diff --git a/README.md b/README.md
index f826e33..0017d8d 100644
--- a/README.md
+++ b/README.md
@@ -305,6 +305,7 @@ See [tests/test_mapper/test_schema_mapper.py](tests/test_schema_mapper/test_sche
## Not supported
- Aggregation
+- ...
## Why another framework?
@@ -337,6 +338,7 @@ precise mappings between *entities* (e.g. schema.org Person is the same as DBPed
that many people wanted to extend the language to perform more complex mappings. To address this, we
help a workshop at the Biocuration conference in Padua, Italy in 2022.
+- [Discussion](https://github.com/orgs/linkml/discussions/1829)
- [SSSOM paper](https://academic.oup.com/database/article/doi/10.1093/database/baac035/6591806)
- [SSSOM Update 2023](https://ceur-ws.org/Vol-3591/om2023_STpaper3.pdf)
- [SSSOM Complex Mappings Workshop 2023](https://www.youtube.com/playlist?list=PLqu_J7ADQtKyX55F7RqZtaSS7TwGd3MoR)
diff --git a/notebooks/Tutorial.ipynb b/notebooks/Tutorial.ipynb
index 84008af..73a00a9 100644
--- a/notebooks/Tutorial.ipynb
+++ b/notebooks/Tutorial.ipynb
@@ -24,8 +24,8 @@
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- "end_time": "2024-01-03T02:07:05.802136Z",
- "start_time": "2024-01-03T02:07:05.768310Z"
+ "end_time": "2024-01-17T22:29:59.302402Z",
+ "start_time": "2024-01-17T22:29:58.965289Z"
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+ "end_time": "2024-01-17T22:29:59.378265Z",
+ "start_time": "2024-01-17T22:29:58.988218Z"
}
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+ "end_time": "2024-01-17T22:30:01.239725Z",
+ "start_time": "2024-01-17T22:29:59.312872Z"
}
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@@ -166,8 +166,8 @@
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+ "start_time": "2024-01-17T22:30:01.238874Z"
}
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@@ -191,7 +191,7 @@
{
"data": {
"image/svg+xml": "\n\n\n\n\n",
- "text/plain": ""
+ "text/plain": ""
},
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"metadata": {},
@@ -204,8 +204,8 @@
"metadata": {
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"ExecuteTime": {
- "end_time": "2024-01-03T02:07:06.816125Z",
- "start_time": "2024-01-03T02:07:06.369496Z"
+ "end_time": "2024-01-17T22:30:02.244818Z",
+ "start_time": "2024-01-17T22:30:01.486984Z"
}
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@@ -249,8 +249,8 @@
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- "end_time": "2024-01-03T02:07:06.829871Z",
- "start_time": "2024-01-03T02:07:06.823308Z"
+ "end_time": "2024-01-17T22:30:02.251017Z",
+ "start_time": "2024-01-17T22:30:02.241183Z"
}
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"id": "9f4d1fc4ca97f80c"
@@ -336,8 +336,8 @@
"metadata": {
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"ExecuteTime": {
- "end_time": "2024-01-03T02:07:06.853312Z",
- "start_time": "2024-01-03T02:07:06.832158Z"
+ "end_time": "2024-01-17T22:30:02.260147Z",
+ "start_time": "2024-01-17T22:30:02.253561Z"
}
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@@ -398,8 +398,8 @@
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"ExecuteTime": {
- "end_time": "2024-01-03T02:07:06.903169Z",
- "start_time": "2024-01-03T02:07:06.848243Z"
+ "end_time": "2024-01-17T22:30:02.326085Z",
+ "start_time": "2024-01-17T22:30:02.258015Z"
}
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"id": "789a7b6535ab410f"
@@ -422,7 +422,7 @@
{
"data": {
"image/svg+xml": "\n\n\n\n\n",
- "text/plain": ""
+ "text/plain": ""
},
"execution_count": 9,
"metadata": {},
@@ -435,8 +435,8 @@
"metadata": {
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"ExecuteTime": {
- "end_time": "2024-01-03T02:07:07.250708Z",
- "start_time": "2024-01-03T02:07:06.913474Z"
+ "end_time": "2024-01-17T22:30:03.283023Z",
+ "start_time": "2024-01-17T22:30:02.345894Z"
}
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@@ -470,8 +470,8 @@
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"ExecuteTime": {
- "end_time": "2024-01-03T02:07:07.250930Z",
- "start_time": "2024-01-03T02:07:07.244685Z"
+ "end_time": "2024-01-17T22:30:03.283868Z",
+ "start_time": "2024-01-17T22:30:03.278695Z"
}
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@@ -528,8 +528,8 @@
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"ExecuteTime": {
- "end_time": "2024-01-03T02:07:07.256503Z",
- "start_time": "2024-01-03T02:07:07.252109Z"
+ "end_time": "2024-01-17T22:30:03.290589Z",
+ "start_time": "2024-01-17T22:30:03.286701Z"
}
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@@ -608,8 +608,8 @@
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"ExecuteTime": {
- "end_time": "2024-01-03T02:07:07.271763Z",
- "start_time": "2024-01-03T02:07:07.266055Z"
+ "end_time": "2024-01-17T22:30:03.323328Z",
+ "start_time": "2024-01-17T22:30:03.300567Z"
}
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@@ -649,8 +649,8 @@
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- "end_time": "2024-01-03T02:07:07.329627Z",
- "start_time": "2024-01-03T02:07:07.293054Z"
+ "end_time": "2024-01-17T22:30:03.365363Z",
+ "start_time": "2024-01-17T22:30:03.321298Z"
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@@ -674,8 +674,8 @@
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+ "start_time": "2024-01-17T22:30:03.370531Z"
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@@ -734,8 +734,8 @@
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+ "end_time": "2024-01-17T22:30:03.629604Z",
+ "start_time": "2024-01-17T22:30:03.624546Z"
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@@ -760,8 +760,8 @@
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- "start_time": "2024-01-03T02:07:07.640190Z"
+ "end_time": "2024-01-17T22:30:03.630816Z",
+ "start_time": "2024-01-17T22:30:03.629262Z"
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@@ -776,8 +776,8 @@
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+ "end_time": "2024-01-17T22:30:03.661717Z",
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@@ -792,8 +792,8 @@
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+ "end_time": "2024-01-17T22:30:03.709283Z",
+ "start_time": "2024-01-17T22:30:03.667849Z"
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+ "end_time": "2024-01-17T22:30:03.739195Z",
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@@ -909,8 +909,8 @@
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+ "start_time": "2024-01-17T22:30:03.782845Z"
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diff --git a/poetry.lock b/poetry.lock
index a5de47e..16c3dca 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -25,24 +25,26 @@ files = [
[[package]]
name = "anyio"
-version = "3.6.2"
+version = "4.2.0"
description = "High level compatibility layer for multiple asynchronous event loop implementations"
category = "dev"
optional = false
-python-versions = ">=3.6.2"
+python-versions = ">=3.8"
files = [
- {file = "anyio-3.6.2-py3-none-any.whl", hash = "sha256:fbbe32bd270d2a2ef3ed1c5d45041250284e31fc0a4df4a5a6071842051a51e3"},
- {file = "anyio-3.6.2.tar.gz", hash = "sha256:25ea0d673ae30af41a0c442f81cf3b38c7e79fdc7b60335a4c14e05eb0947421"},
+ {file = "anyio-4.2.0-py3-none-any.whl", hash = "sha256:745843b39e829e108e518c489b31dc757de7d2131d53fac32bd8df268227bfee"},
+ {file = "anyio-4.2.0.tar.gz", hash = "sha256:e1875bb4b4e2de1669f4bc7869b6d3f54231cdced71605e6e64c9be77e3be50f"},
]
[package.dependencies]
+exceptiongroup = {version = ">=1.0.2", markers = "python_version < \"3.11\""}
idna = ">=2.8"
sniffio = ">=1.1"
+typing-extensions = {version = ">=4.1", markers = "python_version < \"3.11\""}
[package.extras]
-doc = ["packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"]
-test = ["contextlib2", "coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "mock (>=4)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (<0.15)", "uvloop (>=0.15)"]
-trio = ["trio (>=0.16,<0.22)"]
+doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"]
+test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"]
+trio = ["trio (>=0.23)"]
[[package]]
name = "appnope"
@@ -58,23 +60,24 @@ files = [
[[package]]
name = "argon2-cffi"
-version = "21.3.0"
-description = "The secure Argon2 password hashing algorithm."
