Merge branch 'master' into testdocker

CONTRIBUTING.md

@@ -122,6 +122,14 @@ preserving protected files. TBD how to determine protected
 files. Obviously the edit file should not be touched. Could use git
 log to determine if any modifications have been made?
 
+## Setting up a new machine for ODK development
+
+In order to build and publish ODK, you need the following:
+
+1. `docker` installed
+2. have `git` installed
+3. have a git user.name and user.email set
+
 ## General SOP for ODK release and publication
 
 * Put the `master` branch in the state we want for release (i.e. merge any approved PR that we want included in that release, etc.).

constraints.txt

@@ -1,5 +1,6 @@
 airium==0.2.5
 alabaster==0.7.13
+annotated-types==0.5.0
 antlr4-python3-runtime==4.9.3
 anyio==3.7.1
 appdirs==1.4.4
@@ -14,32 +15,31 @@ backcall==0.2.0
 bcp47==0.0.4
 beautifulsoup4==4.12.2
 bidict==0.22.1
-bioregistry==0.9.90
 black==21.12b0
 bleach==6.0.0
-bmt==1.1.0
+bmt==1.1.1
 cachetools==5.3.1
 cattrs==23.1.2
 certifi==2023.7.22
 cffi==1.15.1
 CFGraph==0.2.1
-chardet==5.1.0
+chardet==5.2.0
 charset-normalizer==3.2.0
 class-resolver==0.4.2
 click==8.1.6
 colorama==0.4.6
-comm==0.1.3
+comm==0.1.4
 commonmark==0.9.1
 contourpy==1.1.0
-cryptography==41.0.2
-curies==0.5.7
+cryptography==41.0.3
+curies==0.6.0
 cycler==0.11.0
 dacite==1.8.1
 daff==1.3.46
 dataclasses==0.6
 dataclasses-json==0.5.14
 dataclasses-jsonschema==2.16.0
-debugpy==1.6.7
+debugpy==1.6.7.post1
 decorator==5.1.1
 defusedxml==0.7.1
 Deprecated==1.2.14
@@ -52,23 +52,23 @@ dosdp==0.1.10.dev1
 EditorConfig==0.12.3
 et-xmlfile==1.1.0
 eutils==0.6.0
-exceptiongroup==1.1.2
+exceptiongroup==1.1.3
 executing==1.2.0
 fastjsonschema==2.18.0
 fastobo==0.12.2
 filelock==3.12.2
 flake8==6.1.0
-fonttools==4.41.1
+fonttools==4.42.0
 fqdn==1.5.1
-funowl==0.1.12
+funowl==0.2.3
 ghp-import==2.1.0
 google==3.0.0
 google-api-core==2.11.1
-google-api-python-client==2.95.0
+google-api-python-client==2.96.0
 google-auth==2.22.0
 google-auth-httplib2==0.1.0
 google-auth-oauthlib==1.0.0
-googleapis-common-protos==1.59.1
+googleapis-common-protos==1.60.0
 graphviz==0.20.1
 greenlet==2.0.1
 gspread==5.10.0
@@ -80,10 +80,10 @@ ijson==3.2.3
 imagesize==1.4.1
 importlib-metadata==6.8.0
 iniconfig==2.0.0
-ipykernel==6.25.0
+ipykernel==6.25.1
 ipython==8.14.0
 ipython-genutils==0.2.0
-ipywidgets==8.0.7
+ipywidgets==8.1.0
 isodate==0.6.1
 isoduration==20.11.0
 j2cli==0.3.10
@@ -101,9 +101,9 @@ jsonlines==3.1.0
 jsonpatch==1.33
 jsonpath-ng==1.5.3
 jsonpath-rw==1.4.0
-jsonpickle==3.0.1
+jsonpickle==3.0.2
 jsonpointer==2.4
-jsonschema==4.18.4
+jsonschema==4.19.0
 jsonschema-specifications==2023.7.1
 jsonschema2md==0.9.0
 jsonstreams==0.6.0
@@ -115,21 +115,21 @@ jupyter_client==8.3.0
 jupyter_core==5.3.1
 jupyter_server==2.7.0
 jupyter_server_terminals==0.4.4
-jupyterlab==4.0.3
+jupyterlab==4.0.5
 jupyterlab-pygments==0.2.2
 jupyterlab-widgets==3.0.8
 jupyterlab_server==2.24.0
 keyring==24.2.0
 kgcl-rdflib==0.5.0
-kgcl-schema==0.5.0
+kgcl-schema==0.6.0
 kgx==1.7.2
 kiwisolver==1.4.4
 lark==1.1.7
 lightrdf==0.3.1
 linkml==1.5.6
 linkml-dataops==0.1.0
-linkml-renderer==0.2.0
-linkml-runtime==1.5.5
+linkml-renderer==0.3.0
+linkml-runtime==1.5.6
 lxml==4.9.3
 Markdown==3.4.4
 markdown-it-py==3.0.0
@@ -142,14 +142,14 @@ mccabe==0.7.0
 mdurl==0.1.2
