pyobo 0.12.11__tar.gz → 0.12.13__tar.gz

{pyobo-0.12.11 → pyobo-0.12.13}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyobo
-Version: 0.12.11
+Version: 0.12.13
 Summary: A python package for handling and generating OBO
 Keywords: snekpack,cookiecutter,ontologies,biomedical ontologies,life sciences,natural sciences,bioinformatics,cheminformatics,Open Biomedical Ontologies,OBO
 Author: Charles Tapley Hoyt
@@ -55,7 +55,7 @@ Requires-Dist: nih-reporter-downloader>=0.0.1
 Requires-Dist: typing-extensions
 Requires-Dist: rdflib
 Requires-Dist: obographs>=0.0.8
-Requires-Dist: sssom-pydantic
+Requires-Dist: sssom-pydantic>=0.1.1
 Requires-Dist: psycopg2-binary ; extra == 'drugcentral'
 Requires-Dist: ssslm[gilda] ; extra == 'gilda'
 Requires-Dist: ssslm[gilda-slim] ; extra == 'gilda-slim'
@@ -523,20 +523,6 @@ Alternatively, install using pip:
 $ python3 -m pip install -e .
 ```
 
-### Updating Package Boilerplate
-
-This project uses `cruft` to keep boilerplate (i.e., configuration, contribution
-guidelines, documentation configuration) up-to-date with the upstream
-cookiecutter package. Install cruft with either `uv tool install cruft` or
-`python3 -m pip install cruft` then run:
-
-```console
-$ cruft update
-```
-
-More info on Cruft's update command is available
-[here](https://github.com/cruft/cruft?tab=readme-ov-file#updating-a-project).
-
 ### 🥼 Testing
 
 After cloning the repository and installing `tox` with
@@ -574,8 +560,21 @@ only that Sphinx can build the documentation in an isolated environment (i.e.,
 with `tox -e docs-test`) but also that
 [ReadTheDocs can build it too](https://docs.readthedocs.io/en/stable/pull-requests.html).
 
+</details>
+
+## 🧑‍💻 For Maintainers
+
+<details>
+  <summary>See maintainer instructions</summary>
+
+### Initial Configuration
+
 #### Configuring ReadTheDocs
 
+[ReadTheDocs](https://readthedocs.org) is an external documentation hosting
+service that integrates with GitHub's CI/CD. Do the following for each
+repository:
+
 1. Log in to ReadTheDocs with your GitHub account to install the integration at
    https://readthedocs.org/accounts/login/?next=/dashboard/
 2. Import your project by navigating to https://readthedocs.org/dashboard/import
@@ -584,12 +583,10 @@ with `tox -e docs-test`) but also that
    (i.e., with spaces and capital letters)
 4. Click next, and you're good to go!
 
-### 📦 Making a Release
-
-#### Configuring Zenodo
+#### Configuring Archival on Zenodo
 
 [Zenodo](https://zenodo.org) is a long-term archival system that assigns a DOI
-to each release of your package.
+to each release of your package. Do the following for each repository:
 
 1. Log in to Zenodo via GitHub with this link:
    https://zenodo.org/oauth/login/github/?next=%2F. This brings you to a page
@@ -609,10 +606,10 @@ the DOI for the release and link to the Zenodo record for it.
 
 #### Registering with the Python Package Index (PyPI)
 
-You only have to do the following steps once.
+The [Python Package Index (PyPI)](https://pypi.org) hosts packages so they can
+be easily installed with `pip`, `uv`, and equivalent tools.
 
-1. Register for an account on the
-   [Python Package Index (PyPI)](https://pypi.org/account/register)
+1. Register for an account [here](https://pypi.org/account/register)
 2. Navigate to https://pypi.org/manage/account and make sure you have verified
    your email address. A verification email might not have been sent by default,
    so you might have to click the "options" dropdown next to your address to get
@@ -623,9 +620,11 @@ You only have to do the following steps once.
    2-factor authentication
 4. Issue an API token from https://pypi.org/manage/account/token
 
+This only needs to be done once per developer.
+
 #### Configuring your machine's connection to PyPI
 
-You have to do the following steps once per machine.
+This needs to be done once per machine.
 
 ```console
 $ uv tool install keyring
@@ -635,6 +634,8 @@ $ keyring set https://test.pypi.org/legacy/ __token__
 
 Note that this deprecates previous workflows using `.pypirc`.
 
+### 📦 Making a Release
+
 #### Uploading to PyPI
 
 After installing the package in development mode and installing `tox` with
@@ -672,4 +673,18 @@ This script does the following:
 
 This will trigger Zenodo to assign a DOI to your release as well.
 
