tomoscan 2.2.0.dev0__tar.gz → 2.2.2__tar.gz

{tomoscan-2.2.0.dev0/tomoscan.egg-info → tomoscan-2.2.2}/PKG-INFO

@@ -1,62 +1,59 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: tomoscan
-Version: 2.2.0.dev0
-Summary: "utilitary to access tomography data at esrf"
-Home-page: https://gitlab.esrf.fr/tomotools/tomoscan
-Author: Henri Payno, Pierre Paleo, Pierre-Olivier Autran, Jérôme Lesaint, Alessandro Mirone
-Author-email: henri.payno@esrf.fr, pierre.paleo@esrf.fr, pierre-olivier.autran@esrf.fr, jerome.lesaint@esrf.fr, mirone@esrf.fr
+Version: 2.2.2
+Summary: Utility to access tomography data at ESRF
+Author-email: Henri Payno <henri.payno@esrf.fr>, Pierre Paleo <pierre.paleo@esrf.fr>, Pierre-Olivier Autran <pierre-olivier.autran@esrf.fr>, Jérôme Lesaint <jerome.lesaint@esrf.fr>, Alessandro Mirone <mirone@esrf.fr>
 License: MIT
-Project-URL: Bug Tracker, https://gitlab.esrf.fr/tomotools/tomoscan/-/issues
+Keywords: NXtomo,nexus,tomography,esrf,bliss-tomo
 Classifier: Intended Audience :: Education
 Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Classifier: Environment :: Console
 Classifier: Environment :: X11 Applications :: Qt
 Classifier: Operating System :: POSIX
 Classifier: Natural Language :: English
 Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
-Requires-Python: >=3.6
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: setuptools
+Requires-Dist: defusedxml
 Requires-Dist: h5py>=3.0
+Requires-Dist: hdf5plugin
+Requires-Dist: blosc2-grok
 Requires-Dist: silx>=2.0
 Requires-Dist: lxml
 Requires-Dist: dicttoxml
 Requires-Dist: packaging
 Requires-Dist: psutil
-Requires-Dist: nxtomo>=1.3.0dev8
-Requires-Dist: pyunitsystem>=2.0.0a
-Requires-Dist: numpy<2.0
+Requires-Dist: nxtomo>=2.0.0dev0
+Requires-Dist: numpy
 Requires-Dist: packaging>=22.0
+Requires-Dist: pint
 Provides-Extra: full
-Requires-Dist: glymur; extra == "full"
-Requires-Dist: imageio; extra == "full"
+Requires-Dist: glymur<0.14; python_version <= "3.9" and extra == "full"
+Requires-Dist: glymur; python_version > "3.9" and extra == "full"
 Requires-Dist: tqdm; extra == "full"
 Requires-Dist: tifffile[zarr]>=2023.7.4; python_version >= "3.10" and extra == "full"
 Requires-Dist: tifffile; python_version < "3.10" and extra == "full"
 Requires-Dist: zarr; python_version < "3.10" and extra == "full"
 Requires-Dist: fsspec; python_version < "3.10" and extra == "full"
 Provides-Extra: test
-Requires-Dist: glymur; extra == "test"
-Requires-Dist: imageio; extra == "test"
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: python-gitlab; extra == "test"
+Requires-Dist: glymur<0.14; python_version <= "3.9" and extra == "test"
+Requires-Dist: glymur; python_version > "3.9" and extra == "test"
 Requires-Dist: tqdm; extra == "test"
 Requires-Dist: tifffile[zarr]>=2023.7.4; python_version >= "3.10" and extra == "test"
 Requires-Dist: tifffile; python_version < "3.10" and extra == "test"
 Requires-Dist: zarr; python_version < "3.10" and extra == "test"
 Requires-Dist: fsspec; python_version < "3.10" and extra == "test"
-Requires-Dist: pytest; extra == "test"
-Requires-Dist: python-gitlab; extra == "test"
 Provides-Extra: doc
-Requires-Dist: glymur; extra == "doc"
-Requires-Dist: imageio; extra == "doc"
-Requires-Dist: tqdm; extra == "doc"
-Requires-Dist: tifffile[zarr]>=2023.7.4; python_version >= "3.10" and extra == "doc"
-Requires-Dist: tifffile; python_version < "3.10" and extra == "doc"
-Requires-Dist: zarr; python_version < "3.10" and extra == "doc"
-Requires-Dist: fsspec; python_version < "3.10" and extra == "doc"
 Requires-Dist: Sphinx<5.2.0,>=4.0.0; extra == "doc"
 Requires-Dist: nbsphinx; extra == "doc"
 Requires-Dist: pandoc; extra == "doc"
@@ -67,9 +64,14 @@ Requires-Dist: h5glance; extra == "doc"
 Requires-Dist: pydata_sphinx_theme; extra == "doc"
 Requires-Dist: sphinx-design; extra == "doc"
 Requires-Dist: sphinx-autodoc-typehints; extra == "doc"
-Provides-Extra: setup-requires
-Requires-Dist: setuptools; extra == "setup-requires"
-Requires-Dist: numpy; extra == "setup-requires"
+Requires-Dist: glymur<0.14; python_version <= "3.9" and extra == "doc"
+Requires-Dist: glymur; python_version > "3.9" and extra == "doc"
+Requires-Dist: tqdm; extra == "doc"
+Requires-Dist: tifffile[zarr]>=2023.7.4; python_version >= "3.10" and extra == "doc"
+Requires-Dist: tifffile; python_version < "3.10" and extra == "doc"
+Requires-Dist: zarr; python_version < "3.10" and extra == "doc"
+Requires-Dist: fsspec; python_version < "3.10" and extra == "doc"
+Dynamic: license-file
 