 mergedeep==1.3.4
 mistune==3.0.1
-mkdocs==1.5.1
+mkdocs==1.5.2
 mkdocs-material==9.1.21
 mkdocs-material-extensions==1.1.1
 mkdocs-mermaid2-plugin==0.6.0
 mkdocs-table-reader-plugin==2.0.1
 more-click==0.1.2
-more-itertools==10.0.0
-mypy==1.4.1
+more-itertools==10.1.0
+mypy==1.5.0
 mypy-extensions==1.0.0
 nbclient==0.8.0
 nbconvert==7.7.3
@@ -158,19 +158,19 @@ ndex2==3.5.1
 neo4j==4.3.0
 nest-asyncio==1.5.7
 networkx==3.1
-notebook==7.0.0
+notebook==7.0.2
 notebook_shim==0.2.3
-numpy==1.25.1
-oaklib==0.5.12
+numpy==1.25.2
+oaklib==0.5.15
 oauthlib==3.2.2
 ols-client==0.1.4
-ontobio==2.7.13
+ontobio==2.8.8
 ontodev-cogs==0.3.3
 ontodev-gizmos==0.3.2
 ontoportal-client==0.0.4
 openpyxl==3.1.2
 ordered-set==4.1.0
-overrides==7.3.1
+overrides==7.4.0
 packaging==23.1
 pandas==2.0.3
 pandocfilters==1.5.0
@@ -183,7 +183,7 @@ pickleshare==0.7.5
 Pillow==10.0.0
 pkginfo==1.9.6
 platformdirs==3.10.0
-plotly==5.15.0
+plotly==5.16.0
 pluggy==1.2.0
 ply==3.11
 prefixcommons==0.1.12
@@ -192,7 +192,7 @@ prologterms==0.0.6
 prometheus-client==0.17.1
 prompt-toolkit==3.0.39
 pronto==2.5.4
-protobuf==4.23.4
+protobuf==4.24.0
 psutil==5.9.5
 ptyprocess==0.7.0
 pure-eval==0.2.2
@@ -201,16 +201,17 @@ pyasn1==0.5.0
 pyasn1-modules==0.3.0
 pycodestyle==2.11.0
 pycparser==2.21
-pydantic==1.10.12
+pydantic==2.1.1
+pydantic_core==2.4.0
 pydotplus==2.0.2
 pyflakes==3.1.0
-PyGithub==1.59.0
-Pygments==2.15.1
+PyGithub==1.59.1
+Pygments==2.16.1
 PyJSG==0.11.10
 PyJWT==2.8.0
 pymdown-extensions==10.1
 PyNaCl==1.5.0
-pyparsing==3.0.9
+pyparsing==2.4.7
 PyShEx==0.8.1
 PyShExC==0.9.1
 pysolr==3.9.0
@@ -224,17 +225,17 @@ PyTrie==0.4.0
 pytz==2023.3
 PyYAML==6.0.1
 pyyaml_env_tag==0.1
-pyzmq==25.1.0
+pyzmq==25.1.1
 qtconsole==5.4.3
 QtPy==2.3.1
 ratelimit==2.2.1
-rdflib==6.3.2
+rdflib==7.0.0
 rdflib-jsonld==0.6.1
 rdflib-shim==1.0.3
 readme-renderer==40.0
 recommonmark==0.7.1
-referencing==0.30.0
-regex==2023.6.3
+referencing==0.30.2
+regex==2023.8.8
 requests==2.31.0
 requests-cache==1.1.0
 requests-oauthlib==1.3.1
@@ -243,7 +244,7 @@ rfc3339-validator==0.1.4
 rfc3986==2.0.0
 rfc3986-validator==0.1.1
 rfc3987==1.3.8
-rich==13.5.1
+rich==13.5.2
 rpds-py==0.9.2
 rsa==4.9
 ruamel.yaml==0.17.32
@@ -265,17 +266,17 @@ SPARQLWrapper==2.0.0
 Sphinx==5.3.0
 sphinx-click==4.4.0
 sphinx-rtd-theme==1.2.2
-sphinxcontrib-applehelp==1.0.4
-sphinxcontrib-devhelp==1.0.2
-sphinxcontrib-htmlhelp==2.0.1
+sphinxcontrib-applehelp==1.0.6
+sphinxcontrib-devhelp==1.0.4
+sphinxcontrib-htmlhelp==2.0.3
 sphinxcontrib-jquery==4.1
 sphinxcontrib-jsmath==1.0.1
-sphinxcontrib-qthelp==1.0.3
-sphinxcontrib-serializinghtml==1.1.5
+sphinxcontrib-qthelp==1.0.5
+sphinxcontrib-serializinghtml==1.1.7
 SQLAlchemy==2.0.19
 SQLAlchemy-Utils==0.38.3
-sssom==0.3.36
-sssom-schema==0.14.0
+sssom==0.3.40
+sssom-schema==0.15.0
 stack-data==0.6.2
 stringcase==1.2.0
 tabulate==0.9.0
@@ -286,10 +287,10 @@ terminaltables==3.1.10
 tinycss2==1.2.1
 toml==0.10.2
 tomli==1.2.3
-tornado==6.3.2
+tornado==6.3.3
 tox==3.25.1
 tox-docker==4.1.0
-tqdm==4.65.0
+tqdm==4.66.1
 traitlets==5.9.0
 tsvalid==0.0.3
 twine==4.0.2
@@ -301,8 +302,8 @@ uri-template==1.3.0
 uritemplate==4.1.1
 url-normalize==1.4.3
 urllib3==1.26.16
-validators==0.20.0
-virtualenv==20.24.2
+validators==0.21.2
+virtualenv==20.24.3
 watchdog==3.0.0
 wcwidth==0.2.6
 webcolors==1.13