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merge master -Dorg -Ssuccess-only: PR 187 (Rtd)
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‎.bumpversion.cfg

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[bumpversion:part:build]
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[bumpversion:file:setup.py]
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[bumpversion:file:docs/conf.py]

‎.gitignore

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*.pyc
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.gitignore
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*.DS_Store*
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docs/_build

‎.readthedocs.yml

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# Required
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version: 2
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build:
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os: "ubuntu-22.04"
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tools:
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python: "3.11"
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# Build documentation in the docs/ directory with Sphinx
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sphinx:
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configuration: docs/conf.py
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python:
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install:
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- requirements: docs/requirements.txt

‎README.rst

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.. image:: https://github.com/ome/omero-scripts/workflows/OMERO/badge.svg
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:target: https://github.com/ome/omero-scripts/actions
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.. image:: https://github.com/ome/omero-scripts/workflows/sphinx/badge.svg
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:target: https://github.com/ome/omero-scripts/actions
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.. image:: https://badge.fury.io/py/omero-scripts.svg
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:target: https://badge.fury.io/py/omero-scripts
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@@ -12,34 +15,37 @@ OMERO.scripts API. All scripts (e.g. ``*.py``) present in the
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directory will be automatically distributed with all binary
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builds. Which file-endings will be detected and how they
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will be launched are both configured centrally in the server.
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``.py``, ``.jy", and ``.m`` (MATLAB) files should all be detected
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``.py``, ``.jy``, and ``.m`` (MATLAB) files should all be detected
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by default starting with OMERO 5.
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Categories
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----------
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==========
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Scripts are separated into several categories, one per directory.
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| In the directory | should be scripts which ... |
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| ---------------- | --------------------- |
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+------------------------+-------------------------------------------------------------------------------+
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| Directory | Description |
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+========================+===============================================================================+
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| **analysis_scripts** | crunch images to produce numerical results and similar tasks |
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+------------------------+-------------------------------------------------------------------------------+
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| **export_scripts** | take one or more images as an input, and produce a representation for exchange|
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+------------------------+-------------------------------------------------------------------------------+
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| **figure_scripts** | take one or more images as an input, and produce a summary representation |
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| **hcs_scripts** | work with screens/plates/wells rather than just images |
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+------------------------+-------------------------------------------------------------------------------+
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| **import_scripts** | are run on images after import for extra processing |
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| **processing_scripts** | create new images from existing images or other data |
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| **setup_scripts** | are executed once, often by administrators, to configure OMERO itself |
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+------------------------+-------------------------------------------------------------------------------+
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| **util_scripts** | perform other miscellaneous tasks like cleaning up or optimizing OMERO itself |
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+------------------------+-------------------------------------------------------------------------------+
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Scripts which would like to rely on other scripts can
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use:
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use::
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import omero.<sub_dir>.<script_name>
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For this to work, the official script in question must
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be properly importable, i.e.:
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be properly importable, i.e.::
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def run():
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client = omero.scripts.client(...)
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OMERO User Scripts
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------------------
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==================
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If you would like to provide your own scripts for others to install
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into their OMERO installations, please see http://openmicroscopy.org/info/scripts
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into their OMERO installations, please see https://openmicroscopy.org/info/scripts
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Testing
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-------
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=======
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Integration tests under ``test/`` require an OMERO server with scripts installed.
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The tests are run by Travis for open PRs using omero-test-infra to deploy OMERO
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via Docker containers.
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To run tests locally:
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To run tests locally::
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# All tests
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$ python setup.py test
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# Single test in a single file
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$ python setup.py test -t test/integration/test_util_scripts.py -k test_dataset_to_plate
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Usage
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=====
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See https://omero-scripts.readthedocs.io/en/stable/
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Release process
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===============
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This repository uses `bump2version <https://pypi.org/project/bump2version/>`_ to manage version numbers.
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To tag a release run::
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$ bumpversion release
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This will remove the ``.dev0`` suffix from the current version, commit, and tag the release.
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To switch back to a development version run::
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$ bumpversion --no-tag [major|minor|patch]
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specifying ``major``, ``minor`` or ``patch`` depending on whether the development branch will be a `major, minor or patch release <https://semver.org/>`_. This will also add the ``.dev0`` suffix.
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Remember to ``git push`` all commits and tags.s essential.
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The CI pipeline will automatically deploy the tag onto PyPI.
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Copyright
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---------
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=========
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2010-2020, The Open Microscopy Environment
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2010-2021, The Open Microscopy Environment

‎docs/Makefile

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# Minimal makefile for Sphinx documentation
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#
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# You can set these variables from the command line, and also
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# from the environment for the first two.
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SPHINXOPTS ?=
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SPHINXBUILD ?= sphinx-build
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SOURCEDIR = .
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BUILDDIR = _build
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# Put it first so that "make" without argument is like "make help".
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help:
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@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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.PHONY: help Makefile
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# Catch-all target: route all unknown targets to Sphinx using the new
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# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
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%: Makefile
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@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

‎docs/analysis_scripts.rst

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Analysis scripts
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================
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Kymograph
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---------
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.. automodule:: Kymograph
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:members:
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Kymograph Analysis
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------------------
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.. automodule:: Kymograph_Analysis
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:members:
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Plot Profile
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------------
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.. automodule:: Plot_Profile
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:members:

