update name

.github/workflows/build-main.yml

@@ -30,7 +30,7 @@ jobs:
         pip install .[test]
     - name: Test with pytest
       run: |
-        pytest --cov-report xml --cov=leonardo leonardo/tests/
+        pytest --cov-report xml --cov=leonardo_toolset leonardo_toolset/tests/
     - name: Upload codecov
       uses: codecov/codecov-action@v1
 
@@ -49,10 +49,10 @@ jobs:
         pip install .[test]
     - name: Lint with flake8
       run: |
-        flake8 leonardo --count --verbose --show-source --statistics
+        flake8 leonardo_toolset --count --verbose --show-source --statistics
     - name: Check with black
       run: |
-        black --check leonardo
+        black --check leonardo_toolset
 
   publish:
     if: "contains(github.event.head_commit.message, 'Bump version')"

.github/workflows/test-and-lint.yml

@@ -22,7 +22,7 @@ jobs:
         pip install .[test]
     - name: Test with pytest
       run: |
-        pytest leonardo/tests/
+        pytest leonardo_toolset/tests/
     - name: Upload codecov
       uses: codecov/codecov-action@v1
 
@@ -41,7 +41,7 @@ jobs:
         pip install .[test]
     - name: Lint with flake8
       run: |
-        flake8 leonardo --count --verbose --show-source --statistics
+        flake8 leonardo_toolset --count --verbose --show-source --statistics
     - name: Check with black
       run: |
-        black --check leonardo
+        black --check leonardo_toolset

.gitignore

@@ -67,7 +67,7 @@ instance/
 
 # Sphinx documentation
 docs/_build/
-docs/leonardo.*rst
+docs/leonardo_toolset.*rst
 
 # PyBuilder
 target/

CONTRIBUTING.md

@@ -5,20 +5,20 @@ helps, and credit will always be given.
 
 ## Get Started!
 
-Ready to contribute? Here's how to set up `leonardo` for local development.
+Ready to contribute? Here's how to set up `leonard_toolset` for local development.
 
-1. Fork the `leonardo` repo on GitHub.
+1. Fork the `leonardo_toolset` repo on GitHub.
 
 2. Clone your fork locally:
 
     ```bash
-    git clone [email protected]:{your_name_here}/leonardo.git
+    git clone [email protected]:{your_name_here}/leonardo_toolset.git
     ```
 
 3. Install the project in editable mode. (It is also recommended to work in a virtualenv or anaconda environment):
 
     ```bash
-    cd leonardo/
+    cd leonardo_toolset/
     pip install -e .[dev]
     ```
 

MANIFEST.in

@@ -7,4 +7,4 @@ recursive-exclude * __pycache__
 recursive-exclude * *.py[co]
 
 recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif
-graft leonardo/data
+graft leonardo_toolset/data

Makefile

@@ -49,9 +49,9 @@ build: ## run tox / run tests and lint
 	tox
 
 gen-docs: ## generate Sphinx HTML documentation, including API docs
-	rm -f docs/leonardo*.rst
+	rm -f docs/leonardo_toolset*.rst
 	rm -f docs/modules.rst
-	sphinx-apidoc -o docs/ leonardo **/tests/
+	sphinx-apidoc -o docs/ leonardo_toolset **/tests/
 	$(MAKE) -C docs html
 
 docs: ## generate Sphinx HTML documentation, including API docs, and serve to browser

README.md

@@ -1,6 +1,6 @@
 # Leonardo: a toolset to remove sample-induced aberrations in light sheet microscopy images 
 
-[![Build Status](https://github.com/peng-lab/leonardo/workflows/Build%20Main/badge.svg)](https://github.com/peng-lab/leonardo/actions)
+[![Build Status](https://github.com/peng-lab/leonardo_toolset/workflows/Build%20Main/badge.svg)](https://github.com/peng-lab/leonardo_toolset/actions)
 ---
 
 *Leonardo* is a toolbox able to resolve all sample-induced aberrations in selective plane illumination microscopy (SPIM, also called light-sheet fluorescence microscopy, LSFM) by using two major modules: (1) **DeStripe** removes the stripe artifacts caused by light absorption; (2) **FUSE** reconstructs one single high-quality image from dual-sided illumination and/or dual-sided detection while eliminating optical distortions (ghosts) caused by light refraction. 
@@ -11,15 +11,15 @@ https://leonardo-lsfm.readthedocs.io/en/latest/installation.html
 
