From 2be37da69c5c10c508b7ce6949bc88dc30f63a5a Mon Sep 17 00:00:00 2001
From: Sujay Patil <sujaysanjeev.patil@gmail.com>
Date: Thu, 16 Dec 2021 10:56:48 -0800
Subject: [PATCH 01/15] deprecated support for setuptools

---
 setup.cfg | 37 -------------------------------------
 setup.py  | 12 ------------
 2 files changed, 49 deletions(-)
 delete mode 100644 setup.cfg
 delete mode 100644 setup.py

diff --git a/setup.cfg b/setup.cfg
deleted file mode 100644
index 88a38bfa..00000000
--- a/setup.cfg
+++ /dev/null
@@ -1,37 +0,0 @@
-[metadata]
-name = linkml_runtime
-url = https://github.com/biolink/linkml-runtime
-author = Harold Solbrig
-author-email = solbrig@jhu.edu
-summary = LinkML Runtime Environment
-description = Runtime Environment for the Linked Open Data Modeling Language
-home-page = http://linkml.github.io/linkml-runtime
-license = CC0 1.0 Universal
-python-requires = >=3.7
-classifiers =
-    Development Status :: 4 - Beta
-    Environment :: Console
-    Intended Audience :: Developers
-    Intended Audience :: Science/Research
-    Intended Audience :: Healthcare Industry
-    License :: CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
-    Programming Language :: Python :: 3 :: Only
-    Programming Language :: Python :: 3.7
-    Programming Language :: Python :: 3.8
-    Programming Language :: Python :: 3.9
-keywords =
-    linkml
-    lod
-    rdf
-    owl
-    yaml
-    model
-    metamodel
-
-[files]
-packages =
-    linkml_runtime
-
-[entry_points]
-console_scripts =
-    comparefiles = linkml_runtime.utils.comparefiles:cli
diff --git a/setup.py b/setup.py
deleted file mode 100644
index aa6b10fe..00000000
--- a/setup.py
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env python
-import sys
-from setuptools import setup
-from warnings import warn
-
-if sys.version_info < (3, 7, 0):
-    warn(f"Some URL processing will fail with python 3.7.5 or earlier.  Current version: {sys.version_info}")
-
-setup(
-    setup_requires=['pbr'],
-    pbr=True,
-)

From d82f4f751bac87159ade15f113a0e200cecf1ecc Mon Sep 17 00:00:00 2001
From: Sujay Patil <sujaysanjeev.patil@gmail.com>
Date: Thu, 16 Dec 2021 10:57:30 -0800
Subject: [PATCH 02/15] updated ChangeLog to include latest release summaries

---
 ChangeLog | 84 ++++++++++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 83 insertions(+), 1 deletion(-)

diff --git a/ChangeLog b/ChangeLog
index 275cf8a6..86f50c2d 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,7 +1,89 @@
 CHANGES
 =======
 
-* Update to latest model
+v1.1.10
+-------
+* Extended SchemaUsage to include inferred slot
+* Minor README changes
+* Added binder badge
+* Added poetry support to the repository
+
+v1.1.9
+------
+* Same as v1.1.8
+
+v1.1.8
+------
+* Returned class names by all_class() should match name in Python dataclass
+* SchemaView rdflib loader methods
+* Fixed get_mapping_index method
+* Added inverse and is_mixin methods
+* Added function to return schema elements by id_prefixes
+
+v1.1.7
+------
+* Added flag for unmappable rdf predicates
+* Fixed propagation over slot_usage
+
+v1.1.6
+------
+* Added support for rdfs:Resource as a type uri
+
+v1.1.5
+------
+* Hotfixes to conditional rules released as part of v1.1.4
+
+v1.1.4
+------
+* Added simple set of conditional rules that apply to instances of classes
+
+v1.1.3
+------
+* Bugfix in utils.comparefiles: detecting missing files
+* Ensured get_uri is populated for attributes Ensuring fresh copy of induced slot
+* Added makefile to sync linkml-model
+* Added method to SchemaView to get descendants of a slot
+* New rdf dumper - bypasses existing jsonld based method and does a direct conversion from elements to rdflib
+
+v1.1.2
+------
+* Added deduplication functionality for enums
+* Added click cli for SchemaView
+
+v1.1.1
+------
+* Exclude tombstoned rdflib-jsonld
+
+v1.1.0
+------
+* Fixed serialization of enums in json_dumper
+
+v1.0.16
+-------
+* Fix for induced_slot() returning incorrect range
+
+v1.0.15
+-------
+* Bumped json-flattener requirement
+* Added param to schemaview traversal methods to control traversal over is_a
+* Added more tests for schemaview
+
+v1.0.14
+-------
+* Added inject_type to as_json_object to optionally suppress `@type` declarations
+* Added csv loaders and dumpers to runtime, fixes  linkml/linkml-csv#1
+* Additional methods in schemaview
+  * get_identifier
+  * is_inlined
+
+v1.0.13
+-------
+
+* Added new module: schemaviews
+  * Dynamic inferred views over schemas
+  * See [examples](https://github.com/linkml/linkml-runtime/tree/main/notebooks)
+* Replace hyphen with underscore when underscoring names
+* Incorporates 1.0.4 metamodel
 
 v1.0.12
 -------

From 6c8efd400daa2c41201179d01e96701c10a52a29 Mon Sep 17 00:00:00 2001
From: Sujay Patil <sujaysanjeev.patil@gmail.com>
Date: Wed, 5 Jan 2022 12:13:12 -0800
Subject: [PATCH 03/15] add recipe for package release process

---
 CONTRIBUTING.md | 21 ++++++++++++++++++---
 1 file changed, 18 insertions(+), 3 deletions(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 3992c94f..e3718dc7 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -63,10 +63,25 @@ poetry run pytest
 
 ## Release process
 
-Once the code has been merged into the `main` branch on this repo, there are two processes that need to be completed to ensure a release is complete.
+Once the code has been merged into the `main` branch on this repo, there are a few steps that need to be completed to ensure a release is complete.
 
-* You should use the [releases](https://github.com/linkml/linkml-runtime/releases) section of the Github repo to draft a new release. Click on the *draft a new release* button. Annotate the release with a tag. Conventionally tags are prefixed with `v` so choose an appropriately versioned tag number. Ex., `v1.1.9` and such. Leave the default `main` branch as the target. Use the same tag number for the release title as well. After that, use Github's autogenerated CHANGELOG button to generate release notes. If it's possible to simplify the notes and make it more succinct, you should. 
-* Once a release is created, a [Github Action](.github/workflows/pypi-publish.yaml) will take care of publishing the package to PyPI for you. Verify that the latest release has been deployed to PyPI [here](https://pypi.org/project/linkml-runtime/).
+* Update the version number in the [pyproject.toml](pyproject.toml) file.
+
+Note: Ensure that the latest release tag and the version number in the `pyproject.toml` file are in sync, otherwise there might be problems with the Github Action auto deploying the package to PyPI.
+
+* If there are any new authors on the repository, add them to the [AUTHORS](AUTHORS) file.
+* Update the [ChangeLog](ChangeLog) with a brief summary of the changes introduced in the latest release.
+
+### Creating a release
+
+* Use the [releases](https://github.com/linkml/linkml-runtime/releases) section of the Github interface to draft a new release.
+* Click on the *draft a new release* button. Annotate the release with a tag.
+* Conventionally tags are prefixed with `v` so choose an appropriately versioned tag number. Ex., `v1.1.9` and such.
+* Leave the default `main` branch as the target. Use the same tag number for the release title as well. After that, use Github's autogenerated CHANGELOG button to generate release notes. If it's possible to simplify the notes and make it more succinct, you should. 
+* Once a release is created, a [Github Action](.github/workflows/pypi-publish.yaml) will take care of publishing the package to PyPI for you.
+
+* Navigate to the [Actions](https://github.com/linkml/linkml-runtime/actions) tab, and verify that there is a ✅ next to the release tag that was just created. For ex., [v1.1.15](https://github.com/linkml/linkml-runtime/actions/runs/1656285916).
+* Finally, check the package page on [PyPI](https://pypi.org/project/linkml-runtime/) to make sure the latest release was published.
 
