From 3f8473ac1ff7249be04e1119fcfb358ec0486923 Mon Sep 17 00:00:00 2001 From: rettigl Date: Tue, 24 Oct 2023 23:16:33 +0200 Subject: [PATCH 01/25] add github action to update dependencies using poetry --- .github/dependabot.yml | 9 ----- .github/workflows/update_dependencies.yml | 43 +++++++++++++++++++++++ 2 files changed, 43 insertions(+), 9 deletions(-) delete mode 100644 .github/dependabot.yml create mode 100644 .github/workflows/update_dependencies.yml diff --git a/.github/dependabot.yml b/.github/dependabot.yml deleted file mode 100644 index 9a396b31..00000000 --- a/.github/dependabot.yml +++ /dev/null @@ -1,9 +0,0 @@ -version: 2 -updates: - - package-ecosystem: "pip" - directory: "/" - schedule: - interval: "weekly" - allow: - - dependency-type: "all" - versioning-strategy: "lockfile-only" diff --git a/.github/workflows/update_dependencies.yml b/.github/workflows/update_dependencies.yml new file mode 100644 index 00000000..62fa278b --- /dev/null +++ b/.github/workflows/update_dependencies.yml @@ -0,0 +1,43 @@ +name: Generate requirements.txt for readthedocs + +on: + schedule: + - cron: '0 1 * * 1' + push: + workflow_dispatch: + +jobs: + update_dependencies: + runs-on: ubuntu-latest + steps: + # Check out repo and set up Python + - uses: actions/checkout@v3 + with: + lfs: true + + # Use cached python and dependencies, install poetry + - name: "Setup Python, Poetry and Dependencies" + uses: packetcoders/action-setup-cache-python-poetry@main + with: + python-version: 3.8 + poetry-version: 1.2.2 + + # update poetry lockfile + - name: "Update poetry lock file" + id: update + run: | + update_output=$(poetry run poetry update) + echo "update_output=$update_output" >> $GITHUB_OUTPUT + status=$(git status | grep poetry.lock) + echo "status=$status" >> $GITHUB_OUTPUT + + # create pull request if necessary + - name: "Create Pull Request" + uses: peter-evans/create-pull-request@v5 + if: ${{ steps.update.outputs.status != '' }} + with: + commit-message: Update dependencies + title: "Update dependencies" + body: | + - Dependency updates + ${{ steps.update.outputs.update_output }} From 72d6442f953053e060aeb71cf62eee4f779e3ddf Mon Sep 17 00:00:00 2001 From: rettigl Date: Tue, 24 Oct 2023 23:28:17 +0200 Subject: [PATCH 02/25] remove variables for testing --- .github/workflows/update_dependencies.yml | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/.github/workflows/update_dependencies.yml b/.github/workflows/update_dependencies.yml index 62fa278b..860d035b 100644 --- a/.github/workflows/update_dependencies.yml +++ b/.github/workflows/update_dependencies.yml @@ -1,4 +1,4 @@ -name: Generate requirements.txt for readthedocs +name: Update depencies in poetry lockfile on: schedule: @@ -26,18 +26,13 @@ jobs: - name: "Update poetry lock file" id: update run: | - update_output=$(poetry run poetry update) - echo "update_output=$update_output" >> $GITHUB_OUTPUT - status=$(git status | grep poetry.lock) - echo "status=$status" >> $GITHUB_OUTPUT + poetry run poetry update # create pull request if necessary - name: "Create Pull Request" uses: peter-evans/create-pull-request@v5 - if: ${{ steps.update.outputs.status != '' }} with: commit-message: Update dependencies title: "Update dependencies" body: | - Dependency updates - ${{ steps.update.outputs.update_output }} From 4ec40ed05a8fa3d69b63430eccf3658c7d2e6302 Mon Sep 17 00:00:00 2001 From: rettigl Date: Tue, 24 Oct 2023 23:51:45 +0200 Subject: [PATCH 03/25] add poetry self update, and try once more status check --- .github/workflows/update_dependencies.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.github/workflows/update_dependencies.yml b/.github/workflows/update_dependencies.yml index 860d035b..becf71e5 100644 --- a/.github/workflows/update_dependencies.yml +++ b/.github/workflows/update_dependencies.yml @@ -26,13 +26,18 @@ jobs: - name: "Update poetry lock file" id: update run: | + poetry run poetry self update poetry run poetry update + status=$(git status | grep poetry.lock) + echo "status=$status" >> $GITHUB_OUTPUT # create pull request if necessary - name: "Create Pull Request" uses: peter-evans/create-pull-request@v5 + if: ${{ steps.update.outputs.status != '' }} with: commit-message: Update dependencies title: "Update dependencies" body: | - Dependency updates + ${{ steps.update.outputs.update_output }} From 68213875d36bd4042b423d3318d4acd2f5ec40c8 Mon Sep 17 00:00:00 2001 From: rettigl Date: Wed, 25 Oct 2023 00:08:44 +0200 Subject: [PATCH 04/25] manual lockfile update --- poetry.lock | 449 ++++++++++++---------------------------------------- 1 file changed, 102 insertions(+), 347 deletions(-) diff --git a/poetry.lock b/poetry.lock index 00722c26..d6b53807 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,10 +1,9 @@ -# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. [[package]] name = "alabaster" version = "0.7.13" description = "A configurable sidebar-enabled Sphinx theme" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -16,7 +15,6 @@ files = [ name = "anyio" version = "4.0.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" -category = "main" optional = true python-versions = ">=3.8" files = [ @@ -38,7 +36,6 @@ trio = ["trio (>=0.22)"] name = "appnope" version = "0.1.3" description = "Disable App Nap on macOS >= 10.9" -category = "main" optional = false python-versions = "*" files = [ @@ -50,7 +47,6 @@ files = [ name = "argon2-cffi" version = "23.1.0" description = "Argon2 for Python" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -71,7 +67,6 @@ typing = ["mypy"] name = "argon2-cffi-bindings" version = "21.2.0" description = "Low-level CFFI bindings for Argon2" -category = "main" optional = true python-versions = ">=3.6" files = [ @@ -109,7 +104,6 @@ tests = ["pytest"] name = "arrow" version = "1.3.0" description = "Better dates & times for Python" -category = "main" optional = true python-versions = ">=3.8" files = [ @@ -123,13 +117,12 @@ types-python-dateutil = ">=2.8.10" [package.extras] doc = ["doc8", "sphinx (>=7.0.0)", "sphinx-autobuild", "sphinx-autodoc-typehints", "sphinx_rtd_theme (>=1.3.0)"] -test = ["dateparser (>=1.0.0,<2.0.0)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (>=3.0.0,<4.0.0)"] +test = ["dateparser (==1.*)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (==3.*)"] [[package]] name = "asciitree" version = "0.3.3" description = "Draws ASCII trees." -category = "main" optional = false python-versions = "*" files = [ @@ -140,7 +133,6 @@ files = [ name = "ase" version = "3.22.1" description = "Atomic Simulation Environment" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -161,7 +153,6 @@ test = ["pytest (>=5.0.0)", "pytest-mock (>=3.3.0)", "pytest-xdist (>=1.30.0)"] name = "asteval" version = "0.9.31" description = "Safe, minimalistic evaluator of python expression using ast module" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -179,7 +170,6 @@ test = ["coverage", "pytest", "pytest-cov"] name = "astropy" version = "5.2.2" description = "Astronomy and astrophysics core library" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -233,7 +223,6 @@ test-all = ["coverage[toml]", "ipython (>=4.2)", "objgraph", "pytest (>=7.0)", " name = "asttokens" version = "2.4.0" description = "Annotate AST trees with source code positions" -category = "main" optional = false python-versions = "*" files = [ @@ -251,7 +240,6 @@ test = ["astroid", "pytest"] name = "async-lru" version = "2.0.4" description = "Simple LRU cache for asyncio" -category = "main" optional = true python-versions = ">=3.8" files = [ @@ -266,7 +254,6 @@ typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""} name = "attrs" version = "23.1.0" description = "Classes Without Boilerplate" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -283,14 +270,13 @@ tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pyte [[package]] name = "babel" -version = "2.13.0" +version = "2.13.1" description = "Internationalization utilities" -category = "main" optional = false python-versions = ">=3.7" files = [ - {file = "Babel-2.13.0-py3-none-any.whl", hash = "sha256:fbfcae1575ff78e26c7449136f1abbefc3c13ce542eeb13d43d50d8b047216ec"}, - {file = "Babel-2.13.0.tar.gz", hash = "sha256:04c3e2d28d2b7681644508f836be388ae49e0cfe91465095340395b60d00f210"}, + {file = "Babel-2.13.1-py3-none-any.whl", hash = "sha256:7077a4984b02b6727ac10f1f7294484f737443d7e2e66c5e4380e41a3ae0b4ed"}, + {file = "Babel-2.13.1.tar.gz", hash = "sha256:33e0952d7dd6374af8dbf6768cc4ddf3ccfefc244f9986d4074704f2fbd18900"}, ] [package.dependencies] @@ -303,7 +289,6 @@ dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"] name = "backcall" version = "0.2.0" description = "Specifications for callback functions passed in to an API" -category = "main" optional = false python-versions = "*" files = [ @@ -315,7 +300,6 @@ files = [ name = "backports-zoneinfo" version = "0.2.1" description = "Backport of the standard library zoneinfo module" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -344,7 +328,6 @@ tzdata = ["tzdata"] name = "beautifulsoup4" version = "4.12.2" description = "Screen-scraping library" -category = "main" optional = true python-versions = ">=3.6.0" files = [ @@ -363,7 +346,6 @@ lxml = ["lxml"] name = "bleach" version = "6.1.0" description = "An easy safelist-based HTML-sanitizing tool." -category = "main" optional = true python-versions = ">=3.8" files = [ @@ -382,7 +364,6 @@ css = ["tinycss2 (>=1.1.0,<1.3)"] name = "bokeh" version = "2.4.3" description = "Interactive plots and applications in the browser from Python" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -403,7 +384,6 @@ typing-extensions = ">=3.10.0" name = "cattrs" version = "23.1.2" description = "Composable complex class support for attrs and dataclasses." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -429,7 +409,6 @@ ujson = ["ujson (>=5.4.0,<6.0.0)"] name = "certifi" version = "2023.7.22" description = "Python package for providing Mozilla's CA Bundle." -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -441,7 +420,6 @@ files = [ name = "cffi" version = "1.16.0" description = "Foreign Function Interface for Python calling C code." -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -506,7 +484,6 @@ pycparser = "*" name = "charset-normalizer" version = "3.3.1" description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." -category = "main" optional = false python-versions = ">=3.7.0" files = [ @@ -606,7 +583,6 @@ files = [ name = "click" version = "8.1.7" description = "Composable command line interface toolkit" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -621,7 +597,6 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""} name = "cloudpickle" version = "3.0.0" description = "Pickler class to extend the standard pickle.Pickler functionality" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -633,7 +608,6 @@ files = [ name = "colorama" version = "0.4.6" description = "Cross-platform colored terminal text." -category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" files = [ @@ -645,7 +619,6 @@ files = [ name = "comm" version = "0.1.4" description = "Jupyter Python Comm implementation, for usage in ipykernel, xeus-python etc." -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -665,7 +638,6 @@ typing = ["mypy (>=0.990)"] name = "commonmark" version = "0.9.1" description = "Python parser for the CommonMark Markdown spec" -category = "main" optional = false python-versions = "*" files = [ @@ -680,7 +652,6 @@ test = ["flake8 (==3.7.8)", "hypothesis (==3.55.3)"] name = "contourpy" version = "1.1.1" description = "Python library for calculating contours of 2D quadrilateral grids" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -752,7 +723,6 @@ test-no-images = ["pytest", "pytest-cov", "wurlitzer"] name = "coverage" version = "7.3.2" description = "Code coverage measurement for Python" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -820,7 +790,6 @@ toml = ["tomli"] name = "cramjam" version = "2.7.0" description = "Thin Python bindings to de/compression algorithms in Rust" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -892,7 +861,6 @@ dev = ["black (==22.3.0)", "hypothesis", "numpy", "pytest (>=5.30)", "pytest-xdi name = "cycler" version = "0.12.1" description = "Composable style cycles" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -908,7 +876,6 @@ tests = ["pytest", "pytest-cov", "pytest-xdist"] name = "dask" version = "2022.12.1" description = "Parallel PyData with Task Scheduling" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -938,7 +905,6 @@ test = ["pandas[test]", "pre-commit", "pytest", "pytest-rerunfailures", "pytest- name = "debugpy" version = "1.8.0" description = "An implementation of the Debug Adapter Protocol for Python" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -966,7 +932,6 @@ files = [ name = "decorator" version = "5.1.1" description = "Decorators for Humans" -category = "main" optional = false python-versions = ">=3.5" files = [ @@ -978,7 +943,6 @@ files 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interact with Git repositories" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1433,7 +1376,6 @@ test = ["black", "coverage[toml]", "ddt (>=1.1.1,!