From d5a72bdf3907f257277233e8b253d7a2b694f410 Mon Sep 17 00:00:00 2001 From: Christopher Doris Date: Fri, 6 Sep 2024 11:13:31 +0100 Subject: [PATCH 1/9] build with hatchling and uv --- pyproject.toml | 20 +- uv.lock | 1089 ++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 1097 insertions(+), 12 deletions(-) create mode 100644 uv.lock diff --git a/pyproject.toml b/pyproject.toml index ffd69434..60f9a59a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [build-system] -requires = ["setuptools>=42", "wheel"] -build-backend = "setuptools.build_meta" +requires = ["hatchling"] +build-backend = "hatchling.build" [project] name = "juliacall" @@ -10,17 +10,13 @@ readme = { file = "README.md", content-type = "text/markdown" } classifiers = [ "Programming Language :: Python :: 3", "License :: OSI Approved :: MIT License", - "Operating System :: OS Independent" + "Operating System :: OS Independent", ] -requires-python = ">=3.8" +requires-python = "~=3.8" 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a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -20,13 +20,16 @@ jobs: arch: [x64] # x86 unsupported by MicroMamba os: [ubuntu-latest, windows-latest, macos-latest] jlversion: ['1','1.6'] + steps: - uses: actions/checkout@v2 + - name: Set up Julia ${{ matrix.jlversion }} uses: julia-actions/setup-julia@v1 with: version: ${{ matrix.jlversion }} arch: ${{ matrix.arch }} + - uses: actions/cache@v1 env: cache-name: cache-artifacts @@ -37,19 +40,24 @@ jobs: ${{ runner.os }}-test-${{ env.cache-name }}- ${{ runner.os }}-test- ${{ runner.os }}- + - name: Build package uses: julia-actions/julia-buildpkg@v1 + - name: Run tests uses: julia-actions/julia-runtest@v1 env: JULIA_DEBUG: PythonCall JULIA_NUM_THREADS: '2' + - name: Process coverage uses: julia-actions/julia-processcoverage@v1 + - name: Upload coverage to Codecov uses: codecov/codecov-action@v2 env: CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} + python: name: Test (${{ matrix.os }}, python ${{ matrix.pyversion }}) runs-on: ${{ matrix.os }} @@ -58,33 +66,43 @@ jobs: matrix: os: [ubuntu-latest, windows-latest, macos-latest] pyversion: ["3.x", "3.8"] + steps: - uses: actions/checkout@v3 + - name: Set up Python ${{ matrix.pyversion }} uses: actions/setup-python@v4 with: python-version: ${{ matrix.pyversion }} + - name: Set up Julia uses: julia-actions/setup-julia@v1 with: version: '1' + + - name: Set up UV + uses: astral-sh/setup-uv@v2 + - name: Install dependencies run: | - python -m pip install --upgrade pip - pip install flake8 pytest pytest-cov nbval numpy cp pysrc/juliacall/juliapkg-dev.json pysrc/juliacall/juliapkg.json + uv sync + uv pip install numpy # todo: move into dev-dependencies pip install -e . + - name: Lint with flake8 run: | # stop the build if there are Python syntax errors or undefined names - flake8 . --count --select=E9,F63,F7,F82 --ignore=F821 --show-source --statistics + uv run flake8 . --count --select=E9,F63,F7,F82 --ignore=F821 --show-source --statistics # exit-zero treats all errors as warnings. 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diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index b834e234..5b772b93 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -89,12 +89,8 @@ jobs: - name: Install dependencies run: uv sync - - name: Lint with flake8 - run: | - # stop the build if there are Python syntax errors or undefined names - uv run flake8 ./pysrc --count --select=E9,F63,F7,F82 --ignore=F821 --show-source --statistics - # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide - uv run flake8 ./pysrc --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics + - name: Lint with ruff + run: uv run ruff check --statistics - name: Run tests run: | diff --git a/pyproject.toml b/pyproject.toml index 913d46ab..af0256fa 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,10 +20,13 @@ packages = ["pysrc/juliacall"] [tool.uv] dev-dependencies = [ - "flake8", + "ruff", "pytest", "pytest-cov", "nbval", "numpy", "numpy ~=2.0; python_version >= '3.10'", ] + +[tool.ruff.lint] +select = ["F", "E", "W", "I"] From 16e5940b2a4abe3348f2d5f6c86ecf4f36ef565a Mon Sep 17 00:00:00 2001 From: Christopher Doris Date: Sat, 7 Sep 2024 17:37:44 +0100 Subject: [PATCH 6/9] show full ruff output --- .github/workflows/tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 5b772b93..4cb73394 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -90,7 +90,7 @@ jobs: run: uv sync - name: Lint with ruff - run: uv run ruff check --statistics + run: uv run ruff check - name: Run tests run: | From 985c37833032d3231ad69eaab61d9c5433f63559 Mon Sep 17 00:00:00 2001 From: Christopher Doris Date: Sat, 7 Sep 2024 17:41:19 +0100 Subject: [PATCH 7/9] linting fixes --- examples/flux.ipynb | 6 ++++-- pysrc/juliacall/__init__.py | 4 ++-- pysrc/juliacall/importer.py | 5 +++-- pysrc/juliacall/ipython.py | 8 +++++--- pysrc/juliacall/matplotlib.py | 3 ++- pytest/test_all.py | 3 +++ src/C/find_libpython.py | 6 +++--- 7 files changed, 22 insertions(+), 13 deletions(-) diff --git a/examples/flux.ipynb b/examples/flux.ipynb index c15d8d17..aa290d0f 100644 --- a/examples/flux.ipynb +++ b/examples/flux.ipynb @@ -7,8 +7,10 @@ "metadata": {}, "outputs": [], "source": [ - "import numpy as np, matplotlib.pyplot as plt\n", - "from juliacall import Main as jl, convert as jlconvert" + "import matplotlib.pyplot as plt\n", + "import numpy as np\n", + "from juliacall import Main as jl\n", + "from juliacall import convert as jlconvert" ] }, { diff --git a/pysrc/juliacall/__init__.py b/pysrc/juliacall/__init__.py index 6bc61fd4..7e9e043b 100644 --- a/pysrc/juliacall/__init__.py +++ b/pysrc/juliacall/__init__.py @@ -50,10 +50,10 @@ def backtrace(self): def init(): import atexit - import os import ctypes as c - import sys + import os import subprocess + import sys import warnings # importing pytorch before juliacall sometimes causes segfaults. TODO: remove diff --git a/pysrc/juliacall/importer.py b/pysrc/juliacall/importer.py index 6aea2750..6f386901 100644 --- a/pysrc/juliacall/importer.py +++ b/pysrc/juliacall/importer.py @@ -21,10 +21,11 @@ import io import os import sys - -from . import newmodule, Base from importlib.machinery import ModuleSpec, SourceFileLoader +from . import Base, newmodule + + class Finder: def __init__(self, jlext='.jl', pyext='.py'): self.jlext = jlext diff --git a/pysrc/juliacall/ipython.py b/pysrc/juliacall/ipython.py index 7edc43a4..99eec4da 100644 --- a/pysrc/juliacall/ipython.py +++ b/pysrc/juliacall/ipython.py @@ -12,17 +12,19 @@ - Calling Julia's 'display(x)' function will display 'x' in IPython. """ -from IPython.core.magic import Magics, magics_class, line_cell_magic -from . import Main, PythonCall +from IPython.core.magic import Magics, line_cell_magic, magics_class + import __main__ +from . import Main, PythonCall + _set_var = Main.seval("(k, v) -> @eval $(Symbol(k)) = $v") _get_var = Main.seval("k -> hasproperty(Main, Symbol(k)) ? PythonCall.pyjlraw(getproperty(Main, Symbol(k))) : nothing") _egal = Main.seval("===") @magics_class class JuliaMagics(Magics): - + @line_cell_magic def julia(self, line, cell=None): # parse the line and cell into code and variables diff --git a/pysrc/juliacall/matplotlib.py b/pysrc/juliacall/matplotlib.py index d20debb8..d25cff9d 100644 --- a/pysrc/juliacall/matplotlib.py +++ b/pysrc/juliacall/matplotlib.py @@ -2,8 +2,9 @@ Minimal matplotlib backend which shows plots using Julia's display mechanism. """ -from matplotlib.backend_bases import Gcf, FigureManagerBase +from matplotlib.backend_bases import FigureManagerBase, Gcf from matplotlib.backends.backend_agg import FigureCanvasAgg + from juliacall import Base as jl FigureCanvas = FigureCanvasAgg diff --git a/pytest/test_all.py b/pytest/test_all.py index a895398a..c92da5db 100644 --- a/pytest/test_all.py +++ b/pytest/test_all.py @@ -4,6 +4,8 @@ def test_import(): import juliacall + juliacall + def test_newmodule(): import