From 5f1e4b6a5c1f69a58746cd36534a91510d3a6e46 Mon Sep 17 00:00:00 2001 From: Dominik Gresch Date: Fri, 21 Feb 2025 00:25:00 +0100 Subject: [PATCH] Update dependencies - remove dependency upper limits - update poetry lockfile - adapt to numpy 2.x (use np.round instead of np.round_) - get rid of CI workflow interpolation step - update pre-commit hooks --- .github/workflows/ci.yml | 2 +- .github/workflows_source/ci.yml | 99 - .pre-commit-config.yaml | 42 +- doc/source/conf.py | 1 - poetry.lock | 3189 ++++++++++++++++++----------- pyproject.toml | 54 +- src/z2pack/fp/kpoint.py | 4 +- src/z2pack/line/_result.py | 2 +- src/z2pack/line/_run.py | 2 +- src/z2pack/surface/_result.py | 2 +- src/z2pack/volume/_result.py | 2 +- utils/interpolate_yaml_anchors.py | 58 - 12 files changed, 2072 insertions(+), 1385 deletions(-) delete mode 100644 .github/workflows_source/ci.yml delete mode 100755 utils/interpolate_yaml_anchors.py diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index c84f9f3a..4cfcf741 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -40,7 +40,7 @@ jobs: env: READTHEDOCS: 'True' run: SPHINXOPTS='-nW' make -C doc html - - uses: actions/upload-artifact@v2 + - uses: actions/upload-artifact@v4 with: name: doc-build path: doc/build/html diff --git a/.github/workflows_source/ci.yml b/.github/workflows_source/ci.yml deleted file mode 100644 index 4cbfc8bc..00000000 --- a/.github/workflows_source/ci.yml +++ /dev/null @@ -1,99 +0,0 @@ -name: Continuous Integration - -on: - pull_request: - push: - tags: - - "*" - branches: - - main - workflow_dispatch: - inputs: - -_anchors: - checkout: &CHECKOUT - name: Checkout code - uses: actions/checkout@v2 - - apt-dependencies: &APT_DEPENDENCIES - name: Install apt dependencies - run: | - sudo apt update -qq - sudo apt install -qq graphviz - - pip-cache: &PIP_CACHE - uses: actions/cache@v2 - with: - path: ~/.cache/pip - key: pip-${{ matrix.python-version }}-${{ matrix.install-type }}-${{ hashFiles('**/setup.json') }} - restore-keys: pip-${{ matrix.python-version }}-${{ matrix.install-type }} - - python-setup: &PYTHON_SETUP - name: Set up Python - uses: actions/setup-python@v2 - with: - python-version: ${{ matrix.python-version }} - - install-project: &INSTALL_PROJECT - name: Install the python project - env: - INSTALL_TYPE: ${{ matrix.install-type }} - run: .ci/install_script.sh - -jobs: - docs: - runs-on: ubuntu-latest - strategy: - matrix: - python-version: ["3.12"] - install-type: [dev] - steps: - - *CHECKOUT - - *APT_DEPENDENCIES - - *PIP_CACHE - - *PYTHON_SETUP - - *INSTALL_PROJECT - - name: Build documentation - env: - READTHEDOCS: "True" - run: SPHINXOPTS='-nW' make -C doc html - - uses: actions/upload-artifact@v2 - with: - name: doc-build - path: doc/build/html - - pre-commit: - runs-on: ubuntu-latest - strategy: - matrix: - python-version: ["3.12"] - install-type: [dev] - steps: - - *CHECKOUT - - *APT_DEPENDENCIES - - *PIP_CACHE - - *PYTHON_SETUP - - *INSTALL_PROJECT - - name: Run pre-commit - run: pre-commit run --all-files || ( git status --short ; git diff ; exit 1 ) - tests: - runs-on: ubuntu-latest - strategy: - matrix: - python-version: ["3.9", "3.10", "3.11", "3.12"] - install-type: [dev] - include: - - python-version: "3.12" - install-type: dev_sdist - - python-version: "3.12" - install-type: dev_bdist_wheel - steps: - - *CHECKOUT - - *APT_DEPENDENCIES - - *PIP_CACHE - - *PYTHON_SETUP - - *INSTALL_PROJECT - - name: Run pytest - run: pytest --cov=z2pack --cov-config=.coveragerc - - name: Run codecov - run: codecov diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 4e297e66..ce79136d 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,49 +1,31 @@ repos: - repo: https://github.com/asottile/pyupgrade - rev: v3.15.2 + rev: v3.19.1 hooks: - id: pyupgrade args: [--py39-plus] - repo: https://github.com/psf/black - rev: 24.3.0 + rev: 25.1.0 hooks: - id: black - repo: https://github.com/pycqa/isort - rev: 5.13.2 + rev: 6.0.0 hooks: - id: isort +- repo: https://github.com/python-poetry/poetry/ + rev: "2.1.1" + hooks: + - id: poetry-check + name: "poetry: check pyproject.toml syntax" + - id: poetry-check + name: "poetry: check poetry.lock consistency" + args: ["--lock"] + files: '^(pyproject\.toml|poetry\.lock)$' - repo: local hooks: - - id: poetry-pyproject-check - name: "poetry: pyproject.toml check" - language: system - entry: poetry - args: ["check"] - files: '^(pyproject\.toml)$' - pass_filenames: false - - - id: poetry-lockfile-consistency - name: "poetry: lockfile consistency check" - language: system - entry: poetry - args: ['lock', '--check'] - files: '^(pyproject\.toml)|(poetry\.lock)$' - pass_filenames: false - - id: pylint name: pylint entry: pylint language: system types: [python] exclude: '^(doc/)|(examples/)|(futures/)|(utils/)' - - - id: interpolate-workflows - name: Interpolate Github workflows - entry: python ./utils/interpolate_yaml_anchors.py - language: system - files: | - (?x)^( - .github/(.)*| - utils/interpolate_yaml_anchors.py - )$ - pass_filenames: false diff --git a/doc/source/conf.py b/doc/source/conf.py index e9039165..53dce36e 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -120,7 +120,6 @@ # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. html_theme = "sphinx_rtd_theme" -html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the diff --git a/poetry.lock b/poetry.lock index 918a5fbe..7241d8cd 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.1.1 and should not be changed by hand. [[package]] name = "alabaster" @@ -6,67 +6,55 @@ version = "0.7.16" description = "A light, configurable Sphinx theme" optional = false python-versions = ">=3.9" +groups = ["dev"] +markers = "python_version < \"3.11\"" files = [ {file = "alabaster-0.7.16-py3-none-any.whl", hash = "sha256:b46733c07dce03ae4e150330b975c75737fa60f0a7c591b6c8bf4928a28e2c92"}, {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"}, ] [[package]] -name = "astroid" -version = "3.2.4" -description = "An abstract syntax tree for Python with inference support." -optional = false -python-versions = ">=3.8.0" -files = [ - {file = "astroid-3.2.4-py3-none-any.whl", hash = "sha256:413658a61eeca6202a59231abb473f932038fbcbf1666587f66d482083413a25"}, - {file = "astroid-3.2.4.tar.gz", hash = "sha256:0e14202810b30da1b735827f78f5157be2bbd4a7a59b7707ca0bfc2fb4c0063a"}, -] - -[package.dependencies] -typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""} - -[[package]] -name = "atomicwrites" -version = "1.4.1" -description = "Atomic file writes." +name = "alabaster" +version = "1.0.0" +description = "A light, configurable Sphinx theme" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +python-versions = ">=3.10" +groups = ["dev"] +markers = "python_version >= \"3.11\"" files = [ - {file = "atomicwrites-1.4.1.tar.gz", hash = "sha256:81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11"}, + {file = "alabaster-1.0.0-py3-none-any.whl", hash = "sha256:fc6786402dc3fcb2de3cabd5fe455a2db534b371124f1f21de8731783dec828b"}, + {file = "alabaster-1.0.0.tar.gz", hash = "sha256:c00dca57bca26fa62a6d7d0a9fcce65f3e026e9bfe33e9c538fd3fbb2144fd9e"}, ] [[package]] -name = "attrs" -version = "23.2.0" -description = "Classes Without Boilerplate" +name = "astroid" +version = "3.3.8" +description = "An abstract syntax tree for Python with inference support." optional = false -python-versions = ">=3.7" +python-versions = ">=3.9.0" +groups = ["dev"] files = [ - {file = "attrs-23.2.0-py3-none-any.whl", hash = "sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1"}, - {file = "attrs-23.2.0.tar.gz", hash = "sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30"}, + {file = "astroid-3.3.8-py3-none-any.whl", hash = "sha256:187ccc0c248bfbba564826c26f070494f7bc964fd286b6d9fff4420e55de828c"}, + {file = "astroid-3.3.8.tar.gz", hash = "sha256:a88c7994f914a4ea8572fac479459f4955eeccc877be3f2d959a33273b0cf40b"}, ] -[package.extras] -cov = ["attrs[tests]", "coverage[toml] (>=5.3)"] -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-mypy = ["mypy (>=1.6)", "pytest-mypy-plugins"] -tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist[psutil]"] +[package.dependencies] +typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""} [[package]] name = "babel" -version = "2.14.0" +version = "2.17.0" description = "Internationalization utilities" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" +groups = ["dev"] files = [ - {file = "Babel-2.14.0-py3-none-any.whl", hash = "sha256:efb1a25b7118e67ce3a259bed20545c29cb68be8ad2c784c83689981b7a57287"}, - {file = "Babel-2.14.0.tar.gz", hash = "sha256:6919867db036398ba21eb5c7a0f6b28ab8cbc3ae7a73a44ebe34ae74a4e7d363"}, + {file = "babel-2.17.0-py3-none-any.whl", hash = "sha256:4d0b53093fdfb4b21c92b5213dba5a1b23885afa8383709427046b21c366e5f2"}, + {file = "babel-2.17.0.tar.gz", hash = "sha256:0c54cffb19f690cdcc52a3b50bcbf71e07a808d1c80d549f2459b9d2cf0afb9d"}, ] [package.extras] -dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"] +dev = ["backports.zoneinfo ; 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-description = "Automating the computation of topological numbers of band-structures.." -authors = ["Dominik Gresch "] +version = "2.2.1" +description = "Automating the computation of topological numbers of band-structures." +authors = [{ name ="Dominik Gresch", email = "mail@greschd.ch" }] license = "GPL" readme = "README.md" documentation = "https://z2pack.greschd.ch" @@ -37,33 +37,30 @@ keywords = [ packages = [ { include = "z2pack", from = "src" }, ] +requires-python = ">=3.9" +dependencies = [ + "numpy>=1.20", + "scipy>=1.7", + "decorator>=5.0", + "blessings>=1.7", + "sortedcontainers>=2.4.0", + "msgpack>=1.0", + "fsc.locker>=1.1.0", + "fsc.formatting>=1.0.0", + "fsc.iohelper>=1.0.3", +] -[tool.poetry.dependencies] -python = ">=3.9,<3.13" -numpy = "^1.20" -scipy = "^1.7" -decorator = "^5.0" -blessings = "^1.7" -sortedcontainers = "^2.4.0" -msgpack = "^1.0" -"fsc.locker" = "^1.1.0" -"fsc.formatting" = "^1.0.0" -"fsc.iohelper" = "^1.0.3" -matplotlib = { version = "^3", optional = true } -tbmodels = { version = "^1.1", optional = true } +[project.optional-dependencies] +plot = [ "matplotlib>=3" ] +tb = [ "tbmodels>=1.1" ] [tool.poetry.group.dev.dependencies] -sphinx = "^5" -sphinx-rtd-theme = "^1.1.1" -pytest = "^6" -pytest-cov = "^4.0.0" -pre-commit = "^3.0.0" -pylint = "^3" -"ruamel.yaml" = "^0.17" - -[tool.poetry.extras] -plot = ["matplotlib"] -tb = ["tbmodels"] +sphinx = ">=5" +sphinx-rtd-theme = ">=1.1.1" +pytest = ">=6" +pytest-cov = ">=4.0.0" +pre-commit = ">=3.0.0" +pylint = ">=3" [tool.black] line-length = 100 @@ -108,6 +105,7 @@ disable = [ "consider-using-f-string", "use-dict-literal", "too-many-arguments", + "too-many-positional-arguments", ] [tool.pylint.design] diff --git a/src/z2pack/fp/kpoint.py b/src/z2pack/fp/kpoint.py index bd28be83..ef0a89d2 100644 --- a/src/z2pack/fp/kpoint.py +++ b/src/z2pack/fp/kpoint.py @@ -45,7 +45,7 @@ def _check_dim(fct, kpt): def _check_closed(fct, kpt): """Checks whether the k-point list forms a closed loop.""" delta = kpt[-1] - kpt[0] - if not np.isclose(np.round_(delta), delta).all(): + if not np.isclose(np.round(delta), delta).all(): raise ValueError("The k-point line does not form a closed loop.") return fct(kpt) @@ -133,7 +133,7 @@ def wannier90_nnkpts(kpt): num_kpt = len(kpt) - 1 bz_diff = [np.zeros(3, dtype=int) for _ in range(num_kpt - 1)] # check whether the last k-point is in a different UC - bz_diff.append(np.array(np.round_(kpt[-1] - kpt[0]), dtype=int)) + bz_diff.append(np.array(np.round(kpt[-1] - kpt[0]), dtype=int)) string = "begin nnkpts\n" for i, k in enumerate(bz_diff): j = (i + 1) % num_kpt diff --git a/src/z2pack/line/_result.py b/src/z2pack/line/_result.py index d11eb669..271814cb 100644 --- a/src/z2pack/line/_result.py +++ b/src/z2pack/line/_result.py @@ -1,4 +1,4 @@ -""""Defines the result (data + convergence information) object for line calculations.""" +""" "Defines the result (data + convergence information) object for line calculations.""" from .._result import Result diff --git a/src/z2pack/line/_run.py b/src/z2pack/line/_run.py index 017cd336..25e003f1 100644 --- a/src/z2pack/line/_run.py +++ b/src/z2pack/line/_run.py @@ -114,7 +114,7 @@ def _run_line_impl(*controls, system, line, save_file=None, init_result=None, se """ # check if the line function is closed (up to an inverse lattice vector) delta = np.array(line(1)) - np.array(line(0)) - if not np.isclose(np.round_(delta), delta).all(): + if not np.isclose(np.round(delta), delta).all(): raise ValueError( "Start and end points of the line differ by {}, which is not an inverse lattice vector.".format( delta diff --git a/src/z2pack/surface/_result.py b/src/z2pack/surface/_result.py index e06b726b..ec935bab 100644 --- a/src/z2pack/surface/_result.py +++ b/src/z2pack/surface/_result.py @@ -1,4 +1,4 @@ -""""Defines the result (data + convergence information) object for surface calculations.""" +""" "Defines the result (data + convergence information) object for surface calculations.""" from .._result import Result diff --git a/src/z2pack/volume/_result.py b/src/z2pack/volume/_result.py index f313a075..e7db87b6 100644 --- a/src/z2pack/volume/_result.py +++ b/src/z2pack/volume/_result.py @@ -1,4 +1,4 @@ -""""Defines the result (data + convergence information) object for volume calculations.""" +""" "Defines the result (data + convergence information) object for volume calculations.""" from .._result import Result diff --git a/utils/interpolate_yaml_anchors.py b/utils/interpolate_yaml_anchors.py deleted file mode 100755 index a62bf96c..00000000 --- a/utils/interpolate_yaml_anchors.py +++ /dev/null @@ -1,58 +0,0 @@ -#!/usr/bin/env python - -# Copyright © 2020 Elijah Shaw-Rutschman - -# Permission is hereby granted, free of charge, to any person obtaining a copy -# of this software and associated documentation files (the “Software”), to deal -# in the Software without restriction, including without limitation the rights -# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -# copies of the Software, and to permit persons to whom the Software is -# furnished to do so, subject to the following conditions: -# -# The above copyright notice and this permission notice shall be included in all -# copies or substantial portions of the Software. -# -# THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -# SOFTWARE. -""" -Interpolates aliases in YAML. -""" - -import pathlib - -from ruamel import yaml - - -class InterpolatingDumper(yaml.RoundTripDumper): - def ignore_aliases(self, data): - # Always interpolate aliases - return True - - -def interpolate_aliases(in_stream, out_stream): - data = yaml.load(in_stream, Loader=yaml.RoundTripLoader) - if "_anchors" in data: - # Remove top-level _anchors section - del data["_anchors"] - out_stream.write(yaml.dump(data, Dumper=InterpolatingDumper)) - - -if __name__ == "__main__": - ROOT_DIR = pathlib.Path(__file__).absolute().parent.parent - GITHUB_DIR = ROOT_DIR / ".github" - - TEMPLATE_DIR = GITHUB_DIR / "workflows_source" - assert TEMPLATE_DIR.exists() - - WORKFLOW_DIR = GITHUB_DIR / "workflows" - assert WORKFLOW_DIR.exists() - - for in_file in TEMPLATE_DIR.iterdir(): - out_file = WORKFLOW_DIR / in_file.name - with open(in_file) as in_f, open(out_file, "w") as out_f: - interpolate_aliases(in_f, out_f)