=1.4.3)", "mock", "mypy", "pre name = "h5py" version = "3.10.0" description = "Read and write HDF5 files from Python" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1469,28 +1411,24 @@ numpy = ">=1.17.3" [[package]] name = "hyperspy" -version = "1.7.5" +version = "1.7.4" description = "Multidimensional data analysis toolbox" -category = "main" optional = false python-versions = "~=3.6" files = [ - {file = "hyperspy-1.7.5-cp310-cp310-macosx_11_0_x86_64.whl", hash = "sha256:191a72056c0bbc549432984cd684a527c25cf61fcceefade30cb38844693e5d7"}, - {file = "hyperspy-1.7.5-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:8aadca559dec0ab015e2908d255f9f1bbc10804f2f6e4647a392bdbd5288b73d"}, - {file = "hyperspy-1.7.5-cp310-cp310-win_amd64.whl", hash = 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"sha256:74258224fc33d58f53113cf955e8d51bf01386b91492927d0d1b6b341a765ad7"}, - {file = "pooch-1.7.0.tar.gz", hash = "sha256:f174a1041b6447f0eef8860f76d17f60ed2f857dc0efa387a7f08228af05d998"}, + {file = "pooch-1.8.0-py3-none-any.whl", hash = "sha256:1bfba436d9e2ad5199ccad3583cca8c241b8736b5bb23fe67c213d52650dbb66"}, + {file = "pooch-1.8.0.tar.gz", hash = "sha256:f59981fd5b9b5d032dcde8f4a11eaa492c2ac6343fae3596a2fdae35fc54b0a0"}, ] [package.dependencies] @@ -3617,7 +3471,6 @@ xxhash = ["xxhash (>=1.4.3)"] name = "pprintpp" version = "0.4.0" description = "A drop-in replacement for pprint that's actually pretty" -category = "dev" optional = false python-versions = "*" files = [ @@ -3629,7 +3482,6 @@ files = [ name = "prettytable" version = "3.9.0" description = "A simple Python library for easily displaying tabular data in a visually appealing ASCII table format" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3647,7 +3499,6 @@ tests = ["pytest", "pytest-cov", "pytest-lazy-fixture"] name = "prometheus-client" version = "0.17.1" description = "Python client for the Prometheus monitoring system." -category = "main" optional = true python-versions = ">=3.6" files = [ @@ -3662,7 +3513,6 @@ twisted = ["twisted"] name = "prompt-toolkit" version = "3.0.39" description = "Library for building powerful interactive command lines in Python" -category = "main" optional = false python-versions = ">=3.7.0" files = [ @@ -3677,7 +3527,6 @@ wcwidth = "*" name = "psutil" version = "5.9.6" description = "Cross-platform lib for process and system monitoring in Python." -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" files = [ @@ -3706,7 +3555,6 @@ test = ["enum34", "ipaddress", "mock", "pywin32", "wmi"] name = "ptyprocess" version = "0.7.0" description = "Run a subprocess in a pseudo terminal" -category = "main" optional = false python-versions = "*" files = [ @@ -3718,7 +3566,6 @@ files = [ name = "pure-eval" version = "0.2.2" description = "Safely evaluate AST nodes without side effects" -category = "main" optional = false python-versions = "*" files = [ @@ -3733,7 +3580,6 @@ tests = ["pytest"] name = "py" version = "1.11.0" description = "library with cross-python path, ini-parsing, io, code, log facilities" -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -3745,7 +3591,6 @@ files = [ name = "pyarrow" version = "13.0.0" description = "Python library for Apache Arrow" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3787,7 +3632,6 @@ numpy = ">=1.16.6" name = "pycifrw" version = "4.4.5" description = "CIF/STAR file support for Python" -category = "main" optional = false python-versions = "*" files = [ @@ -3801,7 +3645,6 @@ files = [ name = "pycparser" version = "2.21" description = "C parser in Python" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -3813,7 +3656,6 @@ files = [ name = "pyerfa" version = "2.0.0.3" description = "Python bindings for ERFA" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3870,7 +3712,6 @@ test = ["pytest", "pytest-doctestplus (>=0.7)"] name = "pyfai" version = "2023.9.0" description = "Python implementation of fast azimuthal integration" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3922,7 +3763,6 @@ opencl = ["pyopencl"] name = "pygments" version = "2.16.1" description = "Pygments is a syntax highlighting package written in Python." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3937,7 +3777,6 @@ plugins = ["importlib-metadata"] name = "pynxtools" version = "0.0.5" description = "Extend NeXus for materials science experiment and serve as a NOMAD parser implementation for NeXus." -category = "main" optional = false python-versions = "<3.11,>=3.8" files = [ @@ -3975,7 +3814,6 @@ dev = ["mypy", "pip-tools", "pycodestyle", "pylint", "pytest", "pytest-cov", "py name = "pyparsing" version = "3.1.1" description = "pyparsing module - Classes and methods to define and execute parsing grammars" -category = "main" optional = false python-versions = ">=3.6.8" files = [ @@ -3988,14 +3826,13 @@ diagrams = ["jinja2", "railroad-diagrams"] [[package]] name = "pytest" -version = "7.4.2" +version = "7.4.3" description = "pytest: simple powerful testing with Python" -category = "dev" optional = false python-versions = ">=3.7" files = [ - {file = "pytest-7.4.2-py3-none-any.whl", hash = "sha256:1d881c6124e08ff0a1bb75ba3ec0bfd8b5354a01c194ddd5a0a870a48d99b002"}, - {file = "pytest-7.4.2.tar.gz", hash = "sha256:a766259cfab564a2ad52cb1aae1b881a75c3eb7e34ca3779697c23ed47c47069"}, + {file = "pytest-7.4.3-py3-none-any.whl", hash = "sha256:0d009c083ea859a71b76adf7c1d502e4bc170b80a8ef002da5806527b9591fac"}, + {file = "pytest-7.4.3.tar.gz", hash = "sha256:d989d136982de4e3b29dabcc838ad581c64e8ed52c11fbe86ddebd9da0818cd5"}, ] [package.dependencies] @@ -4013,7 +3850,6 @@ testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "no name = "pytest-clarity" version = "1.0.1" description = "A plugin providing an alternative, colourful diff output for failing assertions." -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -4029,7 +3865,6 @@ rich = ">=8.0.0" name = "pytest-cov" version = "3.0.0" description = "Pytest plugin for measuring coverage." -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -4048,7 +3883,6 @@ testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtuale name = "pytest-forked" version = "1.6.0" description = "run tests in isolated forked subprocesses" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -4064,7 +3898,6 @@ pytest = ">=3.10" name = "pytest-xdist" version = "2.5.0" description = "pytest xdist plugin for distributed testing and loop-on-failing modes" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -4086,7 +3919,6 @@ testing = ["filelock"] name = "python-dateutil" version = "2.8.2" description = "Extensions to the standard Python datetime module" -category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7" files = [ @@ -4101,7 +3933,6 @@ six = ">=1.5" name = "python-json-logger" version = "2.0.7" description = "A python library adding a json log formatter" -category = "main" optional = true python-versions = ">=3.6" files = [ @@ -4113,7 +3944,6 @@ files = [ name = "pytz" version = "2023.3.post1" description = "World timezone definitions, modern and historical" -category = "main" optional = false python-versions = "*" files = [ @@ -4125,7 +3955,6 @@ files = [ name = "pytz-deprecation-shim" version = "0.1.0.post0" description = "Shims to make deprecation of pytz easier" -category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7" files = [ @@ -4141,7 +3970,6 @@ tzdata = {version = "*", markers = "python_version >= \"3.6\""} name = "pywavelets" version = "1.4.1" description = "PyWavelets, wavelet transform module" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4179,7 +4007,6 @@ numpy = ">=1.17.3" name = "pywin32" version = "306" description = "Python for Window Extensions" -category = "main" optional = false python-versions = "*" files = [ @@ -4203,7 +4030,6 @@ files = [ name = "pywinpty" version = "2.0.12" description = "Pseudo terminal support for Windows from Python." -category = "main" optional = true python-versions = ">=3.8" files = [ @@ -4219,7 +4045,6 @@ files = [ name = "pyxem" version = "0.15.1" description = "multi-dimensional diffraction microscopy" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4254,7 +4079,6 @@ tests = ["coverage (>=5.0)", "coveralls (>=1.10)", "pytest (>=5.0)", "pytest-cov name = "pyyaml" version = "6.0.1" description = "YAML parser and emitter for Python" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -4304,7 +4128,6 @@ files = [ name = "pyzmq" version = "25.1.1" description = "Python bindings for 0MQ" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -4410,7 +4233,6 @@ cffi = {version = "*", markers = "implementation_name == \"pypy\""} name = "qtconsole" version = "5.4.4" description = "Jupyter Qt console" -category = "main" optional = true python-versions = ">= 3.7" files = [ @@ -4435,14 +4257,13 @@ test = ["flaky", "pytest", "pytest-qt"] [[package]] name = "qtpy" -version = "2.4.0" +version = "2.4.1" description = "Provides an abstraction layer on top of the various Qt bindings (PyQt5/6 and PySide2/6)." -category = "main" optional = true python-versions = ">=3.7" files = [ - {file = "QtPy-2.4.0-py3-none-any.whl", hash = "sha256:4d4f045a41e09ac9fa57fcb47ef05781aa5af294a0a646acc1b729d14225e741"}, - {file = "QtPy-2.4.0.tar.gz", hash = "sha256:db2d508167aa6106781565c8da5c6f1487debacba33519cedc35fa8997d424d4"}, + {file = "QtPy-2.4.1-py3-none-any.whl", hash = "sha256:1c1d8c4fa2c884ae742b069151b0abe15b3f70491f3972698c683b8e38de839b"}, + {file = "QtPy-2.4.1.tar.gz", hash = "sha256:a5a15ffd519550a1361bdc56ffc07fda56a6af7292f17c7b395d4083af632987"}, ] [package.dependencies] @@ -4455,7 +4276,6 @@ test = ["pytest (>=6,!=7.0.0,!=7.0.1)", "pytest-cov (>=3.0.0)", "pytest-qt"] name = "radioactivedecay" version = "0.4.21" description = "A Python package for radioactive decay modelling that supports 1252 radionuclides, decay chains, branching, and metastable states." -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -4476,7 +4296,6 @@ sympy = "*" name = "recommonmark" version = "0.7.1" description = "A docutils-compatibility bridge to CommonMark, enabling you to write CommonMark inside of Docutils & Sphinx projects." -category = "main" optional = false python-versions = "*" files = [ @@ -4493,7 +4312,6 @@ sphinx = ">=1.3.1" name = "referencing" version = "0.30.2" description = "JSON Referencing + Python" -category = "main" optional = true python-versions = ">=3.8" files = [ @@ -4509,7 +4327,6 @@ rpds-py = ">=0.7.0" name = "requests" version = "2.31.0" description = "Python HTTP for Humans." