diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index 6014d6c2..9914d10a 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -9,19 +9,19 @@ jobs: runs-on: windows-latest steps: - - uses: actions/checkout@v2 - - uses: actions/setup-python@v1 + - uses: actions/checkout@v3 + - uses: actions/setup-python@v4 with: - python-version: 3.7 - architecture: x64 + python-version: 3.9 - - name: Install with poetry + - name: Install dependencies run: | - pip install poetry - - - name: Build with poetry - run: poetry build - - - name: Publish with poetry - run: | - poetry publish -u ${{ secrets.pypi_user }} -p ${{ secrets.pypi_pw }} + python -m pip install --upgrade pip + pip install setuptools wheel twine + python setup.py sdist bdist_wheel + + - name: Publish package + uses: pypa/gh-action-pypi-publish@master + with: + user: __token__ + password: ${{ secrets.PYPI_TOKEN }} diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index dd611b7e..c8f16d97 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -1,10 +1,18 @@ name: build on: - push: - branches: [ master ] pull_request: - branches: [ master ] + branches: + - main + types: + - opened + - reopened + - synchronize + - ready_for_review + push: + branches: + - main + workflow_dispatch: jobs: build: @@ -16,30 +24,29 @@ jobs: python-version: [3.7, 3.8, 3.9] steps: - - uses: actions/checkout@v1 + - uses: actions/checkout@v3 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v1 + uses: actions/setup-python@v4 with: python-version: ${{ matrix.python-version }} architecture: x64 + - uses: actions/cache@v3 + with: + path: ${{ env.pythonLocation }} + key: ${{ env.pythonLocation }}-${{ hashFiles('setup.cfg') }} + + - name: Install + run: | + python -m pip install -e .[develop] + - name: Lint with flake8 run: | - pip install flake8 # stop the build if there are Python syntax errors or undefined names flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics --ignore E501 - - name: Install with poetry - run: | - pip install poetry - # poetry install --no-dev - poetry install - - name: Test with pytest run: | - poetry run pytest tests - - - name: Build with poetry - run: poetry build + pytest tests diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 7eeb63a9..41e348f0 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -2,7 +2,7 @@ # See https://pre-commit.com/hooks.html for more hooks repos: - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v3.4.0 + rev: v4.4.0 hooks: - id: trailing-whitespace args: [--markdown-linebreak-ext=md] @@ -17,26 +17,26 @@ repos: # - id: check-json # - id: check-added-large-files - repo: https://github.com/myint/docformatter - rev: v1.4 + rev: v1.5.0 hooks: - id: docformatter - repo: https://github.com/asottile/reorder_python_imports - rev: v2.5.0 + rev: v3.9.0 hooks: - id: reorder-python-imports args: [--py3-plus] - repo: https://github.com/pre-commit/mirrors-autopep8 - rev: v1.5.7 + rev: v2.0.1 hooks: - id: autopep8 args: ['--in-place', '--ignore=E501,W504'] - repo: https://github.com/asottile/pyupgrade - rev: v2.15.0 + rev: v3.3.1 hooks: - id: pyupgrade args: ['--py36-plus'] - - repo: https://github.com/PyCQA/flake8 - rev: '5.0.4' +- repo: https://github.com/PyCQA/flake8 + rev: '6.0.0' hooks: - id: flake8 args: ['--statistics', '--ignore=F401,F403,F405,F821,F841,E265,E501,A003'] @@ -51,8 +51,8 @@ repos: 'flake8-type-annotations', 'flake8-builtins', ] -- repo: https://github.com/kynan/nbstripout - rev: 0.4.0 - hooks: - - id: nbstripout - files: ".ipynb" +- repo: https://github.com/kynan/nbstripout + rev: 0.6.1 + hooks: + - id: nbstripout + files: ".ipynb" diff --git a/MANIFEST.in b/MANIFEST.in new file mode 100644 index 00000000..2c98f92d --- /dev/null +++ b/MANIFEST.in @@ -0,0 +1,29 @@ +include .pre-commit-config.yaml +include THANKS.md +include LICENCE +include notebooks/*.ipynb +include notebooks/nav.nav +include notebooks/readme.md +include docs/*.md +include docs/*.png +include docs/*.py +include requirements.txt +include scripts/*.py +include setup_win.bat +include tests/*.py +include tests/config/*.yaml +include tests/config/*/*.yaml +include instamatic/camera/*.dll +include instamatic/camera/*.h +include instamatic/camera/*.lockfile +include instamatic/camera/*.md +include instamatic/camera/tpx/*.bpc +include instamatic/camera/tpx/*.dacs +include instamatic/camera/tpx/*.txt +include instamatic/config/*.yaml +include instamatic/config/alignments/*.yaml +include instamatic/config/calibration/*.yaml +include instamatic/config/camera/*.yaml +include instamatic/config/microscope/*.yaml +include instamatic/config/scripts/*.md +include instamatic.neural_network/*.p \ No newline at end of file diff --git a/poetry.lock b/poetry.lock deleted file mode 100644 index 9cf95d9e..00000000 --- a/poetry.lock +++ /dev/null @@ -1,1411 +0,0 @@ -[[package]] -name = "appnope" -version = "0.1.2" -description = "Disable App Nap on macOS >= 10.9" -category = "main" -optional = false -python-versions = "*" - -[[package]] -name = "asteval" -version = "0.9.25" -description = "Safe, minimalistic evaluator of python expression using ast module" -category = "main" -optional = false -python-versions = ">=3.6" - -[[package]] -name = "atomicwrites" -version = "1.4.0" -description = "Atomic file writes." -category = "dev" -optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" - -[[package]] -name = "attrs" -version = "21.2.0" -description = "Classes Without Boilerplate" -category = "dev" -optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" - -[package.extras] -dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit"] -docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"] -tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface"] -tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins"] - -[[package]] -name = "backcall" -version = "0.2.0" -description = "Specifications for callback functions passed in to an API" -category = "main" -optional = false -python-versions = "*" - -[[package]] -name = "backports.entry-points-selectable" -version = "1.1.0" -description = "Compatibility shim providing selectable entry points for older implementations" -category = "dev" -optional = false -python-versions = ">=2.7" - -[package.dependencies] -importlib-metadata = {version = "*", markers = "python_version < \"3.8\""} - -[package.extras] -docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"] -testing = ["pytest (>=4.6)", "pytest-flake8", "pytest-cov", "pytest-black (>=0.3.7)", "pytest-mypy", "pytest-checkdocs (>=2.4)", "pytest-enabler (>=1.0.1)"] - -[[package]] -name = "build" -version = "0.6.1" -description = "A simple, correct PEP517 package builder" -category = "dev" -optional = false -python-versions = ">=3.6" - -[package.dependencies] -colorama = {version = "*", markers = "os_name == \"nt\""} -importlib-metadata = {version = ">=0.22", markers = "python_version < \"3.8\""} -packaging = ">=19.0" -pep517 = ">=0.9.1" -tomli = ">=1.0.0" - -[package.extras] -docs = ["furo (>=2020.11.19b18)", "sphinx (>=3.0,<4.0)", "sphinx-argparse-cli (>=1.5)", "sphinx-autodoc-typehints (>=1.10)"] -test = ["filelock (>=3)", "pytest (>=4)", "pytest-cov (>=2)", "pytest-mock (>=2)", "pytest-rerunfailures (>=9.1)", "pytest-xdist (>=1.34)", "setuptools (>=42.0.0)", "toml (>=0.10.0)", "wheel (>=0.36.0)"] -typing = ["mypy (==0.910)", "typing-extensions (>=3.7.4.3)"] -virtualenv = ["virtualenv (>=20.0.35)"] - -[[package]] -name = "cached-property" -version = "1.5.2" -description = "A decorator for caching properties in classes." -category = "main" -optional = false -python-versions = "*" - -[[package]] -name = "cfgv" -version = "3.3.0" -description = "Validate configuration and produce human readable error messages." -category = "dev" -optional = false -python-versions = ">=3.6.1" - -[[package]] -name = "check-manifest" -version = "0.46" -description = "Check MANIFEST.in in a Python source package for completeness" -category = "dev" -optional = false -python-versions = ">=3.6" - -[package.dependencies] -build = ">=0.1" -toml = "*" - -[package.extras] -test = ["mock (>=3.0.0)", "pytest"] - -[[package]] -name = "colorama" -version = "0.4.4" -description = "Cross-platform colored terminal text." -category = "main" -optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" - -[[package]] -name = "comtypes" -version = "1.1.10" -description = "Pure Python COM package" -category = "main" -optional = false -python-versions = "*" - -[[package]] -name = "coverage" -version = "4.4.2" -description = "Code coverage measurement for Python" -category = "dev" -optional = false -python-versions = "*" - -[[package]] -name = "cycler" -version = "0.10.0" -description = "Composable style cycles" -category = "main" -optional = false -python-versions = "*" - -[package.dependencies] -six = "*" - -[[package]] -name = "decorator" -version = "5.0.9" -description = "Decorators for Humans" -category = "main" -optional = false -python-versions = ">=3.5" - -[[package]] -name = "distlib" -version = "0.3.2" -description = "Distribution utilities" -category = "dev" -optional = false -python-versions = "*" - -[[package]] -name = "filelock" -version = "3.0.12" -description = "A platform independent file lock." -category = "dev" -optional = false -python-versions = "*" - -[[package]] -name = "future" -version = "0.18.2" -description = "Clean single-source support for Python 3 and 2" -category = "main" -optional = false -python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" - -[[package]] -name = "h5py" -version = "3.3.0" -description = "Read and write HDF5 files from Python" -category = "main" -optional = false -python-versions = ">=3.7" - -[package.dependencies] -cached-property = {version = "*", markers = "python_version < \"3.8\""} -numpy = [ - {version = ">=1.14.5", markers = "python_version == \"3.7\""}, - {version = ">=1.17.5", markers = "python_version == \"3.8\""}, - {version = ">=1.19.3", markers = "python_version >= \"3.9\""}, -] - -[[package]] -name = "identify" -version = "2.2.11" -description = "File identification library for Python" -category = "dev" -optional = false -python-versions = ">=3.6.1" - -[package.extras] -license = ["editdistance-s"] - -[[package]] -name = "imageio" -version = "2.9.0" -description = "Library for reading and writing a wide range of image, video, scientific, and volumetric data formats." -category = "main" -optional = false -python-versions = ">=3.5" - -[package.dependencies] -numpy = "*" -pillow = "*" - -[package.extras] -ffmpeg = ["imageio-ffmpeg"] -fits = ["astropy"] -full = ["astropy", "gdal", "imageio-ffmpeg", "itk"] -gdal = ["gdal"] -itk = ["itk"] - -[[package]] -name = "importlib-metadata" -version = "4.6.3" -description = "Read metadata from Python packages" -category = "dev" -optional = false -python-versions = ">=3.6" - -[package.dependencies] -typing-extensions = {version = ">=3.6.4", markers = "python_version < \"3.8\""} -zipp = ">=0.5" - -[package.extras] -docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"] -perf = ["ipython"] -testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"] - -[[package]] -name = "iniconfig" -version = "1.1.1" -description = "iniconfig: brain-dead simple config-ini parsing" -category = "dev" -optional = false -python-versions = "*" - -[[package]] -name = "ipython" -version = "7.26.0" -description = "IPython: Productive Interactive Computing" -category = "main" -optional = false -python-versions = ">=3.7" - -[package.dependencies] -appnope = {version = "*", markers = "sys_platform == \"darwin\""} -backcall = "*" -colorama = {version = "*", markers = "sys_platform == \"win32\""} -decorator = "*" -jedi = ">=0.16" -matplotlib-inline = "*" -pexpect = {version = ">4.3", markers = "sys_platform != \"win32\""} -pickleshare = "*" -prompt-toolkit = ">=2.0.0,<3.0.0 || >3.0.0,<3.0.1 || >3.0.1,<3.1.0" -pygments = "*" -traitlets = ">=4.2" - -[package.extras] -all = ["Sphinx (>=1.3)", "ipykernel", "ipyparallel", "ipywidgets", "nbconvert", "nbformat", "nose (>=0.10.1)", "notebook", "numpy (>=1.17)", "pygments", "qtconsole", "requests", "testpath"] -doc = ["Sphinx (>=1.3)"] -kernel = ["ipykernel"] -nbconvert = ["nbconvert"] -nbformat = ["nbformat"] -notebook = ["notebook", "ipywidgets"] -parallel = ["ipyparallel"] -qtconsole = ["qtconsole"] -test = ["nose (>=0.10.1)", "requests", "testpath", "pygments", "nbformat", "ipykernel", "numpy (>=1.17)"] - -[[package]] -name = "ipython-genutils" -version = "0.2.0" -description = "Vestigial utilities from IPython" -category = "main" -optional = false -python-versions = "*" - -[[package]] -name = "jedi" -version = "0.18.0" -description = "An autocompletion tool for Python that can be used for text editors." -category = "main" -optional = false -python-versions = ">=3.6" - -[package.dependencies] -parso = ">=0.8.0,<0.9.0" - -[package.extras] -qa = ["flake8 (==3.8.3)", "mypy (==0.782)"] -testing = ["Django (<3.1)", "colorama", "docopt", "pytest (<6.0.0)"] - -[[package]] -name = "kiwisolver" -version = "1.3.1" -description = "A fast implementation of the Cassowary constraint solver" -category = "main" -optional = false -python-versions = ">=3.6" - -[[package]] -name = "lmfit" -version = "1.0.2" -description = "Least-Squares Minimization with Bounds and Constraints" -category = "main" -optional = false -python-versions = ">=3.6" - -[package.dependencies] -asteval = ">=0.9.16" -numpy = ">=1.16" -scipy = ">=1.2" -uncertainties = ">=3.0.1" - -[[package]] -name = "matplotlib" -version = "3.4.2" -description = "Python plotting package" -category = "main" -optional = false -python-versions = ">=3.7" - -[package.dependencies] -cycler = ">=0.10" -kiwisolver = ">=1.0.1" -numpy = ">=1.16" -pillow = ">=6.2.0" -pyparsing = ">=2.2.1" -python-dateutil = ">=2.7" - -[[package]] -name = "matplotlib-inline" -version = "0.1.2" -description = "Inline Matplotlib backend for Jupyter" -category = "main" -optional = false -python-versions = ">=3.5" - -[package.dependencies] -traitlets = "*" - -[[package]] -name = "mrcfile" -version = "1.3.0" -description = "MRC file I/O library" -category = "main" -optional = false -python-versions = "*" - -[package.dependencies] -numpy = ">=1.12.0" - -[[package]] -name = "networkx" -version = "2.6.2" -description = "Python package for creating and manipulating graphs and networks" -category = "main" -optional = false -python-versions = ">=3.7" - -[package.extras] -default = ["numpy (>=1.19)", "scipy (>=1.5,!=1.6.1)", "matplotlib (>=3.3)", "pandas (>=1.1)"] -developer = ["black (==21.5b1)", "pre-commit (>=2.12)"] -doc = ["sphinx (>=4.0,<5.0)", "pydata-sphinx-theme (>=0.6,<1.0)", "sphinx-gallery (>=0.9,<1.0)", "numpydoc (>=1.1)", "pillow (>=8.2)", "nb2plots (>=0.6)", "texext (>=0.6.6)"] -extra = ["lxml (>=4.5)", "pygraphviz (>=1.7)", "pydot (>=1.4.1)"] -test = ["pytest (>=6.2)", "pytest-cov (>=2.12)", "codecov (>=2.1)"] - 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-[[package]] -name = "platformdirs" -version = "2.2.0" -description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." -category = "dev" -optional = false -python-versions = ">=3.6" - -[package.extras] -docs = ["Sphinx (>=4)", "furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)"] -test = ["appdirs (==1.4.4)", "pytest (>=6)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)"] - -[[package]] -name = "pluggy" -version = "0.13.1" -description = "plugin and hook calling mechanisms for python" -category = "dev" -optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" - -[package.dependencies] -importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""} - -[package.extras] -dev = ["pre-commit", "tox"] - -[[package]] -name = "pre-commit" -version = "2.13.0" -description = "A framework for managing and maintaining multi-language pre-commit hooks." -category = "dev" -optional = false -python-versions = ">=3.6.1" - -[package.dependencies] -cfgv = ">=2.0.0" -identify = ">=1.0.0" -importlib-metadata = {version = "*", markers = "python_version < \"3.8\""} -nodeenv = ">=0.11.1" -pyyaml = ">=5.1" -toml = "*" -virtualenv = ">=20.0.8" - -[[package]] -name = "prompt-toolkit" -version = "3.0.19" -description = "Library for building powerful interactive command lines in Python" -category = "main" -optional = false -python-versions = ">=3.6.1" - -[package.dependencies] -wcwidth = "*" - -[[package]] -name = "ptyprocess" -version = "0.7.0" -description = "Run a subprocess in a pseudo terminal" -category = "main" -optional = false -python-versions = "*" - -[[package]] -name = "py" -version = "1.10.0" -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.*" - -[[package]] -name = "pygments" -version = "2.9.0" -description = "Pygments is a syntax highlighting package written in Python." -category = "main" -optional = false -python-versions = ">=3.5" - 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'Topic :: Scientific/Engineering :: Human Machine Interfaces', - 'Topic :: Scientific/Engineering :: Chemistry', - 'Topic :: Software Development :: Libraries', -] -homepage = 'http://github.com/instamatic-dev/instamatic' -repository = 'https://github.com/instamatic-dev/instamatic' -documentation = 'https://instamatic.readthedocs.io/' -authors = ['Stef Smeets '] -maintainers = ['Stef Smeets '] -readme = 'readme.md' -keywords = [ - 'electron-crystallography', - 'electron-microscopy', - 'electron-diffraction', - 'serial-crystallography', - '3D-electron-diffraction', - 'micro-ed', - 'data-collection', - 'automation' -] -include = [ - '.pre-commit-config.yaml', - 'THANKS.md', - 'LICENCE', - 'notebooks/*.ipynb', - 'notebooks/nav.nav', - 'notebooks/readme.md', - 'docs/*.md', - 'docs/*.png', - 'docs/*.py', - 'requirements.txt', - 'scripts/*.py', - 'setup_win.bat', - 'tests/*.py', - 'tests/config/*.yaml', - 'tests/config/*/*.yaml', -] - -[tool.poetry.dependencies] -python = ">=3.7.0" -comtypes = '>=1.1.7' -h5py = '>=2.10.0' -ipython = '>=7.11.1' -lmfit = '>=1.0.0' -matplotlib = '>=3.1.2' -mrcfile = '>=1.1.2' -numpy = '>=1.17.3' -pandas = '>=1.0.0' -pillow = '>=7.0.0' -pywinauto = '>=0.6.8' -pyyaml = '>=5.3' -scikit-image = '>=0.17.1' -scipy = '>=1.3.2' -tifffile = '>=2019.7.26.2' -tqdm = '>=4.41.1' -virtualbox = '>=2.0.0' -pyserialem = '>=0.3.2' -# serval-toolkit = { version = ">=0.05", optional = true } - -[tool.poetry.dev-dependencies] -check-manifest = '*' -pre-commit = '*' -pytest = '>=5.4.1' -pytest-cov = '>=2.8.1' - -[tool.poetry.extras] -serval = ["serval-toolkit"] - -[tool.poetry.scripts] -# main -instamatic = 'instamatic.main:main' -'instamatic.controller' = 'instamatic.TEMController.TEMController:main_entry' -# experiments -'instamatic.serialed' = 'instamatic.experiments.serialed.experiment:main' -'instamatic.camera' = 'instamatic.camera.camera:main_entry' -# calibrate -'instamatic.calibrate_stage_lowmag' = 'instamatic.calibrate.calibrate_stage_lowmag:main_entry' -'instamatic.calibrate_stage_mag1' = 