juliacall @@ -123,6 +125,7 @@ def test_call_nogil(yld, raw): """Tests that we can execute Julia code in parallel by releasing the GIL.""" from concurrent.futures import ThreadPoolExecutor, wait from time import time + from juliacall import Main as jl # julia implementation of sleep which unlocks the GIL diff --git a/src/C/find_libpython.py b/src/C/find_libpython.py index 422a0200..181ec25f 100644 --- a/src/C/find_libpython.py +++ b/src/C/find_libpython.py @@ -27,14 +27,14 @@ # OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION # WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. -from __future__ import print_function, absolute_import +from __future__ import absolute_import, print_function -from logging import getLogger import ctypes.util import functools import os import sys import sysconfig +from logging import getLogger logger = getLogger("find_libpython") @@ -97,7 +97,7 @@ def _linked_libpython_windows(): """ Based on: https://stackoverflow.com/a/16659821 """ - from ctypes.wintypes import HANDLE, LPWSTR, DWORD + from ctypes.wintypes import DWORD, HANDLE, LPWSTR GetModuleFileName = ctypes.windll.kernel32.GetModuleFileNameW GetModuleFileName.argtypes = [HANDLE, LPWSTR, DWORD] From 67abf66ecdf1ff8dec3ce7491c3ff9aa6975ebc1 Mon Sep 17 00:00:00 2001 From: Christopher Doris Date: Sat, 7 Sep 2024 17:45:57 +0100 Subject: [PATCH 8/9] ignore some innocuous rules --- pyproject.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pyproject.toml b/pyproject.toml index af0256fa..a898b4e9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -30,3 +30,4 @@ dev-dependencies = [ [tool.ruff.lint] select = ["F", "E", "W", "I"] +ignore = ["E501", "E731"] From 99aae09eea6d40427bf7b220628ffd202187e64e Mon Sep 17 00:00:00 2001 From: Christopher Doris Date: Sat, 7 Sep 2024 17:46:35 +0100 Subject: [PATCH 9/9] noqa for missing references to julia modules --- pysrc/juliacall/__init__.py | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/pysrc/juliacall/__init__.py b/pysrc/juliacall/__init__.py index 7e9e043b..bd10a82b 100644 --- a/pysrc/juliacall/__init__.py +++ b/pysrc/juliacall/__init__.py @@ -9,7 +9,7 @@ def newmodule(name): "A new module with the given name." global _newmodule if _newmodule is None: - _newmodule = Main.seval("name -> (n1=Symbol(name); n2=gensym(n1); Main.@eval(module $n2; module $n1; end; end); Main.@eval $n2.$n1)") + _newmodule = Main.seval("name -> (n1=Symbol(name); n2=gensym(n1); Main.@eval(module $n2; module $n1; end; end); Main.@eval $n2.$n1)") # noqa: F821 return _newmodule(name) _convert = None @@ -18,15 +18,15 @@ def convert(T, x): "Convert x to a Julia T." global _convert if _convert is None: - _convert = PythonCall.JlWrap.seval("pyjlcallback((T,x)->pyjl(pyconvert(pyjlvalue(T)::Type,x)))") + _convert = PythonCall.JlWrap.seval("pyjlcallback((T,x)->pyjl(pyconvert(pyjlvalue(T)::Type,x)))") # noqa: F821 return _convert(T, x) def interactive(enable=True): "Allow the Julia event loop to run in the background of the Python REPL." if enable: - PythonCall.Compat._set_python_input_hook() + PythonCall.Compat._set_python_input_hook() # noqa: F821 else: - PythonCall.Compat._unset_python_input_hook() + PythonCall.Compat._unset_python_input_hook() # noqa: F821 class JuliaError(Exception): "An error arising in Julia code." @@ -36,9 +36,9 @@ def __str__(self): e = self.exception b = self.backtrace if b is None: - return Base.sprint(Base.showerror, e) + return Base.sprint(Base.showerror, e) # noqa: F821 else: - return Base.sprint(Base.showerror, e, b) + return Base.sprint(Base.showerror, e, b) # noqa: F821 @property def exception(self): return self.args[0] @@ -241,7 +241,7 @@ def jlstr(x): CONFIG['inited'] = True if CONFIG['opt_handle_signals'] is None: - if Base.Threads.nthreads() > 1: + if Base.Threads.nthreads() > 1: # noqa: F821 # a warning to help multithreaded users # TODO: should we set PYTHON_JULIACALL_HANDLE_SIGNALS=yes whenever PYTHON_JULIACALL_THREADS != 1? warnings.warn(