 ## Installation
 
-**Stable Release:** `pip install leonardo`<br>
-**Development Head:** `pip install git+https://github.com/peng-lab/leonardo.git`
+**Stable Release:** `pip install leonardo_toolset`<br>
+**Development Head:** `pip install git+https://github.com/peng-lab/leonardo_toolset.git`
 
-**Full software including napari plugins:** `pip install leonardo[napari]`<br>
+**Full software including napari plugins:** `pip install leonardo_toolset[napari]`<br>
 
-This **Leonardo** package contains everything you need for using the toolset, including batch processing support for different workflows, such as running destriping then fusion. If you need only one specific component, you can find more info below:
+This **leonardo_toolset** package contains everything you need for using the toolset, including batch processing support for different workflows, such as running destriping then fusion. If you need only one specific component, you can find more info below:
 
 <details>
-    <summary>More details about the Leonardo package</summary>
+    <summary>More details about the leonardo_toolset package</summary>
 
     ## packages for core componets:
 

docs/Makefile

@@ -4,7 +4,7 @@
 # You can set these variables from the command line.
 SPHINXOPTS    =
 SPHINXBUILD   = python -msphinx
-SPHINXPROJ    = leonardo
+SPHINXPROJ    = leonardo_toolset
 SOURCEDIR     = .
 BUILDDIR      = _build
 

docs/conf.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# leonardo documentation build configuration file, created by
+# leonardo_toolset documentation build configuration file, created by
 # sphinx-quickstart on Fri Jun  9 13:47:02 2017.
 #
 # This file is execfile()d with the current directory set to its
@@ -23,7 +23,7 @@
 
 import sphinx_rtd_theme
 
-import leonardo
+import leonardo_toolset
 
 sys.path.insert(0, os.path.abspath(".."))
 
@@ -69,7 +69,7 @@
 master_doc = "index"
 
 # General information about the project.
-project = u"Leonardo"
+project = u"leonardo_toolset"
 copyright = u'2024, Yu Liu'
 author = u"Yu Liu"
 
@@ -78,9 +78,9 @@
 # the built documents.
 #
 # The short X.Y version.
-version = leonardo.__version__
+version = leonardo_toolset.__version__
 # The full version, including alpha/beta/rc tags.
-release = leonardo.__version__
+release = leonardo_toolset.__version__
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -126,7 +126,7 @@
 # -- Options for HTMLHelp output ---------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = "leonardodoc"
+htmlhelp_basename = "leonardo_toolsetdoc"
 
 
 # -- Options for LaTeX output ------------------------------------------
@@ -153,8 +153,8 @@
 # (source start file, target name, title, author, documentclass
 # [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, "leonardo.tex",
-     u"Leonardo Documentation",
+    (master_doc, "leonardo_toolset.tex",
+     u"leonardo_toolset Documentation",
      u"Yu Liu", "manual"),
 ]
 
@@ -164,8 +164,8 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, "leonardo",
-     u"Leonardo Documentation",
+    (master_doc, "leonardo_toolset",
+     u"leonardo_toolset Documentation",
      [author], 1)
 ]
 
@@ -176,10 +176,10 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, "leonardo",
-     u"Leonardo Documentation",
+    (master_doc, "leonardo_toolset",
+     u"leonardo_toolset Documentation",
      author,
-     "leonardo",
+     "leonardo_toolset",
      "One line description of project.",
      "Miscellaneous"),
 ]

docs/index.rst

@@ -1,4 +1,4 @@
-Welcome to Leonardo's documentation!
+Welcome to leonardo_toolset's documentation!
 ======================================
 
 .. toctree::

docs/installation.rst

@@ -8,13 +8,13 @@ Installation
 Stable release
 --------------
 
-To install Leonardo, run this command in your terminal:
+To install leonardo_toolset, run this command in your terminal:
 
 .. code-block:: console
 
-    $ pip install leonardo
+    $ pip install leonardo_toolset
 
-This is the preferred method to install Leonardo, as it will always install the most recent stable release.
+This is the preferred method to install Leonardo_toolset, as it will always install the most recent stable release.
 
 If you don't have `pip`_ installed, this `Python installation guide`_ can guide
 you through the process.
@@ -26,19 +26,19 @@ you through the process.
 From sources
 ------------
 
-The sources for Leonardo can be downloaded from the `Github repo`_.
+The sources for leonardo_toolset can be downloaded from the `Github repo`_.
 
