renamed deepfinder to exodeepfinder

README.md

@@ -1,16 +1,16 @@
-# napari-deepfinder
+# napari-exodeepfinder
 
-[![License GNU GPL v3.0](https://img.shields.io/pypi/l/napari-deepfinder.svg?color=green)](https://github.com/deep-finder/napari-deepfinder/raw/main/LICENSE)
-[![PyPI](https://img.shields.io/pypi/v/napari-deepfinder.svg?color=green)](https://pypi.org/project/napari-deepfinder)
-[![Python Version](https://img.shields.io/pypi/pyversions/napari-deepfinder.svg?color=green)](https://python.org)
-[![tests](https://github.com/deep-finder/napari-deepfinder/workflows/tests/badge.svg)](https://github.com/deep-finder/napari-deepfinder/actions)
-[![codecov](https://codecov.io/gh/deep-finder/napari-deepfinder/branch/main/graph/badge.svg)](https://codecov.io/gh/deep-finder/napari-deepfinder)
-[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-deepfinder)](https://napari-hub.org/plugins/napari-deepfinder)
+[![License GNU GPL v3.0](https://img.shields.io/pypi/l/napari-exodeepfinder.svg?color=green)](https://github.com/deep-finder/napari-exodeepfinder/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/napari-exodeepfinder.svg?color=green)](https://pypi.org/project/napari-exodeepfinder)
+[![Python Version](https://img.shields.io/pypi/pyversions/napari-exodeepfinder.svg?color=green)](https://python.org)
+[![tests](https://github.com/deep-finder/napari-exodeepfinder/workflows/tests/badge.svg)](https://github.com/deep-finder/napari-exodeepfinder/actions)
+[![codecov](https://codecov.io/gh/deep-finder/napari-exodeepfinder/branch/main/graph/badge.svg)](https://codecov.io/gh/deep-finder/napari-exodeepfinder)
+[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-exodeepfinder)](https://napari-hub.org/plugins/napari-exodeepfinder)
 
-A napari plugin for the DeepFinder library which includes display, annotation, target generation, segmentation and clustering functionalities.
+A napari plugin for the ExoDeepFinder library which includes display, annotation, target generation, segmentation and clustering functionalities.
 An orthoslice view has been added for an easier visualisation and annotation process.
 
-**The documentation for users is available [here](https://deep-finder.github.io/napari-deepfinder/).**
+**The documentation for users is available [here](https://deep-finder.github.io/napari-exodeepfinder/).**
 
 ----------------------------------
 
@@ -26,15 +26,9 @@ https://napari.org/plugins/index.html
 
 ## Installation
 
-You can install `napari-deepfinder` via [pip]:
-
-    pip install napari-deepfinder
-
-
-
-To install latest development version :
-
-    pip install git+https://github.com/deep-finder/napari-deepfinder.git
+1. Create a conda environment with python 3.10: `conda create -n napari-exodeepfinder python=3.10`
+1. Activate the environment: `conda activate napari-exodeepfinder`
+1. Install napari: `pip install napari-exodeepfinder`
 
 
 ## Contributing
@@ -45,7 +39,7 @@ the coverage at least stays the same before you submit a pull request.
 ## License
 
 Distributed under the terms of the [GNU GPL v3.0] license,
-"napari-deepfinder" is free and open source software
+"napari-exodeepfinder" is free and open source software
 
 ## Issues
 
@@ -62,7 +56,7 @@ If you encounter any problems, please [file an issue] along with a detailed desc
 [Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
 [cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin
 
-[file an issue]: https://github.com/deep-finder/napari-deepfinder/issues
+[file an issue]: https://github.com/deep-finder/napari-exodeepfinder/issues
 
 [napari]: https://github.com/napari/napari
 [tox]: https://tox.readthedocs.io/en/latest/

docs/about.rst

@@ -1,8 +1,6 @@
 About
 =====
 
-`napari-deepfinder` is a napari plugin for the `DeepFinder library <https://deepfinder.readthedocs.io/en/latest/>`_ which includes display, annotation, target generation,
-segmentation and clustering functionalities. An orthoslice view has been added for an easier visualisation and
-annotation process.
+`napari-exodeepfinder` is a napari plugin for [ExoDeepFinder](https://github.com/deep-finder/tirfm-deepfinder) which includes display, annotation, target generation, segmentation and clustering functionalities. An orthoslice view has been added for an easier visualisation and annotation process.
 