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4531,7 +4348,6 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"] name = "requests-cache" version = "1.1.0" description = "A persistent cache for python requests" -category = "main" optional = false python-versions = ">=3.7,<4.0" files = [ @@ -4562,7 +4378,6 @@ yaml = ["pyyaml (>=5.4)"] name = "rfc3339-validator" version = "0.1.4" description = "A pure python RFC3339 validator" -category = "main" optional = true python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -4577,7 +4392,6 @@ six = "*" name = "rfc3986-validator" version = "0.1.1" description = "Pure python rfc3986 validator" -category = "main" optional = true python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -4589,7 +4403,6 @@ files = [ name = "rich" version = "13.6.0" description = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal" -category = "dev" optional = false python-versions = ">=3.7.0" files = [ @@ -4609,7 +4422,6 @@ jupyter = ["ipywidgets (>=7.5.1,<9)"] name = "rpds-py" version = "0.10.6" description = "Python bindings to Rust's persistent data structures (rpds)" -category = "main" optional = true python-versions = ">=3.8" files = [ @@ -4718,7 +4530,6 @@ files = [ name = "scikit-image" version = "0.21.0" description = "Image processing in Python" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4769,7 +4580,6 @@ test = ["asv", "matplotlib (>=3.5)", "pooch (>=1.6.0)", "pytest (>=7.0)", "pytes name = "scikit-learn" version = "1.3.2" description = "A set of python modules for machine learning and data mining" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4817,7 +4627,6 @@ tests = ["black (>=23.3.0)", "matplotlib (>=3.1.3)", "mypy (>=1.3)", "numpydoc ( name = "scipy" version = "1.10.1" description = "Fundamental algorithms for scientific computing in Python" -category = "main" optional = false python-versions = "<3.12,>=3.8" files = [ @@ -4856,7 +4665,6 @@ test = ["asv", "gmpy2", "mpmath", "pooch", "pytest", "pytest-cov", "pytest-timeo name = "send2trash" version = "1.8.2" description = "Send file to trash natively under Mac OS X, Windows and Linux" -category = "main" optional = true python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7" files = [ @@ -4873,7 +4681,6 @@ win32 = ["pywin32"] name = "setuptools" version = "68.2.2" description = "Easily download, build, install, upgrade, and uninstall Python packages" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4890,7 +4697,6 @@ testing-integration = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "jar name = "setuptools-scm" version = "8.0.4" description = "the blessed package to manage your versions by scm tags" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4913,7 +4719,6 @@ test = ["build", "pytest", "rich", "wheel"] name = "silx" version = "1.1.2" description = "Software library for X-ray data analysis" -category = "main" optional = false python-versions = ">=3.5" files = [ @@ -4960,7 +4765,6 @@ test = ["pytest", "pytest-mock", "pytest-xvfb"] name = "six" version = "1.16.0" description = "Python 2 and 3 compatibility utilities" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -4972,7 +4776,6 @@ files = [ name = "smmap" version = "5.0.1" description = "A pure Python implementation of a sliding window memory map manager" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4984,7 +4787,6 @@ files = [ name = "sniffio" version = "1.3.0" description = "Sniff out which async library your code is running under" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -4996,7 +4798,6 @@ files = [ name = "snowballstemmer" version = "2.2.0" description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms." -category = "main" optional = false python-versions = "*" files = [ @@ -5008,7 +4809,6 @@ files = [ name = "soupsieve" version = "2.5" description = "A modern CSS selector implementation for Beautiful Soup." -category = "main" optional = true python-versions = ">=3.8" files = [ @@ -5020,7 +4820,6 @@ files = [ name = "sparse" version = "0.14.0" description = "Sparse n-dimensional arrays" -category = "main" optional = false python-versions = ">=3.8, <4" files = [ @@ -5043,7 +4842,6 @@ tox = ["dask[array]", "pytest (>=3.5)", "pytest-black", "pytest-cov", "tox"] name = "sphinx" version = "7.1.2" description = "Python documentation generator" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -5080,7 +4878,6 @@ test = ["cython", "filelock", "html5lib", "pytest (>=4.6)"] name = "sphinx-autodoc-typehints" version = "1.24.0" description = "Type hints (PEP 484) support for the Sphinx autodoc extension" -category = "main" optional = true python-versions = ">=3.8" files = [ @@ -5101,7 +4898,6 @@ testing = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "diff-cover (>=7.5)", "p name = "sphinx-basic-ng" version = "1.0.0b2" description = "A modern skeleton for Sphinx themes." -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -5119,7 +4915,6 @@ docs = ["furo", "ipython", "myst-parser", "sphinx-copybutton", "sphinx-inline-ta name = "sphinx-rtd-theme" version = "1.3.0" description = "Read the Docs theme for Sphinx" -category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7" files = [ @@ -5139,7 +4934,6 @@ dev = ["bump2version", "sphinxcontrib-httpdomain", "transifex-client", "wheel"] name = "sphinxcontrib-applehelp" version = "1.0.4" description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -5155,7 +4949,6 @@ test = ["pytest"] name = "sphinxcontrib-devhelp" version = "1.0.2" description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp document." -category = "main" optional = false python-versions = ">=3.5" files = [ @@ -5171,7 +4964,6 @@ test = ["pytest"] name = "sphinxcontrib-htmlhelp" version = "2.0.1" description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -5187,7 +4979,6 @@ test = ["html5lib", "pytest"] name = "sphinxcontrib-jquery" version = "4.1" description = "Extension to include jQuery on newer Sphinx releases" -category = "main" optional = false python-versions = ">=2.7" files = [ @@ -5202,7 +4993,6 @@ Sphinx = ">=1.8" name = "sphinxcontrib-jsmath" version = "1.0.1" description = "A sphinx extension which renders display math in HTML via JavaScript" -category = "main" optional = false python-versions = ">=3.5" files = [ @@ -5217,7 +5007,6 @@ test = ["flake8", "mypy", "pytest"] name = "sphinxcontrib-qthelp" version = "1.0.3" description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp document." -category = "main" optional = false python-versions = ">=3.5" files = [ @@ -5233,7 +5022,6 @@ test = ["pytest"] name = "sphinxcontrib-serializinghtml" version = "1.1.5" description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)." -category = "main" optional = false python-versions = ">=3.5" files = [ @@ -5249,7 +5037,6 @@ test = ["pytest"] name = "sphinxcontrib-websupport" version = "1.2.4" description = "Sphinx API for Web Apps" -category = "main" optional = true python-versions = ">=3.5" files = [ @@ -5268,7 +5055,6 @@ test = ["Sphinx", "pytest", "sqlalchemy", "whoosh"] name = "stack-data" version = "0.6.3" description = "Extract data from python stack frames and tracebacks for informative displays" -category = "main" optional = false python-versions = "*" files = [ @@ -5288,7 +5074,6 @@ tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"] name = "symmetrize" version = "0.5.5" description = "Symmetrization and centering of 2D pattern using nonrigid point set registration" -category = "main" optional = false python-versions = "*" files = [ @@ -5312,7 +5097,6 @@ sphinx-rtd-theme = "*" name = "sympy" version = "1.12" description = "Computer algebra system (CAS) in Python" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -5327,7 +5111,6 @@ mpmath = ">=0.19" name = "terminado" version = "0.17.1" description = "Tornado websocket backend for the Xterm.js Javascript terminal emulator library." -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -5348,7 +5131,6 @@ test = ["pre-commit", "pytest (>=7.0)", "pytest-timeout"] name = "threadpoolctl" version = "3.2.0" description = "threadpoolctl" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -5360,7 +5142,6 @@ files = [ name = "tifffile" version = "2022.10.10" description = "Read and write TIFF files" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -5378,7 +5159,6 @@ all = ["fsspec", "imagecodecs (>=2022.2.22)", "lxml", "matplotlib (>=3.3)", "zar name = "tinycss2" version = "1.2.1" description = "A tiny CSS parser" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -5397,7 +5177,6 @@ test = ["flake8", "isort", "pytest"] name = "tomli" version = "2.0.1" description = "A lil' TOML parser" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -5409,7 +5188,6 @@ files = [ name = "tomlkit" version = "0.12.1" description = "Style preserving TOML library" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -5421,7 +5199,6 @@ files = [ name = "toolz" version = "0.12.0" description = "List processing tools and functional utilities" -category = "main" optional = false python-versions = ">=3.5" files = [ @@ -5433,7 +5210,6 @@ files = [ name = "tornado" version = "6.3.3" description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed." -category = "main" optional = false python-versions = ">= 3.8" files = [ @@ -5454,7 +5230,6 @@ files = [ name = "tqdm" version = "4.66.1" description = "Fast, Extensible Progress Meter" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -5475,7 +5250,6 @@ telegram = ["requests"] name = "traitlets" version = "5.11.2" description = "Traitlets Python configuration system" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -5491,7 +5265,6 @@ test = ["argcomplete (>=3.0.3)", "mypy (>=1.5.1)", "pre-commit", "pytest (>=7.0, name = "traits" version = "6.4.3" description = "Observable typed attributes for Python classes" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -5566,7 +5339,6 @@ test = ["Cython", "PySide6", "Sphinx", "flake8", "flake8-ets", "mypy", "numpy", name = "transforms3d" version = "0.4.1" description = "Functions for 3D coordinate transformations" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -5577,7 +5349,6 @@ files = [ name = "types-python-dateutil" version = "2.8.19.14" description = "Typing stubs for python-dateutil" -category = "main" optional = true python-versions = "*" files = [ @@ -5589,7 +5360,6 @@ files = [ name = "typing-extensions" version = "4.8.0" description = "Backported and Experimental Type Hints for Python 3.8+" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -5601,7 +5371,6 @@ files = [ name = "tzdata" version = "2023.3" description = "Provider of IANA time zone data" -category = "main" optional = false python-versions = ">=2" files = [ @@ -5613,7 +5382,6 @@ files = [ name = "tzlocal" version = "4.3" description = "tzinfo object for the local timezone" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -5633,7 +5401,6 @@ devenv = ["black", "check-manifest", "flake8", "pyroma", "pytest (>=4.3)", "pyte name = "uncertainties" version = "3.1.7" description = "Transparent calculations with uncertainties on the quantities involved (aka error propagation); fast calculation of derivatives" -category = "main" optional = false python-versions = "*" files = [ @@ -5654,7 +5421,6 @@ tests = ["nose", "numpy"] name = "uri-template" version = "1.3.0" description = "RFC 6570 URI Template Processor" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -5669,7 +5435,6 @@ dev = ["flake8", "flake8-annotations", "flake8-bandit", "flake8-bugbear", "flake name = "url-normalize" version = "1.4.3" description = "URL normalization for Python" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" files = [ @@ -5684,7 +5449,6 @@ six = "*" name = "urllib3" version = "2.0.7" description = "HTTP library with thread-safe connection pooling, file post, and more." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -5702,7 +5466,6 @@ zstd = ["zstandard (>=0.18.0)"] name = "wcwidth" version = "0.2.8" description = "Measures the displayed width of unicode strings in a terminal" -category = "main" optional = false python-versions = "*" files = [ @@ -5714,7 +5477,6 @@ files = [ name = "webcolors" version = "1.13" description = "A library for working with the color formats defined by HTML and CSS." -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -5730,7 +5492,6 @@ tests = ["pytest", "pytest-cov"] name = "webencodings" version = "0.5.1" description = "Character encoding aliases for legacy web content" -category = "main" optional = true python-versions = "*" files = [ @@ -5742,7 +5503,6 @@ files = [ name = "websocket-client" version = "1.6.4" description = "WebSocket client for Python with low level API options" -category = "main" optional = true python-versions = ">=3.8" files = [ @@ -5759,7 +5519,6 @@ test = ["websockets"] name = "widgetsnbextension" version = "4.0.9" description = "Jupyter interactive widgets for Jupyter Notebook" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -5771,7 +5530,6 @@ files = [ name = "xarray" version = "0.20.2" description = "N-D labeled arrays and datasets in Python" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -5795,7 +5553,6 @@ viz = ["matplotlib", "nc-time-axis", "seaborn"] name = "zarr" version = "2.16.1" description = "An implementation of chunked, compressed, N-dimensional arrays for Python" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -5817,7 +5574,6 @@ jupyter = ["ipytree (>=0.2.2)", "ipywidgets (>=8.0.0)", "notebook"] name = "zipfile37" version = "0.1.3" description = "Read and write ZIP files - backport of the zipfile module from Python 3.7" -category = "main" optional = false python-versions = "*" files = [ @@ -5828,7 +5584,6 @@ files = [ name = "zipp" version = "3.17.0" description = "Backport of pathlib-compatible object wrapper for zip files" -category = "main" optional = false python-versions = ">=3.8" files = [ From 3ac390ff0810d67f7d2397e5ef32b2a12bbab414 Mon Sep 17 00:00:00 2001 From: rettigl Date: Wed, 25 Oct 2023 16:33:18 +0200 Subject: [PATCH 05/25] add authentication via app --- .github/workflows/update_dependencies.yml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/.github/workflows/update_dependencies.yml b/.github/workflows/update_dependencies.yml index becf71e5..5e9ac1cb 100644 --- a/.github/workflows/update_dependencies.yml +++ b/.github/workflows/update_dependencies.yml @@ -15,6 +15,12 @@ jobs: with: lfs: true + - uses: tibdex/github-app-token@v1 + id: generate-token + with: + app_id: ${{ secrets.APP_ID }} + private_key: ${{ secrets.APP_PRIVATE_KEY }} + # Use cached python and dependencies, install poetry - name: "Setup Python, Poetry and Dependencies" uses: packetcoders/action-setup-cache-python-poetry@main @@ -30,6 +36,7 @@ jobs: poetry run poetry update status=$(git status | grep poetry.lock) echo "status=$status" >> $GITHUB_OUTPUT + echo $status # create pull request if necessary - name: "Create Pull Request" From 6a7cee77b2c07adef09905974c326d4ca7133cb1 Mon Sep 17 00:00:00 2001 From: rettigl Date: Wed, 25 Oct 2023 16:43:49 +0200 Subject: [PATCH 06/25] use token... --- .github/workflows/update_dependencies.