+version = "23.1.0"
+description = "Argon2 for Python"
category = "dev"
optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
files = [
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[package.dependencies]
argon2-cffi-bindings = "*"
[package.extras]
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-docs = ["furo", "sphinx", "sphinx-notfound-page"]
-tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pytest"]
+dev = ["argon2-cffi[tests,typing]", "tox (>4)"]
+docs = ["furo", "myst-parser", "sphinx", "sphinx-copybutton", "sphinx-notfound-page"]
+tests = ["hypothesis", "pytest"]
+typing = ["mypy"]
[[package]]
name = "argon2-cffi-bindings"
@@ -116,29 +119,34 @@ tests = ["pytest"]
[[package]]
name = "arrow"
-version = "1.2.3"
+version = "1.3.0"
description = "Better dates & times for Python"
category = "dev"
optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
files = [
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]
[package.dependencies]
python-dateutil = ">=2.7.0"
+types-python-dateutil = ">=2.8.10"
+
+[package.extras]
+doc = ["doc8", "sphinx (>=7.0.0)", "sphinx-autobuild", "sphinx-autodoc-typehints", "sphinx_rtd_theme (>=1.3.0)"]
+test = ["dateparser (>=1.0.0,<2.0.0)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (>=3.0.0,<4.0.0)"]
[[package]]
name = "asteval"
-version = "0.9.29"
+version = "0.9.31"
description = "Safe, minimalistic evaluator of python expression using ast module"
category = "main"
optional = false
python-versions = ">=3.7"
files = [
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- {file = "asteval-0.9.29.tar.gz", hash = "sha256:ab98c61ba9394149c774ae7861497e9c32580301aa693ca19746997216c31fab"},
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+ {file = "asteval-0.9.31.tar.gz", hash = "sha256:a2da066b6696dba9835c5f7dec63e0ffb5bd2b4e3bb5f0b9a604aeafb17d833d"},
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@@ -149,53 +157,73 @@ test = ["coverage", "pytest", "pytest-cov"]
[[package]]
name = "asttokens"
-version = "2.2.1"
+version = "2.4.1"
description = "Annotate AST trees with source code positions"
category = "dev"
optional = false
python-versions = "*"
files = [
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+ {file = "asttokens-2.4.1.tar.gz", hash = "sha256:b03869718ba9a6eb027e134bfdf69f38a236d681c83c160d510768af11254ba0"},
]
[package.dependencies]
-six = "*"
+six = ">=1.12.0"
[package.extras]
-test = ["astroid", "pytest"]
+astroid = ["astroid (>=1,<2)", "astroid (>=2,<4)"]
+test = ["astroid (>=1,<2)", "astroid (>=2,<4)", "pytest"]
+
+[[package]]
+name = "async-lru"
+version = "2.0.4"
+description = "Simple LRU cache for asyncio"
+category = "dev"
+optional = false
+python-versions = ">=3.8"
+files = [
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+[package.dependencies]
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[[package]]
name = "attrs"
-version = "23.1.0"
+version = "23.2.0"
description = "Classes Without Boilerplate"
category = "main"
optional = false
python-versions = ">=3.7"
files = [
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]
[package.extras]
cov = ["attrs[tests]", "coverage[toml] (>=5.3)"]
-dev = ["attrs[docs,tests]", "pre-commit"]
+dev = ["attrs[tests]", "pre-commit"]
docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"]
tests = ["attrs[tests-no-zope]", "zope-interface"]
-tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+tests-mypy = ["mypy (>=1.6)", "pytest-mypy-plugins"]
+tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist[psutil]"]
[[package]]
-name = "backcall"
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+name = "babel"
+version = "2.14.0"
+description = "Internationalization utilities"
category = "dev"
optional = false
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packaging = "*"
psutil = "*"
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tornado = ">=6.1"
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decorator = "*"
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traitlets = ">=4.3.1"
-widgetsnbextension = ">=4.0.7,<4.1.0"
+widgetsnbextension = ">=4.0.9,<4.1.0"
[package.extras]
test = ["ipykernel", "jsonschema", "pytest (>=3.6.0)", "pytest-cov", "pytz"]
@@ -1048,23 +1103,23 @@ arrow = ">=0.15.0"
[[package]]
name = "jedi"
-version = "0.18.2"
+version = "0.19.1"
description = "An autocompletion tool for Python that can be used for text editors."