'instamatic.calibrate.calibrate_stage_mag1:main_entry' -'instamatic.calibrate_beamshift' = 'instamatic.calibrate.calibrate_beamshift:main_entry' -'instamatic.calibrate_directbeam' = 'instamatic.calibrate.calibrate_directbeam:main_entry' -'instamatic.calibrate_stagematrix' = 'instamatic.calibrate.calibrate_stagematrix:main_entry' -'instamatic.flatfield' = 'instamatic.processing.flatfield:main_entry' -'instamatic.stretch_correction' = 'instamatic.processing.stretch_correction:main_entry' -# tools -'instamatic.browser' = 'scripts.browser:main' -'instamatic.viewer' = 'scripts.viewer:main' -'instamatic.defocus_helper' = 'instamatic.gui.defocus_button:main' -'instamatic.find_crystals' = 'instamatic.processing.find_crystals:main_entry' -'instamatic.find_crystals_ilastik' = 'instamatic.processing.find_crystals_ilastik:main_entry' -'instamatic.learn' = 'scripts.learn:main_entry' -# server -'instamatic.temserver' = 'instamatic.server.tem_server:main' -'instamatic.camserver' = 'instamatic.server.cam_server:main' -'instamatic.dialsserver' = 'instamatic.server.dials_server:main' -'instamatic.VMserver' = 'instamatic.server.vm_ubuntu_server:main' -'instamatic.xdsserver' = 'instamatic.server.xds_server:main' -'instamatic.temserver_fei' = 'instamatic.server.TEMServer_FEI:main' -'instamatic.goniotoolserver' = 'instamatic.server.goniotool_server:main' -# setup -'instamatic.autoconfig' = 'instamatic.config.autoconfig:main' - -[tool.poetry.urls] -'Bug Reports' = 'https://github.com/instamatic-dev/instamatic/issues' - -[tool.dephell.main] -from = {format = 'poetry', path = 'pyproject.toml'} -to = {format = 'setuppy', path = 'setup.py'} -versioning = 'semver' - [build-system] -requires = ['poetry>=0.12'] -build-backend = 'poetry.masonry.api' +requires = ["setuptools>=40.6.0", "wheel"] +build-backend = "setuptools.build_meta" diff --git a/setup.cfg b/setup.cfg new file mode 100644 index 00000000..de6bf970 --- /dev/null +++ b/setup.cfg @@ -0,0 +1,109 @@ +# see documentation, e.g. +# - https://packaging.python.org/tutorials/packaging-projects/#configuring-metadata +# - https://setuptools.readthedocs.io/en/latest/userguide/declarative_config.html +# - https://www.python.org/dev/peps/pep-0314/ + +[metadata] +author = Stef Smeets +author_email = s.smeets@esciencecenter.nl +classifiers = + Programming Language :: Python :: 3.7 + Programming Language :: Python :: 3.8 + Programming Language :: Python :: 3.9 + Development Status :: 5 - Production/Stable + Intended Audience :: Science/Research + License :: OSI Approved :: BSD License + Operating System :: Microsoft :: Windows + Topic :: Scientific/Engineering :: Human Machine Interfaces + Topic :: Scientific/Engineering :: Chemistry + Topic :: Software Development :: Libraries +description = DPython program for automated electron diffraction data collection +keywords = + electron-crystallography + electron-microscopy + electron-diffraction + serial-crystallography + 3D-electron-diffraction + micro-ed + data-collection + automation +long_description = file: README.md +long_description_content_type = text/markdown +name = instamatic +project_urls = + Bug Tracker = hhttp://github.com/instamatic-dev/instamatic/issues + Documentation = https://instamatic.readthedocs.io/ +url = http://github.com/instamatic-dev/instamatic +version = 1.7.0 + + +[options] +zip_safe = False +include_package_data = True +packages = find: +install_requires = + comtypes >= 1.1.7 + h5py >= 2.10.0 + ipython >= 7.11.1 + lmfit >= 1.0.0 + matplotlib >= 3.1.2 + mrcfile >= 1.1.2 + numpy >= 1.17.3 + pandas >= 1.0.0 + pillow >= 7.0.0 + pywinauto >= 0.6.8 + pyyaml >= 5.3 + scikit-image >= 0.17.1 + scipy >= 1.3.2 + tifffile >= 2019.7.26.2 + tqdm >= 4.41.1 + virtualbox >= 2.0.0 + pyserialem >= 0.3.2 + + +[options.extras_require] +develop = + check-manifest + pre-commit + flake8 + pytest >= 5.4.1 + pytest-cov >= 2.8.1 +serval = + serval-toolkit + + +[options.packages.find] +include = instamatic, instamatic.