 # tomoscan
 

tomoscan-2.2.2/doc/conf.py

@@ -0,0 +1,360 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+#
+# Orange3 Example Add-on documentation build configuration file, created by
+# sphinx-quickstart on Fri Aug 21 11:28:31 2015.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+# sys.path.insert(0, os.path.abspath('.'))
+project = "tomoscan"
+
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+# sys.path.insert(0, os.path.abspath('.'))
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension modules names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.autosummary",
+    "sphinx_design",
+    "nbsphinx",
+    "sphinx_autodoc_typehints",
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+source_suffix = [".rst", ".md"]
+
+# The encoding of source files.
+# source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = "index"
+
+# General information about the project.
+project = "tomoscan"
+copyright = "2016-2023, ESRF"
+author = "ESRF"
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = "2.2"
+# The full version, including alpha/beta/rc tags.
+release = "2.2"
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = "en"
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+# today = ''
+# Else, today_fmt is used as the format for a strftime call.
+# today_fmt = '%B %d, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+exclude_patterns = [
+    "build",
+    "**.ipynb_checkpoints",
+    "*intensity_norm.ipynb",
+    "*tutorials/intensity_norm*",
+]
+
+# The reST default role (used for this markup: `text`) to use for all
+# documents.
+# default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+# add_function_parentheses = True
+
+# If true, the current modules name will be prepended to all description
+# unit titles (such as .. function::).
+# add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+# show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = "sphinx"
+
+# A list of ignored prefixes for modules index sorting.
+# modindex_common_prefix = []
+
+# If true, keep warnings as "system message" paragraphs in the built documents.
+# keep_warnings = False
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+
+
+# -- Options for HTML output ----------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+html_theme = "pydata_sphinx_theme"
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+# html_theme_options = {}
+
+# Add any paths that contain custom themes here, relative to this directory.
+# html_theme_path = []
+
+# The name for this set of Sphinx documents.  If None, it defaults to
+# "<project> v<release> documentation".
+# html_title = None
+
+# A shorter title for the navigation bar.  Default is the same as html_title.
+# html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+html_logo = "img/tomoscan.png"
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+# html_favicon = None
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ["_static"]
+
+# Add any extra paths that contain custom files (such as robots.txt or
+# .htaccess) here, relative to this directory. These files are copied
+# directly to the root of the documentation.
+# html_extra_path = []
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+# html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+# html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+# html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+# html_additional_pages = {}
+
+# If false, no modules index is generated.
+# html_domain_indices = True
+
+# If false, no index is generated.
+# html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+# html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+# html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+# html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+# html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it.  The value of this option must be the
+# base URL from which the finished HTML is served.
+# html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+# html_file_suffix = None
+