category = "dev"
optional = false
python-versions = ">=3.6"
files = [
- {file = "jedi-0.18.2-py2.py3-none-any.whl", hash = "sha256:203c1fd9d969ab8f2119ec0a3342e0b49910045abe6af0a3ae83a5764d54639e"},
- {file = "jedi-0.18.2.tar.gz", hash = "sha256:bae794c30d07f6d910d32a7048af09b5a39ed740918da923c6b780790ebac612"},
+ {file = "jedi-0.19.1-py2.py3-none-any.whl", hash = "sha256:e983c654fe5c02867aef4cdfce5a2fbb4a50adc0af145f70504238f18ef5e7e0"},
+ {file = "jedi-0.19.1.tar.gz", hash = "sha256:cf0496f3651bc65d7174ac1b7d043eff454892c708a87d1b683e57b569927ffd"},
]
[package.dependencies]
-parso = ">=0.8.0,<0.9.0"
+parso = ">=0.8.3,<0.9.0"
[package.extras]
docs = ["Jinja2 (==2.11.3)", "MarkupSafe (==1.1.1)", "Pygments (==2.8.1)", "alabaster (==0.7.12)", "babel (==2.9.1)", "chardet (==4.0.0)", "commonmark (==0.8.1)", "docutils (==0.17.1)", "future (==0.18.2)", "idna (==2.10)", "imagesize (==1.2.0)", "mock (==1.0.1)", "packaging (==20.9)", "pyparsing (==2.4.7)", "pytz (==2021.1)", "readthedocs-sphinx-ext (==2.1.4)", "recommonmark (==0.5.0)", "requests (==2.25.1)", "six (==1.15.0)", "snowballstemmer (==2.1.0)", "sphinx (==1.8.5)", "sphinx-rtd-theme (==0.4.3)", "sphinxcontrib-serializinghtml (==1.1.4)", "sphinxcontrib-websupport (==1.2.4)", "urllib3 (==1.26.4)"]
-qa = ["flake8 (==3.8.3)", "mypy (==0.782)"]
-testing = ["Django (<3.1)", "attrs", "colorama", "docopt", "pytest (<7.0.0)"]
+qa = ["flake8 (==5.0.4)", "mypy (==0.971)", "types-setuptools (==67.2.0.1)"]
+testing = ["Django", "attrs", "colorama", "docopt", "pytest (<7.0.0)"]
[[package]]
name = "jinja2"
@@ -1086,13 +1141,13 @@ i18n = ["Babel (>=2.7)"]
[[package]]
name = "jsbeautifier"
-version = "1.14.7"
+version = "1.14.11"
description = "JavaScript unobfuscator and beautifier."
category = "dev"
optional = false
python-versions = "*"
files = [
- {file = "jsbeautifier-1.14.7.tar.gz", hash = "sha256:77993254db1ff6f84eb6e1d75e3b6b72cba2ef20813a585b2d81e8e5e3c713c6"},
+ {file = "jsbeautifier-1.14.11.tar.gz", hash = "sha256:6b632581ea60dd1c133cd25a48ad187b4b91f526623c4b0fb5443ef805250505"},
]
[package.dependencies]
@@ -1115,6 +1170,21 @@ files = [
click = "*"
pyyaml = "*"
+[[package]]
+name = "json5"
+version = "0.9.14"
+description = "A Python implementation of the JSON5 data format."
+category = "dev"
+optional = false
+python-versions = "*"
+files = [
+ {file = "json5-0.9.14-py2.py3-none-any.whl", hash = "sha256:740c7f1b9e584a468dbb2939d8d458db3427f2c93ae2139d05f47e453eae964f"},
+ {file = "json5-0.9.14.tar.gz", hash = "sha256:9ed66c3a6ca3510a976a9ef9b8c0787de24802724ab1860bc0153c7fdd589b02"},
+]
+
+[package.extras]
+dev = ["hypothesis"]
+
[[package]]
name = "jsonasobj"
version = "1.3.1"
@@ -1144,14 +1214,14 @@ hbreader = "*"
[[package]]
name = "jsonpatch"
-version = "1.32"
+version = "1.33"
description = "Apply JSON-Patches (RFC 6902)"
category = "dev"
optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*"
files = [
- {file = "jsonpatch-1.32-py2.py3-none-any.whl", hash = "sha256:26ac385719ac9f54df8a2f0827bb8253aa3ea8ab7b3368457bcdb8c14595a397"},
- {file = "jsonpatch-1.32.tar.gz", hash = "sha256:b6ddfe6c3db30d81a96aaeceb6baf916094ffa23d7dd5fa2c13e13f8b6e600c2"},
+ {file = "jsonpatch-1.33-py2.py3-none-any.whl", hash = "sha256:0ae28c0cd062bbd8b8ecc26d7d164fbbea9652a1a3693f3b956c1eae5145dade"},
+ {file = "jsonpatch-1.33.tar.gz", hash = "sha256:9fcd4009c41e6d12348b4a0ff2563ba56a2923a7dfee731d004e212e1ee5030c"},
]
[package.dependencies]
@@ -1159,56 +1229,55 @@ jsonpointer = ">=1.9"
[[package]]
name = "jsonpath-ng"
-version = "1.5.3"
+version = "1.6.0"
description = "A final implementation of JSONPath for Python that aims to be standard compliant, including arithmetic and binary comparison operators and providing clear AST for metaprogramming."