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/update_dependencies.yml b/.github/workflows/update_dependencies.yml index 5e9ac1cb..f7975db4 100644 --- a/.github/workflows/update_dependencies.yml +++ b/.github/workflows/update_dependencies.yml @@ -34,7 +34,7 @@ jobs: run: | poetry run poetry self update poetry run poetry update - status=$(git status | grep poetry.lock) + status=$(git status) echo "status=$status" >> $GITHUB_OUTPUT echo $status @@ -43,6 +43,7 @@ jobs: uses: peter-evans/create-pull-request@v5 if: ${{ steps.update.outputs.status != '' }} with: + token: ${{ steps.generate-token.outputs.token }} commit-message: Update dependencies title: "Update dependencies" body: | From cfbb3b4bac88a1e91d2ae5ace051269ccaf67acc Mon Sep 17 00:00:00 2001 From: rettigl Date: Wed, 25 Oct 2023 16:52:37 +0200 Subject: [PATCH 07/25] remove debug printout --- .github/workflows/update_dependencies.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/update_dependencies.yml b/.github/workflows/update_dependencies.yml index f7975db4..aa18f6cf 100644 --- a/.github/workflows/update_dependencies.yml +++ b/.github/workflows/update_dependencies.yml @@ -36,7 +36,6 @@ jobs: poetry run poetry update status=$(git status) echo "status=$status" >> $GITHUB_OUTPUT - echo $status # create pull request if necessary - name: "Create Pull Request" From ad22547047df8c10eca2bf68388353fd975b0920 Mon Sep 17 00:00:00 2001 From: rettigl Date: Wed, 25 Oct 2023 17:04:39 +0200 Subject: [PATCH 08/25] revert --- .github/workflows/update_dependencies.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/update_dependencies.yml b/.github/workflows/update_dependencies.yml index aa18f6cf..6a7566ec 100644 --- a/.github/workflows/update_dependencies.yml +++ b/.github/workflows/update_dependencies.yml @@ -34,7 +34,7 @@ jobs: run: | poetry run poetry self update poetry run poetry update - status=$(git status) + status=$(git status | grep poetry.lock) echo "status=$status" >> $GITHUB_OUTPUT # create pull request if necessary From d39a38741a5c20e026e7d1b2831292b558be692c Mon Sep 17 00:00:00 2001 From: rettigl Date: Thu, 26 Oct 2023 00:22:01 +0200 Subject: [PATCH 09/25] try multiline string storage --- .github/workflows/update_dependencies.yml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/.github/workflows/update_dependencies.yml b/.github/workflows/update_dependencies.yml index 6a7566ec..4872977b 100644 --- a/.github/workflows/update_dependencies.yml +++ b/.github/workflows/update_dependencies.yml @@ -33,9 +33,12 @@ jobs: id: update run: | poetry run poetry self update - poetry run poetry update + UPDATE_OUTPUT = $(poetry run poetry update) status=$(git status | grep poetry.lock) echo "status=$status" >> $GITHUB_OUTPUT + echo "UPDATE_OUTPUT<> $GITHUB_OUTPUT + echo "$UPDATE_OUTPUT" >> $GITHUB_OUTPUT + echo "EOF" >> $GITHUB_OUTPUT # create pull request if necessary - name: "Create Pull Request" @@ -47,4 +50,4 @@ jobs: title: "Update dependencies" body: | - Dependency updates - ${{ steps.update.outputs.update_output }} + - ${{ steps.update.outputs.UPDATE_OUTPUT }} From 084dd3ff7fbca42f3d3a9950585a164e4c1534a7 Mon Sep 17 00:00:00 2001 From: rettigl Date: Thu, 26 Oct 2023 00:26:42 +0200 Subject: [PATCH 10/25] remove spaces --- .github/workflows/update_dependencies.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/update_dependencies.yml b/.github/workflows/update_dependencies.yml index 4872977b..c532675c 100644 --- a/.github/workflows/update_dependencies.yml +++ b/.github/workflows/update_dependencies.yml @@ -33,7 +33,7 @@ jobs: id: update run: | poetry run poetry self update - UPDATE_OUTPUT = $(poetry run poetry update) + UPDATE_OUTPUT=$(poetry run poetry update) status=$(git status | grep poetry.lock) echo "status=$status" >> $GITHUB_OUTPUT echo "UPDATE_OUTPUT<> $GITHUB_OUTPUT From d2e716d24446c4f17abdc89b74cf5eb0121e71aa Mon Sep 17 00:00:00 2001 From: rettigl Date: Thu, 26 Oct 2023 00:39:36 +0200 Subject: [PATCH 11/25] add cosmetic updates, and try better conditional check --- .github/workflows/update_dependencies.yml | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/.github/workflows/update_dependencies.yml b/.github/workflows/update_dependencies.yml index c532675c..cd286cbb 100644 --- a/.github/workflows/update_dependencies.yml +++ b/.github/workflows/update_dependencies.yml @@ -33,21 +33,23 @@ jobs: id: update run: | poetry run poetry self update - UPDATE_OUTPUT=$(poetry run poetry update) - status=$(git status | grep poetry.lock) - echo "status=$status" >> $GITHUB_OUTPUT + exec 5>&1 + UPDATE_OUTPUT=$(poetry run poetry update|tee >(cat - >&5)) echo "UPDATE_OUTPUT<> $GITHUB_OUTPUT echo "$UPDATE_OUTPUT" >> $GITHUB_OUTPUT echo "EOF" >> $GITHUB_OUTPUT + STATUS=$(git status | grep poetry.lock) + echo "STATUS=$STATUS" >> $GITHUB_OUTPUT + # create pull request if necessary - name: "Create Pull Request" uses: peter-evans/create-pull-request@v5 - if: ${{ steps.update.outputs.status != '' }} + if: ${{ contains(steps.update.outputs.STATUS, 'poetry.lock') }} with: token: ${{ steps.generate-token.outputs.token }} commit-message: Update dependencies title: "Update dependencies" body: | - - Dependency updates - - ${{ steps.update.outputs.UPDATE_OUTPUT }} + Dependency updates using Poetry: + ${{ steps.update.outputs.UPDATE_OUTPUT }} From e437a46d37b5fe90d2a89b789ebbd6130dcfd880 Mon Sep 17 00:00:00 2001 From: rettigl Date: Thu, 26 Oct 2023 00:45:00 +0200 Subject: [PATCH 12/25] manually update poetry.lock --- poetry.lock | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/poetry.lock b/poetry.lock index d6b53807..86ec3ead 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1600,13 +1600,13 @@ files = [ [[package]] name = "ipykernel" -version = "6.25.2" +version = "6.26.0" description = "IPython Kernel for Jupyter" optional = false python-versions = ">=3.8" files = [ - {file = "ipykernel-6.25.2-py3-none-any.whl", hash = "sha256:2e2ee359baba19f10251b99415bb39de1e97d04e1fab385646f24f0596510b77"}, - {file = "ipykernel-6.25.2.tar.gz", hash = "sha256:f468ddd1f17acb48c8ce67fcfa49ba6d46d4f9ac0438c1f441be7c3d1372230b"}, + {file = "ipykernel-6.26.0-py3-none-any.whl", hash = "sha256:3ba3dc97424b87b31bb46586b5167b3161b32d7820b9201a9e698c71e271602c"}, + {file = "ipykernel-6.26.0.tar.gz", hash = "sha256:553856658eb8430bbe9653ea041a41bff63e9606fc4628873fc92a6cf3abd404"}, ] [package.dependencies] @@ -1911,13 +1911,13 @@ qtconsole = "*" [[package]] name = "jupyter-client" -version = "8.4.0" +version = "8.5.0" description = "Jupyter protocol implementation and client libraries" optional = false python-versions = ">=3.8" files = [ - {file = "jupyter_client-8.4.0-py3-none-any.whl", hash = "sha256:6a2a950ec23a8f62f9e4c66acec7f0ea6c7d1f80ba0992e747b10c56ce2e6dbe"}, - {file = "jupyter_client-8.4.0.tar.gz", hash = "sha256:dc1b857d5d7d76ac101766c6e9b646bf18742721126e72e5d484c75a993cada2"}, + {file = "jupyter_client-8.5.0-py3-none-any.whl", hash = "sha256:c3877aac7257ec68d79b5c622ce986bd2a992ca42f6ddc9b4dd1da50e89f7028"}, + {file = "jupyter_client-8.5.0.tar.gz", hash = "sha256:e8754066510ce456358df363f97eae64b50860f30dc1fe8c6771440db3be9a63"}, ] [package.dependencies] @@ -2018,13 +2018,13 @@ jupyter-server = ">=1.1.2" [[package]] name = "jupyter-server" -version = "2.8.0" +version = "2.9.1" description = "The backend—i.e. core services, APIs, and REST endpoints—to Jupyter web applications." optional = true python-versions = ">=3.8" files = [ - {file = "jupyter_server-2.8.0-py3-none-any.whl", hash = "sha256:c57270faa6530393ae69783a2d2f1874c718b9f109080581ea076b05713249fa"}, - {file = "jupyter_server-2.8.0.tar.gz", hash = "sha256:b11e2ba80667c75f55630faf8ac3d5809f8734f9006d65cce117c46a0a516ab8"}, + {file = "jupyter_server-2.9.1-py3-none-any.whl", hash = "sha256:21ad1a3d455d5a79ce4bef5201925cd17510c17898cf9d54e3ccfb6b12734948"}, + {file = "jupyter_server-2.9.1.tar.gz", hash = "sha256:9ba71be4b9c16e479e4c50c929f8ac4b1015baf90237a08681397a98c76c7e5e"}, ] [package.dependencies] @@ -5248,18 +5248,18 @@ telegram = ["requests"] [[package]] name = "traitlets" -version = "5.11.2" +version = "5.12.0" description = "Traitlets Python configuration system" optional = false python-versions = ">=3.8" files = [ - {file = "traitlets-5.11.2-py3-none-any.whl", hash = "sha256:98277f247f18b2c5cabaf4af369187754f4fb0e85911d473f72329db8a7f4fae"}, - {file = "traitlets-5.11.2.tar.gz", hash = "sha256:7564b5bf8d38c40fa45498072bf4dc5e8346eb087bbf1e2ae2d8774f6a0f078e"}, + {file = "traitlets-5.12.0-py3-none-any.whl", hash = "sha256:81539f07f7aebcde2e4b5ab76727f53eabf18ad155c6ed7979a681411602fa47"}, + {file = "traitlets-5.12.0.tar.gz", hash = "sha256:833273bf645d8ce31dcb613c56999e2e055b1ffe6d09168a164bcd91c36d5d35"}, ] [package.extras] docs = ["myst-parser", 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of git status --- .github/workflows/update_dependencies.yml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/update_dependencies.yml b/.github/workflows/update_dependencies.yml index cd286cbb..141075f7 100644 --- a/.github/workflows/update_dependencies.yml +++ b/.github/workflows/update_dependencies.yml @@ -39,8 +39,10 @@ jobs: echo "$UPDATE_OUTPUT" >> $GITHUB_OUTPUT echo "EOF" >> $GITHUB_OUTPUT - STATUS=$(git status | grep poetry.lock) - echo "STATUS=$STATUS" >> $GITHUB_OUTPUT + STATUS=$(git status|tee >(cat - >&5)) + echo "STATUS<> $GITHUB_OUTPUT + echo "$STATUS" >> $GITHUB_OUTPUT + echo "EOF" >> $GITHUB_OUTPUT # create pull request if necessary - name: "Create Pull Request" From 7b972020da6d03f16f3f5cf39aee8494b958e056 Mon Sep 17 00:00:00 2001 From: rettigl Date: Thu, 26 Oct 2023 01:07:15 +0200 Subject: [PATCH 15/25] remove push trigger --- .github/workflows/update_dependencies.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/update_dependencies.yml b/.github/workflows/update_dependencies.yml index 141075f7..e3b7985a 100644 --- a/.github/workflows/update_dependencies.yml +++ b/.github/workflows/update_dependencies.yml @@ -3,7 +3,6 @@ name: Update depencies in poetry lockfile on: schedule: - cron: '0 1 * * 1' - push: workflow_dispatch: jobs: From 25f16b17be30181cf5a06b5c262504720186b8d1 Mon Sep 17 00:00:00 2001 From: rettigl Date: Thu, 26 Oct 2023 12:46:23 +0200 Subject: [PATCH 16/25] add docs/requirements.txt update, and try removing poetry run --- .github/workflows/update_dependencies.yml | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/.github/workflows/update_dependencies.yml b/.github/workflows/update_dependencies.yml index e3b7985a..7b26e136 100644 --- a/.github/workflows/update_dependencies.yml +++ b/.github/workflows/update_dependencies.yml @@ -4,6 +4,7 @@ on: schedule: - cron: '0 1 * * 1' workflow_dispatch: + push: jobs: update_dependencies: @@ -31,13 +32,20 @@ jobs: - name: "Update poetry lock file" id: update run: | - poetry run poetry self update + poetry self update exec 5>&1 - UPDATE_OUTPUT=$(poetry run poetry update|tee >(cat - >&5)) + UPDATE_OUTPUT=$(poetry update|tee >(cat - >&5)) echo "UPDATE_OUTPUT<> $GITHUB_OUTPUT echo "$UPDATE_OUTPUT" >> $GITHUB_OUTPUT echo "EOF" >> $GITHUB_OUTPUT + - name: Export requirements.txt + run: | + poetry export --without-hashes --format=requirements.txt -o docs/requirements.txt -E docs -E notebook + + - name: Obtain git status + id: status + run: | STATUS=$(git status|tee >(cat - >&5)) echo "STATUS<> $GITHUB_OUTPUT echo "$STATUS" >> $GITHUB_OUTPUT @@ -46,7 +54,7 @@ jobs: # create pull request if necessary - name: "Create Pull Request" uses: peter-evans/create-pull-request@v5 - if: ${{ contains(steps.update.outputs.STATUS, 'poetry.lock') }} + if: ${{ contains(steps.status.outputs.STATUS, 'poetry.lock') || contains(steps.status.outputs.STATUS, 'requirements.txt')}} with: token: ${{ steps.generate-token.outputs.token }} commit-message: Update dependencies From 28a7a6e46b4250aa4e30e62901e9cee5d70201bf Mon Sep 17 00:00:00 2001 From: rettigl Date: Thu, 26 Oct 2023 12:50:30 +0200 Subject: [PATCH 17/25] remove push trigger --- .github/workflows/update_dependencies.