Scheduled weekly dependency update for week 35 #1090

Workflow file for this run

.github/workflows/pr-test.yml at dbaf9c1

	name: Pull Request CI

	# Controls when the action will run. Triggers the workflow on push or pull request
	# events but only for the master branch
	on:
	workflow_dispatch:
	pull_request:
	paths:
	- requirements-test-libraries.txt

	env:
	# Colored pytest output on CI despite not having a tty
	FORCE_COLOR: 1
	# Enable strict unpack mode to catch file duplication problems in onefile builds (at executable run-time).
	PYINSTALLER_STRICT_UNPACK_MODE: 1
	# Enable strict collect mode to catch file duplication problems in PKG/Carchive (onefile builds) or COLLECT
	# (onedir builds) at build time.
	PYINSTALLER_STRICT_COLLECT_MODE: 1
	# Enable strict handling of codesign errors for macOS bundles.
	PYINSTALLER_STRICT_BUNDLE_CODESIGN_ERROR: 1
	# Enable strict verification of macOS bundles w.r.t. the code-signing requirements.
	PYINSTALLER_VERIFY_BUNDLE_SIGNATURE: 1

	permissions:
	contents: read # to fetch code (actions/checkout)

	jobs:
	test:
	runs-on: ${{ matrix.os }}
	strategy:
	matrix:
	python-version: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13', '3.14']
	pyinstaller: ["https://github.com/pyinstaller/pyinstaller/archive/develop.zip"]
	os: ["macos-15", "macos-15-intel", "ubuntu-24.04", "windows-latest"]
	fail-fast: false

	env:
	# Rebuild bootloader when installing PyInstaller from develop branch
	PYINSTALLER_COMPILE_BOOTLOADER: 1

	steps:
	- uses: actions/checkout@v6

	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v6
	with:
	python-version: ${{ matrix.python-version }}

	- name: Limit dependencies to only new/changed libraries.
	if: "${{ github.event.pull_request }}"
	shell: bash
	run: \|
	git fetch origin ${{ github.base_ref }}
	set +e
	# NOTE: we need to be compatible with both GNU diff and Apple/FreeBSD diff
	diff \
	<(git show origin/${{ github.base_ref }}:requirements-test-libraries.txt) \
	<(git show HEAD:requirements-test-libraries.txt) \
	\| grep -E "^>" \| sed "s/^> //" \
	> requirements-test-libraries.txt
	set -e
	echo '-r requirements-test.txt' >> requirements-test-libraries.txt
	cat requirements-test-libraries.txt

	- name: Set up .NET Core for pythonnet tests
	uses: actions/setup-dotnet@v5
	with:
	dotnet-version: '6.x'

	# Install MariaDB Connector/C from official MariaDB Community Server
	# repository; the version shipped with ubuntu may be too old for
	# the "mariadb" python package.
	#
	# NOTE: the sha256sum for mariadb_repo_setup installation script is available at:
	# https://mariadb.com/docs/server/server-management/install-and-upgrade-mariadb/installing-mariadb/binary-packages/mariadb-package-repository-setup-and-usage#versions
	# (make sure to switch to "mariadb_repo_setup" tab!)
	- name: Install MariaDB Connector/C
	if: startsWith(matrix.os, 'ubuntu')
	run: \|
	sudo apt-get update
	sudo apt-get install -y wget apt-transport-https
	wget https://downloads.mariadb.com/MariaDB/mariadb_repo_setup
	echo "7325ac7755809ca3312b446bd832542421699298f25b701f9a111bb42df0c7c1 mariadb_repo_setup" \| sha256sum -c -
	chmod +x mariadb_repo_setup
	sudo ./mariadb_repo_setup --skip-maxscale
	sudo apt-get install -y libmariadb3 libmariadb-dev