 ## Testing
 

From 0e7b6d4cd64b0ee6dacef67710478ebcb3ea37d9 Mon Sep 17 00:00:00 2001
From: Sierra Taylor Moxon <sierra.taylor@gmail.com>
Date: Thu, 13 Jan 2022 12:15:42 -0800
Subject: [PATCH 04/15] try making a pypi release with automatic versioning

---
 .github/workflows/pypi-publish.yaml | 4 +++-
 pyproject.toml                      | 2 +-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pypi-publish.yaml b/.github/workflows/pypi-publish.yaml
index e847145f..b9eb0693 100644
--- a/.github/workflows/pypi-publish.yaml
+++ b/.github/workflows/pypi-publish.yaml
@@ -27,7 +27,9 @@ jobs:
       run: poetry install --no-interaction
 
     - name: Build source and wheel archives
-      run: poetry build
+      run: |
+        poetry version $(git describe --tags --abbrev=0)
+        poetry build
 
     - name: Publish distribution 📦 to PyPI
       uses: pypa/gh-action-pypi-publish@v1.2.2
diff --git a/pyproject.toml b/pyproject.toml
index 372f4e4c..996ad947 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "linkml_runtime"
-version = "1.1.15"
+version = "0.0.0"
 description = "Runtime environment for LinkML, the Linked open data modeling language"
 authors = [
     "Chris Mungall <cjmungall@lbl.gov>",

From eee4022af8acacbac0a6f6be663c7f517599b655 Mon Sep 17 00:00:00 2001
From: Sierra Taylor Moxon <sierra.taylor@gmail.com>
Date: Thu, 13 Jan 2022 12:37:14 -0800
Subject: [PATCH 05/15] attempt to set __version__

---
 linkml_runtime/__init__.py | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/linkml_runtime/__init__.py b/linkml_runtime/__init__.py
index c864200b..8a27553b 100644
--- a/linkml_runtime/__init__.py
+++ b/linkml_runtime/__init__.py
@@ -4,6 +4,11 @@
 import rdflib_shim
 shim = rdflib_shim.RDFLIB_SHIM
 
+try:
+    import importlib.metadata as importlib_metadata
+except ModuleNotFoundError:
+    import importlib_metadata
+
 LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/')
 TCCM = CurieNamespace('tccm', 'https://ontologies.r.us/tccm/')
 OWL = CurieNamespace('owl', OWL)
@@ -12,6 +17,9 @@
 SKOS = CurieNamespace('skos', SKOS)
 XSD = CurieNamespace('xsd', XSD)
 
+__version__ = importlib_metadata.version(__name__)
+
+
 class MappingError(ValueError):
     """
     An error when mapping elements of a LinkML model to runtime objects

From 6d8c717fad36ae2bce97c2176d3b7b5fa2657a58 Mon Sep 17 00:00:00 2001
From: Sierra Taylor Moxon <sierra.taylor@gmail.com>
Date: Thu, 13 Jan 2022 12:45:02 -0800
Subject: [PATCH 06/15] remove tests at PUSH, keep at PR

---
 .github/workflows/main.yaml      | 2 +-
 tests/test_utils/test_version.py | 3 +++
 2 files changed, 4 insertions(+), 1 deletion(-)
 create mode 100644 tests/test_utils/test_version.py

diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
index 5e504df7..edd081ef 100644
--- a/.github/workflows/main.yaml
+++ b/.github/workflows/main.yaml
@@ -4,7 +4,7 @@
 
 name: Build and test linkml-runtime
 
-on: [push, pull_request]
+on: [pull_request]
 
 jobs:
   test:
diff --git a/tests/test_utils/test_version.py b/tests/test_utils/test_version.py
new file mode 100644
index 00000000..950c85aa
--- /dev/null
+++ b/tests/test_utils/test_version.py
@@ -0,0 +1,3 @@
+import linkml_runtime
+
+print(linkml_runtime.__version__)
\ No newline at end of file

From ab10150c671b5262d0d34e311196059f826662d0 Mon Sep 17 00:00:00 2001
From: Sujay Patil <sujaysanjeev.patil@gmail.com>
Date: Thu, 13 Jan 2022 13:02:37 -0800
Subject: [PATCH 07/15] update test_version unit test

---
 tests/test_utils/test_version.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/tests/test_utils/test_version.py b/tests/test_utils/test_version.py
index 950c85aa..7df18eab 100644
--- a/tests/test_utils/test_version.py
+++ b/tests/test_utils/test_version.py
@@ -1,3 +1,7 @@
+import unittest
+
 import linkml_runtime
 
-print(linkml_runtime.__version__)
\ No newline at end of file
+class TestPackageVersion(unittest.TestCase):
+    def test_package_version(self):
+        self.assertIsNotNone(linkml_runtime.__version__)

From 7d237a2c2be5c0c1f782d8a1bafddf247f831594 Mon Sep 17 00:00:00 2001
From: Sujay Patil <sujaysanjeev.patil@gmail.com>
Date: Thu, 13 Jan 2022 13:12:15 -0800
Subject: [PATCH 08/15] add comment and include importlib-metadata as
 dependency

---
 linkml_runtime/__init__.py | 3 +++
 pyproject.toml             | 1 +
 2 files changed, 4 insertions(+)

diff --git a/linkml_runtime/__init__.py b/linkml_runtime/__init__.py
index 8a27553b..c12e4d74 100644
--- a/linkml_runtime/__init__.py
+++ b/linkml_runtime/__init__.py
@@ -4,6 +4,9 @@
 import rdflib_shim
 shim = rdflib_shim.RDFLIB_SHIM
 
+# use importlib.metadata to read the version provided
+# by the package during installation. Do not hardcode
+# the version in the code
 try:
     import importlib.metadata as importlib_metadata
 except ModuleNotFoundError:
diff --git a/pyproject.toml b/pyproject.toml
index 996ad947..ceb66613 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -58,6 +58,7 @@ shexjsg = "==0.*,>=0.7.0"
 
 [tool.poetry.dev-dependencies]
 coverage = "^6.2"
+importlib-metadata = {version = "^1.0", python = "<3.8"}
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]

From 340c925e09ce5885a4b24e965cf0eb2f32b4d8e6 Mon Sep 17 00:00:00 2001
From: Sierra Taylor Moxon <sierra.taylor@gmail.com>
Date: Fri, 14 Jan 2022 13:24:46 -0800
Subject: [PATCH 09/15] updating readme

---
 CONTRIBUTING.md | 30 ++----------------------------
 1 file changed, 2 insertions(+), 28 deletions(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index e3718dc7..edc7310d 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -14,14 +14,6 @@ You can use the [Issues](https://github.com/linkml/linkml-runtime/issues) tab to
 * Explain which behavior you expected to see instead and why.
 * Provide screenshots of the expected or actual behaviour where applicable.
 
-## General contribution instructions
-
-1. Follow the [Github docs](https://docs.github.com/en/get-started/quickstart/fork-a-repo) to make a copy (a fork) of the repository to your own Github account.
-2. [Clone the forked repository](https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository) to your local machine so you can begin making changes.
-3. Make sure this repository is set as the [upstream remote repository](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/configuring-a-remote-for-a-fork) so you are able to fetch the latest commits.
-4. Push all your changes to a development branch, which is ideally a copy of the `main` branch of this repository.
-5. Create pull requests from the development branch into the `main` branch when the code is ready to be merged into production.
-
 ### The development lifecycle
 
 1. Create a bug fix or feature development branch, based off the `main` branch of the upstream repo, and not your fork. Name the branch appropriately, briefly summarizing the bug fix or feature request. If none come to mind, you can include the issue number in the branch name. Some examples of branch names are, `bugfix/breaking-pipfile-error` or `feature/add-click-cli-layer`, or `bugfix/issue-414`
@@ -36,25 +28,13 @@ Note: All the development must be done on a branch on your fork.
 ## Development environment setup
 
 1. Install [poetry](https://python-poetry.org/docs/#installation).
-2. Clone the [linkml-runtime](https://github.com/linkml/linkml-runtime) repository.
-
-```
-git clone https://github.com/linkml/linkml-runtime.git
-```
-
-3. Change directory to the cloned `linkml-runtime` repo.
-
-```
-cd linkml-runtime
-```
-
-4. Install all the dependencies from your project, which are typically specified in a `poetry.lock` file.
+2. Install all the dependencies from your project, which are typically specified in a `poetry.lock` file.
 
 ```
 poetry install
 ```
 
-5. Run any python scripts or CLI commands by prefixing with `poetry run`.
+3. Run any python scripts or CLI commands by prefixing with `poetry run`.
 
 ```
 poetry run python your_script.py
@@ -65,17 +45,12 @@ poetry run pytest
 
 Once the code has been merged into the `main` branch on this repo, there are a few steps that need to be completed to ensure a release is complete.
 
-* Update the version number in the [pyproject.toml](pyproject.toml) file.
-
-Note: Ensure that the latest release tag and the version number in the `pyproject.toml` file are in sync, otherwise there might be problems with the Github Action auto deploying the package to PyPI.
-
 * If there are any new authors on the repository, add them to the [AUTHORS](AUTHORS) file.
 * Update the [ChangeLog](ChangeLog) with a brief summary of the changes introduced in the latest release.
 
 ### Creating a release
 
 * Use the [releases](https://github.com/linkml/linkml-runtime/releases) section of the Github interface to draft a new release.
-* Click on the *draft a new release* button. Annotate the release with a tag.
 * Conventionally tags are prefixed with `v` so choose an appropriately versioned tag number. Ex., `v1.1.9` and such.
 * Leave the default `main` branch as the target. Use the same tag number for the release title as well. After that, use Github's autogenerated CHANGELOG button to generate release notes. If it's possible to simplify the notes and make it more succinct, you should. 
 * Once a release is created, a [Github Action](.github/workflows/pypi-publish.yaml) will take care of publishing the package to PyPI for you.
@@ -89,7 +64,6 @@ All code added to the linkml-runtime source must have tests. The repo uses pytes
 
 You can run the test suite in the following way:
 