category = "dev"
optional = false
python-versions = "*"
files = [
- {file = "jsonpath-ng-1.5.3.tar.gz", hash = "sha256:a273b182a82c1256daab86a313b937059261b5c5f8c4fa3fc38b882b344dd567"},
- {file = "jsonpath_ng-1.5.3-py2-none-any.whl", hash = "sha256:f75b95dbecb8a0f3b86fd2ead21c2b022c3f5770957492b9b6196ecccfeb10aa"},
- {file = "jsonpath_ng-1.5.3-py3-none-any.whl", hash = "sha256:292a93569d74029ba75ac2dc3d3630fc0e17b2df26119a165fa1d498ca47bf65"},
+ {file = "jsonpath-ng-1.6.0.tar.gz", hash = "sha256:5483f8e9d74c39c9abfab554c070ae783c1c8cbadf5df60d561bc705ac68a07e"},
+ {file = "jsonpath_ng-1.6.0-py3-none-any.whl", hash = "sha256:6fd04833412c4b3d9299edf369542f5e67095ca84efa17cbb7f06a34958adc9f"},
]
[package.dependencies]
-decorator = "*"
ply = "*"
-six = "*"
[[package]]
name = "jsonpointer"
-version = "2.3"
+version = "2.4"
description = "Identify specific nodes in a JSON document (RFC 6901)"
category = "dev"
optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*"
files = [
- {file = "jsonpointer-2.3-py2.py3-none-any.whl", hash = "sha256:51801e558539b4e9cd268638c078c6c5746c9ac96bc38152d443400e4f3793e9"},
- {file = "jsonpointer-2.3.tar.gz", hash = "sha256:97cba51526c829282218feb99dab1b1e6bdf8efd1c43dc9d57be093c0d69c99a"},
+ {file = "jsonpointer-2.4-py2.py3-none-any.whl", hash = "sha256:15d51bba20eea3165644553647711d150376234112651b4f1811022aecad7d7a"},
+ {file = "jsonpointer-2.4.tar.gz", hash = "sha256:585cee82b70211fa9e6043b7bb89db6e1aa49524340dde8ad6b63206ea689d88"},
]
[[package]]
name = "jsonschema"
-version = "4.17.3"
+version = "4.20.0"
description = "An implementation of JSON Schema validation for Python"
category = "main"
optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
files = [
- {file = "jsonschema-4.17.3-py3-none-any.whl", hash = "sha256:a870ad254da1a8ca84b6a2905cac29d265f805acc57af304784962a2aa6508f6"},
- {file = "jsonschema-4.17.3.tar.gz", hash = "sha256:0f864437ab8b6076ba6707453ef8f98a6a0d512a80e93f8abdb676f737ecb60d"},
+ {file = "jsonschema-4.20.0-py3-none-any.whl", hash = "sha256:ed6231f0429ecf966f5bc8dfef245998220549cbbcf140f913b7464c52c3b6b3"},
+ {file = "jsonschema-4.20.0.tar.gz", hash = "sha256:4f614fd46d8d61258610998997743ec5492a648b33cf478c1ddc23ed4598a5fa"},
]
[package.dependencies]
-attrs = ">=17.4.0"
+attrs = ">=22.2.0"
fqdn = {version = "*", optional = true, markers = "extra == \"format-nongpl\""}
idna = {version = "*", optional = true, markers = "extra == \"format-nongpl\""}
isoduration = {version = "*", optional = true, markers = "extra == \"format-nongpl\""}
jsonpointer = {version = ">1.13", optional = true, markers = "extra == \"format-nongpl\""}
-pyrsistent = ">=0.14.0,<0.17.0 || >0.17.0,<0.17.1 || >0.17.1,<0.17.2 || >0.17.2"
+jsonschema-specifications = ">=2023.03.6"
+referencing = ">=0.28.4"
rfc3339-validator = {version = "*", optional = true, markers = "extra == \"format-nongpl\""}
rfc3986-validator = {version = ">0.1.0", optional = true, markers = "extra == \"format-nongpl\""}
rfc3987 = {version = "*", optional = true, markers = "extra == \"format\""}
+rpds-py = ">=0.7.1"
uri-template = {version = "*", optional = true, markers = "extra == \"format-nongpl\""}
webcolors = {version = ">=1.11", optional = true, markers = "extra == \"format-nongpl\""}
@@ -1216,6 +1285,21 @@ webcolors = {version = ">=1.11", optional = true, markers = "extra == \"format-n
format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"]
format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=1.11)"]
+[[package]]
+name = "jsonschema-specifications"
+version = "2023.12.1"
+description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry"
+category = "main"
+optional = false
+python-versions = ">=3.8"
+files = [
+ {file = "jsonschema_specifications-2023.12.1-py3-none-any.whl", hash = "sha256:87e4fdf3a94858b8a2ba2778d9ba57d8a9cafca7c7489c46ba0d30a8bc6a9c3c"},
+ {file = "jsonschema_specifications-2023.12.1.tar.gz", hash = "sha256:48a76787b3e70f5ed53f1160d2b81f586e4ca6d1548c5de7085d1682674764cc"},
+]
+
+[package.dependencies]
+referencing = ">=0.31.0"
+
[[package]]
name = "jupyter"
version = "1.0.0"
@@ -1239,14 +1323,14 @@ qtconsole = "*"
[[package]]
name = "jupyter-client"
-version = "8.2.0"
+version = "8.6.0"
description = "Jupyter protocol implementation and client libraries"
category = "dev"
optional = false
python-versions = ">=3.8"
files = [
- {file = "jupyter_client-8.2.0-py3-none-any.whl", hash = "sha256:b18219aa695d39e2ad570533e0d71fb7881d35a873051054a84ee2a17c4b7389"},
- {file = "jupyter_client-8.2.0.tar.gz", hash = "sha256:9fe233834edd0e6c0aa5f05ca2ab4bdea1842bfd2d8a932878212fc5301ddaf0"},
+ {file = "jupyter_client-8.6.0-py3-none-any.whl", hash = "sha256:909c474dbe62582ae62b758bca86d6518c85234bdee2d908c778db6d72f39d99"},
+ {file = "jupyter_client-8.6.0.tar.gz", hash = "sha256:0642244bb83b4764ae60d07e010e15f0e2d275ec4e918a8f7b80fbbef3ca60c7"},
]
[package.dependencies]
@@ -1288,14 +1372,14 @@ test = ["flaky", "pexpect", "pytest"]
[[package]]
name = "jupyter-core"
-version = "5.3.0"
+version = "5.7.1"
description = "Jupyter core package. A base package on which Jupyter projects rely."