‎docs/conf.py

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# Configuration file for the Sphinx documentation builder.
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#
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# This file only contains a selection of the most common options. For a full
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# list see the documentation:
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# https://www.sphinx-doc.org/en/master/usage/configuration.html
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from datetime import datetime
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import os
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import sys
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from sphinx.util import logging
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logger = logging.getLogger(__name__)
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# -- Path setup --------------------------------------------------------------
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# If extensions (or modules to document with autodoc) are in another directory,
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# add these directories to sys.path here. If the directory is relative to the
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# documentation root, use os.path.abspath to make it absolute, like shown here.
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#
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def get_scripts(directory):
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"""
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Find all the scripts available
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"""
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scripts = []
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# Walk the tree.
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for root, directories, files in os.walk(directory):
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for filename in files:
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if filename.endswith(".py") and "_init_" not in filename:
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scripts.append(filename.replace('\n', '').replace(".py", ""))
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return scripts
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def find_scripts_entry(file_name):
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"""
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Find the entries corresponding to the scripts.
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"""
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with open(file_name) as file:
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lines = file.readlines()
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entries = []
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for line in lines:
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if "automodule" in line:
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values = line.split(".. automodule::")
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entries.append(values[1].replace('\n', '').strip())
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return entries
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def compare(list1, list2):
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"""
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Return the elements not common to both lists
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"""
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return [i for i in list1 + list2 if i not in list1 or i not in list2]
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# List of directories to scan and add the path.
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directories = ['../omero/analysis_scripts', '../omero/export_scripts',
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'../omero/figure_scripts', '../omero/import_scripts',
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'../omero/util_scripts']
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scripts = []
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entries = []
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for d in directories:
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sys.path.insert(0, d)
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scripts.extend(get_scripts(d))
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p = d.split("/")
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name = "%s.rst" % (p[len(p) - 1])
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entries.extend(find_scripts_entry(name))
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# Indicate the scripts not listed for documentation
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if len(entries) < len(scripts):
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common = compare(scripts, entries)
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logger.warning("automodule entries missing for:\n" + '\n'.join(common))
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# -- Project information -----------------------------------------------------
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# The master toctree document.
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master_doc = 'index'
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project = u'omero scripts'
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now = datetime.now()
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author = u'Open Microscopy Environment'
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copyright = u'2016-%d, %s ' % (now.year, author)
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# The full version, including alpha/beta/rc tags
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# The short X.Y version.
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version = '5.6.2.dev0'
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release = version
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# -- General configuration ---------------------------------------------------
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extlinks = {}
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# Add any Sphinx extension module names here, as strings. They can be
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# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
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# ones.
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extensions = [
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'sphinx.ext.autodoc',
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'sphinx.ext.extlinks',
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'sphinx_rtd_theme',
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]
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# Add any paths that contain templates here, relative to this directory.
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templates_path = ['_templates']
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# List of patterns, relative to source directory, that match files and
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# directories to ignore when looking for source files.
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# This pattern also affects html_static_path and html_extra_path.
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exclude_patterns = [u'_build', 'Thumbs.db', '.DS_Store']
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# Build docs without external dependencies
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autodoc_mock_imports = ['numpy', 'omero-py', 'omero', "PIL"]
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# The name of the Pygments (syntax highlighting) style to use.
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pygments_style = 'sphinx'
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# -- Options for HTML output -------------------------------------------------
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# The theme to use for HTML and HTML Help pages. See the documentation for
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# a list of builtin themes.
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#
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html_theme = 'default'
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# Add any paths that contain custom static files (such as style sheets) here,
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# relative to this directory. They are copied after the builtin static files,
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# so a file named "default.css" will overwrite the builtin "default.css".
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html_static_path = []
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# Grouping the document tree into LaTeX files. List of tuples
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# (source start file, target name, title,
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# author, documentclass [howto, manual, or own class]).
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latex_documents = [
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(master_doc, 'OMEROScripts.tex', u'OMERO Scripts Documentation',
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author, 'manual'),
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]
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# -- Options for manual page output ------------------------------------------
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# One entry per manual page. List of tuples
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# (source start file, name, description, authors, manual section).
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man_pages = [
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(master_doc, 'omeroscripts', u'OMERO Scripts Documentation',
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[author], 1)
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]
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# -- Options for Texinfo output ----------------------------------------------
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# Grouping the document tree into Texinfo files. List of tuples
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# (source start file, target name, title, author,
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# dir menu entry, description, category)
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texinfo_documents = [
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(master_doc, 'OMEROScripts', u'OMERO Script Documentation',
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author, 'OMEROScripts', 'One line description of project.',
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'Miscellaneous'),
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]
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# -- Options for Epub output -------------------------------------------------
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# Bibliographic Dublin Core info.
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epub_title = project
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# The unique identifier of the text. This can be a ISBN number
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# or the project homepage.
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#
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# epub_identifier = ''
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# A unique identification for the text.
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#
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# epub_uid = ''
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# A list of files that should not be packed into the epub file.
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epub_exclude_files = ['search.html']

‎docs/export_scripts.rst

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Export scripts
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==============
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Batch Image Export
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------------------
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.. automodule:: Batch_Image_Export
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:members:
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Batch ROI Export
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----------------
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.. automodule:: Batch_ROI_Export
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:members:
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Make Movie
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----------
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.. automodule:: Make_Movie
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:members:

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