-
 ```
 poetry run python -m unittest discover
 ```

From b554c2e21dcc1277439b57b3f957eb8b4a2bc465 Mon Sep 17 00:00:00 2001
From: cmungall <cjm@berkeleybop.org>
Date: Fri, 14 Jan 2022 17:18:40 -0800
Subject: [PATCH 10/15] adding merge_imports fixing merge bug, fixes #566

---
 linkml_runtime/utils/schemaview.py  | 23 ++++++++++++++++++-----
 tests/test_utils/test_schemaview.py | 15 +++++++++++++++
 2 files changed, 33 insertions(+), 5 deletions(-)

diff --git a/linkml_runtime/utils/schemaview.py b/linkml_runtime/utils/schemaview.py
index 7e0e438b..aba7ff78 100644
--- a/linkml_runtime/utils/schemaview.py
+++ b/linkml_runtime/utils/schemaview.py
@@ -1204,19 +1204,32 @@ def merge_schema(self, schema: SchemaDefinition) -> None:
         dest = self.schema
         for k, v in schema.prefixes.items():
             if k not in dest.prefixes:
-                dest.prefixes[k] = copy(y)
+                dest.prefixes[k] = copy(v)
         for k, v in schema.classes.items():
             if k not in dest.classes:
-                dest.classes[k] = copy(y)
+                dest.classes[k] = copy(v)
         for k, v in schema.slots.items():
             if k not in dest.slots:
-                dest.slots[k] = copy(y)
+                dest.slots[k] = copy(v)
         for k, v in schema.types.items():
             if k not in dest.types:
-                dest.types[k] = copy(y)
+                dest.types[k] = copy(v)
         for k, v in schema.enums.items():
             if k not in dest.types:
-                dest.enums[k] = copy(y)
+                dest.enums[k] = copy(v)
+        self.set_modified()
+
+    def merge_imports(self):
+        """
+        Merges the full imports closure
+
+        :return:
+        """
+        schema = self.schema
+        to_merge = [s2 for s2 in self.all_schema(imports=True) if s2 != schema]
+        for s2 in to_merge:
+            self.merge_schema(s2)
+        schema.imports = []
         self.set_modified()
 
     def copy_schema(self, new_name: str = None) -> SchemaDefinition:
diff --git a/tests/test_utils/test_schemaview.py b/tests/test_utils/test_schemaview.py
index d50310a9..aeecdebf 100644
--- a/tests/test_utils/test_schemaview.py
+++ b/tests/test_utils/test_schemaview.py
@@ -1,6 +1,7 @@
 import os
 import unittest
 import logging
+from copy import copy
 
 from linkml_runtime.linkml_model.meta import SchemaDefinition, ClassDefinition, SlotDefinitionName, SlotDefinition
 from linkml_runtime.loaders.yaml_loader import YAMLLoader
@@ -274,6 +275,20 @@ def test_imports(self):
 
         assert view.get_uri('string') == 'xsd:string'
 
+    def test_merge_imports(self):
+        """
+        ensure merging and merging imports closure works
+        """
+        view = SchemaView(SCHEMA_WITH_IMPORTS)
+        all_c = copy(view.all_classes())
+        all_c_noi = copy(view.all_classes(imports=False))
+        assert len(all_c_noi) < len(all_c)
+        view.merge_imports()
+        all_c2 = copy(view.all_classes())
+        self.assertCountEqual(all_c, all_c2)
+        all_c2_noi = copy(view.all_classes(imports=False))
+        assert len(all_c2_noi) == len(all_c2)
+
     def test_slot_inheritance(self):
         schema = SchemaDefinition(id='test', name='test')
         view = SchemaView(schema)

From 38abf7a73ad902ae5bdaaacc09fcfcc768f48bba Mon Sep 17 00:00:00 2001
From: Sujay Patil <sujaysanjeev.patil@gmail.com>
Date: Fri, 21 Jan 2022 11:54:04 -0800
Subject: [PATCH 11/15] more details added to CONTRIBUTING.md

---
 CONTRIBUTING.md | 24 ++++++++++++++++--------
 1 file changed, 16 insertions(+), 8 deletions(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index edc7310d..44ccf156 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -1,6 +1,6 @@
 # Contribution Guidelines
 
-When contributing to this repository, please first discuss the change you wish to make via an issue, email, or any other method, with the owners of this repository before issuing a pull request.
+When contributing to this repository, please first discuss the changes you wish to make via an issue, email, or any other method, with the owners of this repository before issuing a pull request.
 
 ## How to contribute
 
@@ -13,6 +13,7 @@ You can use the [Issues](https://github.com/linkml/linkml-runtime/issues) tab to
 * Describe the behavior you observed after following the steps and point out what exactly is the problem with that behavior.
 * Explain which behavior you expected to see instead and why.
 * Provide screenshots of the expected or actual behaviour where applicable.
+* Tag the issue with appropriate label names. For ex., if your issue is about a bug that needs to be fixed in the repo, tag the issue with the `bug` label from the list of [labels](https://github.com/linkml/linkml-runtime/labels). If an appropriate label name doesn't exist, create one, with a name that clearly encapsulates the topic of the issue.
 
 ### The development lifecycle
 
@@ -23,7 +24,7 @@ You can use the [Issues](https://github.com/linkml/linkml-runtime/issues) tab to
 
 Note: All the development must be done on a branch on your fork.
 
-> An LBL engineer must review and accept your pull request. A code review (which happens with both the contributor and the reviewer present) is required for contributing.
+> A code review (which happens with both the contributor and the reviewer present) is required for contributing.
 
 ## Development environment setup
 
@@ -37,17 +38,24 @@ poetry install
 3. Run any python scripts or CLI commands by prefixing with `poetry run`.
 
