h5rdmtoolbox 2.8.0__tar.gz → 2.8.2__tar.gz

{h5rdmtoolbox-2.8.0 → h5rdmtoolbox-2.8.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: h5rdmtoolbox
-Version: 2.8.0
+Version: 2.8.2
 Summary: Supporting a FAIR Research Data lifecycle using Python and HDF5.
 Author-email: Matthias Probst <matth.probst@gmail.com>
 License-Expression: MIT
@@ -37,11 +37,11 @@ Requires-Dist: python-forge==18.6.0
 Requires-Dist: requests>=2.32.4
 Requires-Dist: pydantic~=2.8
 Requires-Dist: rdflib~=7.1
-Requires-Dist: click>=8.1.7
+Requires-Dist: typer>=0.12
 Requires-Dist: cftime>=1.6.4
 Requires-Dist: pyshacl<1.0.0,>=0.30.1
 Provides-Extra: database
-Requires-Dist: pymongo<=4.10.1,>=4.2.0; extra == "database"
+Requires-Dist: pymongo<=4.10.1,>=4.6.3; extra == "database"
 Provides-Extra: layout-validation
 Requires-Dist: tabulate<=0.9.0,>=0.8.10; extra == "layout-validation"
 Provides-Extra: csv
@@ -81,7 +81,7 @@ Requires-Dist: h5rdmtoolbox[complete,docs]; extra == "complete-with-docs"
 Provides-Extra: server
 Requires-Dist: fastapi>=0.95; extra == "server"
 Requires-Dist: uvicorn[standard]>=0.22; extra == "server"
-Requires-Dist: jinja2>=3.1; extra == "server"
+Requires-Dist: jinja2>=3.1.6; extra == "server"
 Dynamic: license-file
 
 # HDF5 Research Data Management Toolbox
@@ -91,6 +91,7 @@ Dynamic: license-file
 [![Documentation Status](https://readthedocs.org/projects/h5rdmtoolbox/badge/?version=latest)](https://h5rdmtoolbox.readthedocs.io/en/latest/?badge=latest)
 [![PyPI version](https://badge.fury.io/py/h5RDMtoolbox.svg)](https://badge.fury.io/py/h5RDMtoolbox)
 ![pyvers](https://img.shields.io/badge/python-3.9%20%7C%203.10%20%7C%203.11%20%7C%203.12%20%7C%203.13-blue)
+[![Paper](https://img.shields.io/badge/Paper-View-green?style=flat&logo=adobeacrobatreader)](https://preprints.inggrid.org/repository/view/23/)
 