*, instamatic.experiments.* + +[options.entry_points] +console_scripts = + instamatic = instamatic.main:main + instamatic.controller = instamatic.TEMController.TEMController:main_entry + # experiments + instamatic.serialed = instamatic.experiments.serialed.experiment:main + instamatic.camera = instamatic.camera.camera:main_entry + # calibrate + instamatic.calibrate_stage_lowmag = instamatic.calibrate.calibrate_stage_lowmag:main_entry + instamatic.calibrate_stage_mag1 = instamatic.calibrate.calibrate_stage_mag1:main_entry + instamatic.calibrate_beamshift = instamatic.calibrate.calibrate_beamshift:main_entry + instamatic.calibrate_directbeam = instamatic.calibrate.calibrate_directbeam:main_entry + instamatic.calibrate_stagematrix = instamatic.calibrate.calibrate_stagematrix:main_entry + instamatic.flatfield = instamatic.processing.flatfield:main_entry + instamatic.stretch_correction = instamatic.processing.stretch_correction:main_entry + # tools + instamatic.browser = scripts.browser:main + instamatic.viewer = scripts.viewer:main + instamatic.defocus_helper = instamatic.gui.defocus_button:main + instamatic.find_crystals = instamatic.processing.find_crystals:main_entry + instamatic.find_crystals_ilastik = instamatic.processing.find_crystals_ilastik:main_entry + instamatic.learn = scripts.learn:main_entry + # server + instamatic.temserver = instamatic.server.tem_server:main + instamatic.camserver = instamatic.server.cam_server:main + instamatic.dialsserver = instamatic.server.dials_server:main + instamatic.VMserver = instamatic.server.vm_ubuntu_server:main + instamatic.xdsserver = instamatic.server.xds_server:main + instamatic.temserver_fei = instamatic.server.TEMServer_FEI:main + instamatic.goniotoolserver = instamatic.server.goniotool_server:main + # setup + instamatic.autoconfig = instamatic.config.autoconfig:main diff --git a/setup.py b/setup.py index a69ce4ee..60684932 100644 --- a/setup.py +++ b/setup.py @@ -1,129 +1,3 @@ -try: - from setuptools import setup -except ImportError: - from distutils.core import setup +from setuptools import setup - -import os.path - -readme = '' -here = os.path.abspath(os.path.dirname(__file__)) -readme_path = os.path.join(here, 'readme.md') -if os.path.exists(readme_path): - with open(readme_path, 'rb') as stream: - readme = stream.read().decode('utf8') - - -setup( - long_description=readme, - name='instamatic', - version='1.7.0', - description='Python program for automated electron diffraction data collection', - python_requires='>=3.7', - project_urls={ - 'homepage': 'https://github.com/instamatic-dev/instamatic', - 'repository': 'https://github.com/instamatic-dev/instamatic', - 'documentation': 'https://instamatic.readthedocs.io/'}, - author='Stef Smeets', - author_email='s.smeets@esciencecenter.nl', - keywords='electron-crystallography electron-microscopy electron-diffraction serial-crystallography 3D-electron-diffraction micro-ed data-collection automation', - classifiers=[ - 'Programming Language :: Python :: 3.7', - 'Programming Language :: Python :: 3.8', - 'Programming Language :: Python :: 3.9', - 'Development Status :: 5 - Production/Stable', - 'Intended Audience :: Science/Research', - 'License :: OSI Approved :: BSD License', - 'Operating System :: Microsoft :: Windows', - 'Topic :: Scientific/Engineering :: Human Machine Interfaces', - 'Topic :: Scientific/Engineering :: Chemistry', - 'Topic :: Software Development :: Libraries'], - entry_points={ - 'console_scripts': [ - 'instamatic = instamatic.main:main', - 'instamatic.controller = instamatic.TEMController.TEMController:main_entry', - 'instamatic.serialed = instamatic.experiments.serialed.experiment:main', - 'instamatic.camera = instamatic.camera.camera:main_entry', - 'instamatic.calibrate_stage_lowmag = instamatic.calibrate.calibrate_stage_lowmag:main_entry', - 'instamatic.calibrate_stage_mag1 = instamatic.calibrate.calibrate_stage_mag1:main_entry', - 'instamatic.calibrate_beamshift = instamatic.calibrate.calibrate_beamshift:main_entry', - 'instamatic.calibrate_directbeam = instamatic.calibrate.calibrate_directbeam:main_entry', - 'instamatic.calibrate_stagematrix = instamatic.calibrate.calibrate_stagematrix:main_entry', - 'instamatic.flatfield = instamatic.processing.flatfield:main_entry', - 'instamatic.stretch_correction = instamatic.processing.stretch_correction:main_entry', - 'instamatic.browser = scripts.browser:main', - 'instamatic.viewer = scripts.viewer:main', - 'instamatic.defocus_helper = instamatic.gui.defocus_button:main', - 'instamatic.find_crystals = instamatic.processing.find_crystals:main_entry', - 'instamatic.find_crystals_ilastik = instamatic.processing.find_crystals_ilastik:main_entry', - 'instamatic.learn = scripts.learn:main_entry', - 'instamatic.temserver = instamatic.server.tem_server:main', - 'instamatic.camserver = instamatic.server.cam_server:main', - 'instamatic.dialsserver = instamatic.server.dials_server:main', - 'instamatic.VMserver = instamatic.server.vm_ubuntu_server:main', - 'instamatic.xdsserver = instamatic.server.xds_server:main', - 'instamatic.temserver_fei = instamatic.server.TEMServer_FEI:main', - 'instamatic.goniotoolserver = instamatic.server.goniotool_server:main', - 'instamatic.autoconfig = instamatic.config.autoconfig:main']}, - packages=[ - 'instamatic', - 'instamatic.TEMController', - 'instamatic.calibrate', - 'instamatic.camera', - 'instamatic.config', - 'instamatic.experiments', - 'instamatic.experiments.autocred', - 'instamatic.experiments.cred', - 'instamatic.experiments.cred_gatan', - 'instamatic.experiments.cred_tvips', - 'instamatic.experiments.red', - 'instamatic.experiments.serialed', - 'instamatic.formats', - 'instamatic.gui', - 'instamatic.neural_network', - 'instamatic.processing', - 'instamatic.server', - 'instamatic.utils'], - package_data={ - 'instamatic.camera': [ - '*.dll', - '*.h', - '*.lockfile', - '*.md', - 'tpx/*.bpc', - 'tpx/*.dacs', - 'tpx/*.txt'], - 'instamatic.config': [ - '*.yaml', - 'alignments/*.yaml', - 'calibration/*.yaml', - 'camera/*.yaml', - 'microscope/*.yaml', - 'scripts/*.md'], - 'instamatic.neural_network': ['*.p']}, - install_requires=[ - 'comtypes>=1.1.7', - 'h5py>=2.10.0', - 'ipython>=7.11.1', - 'lmfit>=1.0.0', - 'matplotlib>=3.1.2', - 'mrcfile>=1.1.2', - 'numpy>=1.17.3', - 'pandas>=1.0.0', - 'pillow>=7.0.0', - 'pyserialem>=0.3.0', - 'pywinauto>=0.6.8', - 'pyyaml>=5.3', - 'scikit-image>=0.17.1', - 'scipy>=1.3.2', - 'tifffile>=2019.7.26.2', - 'tqdm>=4.41.1', - 'virtualbox>=2.0.0'], - extras_require={ - 'dev': [ - 'check-manifest', - 'pre-commit', - 'pytest>=5.4.1', - 'pytest-cov>=2.8.1'], - 'serval': ['serval-toolkit>=0.05']}, -) +setup() diff --git a/tests/test_ctrl.py b/tests/test_ctrl.py index fecc969a..916dd70f 100644 --- a/tests/test_ctrl.py +++ b/tests/test_ctrl.py @@ -58,12 +58,13 @@ def test_stage(ctrl): stage.set(x=0, y=0, z=0) stage.move_in_projection(delta_x=1, delta_y=1) - assert pytest.approx(abs(stage.y) + abs(stage.z), np.sqrt(2)) + + assert abs(stage.y) + abs(stage.z) == pytest.approx(np.sqrt(2)) assert stage.x == 1 stage.set(x=0, y=0, z=0) stage.move_along_optical_axis(1) - assert pytest.approx(abs(stage.y) + abs(stage.z), np.sqrt(2)) + assert abs(stage.y) + abs(stage.z) == pytest.approx(np.sqrt(2)) stage.xy = (0, 0) stage.move_xy_with_backlash_correction(shift_x=100, shift_y=100)