REL: Release 1.0.0

.gitignore

@@ -66,6 +66,7 @@ instance/
 
 # Sphinx documentation
 docs/_build/
+docs/_notebooks/
 docs/_autosummary/
 
 # PyBuilder

.readthedocs.yml

@@ -27,6 +27,7 @@ build:
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: "3.7"
+  version: "3.8"
   install:
       - requirements: requirements.txt
+      - requirements: docs/requirements.txt

.travis.yml

@@ -47,6 +47,7 @@ deploy:
   - provider: pypi
     server: https://test.pypi.org/legacy/
     distributions: sdist bdist_wheel
+    skip_existing: true
     user: __token__
     password:
       secure: a5EoBz4NAQWB0EmgQCKpDRtISy76uNt2dWYZURzTW5v7V2GHyP+drNDWW5HNN0qoLK8pYXBGS47DqJtNDD0+k4G1ogINQKTENWI/oAxXrI8mwAAEhp+2uhHBGSWUX0jlnfRD3VX3M4zSy0DEszGONrJMiJyfRAKNa+P1FPp7AFjRKh8keivCLXgL3Y27OfyBKf4wgy/EnlK2P/BkO9fhPLfDNdBAXikrOCTmG7b0MIRpSXdOqtgo0QtR8t2tQnekke14iH4oTlhEMq2+X875Fejg3n686mXvmTrenLNyZiO0PW4MXAsc5PEES3F2yyLVyk9tHhp54eBErhg60jr2q5GqkX+QBA9wooXcWoLdB+fKJbv4I4XtiMQ68B/1RLvQwWTUjMp520eFBc1dD3HiCEj0KuoplaxFWAgJoAAawC6/TrSpACgb1Cw1M5XcOb3dzUN4hduuvYp8emcixmc0mufrK1QU62u9320rMMF7HZJuLCg4GVHryWqBlc6u6kQrmnF+xU36ms0Deamjzb96TfA2W+DEG2N2dtxmbYEIaLyKZnpLhCV5FZDai4AK5nW9Hst6w/dDU7kYiHwM962ArEKApFuoF4mbNJe3EALR2xlNINZRaEqY+XPXtjODY7g/3bajsDfxEjKB9RTBxq9mL49ioxlXGRTvS7VhU+n6BE0=

AUTHORS.md

@@ -12,12 +12,13 @@ Development Lead
 - Mostafa Jahanifar <mostafajahanifar>
 - David Epstein <DavidBAEpstein>
 - Srijay Deshpande <Srijay-lab>
+- George Hadjigeorgiou <ghadjigeorghiou>
+- Adam Shephard <adamshephard>
+- Wenqi Lu <wenqi006>
 - Saad Bashir <rajasaad>
 
 Contributors
 ------------
 
-- George Hadjigeorgiou <ghadjigeorghiou>
 - Rob Jewsbury <R-J96>
-- Jev Gamper <jgamper>
-
+- Mohsin Bilal <>

CITATION.cff

@@ -0,0 +1,49 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+- family-names: "Pocock"
+  given-names: "Johnathan"
+  orcid: "https://orcid.org/0000-0002-2866-981X"
+- family-names: "Graham"
+  given-names: "Simon"
+  orcid: "https://orcid.org/0000-0002-2214-8212"
+- family-names: "Vu"
+  given-names: "Quoc Dang"
+  orcid: "https://orcid.org/0000-0003-2075-9201"
+- family-names: "Jahanifar"
+  given-names: "Mostafa"
+  orcid: "https://orcid.org/0000-0001-5842-0460"
+- family-names: "Deshpande"
+  given-names: "Srijay"
+  orcid: "https://orcid.org/0000-0003-3923-2944"
+- family-names: "Hadjigeorghiou"
+  given-names: "Giorgios"
+  orcid: "https://orcid.org/0000-0003-2734-8915"
+- family-names: "Shephard"
+  given-names: "Adam"
+  orcid: "https://orcid.org/0000-0003-0969-2990"
+- family-names: "Bashir"
+  given-names: "Raja Muhammad Saad"
+  orcid: "https://orcid.org/0000-0002-8984-696"
+- family-names: "Bilal"
+  given-names: "Mohsin"
+  orcid: "https://orcid.org/0000-0001-8632-2729"
+- family-names: "Lu"
+  given-names: "Wenqi"
+  orcid: "https://orcid.org/0000-0002-7838-0918"
+- family-names: "Epstein"
+  given-names: "David"
+  orcid: "https://orcid.org/0000-0001-8634-7168"
+- family-names: "Minhas"
+  given-names: "Fayyaz"
+  orcid: "https://orcid.org/0000-0001-9129-1189"
+- family-names: "Rajpoot"
+  given-names: "Nasir M."
+  orcid: "https://orcid.org/0000-0002-4706-1308"
+- family-names: "Raza"
+  given-names: "Shan E Ahmed"
+  orcid: "https://orcid.org/0000-0002-1097-1738"
+title: "TIAToolbox: An End-to-End Toolbox for Advanced Tissue Image Analytics"
+version: 1.0.0
+date-released: 2021-12-23
+url: "https://github.com/TissueImageAnalytics/tiatoolbox"