 A Python package that helps researchers achieve sustainable 
 [**FAIR (Findable, Accessible, Interoperable, Reusable)**](https://www.nature.com/articles/sdata201618) data management with HDF5 files. The toolbox provides a comprehensive
@@ -169,7 +170,7 @@ Below we show the first two serializations.
     schema:description "Room temperature measurements" .
 ```
 
-`ttl_ctx`:
+`ttl_struc`:
 ```ttl
 @prefix hdf: <http://purl.allotrope.org/ontologies/hdf5/1.8#> .
 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@@ -255,8 +256,14 @@ To inspect files in a browser, run:
 h5tbx serve example.h5
 h5tbx serve data/ --h5ext=.h5 --h5ext=.hdf5
 ```
+This allows you to serve a single HDF5 file or a directory of HDF5 files, and view their metadata and structure in a web interface.
+
+You may perform SPARQL queries or view the file as a graph, as shown below:
+
+<p align="center">
+  <img src="docs/_static/screenshot-served-hdf5-as-graph.png" alt="Serve UI screenshot" width="640">
+</p>
 
-The local web app links to Turtle, JSON-LD, N-Triples, RDF/XML, an interactive graph view, SPARQL query editor, graph metrics, and SHACL validation. Per-file buttons are scoped to that file; the landing page also offers a separate combined graph section for all served files plus loaded enrichment. Combined graph visualization is reduced by default with node/edge limits and search controls, and combined metrics skip exact largest-distance computation on very large graphs to keep the local server responsive. HDF5 object URLs such as `/example.h5/group/dataset` dereference to a browser HTML page by default, while `Accept: text/turtle`, `Accept: application/ld+json`, or `?format=ttl|jsonld|nt|xml|html` return the requested representation. For published DOI-style file URIs, use `/resolve?iri=https://doi.org/...%23path` to resolve an exact external RDF subject locally. The resolver uses the first matching served HDF5 subject, caches all served files in one shared query graph, and enriches that graph with known ontology TTL sources, QUDT unit definitions, Zenodo RDF attachments, generic ontology documents, and Wikidata direct claims where applicable. URI values in resource pages link back into `/resolve?iri=...` so browsing stays inside the local app; if a browser request cannot be resolved locally, the app opens the original IRI in a new tab as a fallback. `h5tbx serve` accepts files and folders; folder discovery uses `.h5`, `.hdf`, and `.hdf5` by default, or repeated `--h5ext` values. `--local-iri-pattern` is optional and only limits which external IRIs get local resolver links in the graph view. If no filename is provided, `h5tbx serve` lists all matching HDF5 files in the current directory.
 
 The same graph metrics are available from Python:
 
@@ -312,7 +319,7 @@ module implements the main interface between the user and the HDF5 file. It
 extends the features of the underlying `h5py` library. Some of the features are implemented in other modules, hence the
 wrapper module depends on the convention, database and linked data (ld) module.
 
-<a href="https://h5rdmtoolbox.readthedocs.io/en/latest/"><img src="docs/_static/h5tbx_modules.svg" alt="H5TBX modules" style="widht:600px;"></a>
+<a href="https://h5rdmtoolbox.readthedocs.io/en/latest/"><img src="docs/_static/h5tbx_modules.svg" alt="H5TBX modules" style="width:600px;"></a>
 
 Current implementation highlights in the modules:
 
@@ -326,7 +333,7 @@ Current implementation highlights in the modules:
 - For the **repository** module, a Zenodo interface is implemented. Zenodo is a repository, which allows to upload and
   download data with a persistent identifier.
 - For the **convention** module,
-  the [standard attributes](https://h5rdmtoolbox.readthedocs.io/en/latest/conventions/standard_attributes_and_conventions.html)
+  the [standard attributes](https://h5rdmtoolbox.readthedocs.io/en/latest/userguide/convention/index.html)
   are implemented.
 - The **layout** module allows to define expectations on the internal layout (object names, location, attributes,
   properties) of HDF5 files.
@@ -350,7 +357,7 @@ A paper is published in the journal [inggrid](https://preprints.inggrid.org/repo
 
 ## Installation
 
-Use python 3.9 or higher (automatic testing is performed until 3.13). If you are a regular user, you can install the
+Use Python 3.9 through 3.13. If you are a regular user, you can install the
 package via pip:
 
     pip install h5RDMtoolbox
@@ -359,7 +366,7 @@ package via pip:
 
 Developers may clone the repository and install the package from source. Clone the repository first:
 
-    git clone https://github.com/matthiasprobst/h5RDMtoolbox.git@main