category = "dev"
optional = false
python-versions = ">=3.8"
files = [
- {file = "jupyter_core-5.3.0-py3-none-any.whl", hash = "sha256:d4201af84559bc8c70cead287e1ab94aeef3c512848dde077b7684b54d67730d"},
- {file = "jupyter_core-5.3.0.tar.gz", hash = "sha256:6db75be0c83edbf1b7c9f91ec266a9a24ef945da630f3120e1a0046dc13713fc"},
+ {file = "jupyter_core-5.7.1-py3-none-any.whl", hash = "sha256:c65c82126453a723a2804aa52409930434598fd9d35091d63dfb919d2b765bb7"},
+ {file = "jupyter_core-5.7.1.tar.gz", hash = "sha256:de61a9d7fc71240f688b2fb5ab659fbb56979458dc66a71decd098e03c79e218"},
]
[package.dependencies]
@@ -1304,25 +1388,26 @@ pywin32 = {version = ">=300", markers = "sys_platform == \"win32\" and platform_
traitlets = ">=5.3"
[package.extras]
-docs = ["myst-parser", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "traitlets"]
+docs = ["myst-parser", "pydata-sphinx-theme", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "traitlets"]
test = ["ipykernel", "pre-commit", "pytest", "pytest-cov", "pytest-timeout"]
[[package]]
name = "jupyter-events"
-version = "0.6.3"
+version = "0.9.0"
description = "Jupyter Event System library"
category = "dev"
optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
files = [
- {file = "jupyter_events-0.6.3-py3-none-any.whl", hash = "sha256:57a2749f87ba387cd1bfd9b22a0875b889237dbf2edc2121ebb22bde47036c17"},
- {file = "jupyter_events-0.6.3.tar.gz", hash = "sha256:9a6e9995f75d1b7146b436ea24d696ce3a35bfa8bfe45e0c33c334c79464d0b3"},
+ {file = "jupyter_events-0.9.0-py3-none-any.whl", hash = "sha256:d853b3c10273ff9bc8bb8b30076d65e2c9685579db736873de6c2232dde148bf"},
+ {file = "jupyter_events-0.9.0.tar.gz", hash = "sha256:81ad2e4bc710881ec274d31c6c50669d71bbaa5dd9d01e600b56faa85700d399"},
]
[package.dependencies]
-jsonschema = {version = ">=3.2.0", extras = ["format-nongpl"]}
+jsonschema = {version = ">=4.18.0", extras = ["format-nongpl"]}
python-json-logger = ">=2.0.4"
pyyaml = ">=5.3"
+referencing = "*"
rfc3339-validator = "*"
rfc3986-validator = ">=0.1.1"
traitlets = ">=5.3"
@@ -1330,18 +1415,34 @@ traitlets = ">=5.3"
[package.extras]
cli = ["click", "rich"]
docs = ["jupyterlite-sphinx", "myst-parser", "pydata-sphinx-theme", "sphinxcontrib-spelling"]
-test = ["click", "coverage", "pre-commit", "pytest (>=7.0)", "pytest-asyncio (>=0.19.0)", "pytest-console-scripts", "pytest-cov", "rich"]
+test = ["click", "pre-commit", "pytest (>=7.0)", "pytest-asyncio (>=0.19.0)", "pytest-console-scripts", "rich"]
+
+[[package]]
+name = "jupyter-lsp"
+version = "2.2.1"
+description = "Multi-Language Server WebSocket proxy for Jupyter Notebook/Lab server"
+category = "dev"
+optional = false
+python-versions = ">=3.8"
+files = [
+ {file = "jupyter-lsp-2.2.1.tar.gz", hash = "sha256:b17fab6d70fe83c8896b0cff59237640038247c196056b43684a0902b6a9e0fb"},
+ {file = "jupyter_lsp-2.2.1-py3-none-any.whl", hash = "sha256:17a689910c5e4ae5e7d334b02f31d08ffbe98108f6f658fb05e4304b4345368b"},
+]
+
+[package.dependencies]
+importlib-metadata = {version = ">=4.8.3", markers = "python_version < \"3.10\""}
+jupyter-server = ">=1.1.2"
[[package]]
name = "jupyter-server"
-version = "2.5.0"
+version = "2.12.2"
description = "The backend—i.e. core services, APIs, and REST endpoints—to Jupyter web applications."
category = "dev"
optional = false
python-versions = ">=3.8"
files = [
- {file = "jupyter_server-2.5.0-py3-none-any.whl", hash = "sha256:e6bc1e9e96d7c55b9ce9699ff6cb9a910581fe7349e27c40389acb67632e24c0"},
- {file = "jupyter_server-2.5.0.tar.gz", hash = "sha256:9fde612791f716fd34d610cd939704a9639643744751ba66e7ee8fdc9cead07e"},
+ {file = "jupyter_server-2.12.2-py3-none-any.whl", hash = "sha256:abcfa33f98a959f908c8733aa2d9fa0101d26941cbd49b148f4cef4d3046fc61"},
+ {file = "jupyter_server-2.12.2.tar.gz", hash = "sha256:5eae86be15224b5375cdec0c3542ce72ff20f7a25297a2a8166a250bb455a519"},
]
[package.dependencies]
@@ -1350,34 +1451,35 @@ argon2-cffi = "*"
jinja2 = "*"
jupyter-client = ">=7.4.4"
jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
-jupyter-events = ">=0.4.0"
+jupyter-events = ">=0.9.0"
jupyter-server-terminals = "*"
nbconvert = ">=6.4.4"
nbformat = ">=5.3.0"
+overrides = "*"
packaging = "*"
prometheus-client = "*"
pywinpty = {version = "*", markers = "os_name == \"nt\""}
pyzmq = ">=24"
-send2trash = "*"
+send2trash = ">=1.8.2"
terminado = ">=0.8.3"
tornado = ">=6.2.0"
traitlets = ">=5.6.0"
websocket-client = "*"
[package.extras]
-docs = ["docutils (<0.20)", "ipykernel", "jinja2", "jupyter-client", "jupyter-server", "mistune (<1.0.0)", "myst-parser", "nbformat", "prometheus-client", "pydata-sphinx-theme", "send2trash", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-openapi", "sphinxcontrib-spelling", "sphinxemoji", "tornado", "typing-extensions"]
-test = ["ipykernel", "pre-commit", "pytest (>=7.0)", "pytest-console-scripts", "pytest-jupyter[server] (>=0.4)", "pytest-timeout", "requests"]
+docs = ["ipykernel", "jinja2", "jupyter-client", "jupyter-server", "myst-parser", "nbformat", "prometheus-client", "pydata-sphinx-theme", "send2trash", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-openapi (>=0.8.0)", "sphinxcontrib-spelling", "sphinxemoji", "tornado", "typing-extensions"]
+test = ["flaky", "ipykernel", "pre-commit", "pytest (>=7.0)", "pytest-console-scripts", "pytest-jupyter[server] (>=0.4)", "pytest-timeout", "requests"]
[[package]]
name = "jupyter-server-terminals"
-version = "0.4.4"
+version = "0.5.1"
description = "A Jupyter Server Extension Providing Terminals."
category = "dev"
optional = false
python-versions = ">=3.8"
files = [
- {file = "jupyter_server_terminals-0.4.4-py3-none-any.whl", hash = "sha256:75779164661cec02a8758a5311e18bb8eb70c4e86c6b699403100f1585a12a36"},
- {file = "jupyter_server_terminals-0.4.4.tar.gz", hash = "sha256:57ab779797c25a7ba68e97bcfb5d7740f2b5e8a83b5e8102b10438041a7eac5d"},
+ {file = "jupyter_server_terminals-0.5.1-py3-none-any.whl", hash = "sha256:5e63e947ddd97bb2832db5ef837a258d9ccd4192cd608c1270850ad947ae5dd7"},
+ {file = "jupyter_server_terminals-0.5.1.tar.gz", hash = "sha256:16d3be9cf48be6a1f943f3a6c93c033be259cf4779184c66421709cf63dccfea"},
]
[package.dependencies]
@@ -1385,33 +1487,111 @@ pywinpty = {version = ">=2.0.3", markers = "os_name == \"nt\""}
terminado = ">=0.8.3"
[package.extras]
-docs = ["jinja2", "jupyter-server", "mistune (<3.0)", "myst-parser", "nbformat", "packaging", "pydata-sphinx-theme", "sphinxcontrib-github-alt", "sphinxcontrib-openapi", "sphinxcontrib-spelling", "sphinxemoji", "tornado"]
-test = ["coverage", "jupyter-server (>=2.0.0)", "pytest (>=7.0)", "pytest-cov", "pytest-jupyter[server] (>=0.5.3)", "pytest-timeout"]
+docs = ["jinja2", "jupyter-server", "mistune (<4.0)", "myst-parser", "nbformat", "packaging", "pydata-sphinx-theme", "sphinxcontrib-github-alt", "sphinxcontrib-openapi", "sphinxcontrib-spelling", "sphinxemoji", "tornado"]
+test = ["jupyter-server (>=2.0.0)", "pytest (>=7.0)", "pytest-jupyter[server] (>=0.5.3)", "pytest-timeout"]
+
+[[package]]
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optional = false
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pyyaml = ">=5.1"
pyyaml-env-tag = ">=0.1"
watchdog = ">=2.0"
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description = "Extension pack for Python Markdown and MkDocs Material."
