From 3ca8a7b57383a87b56fb713126169dccbaf45c88 Mon Sep 17 00:00:00 2001 From: David Orme Date: Fri, 13 Dec 2024 19:39:00 +0000 Subject: [PATCH 1/5] Adding pyrealm --- poetry.lock | 145 +++++++++++++++++++++++++++++++++++++++++++++++-- pyproject.toml | 1 + 2 files changed, 141 insertions(+), 5 deletions(-) diff --git a/poetry.lock b/poetry.lock index ae7951a95..7d92e33a2 100644 --- a/poetry.lock +++ b/poetry.lock @@ -727,6 +727,19 @@ files = [ docs = ["ipython", "matplotlib", "numpydoc", "sphinx"] tests = ["pytest", "pytest-cov", "pytest-xdist"] +[[package]] +name = "dacite" +version = "1.8.1" +description = "Simple creation of data classes from dictionaries." +optional = false +python-versions = ">=3.6" +files = [ + {file = "dacite-1.8.1-py3-none-any.whl", hash = "sha256:cc31ad6fdea1f49962ea42db9421772afe01ac5442380d9a99fcf3d188c61afe"}, +] + +[package.extras] +dev = ["black", "coveralls", "mypy", "pre-commit", "pylint", "pytest (>=5)", "pytest-benchmark", "pytest-cov"] + [[package]] name = "dask" version = "2024.12.0" @@ -2025,6 +2038,48 @@ files = [ {file = "markupsafe-3.0.1.tar.gz", hash = "sha256:3e683ee4f5d0fa2dde4db77ed8dd8a876686e3fc417655c2ece9a90576905344"}, ] +[[package]] +name = "marshmallow" +version = "3.23.1" +description = "A lightweight library for converting complex datatypes to and from native Python datatypes." +optional = false +python-versions = ">=3.9" +files = [ + {file = "marshmallow-3.23.1-py3-none-any.whl", hash = "sha256:fece2eb2c941180ea1b7fcbd4a83c51bfdd50093fdd3ad2585ee5e1df2508491"}, + {file = "marshmallow-3.23.1.tar.gz", hash = "sha256:3a8dfda6edd8dcdbf216c0ede1d1e78d230a6dc9c5a088f58c4083b974a0d468"}, +] + +[package.dependencies] +packaging = ">=17.0" + +[package.extras] +dev = ["marshmallow[tests]", "pre-commit (>=3.5,<5.0)", "tox"] +docs = ["alabaster (==1.0.0)", "autodocsumm (==0.2.14)", "sphinx (==8.1.3)", "sphinx-issues (==5.0.0)", "sphinx-version-warning (==1.1.2)"] +tests = ["pytest", "simplejson"] + +[[package]] +name = "marshmallow-dataclass" +version = "8.7.1" +description = "Python library to convert dataclasses into marshmallow schemas." +optional = false +python-versions = ">=3.8" +files = [ + {file = "marshmallow_dataclass-8.7.1-py3-none-any.whl", hash = "sha256:405cbaaad9cea56b3de2f85eff32a9880e3bf849f652e7f6de7395e4b1ddc072"}, + {file = "marshmallow_dataclass-8.7.1.tar.gz", hash = "sha256:4fb80e1bf7b31ce1b192aa87ffadee2cedb3f6f37bb0042f8500b07e6fad59c4"}, +] + +[package.dependencies] +marshmallow = ">=3.18.0" +typeguard = ">=4.0,<5" +typing-extensions = {version = ">=4.2.0", markers = "python_version < \"3.11\""} +typing-inspect = ">=0.9.0" + +[package.extras] +dev = ["pre-commit (>=2.17,<3.0)", "pytest (>=5.4)", "pytest-mypy-plugins (>=1.2.0)", "sphinx"] +docs = ["sphinx"] +lint = ["pre-commit (>=2.17,<3.0)"] +tests = ["pytest (>=5.4)", "pytest-mypy-plugins (>=1.2.0)"] + [[package]] name = "matplotlib" version = "3.9.3" @@ -2653,6 +2708,21 @@ sql-other = ["SQLAlchemy (>=2.0.0)", "adbc-driver-postgresql (>=0.8.0)", "adbc-d test = ["hypothesis (>=6.46.1)", "pytest (>=7.3.2)", "pytest-xdist (>=2.2.0)"] xml = ["lxml (>=4.9.2)"] +[[package]] +name = "pandas-stubs" +version = "2.2.3.241126" +description = "Type annotations for pandas" +optional = false +python-versions = ">=3.10" +files = [ + {file = "pandas_stubs-2.2.3.241126-py3-none-any.whl", hash = "sha256:74aa79c167af374fe97068acc90776c0ebec5266a6e5c69fe11e9c2cf51f2267"}, + {file = "pandas_stubs-2.2.3.241126.tar.gz", hash = "sha256:cf819383c6d9ae7d4dabf34cd47e1e45525bb2f312e6ad2939c2c204cb708acd"}, +] + +[package.dependencies] +numpy = ">=1.23.5" +types-pytz = ">=2022.1.1" + [[package]] name = "pandocfilters" version = "1.5.1" @@ -3058,6 +3128,27 @@ files = [ [package.extras] diagrams = ["jinja2", "railroad-diagrams"] +[[package]] +name = "pyrealm" +version = "2.0.0rc1" +description = "Python tools for modelling plant productivity and demography." +optional = false +python-versions = ">=3.10" +files = [ + {file = "pyrealm-2.0.0rc1-py3-none-any.whl", hash = "sha256:63d573d41bfdfb3c041b966f94c7bbd836aff62476b7f842286bb43616bfa9ab"}, + {file = "pyrealm-2.0.0rc1.tar.gz", hash = "sha256:adf9cadbad85642eefa09d7511a302ad1463ec7b3be3cd60a90c4084d2c8053c"}, +] + +[package.dependencies] +dacite = ">=1.6.0,<2.0.0" +marshmallow = ">=3.22.0,<4.0.0" +marshmallow-dataclass = ">=8.7.0,<9.0.0" +numpy = ">=2.1,<2.2" +pandas = ">=2.2.2,<3.0.0" +pandas-stubs = ">=2.2.2.240909,<3.0.0.0" +scipy = ">=1.7.3,<2.0.0" +tabulate = ">=0.8.10,<0.9.0" + [[package]] name = "pytest" version = "8.3.4" @@ -4194,13 +4285,13 @@ tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"] [[package]] name = "tabulate" -version = "0.9.0" +version = "0.8.10" description = "Pretty-print tabular data" optional = false -python-versions = ">=3.7" +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ - {file = "tabulate-0.9.0-py3-none-any.whl", hash = "sha256:024ca478df22e9340661486f85298cff5f6dcdba14f3813e8830015b9ed1948f"}, - {file = "tabulate-0.9.0.tar.gz", hash = "sha256:0095b12bf5966de529c0feb1fa08671671b3368eec77d7ef7ab114be2c068b3c"}, + {file = "tabulate-0.8.10-py3-none-any.whl", hash = "sha256:0ba055423dbaa164b9e456abe7920c5e8ed33fcc16f6d1b2f2d152c8e1e8b4fc"}, + {file = "tabulate-0.8.10.tar.gz", hash = "sha256:6c57f3f3dd7ac2782770155f3adb2db0b1a269637e42f27599925e64b114f519"}, ] [package.extras] @@ -4364,6 +4455,24 @@ files = [ docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"] test = ["argcomplete (>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0,<8.2)", "pytest-mock", "pytest-mypy-testing"] +[[package]] +name = "typeguard" +version = "4.4.1" +description = "Run-time type checker for Python" +optional = false +python-versions = ">=3.9" +files = [ + {file = "typeguard-4.4.1-py3-none-any.whl", hash = "sha256:9324ec07a27ec67fc54a9c063020ca4c0ae6abad5e9f0f9804ca59aee68c6e21"}, + {file = "typeguard-4.4.1.tar.gz", hash = "sha256:0d22a89d00b453b47c49875f42b6601b961757541a2e1e0ef517b6e24213c21b"}, +] + +[package.dependencies] +typing-extensions = ">=4.10.0" + +[package.extras] +doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme (>=1.3.0)"] +test = ["coverage[toml] (>=7)", "mypy (>=1.2.0)", "pytest (>=7)"] + [[package]] name = "types-dataclasses" version = "0.6.6" @@ -4400,6 +4509,17 @@ files = [ {file = "types_python_dateutil-2.9.0.20241003-py3-none-any.whl", hash = "sha256:250e1d8e80e7bbc3a6c99b907762711d1a1cdd00e978ad39cb5940f6f0a87f3d"}, ] +[[package]] +name = "types-pytz" +version = "2024.2.0.20241003" +description = "Typing stubs for pytz" +optional = false +python-versions = ">=3.8" +files = [ + {file = "types-pytz-2024.2.0.20241003.tar.gz", hash = "sha256:575dc38f385a922a212bac00a7d6d2e16e141132a3c955078f4a4fd13ed6cb44"}, + {file = "types_pytz-2024.2.0.20241003-py3-none-any.whl", hash = "sha256:3e22df1336c0c6ad1d29163c8fda82736909eb977281cb823c57f8bae07118b7"}, +] + [[package]] name = "types-requests" version = "2.32.0.20241016" @@ -4439,6 +4559,21 @@ files = [ {file = "typing_extensions-4.12.2.tar.gz", hash = "sha256:1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8"}, ] +[[package]] +name = "typing-inspect" +version = "0.9.0" +description = "Runtime inspection utilities for typing module." +optional = false +python-versions = "*" +files = [ + {file = "typing_inspect-0.9.0-py3-none-any.whl", hash = "sha256:9ee6fc59062311ef8547596ab6b955e1b8aa46242d854bfc78f4f6b0eff35f9f"}, + {file = "typing_inspect-0.9.0.tar.gz", hash = "sha256:b23fc42ff6f6ef6954e4852c1fb512cdd18dbea03134f91f856a95ccc9461f78"}, +] + +[package.dependencies] +mypy-extensions = ">=0.3.0" +typing-extensions = ">=3.7.4" + [[package]] name = "tzdata" version = "2024.2" @@ -4601,4 +4736,4 @@ type = ["pytest-mypy"] [metadata] lock-version = "2.0" python-versions = ">=3.10,<3.13" -content-hash = "24c8405fe6ac3f9ab5de5dd7abcc2c9b9d7cd0f6ab6715709b5da5f1f61b45e4" +content-hash = "71a24bc9b34165aa9eb553b60b41ec1fdeca692c536c49d7b607e83b9a45a60d" diff --git a/pyproject.toml b/pyproject.toml index d3b5e6c61..7c3b8a672 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -43,6 +43,7 @@ tomli = {version = "^2.0.1", python = "<3.11"} tomli-w = "^1.0.0" tqdm = "^4.66.2" xarray = "^2024.06.0" +pyrealm = {version = "2.0.0-rc.1", allow-prereleases = true} [tool.poetry.group.types.dependencies] types-dataclasses = "^0.6.6" From 214bfbbcdcb6863cf98ee33c83590099e7c1c3ba Mon Sep 17 00:00:00 2001 From: David Orme Date: Sat, 14 Dec 2024 18:22:20 +0000 Subject: [PATCH 2/5] Better way of adding pyrealm --- docs/source/using_the_ve/data/data.md | 2 +- docs/source/using_the_ve/virtual_ecosystem_in_use.md | 2 +- .../implementation/core_components_overview.md | 2 +- poetry.lock | 2 +- pyproject.toml | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/source/using_the_ve/data/data.md b/docs/source/using_the_ve/data/data.md index c4dc61ad1..a25dd125e 100644 --- a/docs/source/using_the_ve/data/data.md +++ b/docs/source/using_the_ve/data/data.md @@ -20,7 +20,7 @@ language_info: name: python nbconvert_exporter: python pygments_lexer: ipython3 - version: 3.11.9 + version: 3.10.14 --- # Adding and using data with the Virtual Ecosystem diff --git a/docs/source/using_the_ve/virtual_ecosystem_in_use.md b/docs/source/using_the_ve/virtual_ecosystem_in_use.md index 12ee3c683..d44926d0b 100644 --- a/docs/source/using_the_ve/virtual_ecosystem_in_use.md +++ b/docs/source/using_the_ve/virtual_ecosystem_in_use.md @@ -19,7 +19,7 @@ language_info: name: python nbconvert_exporter: python pygments_lexer: ipython3 - version: 3.11.9 + version: 3.10.14 --- # Using the Virtual Ecosystem diff --git a/docs/source/virtual_ecosystem/implementation/core_components_overview.md b/docs/source/virtual_ecosystem/implementation/core_components_overview.md index 1207c75b5..9b356d014 100644 --- a/docs/source/virtual_ecosystem/implementation/core_components_overview.md +++ b/docs/source/virtual_ecosystem/implementation/core_components_overview.md @@ -20,7 +20,7 @@ language_info: name: python nbconvert_exporter: python pygments_lexer: ipython3 - version: 3.11.9 + version: 3.10.14 --- # Implementation of the core components diff --git a/poetry.lock b/poetry.lock index 7d92e33a2..a22063bc5 100644 --- a/poetry.lock +++ b/poetry.lock @@ -4736,4 +4736,4 @@ type = ["pytest-mypy"] [metadata] lock-version = "2.0" python-versions = ">=3.10,<3.13" -content-hash = "71a24bc9b34165aa9eb553b60b41ec1fdeca692c536c49d7b607e83b9a45a60d" +content-hash = "811e8e25d4c8b6c854b9d45d2e19608a3d23fb881497e7c120e0ac46816a71e0" diff --git a/pyproject.toml b/pyproject.toml index 7c3b8a672..ee275852e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -43,7 +43,7 @@ tomli = {version = "^2.0.1", python = "<3.11"} tomli-w = "^1.0.0" tqdm = "^4.66.2" xarray = "^2024.06.0" -pyrealm = {version = "2.0.0-rc.1", allow-prereleases = true} +pyrealm = {version = "^2.0.0rc1", allow-prereleases = true} [tool.poetry.group.types.dependencies] types-dataclasses = "^0.6.6" From a853babe6ff8308e7d8a9aefe5319d9ca912fc6b Mon Sep 17 00:00:00 2001 From: David Orme Date: Sun, 15 Dec 2024 16:01:25 +0000 Subject: [PATCH 3/5] Pinning numpy under 2.2.0 --- pyproject.toml | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index ee275852e..a2b659873 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -30,20 +30,20 @@ version = "0.1.1a6" ve_run = "virtual_ecosystem.entry_points:ve_run_cli" [tool.poetry.dependencies] -Shapely = "^2.0" -dask = ">=2023.6,<2025.0" -dpath = "^2.0.6" -jsonschema = "^4.14.0" -netcdf4 = "^1.6.5" -numpy = "^2.0" -pint = "^0.24.1" -python = ">=3.10,<3.13" -scipy = "^1.9.0" -tomli = {version = "^2.0.1", python = "<3.11"} -tomli-w = "^1.0.0" -tqdm = "^4.66.2" -xarray = "^2024.06.0" -pyrealm = {version = "^2.0.0rc1", allow-prereleases = true} +Shapely = "^2.0" +dask = ">=2023.6,<2025.0" +dpath = "^2.0.6" +jsonschema = "^4.14.0" +netcdf4 = "^1.6.5" +numpy = "~2.1" # Pinning numpy less than 2.2.0 until this resolves: https://github.com/numpy/numpy/issues/27957 +pint = "^0.24.1" +pyrealm = {version = "^2.0.0rc1", allow-prereleases = true} +python = ">=3.10,<3.13" +scipy = "^1.9.0" +tomli = {version = "^2.0.1", python = "<3.11"} +tomli-w = "^1.0.0" +tqdm = "^4.66.2" +xarray = "^2024.06.0" [tool.poetry.group.types.dependencies] types-dataclasses = "^0.6.6" From a6a296f5b6ed7ae816c11c99c31c3da52de92a4b Mon Sep 17 00:00:00 2001 From: David Orme Date: Sun, 15 Dec 2024 16:02:07 +0000 Subject: [PATCH 4/5] poetry lock --- poetry.lock | 1546 +++++++++++++++++++++++++-------------------------- 1 file changed, 767 insertions(+), 779 deletions(-) diff --git a/poetry.lock b/poetry.lock index a22063bc5..cdf03b0a9 100644 --- a/poetry.lock +++ b/poetry.lock @@ -13,24 +13,24 @@ files = [ [[package]] name = "anyio" -version = "4.6.2.post1" +version = "4.7.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" optional = false python-versions = ">=3.9" files = [ - {file = "anyio-4.6.2.post1-py3-none-any.whl", hash = "sha256:6d170c36fba3bdd840c73d3868c1e777e33676a69c3a72cf0a0d5d6d8009b61d"}, - {file = "anyio-4.6.2.post1.tar.gz", hash = "sha256:4c8bc31ccdb51c7f7bd251f51c609e038d63e34219b44aa86e47576389880b4c"}, + {file = "anyio-4.7.0-py3-none-any.whl", hash = "sha256:ea60c3723ab42ba6fff7e8ccb0488c898ec538ff4df1f1d5e642c3601d07e352"}, + {file = "anyio-4.7.0.tar.gz", hash = "sha256:2f834749c602966b7d456a7567cafcb309f96482b5081d14ac93ccd457f9dd48"}, ] [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\""} +typing_extensions = {version = ">=4.5", markers = "python_version < \"3.13\""} [package.extras] -doc = ["Sphinx (>=7.4,<8.0)", "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", "truststore (>=0.9.1)", "uvloop (>=0.21.0b1)"] +doc = ["Sphinx (>=7.4,<8.0)", "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", "truststore (>=0.9.1)", "uvloop (>=0.21)"] trio = ["trio (>=0.26.1)"] [[package]] @@ -122,21 +122,18 @@ test = ["dateparser (==1.