+    git clone --branch main https://github.com/matthiasprobst/h5RDMtoolbox.git
 
 Then, run
 
@@ -381,6 +388,7 @@ specific to the features of the package:
 - `numpy`: Scientific computing, handling of arrays
 - `matplotlib`: Plotting
 - `appdirs`: Managing user and application directories
+- `importlib_resources`: Accessing package resources consistently
 - `packaging`: Version handling
 - `IPython`: Pretty display of data in notebooks
 - `regex`: Working with regular expressions
@@ -393,14 +401,17 @@ specific to the features of the package:
 - `pint`: Allows working with units
 - `pint_xarray`: Working with units for usage with xarray
 - `python-forge`: Used to update function signatures when using
-  the [standard attributes](https://h5rdmtoolbox.readthedocs.io/en/latest/conventions/standard_attributes_and_conventions.html)
+  the [standard attributes](https://h5rdmtoolbox.readthedocs.io/en/latest/userguide/convention/index.html)
 - `pydantic`: Used to
-  validate [standard attributes](https://h5rdmtoolbox.readthedocs.io/en/latest/conventions/standard_attributes_and_conventions.html)
+  validate [standard attributes](https://h5rdmtoolbox.readthedocs.io/en/latest/userguide/convention/index.html)
 - `pyyaml`: Reading and writing of yaml files, e.g. metadata definitions (conventions). Note, lower versions
   collide with python 3.11
 - `requests`: Used to download files from the internet or validate URLs, e.g. metadata definitions (conventions)
 - `rdflib`: Used to enable working with RDF
 - `ontolutils`: Required to work with RDF and derive semantic description of HDF5 file content
+- `cftime`: Handling non-standard calendars and time coordinates
+- `pyshacl`: Validating RDF graphs against SHACL shapes
+- `typer`: Providing the `h5tbx` command-line interface
 
 #### Optional dependencies
 
@@ -408,9 +419,9 @@ To run unit tests or to enable certain features, additional dependencies must be
 
 Install optional dependencies by specifying them in square brackets after the package name, e.g.:
 
-    pip install h5RDMtoolbox[mongodb]
+    pip install h5RDMtoolbox[database]
 
-[mongodb]
+[database]
 
 - `pymongo`: Database solution for HDF5 files
 
@@ -425,6 +436,10 @@ Install optional dependencies by specifying them in square brackets after the pa
 - `python-gitlab`: Access to gitlab repositories
 - `pypandoc`: Conversion of markdown files to html
 
+Other supported extras are `layout_validation`, `catalog`, `gui`, `server`, `test`, `docs`, `complete`, and
+`complete-with-docs`. See the [installation guide](https://h5rdmtoolbox.readthedocs.io/en/latest/gettingstarted/installation.html)
+for their purpose. The authoritative dependency lists and version constraints are in [`pyproject.toml`](./pyproject.toml).
+
 ## Citing the package
 
 If you intend to use the package in your work, you may cite the software itself as published on paper in the
@@ -457,10 +472,10 @@ Here is the BibTeX entry:
 Feel free to contribute. Make sure to write `docstrings` to your methods and classes and please write tests and use PEP
 8 (https://peps.python.org/pep-0008/)
 
-Please write tests for your code and put them into the `test/` folder. Visit the [README file](./tests/README.md) in the
-test-folder for more information.
+Please write tests for your code and put them into the `tests/` folder. Visit the [README file](./tests/README.md) in the
+tests folder for more information.
 
-Pleas also add a jupyter notebook in the `docs/` folder in order to document your code. Please visit
+Please also add a Jupyter notebook in the `docs/` folder in order to document your code. Please visit
 the [README file](./docs/README.md) in the docs-folder for more information on how to compile the documentation.
 
 Please use the **numpy style for the docstrings**:

{h5rdmtoolbox-2.8.0 → h5rdmtoolbox-2.8.2}/README.md

@@ -5,6 +5,7 @@
 [![Documentation Status](https://readthedocs.org/projects/h5rdmtoolbox/badge/?version=latest)](https://h5rdmtoolbox.readthedocs.io/en/latest/?badge=latest)
 [![PyPI version](https://badge.fury.io/py/h5RDMtoolbox.svg)](https://badge.fury.io/py/h5RDMtoolbox)
 ![pyvers](https://img.shields.io/badge/python-3.9%20%7C%203.10%20%7C%203.11%20%7C%203.12%20%7C%203.13-blue)
+[![Paper](https://img.shields.io/badge/Paper-View-green?style=flat&logo=adobeacrobatreader)](https://preprints.inggrid.org/repository/view/23/)
 
 A Python package that helps researchers achieve sustainable 
 [**FAIR (Findable, Accessible, Interoperable, Reusable)**](https://www.nature.com/articles/sdata201618) data management with HDF5 files. The toolbox provides a comprehensive
@@ -83,7 +84,7 @@ Below we show the first two serializations.
     schema:description "Room temperature measurements" .
 ```
 