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/update_dependencies.yml b/.github/workflows/update_dependencies.yml index 7b26e136..95c18c83 100644 --- a/.github/workflows/update_dependencies.yml +++ b/.github/workflows/update_dependencies.yml @@ -4,7 +4,6 @@ on: schedule: - cron: '0 1 * * 1' workflow_dispatch: - push: jobs: update_dependencies: From 60d27650a933519be64b36d9d59ab6d09c1dba1e Mon Sep 17 00:00:00 2001 From: rettigl Date: Thu, 26 Oct 2023 12:51:40 +0200 Subject: [PATCH 18/25] remove generate_requirements workflow --- .github/workflows/generate-requirements.yml | 21 --------------------- 1 file changed, 21 deletions(-) delete mode 100644 .github/workflows/generate-requirements.yml diff --git a/.github/workflows/generate-requirements.yml b/.github/workflows/generate-requirements.yml deleted file mode 100644 index f971a3d8..00000000 --- a/.github/workflows/generate-requirements.yml +++ /dev/null @@ -1,21 +0,0 @@ -name: Generate requirements.txt for readthedocs - -on: - push: - branches: [main] - -jobs: - generate-requirements: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v3 - with: - lfs: true - - name: Set up Python 3.8 - uses: actions/setup-python@v4 - with: - python-version: 3.8 - - name: Install Poetry - run: curl -sSL https://install.python-poetry.org | python3 - - - name: Export requirements.txt - run: poetry export --without-hashes --format=requirements.txt -o docs/requirements.txt -E docs -E notebook From 45f6763cd5cb01672e8f99077db2458bf78a64b9 Mon Sep 17 00:00:00 2001 From: rettigl Date: Thu, 26 Oct 2023 12:58:19 +0200 Subject: [PATCH 19/25] fix tunneling of git status output --- .github/workflows/update_dependencies.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/update_dependencies.yml b/.github/workflows/update_dependencies.yml index 95c18c83..f978f869 100644 --- a/.github/workflows/update_dependencies.yml +++ b/.github/workflows/update_dependencies.yml @@ -45,6 +45,7 @@ jobs: - name: Obtain git status id: status run: | + exec 5>&1 STATUS=$(git status|tee >(cat - >&5)) echo "STATUS<> $GITHUB_OUTPUT echo "$STATUS" >> $GITHUB_OUTPUT From 1709c18c32f5244b4401647673fe6eba1777f7f8 Mon Sep 17 00:00:00 2001 From: rettigl Date: Thu, 26 Oct 2023 12:59:11 +0200 Subject: [PATCH 20/25] remove push trigger --- tests/data/config/config_local.yaml | 180 ++++++++++++++++++++++++++++ 1 file changed, 180 insertions(+) create mode 100644 tests/data/config/config_local.yaml diff --git a/tests/data/config/config_local.yaml b/tests/data/config/config_local.yaml new file mode 100644 index 00000000..05de06b1 --- /dev/null +++ b/tests/data/config/config_local.yaml @@ -0,0 +1,180 @@ +core: + loader: mpes + use_copy_tool: True + copy_tool_source: "/mnt/pcshare/" + copy_tool_dest: "/scratch/localDataStore/" + copy_tool_kwds: + ntasks: 20 + gid: 5050 + +dataframe: + hdf5_groupnames: ["Stream_0", "Stream_1", "Stream_2", "Stream_4"] + hdf5_aliases: + Stream_0: "X" + Stream_1: "Y" + Stream_2: "t" + Stream_4: "ADC" + time_stamp_alias: "timeStamps" + ms_markers_group: "msMarkers" + first_event_time_stamp_key: "FirstEventTimeStamp" + jitter_cols: ["X", "Y", "t", "ADC"] + x_column: "X" + y_column: "Y" + tof_column: "t" + corrected_tof_column: "tm" + adc_column: "ADC" + energy_column: "E" + corrected_x_column: "Xm" + corrected_y_column: "Ym" + kx_column: "kx" + ky_column: "ky" + delay_column: "delay" + tof_binwidth: 4.125e-12 + tof_binning: 2 + +energy: + bins: 1000 + ranges: [64000, 69000] + bias_key: "@KTOF:Lens:Sample:V" + normalize: True + normalize_span: 7 + normalize_order: 1 + fastdtw_radius: 2 + peak_window: 7 + calibration_method: "lmfit" + energy_scale: "kinetic" + tof_fermi: 132250 + x_width: [-20, 20] + y_width: [-20, 20] + tof_width: [-300, 500] + color_clip: 300 + correction: + correction_type: "Lorentzian" + amplitude: 2.5 + center: [730.0, 730.0] + kwds: + gamma: 920.0 + calibration: + d: 1.058206295066418 + t0: 7.684410678887588e-07 + E0: -30.440035779171833 + energy_scale: "kinetic" + +momentum: + axes: ["@x_column", "@y_column", "@tof_column"] + bins: [512, 512, 300] + ranges: [[-256, 1792], [-256, 1792], [66000, 68000]] + detector_ranges: [[0, 2048], [0, 2048]] + center_pixel: [256, 256] + sigma: 5 + fwhm: 8 + sigma_radius: 1 + center_det: "centroidnn" + calibration: + coeffs: [0.012389400615413859, 0.012389400615413859] + x_center: 256.0 + y_center: 256.0 + rstart: -256. + cstart: -256. + rstep: 4.0 + cstep: 4.0 + dfield_file: "../tests/data/config/dfield.npy" + +delay: + adc_range: [1900, 25600] + adc_binning: 2 + p1_key: "@trARPES:DelayStage:p1" + p2_key: "@trARPES:DelayStage:p2" + t0_key: "@trARPES:DelayStage:t0" + +binning: + hist_mode: "numba" + mode: "fast" + pbar: True + num_cores: 20 + threads_per_worker: 4 + threadpool_API: "blas" + +histogram: + bins: [80, 80, 80, 80] + axes: ["X", "Y", "t", "ADC"] + ranges: [[0, 1800], [0, 1800], [65000, 69000], [0, 9000], ] + +metadata: + epics_pvs: ["KTOF:Lens:Extr:I", "trARPES:Carving:TEMP_RBV", "trARPES:XGS600:PressureAC:P_RD", "KTOF:Lens:UDLD:V", "KTOF:Lens:Sample:V", "KTOF:Apertures:m1.RBV", "KTOF:Apertures:m2.RBV", "KTOF:Apertures:m3.RBV", "trARPES:Carving:TRX.RBV", "trARPES:Carving:TRY.RBV", "trARPES:Carving:TRZ.RBV", "trARPES:Carving:THT.RBV", "trARPES:Carving:PHI.RBV", "trARPES:Carving:OMG.RBV"] + fa_in_channel: 'KTOF:Apertures:m1.RBV' + fa_hor_channel: 'KTOF:Apertures:m2.RBV' + ca_in_channel: 'KTOF:Apertures:m3.RBV' + aperture_config: + "2018-01-23T19:35:15": + fa_size: + 750.: [[-3.0, -1.4], [-5.4, -4.6]] + grid: [[-3.0, -1.4], [0.15, 1.75]] + 1500.: [[-3.0, -1.4], [6.25, 7.75]] + 200.: [[3.3, 4.4], [-5.4, -4.6]] + 500.: [[3.3, 4.4], [0.15, 1.75]] + 1000.: [[3.3, 4.4], [6.25, 7.75]] + 20.: [[9.6, 10.1], [-5.4, -4.6]] + 50.: [[9.6, 10.1], [0.15, 1.75]] + 100.: [[9.6, 10.1], [6.25, 7.75]] + open: [[-15, -9.0], [-15, -8.9]] + ca_size: + 50.: [8.0, 8.4] + 200.: [-0.5, -0.9] + 100: [3.4, 3.8] + grid: [-5.3, -5.9] + open: [-12.0, -8] + "2020-01-23T19:35:15": + fa_size: + 750.: [[-6.2, -4.8], [5.0, 6.0]] + grid: [[-6.2, -4.8], [-0.7, -0.3]] + 500.: [[-6.2, -4.8], [-7.0, -6.0]] + 200.: [[0.5, 0.9], [-0.7, -0.3]] + 100.: [[0.5, 0.9], [-7.0, -6.0]] + 300.: [[0.5, 0.9], [5.0, 6.0]] + 10.: [[6.5, 6.9], [-7.0, -6.0]] + 20.: [[6.5, 6.9], [-0.7, -0.3]] + 50.: [[6.5, 6.9], [5.0, 6.0]] + open: [[-15, -8.5], [-15, -8.9]] + ca_size: + 50.: [9.0, 11.0] + 300.: [-0.1, 0.1] + 200.: [0.7, 1.5] + 100: [5.1, 5.9] + grid: [-5.5, -5.2] + open: [-15, -8.5] + lens_mode_config: + "6kV_kmodem4.0_20VTOF_v3.sav": + Extr: 6000.0 + UCA: 1200 + UFA: 600.0 + Z1: 2452.9 + Z2: 1489.9 + A: 420.07 + B: 2494.8 + C: 489.2 + D: 228.05 + E: 113.82 + F: 54.232 + G: 20.0 + H: 25.5 + I: 36.0 + TOF: 20.0 + MCPfront: 20.0 + "6kV_kmodem4.0_30VTOF_453ns_focus.sav": + Extr: 6000.0 + UCA: 1200 + UFA: 600.0 + Z1: 2452.9 + Z2: 1489.9 + A: 403.07 + B: 2500 + C: 422.25 + D: 208.88 + E: 199.49 + F: 68.735 + G: 30.0 + H: 30.0 + I: 44.5 + TOF: 30.0 + MCPfront: 30.0 From 4f55c05572f2233ee9154ada2fffa1b6a6f7f606 Mon Sep 17 00:00:00 2001 From: rettigl Date: Thu, 26 Oct 2023 13:00:40 +0200 Subject: [PATCH 21/25] add push action --- .github/workflows/update_dependencies.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/update_dependencies.yml b/.github/workflows/update_dependencies.yml index f978f869..4dd3e0af 100644 --- a/.github/workflows/update_dependencies.yml +++ b/.github/workflows/update_dependencies.yml @@ -4,6 +4,7 @@ on: schedule: - cron: '0 1 * * 1' workflow_dispatch: + push: jobs: update_dependencies: From cfbaed22231b69d3276b445a87f72dd622e2da03 Mon Sep 17 00:00:00 2001 From: rettigl Date: Thu, 26 Oct 2023 11:03:43 +0000 Subject: [PATCH 22/25] Update dependencies --- docs/requirements.txt | 188 ++++++++++++++++++++++-------------------- poetry.lock | 9 +- 2 files changed, 104 insertions(+), 93 deletions(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index 22a0694b..63c82205 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,35 +1,37 @@ alabaster==0.7.13 ; python_version >= "3.8" and python_version < "3.11" -anyio==3.7.1 ; python_version >= "3.8" and python_version < "3.11" -appnope==0.1.3 ; python_version >= "3.8" and python_version < "3.11" and platform_system == "Darwin" or python_version >= "3.8" and python_version < "3.11" and sys_platform == "darwin" +anyio==4.0.0 ; python_version >= "3.8" and python_version < "3.11" +appnope==0.1.3 ; python_version >= "3.8" and python_version < "3.11" and (platform_system == "Darwin" or sys_platform == "darwin") argon2-cffi-bindings==21.2.0 ; python_version >= "3.8" and python_version < "3.11" -argon2-cffi==21.3.0 ; python_version >= "3.8" and python_version < "3.11" -arrow==1.2.3 ; python_version >= "3.8" and python_version < "3.11" -asciitree==0.3.3 ; python_version >= "3.8" and python_version < "3.11" and platform_machine == "x86_64" or python_version >= "3.8" and python_version < "3.11" and platform_machine == "AMD64" +argon2-cffi==23.1.0 ; python_version >= "3.8" and python_version < "3.11" +arrow==1.3.0 ; python_version >= "3.8" and python_version < "3.11" +asciitree==0.3.3 ; python_version >= "3.8" and python_version < "3.11" and (platform_machine == "x86_64" or platform_machine == "AMD64") ase==3.22.1 ; python_version >= "3.8" and python_version < "3.11" asteval==0.9.31 ; python_version >= "3.8" and python_version < "3.11" astropy==5.2.2 ; python_version >= "3.8" and python_version < "3.11" -asttokens==2.2.1 ; python_version >= "3.8" and python_version < "3.11" +asttokens==2.4.1 ; python_version >= "3.8" and python_version < "3.11" +async-lru==2.0.4 ; python_version >= "3.8" and python_version < "3.11" attrs==23.1.0 ; python_version >= "3.8" and python_version < "3.11" -babel==2.12.1 ; python_version >= "3.8" and python_version < "3.11" +babel==2.13.1 ; python_version >= "3.8" and python_version < "3.11" backcall==0.2.0 ; python_version >= "3.8" and python_version < "3.11" +backports-zoneinfo==0.2.1 ; python_version >= "3.8" and python_version < "3.9" beautifulsoup4==4.12.2 ; python_version >= "3.8" and python_version < "3.11" -bleach==6.0.0 ; python_version >= "3.8" and python_version < "3.11" +bleach==6.1.0 ; python_version >= "3.8" and python_version < "3.11" bokeh==2.4.3 ; python_version >= "3.8" and python_version < "3.11" cattrs==23.1.2 ; python_version >= "3.8" and python_version < "3.11" certifi==2023.7.22 ; python_version >= "3.8" and python_version < "3.11" -cffi==1.15.1 ; python_version >= "3.8" and python_version < "3.11" -charset-normalizer==3.2.0 ; python_version >= "3.8" and python_version < "3.11" -click==8.1.6 ; python_version >= "3.8" and python_version < "3.11" -cloudpickle==2.2.1 ; python_version >= "3.8" and python_version < "3.11" -colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.11" and platform_system == "Windows" or python_version >= "3.8" and python_version < "3.11" and sys_platform == "win32" +cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.11" +charset-normalizer==3.3.1 ; python_version >= "3.8" and python_version < "3.11" +click==8.1.7 ; python_version >= "3.8" and python_version < "3.11" +cloudpickle==3.0.0 ; python_version >= "3.8" and python_version < "3.11" +colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.11" and (platform_system == "Windows" or sys_platform == "win32") comm==0.1.4 ; python_version >= "3.8" and python_version < "3.11" commonmark==0.9.1 ; python_version >= "3.8" and python_version < "3.11" -contourpy==1.1.0 ; python_version >= "3.8" and python_version < "3.11" +contourpy==1.1.1 ; python_version >= "3.8" and python_version < "3.11" cramjam==2.7.0 ; python_version >= "3.8" and python_version < "3.11" -cycler==0.11.0 ; python_version >= "3.8" and python_version < "3.11" +cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.11" dask==2022.12.1 ; python_version >= "3.8" and python_version < "3.11" dask[array]==2022.12.1 ; python_version >= "3.8" and python_version < "3.11" -debugpy==1.6.7.post1 ; python_version >= "3.8" and python_version < "3.11" +debugpy==1.8.0 ; python_version >= "3.8" and python_version < "3.11" decorator==5.1.1 ; python_version >= "3.8" and python_version < "3.11" defusedxml==0.7.1 ; python_version >= "3.8" and python_version < "3.11" diffpy-structure==3.1.0 ; python_version >= "3.8" and python_version < "3.11" @@ -37,61 +39,60 @@ diffsims==0.5.2 ; python_version >= "3.8" and python_version < "3.11" dill==0.3.7 ; python_version >= "3.8" and python_version < "3.11" docutils==0.18.1 ; python_version >= "3.8" and python_version < "3.11" entrypoints==0.4 ; python_version >= "3.8" and python_version < "3.11" -exceptiongroup==1.1.2 ; python_version >= "3.8" and python_version < "3.11" -executing==1.2.0 ; python_version >= "3.8" and python_version < "3.11" +exceptiongroup==1.1.3 ; python_version >= "3.8" and python_version < "3.11" +executing==2.0.0 ; python_version >= "3.8" and