From 5b53f684f0efe0a77aecf1918177882d67e6eca6 Mon Sep 17 00:00:00 2001 From: Niko Ehrenfeuchter Date: Thu, 20 Mar 2025 14:40:19 +0100 Subject: [PATCH 1/3] Remove ipython from dev-dependencies --- poetry.lock | 251 +------------------------------------------------ pyproject.toml | 1 - 2 files changed, 1 insertion(+), 251 deletions(-) diff --git a/poetry.lock b/poetry.lock index 03015af8..b0ee2a39 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,20 +1,5 @@ # This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. -[[package]] -name = "asttokens" -version = "3.0.0" -description = "Annotate AST trees with source code positions" -optional = false -python-versions = ">=3.8" -files = [ - {file = "asttokens-3.0.0-py3-none-any.whl", hash = "sha256:e3078351a059199dd5138cb1c706e6430c05eff2ff136af5eb4790f9d28932e2"}, - {file = "asttokens-3.0.0.tar.gz", hash = "sha256:0dcd8baa8d62b0c1d118b399b2ddba3c4aff271d0d7a9e0d4c1681c79035bbc7"}, -] - -[package.extras] -astroid = ["astroid (>=2,<4)"] -test = ["astroid (>=2,<4)", "pytest", "pytest-cov", "pytest-xdist"] - [[package]] name = "colorama" version = "0.4.6" @@ -104,17 +89,6 @@ tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.1 [package.extras] toml = ["tomli"] -[[package]] -name = "decorator" -version = "5.1.1" -description = "Decorators for Humans" -optional = false -python-versions = ">=3.5" -files = [ - {file = "decorator-5.1.1-py3-none-any.whl", hash = "sha256:b8c3f85900b9dc423225913c5aace94729fe1fa9763b38939a95226f02d37186"}, - {file = "decorator-5.1.1.tar.gz", hash = "sha256:637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330"}, -] - [[package]] name = "exceptiongroup" version = "1.2.2" @@ -129,20 +103,6 @@ files = [ [package.extras] test = ["pytest (>=6)"] -[[package]] -name = "executing" -version = "2.2.0" -description = "Get the currently executing AST node of a frame, and other information" -optional = false -python-versions = ">=3.8" -files = [ - {file = "executing-2.2.0-py2.py3-none-any.whl", hash = "sha256:11387150cad388d62750327a53d3339fad4888b39a6fe233c3afbb54ecffd3aa"}, - {file = "executing-2.2.0.tar.gz", hash = "sha256:5d108c028108fe2551d1a7b2e8b713341e2cb4fc0aa7dcf966fa4327a5226755"}, -] - -[package.extras] -tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipython", "littleutils", "pytest", "rich"] - [[package]] name = "imcf-fiji-mocks" version = "0.8.0a0" @@ -165,77 +125,6 @@ files = [ {file = "iniconfig-2.0.0.tar.gz", hash = "sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3"}, ] -[[package]] -name = "ipython" -version = "8.32.0" -description = "IPython: Productive Interactive Computing" -optional = false -python-versions = ">=3.10" -files = [ - {file = "ipython-8.32.0-py3-none-any.whl", hash = "sha256:cae85b0c61eff1fc48b0a8002de5958b6528fa9c8defb1894da63f42613708aa"}, - {file = "ipython-8.32.0.tar.gz", hash = "sha256:be2c91895b0b9ea7ba49d33b23e2040c352b33eb6a519cca7ce6e0c743444251"}, -] - -[package.dependencies] -colorama = {version = "*", markers = "sys_platform == \"win32\""} -decorator = "*" -exceptiongroup = {version = "*", markers = "python_version < \"3.11\""} -jedi = ">=0.16" -matplotlib-inline = "*" -pexpect = {version = ">4.3", markers = "sys_platform != \"win32\" and sys_platform != \"emscripten\""} -prompt_toolkit = ">=3.0.41,<3.1.0" -pygments = ">=2.4.0" -stack_data = "*" -traitlets = ">=5.13.0" -typing_extensions = {version = ">=4.6", markers = "python_version < \"3.12\""} - -[package.extras] -all = ["ipython[black,doc,kernel,matplotlib,nbconvert,nbformat,notebook,parallel,qtconsole]", "ipython[test,test-extra]"] -black = ["black"] -doc = ["docrepr", "exceptiongroup", "intersphinx_registry", "ipykernel", "ipython[test]", "matplotlib", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "sphinxcontrib-jquery", "tomli", "typing_extensions"] -kernel = ["ipykernel"] -matplotlib = ["matplotlib"] -nbconvert = ["nbconvert"] -nbformat = ["nbformat"] -notebook = ["ipywidgets", "notebook"] -parallel = ["ipyparallel"] -qtconsole = ["qtconsole"] -test = ["packaging", "pickleshare", "pytest", "pytest-asyncio (<0.22)", "testpath"] -test-extra = ["curio", "ipython[test]", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.23)", "pandas", "trio"] - -[[package]] -name = "jedi" -version = "0.19.2" -description = "An autocompletion tool for Python that can be used for text editors." -optional = false -python-versions = ">=3.6" -files = [ - {file = "jedi-0.19.2-py2.py3-none-any.whl", hash = "sha256:a8ef22bde8490f57fe5c7681a3c83cb58874daf72b4784de3cce5b6ef6edb5b9"}, - {file = "jedi-0.19.2.tar.gz", hash = "sha256:4770dc3de41bde3966b02eb84fbcf557fb33cce26ad23da12c742fb50ecb11f0"}, -] - -[package.dependencies] -parso = ">=0.8.4,<0.9.0" - -[package.extras] -docs = ["Jinja2 (==2.11.3)", "MarkupSafe (==1.1.1)", "Pygments (==2.8.1)", "alabaster (==0.7.12)", "babel (==2.9.1)", "chardet (==4.0.0)", "commonmark (==0.8.1)", "docutils (==0.17.1)", "future (==0.18.2)", "idna (==2.10)", "imagesize (==1.2.0)", "mock (==1.0.1)", "packaging (==20.9)", "pyparsing (==2.4.7)", "pytz (==2021.1)", "readthedocs-sphinx-ext (==2.1.4)", "recommonmark (==0.5.0)", "requests (==2.25.1)", "six (==1.15.0)", "snowballstemmer (==2.1.0)", "sphinx (==1.8.5)", "sphinx-rtd-theme (==0.4.3)", "sphinxcontrib-serializinghtml (==1.1.4)", "sphinxcontrib-websupport (==1.2.4)", "urllib3 (==1.26.4)"] -qa = ["flake8 (==5.0.4)", "mypy (==0.971)", "types-setuptools (==67.2.0.1)"] -testing = ["Django", "attrs", "colorama", "docopt", "pytest (<9.0.0)"] - -[[package]] -name = "matplotlib-inline" -version = "0.1.7" -description = "Inline Matplotlib backend for Jupyter" -optional = false -python-versions = ">=3.8" -files = [ - {file = "matplotlib_inline-0.1.7-py3-none-any.whl", hash = "sha256:df192d39a4ff8f21b1895d72e6a13f5fcc5099f00fa84384e0ea28c2cc0653ca"}, - {file = "matplotlib_inline-0.1.7.tar.gz", hash = "sha256:8423b23ec666be3d16e16b60bdd8ac4e86e840ebd1dd11a30b9f117f2fa0ab90"}, -] - -[package.dependencies] -traitlets = "*" - [[package]] name = "olefile" version = "0.46" @@ -257,35 +146,6 @@ files = [ {file = "packaging-24.2.tar.gz", hash = "sha256:c228a6dc5e932d346bc5739379109d49e8853dd8223571c7c5b55260edc0b97f"}, ] -[[package]] -name = "parso" -version = "0.8.4" -description = "A Python Parser" -optional = false -python-versions = ">=3.6" -files = [ - {file = "parso-0.8.4-py2.py3-none-any.whl", hash = "sha256:a418670a20291dacd2dddc80c377c5c3791378ee1e8d12bffc35420643d43f18"}, - {file = "parso-0.8.4.tar.gz", hash = "sha256:eb3a7b58240fb99099a345571deecc0f9540ea5f4dd2fe14c2a99d6b281ab92d"}, -] - -[package.extras] -qa = ["flake8 (==5.0.4)", "mypy (==0.971)", "types-setuptools (==67.2.0.1)"] -testing = ["docopt", "pytest"] - -[[package]] -name = "pexpect" -version = "4.9.0" -description = "Pexpect allows easy control of interactive console applications." -optional = false -python-versions = "*" -files = [ - {file = "pexpect-4.9.0-py2.py3-none-any.whl", hash = "sha256:7236d1e080e4936be2dc3e326cec0af72acf9212a7e1d060210e70a47e253523"}, - {file = "pexpect-4.9.0.tar.gz", hash = "sha256:ee7d41123f3c9911050ea2c2dac107568dc43b2d3b0c7557a33212c398ead30f"}, -] - -[package.dependencies] -ptyprocess = ">=0.5" - [[package]] name = "pluggy" version = "1.5.0" @@ -301,59 +161,6 @@ files = [ dev = ["pre-commit", "tox"] testing = ["pytest", "pytest-benchmark"] -[[package]] -name = "prompt-toolkit" -version = "3.0.50" -description = "Library