 ```
-poetry run python your_script.py
-poetry run pytest
+poetry run python your_script.py  # ex of how to run standalone python script
+poetry run pytest # ex of how to invoke CLI tools
+```
+
+4. Refer to the poetry docs for details on how to use the [add](https://python-poetry.org/docs/cli/#add), [update](https://python-poetry.org/docs/cli/#update) and [remove](https://python-poetry.org/docs/cli/#remove) commands.
+
+### Creating `requirements.txt`
+
+To export the list of dependents from the `poetry.lock` file into a `requirements.txt` file, use the following command:
+
+```
+poetry export -f requirements.txt --output requirements.txt
 ```
 
 ## Release process
 
 Once the code has been merged into the `main` branch on this repo, there are a few steps that need to be completed to ensure a release is complete.
 
-* If there are any new authors on the repository, add them to the [AUTHORS](AUTHORS) file.
-* Update the [ChangeLog](ChangeLog) with a brief summary of the changes introduced in the latest release.
-
 ### Creating a release
 
 * Use the [releases](https://github.com/linkml/linkml-runtime/releases) section of the Github interface to draft a new release.
@@ -60,7 +68,7 @@ Once the code has been merged into the `main` branch on this repo, there are a f
 
 ## Testing
 
-All code added to the linkml-runtime source must have tests. The repo uses pytest to run tests. The test code is located in the tests subdirectory.
+All code added to the linkml-runtime source must have tests. The repo uses the native `unittest` module to run tests. The test code is located in the tests subdirectory.
 
 You can run the test suite in the following way:
 

From 5376550729899814d4ce2e04ed4ceb32221e3a2a Mon Sep 17 00:00:00 2001
From: Sujay Patil <sujaysanjeev.patil@gmail.com>
Date: Fri, 21 Jan 2022 11:58:55 -0800
Subject: [PATCH 12/15] sync poetry.lock with deps listed in pyproject.toml

---
 poetry.lock | 145 +++++++++++++++++++++++++++-------------------------
 1 file changed, 74 insertions(+), 71 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 35a7cd9e..ac71e9da 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -8,17 +8,17 @@ python-versions = "*"
 
 [[package]]
 name = "attrs"
-version = "21.2.0"
+version = "21.4.0"
 description = "Classes Without Boilerplate"
 category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [package.extras]
-dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit"]
+dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"]
 docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"]
-tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface"]
-tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins"]
+tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "cloudpickle"]
+tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "cloudpickle"]
 
 [[package]]
 name = "cachetools"
@@ -38,7 +38,7 @@ python-versions = "*"
 
 [[package]]
 name = "charset-normalizer"
-version = "2.0.9"
+version = "2.0.10"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 category = "main"
 optional = false
@@ -94,7 +94,7 @@ dev = ["tox", "bump2version (<1)", "sphinx (<2)", "importlib-metadata (<3)", "im
 
 [[package]]
 name = "frozendict"
-version = "2.1.2"
+version = "2.2.0"
 description = "A simple immutable dictionary"
 category = "main"
 optional = false
@@ -118,20 +118,18 @@ python-versions = ">=3.5"
 
 [[package]]
 name = "importlib-metadata"
-version = "4.10.0"
+version = "1.7.0"
 description = "Read metadata from Python packages"
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
 
 [package.dependencies]
-typing-extensions = {version = ">=3.6.4", markers = "python_version < \"3.8\""}
 zipp = ">=0.5"
 
 [package.extras]
-docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
-perf = ["ipython"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"]
+docs = ["sphinx", "rst.linker"]
+testing = ["packaging", "pep517", "importlib-resources (>=1.3)"]
 
 [[package]]
 name = "importlib-resources"
@@ -195,7 +193,7 @@ hbreader = "*"
 
 [[package]]
 name = "jsonschema"
-version = "4.3.2"
+version = "4.4.0"
 description = "An implementation of JSON Schema validation for Python"
 category = "main"
 optional = false
@@ -274,7 +272,7 @@ requests = ["requests"]
 
 [[package]]
 name = "pyparsing"
-version = "3.0.6"
+version = "3.0.7"
 description = "Python parsing module"
 category = "main"
 optional = false
@@ -285,11 +283,11 @@ diagrams = ["jinja2", "railroad-diagrams"]
 
 [[package]]
 name = "pyrsistent"
-version = "0.18.0"
+version = "0.18.1"
 description = "Persistent/Functional/Immutable data structures"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [[package]]
 name = "pyyaml"
@@ -355,7 +353,7 @@ rdflib-jsonld = "0.6.1"
 
 [[package]]
 name = "requests"
-version = "2.26.0"
+version = "2.27.1"
 description = "Python HTTP for Humans."
 category = "main"
 optional = false
@@ -413,7 +411,7 @@ python-versions = ">=3.6"
 
 [[package]]
 name = "urllib3"
-version = "1.26.7"
+version = "1.26.8"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 category = "main"
 optional = false
@@ -434,28 +432,28 @@ python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
 
 [[package]]
 name = "zipp"
-version = "3.6.0"
+version = "3.7.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.extras]
 docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
-testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy"]
 
 [metadata]
 lock-version = "1.1"
 python-versions = "^3.7.1"
-content-hash = "d990cd7da3ae0810757f84a56f3cdddeaec07f7bfff8444d4e843fae0e3679f7"
+content-hash = "3dffa1bd32739026ff1c5b1cadb71ed9dcb7122ca0e5f3926d618fd10a0d17d9"
 
 [metadata.files]
 antlr4-python3-runtime = [
     {file = "antlr4-python3-runtime-4.9.3.tar.gz", hash = "sha256:f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b"},
 ]
 attrs = [
-    {file = "attrs-21.2.0-py2.py3-none-any.whl", hash = "sha256:149e90d6d8ac20db7a955ad60cf0e6881a3f20d37096140088356da6c716b0b1"},
-    {file = "attrs-21.2.0.tar.gz", hash = "sha256:ef6aaac3ca6cd92904cdd0d83f629a15f18053ec84e6432106f7a4d04ae4f5fb"},
+    {file = "attrs-21.4.0-py2.py3-none-any.whl", hash = "sha256:2d27e3784d7a565d36ab851fe94887c5eccd6a463168875832a1be79c82828b4"},
+    {file = "attrs-21.4.0.tar.gz", hash = "sha256:626ba8234211db98e869df76230a137c4c40a12d72445c45d5f5b716f076e2fd"},
 ]
 cachetools = [
     {file = "cachetools-5.0.0-py3-none-any.whl", hash = "sha256:8fecd4203a38af17928be7b90689d8083603073622229ca7077b72d8e5a976e4"},
@@ -466,8 +464,8 @@ certifi = [
     {file = "certifi-2021.10.8.tar.gz", hash = "sha256:78884e7c1d4b00ce3cea67b44566851c4343c120abd683433ce934a68ea58872"},
 ]
 charset-normalizer = [
-    {file = "charset-normalizer-2.0.9.tar.gz", hash = "sha256:b0b883e8e874edfdece9c28f314e3dd5badf067342e42fb162203335ae61aa2c"},
-    {file = "charset_normalizer-2.0.9-py3-none-any.whl", hash = "sha256:1eecaa09422db5be9e29d7fc65664e6c33bd06f9ced7838578ba40d58bdf3721"},
+    {file = "charset-normalizer-2.0.10.tar.gz", hash = "sha256:876d180e9d7432c5d1dfd4c5d26b72f099d503e8fcc0feb7532c9289be60fcbd"},
+    {file = "charset_normalizer-2.0.10-py3-none-any.whl", hash = "sha256:cb957888737fc0bbcd78e3df769addb41fd1ff8cf950dc9e7ad7793f1bf44455"},
 ]
 click = [
     {file = "click-8.0.3-py3-none-any.whl", hash = "sha256:353f466495adaeb40b6b5f592f9f91cb22372351c84caeb068132442a4518ef3"},
@@ -531,18 +529,23 @@ deprecated = [
     {file = "Deprecated-1.2.13.tar.gz", hash = "sha256:43ac5335da90c31c24ba028af536a91d41d53f9e6901ddb021bcc572ce44e38d"},
 ]
 frozendict = [
-    {file = "frozendict-2.1.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:3cbb8bd5ddbdd1db1caa670586b50f9e665e60b1c095add5aa04d9e2bedf5f00"},
-    {file = "frozendict-2.1.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:513a3f3a8ff2767492570c78c158845a1cc7b4c954fc9f78ed313b2463727cae"},
-    {file = "frozendict-2.1.2-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:3b4ac7aafd613959a055818c3e9844822196c874b9c8bf118b6c1419ff1fbbdc"},
-    {file = "frozendict-2.1.2-cp36-cp36m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:bb1ebca998c68c3bf28ce70f14a392431bbe01bfa610e3e9e635176d9ecbba71"},
-    {file = "frozendict-2.1.2-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:c0e09b7159fee7c6dafd727dec2ea7a135f47458dd3996705f9a64e3fca3bf73"},