	- name: Install apt dependencies
	if: startsWith(matrix.os, 'ubuntu')
	run: \|
	sudo apt-get update
	# Set up a virtual screen (for GUI libraries and pynput).
	sudo apt-get install libxcb-xkb-dev xvfb
	Xvfb :99 & echo "DISPLAY=:99" >> $GITHUB_ENV
	# Install PyQt5 (qtmodern) dependencies.
	sudo apt-get install -y libxcb-image0 libxcb-keysyms1 libxcb-render-util0 \
	libxkbcommon-x11-0 libxcb-icccm4 libxcb1 openssl \
	libxcb-randr0-dev libxcb-xtest0-dev libxcb-xinerama0-dev \
	libxcb-shape0-dev libxcb-xkb-dev libopengl0 libegl1 \
	libpulse0 libpulse-mainloop-glib0
	# Install cairo dependencies.
	sudo apt-get install -y libcairo2
	# Install libdiscid (dependency of discid python package).
	sudo apt-get install -y libdiscid0
	# These are dependencies of gmsh
	sudo apt-get install -y libglu1 libgl1 libxrender1 libxcursor1 libxft2 \
	libxinerama1 libgomp1
	# Required by PyGObject (dependency of toga/toga-gtk)
	sudo apt-get install -y gir1.2-gtk-3.0 \
	libcairo2-dev \
	libgirepository1.0-dev gir1.2-girepository-2.0 \
	libgirepository-2.0-dev gir1.2-girepository-3.0
	# Required by pygraphviz
	sudo apt-get install -y graphviz graphviz-dev
	# Contemporary versions of eccodes PyPI wheels provide bundled copies of eccodes library; install a system
	# copy to ensure that the bundled copy is properly collected and used at run-time.
	sudo apt-get install -y libeccodes0

	- name: Install brew dependencies
	if: startsWith(matrix.os, 'macos')
	run: \|
	# `pkg-config` is deprecated and superseded by `pkgconf`, but it is still pre-installed on the GitHub Actions
	# runner. This leads to `brew link` errors when `pkgconf` is installed as part of dependencies. So for now,
	# manually remove `pkg-config` (and specifically, the problematic `pkg-config@0.29.2`).
	brew uninstall pkg-config \|\| :
	brew uninstall pkg-config@0.29.2 \|\| :
	# At the time of writing (end of August 2025), GHA macOS runner images started to pin CMake 3.31.6 via custom
	# tap due to CMake 4.0 not being fully backwards compatible. However, this seems to be preventing us from
	# installing `lsl`, which errors out with:
	# Error: cmake is already installed from local/pinned!
	# Please `brew uninstall cmake` first."
	brew uninstall cmake \|\| :
	# Install cairo dependencies.
	brew install cairo
	# Install pango dependencies (weasyprint hook).
	brew install pango
	# Install libdiscid (dependency of discid python package).
	brew install libdiscid
	# Install lsl library for pylsl
	brew install labstreaminglayer/tap/lsl
	# This one is required by eccodes. Binary wheels with bundled eccodes library are provided for macOS 13+,
	# but we install system package to ensure that the bundled copy is properly collected and used at run-time.
	brew install eccodes
	# Requires by pygraphviz
	brew install graphviz

	# On arm64 macOS runners, Homebrew is installed in /opt/homebrew instead of /usr/local prefix, and
	# its headers and shared libraries are not in the default search path. Add them by setting CPPFLAGS
	# and LDFLAGS. This is required by `pygraphviz`.
	if [ "$(brew --prefix)" = "/opt/homebrew" ]; then
	echo "CPPFLAGS=-I/opt/homebrew/include${CPPFLAGS+ ${CPPFLAGS}}" >> $GITHUB_ENV
	echo "LDFLAGS=-L/opt/homebrew/lib${LDFLAGS+ ${LDFLAGS}}" >> $GITHUB_ENV
	fi

	- name: Install dependencies
	shell: bash
	run: \|
	# Upgrade to the latest pip.
	python -m pip install -U pip setuptools