-`ttl_ctx`:
+`ttl_struc`:
 ```ttl
 @prefix hdf: <http://purl.allotrope.org/ontologies/hdf5/1.8#> .
 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@@ -169,8 +170,14 @@ To inspect files in a browser, run:
 h5tbx serve example.h5
 h5tbx serve data/ --h5ext=.h5 --h5ext=.hdf5
 ```
+This allows you to serve a single HDF5 file or a directory of HDF5 files, and view their metadata and structure in a web interface.
+
+You may perform SPARQL queries or view the file as a graph, as shown below:
+
+<p align="center">
+  <img src="docs/_static/screenshot-served-hdf5-as-graph.png" alt="Serve UI screenshot" width="640">
+</p>
 
-The local web app links to Turtle, JSON-LD, N-Triples, RDF/XML, an interactive graph view, SPARQL query editor, graph metrics, and SHACL validation. Per-file buttons are scoped to that file; the landing page also offers a separate combined graph section for all served files plus loaded enrichment. Combined graph visualization is reduced by default with node/edge limits and search controls, and combined metrics skip exact largest-distance computation on very large graphs to keep the local server responsive. HDF5 object URLs such as `/example.h5/group/dataset` dereference to a browser HTML page by default, while `Accept: text/turtle`, `Accept: application/ld+json`, or `?format=ttl|jsonld|nt|xml|html` return the requested representation. For published DOI-style file URIs, use `/resolve?iri=https://doi.org/...%23path` to resolve an exact external RDF subject locally. The resolver uses the first matching served HDF5 subject, caches all served files in one shared query graph, and enriches that graph with known ontology TTL sources, QUDT unit definitions, Zenodo RDF attachments, generic ontology documents, and Wikidata direct claims where applicable. URI values in resource pages link back into `/resolve?iri=...` so browsing stays inside the local app; if a browser request cannot be resolved locally, the app opens the original IRI in a new tab as a fallback. `h5tbx serve` accepts files and folders; folder discovery uses `.h5`, `.hdf`, and `.hdf5` by default, or repeated `--h5ext` values. `--local-iri-pattern` is optional and only limits which external IRIs get local resolver links in the graph view. If no filename is provided, `h5tbx serve` lists all matching HDF5 files in the current directory.
 
 The same graph metrics are available from Python:
 
@@ -226,7 +233,7 @@ module implements the main interface between the user and the HDF5 file. It
 extends the features of the underlying `h5py` library. Some of the features are implemented in other modules, hence the
 wrapper module depends on the convention, database and linked data (ld) module.
 
-<a href="https://h5rdmtoolbox.readthedocs.io/en/latest/"><img src="docs/_static/h5tbx_modules.svg" alt="H5TBX modules" style="widht:600px;"></a>
+<a href="https://h5rdmtoolbox.readthedocs.io/en/latest/"><img src="docs/_static/h5tbx_modules.svg" alt="H5TBX modules" style="width:600px;"></a>
 
 Current implementation highlights in the modules:
 
@@ -240,7 +247,7 @@ Current implementation highlights in the modules:
 - For the **repository** module, a Zenodo interface is implemented. Zenodo is a repository, which allows to upload and
   download data with a persistent identifier.
 - For the **convention** module,
-  the [standard attributes](https://h5rdmtoolbox.readthedocs.io/en/latest/conventions/standard_attributes_and_conventions.html)
+  the [standard attributes](https://h5rdmtoolbox.readthedocs.io/en/latest/userguide/convention/index.html)
   are implemented.
 - The **layout** module allows to define expectations on the internal layout (object names, location, attributes,
   properties) of HDF5 files.
@@ -264,7 +271,7 @@ A paper is published in the journal [inggrid](https://preprints.inggrid.org/repo
 
 ## Installation
 
-Use python 3.9 or higher (automatic testing is performed until 3.13). If you are a regular user, you can install the
+Use Python 3.9 through 3.13. If you are a regular user, you can install the
 package via pip:
 
     pip install h5RDMtoolbox
@@ -273,7 +280,7 @@ package via pip:
 
 Developers may clone the repository and install the package from source. Clone the repository first:
 
-    git clone https://github.com/matthiasprobst/h5RDMtoolbox.git@main
+    git clone --branch main https://github.com/matthiasprobst/h5RDMtoolbox.git
 