-    {file = "frozendict-2.1.2-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:79666516d594ced95a294869988dba2daff89d9d274061f7138e1c49e49428ce"},
-    {file = "frozendict-2.1.2-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:3cdc8602e398d28887484226a493ae6e96ff3532b4368d4d49ab96c5ee7eb61d"},
-    {file = "frozendict-2.1.2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:2cfe6d89d2af7b97726a5f789d73b5298eb067a9348a8cc8f0834fdc5349b125"},
-    {file = "frozendict-2.1.2-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:afaaa4fc0343af15f1153d9e09660f6c388ab1d6d01147bbd7f7979e723258df"},
-    {file = "frozendict-2.1.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:f45f7a724e93653f0d446e0cc99e09bda4835f16de08eb1de3b007537e18daa1"},
-    {file = "frozendict-2.1.2-py3-none-any.whl", hash = "sha256:a0650a673ce6e320e8b25a38f4620f42382c081b2088051c81073a67f14bac32"},
-    {file = "frozendict-2.1.2.tar.gz", hash = "sha256:2eb92fbe8dde37075ed0e5dd3dac88a850a04ccfc646d20f3412b72220ddbaf2"},
+    {file = "frozendict-2.2.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:b39cfcf563b3432d4780bf15769e2de2a2906c46c26fb73a9582b69142621814"},
+    {file = "frozendict-2.2.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:e7198dda9741f3da79db952ecd27607d836727ed320f29438eac565133008c8c"},
+    {file = "frozendict-2.2.0-cp310-cp310-win_amd64.whl", hash = "sha256:3a564bd93767044e740e0f6c59606cf612a143160ace9d2c047c4a297a74329a"},
+    {file = "frozendict-2.2.0-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:2a47f3f7fe52094904777d29f300ad6c11213dd81a8fbdec96aa2d4763104319"},
+    {file = "frozendict-2.2.0-cp36-cp36m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:2bfacb9f75768903495747ddaacb1bf98738fb3e966a27f0627f7f163fd676eb"},
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+    {file = "frozendict-2.2.0-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:722e915421b2d869b236d8de8e0ab42f1e2f7e12d670f9bc3dedfc055550bcb9"},
+    {file = "frozendict-2.2.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:4519f6eb661f268c60a3ea14f000d321159cf5e6db397129ea4921aef3bf2173"},
+    {file = "frozendict-2.2.0-cp37-cp37m-win_amd64.whl", hash = "sha256:9c720e4a19e9b5f48d1b12e193d39765898dff4952320251c0ccd9960631cae9"},
+    {file = "frozendict-2.2.0-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:1708828a3fed512ea8fa18e75622b29e551a5524c14aea0b0364f4472ca15f7d"},
+    {file = "frozendict-2.2.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:ede1bc6b6d734ba36bdcd99659463d96620069281e6bb6f72cbed719d679c1bb"},
+    {file = "frozendict-2.2.0-cp38-cp38-win_amd64.whl", hash = "sha256:f6293ec3181ff98e5ae98f748e8ffe6c937caf14ca9561d3a6d6d02a82c7fbff"},
+    {file = "frozendict-2.2.0-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:ebf36b78ce0a43f7372e94eee8b0327a12c15914e1a29c088f9bcfba20971929"},
+    {file = "frozendict-2.2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:e237adae46cc28eb0355f6d65900e946c0a7bc4536145c6d8e6bbb2b6c28ac2a"},
+    {file = "frozendict-2.2.0-cp39-cp39-win_amd64.whl", hash = "sha256:14ab850309632198b28e74948b800ac75609380a6f779a5779482a3189af7299"},
+    {file = "frozendict-2.2.0-py3-none-any.whl", hash = "sha256:a6d56ec83e5120f273adbf7f3798f78e8775158eee95469cd66e2e28be153ee3"},
+    {file = "frozendict-2.2.0.tar.gz", hash = "sha256:8e3d4735f9a13d1077567e568471663f3244f85ac89b23f8cb31cf231dbe45b9"},
 ]
 hbreader = [
     {file = "hbreader-0.9.1-py3-none-any.whl", hash = "sha256:9a6e76c9d1afc1b977374a5dc430a1ebb0ea0488205546d4678d6e31cc5f6801"},
@@ -553,8 +556,8 @@ idna = [
     {file = "idna-3.3.tar.gz", hash = "sha256:9d643ff0a55b762d5cdb124b8eaa99c66322e2157b69160bc32796e824360e6d"},
 ]
 importlib-metadata = [
-    {file = "importlib_metadata-4.10.0-py3-none-any.whl", hash = "sha256:b7cf7d3fef75f1e4c80a96ca660efbd51473d7e8f39b5ab9210febc7809012a4"},
-    {file = "importlib_metadata-4.10.0.tar.gz", hash = "sha256:92a8b58ce734b2a4494878e0ecf7d79ccd7a128b5fc6014c401e0b61f006f0f6"},
+    {file = "importlib_metadata-1.7.0-py2.py3-none-any.whl", hash = "sha256:dc15b2969b4ce36305c51eebe62d418ac7791e9a157911d58bfb1f9ccd8e2070"},
+    {file = "importlib_metadata-1.7.0.tar.gz", hash = "sha256:90bb658cdbbf6d1735b6341ce708fc7024a3e14e99ffdc5783edea9f9b077f83"},
 ]
 importlib-resources = [
     {file = "importlib_resources-5.4.0-py3-none-any.whl", hash = "sha256:33a95faed5fc19b4bc16b29a6eeae248a3fe69dd55d4d229d2b480e23eeaad45"},
@@ -577,8 +580,8 @@ jsonasobj2 = [
     {file = "jsonasobj2-1.0.4.tar.gz", hash = "sha256:f50b1668ef478004aa487b2d2d094c304e5cb6b79337809f4a1f2975cc7fbb4e"},
 ]
 jsonschema = [
-    {file = "jsonschema-4.3.2-py3-none-any.whl", hash = "sha256:8697a10a5a5edc922d2eb8556c7f35e814436f3ed8278ec2f65d40e9312d7c80"},
-    {file = "jsonschema-4.3.2.tar.gz", hash = "sha256:cca171fb7544de15ccda236bf78d58434d769c9a2ce21d44e0d209e39eeb8876"},
+    {file = "jsonschema-4.4.0-py3-none-any.whl", hash = "sha256:77281a1f71684953ee8b3d488371b162419767973789272434bbc3f29d9c8823"},
+    {file = "jsonschema-4.4.0.tar.gz", hash = "sha256:636694eb41b3535ed608fe04129f26542b59ed99808b4f688aa32dcf55317a83"},
 ]
 lxml = [
     {file = "lxml-4.7.1-cp27-cp27m-macosx_10_14_x86_64.whl", hash = "sha256:d546431636edb1d6a608b348dd58cc9841b81f4116745857b6cb9f8dadb2725f"},
@@ -655,31 +658,31 @@ pyldmod = [
     {file = "PyLDmod-2.0.5.tar.gz", hash = "sha256:afe7515a4c2b53bbff436c93af128599b4f52791cc71e34baecb7662c694feed"},
 ]
 pyparsing = [
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-    {file = "pyparsing-3.0.6.tar.gz", hash = "sha256:d9bdec0013ef1eb5a84ab39a3b3868911598afa494f5faa038647101504e2b81"},
+    {file = "pyparsing-3.0.7-py3-none-any.whl", hash = "sha256:a6c06a88f252e6c322f65faf8f418b16213b51bdfaece0524c1c1bc30c63c484"},
+    {file = "pyparsing-3.0.7.tar.gz", hash = "sha256:18ee9022775d270c55187733956460083db60b37d0d0fb357445f3094eed3eea"},
 ]
 pyrsistent = [
-    {file = "pyrsistent-0.18.0-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:f4c8cabb46ff8e5d61f56a037974228e978f26bfefce4f61a4b1ac0ba7a2ab72"},
-    {file = "pyrsistent-0.18.0-cp36-cp36m-manylinux1_i686.whl", hash = "sha256:da6e5e818d18459fa46fac0a4a4e543507fe1110e808101277c5a2b5bab0cd2d"},
-    {file = "pyrsistent-0.18.0-cp36-cp36m-manylinux1_x86_64.whl", hash = "sha256:5e4395bbf841693eaebaa5bb5c8f5cdbb1d139e07c975c682ec4e4f8126e03d2"},
-    {file = "pyrsistent-0.18.0-cp36-cp36m-win32.whl", hash = "sha256:527be2bfa8dc80f6f8ddd65242ba476a6c4fb4e3aedbf281dfbac1b1ed4165b1"},
-    {file = "pyrsistent-0.18.0-cp36-cp36m-win_amd64.whl", hash = "sha256:2aaf19dc8ce517a8653746d98e962ef480ff34b6bc563fc067be6401ffb457c7"},
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+    {file = "pyrsistent-0.18.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:6bc66318fb7ee012071b2792024564973ecc80e9522842eb4e17743604b5e045"},
+    {file = "pyrsistent-0.18.1-cp39-cp39-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:914474c9f1d93080338ace89cb2acee74f4f666fb0424896fcfb8d86058bf17c"},
+    {file = "pyrsistent-0.18.1-cp39-cp39-win32.whl", hash = "sha256:1b34eedd6812bf4d33814fca1b66005805d3640ce53140ab8bbb1e2651b0d9bc"},
+    {file = "pyrsistent-0.18.1-cp39-cp39-win_amd64.whl", hash = "sha256:e24a828f57e0c337c8d8bb9f6b12f09dfdf0273da25fda9e314f0b684b415a07"},
+    {file = "pyrsistent-0.18.1.tar.gz", hash = "sha256:d4d61f8b993a7255ba714df3aca52700f8125289f84f704cf80916517c46eb96"},
 ]
 pyyaml = [
     {file = "PyYAML-5.4.1-cp27-cp27m-macosx_10_9_x86_64.whl", hash = "sha256:3b2b1824fe7112845700f815ff6a489360226a5609b96ec2190a45e62a9fc922"},
@@ -729,8 +732,8 @@ rdflib-shim = [
     {file = "rdflib_shim-1.0.3.tar.gz", hash = "sha256:d955d11e2986aab42b6830ca56ac6bc9c893abd1d049a161c6de2f1b99d4fc0d"},
 ]
 requests = [
-    {file = "requests-2.26.0-py2.py3-none-any.whl", hash = "sha256:6c1246513ecd5ecd4528a0906f910e8f0f9c6b8ec72030dc9fd154dc1a6efd24"},
-    {file = "requests-2.26.0.tar.gz", hash = "sha256:b8aa58f8cf793ffd8782d3d8cb19e66ef36f7aba4353eec859e74678b01b07a7"},
+    {file = "requests-2.27.1-py2.py3-none-any.whl", hash = "sha256:f22fa1e554c9ddfd16e6e41ac79759e17be9e492b3587efa038054674760e72d"},
+    {file = "requests-2.27.1.tar.gz", hash = "sha256:68d7c56fd5a8999887728ef304a6d12edc7be74f1cfa47714fc8b414525c9a61"},
 ]
 shexjsg = [
     {file = "ShExJSG-0.8.1-py2.py3-none-any.whl", hash = "sha256:33749e8c90a30cca2cb6e23f94268bed5217a6f7c04d584e64fcb6869b60972b"},