-The source code of `napari-deepfinder` is available `here <https://github.com/deep-finder/napari-deepfinder>`_ and the source code of the `DeepFinder` library itself is available `here <https://gitlab.inria.fr/serpico/deep-finder>`_.
+The source code of `napari-exodeepfinder` is available [here](https://github.com/deep-finder/napari-exodeepfinder) and the source code of the `ExoDeepFinder` library itself is available [here](https://github.com/deep-finder/tirfm-deepfinder).

docs/conf.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-# napari-deepfinder documentation build configuration file
+# napari-exodeepfinder documentation build configuration file
 #
 # This file is execfile()d with the current directory set to its
 # containing dir.
@@ -46,8 +46,8 @@
 master_doc = 'index'
 
 # General information about the project.
-project = u'napari-deepfinder'
-copyright = u'2023, napari-deepfinder'
+project = u'napari-exodeepfinder'
+copyright = u'2023, napari-exodeepfinder'
 author = u'Constantin Aronssohn'
 
 # The version info for the project you're documenting, acts as replacement for
@@ -253,7 +253,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, 'napari-cookiecutterplugin_name', u'napari-deepfinder Documentation',
+    (master_doc, 'napari-cookiecutterplugin_name', u'napari-exodeepfinder Documentation',
      [author], 1)
 ]
 
@@ -267,7 +267,7 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-  (master_doc, 'napari-cookiecutterplugin_name', u'napari-deepfinder Documentation',
+  (master_doc, 'napari-cookiecutterplugin_name', u'napari-exodeepfinder Documentation',
    author, 'napari-cookiecutterplugin_name', 'One line description of project.',
    'Miscellaneous'),
 ]

docs/developers.rst

@@ -4,13 +4,13 @@ Developers
 Readers
 -------
 
-.. automodule:: napari_deepfinder._reader
+.. automodule:: napari_exodeepfinder._reader
    :members:
 
 Writers
 -------
 
-.. automodule:: napari_deepfinder._writer
+.. automodule:: napari_exodeepfinder._writer
    :members:
 
 Widgets
@@ -19,28 +19,28 @@ Widgets
 Reorder layers
 ++++++++++++++
 
-.. autofunction:: napari_deepfinder._widget::reorder_widget
+.. autofunction:: napari_exodeepfinder._widget::reorder_widget
 
 Denoising
 +++++++++
 
-.. autofunction:: napari_deepfinder._widget::denoise_widget
+.. autofunction:: napari_exodeepfinder._widget::denoise_widget
 
 Annotation
 ++++++++++
 
-.. autoclass:: napari_deepfinder._widget::AddPointsWidget
+.. autoclass:: napari_exodeepfinder._widget::AddPointsWidget
    :members:
 
 Segmentation
 ++++++++++++
 
-.. automodule:: napari_deepfinder._segmentation_widget
+.. automodule:: napari_exodeepfinder._segmentation_widget
    :members:
 
 Clustering
 ++++++++++
 
-.. automodule:: napari_deepfinder._cluster_widget
+.. automodule:: napari_exodeepfinder._cluster_widget
    :members:
 

docs/guide.rst

@@ -7,14 +7,14 @@ General purpose visualisation
 Open files
 ++++++++++
 
-Once `napari-deepfinder` is installed, you will be able to open the files associated with the cryo-et workflow:
+Once `napari-exodeepfinder` is installed, you will be able to open the files associated with the cryo-et workflow:
 
 * Tomograms and segmentation maps as `.mrc`, `.map`, `.rec`, `.h5`, `.tif` or `.TIF`
 * Annotation object lists as `.xml`, `.ods`, `.xls` or `.xlsx`
 
 .. note:: The following features are all different widgets included in the plugin.
 