	# Install hooks-contrib
	pip install -e .

	# Install test libraries
	pip install --prefer-binary -r requirements-test-libraries.txt

	# Additional implied dependencies of test libraries

	# pyqtgraph requires Qt bindings - use PyQt5
	pip show -qq pyqtgraph && pip install --prefer-binary PyQt5

	# NOTE: specify minimum allowed version for sudachidict-* packages, to prevent pip from installing invalid
	# SudachiDict_full-0.0.0-py3-none-any.whl due to --prefer-binary switch used with pip install...
	pip show -qq sudachipy && pip install --prefer-binary "sudachidict-small>=20230927" "sudachidict-core>=20230927" "sudachidict-full>=20230927"

	# pythainlp requires python-crfsuite, but fails to declare it as a requirement.
	pip show -qq pythainlp && pip install --prefer-binary python-crfsuite

	# tests for various trame-* packages require base trame package as well
	pip show -qq trame-client trame-code trame-components trame-datagrid trame-deckgl trame-formkit trame-grid-layout trame-iframe trame-keycloak trame-leaflet trame-markdown trame-matplotlib trame-mesh-streamer trame-plotly trame-pvui trame-quasar trame-rca trame-router trame-server trame-simput trame-tauri trame-tweakpane trame-vega trame-vtk trame-vtk3d trame-vtklocal trame-vuetify trame-xterm && pip install --prefer-binary trame

	pip show -qq trame-vtk && pip install --prefer-binary vtk pyvista nest-asyncio2 trame-vuetify
	pip show -qq trame-mesh-streamer && pip install --prefer-binary vtk
	pip show -qq trame-rca && pip install --prefer-binary vtk

	# test_xarray_chunk requires dask in addition to xarray
	pip show -qq xarray && pip install --prefer-binary dask

	# Install additional intake plugins for test_intake_plugins
	pip show -qq intake && pip install --prefer-binary intake-xarray

	# test_langchain_with_ollama requires langchain-ollama to be installed together with langchain
	pip show -qq langchain && pip install --prefer-binary langchain-ollama

	# procrastinate depends on psycopg[pool]; the binary extra is required so that psycopg can be
	# imported without a system-provided libpq.
	pip show -qq procrastinate && pip install --prefer-binary psycopg[binary]

	# Install PyInstaller
	pip install ${{ matrix.pyinstaller }}

	# PyTaskbar 0.1.0 does not ship TaskBarLib.tlb with its wheels anymore (in contrast
	# to earlier releases under the PyTaskbarProgress name); apparently users are supposed
	# to download it separately and copy it to their project's directory. Copying to the
	# package's directory also seems to work, and is what our hook is expecting. So until
	# we see what directions subsequent releases take, download and install the file.
	# Applicable only to Windows (PyTaskbar is available only for Windows).
	- name: Download and install TLB for PyTaskbar
	if: startsWith(matrix.os, 'windows')
	shell: python
	run: \|
	import importlib.metadata
	import importlib.util
	import os
	import sys
	import urllib.request

	import packaging.version

	# Check if PyTaskbar is available, and at >= 0.1.0 version.
	try:
	version = importlib.metadata.version('PyTaskbar')
	except importlib.metadata.PackageNotFoundError:
	print("PyTaskbar dist not found.")
	sys.exit() # N/A

	print(f"PyTaskbar version: {version}")

	version = packaging.version.parse(version)
	if version < packaging.version.parse("0.1.0"):
	print("PyTaskbar version is lower than 0.1.0.")
	sys.exit()

	# Determine package's path - attempting to import the package might raise
	# missing library error, so look up the spec and module's search location
	# in it.
	spec = importlib.util.find_spec('PyTaskbar')
	if spec is None:
	print("PyTaskbar spec not found.")
	sys.exit()
	location = spec.submodule_search_locations[0]
	print(f"Package location: {location}")

	# Check if the .tlb file already exists
	tlb_file = os.path.join(location, 'TaskbarLib.tlb')
	if os.path.isfile(tlb_file):
	print(f"TLB file already exists.")
	sys.exit()

	# Download the .tlb file from GitHub releases
	tlb_url = f"https://github.com/N3RDIUM/PyTaskbar/releases/download/{version}/TaskbarLib.tlb"
	print(f"Downloading TLB file from: {tlb_url}")

	urllib.request.urlretrieve(tlb_url, tlb_file)