 You can either clone the public repository:
 
 .. code-block:: console
 
-    $ git clone git://github.com/peng-lab/leonardo
+    $ git clone git://github.com/peng-lab/leonardo_toolset
 
 Or download the `tarball`_:
 
 .. code-block:: console
 
-    $ curl  -OL https://github.com/peng-lab/leonardo/tarball/main
+    $ curl  -OL https://github.com/peng-lab/leonardo_toolset/tarball/main
 
 Once you have a copy of the source, you can install it with:
 
@@ -47,5 +47,5 @@ Once you have a copy of the source, you can install it with:
     $ python setup.py install
 
 
-.. _Github repo: https://github.com/peng-lab/leonardo
-.. _tarball: https://github.com/peng-lab/leonardo/tarball/main
+.. _Github repo: https://github.com/peng-lab/leonardo_toolset
+.. _tarball: https://github.com/peng-lab/leonardo_toolset/tarball/main

docs/make.bat

@@ -9,7 +9,7 @@ if "%SPHINXBUILD%" == "" (
 )
 set SOURCEDIR=.
 set BUILDDIR=_build
-set SPHINXPROJ=leonardo
+set SPHINXPROJ=leonardo_toolset
 
 if "%1" == "" goto help
 

leonardo/__init__.py → leonardo_toolset/__init__.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-"""Top-level package for Leonardo."""
+"""Top-level package for leonardo_toolset."""
 
 __author__ = "Yu Liu"
 __email__ = "[email protected]"
@@ -14,3 +14,6 @@ def get_module_version():
 
 
 from .workflows import workflow_wrapper  # noqa: F401
+from lsfm_fuse import FUSE_illu  # noqa: F401
+from lsfm_fuse import FUSE_illu  # noqa: F401
+from lsfm_destripe import DeStripe  # noqa: F401

leonardo_toolset/bin/__init__.py

@@ -0,0 +1,3 @@
+# -*- coding: utf-8 -*-
+
+"""Bin scripts package for leonardo_toolset."""

leonardo/bin/leonardo_workflow.py → leonardo_toolset/bin/leonardo_workflow.py

@@ -11,7 +11,7 @@
 import sys
 import traceback
 
-from leonardo import workflow_wrapper, get_module_version
+from leonardo_toolset import workflow_wrapper, get_module_version
 
 ###############################################################################
 

leonardo_toolset/tests/__init__.py

@@ -0,0 +1,3 @@
+# -*- coding: utf-8 -*-
+
+"""Unit test package for leonardo_toolset."""

setup.cfg

@@ -7,7 +7,7 @@ tag = True
 search = version="{current_version}"
 replace = version="{new_version}"
 
-[bumpversion:file:leonardo/__init__.py]
+[bumpversion:file:leonardo_toolset/__init__.py]
 search = {current_version}
 replace = {new_version}
 

setup.py

@@ -74,23 +74,23 @@
     description="Leonardo: an LSFM image processing toolset",
     entry_points={
         "console_scripts": [
-            "run_leonardo=leonardo.bin.leonardo_workflow:main"
+            "run_leonardo=leonardo_toolset.bin.leonardo_workflow:main"
         ],
     },
     install_requires=requirements,
     license="MIT license",
     long_description=readme,
     long_description_content_type="text/markdown",
     include_package_data=True,
-    keywords="leonardo",
-    name="leonardo",
+    keywords="leonardo_toolset",
+    name="leonardo_toolset",
     packages=find_packages(exclude=["tests", "*.tests", "*.tests.*"]),
     python_requires=">=3.9",
     setup_requires=setup_requirements,
-    test_suite="leonardo/tests",
+    test_suite="leonardo_toolset/tests",
     tests_require=test_requirements,
     extras_require=extra_requirements,
-    url="https://github.com/peng-lab/leonardo",
+    url="https://github.com/peng-lab/leonardo_toolset",
     # Do not edit this string manually, always use bumpversion
     # Details in CONTRIBUTING.rst
     version="0.0.2",

tox.ini

@@ -6,13 +6,13 @@ envlist = py37, py38, py39, lint
 deps =
     .[test]
 commands =
-    flake8 leonardo --count --verbose --show-source --statistics
-    black --check leonardo
+    flake8 leonardo_toolset --count --verbose --show-source --statistics
+    black --check leonardo_toolset
 
 [testenv]
 setenv =
     PYTHONPATH = {toxinidir}
 deps =
     .[test]
 commands =
-    pytest --basetemp={envtmpdir} --cov-report html --cov=leonardo leonardo/tests/
+    pytest --basetemp={envtmpdir} --cov-report html --cov=leonardo_toolset leonardo_toolset/tests/