 Then, run
 
@@ -295,6 +302,7 @@ specific to the features of the package:
 - `numpy`: Scientific computing, handling of arrays
 - `matplotlib`: Plotting
 - `appdirs`: Managing user and application directories
+- `importlib_resources`: Accessing package resources consistently
 - `packaging`: Version handling
 - `IPython`: Pretty display of data in notebooks
 - `regex`: Working with regular expressions
@@ -307,14 +315,17 @@ specific to the features of the package:
 - `pint`: Allows working with units
 - `pint_xarray`: Working with units for usage with xarray
 - `python-forge`: Used to update function signatures when using
-  the [standard attributes](https://h5rdmtoolbox.readthedocs.io/en/latest/conventions/standard_attributes_and_conventions.html)
+  the [standard attributes](https://h5rdmtoolbox.readthedocs.io/en/latest/userguide/convention/index.html)
 - `pydantic`: Used to
-  validate [standard attributes](https://h5rdmtoolbox.readthedocs.io/en/latest/conventions/standard_attributes_and_conventions.html)
+  validate [standard attributes](https://h5rdmtoolbox.readthedocs.io/en/latest/userguide/convention/index.html)
 - `pyyaml`: Reading and writing of yaml files, e.g. metadata definitions (conventions). Note, lower versions
   collide with python 3.11
 - `requests`: Used to download files from the internet or validate URLs, e.g. metadata definitions (conventions)
 - `rdflib`: Used to enable working with RDF
 - `ontolutils`: Required to work with RDF and derive semantic description of HDF5 file content
+- `cftime`: Handling non-standard calendars and time coordinates
+- `pyshacl`: Validating RDF graphs against SHACL shapes
+- `typer`: Providing the `h5tbx` command-line interface
 
 #### Optional dependencies
 
@@ -322,9 +333,9 @@ To run unit tests or to enable certain features, additional dependencies must be
 
 Install optional dependencies by specifying them in square brackets after the package name, e.g.:
 
-    pip install h5RDMtoolbox[mongodb]
+    pip install h5RDMtoolbox[database]
 
-[mongodb]
+[database]
 
 - `pymongo`: Database solution for HDF5 files
 
@@ -339,6 +350,10 @@ Install optional dependencies by specifying them in square brackets after the pa
 - `python-gitlab`: Access to gitlab repositories
 - `pypandoc`: Conversion of markdown files to html
 
+Other supported extras are `layout_validation`, `catalog`, `gui`, `server`, `test`, `docs`, `complete`, and
+`complete-with-docs`. See the [installation guide](https://h5rdmtoolbox.readthedocs.io/en/latest/gettingstarted/installation.html)
+for their purpose. The authoritative dependency lists and version constraints are in [`pyproject.toml`](./pyproject.toml).
+
 ## Citing the package
 
 If you intend to use the package in your work, you may cite the software itself as published on paper in the
@@ -371,10 +386,10 @@ Here is the BibTeX entry:
 Feel free to contribute. Make sure to write `docstrings` to your methods and classes and please write tests and use PEP
 8 (https://peps.python.org/pep-0008/)
 
-Please write tests for your code and put them into the `test/` folder. Visit the [README file](./tests/README.md) in the
-test-folder for more information.
+Please write tests for your code and put them into the `tests/` folder. Visit the [README file](./tests/README.md) in the
+tests folder for more information.
 
-Pleas also add a jupyter notebook in the `docs/` folder in order to document your code. Please visit
+Please also add a Jupyter notebook in the `docs/` folder in order to document your code. Please visit
 the [README file](./docs/README.md) in the docs-folder for more information on how to compile the documentation.
 
 Please use the **numpy style for the docstrings**:

{h5rdmtoolbox-2.8.0 → h5rdmtoolbox-2.8.2}/h5rdmtoolbox/convention/core.py

@@ -306,7 +306,10 @@ class Convention(AbstractConvention):
 
     @classmethod
     def from_yaml(
-        cls, yaml_filename: Union[str, pathlib.Path], overwrite: bool = False
+        cls,
+        yaml_filename: Union[str, pathlib.Path],
+        overwrite: bool = False,
+        allow_python_validators: bool = True,
     ):
         """Create a convention from a yaml file.
         The YAML file must have the following structure:
@@ -333,6 +336,8 @@ class Convention(AbstractConvention):
             path to the yaml file
         overwrite: bool
             if True, overwrite an existing (registered) convention with the same name
+        allow_python_validators: bool
+            Whether to copy and execute an adjacent ``*_vfuncs.py`` module.
 