-    To open them, click on the `Plugins` menu of napari, select napari-deepfinder` and you will see the list of widgets available.
+    To open them, click on the `Plugins` menu of napari, select napari-exodeepfinder` and you will see the list of widgets available.
     Click on the desired widget of this list to enable or disable it!
 
 Automatic reordering of layers
@@ -60,13 +60,13 @@ From the widget you can:
 Inference phase
 ---------------
 
-.. important:: This phase is only possible once DeepFinder has been trained, training does not happen in this plugin.
+.. important:: This phase is only possible once ExoDeepFinder has been trained, training does not happen in this plugin.
 
 Segmentation
 ++++++++++++
 The `Segmentation` widget serves as a graphical user interface to generate a segmentation map based on the trained DeepFinder model.
 You need to select the file containing the weights of the network and set other parameters.
-Those parameters are mostly explained here: https://deepfinder.readthedocs.io/en/latest/guide.html#segmentation.
+Those parameters are explained here: https://deepfinder.readthedocs.io/en/latest/guide.html#segmentation.
 
 .. important:: Be aware that this step might last several minutes and consume a lot of RAM and computing ressources
     (you can play with the patch size to optimize the segmentation time:

docs/help.rst

@@ -2,4 +2,4 @@ Getting help
 ============
 
 If you discover a bug with the plugin, would like to request a new feature, or need some help,
-please raise an issue on our repository at https://github.com/deep-finder/napari-deepfinder/issues.
+please raise an issue on our repository at https://github.com/deep-finder/napari-exodeepfinder/issues.

docs/index.rst

@@ -1,5 +1,5 @@
 
-Welcome to napari-deepfinder's documentation!
+Welcome to napari-exodeepfinder's documentation!
 ===============================================================
 
 Contents:

docs/quickstart.rst

@@ -7,19 +7,19 @@ A clean environment
 First of all you need a working installation of napari, you can refer to that webpage for more info https://napari.org/#installation .
 
 It is strongly recommended to work with virtual environments (such as virtualenv or conda).
-You can create a new environment especially for your work with `napari-deepfinder`.
-This is really useful and advised, especially because `napari-deepfinder` will install a lot of dependencies (including deepfinder and it's dependencies).
+You can create a new environment especially for your work with `napari-exodeepfinder`.
+This is really useful and advised, especially because `napari-exodeepfinder` will install a lot of dependencies (including ExoDeepFinder and it's dependencies).
 
-Installation of `napari-deepfinder`
+Installation of `napari-exodeepfinder`
 -----------------------------------
 
 The general purpose guide for installing napari plugins is available `here <https://napari.org/plugins/find_and_install_plugin.html>`_.
 
 Basically you need to start napari and go in the plugin menu. There you will find the `Install/Uninstall Plugins` entry, which once clicked opens a new dedicated window.
 There you can either:
 
- * Enter the name `napari-deepfinder`
- * Enter the url https://github.com/deep-finder/napari-deepfinder
+ * Enter the name `napari-exodeepfinder`
+ * Enter the url https://github.com/deep-finder/napari-exodeepfinder
  * Drag and drop the folder of a downloaded copy of the source code of the plugin
 
 .. raw:: html
@@ -28,9 +28,9 @@ There you can either:
    <summary><a>Command line installation for more advanced users</a></summary>
 
 You can also install the plugin through the command line in the virtual environment by using `pip <https://pypi.org/project/pip/>`_:
-    ``pip install napari-deepfinder``
+    ``pip install napari-exodeepfinder``
 or (for the latest development version):
-    ``pip install git+https://github.com/deep-finder/napari-deepfinder.git``
+    ``pip install git+https://github.com/deep-finder/napari-exodeepfinder.git``
 