+### Updating Package Boilerplate
+
+This project uses `cruft` to keep boilerplate (i.e., configuration, contribution
+guidelines, documentation configuration) up-to-date with the upstream
+cookiecutter package. Install cruft with either `uv tool install cruft` or
+`python3 -m pip install cruft` then run:
+
+```console
+$ cruft update
+```
+
+More info on Cruft's update command is available
+[here](https://github.com/cruft/cruft?tab=readme-ov-file#updating-a-project).
+
 </details>

{pyobo-0.12.11 → pyobo-0.12.13}/README.md

@@ -435,20 +435,6 @@ Alternatively, install using pip:
 $ python3 -m pip install -e .
 ```
 
-### Updating Package Boilerplate
-
-This project uses `cruft` to keep boilerplate (i.e., configuration, contribution
-guidelines, documentation configuration) up-to-date with the upstream
-cookiecutter package. Install cruft with either `uv tool install cruft` or
-`python3 -m pip install cruft` then run:
-
-```console
-$ cruft update
-```
-
-More info on Cruft's update command is available
-[here](https://github.com/cruft/cruft?tab=readme-ov-file#updating-a-project).
-
 ### 🥼 Testing
 
 After cloning the repository and installing `tox` with
@@ -486,8 +472,21 @@ only that Sphinx can build the documentation in an isolated environment (i.e.,
 with `tox -e docs-test`) but also that
 [ReadTheDocs can build it too](https://docs.readthedocs.io/en/stable/pull-requests.html).
 
+</details>
+
+## 🧑‍💻 For Maintainers
+
+<details>
+  <summary>See maintainer instructions</summary>
+
+### Initial Configuration
+
 #### Configuring ReadTheDocs
 
+[ReadTheDocs](https://readthedocs.org) is an external documentation hosting
+service that integrates with GitHub's CI/CD. Do the following for each
+repository:
+
 1. Log in to ReadTheDocs with your GitHub account to install the integration at
    https://readthedocs.org/accounts/login/?next=/dashboard/
 2. Import your project by navigating to https://readthedocs.org/dashboard/import
@@ -496,12 +495,10 @@ with `tox -e docs-test`) but also that
    (i.e., with spaces and capital letters)
 4. Click next, and you're good to go!
 
-### 📦 Making a Release
-
-#### Configuring Zenodo
+#### Configuring Archival on Zenodo
 
 [Zenodo](https://zenodo.org) is a long-term archival system that assigns a DOI
-to each release of your package.
+to each release of your package. Do the following for each repository:
 
 1. Log in to Zenodo via GitHub with this link:
    https://zenodo.org/oauth/login/github/?next=%2F. This brings you to a page
@@ -521,10 +518,10 @@ the DOI for the release and link to the Zenodo record for it.
 
 #### Registering with the Python Package Index (PyPI)
 
-You only have to do the following steps once.
+The [Python Package Index (PyPI)](https://pypi.org) hosts packages so they can
+be easily installed with `pip`, `uv`, and equivalent tools.
 
-1. Register for an account on the
-   [Python Package Index (PyPI)](https://pypi.org/account/register)
+1. Register for an account [here](https://pypi.org/account/register)
 2. Navigate to https://pypi.org/manage/account and make sure you have verified
    your email address. A verification email might not have been sent by default,
    so you might have to click the "options" dropdown next to your address to get
@@ -535,9 +532,11 @@ You only have to do the following steps once.
    2-factor authentication
 4. Issue an API token from https://pypi.org/manage/account/token
 
+This only needs to be done once per developer.
+
 #### Configuring your machine's connection to PyPI
 
-You have to do the following steps once per machine.
+This needs to be done once per machine.
 
 ```console
 $ uv tool install keyring
@@ -547,6 +546,8 @@ $ keyring set https://test.pypi.org/legacy/ __token__
 
 Note that this deprecates previous workflows using `.pypirc`.
 
+### 📦 Making a Release
+
 #### Uploading to PyPI
 
 After installing the package in development mode and installing `tox` with
@@ -584,4 +585,18 @@ This script does the following:
 
 This will trigger Zenodo to assign a DOI to your release as well.
 