         Returns
         -------
@@ -364,8 +369,10 @@ class Convention(AbstractConvention):
                 f'YAML file {yaml_filename} does not contain "__contact__". Is the file a valid convention?'
             )
 
+        from . import generate
+
         # check if name already exists!
-        convention_name = attrs["__name__"].lower().replace("-", "_")
+        convention_name = generate.normalize_convention_name(attrs["__name__"])
         if convention_name in [d.name for d in CV_DIR.glob("*")]:
             if not overwrite:
                 return _get_convention_from_dir(attrs["__name__"])
@@ -375,10 +382,10 @@ class Convention(AbstractConvention):
                 f'Convention exists and overwrite is True: Deleting convention "{convention_name}"'
             )
 
-        from . import generate
-
         generate.write_convention_module_from_yaml(
-            yaml_filename, name=attrs["__name__"]
+            yaml_filename,
+            name=attrs["__name__"],
+            allow_python_validators=allow_python_validators,
         )
 
         # add_convention(yaml_filename, name=attrs['__name__'])
@@ -504,9 +511,6 @@ class Convention(AbstractConvention):
         """
         from ..wrapper.core import File
 
-        if not isinstance(file_or_filename, (str, pathlib.Path)):
-            with File(file_or_filename, "r") as f:
-                return self.check(f)
         failed = []
 
         convention = self
@@ -575,13 +579,19 @@ class Convention(AbstractConvention):
                                         )
                                     )
 
-        with File(file_or_filename, "r") as f:
+        def _validate_file(f):
             logger.debug(
                 f"Checking file {file_or_filename} for compliance with convention {self.name}"
             )
             _validate_convention("/", f)
             f.visititems(_validate_convention)
 
+        if isinstance(file_or_filename, (str, pathlib.Path)):
+            with File(file_or_filename, "r") as f:
+                _validate_file(f)
+        else:
+            _validate_file(file_or_filename)
+
         return failed
 
 
@@ -621,8 +631,9 @@ def _import_convention(convention_name) -> "module":
 
 
 def _get_convention_from_dir(convention_name: str) -> "Convention":
-    _convention_name = convention_name.lower().replace("-", "_")
-    assert "-" not in _convention_name
+    from .generate import normalize_convention_name
+
+    _convention_name = normalize_convention_name(convention_name)
     if _convention_name in get_registered_conventions():
         return get_registered_conventions()[convention_name]
     _convention_py_filename = CV_DIR / f"{_convention_name}" / f"{_convention_name}.py"
@@ -799,19 +810,22 @@ def delete(convention: Union[str, Convention]):
         convention_name = convention.name
     else:
         convention_name = convention
-    cv_dir = CV_DIR / convention_name
+    from .generate import normalize_convention_name
+
+    safe_convention_name = normalize_convention_name(convention_name)
+    cv_dir = CV_DIR / safe_convention_name
     if cv_dir.exists():
-        shutil.rmtree(CV_DIR / convention_name)
+        shutil.rmtree(cv_dir)
     cfg._registered_conventions.pop(convention_name, None)
     if convention_name in sys.modules:
         # if the convention (py script) already has been imported, remove it from the list of imported modules:
         del sys.modules[convention_name]
 
 
-def from_file(filename) -> Convention:
+def from_file(filename, allow_python_validators: bool = True) -> Convention:
     """Load a convention from a file. Currently yaml and json files are supported"""
     if filename.suffix == ".yaml":
-        return from_yaml(filename)
+        return from_yaml(filename, allow_python_validators=allow_python_validators)
     elif filename.suffix == ".json":
         return from_json(filename)
     else:
@@ -819,11 +833,17 @@ def from_file(filename) -> Convention:
 
 
 def from_yaml(
-    filename: Union[str, pathlib.Path], overwrite: bool = False
+    filename: Union[str, pathlib.Path],
+    overwrite: bool = False,
+    allow_python_validators: bool = True,
 ) -> Convention:
     """Load a convention from a YAML file. See Convention.from_yaml() for details"""
     logger.debug(f"Reading Convention from yaml file: {filename}")
-    return Convention.from_yaml(filename, overwrite=overwrite)
+    return Convention.from_yaml(
+        filename,
+        overwrite=overwrite,
+        allow_python_validators=allow_python_validators,
+    )
 
 
 def from_json(
@@ -833,7 +853,11 @@ def from_json(
     return Convention.from_json(filename, overwrite=overwrite)
 