category = "dev"
optional = false
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requests = "*"
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-
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jupyter-client = ">=6.1.12"
jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
nbformat = ">=5.1"
-traitlets = ">=5.3"
+traitlets = ">=5.4"
[package.extras]
dev = ["pre-commit"]
docs = ["autodoc-traits", "mock", "moto", "myst-parser", "nbclient[test]", "sphinx (>=1.7)", "sphinx-book-theme", "sphinxcontrib-spelling"]
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+test = ["flaky", "ipykernel (>=6.19.3)", "ipython", "ipywidgets", "nbconvert (>=7.0.0)", "pytest (>=7.0)", "pytest-asyncio", "pytest-cov (>=4.0)", "testpath", "xmltodict"]
[[package]]
name = "nbconvert"
-version = "7.3.1"
+version = "7.14.0"
description = "Converting Jupyter Notebooks"
category = "dev"
optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
files = [
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]
[package.dependencies]
beautifulsoup4 = "*"
-bleach = "*"
+bleach = "!=5.0.0"
defusedxml = "*"
importlib-metadata = {version = ">=3.6", markers = "python_version < \"3.10\""}
jinja2 = ">=3.0"
jupyter-core = ">=4.7"
jupyterlab-pygments = "*"
markupsafe = ">=2.0"
-mistune = ">=2.0.3,<3"
+mistune = ">=2.0.3,<4"
nbclient = ">=0.5.0"
-nbformat = ">=5.1"
+nbformat = ">=5.7"
packaging = "*"
pandocfilters = ">=1.4.1"
pygments = ">=2.4.1"
tinycss2 = "*"
-traitlets = ">=5.0"
+traitlets = ">=5.1"
[package.extras]
all = ["nbconvert[docs,qtpdf,serve,test,webpdf]"]
@@ -1794,19 +1959,19 @@ docs = ["ipykernel", "ipython", "myst-parser", "nbsphinx (>=0.2.12)", "pydata-sp
qtpdf = ["nbconvert[qtpng]"]
qtpng = ["pyqtwebengine (>=5.15)"]
serve = ["tornado (>=6.1)"]
-test = ["ipykernel", "ipywidgets (>=7)", "pre-commit", "pytest", "pytest-dependency"]
-webpdf = ["pyppeteer (>=1,<1.1)"]
+test = ["flaky", "ipykernel", "ipywidgets (>=7.5)", "pytest"]
+webpdf = ["playwright"]
[[package]]
name = "nbformat"
-version = "5.8.0"
+version = "5.9.2"
description = "The Jupyter Notebook format"
category = "dev"
optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
files = [
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+ {file = "nbformat-5.9.2.tar.gz", hash = "sha256:5f98b5ba1997dff175e77e0c17d5c10a96eaed2cbd1de3533d1fc35d5e111192"},
]
[package.dependencies]
@@ -1821,50 +1986,39 @@ test = ["pep440", "pre-commit", "pytest", "testpath"]
[[package]]
name = "nest-asyncio"
-version = "1.5.6"
+version = "1.5.8"
description = "Patch asyncio to allow nested event loops"
category = "dev"
optional = false
python-versions = ">=3.5"
files = [
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+ {file = "nest_asyncio-1.5.8-py3-none-any.whl", hash = "sha256:accda7a339a70599cb08f9dd09a67e0c2ef8d8d6f4c07f96ab203f2ae254e48d"},
+ {file = "nest_asyncio-1.5.8.tar.gz", hash = "sha256:25aa2ca0d2a5b5531956b9e273b45cf664cae2b145101d73b86b199978d48fdb"},
]
[[package]]
name = "notebook"
-version = "6.5.4"
-description = "A web-based notebook environment for interactive computing"
+version = "7.0.6"
+description = "Jupyter Notebook - A web-based notebook environment for interactive computing"
category = "dev"
optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
files = [
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-nbclassic = ">=0.4.7"
-nbconvert = ">=5"
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-prometheus-client = "*"
-pyzmq = ">=17"
-Send2Trash = ">=1.8.0"
-terminado = ">=0.8.3"
-tornado = ">=6.1"
-traitlets = ">=4.2.1"
+jupyter-server = ">=2.4.0,<3"
+jupyterlab = ">=4.0.2,<5"
+jupyterlab-server = ">=2.22.1,<3"
+notebook-shim = ">=0.2,<0.3"
+tornado = ">=6.2.0"
[package.extras]
-docs = ["myst-parser", "nbsphinx", "sphinx", "sphinx-rtd-theme", "sphinxcontrib-github-alt"]
-json-logging = ["json-logging"]
-test = ["coverage", "nbval", "pytest", "pytest-cov", "requests", "requests-unixsocket", "selenium (==4.1.5)", "testpath"]
+dev = ["hatch", "pre-commit"]
+docs = ["myst-parser", "nbsphinx", "pydata-sphinx-theme", "sphinx (>=1.3.6)", "sphinxcontrib-github-alt", "sphinxcontrib-spelling"]
+test = ["importlib-resources (>=5.0)", "ipykernel", "jupyter-server[test] (>=2.4.0,<3)", "jupyterlab-server[test] (>=2.22.1,<3)", "nbval", "pytest (>=7.0)", "pytest-console-scripts", "pytest-timeout", "pytest-tornasync", "requests"]
[[package]]
name = "notebook-shim"
@@ -1914,16 +2068,39 @@ files = [
[package.extras]
dev = ["black", "mypy", "pytest"]
+[[package]]
+name = "overrides"
+version = "7.4.0"
+description = "A decorator to automatically detect mismatch when overriding a method."
