From c1dc47ca25d9e5046eb01e231905124761c2ebe3 Mon Sep 17 00:00:00 2001 From: Michael Milton Date: Tue, 21 May 2024 23:33:02 +1000 Subject: [PATCH 1/3] Add id codegen readme --- codegen/id_mapping/README.md | 4 ++++ 1 file changed, 4 insertions(+) create mode 100644 codegen/id_mapping/README.md diff --git a/codegen/id_mapping/README.md b/codegen/id_mapping/README.md new file mode 100644 index 0000000..90d57de --- /dev/null +++ b/codegen/id_mapping/README.md @@ -0,0 +1,4 @@ +To regenerate the ID mapping types: +```bash +poetry run python codegen/id_mapping/generate.py > unipressed/id_mapping/types.py +``` \ No newline at end of file From 74599d3837cf6518bf9c09efccf2384a09e4f878 Mon Sep 17 00:00:00 2001 From: Michael Milton Date: Thu, 23 May 2024 22:10:10 +1000 Subject: [PATCH 2/3] Add missing __init__, bump dependencies --- poetry.lock | 418 +++++++++--------- pyproject.toml | 5 +- .../dataset/generated_types/__init__.py | 0 3 files changed, 201 insertions(+), 222 deletions(-) create mode 100644 unipressed/dataset/generated_types/__init__.py diff --git a/poetry.lock b/poetry.lock index 3332a72..f37807d 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. [[package]] name = "anyio" @@ -127,6 +127,21 @@ six = ">=1.12.0" astroid = ["astroid (>=1,<2)", "astroid (>=2,<4)"] test = ["astroid (>=1,<2)", "astroid (>=2,<4)", "pytest"] +[[package]] +name = "astunparse" +version = "1.6.3" +description = "An AST unparser for Python" +optional = false +python-versions = "*" +files = [ + {file = "astunparse-1.6.3-py2.py3-none-any.whl", hash = "sha256:c2652417f2c8b5bb325c885ae329bdf3f86424075c4fd1a128674bc6fba4b8e8"}, + {file = "astunparse-1.6.3.tar.gz", hash = "sha256:5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872"}, +] + +[package.dependencies] +six = ">=1.6.1,<2.0" +wheel = ">=0.23.0,<1.0" + [[package]] name = "async-lru" version = "2.0.4" @@ -236,7 +251,6 @@ mypy-extensions = ">=0.4.3" pathspec = ">=0.9.0" platformdirs = ">=2" tomli = {version = ">=1.1.0", markers = "python_full_version < \"3.11.0a7\""} -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\""} [package.extras] @@ -263,17 +277,6 @@ webencodings = "*" [package.extras] css = ["tinycss2 (>=1.1.0,<1.3)"] -[[package]] -name = "cached-property" -version = "1.5.2" -description = "A decorator for caching properties in classes." -optional = false -python-versions = "*" -files = [ - {file = "cached-property-1.5.2.tar.gz", hash = "sha256:9fa5755838eecbb2d234c3aa390bd80fbd3ac6b6869109bfc1b499f7bd89a130"}, - {file = "cached_property-1.5.2-py2.py3-none-any.whl", hash = "sha256:df4f613cf7ad9a588cc381aaf4a512d26265ecebd5eb9e1ba12f1319eb85a6a0"}, -] - [[package]] name = "certifi" version = "2024.2.2" @@ -351,13 +354,13 @@ pycparser = "*" [[package]] name = "cfgv" -version = "3.3.1" +version = "3.4.0" description = "Validate configuration and produce human readable error messages." optional = false -python-versions = ">=3.6.1" +python-versions = ">=3.8" files = [ - {file = "cfgv-3.3.1-py2.py3-none-any.whl", hash = "sha256:c6a0883f3917a037485059700b9e75da2464e6c27051014ad85ba6aaa5884426"}, - {file = "cfgv-3.3.1.tar.gz", hash = "sha256:f5a830efb9ce7a445376bb66ec94c638a9787422f96264c98edc6bdeed8ab736"}, + {file = "cfgv-3.4.0-py2.py3-none-any.whl", hash = "sha256:b7265b1f29fd3316bfcd2b330d63d024f2bfd8bcb8b0272f8e19a504856c48f9"}, + {file = "cfgv-3.4.0.tar.gz", hash = "sha256:e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560"}, ] [[package]] @@ -472,7 +475,6 @@ files = [ [package.dependencies] colorama = {version = "*", markers = "platform_system == \"Windows\""} -importlib-metadata = {version = "*", markers = "python_version < \"3.8\""} [[package]] name = "colorama" @@ -635,18 +637,19 @@ devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benc [[package]] name = "filelock" -version = "3.12.2" +version = "3.14.0" description = "A platform independent file lock." optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "filelock-3.12.2-py3-none-any.whl", hash = "sha256:cbb791cdea2a72f23da6ac5b5269ab0a0d161e9ef0100e653b69049a7706d1ec"}, - {file = "filelock-3.12.2.tar.gz", hash = "sha256:002740518d8aa59a26b0c76e10fb8c6e15eae825d34b6fdf670333fd7b938d81"}, + {file = "filelock-3.14.0-py3-none-any.whl", hash = "sha256:43339835842f110ca7ae60f1e1c160714c5a6afd15a2873419ab185334975c0f"}, + {file = "filelock-3.14.0.tar.gz", hash = "sha256:6ea72da3be9b8c82afd3edcf99f2fffbb5076335a5ae4d03248bb5b6c3eae78a"}, ] [package.extras] -docs = ["furo (>=2023.5.20)", "sphinx (>=7.0.1)", "sphinx-autodoc-typehints (>=1.23,!=1.23.4)"] -testing = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "diff-cover (>=7.5)", "pytest (>=7.3.1)", "pytest-cov (>=4.1)", "pytest-mock (>=3.10)", "pytest-timeout (>=2.1)"] +docs = ["furo (>=2023.9.10)", "sphinx (>=7.2.6)", "sphinx-autodoc-typehints (>=1.25.2)"] +testing = ["covdefaults (>=2.3)", "coverage (>=7.3.2)", "diff-cover (>=8.0.1)", "pytest (>=7.4.3)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)", "pytest-timeout (>=2.2)"] +typing = ["typing-extensions (>=4.8)"] [[package]] name = "fqdn" @@ -678,17 +681,17 @@ dev = ["flake8", "markdown", "twine", "wheel"] [[package]] name = "griffe" -version = "0.30.1" +version = "0.45.1" description = "Signatures for entire Python programs. 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"pytest-flake8", "pytest-mypy (>=0.9.1)"] +docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +testing = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] [metadata] lock-version = "2.0" -python-versions = "^3.7" -content-hash = "ca8afac6b5872e3ae009278a12576baebfe5f8d349b442fc1ea92106357fa6f6" +python-versions = "^3.8" +content-hash = "18ab9be9d34d20eb3da46b9b9a8aac08b4e903ec0bf6c947f97abede9a0c2dad" diff --git a/pyproject.toml b/pyproject.toml index a4ef96e..9b0f945 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,16 +9,17 @@ homepage = "https://multimeric.github.io/Unipressed" repository = "https://github.com/multimeric/Unipressed" [tool.poetry.dependencies] -python = "^3.7" +python = "^3.8" requests = "^2.28.1" typing-extensions = "^4.3.0" +mkdocstrings-python = "^1.10.2" [tool.poetry.group.tests.dependencies] pytest = { version = "^7.1.2" } fastaparser = "^1.1" [tool.poetry.group.docs.dependencies] -mkdocstrings = { extras = ["python"], version = "^0.19.0" } +mkdocstrings = { version = "^0.25.1" } mkdocs = { version = "^1.3.1" } mkdocs-material = { version = "^8.3.9" } mkdocs-include-markdown-plugin = { version = "^3.6.1" } diff --git a/unipressed/dataset/generated_types/__init__.py b/unipressed/dataset/generated_types/__init__.py new file mode 100644 index 0000000..e69de29 From 0a90f4c6c2b15d91233302f966ac204bff304826 Mon Sep 17 00:00:00 2001 From: Michael Milton Date: Thu, 23 May 2024 22:13:05 +1000 Subject: [PATCH 3/3] Use 3.12 and not 3.7 in CI --- .github/workflows/build.yaml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml index 83142a7..91c49c5 100644 --- a/.github/workflows/build.yaml +++ b/.github/workflows/build.yaml @@ -7,7 +7,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"] + python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"] steps: - uses: actions/checkout@v3 @@ -25,14 +25,12 @@ jobs: run: poetry install --with lint --with tests - uses: pre-commit/action@v3.0.0 - if: matrix['python-version'] != '3.7' - name: Test with pytest run: | poetry run pytest - name: Test readme notebook - if: matrix['python-version'] != '3.7' run: | poetry install --with readme poetry run jupyter nbconvert --to markdown README.ipynb