for building powerful interactive command lines in Python" -optional = false -python-versions = ">=3.8.0" -files = [ - {file = "prompt_toolkit-3.0.50-py3-none-any.whl", hash = "sha256:9b6427eb19e479d98acff65196a307c555eb567989e6d88ebbb1b509d9779198"}, - {file = "prompt_toolkit-3.0.50.tar.gz", hash = "sha256:544748f3860a2623ca5cd6d2795e7a14f3d0e1c3c9728359013f79877fc89bab"}, -] - -[package.dependencies] -wcwidth = "*" - -[[package]] -name = "ptyprocess" -version = "0.7.0" -description = "Run a subprocess in a pseudo terminal" -optional = false -python-versions = "*" -files = [ - {file = "ptyprocess-0.7.0-py2.py3-none-any.whl", hash = "sha256:4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35"}, - {file = "ptyprocess-0.7.0.tar.gz", hash = "sha256:5c5d0a3b48ceee0b48485e0c26037c0acd7d29765ca3fbb5cb3831d347423220"}, -] - -[[package]] -name = "pure-eval" -version = "0.2.3" -description = "Safely evaluate AST nodes without side effects" -optional = false -python-versions = "*" -files = [ - {file = "pure_eval-0.2.3-py3-none-any.whl", hash = "sha256:1db8e35b67b3d218d818ae653e27f06c3aa420901fa7b081ca98cbedc874e0d0"}, - {file = "pure_eval-0.2.3.tar.gz", hash = "sha256:5f4e983f40564c576c7c8635ae88db5956bb2229d7e9237d03b3c0b0190eaf42"}, -] - -[package.extras] -tests = ["pytest"] - -[[package]] -name = "pygments" -version = "2.19.1" -description = "Pygments is a syntax highlighting package written in Python." -optional = false -python-versions = ">=3.8" -files = [ - {file = "pygments-2.19.1-py3-none-any.whl", hash = "sha256:9ea1544ad55cecf4b8242fab6dd35a93bbce657034b0611ee383099054ab6d8c"}, - {file = "pygments-2.19.1.tar.gz", hash = "sha256:61c16d2a8576dc0649d9f39e089b5f02bcd27fba10d8fb4dcc28173f7a45151f"}, -] - -[package.extras] -windows-terminal = ["colorama (>=0.4.6)"] - [[package]] name = "pytest" version = "8.3.4" @@ -420,25 +227,6 @@ files = [ {file = "sjlogging-0.5.4.tar.gz", hash = "sha256:5fb1a4e6338088bdbf9d943a867bf1bc6f77031ec48dbb7dd96f09abb0aaaa92"}, ] -[[package]] -name = "stack-data" -version = "0.6.3" -description = "Extract data from python stack frames and tracebacks for informative displays" -optional = false -python-versions = "*" -files = [ - {file = "stack_data-0.6.3-py3-none-any.whl", hash = "sha256:d5558e0c25a4cb0853cddad3d77da9891a08cb85dd9f9f91b9f8cd66e511e695"}, - {file = "stack_data-0.6.3.tar.gz", hash = "sha256:836a778de4fec4dcd1dcd89ed8abff8a221f58308462e1c4aa2a3cf30148f0b9"}, -] - -[package.dependencies] -asttokens = ">=2.1.0" -executing = ">=1.2.0" -pure-eval = "*" - -[package.extras] -tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"] - [[package]] name = "tomli" version = "2.2.1" @@ -480,44 +268,7 @@ files = [ {file = "tomli-2.2.1.tar.gz", hash = "sha256:cd45e1dc79c835ce60f7404ec8119f2eb06d38b1deba146f07ced3bbc44505ff"}, ] -[[package]] -name = "traitlets" -version = "5.14.3" -description = "Traitlets Python configuration system" -optional = false -python-versions = ">=3.8" -files = [ - {file = "traitlets-5.14.3-py3-none-any.whl", hash = "sha256:b74e89e397b1ed28cc831db7aea759ba6640cb3de13090ca145426688ff1ac4f"}, - {file = "traitlets-5.14.3.tar.gz", hash = "sha256:9ed0579d3502c94b4b3732ac120375cda96f923114522847de4b3bb98b96b6b7"}, -] - -[package.extras] -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 = "typing-extensions" -version = "4.12.2" -description = "Backported and Experimental Type Hints for Python 3.8+" -optional = false -python-versions = ">=3.8" -files = [ - {file = "typing_extensions-4.12.2-py3-none-any.whl", hash = "sha256:04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d"}, - {file = "typing_extensions-4.12.2.tar.gz", hash = "sha256:1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8"}, -] - -[[package]] -name = "wcwidth" -version = "0.2.13" -description = "Measures the displayed width of unicode strings in a terminal" -optional = false -python-versions = "*" -files = [ - {file = "wcwidth-0.2.13-py2.py3-none-any.whl", hash = "sha256:3da69048e4540d84af32131829ff948f1e022c1c6bdb8d6102117aac784f6859"}, - {file = "wcwidth-0.2.13.tar.gz", hash = "sha256:72ea0c06399eb286d978fdedb6923a9eb47e1c486ce63e9b4e64fc18303972b5"}, -] - [metadata] lock-version = "2.0" python-versions = ">=3.10" -content-hash = "26f88742f5c3e83b8a39f299398e5784b3689404e83870520d80db6aaa91d6ff" +content-hash = "11318171d20040fce90144782e5dced220d59595cd672cee1037d5f386648eff" diff --git a/pyproject.toml b/pyproject.toml index dda9e34b..50832442 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -27,7 +27,6 @@ python-micrometa = "^15.2.2" sjlogging = ">=0.5.2" [tool.poetry.group.dev.dependencies] -ipython = "^8.17.2" pytest = "^8.0.1" pytest-cov = "^6.0.0" From f3789209665927c6029f3dc64e10a95434dfe8a8 Mon Sep 17 00:00:00 2001 From: Niko Ehrenfeuchter Date: Thu, 20 Mar 2025 15:02:34 +0100 Subject: [PATCH 2/3] Add script to parse dependencies from pyproject.toml MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit NOTE: this was created in order to facilitate the project setup using Python 2 🐍ðŸŠĶ but is currently UNUSED as this opens Pandora's box ðŸŠĪ of versions specified via 🎭 Poetry but incompatible with Python 2 etc. --- .github/workflows/pytest-python2.yml | 4 +++- scripts/parse-python-deps.py | 23 +++++++++++++++++++++++ 2 files changed, 26 insertions(+), 1 deletion(-) create mode 100644 scripts/parse-python-deps.py diff --git a/.github/workflows/pytest-python2.yml b/.github/workflows/pytest-python2.yml index 43381338..91fa23ba 100644 --- a/.github/workflows/pytest-python2.yml +++ b/.github/workflows/pytest-python2.yml @@ -25,7 +25,9 @@ jobs: - name: 🗃 Cache ðŸ“Ķ APT Packages uses: awalsh128/cache-apt-pkgs-action@v1.4.3 with: - packages: xmlstarlet + packages: + xmlstarlet + # python3-tomli # required only for 'parse-python-deps.py' version: 1.0 - name: 🗃 Cache pyenv installation diff --git a/scripts/parse-python-deps.py b/scripts/parse-python-deps.py new file mode 100644 index 00000000..2b076114 --- /dev/null +++ b/scripts/parse-python-deps.py @@ -0,0 +1,23 @@ +#!/usr/bin/env python3 + +"""Parse project dependencies and format them for usage with `pip install`.""" + +# NOTE: requires Ubuntu package 'python3-tomli' to be installed! + +import tomli + +with open("pyproject.toml", "rb") as tomlfile: + pyproject = tomli.load(tomlfile) + +deps_pkg = pyproject["tool"]["poetry"]["dependencies"] +deps_dev = pyproject["tool"]["poetry"]["group"]["dev"]["dependencies"] + +output = "" + +for deps in deps_pkg, deps_dev: + for pkg, ver in deps.items(): + if ver[0] == "^": + ver = f">={ver[1:]}" + output = f'{output} {pkg}{ver}' + +print(output) From b72e685d8070706b3116c72d51cff31e1607d19e Mon Sep 17 00:00:00 2001 From: Niko Ehrenfeuchter Date: Thu, 20 Mar 2025 15:05:26 +0100 Subject: [PATCH 3/3] Install pre-releases of "imcf-fiji-mocks" if available --- scripts/py2-pytest.sh | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/scripts/py2-pytest.sh b/scripts/py2-pytest.sh index f840f4a8..3c8557c1 100755 --- a/scripts/py2-pytest.sh +++ b/scripts/py2-pytest.sh @@ -103,11 +103,14 @@ mv pyproject_.toml pyproject.toml echo "== * Removing 'setup.py'..." rm setup.py +echo "== * Installing dependencies (incl. pre-release and dev versions)..." +vpip install --upgrade --pre \ + imcf-fiji-mocks + echo "== * Installing dependencies..." vpip install \ python-micrometa \ sjlogging \ - "imcf-fiji-mocks>=0.3.0" \ olefile==0.46 \ pytest \ pytest-cov \