python_version < "3.11" fabio==2023.6.0 ; python_version >= "3.8" and python_version < "3.11" fastdtw==0.3.4 ; python_version >= "3.8" and python_version < "3.11" -fasteners==0.18 ; python_version >= "3.8" and python_version < "3.11" and platform_machine == "x86_64" or python_version >= "3.8" and python_version < "3.11" and platform_machine == "AMD64" -fastjsonschema==2.18.0 ; python_version >= "3.8" and python_version < "3.11" +fasteners==0.19 ; python_version >= "3.8" and python_version < "3.11" and (platform_machine == "x86_64" or platform_machine == "AMD64") +fastjsonschema==2.18.1 ; python_version >= "3.8" and python_version < "3.11" fastparquet==0.8.3 ; python_version >= "3.8" and python_version < "3.11" flatdict==4.0.1 ; python_version >= "3.8" and python_version < "3.11" -fonttools==4.42.0 ; python_version >= "3.8" and python_version < "3.11" +fonttools==4.43.1 ; python_version >= "3.8" and python_version < "3.11" fqdn==1.5.1 ; python_version >= "3.8" and python_version < "3.11" -fsspec==2023.6.0 ; python_version >= "3.8" and python_version < "3.11" -furo==2023.7.26 ; python_version >= "3.8" and python_version < "3.11" +fsspec==2023.10.0 ; python_version >= "3.8" and python_version < "3.11" +furo==2023.9.10 ; python_version >= "3.8" and python_version < "3.11" future==0.18.3 ; python_version >= "3.8" and python_version < "3.11" -gitdb==4.0.10 ; python_version >= "3.8" and python_version < "3.11" -gitpython==3.1.32 ; python_version >= "3.8" and python_version < "3.11" -h5grove==1.3.0 ; python_version >= "3.8" and python_version < "3.11" -h5py==3.9.0 ; python_version >= "3.8" and python_version < "3.11" -hyperspy==1.7.5 ; python_version >= "3.8" and python_version < "3.11" +gitdb==4.0.11 ; python_version >= "3.8" and python_version < "3.11" +gitpython==3.1.40 ; python_version >= "3.8" and python_version < "3.11" +h5py==3.10.0 ; python_version >= "3.8" and python_version < "3.11" +hyperspy==1.7.4 ; python_version >= "3.8" and python_version < "3.11" idna==3.4 ; python_version >= "3.8" and python_version < "3.11" ifes-apt-tc-data-modeling==0.0.9 ; python_version >= "3.8" and python_version < "3.11" -imageio==2.27.0 ; python_version >= "3.8" and python_version < "3.11" +imageio==2.31.6 ; python_version >= "3.8" and python_version < "3.11" imagesize==1.4.1 ; python_version >= "3.8" and python_version < "3.11" importlib-metadata==6.8.0 ; python_version >= "3.8" and python_version < "3.11" -importlib-resources==6.0.1 ; python_version >= "3.8" and python_version < "3.10" -ipykernel==6.25.1 ; python_version >= "3.8" and python_version < "3.11" -ipykernel[notebook]==6.25.1 ; python_version >= "3.8" and python_version < "3.11" +importlib-resources==6.1.0 ; python_version >= "3.8" and python_version < "3.10" +ipykernel==6.26.0 ; python_version >= "3.8" and python_version < "3.11" +ipykernel[notebook]==6.26.0 ; python_version >= "3.8" and python_version < "3.11" ipympl==0.9.3 ; python_version >= "3.8" and python_version < "3.11" ipyparallel==8.6.1 ; python_version >= "3.8" and python_version < "3.11" ipython-genutils==0.2.0 ; python_version >= "3.8" and python_version < "3.11" -ipython==8.12.2 ; python_version >= "3.8" and python_version < "3.11" -ipywidgets==7.8.0 ; python_version >= "3.8" and python_version < "3.11" +ipython==8.12.3 ; python_version >= "3.8" and python_version < "3.11" +ipywidgets==8.1.1 ; python_version >= "3.8" and python_version < "3.11" isoduration==20.11.0 ; python_version >= "3.8" and python_version < "3.11" -jedi==0.19.0 ; python_version >= "3.8" and python_version < "3.11" +jedi==0.19.1 ; python_version >= "3.8" and python_version < "3.11" jinja2==3.1.2 ; python_version >= "3.8" and python_version < "3.11" joblib==1.3.2 ; python_version >= "3.8" and python_version < "3.11" json5==0.9.14 ; python_version >= "3.8" and python_version < "3.11" jsonpointer==2.4 ; python_version >= "3.8" and python_version < "3.11" jsonschema-specifications==2023.7.1 ; python_version >= "3.8" and python_version < "3.11" -jsonschema==4.19.0 ; python_version >= "3.8" and python_version < "3.11" -jsonschema[format-nongpl]==4.19.0 ; python_version >= "3.8" and python_version < "3.11" -jupyter-client==8.3.0 ; python_version >= "3.8" and python_version < "3.11" +jsonschema==4.19.1 ; python_version >= "3.8" and python_version < "3.11" +jsonschema[format-nongpl]==4.19.1 ; python_version >= "3.8" and python_version < "3.11" +jupyter-client==8.5.0 ; python_version >= "3.8" and python_version < "3.11" jupyter-console==6.6.3 ; python_version >= "3.8" and python_version < "3.11" -jupyter-core==5.3.1 ; python_version >= "3.8" and python_version < "3.11" -jupyter-events==0.7.0 ; python_version >= "3.8" and python_version < "3.11" +jupyter-core==5.4.0 ; python_version >= "3.8" and python_version < "3.11" +jupyter-events==0.8.0 ; python_version >= "3.8" and python_version < "3.11" +jupyter-lsp==2.2.0 ; python_version >= "3.8" and python_version < "3.11" jupyter-server-terminals==0.4.4 ; python_version >= "3.8" and python_version < "3.11" -jupyter-server==2.7.0 ; python_version >= "3.8" and python_version < "3.11" +jupyter-server==2.9.1 ; python_version >= "3.8" and python_version < "3.11" jupyter[notebook]==1.0.0 ; python_version >= "3.8" and python_version < "3.11" -jupyterlab-h5web==10.0.0 ; python_version >= "3.8" and python_version < "3.11" jupyterlab-pygments==0.2.2 ; python_version >= "3.8" and python_version < "3.11" -jupyterlab-server==2.24.0 ; python_version >= "3.8" and python_version < "3.11" -jupyterlab-widgets==1.1.5 ; python_version >= "3.8" and python_version < "3.11" -jupyterlab==3.5.3 ; python_version >= "3.8" and python_version < "3.11" +jupyterlab-server==2.25.0 ; python_version >= "3.8" and python_version < "3.11" +jupyterlab-widgets==3.0.9 ; python_version >= "3.8" and python_version < "3.11" +jupyterlab==4.0.7 ; python_version >= "3.8" and python_version < "3.11" kikuchipy==0.8.7 ; python_version >= "3.8" and python_version < "3.11" -kiwisolver==1.4.4 ; python_version >= "3.8" and python_version < "3.11" -lark==1.1.7 ; python_version >= "3.8" and python_version < "3.11" +kiwisolver==1.4.5 ; python_version >= "3.8" and python_version < "3.11" +lark==1.1.8 ; python_version >= "3.8" and python_version < "3.11" lazy-loader==0.3 ; python_version >= "3.8" and python_version < "3.11" llvmlite==0.38.1 ; python_version >= "3.8" and python_version < "3.11" lmfit==1.2.2 ; python_version >= "3.8" and python_version < "3.11" @@ -99,83 +100,89 @@ locket==1.0.0 ; python_version >= "3.8" and python_version < "3.11" markupsafe==2.1.3 ; python_version >= "3.8" and python_version < "3.11" matplotlib-inline==0.1.6 ; python_version >= "3.8" and python_version < "3.11" matplotlib-scalebar==0.8.1 ; python_version >= "3.8" and python_version < "3.11" -matplotlib==3.7.2 ; python_version >= "3.8" and python_version < "3.11" -mistune==3.0.1 ; python_version >= "3.8" and python_version < "3.11" +matplotlib==3.7.3 ; python_version >= "3.8" and python_version < "3.11" +mistune==3.0.2 ; python_version >= "3.8" and python_version < "3.11" mpmath==1.3.0 ; python_version >= "3.8" and python_version < "3.11" natsort==8.4.0 ; python_version >= "3.8" and python_version < "3.11" -nbclassic==1.0.0 ; python_version >= "3.8" and python_version < "3.11" nbclient==0.8.0 ; python_version >= "3.8" and python_version < "3.11" -nbconvert==7.7.3 ; python_version >= "3.8" and python_version < "3.11" +nbconvert==7.9.2 ; python_version >= "3.8" and python_version < "3.11" nbformat==5.9.2 ; python_version >= "3.8" and python_version < "3.11" -nest-asyncio==1.5.7 ; python_version >= "3.8" and python_version < "3.11" +nest-asyncio==1.5.8 ; python_version >= "3.8" and python_version < "3.11" networkx==3.1 ; python_version >= "3.8" and python_version < "3.11" +niondata==0.15.3 ; python_version >= "3.8" and python_version < "3.11" +nionswift-io==0.15.1 ; python_version >= "3.8" and python_version < "3.11" +nionswift==0.16.8 ; python_version >= "3.8" and python_version < "3.11" +nionui==0.6.10 ; python_version >= "3.8" and python_version < "3.11" +nionutils==0.4.6 ; python_version >= "3.8" and python_version < "3.11" notebook-shim==0.2.3 ; python_version >= "3.8" and python_version < "3.11" -notebook==6.5.4 ; python_version >= "3.8" and python_version < "3.11" +notebook==7.0.6 ; python_version >= "3.8" and python_version < "3.11" numba==0.55.2 ; python_version >= "3.8" and python_version < "3.11" -numcodecs==0.11.0 ; python_version >= "3.8" and python_version < "3.11" and platform_machine == "x86_64" or python_version >= "3.8" and python_version < "3.11" and platform_machine == "AMD64" -numexpr==2.8.5 ; python_version >= "3.8" and python_version < "3.11" +numcodecs==0.12.1 ; python_version >= "3.8" and python_version < "3.11" and (platform_machine == "x86_64" or platform_machine == "AMD64") +numexpr==2.8.6 ; python_version >= "3.8" and python_version < "3.11" numpy-quaternion==2022.4.3 ; python_version >= "3.8" and python_version < "3.11" -numpy==1.21.6 ; python_version < "3.11" and python_version >= "3.8" +numpy==1.22.4 ; python_version >= "3.8" and python_version < "3.11" opencv-python==4.8.0.74 ; python_version >= "3.8" and python_version < "3.11" orix==0.11.1 ; python_version >= "3.8" and python_version < "3.11" -orjson==3.9.4 ; python_version >= "3.8" and python_version < "3.11" overrides==7.4.0 ; python_version >= "3.8" and python_version < "3.11" -packaging==23.1 ; python_version >= "3.8" and python_version < "3.11" +packaging==23.2 ; python_version >= "3.8" and python_version < "3.11" pandas==1.5.3 ; python_version >= "3.8" and python_version < "3.11" pandocfilters==1.5.0 ; python_version >= "3.8" and python_version < "3.11" parso==0.8.3 ; python_version >= "3.8" and python_version < "3.11" -partd==1.4.0 ; python_version >= "3.8" and python_version < "3.11" +partd==1.4.1 ; python_version >= "3.8" and python_version < "3.11" pexpect==4.8.0 ; python_version >= "3.8" and python_version < "3.11" and sys_platform != "win32" photutils==1.8.0 ; python_version >= "3.8" and python_version < "3.11" pickleshare==0.7.5 ; python_version >= "3.8" and python_version < "3.11" -pillow==10.0.0 ; python_version >= "3.8" and python_version < "3.11" +pillow==10.0.1 ; python_version >= "3.8" and python_version < "3.11" pint==0.21.1 ; python_version >= "3.8" and python_version < "3.11" pkgutil-resolve-name==1.3.10 ; python_version >= "3.8" and python_version < "3.9" -platformdirs==3.10.0 ; python_version >= "3.8" and python_version < "3.11" -pooch==1.7.0 ; python_version >= "3.8" and python_version < "3.11" -prettytable==3.8.0 ; python_version >= "3.8" and python_version < "3.11" +platformdirs==3.11.0 ; python_version >= "3.8" and python_version < "3.11" +pooch==1.8.0 ; python_version >= "3.8" and python_version < "3.11" +prettytable==3.9.0 ; python_version >= "3.8" and python_version < "3.11" prometheus-client==0.17.1 ; python_version >= "3.8" and python_version < "3.11" prompt-toolkit==3.0.39 ; python_version >= "3.8" and python_version < "3.11" -psutil==5.9.5 ; python_version >= "3.8" and python_version < "3.11" -ptyprocess==0.7.0 ; python_version >= "3.8" and python_version < "3.11" and sys_platform != "win32" or python_version >= "3.8" and python_version < "3.11" and os_name != "nt" +psutil==5.9.6 ; python_version >= "3.8" and python_version < "3.11" +ptyprocess==0.7.0 ; python_version >= "3.8" and python_version < "3.11" and (sys_platform != "win32" or os_name != "nt") pure-eval==0.2.2 ; python_version >= "3.8" and python_version < "3.11" +pyarrow==13.0.0 ; python_version >= "3.8" and python_version < "3.11" pycifrw==4.4.5 ; python_version >= "3.8" and python_version < "3.11" pycparser==2.21 ; python_version >= "3.8" and python_version < "3.11" pyerfa==2.0.0.3 ; python_version >= "3.8" and python_version < "3.11" -pyfai==2023.5.0 ; python_version >= "3.8" and python_version < "3.11" +pyfai==2023.9.0 ; python_version >= "3.8" and python_version < "3.11" pygments==2.16.1 ; python_version >= "3.8" and python_version < "3.11" -pynxtools==0.0.2 ; python_version >= "3.8" and python_version < "3.11" -pyparsing==3.0.9 ; python_version >= "3.8" and python_version < "3.11" +pynxtools==0.0.5 ; python_version >= "3.8" and python_version < "3.11" +pyparsing==3.1.1 ; python_version >= "3.8" and python_version < "3.11" python-dateutil==2.8.2 ; python_version >= "3.8" and python_version < "3.11" python-json-logger==2.0.7 ; python_version >= "3.8" and python_version < "3.11" -pytz==2023.3 ; python_version >= "3.8" and python_version < "3.11" +pytz-deprecation-shim==0.1.0.post0 ; python_version >= "3.8" and python_version < "3.11" +pytz==2023.3.post1 ; python_version >= "3.8" and python_version < "3.11" pywavelets==1.4.1 ; python_version >= "3.8" and