 
-def from_repo(repo_interface: RepositoryInterface, name: str):
+def from_repo(
+        repo_interface: RepositoryInterface,
+        name: str,
+        allow_python_validators: bool = False,
+):
     """Download a YAML file from a repository
 
     Parameters
@@ -842,6 +866,9 @@ def from_repo(repo_interface: RepositoryInterface, name: str):
         The repository interface to use for downloading the file
     name: str
         Name of the file to download
+    allow_python_validators: bool
+        Whether to download and execute a repository-provided ``*_vfuncs.py``
+        file. Disabled by default because it is executable code.
     """
     logger.debug(f"Downloading file {name} from repository {repo_interface}")
 
@@ -849,19 +876,20 @@ def from_repo(repo_interface: RepositoryInterface, name: str):
     _suffix = pathlib.Path(name).suffix
     vfunc_filename = name.split(_suffix, 1)
     has_vfunc = False
-    if len(vfunc_filename) == 2:
+    downloaded_vfunc_filename = None
+    if allow_python_validators and len(vfunc_filename) == 2:
         vfunc_filename = f"{vfunc_filename[0]}_vfuncs.py"
         try:
             downloaded_vfunc_filename = repo_interface.download_file(vfunc_filename)
             has_vfunc = True
         except Exception as e:
             logger.debug(f"No vfuncs file found for {name}: {e}")
-    if has_vfunc:
+    if has_vfunc and downloaded_vfunc_filename is not None:
         shutil.copy(
             downloaded_vfunc_filename, filename.parent / downloaded_vfunc_filename.name
         )
     logger.debug(f"File downloaded to {filename}. Now loading convention from file.")
-    return from_file(filename)
+    return from_file(filename, allow_python_validators=allow_python_validators)
 
 
 def from_zenodo(
@@ -869,6 +897,7 @@ def from_zenodo(
     name: str = None,
     overwrite: bool = False,
     force_download: bool = False,
+    allow_python_validators: bool = False,
 ) -> Convention:
     """Download a YAML file from a zenodo repository
 
@@ -885,6 +914,9 @@ def from_zenodo(
         Whether to overwrite existing convention with the same name. Default is False
     force_download: bool
         Whether to force download the file even if it is already cached. Default is False
+    allow_python_validators: bool
+        Whether to download and execute repository-provided validator Python.
+        Disabled by default.
 
     Returns
     -------
@@ -910,10 +942,18 @@ def from_zenodo(
             yaml_matches = [
                 file for file in filenames if pathlib.Path(file).suffix == ".yaml"
             ]
-            vfuns_matches = [file for file in filenames if file.endswith("vfuncs.py")]
+            vfuns_matches = (
+                [file for file in filenames if file.endswith("vfuncs.py")]
+                if allow_python_validators
+                else []
+            )
         else:
             yaml_matches = [file for file in filenames if file == name]
-            vfuns_matches = [file for file in filenames if file == f"{name}_vfuncs.py"]
+            vfuns_matches = (
+                [file for file in filenames if file == f"{name}_vfuncs.py"]
+                if allow_python_validators
+                else []
+            )
             if len(yaml_matches) == 0:
                 raise ValueError(
                     f'No file with name "{name}" found in record {doi_or_recid}'
@@ -927,7 +967,11 @@ def from_zenodo(
             )
             shutil.move(_filename, match)
 
-    return from_yaml(yaml_matches[0], overwrite=overwrite)
+    return from_yaml(
+        yaml_matches[0],
+        overwrite=overwrite,
+        allow_python_validators=allow_python_validators,
+    )
 
 
 def yaml2jsonld(