diff --git a/CHANGELOG.md b/CHANGELOG.md index dee79fe..3958ae5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,22 +7,43 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [Releases](https://github.com/cancerDHC/sheet2linkml/releases) -## [v1.0.0](https://github.com/cancerDHC/sheet2linkml/releases/tag/v1.0.0) +## [Unreleased] -* First working release of `sheet2linkml` -* Package deployed to PyPI -* In its current state, it is meant to be used only as a dependency for ccdhmodel -* It is compatible with Python version 3.9 and higher +## [v1.2.0] - 2021-11-29 +* Separate enums from codeable concepts -## [v1.0.1](https://github.com/cancerDHC/sheet2linkml/releases/tag/v1.0.1) +## [v1.1.1] - 2021-11-11 -* Added `python-dotenv` to list of core dependencies +* Updated minimum Python version from 3.9 to 3.7, thanks to changes from v1.1.0 -## [Unreleased] +## [v1.1.0] - 2021-10-28 + +* Retroactive code style formatting of the entire codebase using Black +* Added a Github Action that checks if checked in code is Black formatted +* Modified the code to be compatible with Python versions 3.7 and 3.8 by using `typing.List` and `typing.Dict` +* Added this CHANGELOG + +## [v1.0.1] - 2021-10-04 -## [v1.0.2] +* Improved README +* Moved `python-dotenv` to list of core dependencies + +## [v1.0.0] - 2021-09-30 + +* Added CONTRIBUTING documentation +* Package deployed to PyPI +* In its current state, it is meant to be used only as a dependency for ccdhmodel +* It is compatible with Python version 3.9 and higher + +## [v0.0.1] - 2021-09-29 + +* First working release of `sheet2linkml` -* Retroactive black formatting of entire codebase -* Github Action that checks if checked in code is black formatted -* Compatible with Python versions 3.7 and 3.8 +[Unreleased]: https://github.com/cancerDHC/sheet2linkml/compare/v1.2.0...HEAD +[v1.2.0]: https://github.com/cancerDHC/sheet2linkml/compare/v1.1.1...v1.2.0 +[v1.1.1]: https://github.com/cancerDHC/sheet2linkml/compare/v1.1.0...v1.1.1 +[v1.1.0]: https://github.com/cancerDHC/sheet2linkml/compare/v1.0.1...v1.1.0 +[v1.0.1]: https://github.com/cancerDHC/sheet2linkml/compare/v1.0.0...v1.0.1 +[v1.0.0]: https://github.com/cancerDHC/sheet2linkml/compare/v0.0.1...v1.0.0 +[v0.0.1]: https://github.com/cancerDHC/sheet2linkml/releases/tag/v0.0.1 diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 43ac44d..6afb96b 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -57,6 +57,30 @@ poetry run black ~/path/to/directory ## Release process +The branch names follow the convention described by the [git flow](https://nvie.com/posts/a-successful-git-branching-model/) +branching model. Release branches are created to support the preparation of a new production release. + +Steps to follow when issuing a new release: + +``` +git checkout -b release-1.2 develop # Switched to a new branch "release-1.2" + +# minor bug fixes and preparing metadata for a release +# e.g., version number, build dates +# commit changes + +# merge changes into "main" +git checkout main # switched to branch "main" +git merge --no-ff release-1.2 # merge into "main" with summary of changes + +# merge changes into "develop" +git checkout develop # switched to branch "develop" +git merge --no-ff release-1.2 # merge into "develop" with summary of changes + +# remove release branch +git branch -d release-1.2 # deleted branch release-1.2 +``` + 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. diff --git a/poetry.lock b/poetry.lock index a73c33f..9d0e33d 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,7 +1,7 @@ [[package]] name = "antlr4-python3-runtime" -version = "4.9.2" -description = "ANTLR 4.9.2 runtime for Python 3.7" +version = "4.9.3" +description = "ANTLR 4.9.3 runtime for Python 3.7" category = "main" optional = false python-versions = "*" @@ -22,7 +22,7 @@ tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (> [[package]] name = "black" -version = "21.9b0" +version = "21.11b1" description = "The uncompromising code formatter." category = "main" optional = false @@ -33,8 +33,9 @@ click = ">=7.1.2" mypy-extensions = ">=0.4.3" pathspec = ">=0.9.0,<1" platformdirs = ">=2" -regex = ">=2020.1.8" +regex = ">=2021.4.4" tomli = ">=0.2.6,<2.0.0" +typed-ast = {version = ">=1.4.2", markers = "python_version < \"3.8\" and implementation_name == \"cpython\""} typing-extensions = [ {version = ">=3.10.0.0", markers = "python_version < \"3.10\""}, {version = "!