From 418deecb764917745be54f1ea7a47b82497dd5b7 Mon Sep 17 00:00:00 2001 From: zethson Date: Mon, 21 Oct 2024 14:54:38 +0200 Subject: [PATCH] Fix Numpy 2.x compatibility Signed-off-by: zethson --- .github/workflows/release.yml | 8 +- .github/workflows/test.yml | 6 +- .travis.yml | 47 - fcsparser/api.py | 7 +- poetry.lock | 2203 +++++++++++++++++---------------- pyproject.toml | 5 +- 6 files changed, 1150 insertions(+), 1126 deletions(-) delete mode 100644 .travis.yml diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index f08c69f..9791344 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -17,13 +17,13 @@ jobs: if: github.ref == 'refs/heads/master' runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Install poetry run: pipx install poetry==$POETRY_VERSION - - name: Set up Python 3.10 - uses: actions/setup-python@v4 + - name: Set up Python 3.11 + uses: actions/setup-python@v5 with: - python-version: "3.10" + python-version: "3.11" cache: "poetry" - name: Build project for distribution run: poetry build diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index cb6bfb5..b794d13 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -13,16 +13,16 @@ jobs: strategy: matrix: python-version: - - "3.8" - "3.9" - "3.10" - "3.11" + - "3.12" steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Install poetry run: pipx install poetry==$POETRY_VERSION - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} cache: "poetry" diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index fddb100..0000000 --- a/.travis.yml +++ /dev/null @@ -1,47 +0,0 @@ -language: python - -sudo: false - - -cache: - directories: - - ~/.cache/pip - -env: - global: - - PIP_WHEEL_DIR=$HOME/.cache/pip/wheels - - PIP_FIND_LINKS=file://$HOME/.cache/pip/wheels - -matrix: - include: - - python: 2.7 - env: PANDAS=0.16.2 - - python: 2.7 - env: PANDAS=0.17.1 - - python: 2.7 - env: PANDAS=0.18.1 - - python: 3.5 - env: PANDAS=0.16.2 - - python: 3.5 - env: PANDAS=0.17.1 - - python: 3.5 - env: PANDAS=0.18.1 - -before_install: - - pip install -U pip - - pip install wheel - - -install: - - pip wheel numpy - - pip wheel -r requirements.test.txt - - - pip install numpy - - pip install -r requirements.test.txt - - pip install pandas==$PANDAS - -script: - - py.test fcsparser/ --cov fcsparser -v --cov-report term-missing - -after_success: - - coveralls diff --git a/fcsparser/api.py b/fcsparser/api.py index 5c8af94..8319605 100644 --- a/fcsparser/api.py +++ b/fcsparser/api.py @@ -577,10 +577,13 @@ def read_data(self, file_handle): ## # Convert to native byte order # This is needed for working with pandas data structures - native_code = "<" if (sys.byteorder == "little") else ">" + sys_is_le = sys.byteorder == 'little' + native_code = '<' if sys_is_le else '>' + swapped_code = '>' if sys_is_le else '<' if endian != native_code: # swaps the actual bytes and also the endianness - data = data.byteswap().newbyteorder() + # updated to be numpy>= 2.0 compliant + data = data.view(data.dtype.newbyteorder(swapped_code)).byteswap() # Mask off high bits if integer type data if text["$DATATYPE"] == "I": diff --git a/poetry.lock b/poetry.lock index 9f1320c..4875eaf 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand. 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= "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"}, - {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"}, + {file = "zipp-3.20.2-py3-none-any.whl", hash = "sha256:a817ac80d6cf4b23bf7f2828b7cabf326f15a001bea8b1f9b49631780ba28350"}, + {file = "zipp-3.20.2.tar.gz", hash = "sha256:bc9eb26f4506fda01b81bcde0ca78103b6e62f991b381fec825435c836edbc29"}, ] [package.extras] -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"] +check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"] +cover = ["pytest-cov"] +doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +enabler = ["pytest-enabler (>=2.2)"] +test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] +type = ["pytest-mypy"] [metadata] lock-version = "2.0" -python-versions = "^3.8.0" -content-hash = "d9bf0297d384414e76761abfe6ab79bd9a52159910edf83fff9ad400531702de" +python-versions = "^3.9.0" +content-hash = "e323019ec3fd0da375434f21db0bec190bc1b2335a474f82cc406d3bcce24d6f" diff --git a/pyproject.toml b/pyproject.toml index c440c73..659a0cf 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -15,9 +15,9 @@ classifiers = [ ] [tool.poetry.dependencies] -python = "^3.8.0" +python = "^3.9.0" pandas = ">=1.5.3" -numpy = "^1" +numpy = ">=1.0,<3.0" [tool.poetry.group.dev.dependencies] jupyterlab = "^3" @@ -62,7 +62,6 @@ ignore_missing_imports = "True" [tool.coverage.run] omit = ["tests/*"] - [build-system] requires = ["poetry-core>=1.0.0"] build-backend = "poetry.core.masonry.api"