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+files = [
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+]
+
[[package]]
name = "packaging"
-version = "23.1"
+version = "23.2"
description = "Core utilities for Python packages"
category = "main"
optional = false
python-versions = ">=3.7"
files = [
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+]
+
+[[package]]
+name = "paginate"
+version = "0.5.6"
+description = "Divides large result sets into pages for easier browsing"
+category = "dev"
+optional = false
+python-versions = "*"
+files = [
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]
[[package]]
@@ -1940,14 +2117,14 @@ files = [
[[package]]
name = "parse"
-version = "1.19.0"
+version = "1.20.0"
description = "parse() is the opposite of format()"
category = "dev"
optional = false
python-versions = "*"
files = [
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[[package]]
@@ -1967,37 +2144,37 @@ qa = ["flake8 (==3.8.3)", "mypy (==0.782)"]
testing = ["docopt", "pytest (<6.0.0)"]
[[package]]
-name = "pexpect"
-version = "4.8.0"
-description = "Pexpect allows easy control of interactive console applications."
+name = "pathspec"
+version = "0.12.1"
+description = "Utility library for gitignore style pattern matching of file paths."
category = "dev"
optional = false
-python-versions = "*"
+python-versions = ">=3.8"
files = [
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-[package.dependencies]
-ptyprocess = ">=0.5"
-
[[package]]
-name = "pickleshare"
-version = "0.7.5"
-description = "Tiny 'shelve'-like database with concurrency support"
+name = "pexpect"
+version = "4.9.0"
+description = "Pexpect allows easy control of interactive console applications."
category = "dev"
optional = false
python-versions = "*"
files = [
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]
+[package.dependencies]
+ptyprocess = ">=0.5"
+
[[package]]
name = "pint"
version = "0.23"
description = "Physical quantities module"
-category = "dev"
+category = "main"
optional = false
python-versions = ">=3.9"
files = [
@@ -2022,30 +2199,30 @@ xarray = ["xarray"]
[[package]]
name = "platformdirs"
-version = "3.5.0"
+version = "4.1.0"
description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
-category = "dev"
+category = "main"
optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
files = [
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-test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.3.1)", "pytest-cov (>=4)", "pytest-mock (>=3.10)"]
+docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.1)", "sphinx-autodoc-typehints (>=1.24)"]
+test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)"]
[[package]]
name = "pluggy"
-version = "1.0.0"
+version = "1.3.0"
description = "plugin and hook calling mechanisms for python"
category = "main"
optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
files = [
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[package.extras]
@@ -2084,37 +2261,37 @@ requests = ">=2.28.1,<3.0.0"
[[package]]
name = "prefixmaps"
-version = "0.1.5"
+version = "0.2.1"
description = "A python library for retrieving semantic prefix maps"
category = "main"
optional = false
-python-versions = ">=3.7.6,<4.0.0"
+python-versions = ">=3.9,<4.0"
files = [
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[package.dependencies]
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-greenlet = "2.0.1"
-importlib-metadata = ">=1.0.0"
+click = ">=8.1.3"
+curies = ">=0.5.3"
+pydantic = ">=2.5,<3.0"
pyyaml = ">=5.3.1"
-typing-extensions = ">=4.4.0,<5.0.0"
+tox = ">=4.11.3,<5.0.0"
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+docs = ["Sphinx[docs] (>=7.2.6,<8.0.0)", "myst-parser[docs] (>=2.0.0,<3.0.0)", "sphinx-autodoc-typehints[docs] (>=1.23.4,<2.0.0)", "sphinx-click[docs] (>=4.3.0,<5.0.0)", "sphinx-rtd-theme[docs] (>=1.0.0,<2.0.0)"]
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[[package]]
name = "prometheus-client"
-version = "0.16.0"
+version = "0.19.0"
description = "Python client for the Prometheus monitoring system."
category = "dev"
optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
files = [
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]
[package.extras]
@@ -2122,14 +2299,14 @@ twisted = ["twisted"]
[[package]]
name = "prompt-toolkit"
-version = "3.0.38"
+version = "3.0.43"
description = "Library for building powerful interactive command lines in Python"
category = "dev"
optional = false
python-versions = ">=3.7.0"
files = [
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]
[package.dependencies]
@@ -2137,26 +2314,28 @@ wcwidth = "*"
[[package]]
name = "psutil"
-version = "5.9.5"
+version = "5.9.7"
description = "Cross-platform lib for process and system monitoring in Python."
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description = "Easily download, build, install, upgrade, and uninstall Python packages"
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category = "dev"
optional = false
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mysql = ["mysqlclient (>=1.4.0)"]
mysql-connector = ["mysql-connector-python"]
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postgresql-psycopg2cffi = ["psycopg2cffi"]
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test = ["pre-commit", "pytest (>=7.0)", "pytest-timeout"]
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python-versions = ">= 3.8"
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]
[[package]]
name = "zipp"
-version = "3.15.0"
+version = "3.17.0"
description = "Backport of pathlib-compatible object wrapper for zip files"
-category = "main"
+category = "dev"
optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
files = [
- {file = "zipp-3.15.0-py3-none-any.whl", hash = "sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556"},
- {file = "zipp-3.15.0.tar.gz", hash = "sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b"},
+ {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"},
+ {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"},
]
[package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
[metadata]
lock-version = "2.0"
python-versions = "^3.9"
-content-hash = "6cf50ad97b83292fa6ae0f7cd1e329a30541e63c75671f658c80c2b7c4093ee6"
+content-hash = "aa8778026cd61fdf9b198224af216dafc02982e92682b2ecb63e3a85d1d0dcc4"
diff --git a/pyproject.toml b/pyproject.toml
index 1da5e61..05e85f5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -11,7 +11,7 @@ linkml-runtime = ">=1.5.2"
asteval = "^0.9.29"
deepdiff = "^6.7.1"
pydantic = "^2.5.3"
-pyoxigraph = "^0.3.22"
+ucumvert = "^0.1.1"
[tool.poetry.dev-dependencies]
pytest = "^7.3.1"
diff --git a/src/linkml_transformer/functions/unit_conversion.py b/src/linkml_transformer/functions/unit_conversion.py
index 28af916..49f771d 100644
--- a/src/linkml_transformer/functions/unit_conversion.py
+++ b/src/linkml_transformer/functions/unit_conversion.py
@@ -1,29 +1,30 @@
"""
Basic unit conversion functions.
-Currently uses pint, which is an optional dependency. But
-note that pint may not work well with UCUM, see:
+Currently only native pint units or UCUM units are supported.
-- https://github.com/hgrecco/pint/issues/1769
+For UCUM, the ucumvert library is used to convert UCUM units to pint units,
+see ``_.
"""
-import re
from enum import Enum
from functools import lru_cache
from typing import Any, Optional
+import lark
+import pint
+from ucumvert import PintUcumRegistry
+
class UnitSystem(str, Enum):
+ """Enumeration of supported unit systems."""