+### Updating Package Boilerplate
+
+This project uses `cruft` to keep boilerplate (i.e., configuration, contribution
+guidelines, documentation configuration) up-to-date with the upstream
+cookiecutter package. Install cruft with either `uv tool install cruft` or
+`python3 -m pip install cruft` then run:
+
+```console
+$ cruft update
+```
+
+More info on Cruft's update command is available
+[here](https://github.com/cruft/cruft?tab=readme-ov-file#updating-a-project).
+
 </details>

{pyobo-0.12.11 → pyobo-0.12.13}/pyproject.toml

@@ -1,10 +1,10 @@
 [build-system]
-requires = ["uv_build>=0.6.6,<1.0"]
+requires = ["uv_build>=0.9.6,<1.0"]
 build-backend = "uv_build"
 
 [project]
 name = "pyobo"
-version = "0.12.11"
+version = "0.12.13"
 description = "A python package for handling and generating OBO"
 readme = "README.md"
 authors = [
@@ -89,7 +89,7 @@ dependencies = [
     "typing_extensions",
     "rdflib",
     "obographs>=0.0.8",
-    "sssom_pydantic",
+    "sssom_pydantic>=0.1.1",
 ]
 
 # see https://peps.python.org/pep-0735/ and https://docs.astral.sh/uv/concepts/dependencies/#dependency-groups
@@ -141,8 +141,8 @@ bump = [
     "bump-my-version",
 ]
 build = [
-    "uv",
-    "uv-build",
+    "uv>=0.9.6",
+    "uv-build>=0.9.6",
 ]
 release = [
     { include-group = "build" },
@@ -315,7 +315,7 @@ known-first-party = [
 docstring-code-format = true
 
 [tool.bumpversion]
-current_version = "0.12.11"
+current_version = "0.12.13"
 parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)(?:-(?P<release>[0-9A-Za-z-]+(?:\\.[0-9A-Za-z-]+)*))?(?:\\+(?P<build>[0-9A-Za-z-]+(?:\\.[0-9A-Za-z-]+)*))?"
 serialize = [
     "{major}.{minor}.{patch}-{release}+{build}",

{pyobo-0.12.11 → pyobo-0.12.13}/src/pyobo/api/xrefs.py

@@ -9,7 +9,7 @@ import curies
 import pandas as pd
 from curies import ReferenceTuple
 from sssom_pydantic import SemanticMapping
-from sssom_pydantic.io import parse_record, parse_row
+from sssom_pydantic.io import row_to_semantic_mapping
 from typing_extensions import Unpack
 
 from .utils import get_version_from_kwargs
@@ -124,12 +124,7 @@ def get_semantic_mappings(
     )
     if converter is None:
         converter = get_converter()
-    rv = []
-    for _, row in df.iterrows():
-        record = parse_row(row.to_dict())
-        mapping = parse_record(record, converter=converter)
-        rv.append(mapping)
-    return rv
+    return [row_to_semantic_mapping(row, converter=converter) for _, row in df.iterrows()]
 
 
 def get_mappings_df(

{pyobo-0.12.11 → pyobo-0.12.13}/src/pyobo/cli/cli.py

@@ -6,10 +6,7 @@ from collections.abc import Iterable
 from functools import lru_cache
 from operator import itemgetter
 
-import bioregistry
 import click
-import humanize
-from tabulate import tabulate
 
 from .database import main as database_main
 from .lookup import lookup
@@ -59,6 +56,9 @@ def clean(remove_obo: bool):
 @main.command()
 def ls():
     """List how big all of the OBO files are."""
+    import humanize
+    from tabulate import tabulate
+
     entries = [(prefix, os.path.getsize(path)) for prefix, path in _iter_cached_obo()]
     entries = [
         (prefix, humanize.naturalsize(size), "✅" if not has_nomenclature_plugin(prefix) else "❌")
@@ -69,6 +69,8 @@ def ls():
 
 def _iter_cached_obo() -> Iterable[tuple[str, str]]:
     """Iterate over cached OBO paths."""
+    import bioregistry
+
     for prefix in os.listdir(RAW_DIRECTORY):
         if prefix in GLOBAL_SKIP or _has_no_download(prefix) or bioregistry.is_deprecated(prefix):
             continue
@@ -83,6 +85,8 @@ def _iter_cached_obo() -> Iterable[tuple[str, str]]:
 
 def _has_no_download(prefix: str) -> bool:
     """Return if the prefix is not available."""
+    import bioregistry
+
     prefix_norm = bioregistry.normalize_prefix(prefix)
     return prefix_norm is not None and prefix_norm in _no_download()
 
@@ -90,6 +94,8 @@ def _has_no_download(prefix: str) -> bool:
 @lru_cache(maxsize=1)
 def _no_download() -> set[str]:
     """Get the list of prefixes not available as OBO."""
+    import bioregistry
+
     return {resource.prefix for resource in bioregistry.resources() if not resource.has_download()}
 
 