python_version < "3.11" pywin32==306 ; sys_platform == "win32" and platform_python_implementation != "PyPy" and python_version >= "3.8" and python_version < "3.11" -pywinpty==2.0.11 ; python_version >= "3.8" and python_version < "3.11" and os_name == "nt" +pywinpty==2.0.12 ; python_version >= "3.8" and python_version < "3.11" and os_name == "nt" pyxem==0.15.1 ; python_version >= "3.8" and python_version < "3.11" pyyaml==6.0.1 ; python_version >= "3.8" and python_version < "3.11" pyzmq==25.1.1 ; python_version >= "3.8" and python_version < "3.11" -qtconsole==5.4.3 ; python_version >= "3.8" and python_version < "3.11" -qtpy==2.3.1 ; python_version >= "3.8" and python_version < "3.11" -radioactivedecay==0.4.20 ; python_version >= "3.8" and python_version < "3.11" +qtconsole==5.4.4 ; python_version >= "3.8" and python_version < "3.11" +qtpy==2.4.1 ; python_version >= "3.8" and python_version < "3.11" +radioactivedecay==0.4.21 ; python_version >= "3.8" and python_version < "3.11" recommonmark==0.7.1 ; python_version >= "3.8" and python_version < "3.11" referencing==0.30.2 ; python_version >= "3.8" and python_version < "3.11" requests-cache==1.1.0 ; python_version >= "3.8" and python_version < "3.11" requests==2.31.0 ; python_version >= "3.8" and python_version < "3.11" rfc3339-validator==0.1.4 ; python_version >= "3.8" and python_version < "3.11" rfc3986-validator==0.1.1 ; python_version >= "3.8" and python_version < "3.11" -rpds-py==0.9.2 ; python_version >= "3.8" and python_version < "3.11" +rpds-py==0.10.6 ; python_version >= "3.8" and python_version < "3.11" scikit-image==0.21.0 ; python_version >= "3.8" and python_version < "3.11" -scikit-learn==1.3.0 ; python_version >= "3.8" and python_version < "3.11" +scikit-learn==1.3.2 ; python_version >= "3.8" and python_version < "3.11" scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.11" send2trash==1.8.2 ; python_version >= "3.8" and python_version < "3.11" -setuptools==68.0.0 ; python_version >= "3.8" and python_version < "3.11" +setuptools-scm==8.0.4 ; python_version >= "3.8" and python_version < "3.11" +setuptools==68.2.2 ; python_version >= "3.8" and python_version < "3.11" silx==1.1.2 ; python_version >= "3.8" and python_version < "3.11" six==1.16.0 ; python_version >= "3.8" and python_version < "3.11" -smmap==5.0.0 ; python_version >= "3.8" and python_version < "3.11" +smmap==5.0.1 ; python_version >= "3.8" and python_version < "3.11" sniffio==1.3.0 ; python_version >= "3.8" and python_version < "3.11" snowballstemmer==2.2.0 ; python_version >= "3.8" and python_version < "3.11" -soupsieve==2.4.1 ; python_version >= "3.8" and python_version < "3.11" +soupsieve==2.5 ; python_version >= "3.8" and python_version < "3.11" sparse==0.14.0 ; python_version >= "3.8" and python_version < "3.11" sphinx-autodoc-typehints[docs]==1.24.0 ; python_version >= "3.8" and python_version < "3.11" sphinx-basic-ng==1.0.0b2 ; python_version >= "3.8" and python_version < "3.11" @@ -191,7 +198,7 @@ sphinxcontrib-jsmath==1.0.1 ; python_version >= "3.8" and python_version < "3.11 sphinxcontrib-qthelp==1.0.3 ; python_version >= "3.8" and python_version < "3.11" sphinxcontrib-serializinghtml==1.1.5 ; python_version >= "3.8" and python_version < "3.11" sphinxcontrib-websupport==1.2.4 ; python_version >= "3.8" and python_version < "3.11" -stack-data==0.6.2 ; python_version >= "3.8" and python_version < "3.11" +stack-data==0.6.3 ; python_version >= "3.8" and python_version < "3.11" symmetrize==0.5.5 ; python_version >= "3.8" and python_version < "3.11" sympy==1.12 ; python_version >= "3.8" and python_version < "3.11" terminado==0.17.1 ; python_version >= "3.8" and python_version < "3.11" @@ -201,22 +208,25 @@ tinycss2==1.2.1 ; python_version >= "3.8" and python_version < "3.11" tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11" tomlkit[docs]==0.12.1 ; python_version >= "3.8" and python_version < "3.11" toolz==0.12.0 ; python_version >= "3.8" and python_version < "3.11" -tornado==6.3.2 ; python_version >= "3.8" and python_version < "3.11" +tornado==6.3.3 ; python_version >= "3.8" and python_version < "3.11" tqdm==4.66.1 ; python_version >= "3.8" and python_version < "3.11" -traitlets==5.9.0 ; python_version >= "3.8" and python_version < "3.11" -traits==6.4.2 ; python_version >= "3.8" and python_version < "3.11" +traitlets==5.12.0 ; python_version >= "3.8" and python_version < "3.11" +traits==6.4.3 ; python_version >= "3.8" and python_version < "3.11" transforms3d==0.4.1 ; python_version >= "3.8" and python_version < "3.11" -typing-extensions==4.7.1 ; python_version >= "3.8" and python_version < "3.11" +types-python-dateutil==2.8.19.14 ; python_version >= "3.8" and python_version < "3.11" +typing-extensions==4.8.0 ; python_version >= "3.8" and python_version < "3.11" +tzdata==2023.3 ; python_version >= "3.8" and python_version < "3.11" +tzlocal==4.3 ; python_version >= "3.8" and python_version < "3.11" uncertainties==3.1.7 ; python_version >= "3.8" and python_version < "3.11" uri-template==1.3.0 ; python_version >= "3.8" and python_version < "3.11" url-normalize==1.4.3 ; python_version >= "3.8" and python_version < "3.11" -urllib3==2.0.4 ; python_version >= "3.8" and python_version < "3.11" -wcwidth==0.2.6 ; python_version >= "3.8" and python_version < "3.11" +urllib3==2.0.7 ; python_version >= "3.8" and python_version < "3.11" +wcwidth==0.2.8 ; python_version >= "3.8" and python_version < "3.11" webcolors==1.13 ; python_version >= "3.8" and python_version < "3.11" webencodings==0.5.1 ; python_version >= "3.8" and python_version < "3.11" -websocket-client==1.6.1 ; python_version >= "3.8" and python_version < "3.11" -widgetsnbextension==3.6.5 ; python_version >= "3.8" and python_version < "3.11" +websocket-client==1.6.4 ; python_version >= "3.8" and python_version < "3.11" +widgetsnbextension==4.0.9 ; python_version >= "3.8" and python_version < "3.11" xarray==0.20.2 ; python_version >= "3.8" and python_version < "3.11" -zarr==2.16.0 ; python_version >= "3.8" and python_version < "3.11" and platform_machine == "x86_64" or python_version >= "3.8" and python_version < "3.11" and platform_machine == "AMD64" +zarr==2.16.1 ; python_version >= "3.8" and python_version < "3.11" and (platform_machine == "x86_64" or platform_machine == "AMD64") zipfile37==0.1.3 ; python_version >= "3.8" and python_version < "3.11" -zipp==3.16.2 ; python_version >= "3.8" and python_version < "3.11" +zipp==3.17.0 ; python_version >= "3.8" and python_version < "3.11" diff --git a/poetry.lock b/poetry.lock index be700b9e..b5466c9d 100644 --- a/poetry.lock +++ b/poetry.lock @@ -221,20 +221,21 @@ test-all = ["coverage[toml]", "ipython (>=4.2)", "objgraph", "pytest (>=7.0)", " [[package]] name = "asttokens" -version = "2.4.0" +version = "2.4.1" description = "Annotate AST trees with source code positions" optional = false python-versions = "*" files = [ - {file = "asttokens-2.4.0-py2.py3-none-any.whl", hash = "sha256:cf8fc9e61a86461aa9fb161a14a0841a03c405fa829ac6b202670b3495d2ce69"}, - {file = "asttokens-2.4.0.tar.gz", hash = "sha256:2e0171b991b2c959acc6c49318049236844a5da1d65ba2672c4880c1c894834e"}, + {file = "asttokens-2.4.1-py2.py3-none-any.whl", hash = "sha256:051ed49c3dcae8913ea7cd08e46a606dba30b79993209636c4875bc1d637bc24"}, + {file = "asttokens-2.4.1.tar.gz", hash = "sha256:b03869718ba9a6eb027e134bfdf69f38a236d681c83c160d510768af11254ba0"}, ] [package.dependencies] six = ">=1.12.0" [package.extras] -test = ["astroid", "pytest"] +astroid = ["astroid (>=1,<2)", "astroid (>=2,<4)"] +test = ["astroid (>=1,<2)", "astroid (>=2,<4)", "pytest"] [[package]] name = "async-lru" From 4b1769f70532ef712f9c6672bd71b001b97c1a47 Mon Sep 17 00:00:00 2001 From: rettigl Date: Thu, 26 Oct 2023 14:39:02 +0200 Subject: [PATCH 23/25] restrict push action to pyproject.toml --- .github/workflows/update_dependencies.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/update_dependencies.yml b/.github/workflows/update_dependencies.yml index 4dd3e0af..c7f08d4b 100644 --- a/.github/workflows/update_dependencies.yml +++ b/.github/workflows/update_dependencies.yml @@ -5,6 +5,8 @@ on: - cron: '0 1 * * 1' workflow_dispatch: push: + paths: + - pyproject.toml jobs: update_dependencies: From 9e35e99e5af0de22d42d325c7c88f8573d3395c3 Mon Sep 17 00:00:00 2001 From: Zain Sohail Date: Thu, 26 Oct 2023 18:19:29 +0200 Subject: [PATCH 24/25] Improve workflows to use github caches (#182) * add dev dependencies for linting * update all workflows to use caches * remove race condition for flash loader tests and remove additional generated buffer files * remove race condition in test_io, and remove generated test files * remove race condition for sed_config.yaml detetion from test_processor.py * produce a coverge file in xml format and use with coveralls * added PR trigger * changed testing file name to include coverage * removed update_requirements.yml * updated poetry.lock --------- Co-authored-by: rettigl --- .github/workflows/linting.yml | 33 ++++ .github/workflows/pylint.yml | 47 ----- .github/workflows/pytest_coveralls.yml | 34 ---- .github/workflows/pytest_muliversion.yml | 40 ----- .github/workflows/testing_coverage.yml | 33 ++++ .github/workflows/testing_multiversion.yml | 30 ++++ poetry.lock | 196 +++++++++++++++++---- pyproject.toml | 7 +- tests/loader/test_loaders.py | 50 ++++++ tests/test_io.py | 19 +- tests/test_processor.py | 21 ++- 11 files changed, 341 insertions(+), 169 deletions(-) create mode 100644 .github/workflows/linting.yml delete mode 100644 .github/workflows/pylint.yml delete mode 100644 .github/workflows/pytest_coveralls.yml delete mode 100644 .github/workflows/pytest_muliversion.yml create mode 100644 .github/workflows/testing_coverage.yml create mode 100644 .github/workflows/testing_multiversion.yml diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml new file mode 100644 index 00000000..c1ee31e3 --- /dev/null +++ b/.github/workflows/linting.yml @@ -0,0 +1,33 @@ +name: linting + +# Triggers the workflow on push for all branches +on: [push] + +jobs: + lint: + runs-on: ubuntu-latest + steps: + # Check out repo and set up Python + - uses: actions/checkout@v3 + with: + lfs: true + + # Use cached python and dependencies, install poetry + - name: "Setup Python, Poetry and Dependencies" + uses: packetcoders/action-setup-cache-python-poetry@main + with: + python-version: 3.8 + poetry-version: 1.2.2 + + # Linting steps, excute all linters even if one fails + - name: pycodestyle + run: + poetry run pycodestyle --ignore=E203,E501,W503 sed tests + - name: pylint + if: ${{ always() }} + run: + poetry run pylint --good-names=i,j,k,ex,x,y,t,k,v,ax,df,ec,mc,dc,ct --disable=fixme,too-many-branches,too-many-locals,too-many-statements,too-many-arguments,too-many-lines,too-many-public-methods,too-many-instance-attributes,too-few-public-methods sed tests + - name: mypy + if: ${{ always() }} + run: + poetry run mypy --ignore-missing-imports --follow-imports=silent --no-strict-optional sed tests \ No newline at end of file diff --git a/.github/workflows/pylint.yml b/.github/workflows/pylint.yml deleted file mode 100644 index c02f7fa2..00000000 --- a/.github/workflows/pylint.yml +++ /dev/null @@ -1,47 +0,0 @@ -# This workflow will install Python dependencies, lint and run tests with a single version of Python -# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions - -name: linting - -on: [push] - -jobs: - build: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v3 - with: - lfs: true - - name: Set up Python 3.8 - uses: actions/setup-python@v4 - with: - python-version: 3.8 - - name: Install dependencies - run: | - git lfs pull - python -m pip install --upgrade pip - pip install pycodestyle pylint mypy pytest types-PyYAML types-requests coverage coveralls - if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - - name: Install package - run: | - python -m pip install . - - name: pycodestyle - run: | - python -m pycodestyle --ignore=E203,E501,W503 sed tests - - name: pylint - if: ${{ always() }} - run: | - python -m pylint --good-names=i,j,k,ex,x,y,t,k,v,ax,df,ec,mc,dc,ct --disable=fixme,too-many-branches,too-many-locals,too-many-statements,too-many-arguments,too-many-lines,too-many-public-methods,too-many-instance-attributes,too-few-public-methods sed tests - - name: mypy - if: ${{ always() }} - run: | - python -m mypy --ignore-missing-imports --follow-imports=silent --no-strict-optional sed tests - - name: Test with pytest - if: ${{ always() }} - run: | - coverage run -m pytest -sv --show-capture=no tests - - name: Submit to coveralls - env: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - run: | - coveralls --service=github diff --git a/.github/workflows/pytest_coveralls.yml