examples/EngMeta.ipynb b/docs/conventions/examples/EngMeta.ipynb
@@ -71,7 +71,7 @@
    ],
    "source": [
     "import h5rdmtoolbox as h5tbx\n",
-    "cv = h5tbx.conventions.from_yaml('EngMeta.yaml')\n",
+    "cv = h5tbx.convention.from_yaml('EngMeta.yaml')\n",
     "cv"
    ]
   },

diff --git a/docs/conventions/examples/Provenance.ipynb b/docs/conventions/examples/Provenance.ipynb
@@ -64,7 +64,7 @@
     }
    ],
    "source": [
-    "cv = h5tbx.conventions.from_zenodo('https://zenodo.org/records/10156750')\n",
+    "cv = h5tbx.convention.from_zenodo('https://zenodo.org/records/10156750')\n",
     "\n",
     "h5tbx.use(cv)"
    ]
@@ -115,7 +115,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from h5rdmtoolbox.conventions.standard_names import accessor"
+    "from h5rdmtoolbox.convention.standard_names import accessor"
    ]
   },
   {

diff --git a/docs/conventions/examples/standard_name_convention.ipynb b/docs/conventions/examples/standard_name_convention.ipynb
@@ -43,7 +43,7 @@
     "import warnings\n",
     "warnings.filterwarnings('ignore')\n",
     "\n",
-    "from h5rdmtoolbox.conventions.standard_names.table import StandardNameTable"
+    "from h5rdmtoolbox.convention.standard_names.table import StandardNameTable"
    ]
   },
   {
@@ -606,7 +606,7 @@
        "\u001b[1mConvention(\"standard name convention\")\u001b[0m\n",
        "contact: https://orcid.org/0000-0001-8729-0482\n",
        "  File.__init__():\n",
-       "    * \u001b[3mstandard_name_table\u001b[0m (default=<h5rdmtoolbox.conventions.consts.DefaultValue object at 0x000001CBD2CD2100>):\n",
+       "    * \u001b[3mstandard_name_table\u001b[0m (default=<h5rdmtoolbox.convention.consts.DefaultValue object at 0x000001CBD2CD2100>):\n",
        "\t\tThe standard name table of the convention.\n",
        "  Group.create_dataset():\n",
        "    * \u001b[3mscale\u001b[0m (default=None):\n",
@@ -628,7 +628,7 @@
     }
    ],
    "source": [
-    "zenodo_cv = h5tbx.conventions.from_zenodo('https://zenodo.org/record/8357399')\n",
+    "zenodo_cv = h5tbx.convention.from_zenodo('https://zenodo.org/record/8357399')\n",
     "sn_cv = zenodo_cv.pop('contact', 'comment', 'references', 'data_type')\n",
     "sn_cv.name = 'standard name convention'\n",
     "sn_cv.register()\n",

diff --git a/docs/conventions/examples/standard_name_interface.ipynb b/docs/conventions/examples/standard_name_interface.ipynb
@@ -43,11 +43,11 @@
    "source": [
     "import h5rdmtoolbox as h5tbx\n",
     "\n",
-    "from h5rdmtoolbox.conventions.standard_names import HDF5StandardNameInterface\n",
+    "from h5rdmtoolbox.convention.standard_names import HDF5StandardNameInterface\n",
     "\n",
     "import numpy as np\n",
     "\n",
-    "cv = h5tbx.conventions.from_zenodo('https://zenodo.org/record/8357399')\n",
+    "cv = h5tbx.convention.from_zenodo('https://zenodo.org/record/8357399')\n",
     "cv.properties[h5tbx.File]['data_type'].make_optional()\n",
     "cv.properties[h5tbx.File]['contact'].make_optional()\n",
     "h5tbx.use(cv)"

diff --git a/docs/conventions/index.rst b/docs/conventions/index.rst
@@ -22,5 +22,4 @@ The following chapters will explain the usage of conventions (standard attribute
 
     ontologies.ipynb
     standard_attributes_and_conventions.ipynb
-    layout.ipynb
     Examples <examples/index>