*)", "pre-commit", "pytest", "pytest-cov", "pytest-mock [[package]] name = "asttokens" -version = "2.4.1" +version = "3.0.0" description = "Annotate AST trees with source code positions" optional = false -python-versions = "*" +python-versions = ">=3.8" files = [ - {file = "asttokens-2.4.1-py2.py3-none-any.whl", hash = "sha256:051ed49c3dcae8913ea7cd08e46a606dba30b79993209636c4875bc1d637bc24"}, - {file = "asttokens-2.4.1.tar.gz", hash = "sha256:b03869718ba9a6eb027e134bfdf69f38a236d681c83c160d510768af11254ba0"}, + {file = "asttokens-3.0.0-py3-none-any.whl", hash = "sha256:e3078351a059199dd5138cb1c706e6430c05eff2ff136af5eb4790f9d28932e2"}, + {file = "asttokens-3.0.0.tar.gz", hash = "sha256:0dcd8baa8d62b0c1d118b399b2ddba3c4aff271d0d7a9e0d4c1681c79035bbc7"}, ] -[package.dependencies] -six = ">=1.12.0" - [package.extras] -astroid = ["astroid (>=1,<2)", "astroid (>=2,<4)"] -test = ["astroid (>=1,<2)", "astroid (>=2,<4)", "pytest"] +astroid = ["astroid (>=2,<4)"] +test = ["astroid (>=2,<4)", "pytest", "pytest-cov", "pytest-xdist"] [[package]] name = "async-lru" @@ -222,31 +219,30 @@ lxml = ["lxml"] [[package]] name = "bleach" -version = "6.1.0" +version = "6.2.0" description = "An easy safelist-based HTML-sanitizing 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e5186fdef15d86e4d58fb20ac65b4ae91e3d51bc Mon Sep 17 00:00:00 2001 From: David Orme Date: Sun, 15 Dec 2024 21:41:47 +0000 Subject: [PATCH 5/5] Pin numpy to 2.1.3 in pre-commit, fix typing issue from mypy update --- .pre-commit-config.yaml | 8 ++++---- virtual_ecosystem/core/registry.py | 4 ++-- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index f8a8aa8b2..c72878584 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -5,18 +5,18 @@ repos: - id: check-merge-conflict - id: debug-statements - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.6.9 + rev: v0.8.3 hooks: - id: ruff # Run the linter. args: [--fix, --exit-non-zero-on-fix] - id: ruff-format # Run the formatter. - repo: https://github.com/pre-commit/mirrors-mypy - rev: "v1.11.2" + rev: "v1.13.0" hooks: - id: mypy - additional_dependencies: [types-jsonschema, xarray, types-tabulate, numpy] + additional_dependencies: [types-jsonschema, xarray, types-tabulate, numpy==2.1.3] - repo: https://github.com/igorshubovych/markdownlint-cli - rev: v0.42.0 + rev: v0.43.0 hooks: - id: markdownlint - repo: https://github.com/mwouts/jupytext diff --git a/virtual_ecosystem/core/registry.py b/virtual_ecosystem/core/registry.py index 03c9eaa2c..756e2f82d 100644 --- a/virtual_ecosystem/core/registry.py +++ b/virtual_ecosystem/core/registry.py @@ -11,7 +11,7 @@ function, which is used to populate the registry with the components of a given module. """ # noqa: D205 -from dataclasses import dataclass, is_dataclass +from dataclasses import dataclass from importlib import import_module, resources from inspect import getmembers, isclass from typing import Any @@ -172,7 +172,7 @@ def register_module(module_name: str) -> None: constants_classes = { class_name: class_obj for class_name, class_obj in getmembers(constants_submodule) - if is_dataclass(class_obj) + if isclass(class_obj) and issubclass(class_obj, ConstantsDataclass) and class_obj is not ConstantsDataclass }