+# Language to be used for generating the HTML full-text search index.
+# Sphinx supports the following languages:
+#   'da', 'de', 'en', 'es', 'fi', 'fr', 'h', 'it', 'ja'
+#   'nl', 'no', 'pt', 'ro', 'r', 'sv', 'tr'
+# html_search_language = 'en'
+
+# A dictionary with options for the search language support, empty by default.
+# Now only 'ja' uses this config value
+# html_search_options = {'type': 'default'}
+
+# The name of a javascript file (relative to the configuration directory) that
+# implements a search results scorer. If empty, the default will be used.
+# html_search_scorer = 'scorer.js'
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = "tomoscan"
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #'papersize': 'letterpaper',
+    # The font size ('10pt', '11pt' or '12pt').
+    #'pointsize': '10pt',
+    # Additional stuff for the LaTeX preamble.
+    #'preamble': '',
+    # Latex figure (float) alignment
+    #'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+# latex_documents = [
+#   (master_doc, 'Orange3ESRFAdd-on.tex', 'Orange3 ESRF Add-on Documentation',
+#    'Biolab', 'manual'),
+# ]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+# latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+# latex_use_parts = False
+
+# If true, show page references after internal links.
+# latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+# latex_show_urls = False
+
+# Documents to append as an appendix to all manuals.
+# latex_appendices = []
+
+# If false, no modules index is generated.
+# latex_domain_indices = True
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [(master_doc, "tomoscan", "tomoscan documentation", [author], 1)]
+
+htmlhelp_pages = [(master_doc, "tomoscan", "tomoscan documentation", [author], 1)]
+
+# If true, show URL addresses after external links.
+# man_show_urls = False
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (
+        master_doc,
+        "tomoscan",
+        "tomoscan Documentation",
+        author,
+        "tomoscan",
+        "utils for getting core information from scan",
+        "Miscellaneous",
+    ),
+]
+
+# Documents to append as an appendix to all manuals.
+# texinfo_appendices = []
+
+# If false, no modules index is generated.
+# texinfo_domain_indices = True
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+# texinfo_show_urls = 'footnote'
+
+# If true, do not generate a @detailmenu in the "Top" node's menu.
+# texinfo_no_detailmenu = False
+
+nbsphinx_timeout = 60
+nbsphinx_allow_errors = True
+
+
+autosummary_generate = True
+
+autodoc_default_flags = [
+    "members",
+    "undoc-members",
+    "show-inheritance",
+]
+
+
+html_theme_options = {
+    "icon_links": [
+        {
+            "name": "pypi",
+            "url": "https://pypi.org/project/tomoscan",
+            "icon": "_static/navbar_icons/pypi.svg",
+            "type": "local",
+        },
+        {
+            "name": "gitlab",
+            "url": "https://gitlab.esrf.fr/tomotools/tomoscan",
+            "icon": "_static/navbar_icons/gitlab.svg",
+            "type": "local",
+        },
+    ],
+    "show_toc_level": 1,
+    "navbar_align": "left",
+    "show_version_warning_banner": True,
+    "navbar_start": ["navbar-logo", "version"],
+    "navbar_center": ["navbar-nav"],
+    "footer_start": ["copyright"],
+    "footer_center": ["sphinx-version"],
+}
+
+html_sidebars = {
+    "community/index": [
+        "sidebar-nav-bs",
+        "custom-template",
+    ],  # This ensures we test for custom sidebars
+    "examples/no-sidebar": [],  # Test what page looks like with no sidebar items
+    "examples/persistent-search-field": ["search-field"],
+    # Blog sidebars
+    # ref: https://ablog.readthedocs.io/manual/ablog-configuration-options/#blog-sidebars
+    "examples/blog/*": [
+        "ablog/postcard.html",
+        "ablog/recentposts.html",
+        "ablog/tagcloud.html",
+        "ablog/categories.html",
+        "ablog/authors.html",
+        "ablog/languages.html",
+        "ablog/locations.html",
+        "ablog/archives.html",
+    ],
+}