	# Some python versions come with initial `setuptools` installation that seems to contain `.opt-1.pyc`
	# files in `__pycache__` directories. During the upgrade, `pip` fails to remove those directories
	# (see: https://github.com/pypa/pip/issues/11835).
	#
	# `setuptools` 75.4 removed its vendored copy of `importlib_resources`, but due to
	# the above issue, the effectively empty directory remains, turning `importlib_resources`
	# into a defunct namespace package, which causes some of our tests to fail.
	#
	# Similar issue arises when upgrading to `setuptools` 82.0.0, which removed `pkg_resources` package;
	# the defunct namespace package arising from the left-over directory causes error in our `pkg_resources`
	# run-time hook (which would otherwise not be collected at all).
	- name: Work around potentially broken setuptools upgrade
	shell: python
	run: \|
	import sys
	import pathlib
	import shutil
	import importlib.util

	PACKAGES = [
	'setuptools._vendor.importlib_resources',
	'pkg_resources',
	]

	def fix_package(package_name):
	try:
	spec = importlib.util.find_spec(package_name)
	except ImportError:
	spec = None # parent package (e.g., setuptools or setuptools._vendor) does not exist
	if spec is None:
	print(f"Did not find {package_name}.")
	return
	elif spec.loader is not None:
	# Not a namespace package (i.e., directory with just __pycache__ sub-directory)
	print(f"Found a valid copy of {package_name}.")
	return

	print(f"Found a defunct copy of {package_name}!")

	# List the contents of package directory for debug purposes
	def list_directory(path, pad=""):
	for child in path.iterdir():
	if child.is_dir():
	print(f"{pad} + {child.name}")
	list_directory(child, pad + " ")
	else:
	print(f"{pad} - {child.name} ({child.stat().st_size} bytes)")

	for path in spec.submodule_search_locations:
	print(f"Listing contents of {path}")
	list_directory(pathlib.Path(path))

	# Remove
	for path in spec.submodule_search_locations:
	print(f"Removing {path}...")
	shutil.rmtree(path)

	for package in PACKAGES:
	fix_package(package)

	- name: Run tests
	run: pytest -v -n logical

	# Conditionally enable slow tests, so that they are ran only if
	# their corresponding packages are explicitly installed but not
	# if they are installed as dependencies of some other package.
	- name: Check if slow tests are required (scikit-learn)
	id: check-scikit-learn
	shell: bash
	run: \|
	grep -E "scikit-learn" requirements-test-libraries.txt && echo "AVAILABLE=yes" >> $GITHUB_OUTPUT \|\| echo "AVAILABLE=no" >> $GITHUB_OUTPUT

	- name: Run slow tests (scikit-learn)
	if: ${{ steps.check-scikit-learn.outputs.AVAILABLE == 'yes' }}
	run: pytest -v -n logical -m slow -k sklearn

	- name: Check if slow tests are required (scikit-image)
	id: check-scikit-image
	shell: bash
	run: \|
	grep -E "scikit-image" requirements-test-libraries.txt && echo "AVAILABLE=yes" >> $GITHUB_OUTPUT \|\| echo "AVAILABLE=no" >> $GITHUB_OUTPUT

	- name: Run slow tests (scikit-image)
	if: ${{ steps.check-scikit-image.outputs.AVAILABLE == 'yes' }}
	run: pytest -v -n logical -m slow -k skimage

	- name: Check if slow tests are required (vtk)
	id: check-vtk
	shell: bash
	run: \|
	grep -E "^vtk==" requirements-test-libraries.txt && echo "AVAILABLE=yes" >> $GITHUB_OUTPUT \|\| echo "AVAILABLE=no" >> $GITHUB_OUTPUT

	- name: Run slow tests (vtk)
	if: ${{ steps.check-vtk.outputs.AVAILABLE == 'yes' }}
	run: pytest -v -n logical -m slow -k test_vtkmodules

Navigation Menu

Uh oh!

Scheduled weekly dependency update for week 35 #1090

Workflow file

Scheduled weekly dependency update for week 35 #1090

Uh oh!

Workflow file for this run