{pyobo-0.12.11 → pyobo-0.12.13}/src/pyobo/cli/database.py

@@ -5,29 +5,11 @@ import warnings
 from collections.abc import Iterable
 from pathlib import Path
 
-import bioregistry
-import bioversions
 import click
 from more_click import verbose_option
 from tqdm.contrib.logging import logging_redirect_tqdm
 from typing_extensions import Unpack
-from zenodo_client import update_zenodo
-
-from .database_utils import (
-    IterHelperHelperDict,
-    _iter_alts,
-    _iter_definitions,
-    _iter_edges,
-    _iter_mappings,
-    _iter_names,
-    _iter_properties,
-    _iter_relations,
-    _iter_species,
-    _iter_synonyms,
-    _iter_typedefs,
-    _iter_xrefs,
-    iter_helper_helper,
-)
+
 from .utils import (
     Clickable,
     directory_option,
@@ -48,7 +30,6 @@ from ..constants import (
     TYPEDEFS_RECORD,
     DatabaseKwargs,
 )
-from ..getters import db_output_helper, get_ontology
 
 __all__ = [
     "main",
@@ -107,6 +88,8 @@ def build(ctx: click.Context, eager_versions: bool, **kwargs: Unpack[DatabaseKwa
     #    sys.exit(1)
 
     if eager_versions:
+        import bioversions
+
         bioversions.get_rows(use_tqdm=True)
 
     with logging_redirect_tqdm():
@@ -143,6 +126,9 @@ def build(ctx: click.Context, eager_versions: bool, **kwargs: Unpack[DatabaseKwa
 @database_annotate
 def cache(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Cache all things."""
+    from .database_utils import iter_helper_helper
+    from ..getters import get_ontology
+
     if zenodo:
         click.echo("no zenodo for caching")
 
@@ -156,9 +142,13 @@ def cache(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> No
 @database_annotate
 def metadata(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Make the prefix-metadata dump."""
+    import bioregistry
+
+    from .database_utils import IterHelperHelperDict, iter_helper_helper
     from ..api import get_metadata
+    from ..getters import db_output_helper
 
-    def _iter_metadata(
+    def _iter_metadata_internal(
         **kwargs: Unpack[IterHelperHelperDict],
     ) -> Iterable[tuple[str, str, str, bool]]:
         for prefix, data in iter_helper_helper(get_metadata, **kwargs):
@@ -166,7 +156,7 @@ def metadata(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) ->
             logger.debug(f"[{prefix}] using version {version}")
             yield prefix, version, data["date"], bioregistry.is_deprecated(prefix)
 
-    it = _iter_metadata(**kwargs)
+    it = _iter_metadata_internal(**kwargs)
     db_output_helper(
         it,
         "metadata",
@@ -181,6 +171,9 @@ def metadata(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) ->
 @database_annotate
 def names(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Make the prefix-identifier-name dump."""
+    from .database_utils import _iter_names
+    from ..getters import db_output_helper
+
     it = _iter_names(**kwargs)
     with logging_redirect_tqdm():
         paths = db_output_helper(
@@ -190,6 +183,8 @@ def names(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> No
             directory=directory,
         )
     if zenodo:
+        from zenodo_client import update_zenodo
+
         # see https://zenodo.org/record/4020486
         update_zenodo(OOH_NA_NA_RECORD, paths)
 
@@ -197,6 +192,9 @@ def names(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> No
 @database_annotate
 def species(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Make the prefix-identifier-species dump."""
+    from .database_utils import _iter_species
+    from ..getters import db_output_helper
+
     with logging_redirect_tqdm():
         it = _iter_species(**kwargs)
         paths = db_output_helper(
@@ -206,6 +204,8 @@ def species(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) ->
             directory=directory,
         )
     if zenodo:
+        from zenodo_client import update_zenodo
+
         # see https://zenodo.org/record/5334738
         update_zenodo(SPECIES_RECORD, paths)
 
@@ -221,6 +221,9 @@ def _extend_skip_set(kwargs: DatabaseKwargs, skip_set: set[str]) -> None:
 @database_annotate
 def definitions(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Make the prefix-identifier-definition dump."""
+    from .database_utils import _iter_definitions
+    from ..getters import db_output_helper
+
     with logging_redirect_tqdm():
         _extend_skip_set(kwargs, {"kegg.pathway", "kegg.genes", "kegg.genome", "umls"})
         it = _iter_definitions(**kwargs)
@@ -231,6 +234,8 @@ def definitions(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs])
             directory=directory,
         )
     if zenodo:
+        from zenodo_client import update_zenodo
+
         # see https://zenodo.org/record/4637061
         update_zenodo(DEFINITIONS_RECORD, paths)
 