@@ -749,8 +752,8 @@ typing-extensions = [
     {file = "typing_extensions-4.0.1.tar.gz", hash = "sha256:4ca091dea149f945ec56afb48dae714f21e8692ef22a395223bcd328961b6a0e"},
 ]
 urllib3 = [
-    {file = "urllib3-1.26.7-py2.py3-none-any.whl", hash = "sha256:c4fdf4019605b6e5423637e01bc9fe4daef873709a7973e195ceba0a62bbc844"},
-    {file = "urllib3-1.26.7.tar.gz", hash = "sha256:4987c65554f7a2dbf30c18fd48778ef124af6fab771a377103da0585e2336ece"},
+    {file = "urllib3-1.26.8-py2.py3-none-any.whl", hash = "sha256:000ca7f471a233c2251c6c7023ee85305721bfdf18621ebff4fd17a8653427ed"},
+    {file = "urllib3-1.26.8.tar.gz", hash = "sha256:0e7c33d9a63e7ddfcb86780aac87befc2fbddf46c58dbb487e0855f7ceec283c"},
 ]
 wrapt = [
     {file = "wrapt-1.13.3-cp27-cp27m-macosx_10_9_x86_64.whl", hash = "sha256:e05e60ff3b2b0342153be4d1b597bbcfd8330890056b9619f4ad6b8d5c96a81a"},
@@ -806,6 +809,6 @@ wrapt = [
     {file = "wrapt-1.13.3.tar.gz", hash = "sha256:1fea9cd438686e6682271d36f3481a9f3636195578bab9ca3382e2f5f01fc185"},
 ]
 zipp = [
-    {file = "zipp-3.6.0-py3-none-any.whl", hash = "sha256:9fe5ea21568a0a70e50f273397638d39b03353731e6cbbb3fd8502a33fec40bc"},
-    {file = "zipp-3.6.0.tar.gz", hash = "sha256:71c644c5369f4a6e07636f0aa966270449561fcea2e3d6747b8d23efaa9d7832"},
+    {file = "zipp-3.7.0-py3-none-any.whl", hash = "sha256:b47250dd24f92b7dd6a0a8fc5244da14608f3ca90a5efcd37a3b1642fac9a375"},
+    {file = "zipp-3.7.0.tar.gz", hash = "sha256:9f50f446828eb9d45b267433fd3e9da8d801f614129124863f9c51ebceafb87d"},
 ]

From 9bafb8550334a28a57dbd4821e53661cfee7b50e Mon Sep 17 00:00:00 2001
From: Sujay Patil <sujaysanjeev.patil@gmail.com>
Date: Fri, 21 Jan 2022 12:02:05 -0800
Subject: [PATCH 13/15] remove redundant AUTHORS and ChangeLog files

---
 AUTHORS   |   6 --
 ChangeLog | 237 ------------------------------------------------------
 2 files changed, 243 deletions(-)
 delete mode 100644 AUTHORS
 delete mode 100644 ChangeLog

diff --git a/AUTHORS b/AUTHORS
deleted file mode 100644
index d4b9c822..00000000
--- a/AUTHORS
+++ /dev/null
@@ -1,6 +0,0 @@
-Chris Mungall <cjm@berkeleybop.org>
-Gaurav Vaidya <gaurav@ggvaidya.com>
-GitHub Action <action@github.com>
-Harold Solbrig <solbrig@jhu.edu>
-cmungall <cjm@berkeleybop.org>
-hsolbrig <solbrig@jhu.edu>
diff --git a/ChangeLog b/ChangeLog
deleted file mode 100644
index 86f50c2d..00000000
--- a/ChangeLog
+++ /dev/null
@@ -1,237 +0,0 @@
-CHANGES
-=======
-
-v1.1.10
--------
-* Extended SchemaUsage to include inferred slot
-* Minor README changes
-* Added binder badge
-* Added poetry support to the repository
-
-v1.1.9
-------
-* Same as v1.1.8
-
-v1.1.8
-------
-* Returned class names by all_class() should match name in Python dataclass
-* SchemaView rdflib loader methods
-* Fixed get_mapping_index method
-* Added inverse and is_mixin methods
-* Added function to return schema elements by id_prefixes
-
-v1.1.7
-------
-* Added flag for unmappable rdf predicates
-* Fixed propagation over slot_usage
-
-v1.1.6
-------
-* Added support for rdfs:Resource as a type uri
-
-v1.1.5
-------
-* Hotfixes to conditional rules released as part of v1.1.4
-
-v1.1.4
-------
-* Added simple set of conditional rules that apply to instances of classes
-
-v1.1.3
-------
-* Bugfix in utils.comparefiles: detecting missing files
-* Ensured get_uri is populated for attributes Ensuring fresh copy of induced slot
-* Added makefile to sync linkml-model
-* Added method to SchemaView to get descendants of a slot
-* New rdf dumper - bypasses existing jsonld based method and does a direct conversion from elements to rdflib
-
-v1.1.2
-------
-* Added deduplication functionality for enums
-* Added click cli for SchemaView
-
-v1.1.1
-------
-* Exclude tombstoned rdflib-jsonld
-
-v1.1.0
-------
-* Fixed serialization of enums in json_dumper
-
-v1.0.16
--------
-* Fix for induced_slot() returning incorrect range
-
-v1.0.15
--------
-* Bumped json-flattener requirement
-* Added param to schemaview traversal methods to control traversal over is_a
-* Added more tests for schemaview
-
-v1.0.14
--------
-* Added inject_type to as_json_object to optionally suppress `@type` declarations
-* Added csv loaders and dumpers to runtime, fixes  linkml/linkml-csv#1
-* Additional methods in schemaview
-  * get_identifier
-  * is_inlined
-
-v1.0.13
--------
-
-* Added new module: schemaviews
-  * Dynamic inferred views over schemas
-  * See [examples](https://github.com/linkml/linkml-runtime/tree/main/notebooks)
-* Replace hyphen with underscore when underscoring names
-* Incorporates 1.0.4 metamodel
-
-v1.0.12
--------
-
-* Added leaf/root methods
-* Added additional methods
-* Adding more examples
-* Adding a new library schemaview
-* replace hyphen with underscore when underscoring names
-* Add the actual test to the pull request action
-
-v1.0.11
--------
-
-* Update test\_issue\_368\_enums.py
-* Try relative paths on linkml\_runtime/linkml\_model/\_\_init\_\_.py
-* Add publish step to update AUTHORS and ChangeLog
-* Test change on AUTHORS
-* Update to copy of linkml-model 1.0.1
-* Replaced \_\_str\_\_() repr of EnumDefinitionImpl
-* Fix syntax for pr-test version in github actions
-* Add a couple more unit tests
-* Further fixes for issue #12.  Introduce \`remove\_empty\_items\` into all dumpers
-* Fix for issue #12
-* Loader now takes root lists
-
-v1.0.10
--------
-
-* Fix an omission on inline generation
-
-v1.0.9
-------
-
-* Sync generated files
-* Add MissingRequiredField to YAMLRoot
-* Phase 1 in adding MissingRequiredField intercept
-* Update main.yaml
-
-v1.0.8
-------
-
-* Fix import error
-* Add sequential dependencies to build process
-* Update Pipfile
-
-v1.0.7
-------
-
-* Automatically generated requirements.txt and requirements-dev.txt
-* Fix for issue #6
-* Automatically generated requirements.txt and requirements-dev.txt
-* Fix issue #3
-
-v1.0.6
-------
-
-* Update json\_loader.py
-* Added notes in Pipfile for next steps
-* Fixing URL for github issue
-
-v1.0.5
-------
-
-* Include JSON-LD files as well for RDF transformations
-
-v1.0.4
-------
-
-* Include yaml files in linkml\_model cpy
-* Another (last) brute force attempt to get rid of pyld
-* Add test for issue #3
-
-v1.0.3
-------
-
-* Changelog
-* Fixed import statement mystery
-* Update w/ solo strings issue
-
-v1.0.2
-------
-
-* One last attempt to brute force this whole thing..
-* Automatically generated requirements.txt and requirements-dev.txt
-* Change dependency to rdflib-pyldmod-compat
-* Trying to force pyld out of the picture (!)
-* Force pyldmod install
-* Create a local image of linkml-model
-* Added \_is\_empty function to YAMLRoot
-
-v1.0.1
-------
-
-* Automatically generated requirements.txt and requirements-dev.txt
-* Switch to jsonasobj2 and pyldmod
-
-v1.0.0
-------
-
-* Fix an issue where the json\_dumper didn't handle contexts correctly
-
-v0.1.6
-------
-
-* Redirect the old \`\_normalize\_inlined\` function to the new code
-* Update readme to have badges
-
-v0.1.5
-------
-
-* Remove all dependencies on linkml\_model with the exception of the unit tests
-* Temporarily fix linkml\_model references
-* Revised form of inlined\_as\_list now operational
-* Add two new test files
-* \_normalize\_inlined\_as\_dict is now working
-* Automatically generated requirements.txt and requirements-dev.txt
-* Tweaks to recognize that JsonObj's are actually dicts but can't claim to be an instance of them
-
-v0.1.4
-------
-
-* Re-add shex\_results\_as\_string to formatutils.py
-
-v0.1.3
-------
-
-* Automatically generated requirements.txt and requirements-dev.txt
-* Py 3.7 compatibility
-
-v0.1.2
-------
-
-* Automatically generated requirements.txt and requirements-dev.txt
-* Switch to a better behaved jsonasobj
-
-v0.1.1
-------
-
-* Automated adding outputs from tests
-* v0.1.0 tag
-
-v0.1.0
-------
-
-* Automatically generated requirements.txt and requirements-dev.txt
-* Should be in good enough shape to be used in the <app>-model package
-* Checkpoint
-* Update ignore
-* checkpoint
-* Initial commit

From 6ec31b3542be8f3a176b818a29c5b0725736f058 Mon Sep 17 00:00:00 2001
From: cmungall <cjm@berkeleybop.org>
Date: Mon, 24 Jan 2022 12:24:53 -0800
Subject: [PATCH 14/15] using logging not print

---
 linkml_runtime/loaders/json_loader.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/linkml_runtime/loaders/json_loader.py b/linkml_runtime/loaders/json_loader.py