b/.github/workflows/pytest_coveralls.yml deleted file mode 100644 index 4909c2a3..00000000 --- a/.github/workflows/pytest_coveralls.yml +++ /dev/null @@ -1,34 +0,0 @@ -# This workflow will install Python dependencies, run tests for a single versions of Python and commit test results to coveralls -# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions - -name: pytest - -on: pull_request - -jobs: - pytest: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v3 - with: - lfs: true - - name: Set up Python 3.8 - uses: actions/setup-python@v4 - with: - python-version: 3.8 - - name: Install dependencies - run: | - git lfs pull - python -m pip install --upgrade pip - python -m pip install pytest coverage coveralls - - name: Install package - run: | - python -m pip install . - - name: Test with pytest - run: | - coverage run -m pytest -sv --show-capture=no tests - - name: Submit to coveralls - env: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - run: | - coveralls --service=github diff --git a/.github/workflows/pytest_muliversion.yml b/.github/workflows/pytest_muliversion.yml deleted file mode 100644 index 955304ea..00000000 --- a/.github/workflows/pytest_muliversion.yml +++ /dev/null @@ -1,40 +0,0 @@ -# This workflow will install Python dependencies, and run tests for multiple versions of Python -# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions - -name: pytest - -on: - push: - branches: [main] - -jobs: - pytest: - runs-on: ubuntu-latest - strategy: - matrix: - python_version: ["3.8", "3.9", "3.10"] - - steps: - - uses: actions/checkout@v3 - with: - lfs: true - - name: Set up Python ${{ matrix.python_version }} - uses: actions/setup-python@v4 - with: - python-version: ${{ matrix.python_version }} - - name: Install dependencies - run: | - git lfs pull - python -m pip install --upgrade pip - python -m pip install pytest coverage coveralls - - name: Install package - run: | - python -m pip install . - - name: Test with pytest - run: | - coverage run -m pytest -sv --show-capture=no tests - - name: Submit to coveralls - env: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - run: | - coveralls --service=github diff --git a/.github/workflows/testing_coverage.yml b/.github/workflows/testing_coverage.yml new file mode 100644 index 00000000..57ac606a --- /dev/null +++ b/.github/workflows/testing_coverage.yml @@ -0,0 +1,33 @@ +name: pytest and coverage report + +# Triggers the workflow on push and PR for all branches +on: [push, pull_request] + +jobs: + pytest: + runs-on: ubuntu-latest + steps: + # Check out repo and set up Python + - name: Check out the repository + uses: actions/checkout@v4 + with: + lfs: true + + # Use cached python and dependencies, install poetry + - name: "Setup Python, Poetry and Dependencies" + uses: packetcoders/action-setup-cache-python-poetry@main + with: + python-version: 3.8 + poetry-version: 1.2.2 + + # Run pytest with coverage report, saving to xml + - name: Run tests on python 3.8 + run: | + poetry run pytest --cov --cov-report xml:cobertura.xml --full-trace --show-capture=no -sv -n auto tests/ + + # Take report and upload to coveralls + - name: Coveralls + uses: coverallsapp/github-action@v2 + with: + github-token: ${{ secrets.GITHUB_TOKEN }} + file: ./cobertura.xml \ No newline at end of file diff --git a/.github/workflows/testing_multiversion.yml b/.github/workflows/testing_multiversion.yml new file mode 100644 index 00000000..1cc090de --- /dev/null +++ b/.github/workflows/testing_multiversion.yml @@ -0,0 +1,30 @@ +name: pytest multiversion + +on: + push: + branches: [ main ] + +jobs: + pytest: + # Using matrix strategy + strategy: + matrix: + python-version: ["3.8", "3.9", "3.10"] + runs-on: ubuntu-latest + 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a/tests/loader/test_loaders.py b/tests/loader/test_loaders.py index 1d744088..3947adfc 100644 --- a/tests/loader/test_loaders.py +++ b/tests/loader/test_loaders.py @@ -1,6 +1,7 @@ """Test cases for loaders used to load dataframes """ import os +from copy import deepcopy from importlib.util import find_spec from pathlib import Path from typing import cast @@ -86,6 +87,15 @@ def test_if_loaders_are_children_of_base_loader(loader: BaseLoader): def test_has_correct_read_dataframe_func(loader: BaseLoader, read_type: str): """Test if all loaders have a valid read function implemented""" assert callable(loader.read_dataframe) + + # Fix for race condition during parallel testing + if loader.__name__ == "flash": + config = deepcopy(loader._config) # pylint: disable=protected-access + config["core"]["paths"]["data_parquet_dir"] = ( + config["core"]["paths"]["data_parquet_dir"] + f"_{read_type}" + ) + loader = get_loader(loader_name="flash", config=config) + if loader.__name__ != "BaseLoader": assert hasattr(loader, "files") assert hasattr(loader, "supported_file_types") @@ -165,6 +175,15 @@ def test_get_count_rate(loader: BaseLoader): Args: loader (BaseLoader): the loader object to test """ + + # Fix for race condition during parallel testing + if loader.__name__ == "flash": + config = deepcopy(loader._config) # pylint: disable=protected-access + config["core"]["paths"]["data_parquet_dir"] = ( + config["core"]["paths"]["data_parquet_dir"] + "_count_rate" + ) + loader = get_loader(loader_name="flash", config=config) + if loader.__name__ != "BaseLoader": loader_name = get_loader_name_from_loader_object(loader) input_folder = os.path.join(test_data_dir, "loader", loader_name) @@ -176,12 +195,23 @@ def test_get_count_rate(loader: BaseLoader): ) loaded_time, loaded_countrate = loader.get_count_rate() if loaded_time is None and loaded_countrate is None: + if loader.__name__ == "flash": + loader = cast(FlashLoader, loader) + _, parquet_data_dir = loader.initialize_paths() + for file in os.listdir(Path(parquet_data_dir, "buffer")): + os.remove(Path(parquet_data_dir, "buffer", file)) pytest.skip("Not implemented") assert len(loaded_time) == len(loaded_countrate) loaded_time2, loaded_countrate2 = loader.get_count_rate(fids=[0]) assert len(loaded_time2) == len(loaded_countrate2) assert len(loaded_time2) < len(loaded_time) + if loader.__name__ == "flash": + loader = cast(FlashLoader, loader) + _, parquet_data_dir = loader.initialize_paths() + for file in os.listdir(Path(parquet_data_dir, "buffer")): + os.remove(Path(parquet_data_dir, "buffer", file)) + @pytest.mark.parametrize("loader", get_all_loaders()) def test_get_elapsed_time(loader: BaseLoader): @@ -190,6 +220,15 @@ def test_get_elapsed_time(loader: BaseLoader): Args: loader (BaseLoader): the loader object to test """ + + # Fix for race condition during parallel testing + if loader.__name__ == "flash": + config = deepcopy(loader._config) # pylint: disable=protected-access + config["core"]["paths"]["data_parquet_dir"] = ( + config["core"]["paths"]["data_parquet_dir"] + "_elapsed_time" + ) + loader = get_loader(loader_name="flash", config=config) + if loader.__name__ != "BaseLoader": loader_name = get_loader_name_from_loader_object(loader) input_folder = os.path.join(test_data_dir, "loader", loader_name) @@ -201,12 +240,23 @@ def test_get_elapsed_time(loader: BaseLoader): ) elapsed_time = loader.get_elapsed_time() if elapsed_time is None: + if loader.__name__ == "flash": + loader = cast(FlashLoader, loader) + _, parquet_data_dir = loader.initialize_paths() + for file in os.listdir(Path(parquet_data_dir, "buffer")): + os.remove(Path(parquet_data_dir, "buffer", file)) pytest.skip("Not implemented") assert elapsed_time > 0 elapsed_time2 = loader.get_elapsed_time(fids=[0]) assert elapsed_time2 > 0 assert elapsed_time > elapsed_time2 + if loader.__name__ == "flash": + loader = cast(FlashLoader, loader) + _, parquet_data_dir = loader.initialize_paths() + for file in os.listdir(Path(parquet_data_dir, "buffer")): + os.remove(Path(parquet_data_dir, "buffer", file)) + def test_mpes_timestamps(): """Function to test if the timestamps are loaded correctly""" diff --git a/tests/test_io.py b/tests/test_io.py index 6b01beb3..1bde7c88 100644 --- a/tests/test_io.py +++ b/tests/test_io.py @@ -1,5 +1,6 @@ """This file contains code that performs several tests for the input/output functions """ +import os import random from pathlib import Path @@ -35,9 +36,10 @@ def test_save_and_load_tiff_array(_da: xr.DataArray): """ nd_array = _da.data if nd_array.ndim > 1: - to_tiff(nd_array, "test") - as_array = load_tiff("test.tiff") + to_tiff(nd_array, f"test1{nd_array.ndim}") + as_array = load_tiff(f"test1{nd_array.ndim}.tiff") np.testing.assert_allclose(nd_array, as_array) + os.remove(f"test1{nd_array.ndim}.tiff") @pytest.mark.parametrize( @@ -51,8 +53,9 @@ def test_save_xarr_to_tiff(_da: xr.DataArray): Args: _da (xr.DataArray): binned DataArray """ - to_tiff(_da, "test") - assert Path("test.tiff").is_file() + to_tiff(_da, f"test2{len(_da.shape)}") + assert Path(f"test2{len(_da.shape)}.tiff").is_file() + os.remove(f"test2{len(_da.shape)}.tiff") @pytest.mark.parametrize( @@ -66,14 +69,15 @@ def test_save_and_load_tiff_xarray(_da: xr.DataArray): rgs: _da (xr.DataArray): binned DataArray """ - to_tiff(_da, "test") - loaded = load_tiff("test.tiff") + to_tiff(_da, f"test3{len(_da.shape)}") + loaded = load_tiff(f"test3{len(_da.shape)}.tiff") dims_order = _sort_dims_for_imagej(_da.dims) transposed = _da.transpose(*dims_order).astype(np.float32) np.testing.assert_allclose( transposed.values, loaded.values, ) + os.remove(f"test3{len(_da.shape)}.tiff") @pytest.mark.parametrize( @@ -87,10 +91,11 @@ def test_save_and_load_hdf5(_da: xr.DataArray): Args: _da (xr.DataArray): binned DataArray """ - faddr = "test.h5" + faddr = f"test{len(_da.shape)}.h5" to_h5(_da, faddr, mode="w") loaded = load_h5(faddr) xr.testing.assert_equal(_da, loaded) np.testing.assert_equal(_da.attrs, loaded.attrs) for axis in _da.coords: np.testing.assert_equal(_da[axis].attrs, loaded[axis].attrs) + os.remove(faddr) diff --git a/tests/test_processor.py b/tests/test_processor.py index 8e7447ec..4d0fca66 100644 --- a/tests/test_processor.py +++ b/tests/test_processor.py @@ -274,7 +274,10 @@ def test_momentum_correction_workflow(features: np.ndarray): ) assert len(processor.mc.pouter_ord) == rotsym processor.generate_splinewarp(use_center=include_center) - processor.save_splinewarp(filename=f"sed_config{len(features)}.yaml", overwrite=True) + processor.save_splinewarp( + filename=f"sed_config_momentum_correction{len(features)}.yaml", + overwrite=True, + ) pouter_ord = processor.mc.pouter_ord cdeform_field = processor.mc.cdeform_field rdeform_field = processor.mc.rdeform_field @@ -282,7 +285,7 @@ def test_momentum_correction_workflow(features: np.ndarray): processor = SedProcessor( folder=df_folder, config=config, - folder_config=f"sed_config{len(features)}.yaml", + folder_config=f"sed_config_momentum_correction{len(features)}.yaml", user_config={}, system_config={}, ) @@ -291,7 +294,7 @@ def test_momentum_correction_workflow(features: np.ndarray): np.testing.assert_allclose(processor.mc.pouter_ord, pouter_ord) np.testing.assert_allclose(processor.mc.cdeform_field, cdeform_field) np.testing.assert_allclose(processor.mc.rdeform_field, rdeform_field) - os.remove(f"sed_config{len(features)}.yaml") + os.remove(f"sed_config_momentum_correction{len(features)}.yaml") def test_pose_adjustment(): @@ -379,10 +382,11 @@ def test_momentum_calibration_workflow(): apply=True, ) assert processor.mc.calibration["kx_scale"] != processor.mc.calibration["ky_scale"] - processor.save_momentum_calibration() + processor.save_momentum_calibration(filename="sed_config_momentum_calibration.yaml") processor = SedProcessor( folder=df_folder, config=config, + folder_config="sed_config_momentum_calibration.yaml", user_config={}, system_config={}, ) @@ -393,7 +397,7 @@ def test_momentum_calibration_workflow(): ) assert "kx" in processor.dataframe.columns assert "ky" in processor.dataframe.columns - os.remove("sed_config.yaml") + os.remove("sed_config_momentum_calibration.yaml") def test_energy_correction(): @@ -538,19 +542,22 @@ def test_energy_calibration_workflow(energy_scale: str, calibration_method: str) method=calibration_method, ) assert processor.ec.calibration["energy_scale"] == energy_scale - processor.save_energy_calibration() + processor.save_energy_calibration( + filename=f"sed_config_energy_calibration_{energy_scale}-{calibration_method}.yaml", + ) processor.append_energy_axis() assert "energy" in processor.dataframe.columns processor = SedProcessor( folder=df_folder + "../mpes/", config=config, + folder_config=f"sed_config_energy_calibration_{energy_scale}-{calibration_method}.yaml", user_config={}, system_config={}, ) processor.append_energy_axis(preview=True) assert "energy" in 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