tomoscan-2.2.2/pyproject.toml

@@ -0,0 +1,108 @@
+[project]
+name = "tomoscan"
+dynamic = ["version"]
+authors = [
+    { name = "Henri Payno", email = "henri.payno@esrf.fr" },
+    { name = "Pierre Paleo", email = "pierre.paleo@esrf.fr" },
+    { name = "Pierre-Olivier Autran", email = "pierre-olivier.autran@esrf.fr" },
+    { name = "Jérôme Lesaint", email = "jerome.lesaint@esrf.fr" },
+    { name = "Alessandro Mirone", email = "mirone@esrf.fr" }
+]
+description = "Utility to access tomography data at ESRF"
+readme = { file = "README.md", content-type = "text/markdown" }
+license = { text = "MIT" }
+requires-python = ">=3.9"
+keywords = ["NXtomo", "nexus", "tomography", "esrf", "bliss-tomo"]
+classifiers = [
+    "Intended Audience :: Education",
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Environment :: Console",
+    "Environment :: X11 Applications :: Qt",
+    "Operating System :: POSIX",
+    "Natural Language :: English",
+    "Topic :: Scientific/Engineering :: Physics",
+    "Topic :: Software Development :: Libraries :: Python Modules"
+]
+
+dependencies = [
+    "setuptools",
+    "defusedxml",
+    "h5py>=3.0",
+    "hdf5plugin",
+    "blosc2-grok",
+    "silx>=2.0",
+    "lxml",
+    "dicttoxml",
+    "packaging",
+    "psutil",
+    "nxtomo>=2.0.0dev0",
+    "numpy",
+    "packaging>=22.0",
+    "pint",
+]
+
+[project.optional-dependencies]
+full = [
+    "glymur<0.14 ; python_version <= '3.9'",
+    "glymur ; python_version > '3.9'",
+    "tqdm",
+    "tifffile[zarr]>=2023.7.4; python_version >= '3.10'",
+    "tifffile; python_version < '3.10'",
+    "zarr; python_version < '3.10'",
+    "fsspec; python_version < '3.10'"
+]
+test = [
+    "pytest",
+    "python-gitlab",
+    "glymur<0.14 ; python_version <= '3.9'",
+    "glymur ; python_version > '3.9'",
+    "tqdm",
+    "tifffile[zarr]>=2023.7.4; python_version >= '3.10'",
+    "tifffile; python_version < '3.10'",
+    "zarr; python_version < '3.10'",
+    "fsspec; python_version < '3.10'"
+]
+doc = [
+    "Sphinx>=4.0.0, <5.2.0",
+    "nbsphinx",
+    "pandoc",
+    "ipykernel",
+    "jupyter_client",
+    "nbconvert",
+    "h5glance",
+    "pydata_sphinx_theme",
+    "sphinx-design",
+    "sphinx-autodoc-typehints",
+    "glymur<0.14 ; python_version <= '3.9'",
+    "glymur ; python_version > '3.9'",
+    "tqdm",
+    "tifffile[zarr]>=2023.7.4; python_version >= '3.10'",
+    "tifffile; python_version < '3.10'",
+    "zarr; python_version < '3.10'",
+    "fsspec; python_version < '3.10'"
+]
+
+[build-system]
+requires = [
+    "setuptools>=61.0",
+    "wheel",
+    "numpy"
+]
+build-backend = "setuptools.build_meta"
+
+[tool.sphinx]
+source-dir = "./doc"
+
+[project.scripts]
+tomoscan = "tomoscan.__main__:main"
+
+[tool.setuptools.dynamic]
+version = { attr = "tomoscan.__version__" }
+
+[tool.setuptools.packages.find]
+where = ["."]

tomoscan-2.2.2/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+