index a4d2c050..2a3e3ac4 100644
--- a/linkml_runtime/loaders/json_loader.py
+++ b/linkml_runtime/loaders/json_loader.py
@@ -1,4 +1,5 @@
 import json
+import logging
 from typing import Union, TextIO, Optional, Dict, Type
 
 from hbreader import FileInfo
@@ -15,8 +16,7 @@ def loader(data: Union[str, dict], _: FileInfo) -> Optional[Dict]:
             data_as_dict = json.loads(data) if isinstance(data, str) else data
             typ = data_as_dict.pop('@type', None)
             if typ and typ != target_class.__name__:
-                # TODO: connect this up with the logging facility or warning?
-                print(f"Warning: input type mismatch. Expected: {target_class.__name__}, Actual: {typ}")
+                logging.warning(f"Warning: input type mismatch. Expected: {target_class.__name__}, Actual: {typ}")
             return self.json_clean(data_as_dict)
 
         if not metadata:

From 75b6b49ededc9bae214e62c73a4e318525d9c5b9 Mon Sep 17 00:00:00 2001
From: Sujay Patil <sujaysanjeev.patil@gmail.com>
Date: Mon, 24 Jan 2022 14:22:41 -0800
Subject: [PATCH 15/15] fix poetry files that are causing Actions to error out

---
 poetry.lock    | 317 +++++++++++++++++++++++++++----------------------
 pyproject.toml |   8 +-
 2 files changed, 178 insertions(+), 147 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index cda2c0e6..ac71e9da 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -8,25 +8,25 @@ python-versions = "*"
 
 [[package]]
 name = "attrs"
-version = "21.2.0"
+version = "21.4.0"
 description = "Classes Without Boilerplate"
 category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [package.extras]
-dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit"]
+dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"]
 docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"]
-tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface"]
-tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins"]
+tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "cloudpickle"]
+tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "cloudpickle"]
 
 [[package]]
 name = "cachetools"
-version = "4.2.4"
+version = "5.0.0"
 description = "Extensible memoizing collections and decorators"
 category = "main"
 optional = false
-python-versions = "~=3.5"
+python-versions = "~=3.7"
 
 [[package]]
 name = "certifi"
@@ -38,7 +38,7 @@ python-versions = "*"
 
 [[package]]
 name = "charset-normalizer"
-version = "2.0.9"
+version = "2.0.10"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 category = "main"
 optional = false
@@ -94,7 +94,7 @@ dev = ["tox", "bump2version (<1)", "sphinx (<2)", "importlib-metadata (<3)", "im
 
 [[package]]
 name = "frozendict"
-version = "2.1.1"
+version = "2.2.0"
 description = "A simple immutable dictionary"
 category = "main"
 optional = false
@@ -118,20 +118,18 @@ python-versions = ">=3.5"
 
 [[package]]
 name = "importlib-metadata"
-version = "4.8.2"
+version = "1.7.0"
 description = "Read metadata from Python packages"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
 
 [package.dependencies]
-typing-extensions = {version = ">=3.6.4", markers = "python_version < \"3.8\""}
 zipp = ">=0.5"
 
 [package.extras]
-docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
-perf = ["ipython"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"]
+docs = ["sphinx", "rst.linker"]
+testing = ["packaging", "pep517", "importlib-resources (>=1.3)"]
 
 [[package]]
 name = "importlib-resources"
@@ -150,7 +148,7 @@ testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-
 
 [[package]]
 name = "isodate"
-version = "0.6.0"
+version = "0.6.1"
 description = "An ISO 8601 date/time/duration parser and formatter"
 category = "main"
 optional = false
@@ -195,7 +193,7 @@ hbreader = "*"
 
 [[package]]
 name = "jsonschema"
-version = "4.2.1"
+version = "4.4.0"
 description = "An implementation of JSON Schema validation for Python"
 category = "main"
 optional = false
@@ -206,6 +204,7 @@ attrs = ">=17.4.0"
 importlib-metadata = {version = "*", markers = "python_version < \"3.8\""}
 importlib-resources = {version = ">=1.4.0", markers = "python_version < \"3.9\""}
 pyrsistent = ">=0.14.0,<0.17.0 || >0.17.0,<0.17.1 || >0.17.1,<0.17.2 || >0.17.2"
+typing-extensions = {version = "*", markers = "python_version < \"3.8\""}
 
 [package.extras]
 format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"]
@@ -213,7 +212,7 @@ format_nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-
 
 [[package]]
 name = "lxml"
-version = "4.6.4"
+version = "4.7.1"
 description = "Powerful and Pythonic XML processing library combining libxml2/libxslt with the ElementTree API."
 category = "main"
 optional = false
@@ -242,7 +241,7 @@ test = ["pytest"]
 
 [[package]]
 name = "pyjsg"
-version = "0.11.6"
+version = "0.11.9"
 description = "Python JSON Schema Grammar interpreter"
 category = "main"
 optional = false
@@ -273,7 +272,7 @@ requests = ["requests"]
 
 [[package]]
 name = "pyparsing"
-version = "3.0.6"
+version = "3.0.7"
 description = "Python parsing module"
 category = "main"
 optional = false
@@ -284,11 +283,11 @@ diagrams = ["jinja2", "railroad-diagrams"]
 
 [[package]]
 name = "pyrsistent"
-version = "0.18.0"
+version = "0.18.1"
 description = "Persistent/Functional/Immutable data structures"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [[package]]
 name = "pyyaml"
@@ -300,22 +299,21 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
 
 [[package]]
 name = "rdflib"
-version = "5.0.0"
+version = "6.1.1"
 description = "RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information."
 category = "main"
 optional = false
-python-versions = "*"
+python-versions = ">=3.7"
 
 [package.dependencies]
+importlib-metadata = {version = "*", markers = "python_version < \"3.8.0\""}
 isodate = "*"
 pyparsing = "*"
-six = "*"
 
 [package.extras]
-docs = ["sphinx (<3)", "sphinxcontrib-apidoc"]
+docs = ["sphinx (<5)", "sphinxcontrib-apidoc"]
 html = ["html5lib"]
-sparql = ["requests"]
-tests = ["html5lib", "networkx", "nose", "doctest-ignore-unicode"]
+tests = ["berkeleydb", "html5lib", "networkx", "pytest", "pytest-cov", "pytest-subtests"]
 
 [[package]]
 name = "rdflib-jsonld"
@@ -341,9 +339,21 @@ pyldmod = "*"
 rdflib = ">=4.2.0"
 testfixtures = "*"
 
+[[package]]
+name = "rdflib-shim"
+version = "1.0.3"
+description = "Shim for rdflib 5 and 6 incompatibilities"
+category = "main"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+rdflib = ">=5.0.0"
+rdflib-jsonld = "0.6.1"
+
 [[package]]
 name = "requests"
-version = "2.26.0"
+version = "2.27.1"
 description = "Python HTTP for Humans."
 category = "main"
 optional = false
@@ -361,14 +371,14 @@ use_chardet_on_py3 = ["chardet (>=3.0.2,<5)"]
 
 [[package]]
 name = "shexjsg"
-version = "0.7.1"
+version = "0.8.1"
 description = "ShExJSG - Astract Syntax Tree for the ShEx 2.0 language"
 category = "main"
 optional = false
 python-versions = "*"
 
 [package.dependencies]
-pyjsg = ">=0.11.5"
+pyjsg = ">=0.11.9"
 
 [[package]]
 name = "six"
@@ -401,7 +411,7 @@ python-versions = ">=3.6"
 
 [[package]]
 name = "urllib3"
-version = "1.26.7"
+version = "1.26.8"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 category = "main"
 optional = false
@@ -422,40 +432,40 @@ python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
 
 [[package]]
 name = "zipp"
-version = "3.6.0"
+version = "3.7.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.extras]
 docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
-testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy"]
 
 [metadata]
 lock-version = "1.1"
 python-versions = "^3.7.1"
-content-hash = "85b3ecabe64aa1a5973ddf4b2ea232cccd7f1b71b57d54b719a4316a3d1d6ac7"
+content-hash = "3dffa1bd32739026ff1c5b1cadb71ed9dcb7122ca0e5f3926d618fd10a0d17d9"
 
 [metadata.files]
 antlr4-python3-runtime = [
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 ]
 attrs = [
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-    {file = "attrs-21.2.0.tar.gz", hash = "sha256:ef6aaac3ca6cd92904cdd0d83f629a15f18053ec84e6432106f7a4d04ae4f5fb"},
+    {file = "attrs-21.4.0-py2.py3-none-any.whl", hash = "sha256:2d27e3784d7a565d36ab851fe94887c5eccd6a463168875832a1be79c82828b4"},
+    {file = "attrs-21.4.0.tar.gz", hash = "sha256:626ba8234211db98e869df76230a137c4c40a12d72445c45d5f5b716f076e2fd"},
 ]
 cachetools = [