=3.10.0.1", markers = "python_version >= \"3.10\""}, @@ -42,9 +43,9 @@ typing-extensions = [ [package.extras] colorama = ["colorama (>=0.4.3)"] -d = ["aiohttp (>=3.6.0)", "aiohttp-cors (>=0.4.0)"] +d = ["aiohttp (>=3.7.4)"] jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"] -python2 = ["typed-ast (>=1.4.2)"] +python2 = ["typed-ast (>=1.4.3)"] uvloop = ["uvloop (>=0.15.2)"] [[package]] @@ -57,7 +58,7 @@ python-versions = "~=3.5" [[package]] name = "certifi" -version = "2021.5.30" +version = "2021.10.8" description = "Python package for providing Mozilla's CA Bundle." category = "main" optional = false @@ -65,7 +66,7 @@ python-versions = "*" [[package]] name = "charset-normalizer" -version = "2.0.6" +version = "2.0.8" description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." category = "main" optional = false @@ -76,7 +77,7 @@ unicode_backport = ["unicodedata2"] [[package]] name = "click" -version = "8.0.1" +version = "8.0.3" description = "Composable command line interface toolkit" category = "main" optional = false @@ -84,6 +85,7 @@ python-versions = ">=3.6" [package.dependencies] colorama = {version = "*", markers = "platform_system == \"Windows\""} +importlib-metadata = {version = "*", markers = "python_version < \"3.8\""} [[package]] name = "colorama" @@ -109,7 +111,7 @@ dev = ["tox", "bump2version (<1)", "sphinx (<2)", "importlib-metadata (<3)", "im [[package]] name = "frozendict" -version = "2.0.6" +version = "2.1.1" description = "A simple immutable dictionary" category = "main" optional = false @@ -117,7 +119,7 @@ python-versions = ">=3.6" [[package]] name = "google-api-core" -version = "2.0.1" +version = "2.2.2" description = "Google API client core library" category = "main" optional = false @@ -125,18 +127,18 @@ python-versions = ">=3.6" [package.dependencies] google-auth = ">=1.25.0,<3.0dev" -googleapis-common-protos = ">=1.6.0,<2.0dev" +googleapis-common-protos = ">=1.52.0,<2.0dev" protobuf = ">=3.12.0" requests = ">=2.18.0,<3.0.0dev" [package.extras] -grpc = ["grpcio (>=1.33.2,<2.0dev)"] +grpc = ["grpcio (>=1.33.2,<2.0dev)", "grpcio-status (>=1.33.2,<2.0dev)"] grpcgcp = ["grpcio-gcp (>=0.2.2)"] grpcio-gcp = ["grpcio-gcp (>=0.2.2)"] [[package]] name = "google-api-python-client" -version = "2.23.0" +version = "2.31.0" description = "Google API Client Library for Python" category = "main" optional = false @@ -147,23 +149,24 @@ google-api-core = ">=1.21.0,<3.0.0dev" google-auth = ">=1.16.0,<3.0.0dev" google-auth-httplib2 = ">=0.1.0" httplib2 = ">=0.15.0,<1dev" -uritemplate = ">=3.0.0,<4dev" +uritemplate = ">=3.0.0,<5" [[package]] name = "google-auth" -version = "2.2.1" +version = "2.3.3" description = "Google Authentication Library" category = "main" optional = false -python-versions = ">= 3.6" +python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*" [package.dependencies] cachetools = ">=2.0.0,<5.0" pyasn1-modules = ">=0.2.1" -rsa = ">=3.1.4,<5" +rsa = {version = ">=3.1.4,<5", markers = "python_version >= \"3.6\""} +six = ">=1.9.0" [package.extras] -aiohttp = ["aiohttp (>=3.6.2,<4.0.0dev)", "requests (>=2.20.0,<3.0.0dev)"] +aiohttp = ["requests (>=2.20.0,<3.0.0dev)", "aiohttp (>=3.6.2,<4.0.0dev)"] pyopenssl = ["pyopenssl (>=20.0.0)"] reauth = ["pyu2f (>=0.1.5)"] @@ -219,23 +222,55 @@ python-versions = ">=3.7" [[package]] name = "httplib2" -version = "0.19.1" +version = "0.20.2" description = "A comprehensive HTTP client library." category = "main" optional = false -python-versions = "*" +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [package.dependencies] -pyparsing = ">=2.4.2,<3" +pyparsing = {version = ">=2.4.2,<3.0.0 || >3.0.0,<3.0.1 || >3.0.1,<3.0.2 || >3.0.2,<3.0.3 || >3.0.3,<4", markers = "python_version > \"3.0\""} [[package]] name = "idna" -version = "3.2" +version = "3.3" description = "Internationalized Domain Names in Applications (IDNA)" category = "main" optional = false python-versions = ">=3.5" +[[package]] +name = "importlib-metadata" +version = "4.8.2" +description = "Read metadata from Python packages" +category = "main" +optional = false +python-versions = ">=3.6" + +[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)"] + +[[package]] +name = "importlib-resources" +version = "5.4.0" +description = "Read resources from Python packages" +category = "main" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""} + +[package.extras] +docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"] +testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-black (>=0.3.7)", "pytest-mypy"] + [[package]] name = "isodate" version = "0.6.0" @@ -283,7 +318,7 @@ hbreader = "*" [[package]] name = "jsonschema" -version = "4.0.1" +version = "4.2.1" description = "An implementation of JSON Schema validation for Python" category = "main" optional = false @@ -291,6 +326,8 @@ python-versions = ">=3.7" [package.dependencies] 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" [package.extras] @@ -299,7 +336,7 @@ format_nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339- [[package]] name = "linkml-runtime" -version = "1.1.2" +version = "1.1.7" description = "LinkML Runtime Environment" category = "main" optional = false @@ -323,7 +360,7 @@ shexjsg = ">=0.7,<1.0" [[package]] name = "lxml" -version = "4.6.3" +version = "4.6.4" description = "Powerful and Pythonic XML processing library combining libxml2/libxslt with the ElementTree API." category = "main" optional = false @@ -393,11 +430,11 @@ test = ["pytest"] [[package]] name = "protobuf" -version = "3.18.0" +version = "3.19.1" description = "Protocol Buffers" category = "main" optional = false -python-versions = "*" +python-versions = ">=3.5" [[package]] name = "pyasn1" @@ -466,11 +503,14 @@ requests = ["requests"] [[package]] name = "pyparsing" -version = "2.4.7" +version = "3.0.6" description = "Python parsing module" category = "main" optional = false -python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" +python-versions = ">=3.6" + +[package.extras] +diagrams = ["jinja2", "railroad-diagrams"] [[package]] name = "pyrsistent" @@ -544,7 +584,7 @@ testfixtures = "*" [[package]] name = "regex" -version = "2021.10.8" +version = "2021.11.10" description = "Alternative regular expression module, to replace re." category = "main" optional = false @@ -585,11 +625,11 @@ rsa = ["oauthlib[signedtoken] (>=3.0.0)"] [[package]] name = "rsa" -version = "4.7.2" +version = "4.8" description = "Pure-Python RSA implementation" category = "main" optional = false -python-versions = ">=3.5, <4" +python-versions = ">=3.6,<4" [package.dependencies] pyasn1 = ">=0.1.3" @@ -628,27 +668,35 @@ test = ["pytest (>=3.6)", "pytest-cov", "pytest-django", "zope.component", "sybi [[package]] name = "tomli" -version = "1.2.1" +version = "1.2.2" description = "A lil' TOML parser" category = "main" optional = false python-versions = ">=3.6" +[[package]] +name = "typed-ast" +version = 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fddfef7..3f32c17 100644 --- a/sheet2linkml/source/gsheetmodel/entity.py +++ b/sheet2linkml/source/gsheetmodel/entity.py @@ -411,13 +411,6 @@ def as_linkml(self, root_uri) -> SlotDefinition: examples = [Example(value=example) for example in examples] attribute_range = self.range - # For CodeableConcepts, we currently replace it with an enumeration. - # In future versions, we will instead constrain the CodeableConcept's codes in some way. - if self.terminology_service and attribute_range == "CodeableConcept": - # Logically, we should be able to set `attribute_range` to the EnumDefinition. - # But LinkML doesn't support that yet. 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