+
UCUM = "ucum"
IEC61360 = "iec61360"
- SI = "si"
+ SI = "SI"
-# TODO: this is currently highly incomplete; consider deriving from established mappings
-MAPPINGS = {
- UnitSystem.UCUM: {
- "mo": "month",
- "Cel": "degC",
- },
+REGISTRIES = {
+ UnitSystem.UCUM: PintUcumRegistry(),
}
@@ -36,6 +37,12 @@ class UndefinedUnitError(Exception):
"""
+class QuantitySyntaxError(Exception):
+ """
+ Raised when a quantity cannot be parsed.
+ """
+
+
class DimensionalityError(Exception):
"""
Raised when a unit conversion cannot be performed.
@@ -51,10 +58,25 @@ def convert_units(
"""
Convert a quantity between units.
+ >>> convert_units(1, "m", "cm")
+ 100.0
+ >>> convert_units(1, "m", "cm", system=UnitSystem.UCUM)
+ 100.0
+ >>> convert_units(1, "m", "cm", system=UnitSystem.SI)
+ 100.0
+ >>> convert_units(1.0, "hectare", "m^2", system=UnitSystem.SI)
+ 10000.0
+ >>> convert_units(1.0, "hectare", "m ** 2", system=UnitSystem.SI)
+ 10000.0
+ >>> convert_units(1.0, "hectare", "m ** 2", system=None)
+ 10000.0
+ >>> convert_units(1.0, "km2", "m2", system=UnitSystem.UCUM)
+ 1000000.0
+
:param magnitude:
:param from_unit:
:param to_unit:
- :return:
+ :return: converted magnitude
"""
import pint
@@ -63,6 +85,8 @@ def convert_units(
to_unit = normalize_unit(to_unit, system)
try:
from_unit_q = ureg.parse_units(from_unit)
+ except lark.exceptions.UnexpectedCharacters:
+ raise UndefinedUnitError(f"Cannot parse unit: {from_unit}")
except pint.errors.UndefinedUnitError:
raise UndefinedUnitError(f"Unknown source unit: {from_unit}")
quantity = magnitude * from_unit_q
@@ -79,7 +103,30 @@ def get_unit_registry(system: Optional[UnitSystem] = None) -> Any:
"""
Get a unit registry.
- :param system:
+ >>> ureg = get_unit_registry(UnitSystem.UCUM)
+ >>> ureg.from_ucum("m/s2.kg")
+
+ >>> str(_)
+ '1.0 kilogram * meter / second ** 2'
+ >>> ureg.from_ucum("m[H2O]{35Cel}") # UCUM code with annotation
+
+ >>> _.to("mbar")
+
+ >>> ureg("degC") # a standard pint unit
+
+ >>> ureg.from_ucum("g/m2")
+
+ >>> _.to(ureg.from_ucum("kg/m2"))
+
+ >>> ureg.from_ucum("nmol/mmol{Cre}")
+
+ >>> sireg = get_unit_registry(UnitSystem.SI)
+ >>> sireg("degC")
+
+ >>> sireg("ha")
+
+
+ :param system: currently only supported values are None or UnitSystem.UCUM
:return:
"""
import pint
@@ -87,54 +134,23 @@ def get_unit_registry(system: Optional[UnitSystem] = None) -> Any:
ureg = pint.UnitRegistry()
if not system:
return ureg
- if system not in MAPPINGS:
- raise NotImplementedError(f"Unknown unit system: {system}")
- for k, v in MAPPINGS[system].items():
- ureg.define(f"{k} = {v}")
- return ureg
+ if system in REGISTRIES:
+ return REGISTRIES[system]
+ if system.value in dir(ureg.sys):
+ ureg.default_system = system.value
+ return ureg
+ raise NotImplementedError(f"Unknown unit system: {system}")
def normalize_unit(unit: str, system: Optional[UnitSystem] = None) -> str:
if system is None:
return unit
if system == UnitSystem.UCUM:
- return remove_ucum_annotations(convert_to_exponential_format(convert_dot_to_slash(unit)))
+ try:
+ return str(get_unit_registry(system).from_ucum(unit))
+ except pint.errors.UndefinedUnitError:
+ raise UndefinedUnitError(f"Unknown unit: {unit}")
+ except lark.exceptions.UnexpectedCharacters:
+ raise UndefinedUnitError(f"Cannot parse unit: {unit}")
else:
return unit
-
-
-def remove_ucum_annotations(code: str) -> str:
- """
- Remove UCUM annotations from text.
-
- >>> remove_ucum_annotations("nmol/mmol{Cre}")
- 'nmol/mmol'
-
- :param text:
- :return:
- """
- # Regular expression to find and replace UCUM annotations
- return re.sub(r"\{.*?\}", "", code)
-
-
-def convert_to_exponential_format(code: str) -> str:
- """
- Convert units like g/m2 to g/m^2 in the given text.
-
- >>> convert_to_exponential_format("g/m2")
- 'g/m^2'
-
- """
- # Regular expression to find and replace units like g/m2 to g/m^2
- return re.sub(r"(\w+)/(\w+)(\d+)", r"\1/\2^\3", code)
-
-
-def convert_dot_to_slash(text):
- """
- Convert units from forms like pmol.umol-1 to pmol/umol in the given text.
-
- >>> convert_dot_to_slash("pmol.umol-1")
- 'pmol/umol'
- """
- # Regular expression to find and replace units like pmol.umol-1 to pmol/umol
- return re.sub(r"(\w+)\.(\w+)-1", r"\1/\2", text)
diff --git a/tests/test_compliance/test_compliance_suite.py b/tests/test_compliance/test_compliance_suite.py
index bad8e4f..3160d56 100644
--- a/tests/test_compliance/test_compliance_suite.py
+++ b/tests/test_compliance/test_compliance_suite.py
@@ -515,8 +515,19 @@ def infer_range(v: Any, typ: Optional[str] = None):
("s1", "s1", "pinknoodles", "m", "ucum_code", 1.0, None, UndefinedUnitError, None),
("s1", "s1", "m/s", "cm/s", "ucum_code", 1.0, 100.0, None, None),
("s1", "s1", "m.s-1", "cm.s-1", "ucum_code", 1.0, 100.0, None, None),
- ("s1", "s1", "g.m2-1", "kg.m2-1", "ucum_code", 1.0, 0.001, None, None),
+ (
+ "s1",
+ "s1",
+ "g.m2-1",
+ "kg.m2-1",
+ "ucum_code",
+ 1.0,
+ 0.001,
+ None,
+ "https://github.com/dalito/ucumvert/issues/8",
+ ),
("height_in_m", "height_in_cm", "m", "cm", "ucum_code", 1.0, 100.0, None, None),
+ ("s1", "s1", "m[H2O]{35Cel}", "m[H2O]{35Cel}", "ucum_code", 1.0, 1.0, None, None),
],
)
def test_simple_unit_conversion(