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-    {file = "cachetools-4.2.4.tar.gz", hash = "sha256:89ea6f1b638d5a73a4f9226be57ac5e4f399d22770b92355f92dcb0f7f001693"},
+    {file = "cachetools-5.0.0-py3-none-any.whl", hash = "sha256:8fecd4203a38af17928be7b90689d8083603073622229ca7077b72d8e5a976e4"},
+    {file = "cachetools-5.0.0.tar.gz", hash = "sha256:486471dfa8799eb7ec503a8059e263db000cdda20075ce5e48903087f79d5fd6"},
 ]
 certifi = [
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     {file = "certifi-2021.10.8.tar.gz", hash = "sha256:78884e7c1d4b00ce3cea67b44566851c4343c120abd683433ce934a68ea58872"},
 ]
 charset-normalizer = [
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-    {file = "charset_normalizer-2.0.9-py3-none-any.whl", hash = "sha256:1eecaa09422db5be9e29d7fc65664e6c33bd06f9ced7838578ba40d58bdf3721"},
+    {file = "charset-normalizer-2.0.10.tar.gz", hash = "sha256:876d180e9d7432c5d1dfd4c5d26b72f099d503e8fcc0feb7532c9289be60fcbd"},
+    {file = "charset_normalizer-2.0.10-py3-none-any.whl", hash = "sha256:cb957888737fc0bbcd78e3df769addb41fd1ff8cf950dc9e7ad7793f1bf44455"},
 ]
 click = [
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@@ -519,8 +529,23 @@ deprecated = [
     {file = "Deprecated-1.2.13.tar.gz", hash = "sha256:43ac5335da90c31c24ba028af536a91d41d53f9e6901ddb021bcc572ce44e38d"},
 ]
 frozendict = [
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-    {file = "frozendict-2.1.1.tar.gz", hash = "sha256:655b879217dd445a2023e16154cc231febef802b5c812d5c2e822280ad69e1dc"},
+    {file = "frozendict-2.2.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:b39cfcf563b3432d4780bf15769e2de2a2906c46c26fb73a9582b69142621814"},
+    {file = "frozendict-2.2.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:e7198dda9741f3da79db952ecd27607d836727ed320f29438eac565133008c8c"},
+    {file = "frozendict-2.2.0-cp310-cp310-win_amd64.whl", hash = "sha256:3a564bd93767044e740e0f6c59606cf612a143160ace9d2c047c4a297a74329a"},
+    {file = "frozendict-2.2.0-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:2a47f3f7fe52094904777d29f300ad6c11213dd81a8fbdec96aa2d4763104319"},
+    {file = "frozendict-2.2.0-cp36-cp36m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:2bfacb9f75768903495747ddaacb1bf98738fb3e966a27f0627f7f163fd676eb"},
+    {file = "frozendict-2.2.0-cp36-cp36m-win_amd64.whl", hash = "sha256:efc138fb1e2c115c39240f60b4b0daf752f1cca591d5f93ac4e788af0665d737"},
+    {file = "frozendict-2.2.0-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:722e915421b2d869b236d8de8e0ab42f1e2f7e12d670f9bc3dedfc055550bcb9"},
+    {file = "frozendict-2.2.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:4519f6eb661f268c60a3ea14f000d321159cf5e6db397129ea4921aef3bf2173"},
+    {file = "frozendict-2.2.0-cp37-cp37m-win_amd64.whl", hash = "sha256:9c720e4a19e9b5f48d1b12e193d39765898dff4952320251c0ccd9960631cae9"},
+    {file = "frozendict-2.2.0-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:1708828a3fed512ea8fa18e75622b29e551a5524c14aea0b0364f4472ca15f7d"},
+    {file = "frozendict-2.2.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:ede1bc6b6d734ba36bdcd99659463d96620069281e6bb6f72cbed719d679c1bb"},
+    {file = "frozendict-2.2.0-cp38-cp38-win_amd64.whl", hash = "sha256:f6293ec3181ff98e5ae98f748e8ffe6c937caf14ca9561d3a6d6d02a82c7fbff"},
+    {file = "frozendict-2.2.0-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:ebf36b78ce0a43f7372e94eee8b0327a12c15914e1a29c088f9bcfba20971929"},
+    {file = "frozendict-2.2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:e237adae46cc28eb0355f6d65900e946c0a7bc4536145c6d8e6bbb2b6c28ac2a"},
+    {file = "frozendict-2.2.0-cp39-cp39-win_amd64.whl", hash = "sha256:14ab850309632198b28e74948b800ac75609380a6f779a5779482a3189af7299"},
+    {file = "frozendict-2.2.0-py3-none-any.whl", hash = "sha256:a6d56ec83e5120f273adbf7f3798f78e8775158eee95469cd66e2e28be153ee3"},
+    {file = "frozendict-2.2.0.tar.gz", hash = "sha256:8e3d4735f9a13d1077567e568471663f3244f85ac89b23f8cb31cf231dbe45b9"},
 ]
 hbreader = [
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@@ -531,16 +556,16 @@ idna = [
     {file = "idna-3.3.tar.gz", hash = "sha256:9d643ff0a55b762d5cdb124b8eaa99c66322e2157b69160bc32796e824360e6d"},
 ]
 importlib-metadata = [
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-    {file = "importlib_metadata-4.8.2.tar.gz", hash = "sha256:75bdec14c397f528724c1bfd9709d660b33a4d2e77387a3358f20b848bb5e5fb"},
+    {file = "importlib_metadata-1.7.0-py2.py3-none-any.whl", hash = "sha256:dc15b2969b4ce36305c51eebe62d418ac7791e9a157911d58bfb1f9ccd8e2070"},
+    {file = "importlib_metadata-1.7.0.tar.gz", hash = "sha256:90bb658cdbbf6d1735b6341ce708fc7024a3e14e99ffdc5783edea9f9b077f83"},
 ]
 importlib-resources = [
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     {file = "importlib_resources-5.4.0.tar.gz", hash = "sha256:d756e2f85dd4de2ba89be0b21dba2a3bbec2e871a42a3a16719258a11f87506b"},
 ]
 isodate = [
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+    {file = "isodate-0.6.1-py2.py3-none-any.whl", hash = "sha256:0751eece944162659049d35f4f549ed815792b38793f07cf73381c1c87cbed96"},
+    {file = "isodate-0.6.1.tar.gz", hash = "sha256:48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9"},
 ]
 json-flattener = [
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@@ -555,70 +580,70 @@ jsonasobj2 = [
     {file = "jsonasobj2-1.0.4.tar.gz", hash = "sha256:f50b1668ef478004aa487b2d2d094c304e5cb6b79337809f4a1f2975cc7fbb4e"},
 ]
 jsonschema = [
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-    {file = "jsonschema-4.2.1.tar.gz", hash = "sha256:390713469ae64b8a58698bb3cbc3859abe6925b565a973f87323ef21b09a27a8"},
+    {file = "jsonschema-4.4.0-py3-none-any.whl", hash = "sha256:77281a1f71684953ee8b3d488371b162419767973789272434bbc3f29d9c8823"},
+    {file = "jsonschema-4.4.0.tar.gz", hash = "sha256:636694eb41b3535ed608fe04129f26542b59ed99808b4f688aa32dcf55317a83"},
 ]
 lxml = [
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-    {file = "lxml-4.6.4-cp310-cp310-manylinux_2_12_i686.manylinux2010_i686.manylinux_2_24_i686.whl", hash = "sha256:38b9de0de3aa689fe9fb9877ae1be1e83b8cf9621f7e62049d0436b9ecf4ad64"},
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 ]
 urllib3 = [
-    {file = "urllib3-1.26.7-py2.py3-none-any.whl", hash = "sha256:c4fdf4019605b6e5423637e01bc9fe4daef873709a7973e195ceba0a62bbc844"},
-    {file = "urllib3-1.26.7.tar.gz", hash = "sha256:4987c65554f7a2dbf30c18fd48778ef124af6fab771a377103da0585e2336ece"},
+    {file = "urllib3-1.26.8-py2.py3-none-any.whl", hash = "sha256:000ca7f471a233c2251c6c7023ee85305721bfdf18621ebff4fd17a8653427ed"},
+    {file = "urllib3-1.26.8.tar.gz", hash = "sha256:0e7c33d9a63e7ddfcb86780aac87befc2fbddf46c58dbb487e0855f7ceec283c"},
 ]
 wrapt = [
     {file = "wrapt-1.13.3-cp27-cp27m-macosx_10_9_x86_64.whl", hash = "sha256:e05e60ff3b2b0342153be4d1b597bbcfd8330890056b9619f4ad6b8d5c96a81a"},
@@ -780,6 +809,6 @@ wrapt = [
     {file = "wrapt-1.13.3.tar.gz", hash = "sha256:1fea9cd438686e6682271d36f3481a9f3636195578bab9ca3382e2f5f01fc185"},
 ]
 zipp = [
-    {file = "zipp-3.6.0-py3-none-any.whl", hash = "sha256:9fe5ea21568a0a70e50f273397638d39b03353731e6cbbb3fd8502a33fec40bc"},
-    {file = "zipp-3.6.0.tar.gz", hash = "sha256:71c644c5369f4a6e07636f0aa966270449561fcea2e3d6747b8d23efaa9d7832"},
+    {file = "zipp-3.7.0-py3-none-any.whl", hash = "sha256:b47250dd24f92b7dd6a0a8fc5244da14608f3ca90a5efcd37a3b1642fac9a375"},
+    {file = "zipp-3.7.0.tar.gz", hash = "sha256:9f50f446828eb9d45b267433fd3e9da8d801f614129124863f9c51ebceafb87d"},
 ]
diff --git a/pyproject.toml b/pyproject.toml
index 86ac4743..ceb66613 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "linkml_runtime"
-version = "1.1.10"
+version = "0.0.0"
 description = "Runtime environment for LinkML, the Linked open data modeling language"
 authors = [
     "Chris Mungall <cjmungall@lbl.gov>",
@@ -49,14 +49,16 @@ jsonschema = ">=3.2.0"
 prefixcommons = "*"
 pyldmod = "*"
 pyyaml = "==5.*,>=5.1.0"
-rdflib = "==5.*,>=5.0.0"
-rdflib-jsonld = "<=0.6.1,>=0.5.0"
+rdflib = ">=5.0.0"
+rdflib-shim = ">=1.0.3"
+rdflib-jsonld = "==0.6.1"
 rdflib-pyldmod-compat = "*"
 requests = "*"
 shexjsg = "==0.*,>=0.7.0"
 
 [tool.poetry.dev-dependencies]
 coverage = "^6.2"
+importlib-metadata = {version = "^1.0", python = "<3.8"}
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]