 .. raw:: html
 

pyproject.toml

@@ -2,8 +2,6 @@
 requires = ["setuptools", "wheel"]
 build-backend = "setuptools.build_meta"
 
-
-
 [tool.black]
 line-length = 79
 

setup.cfg

@@ -1,11 +1,11 @@
 [metadata]
-name = napari-deepfinder
+name = napari-exodeepfinder
 version = 0.0.1
-author = Constantin Aronssohn
+author = Constantin Aronssohn, Arthur Masson
 author_email = [email protected]
-url = https://github.com/deep-finder/napari-deepfinder
+url = https://github.com/deep-finder/napari-exodeepfinder
 license = GPL-3.0-only
-description = A napari plugin for the DeepFinder library which includes display, annotation, target generation, segmentation and clustering functionalities. An orthoslice view has been added for an easier visualisation and annotation process.
+description = A napari plugin for the ExpDeepFinder library which includes display, annotation, target generation, segmentation and clustering functionalities. An orthoslice view has been added for an easier visualisation and annotation process.
 long_description = file: README.md
 long_description_content_type = text/markdown
 classifiers =
@@ -27,10 +27,10 @@ classifiers =
     Operating System :: OS Independent
     License :: OSI Approved :: GNU General Public License v3 (GPLv3)
 project_urls =
-    Bug Tracker = https://github.com/deep-finder/napari-deepfinder/issues
-    Documentation = https://deep-finder.github.io/napari-deepfinder/
-    Source Code = https://github.com/deep-finder/napari-deepfinder
-    User Support = https://github.com/deep-finder/napari-deepfinder/issues
+    Bug Tracker = https://github.com/deep-finder/napari-exodeepfinder/issues
+    Documentation = https://deep-finder.github.io/napari-exodeepfinder/
+    Source Code = https://github.com/deep-finder/napari-exodeepfinder
+    User Support = https://github.com/deep-finder/napari-exodeepfinder/issues
 
 [options]
 packages = find:
@@ -41,7 +41,7 @@ package_dir =
 
 # add your package requirements here
 install_requires =
-    cryoet-deepfinder @ git+ssh://[email protected]:deep-finder/cryoet-deepfinder.git
+    exodeepfinder
     numpy
     magicgui
     qtpy
@@ -55,7 +55,6 @@ install_requires =
     mrcfile
     scipy
 
-
 [options.extras_require]
 testing =
     tox
@@ -71,4 +70,4 @@ where = src
 
 [options.entry_points]
 napari.manifest =
-    napari-deepfinder = napari_deepfinder:napari.yaml
+    napari-exodeepfinder = napari_exodeepfinder:napari.yaml

src/napari_deepfinder/_cluster_widget.py → src/napari_exodeepfinder/_cluster_widget.py

@@ -125,7 +125,7 @@ def launch_process(self):
         return path_objl
 
     def add_cluster(self, path):
-        self.viewer.open(path, plugin='napari-deepfinder')
+        self.viewer.open(path, plugin='napari-exodeepfinder')
         self._launch_clustering.setEnabled(True)
 
     def _run(self):

src/napari_deepfinder/_tests/test_reader.py → src/napari_exodeepfinder/_tests/test_reader.py

@@ -1,4 +1,4 @@
-from napari_deepfinder import napari_get_reader
+from napari_exodeepfinder import napari_get_reader
 import numpy as np
 import mrcfile
 

src/napari_deepfinder/_tests/test_widget.py → src/napari_exodeepfinder/_tests/test_widget.py

@@ -4,7 +4,7 @@
 from scipy.ndimage import uniform_filter
 from qtpy import QtCore
 
-from napari_deepfinder import (
+from napari_exodeepfinder import (
     AddPointsWidget,
     ClusterWidget,
     Orthoslice,