@@ -238,6 +243,9 @@ def definitions(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs])
 @database_annotate
 def typedefs(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Make the typedef prefix-identifier-name dump."""
+    from .database_utils import _iter_typedefs
+    from ..getters import db_output_helper
+
     with logging_redirect_tqdm():
         _extend_skip_set(kwargs, {"ncbigene", "kegg.pathway", "kegg.genes", "kegg.genome"})
         it = _iter_typedefs(**kwargs)
@@ -249,6 +257,8 @@ def typedefs(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) ->
             directory=directory,
         )
     if zenodo:
+        from zenodo_client import update_zenodo
+
         # see https://zenodo.org/record/4644013
         update_zenodo(TYPEDEFS_RECORD, paths)
 
@@ -256,6 +266,9 @@ def typedefs(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) ->
 @database_annotate
 def alts(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Make the prefix-alt-id dump."""
+    from .database_utils import _iter_alts
+    from ..getters import db_output_helper
+
     with logging_redirect_tqdm():
         _extend_skip_set(kwargs, {"kegg.pathway", "kegg.genes", "kegg.genome", "umls"})
         it = _iter_alts(**kwargs)
@@ -266,6 +279,8 @@ def alts(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> Non
             directory=directory,
         )
     if zenodo:
+        from zenodo_client import update_zenodo
+
         # see https://zenodo.org/record/4021476
         update_zenodo(ALTS_DATA_RECORD, paths)
 
@@ -273,6 +288,9 @@ def alts(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> Non
 @database_annotate
 def synonyms(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Make the prefix-identifier-synonym dump."""
+    from .database_utils import _iter_synonyms
+    from ..getters import db_output_helper
+
     with logging_redirect_tqdm():
         _extend_skip_set(kwargs, {"kegg.pathway", "kegg.genes", "kegg.genome"})
         it = _iter_synonyms(**kwargs)
@@ -283,6 +301,8 @@ def synonyms(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) ->
             directory=directory,
         )
     if zenodo:
+        from zenodo_client import update_zenodo
+
         # see https://zenodo.org/record/4021482
         update_zenodo(SYNONYMS_RECORD, paths)
 
@@ -290,6 +310,9 @@ def synonyms(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) ->
 @database_annotate
 def relations(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Make the relation dump."""
+    from .database_utils import _iter_relations
+    from ..getters import db_output_helper
+
     with logging_redirect_tqdm():
         it = _iter_relations(**kwargs)
         paths = db_output_helper(
@@ -307,6 +330,8 @@ def relations(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -
             directory=directory,
         )
     if zenodo:
+        from zenodo_client import update_zenodo
+
         # see https://zenodo.org/record/4625167
         update_zenodo(RELATIONS_RECORD, paths)
 
@@ -314,6 +339,9 @@ def relations(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -
 @database_annotate
 def edges(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Make the edges dump."""
+    from .database_utils import _iter_edges
+    from ..getters import db_output_helper
+
     with logging_redirect_tqdm():
         it = _iter_edges(**kwargs)
         db_output_helper(
@@ -334,6 +362,9 @@ def edges(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> No
 @database_annotate
 def properties(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Make the properties dump."""
+    from .database_utils import _iter_properties
+    from ..getters import db_output_helper
+
     with logging_redirect_tqdm():
         it = _iter_properties(**kwargs)
         paths = db_output_helper(
@@ -344,6 +375,8 @@ def properties(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs])
             directory=directory,
         )
     if zenodo:
+        from zenodo_client import update_zenodo
+
         # see https://zenodo.org/record/4625172
         update_zenodo(PROPERTIES_RECORD, paths)
 
@@ -351,6 +384,9 @@ def properties(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs])
 @database_annotate
 def xrefs(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Make the prefix-identifier-xref dump."""
+    from .database_utils import _iter_xrefs
+    from ..getters import db_output_helper
+
     warnings.warn("Use pyobo.database.mappings instead", DeprecationWarning, stacklevel=2)
     with logging_redirect_tqdm():
         it = _iter_xrefs(**kwargs)
@@ -362,6 +398,8 @@ def xrefs(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> No
             directory=directory,
         )
     if zenodo:
+        from zenodo_client import update_zenodo
+
         # see https://zenodo.org/record/4021477
         update_zenodo(JAVERT_RECORD, paths)
 
@@ -369,6 +407,9 @@ def xrefs(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> No
 @database_annotate
 def mappings(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Make the SSSOM dump."""
+    from .database_utils import _iter_mappings
+    from ..getters import db_output_helper
+
     columns = [
         "subject_id",
         "object_id",