HISTORY.md

@@ -1,6 +1,46 @@
 History
 =======
 
+1.0.0 (2021-12-23)
+------------------
+### Major Updates and Feature Improvements
+- Adds nucleus instance segmentation base class
+  - Adds  [HoVerNet](https://www.sciencedirect.com/science/article/abs/pii/S1361841519301045) architecture
+- Adds multi-task segmentor [HoVerNet+](https://arxiv.org/abs/2108.13904) model
+- Adds <a href="https://www.thelancet.com/journals/landig/article/PIIS2589-7500(2100180-1/fulltext">IDaRS</a> pipeline
+- Adds [SlideGraph](https://arxiv.org/abs/2110.06042) pipeline
+- Adds PCam patch classification models
+- Adds support for stain augmentation feature
+- Adds classes and functions under `tiatoolbox.tools.graph` to enable construction of graphs in a format which can be used with PyG (PyTorch Geometric).
+- Add classes which act as a mutable mapping (dictionary like) structure and enables efficient management of annotations. (#135)
+- Adds example notebook for adding advanced models
+- Adds classes which can generate zoomify tiles from a WSIReader object.
+- Adds WSI viewer using Zoomify/WSIReader API (#212)
+- Adds README to example page for clarity
+- Adds support to override or specify mpp and power
+
+### Changes to API
+- Replaces `models.controller` API with `models.engine`
+- Replaces `CNNPatchPredictor` with `PatchPredictor`
+
+### Bug Fixes and Other Changes
+- Fixes  Fix `filter_coordinates` read wrong resolutions for patch extraction
+- For `PatchPredictor`
+  - `ioconfig` will supersede everything
+  - if `ioconfig` is not provided
+    - If `model` is pretrained (defined in `pretrained_model.yaml` )
+      - Use the yaml ioconfig
+      - Any other input patch reading arguments will overwrite the yaml ioconfig (at the same keyword).
+    - If `model` is not defined, all input patch reading arguments must be provided else exception will be thrown.
+- Improves performance of mask based patch extraction
+
+### Development related changes
+- Improve tests performance for Travis runs
+- Adds feature detection mechanism to detect the platform and installed packages etc.
+- On demand imports for some libraries for performance
+- Improves performance of mask based patch extraction
+
+
 0.8.0 (2021-10-27)
 ------------------
 ### Major Updates and Feature Improvements

Makefile

@@ -57,12 +57,13 @@ test-all: ## run tests on every Python version with tox
 	tox
 
 coverage: ## check code coverage quickly with the default Python
-	pytest  --cov=tiatoolbox --cov-report=term --cov-report=html
+	pytest  --cov=tiatoolbox --cov-report=term --cov-report=html --cov-report=xml
 	$(BROWSER) htmlcov/index.html
 
 docs: ## generate Sphinx HTML documentation, including API docs
 	rm -f docs/tiatoolbox.rst
 	rm -f docs/modules.rst
+	rm -f docs/_autosummary
 	sphinx-apidoc -o docs/ tiatoolbox
 	$(MAKE) -C docs clean
 	$(MAKE) -C docs html

README.md

@@ -1,5 +1,5 @@
 <p align="center">
-  <img src="https://raw.githubusercontent.com/TissueImageAnalytics/tiatoolbox/develop/docs/tia_logo.png">
+  <img src="https://raw.githubusercontent.com/TissueImageAnalytics/tiatoolbox/develop/docs/tiatoolbox-logo.png">
 </p>
 <h1 align="center">TIA Toolbox</h1>
 <p align="center">
@@ -35,8 +35,7 @@ Anyone wanting to contribute to this repository, please first look at our [Wiki]
 ### Links, if needed
 The [bash](https://www.gnu.org/software/bash) shell is available on all commonly encountered platforms. Commands in this README are in bash. Windows users can use the command prompt to install conda and python packages.
 
-
-[`conda`](https://github.com/conda/conda) is a management system for software packages and [virtual environments](https://docs.conda.io/projects/conda/en/latest/user-guide/concepts/environments.html). To get `conda`, download [Anaconda](https://www.anaconda.com/), which includes hundreds of the most useful Python packages, using 2GB disk space. Alternatively, [miniconda](https://docs.conda.io/en/latest/miniconda.html) uses 400MB, and packages can be added as needed.
+[conda](https://github.com/conda/conda) is a management system for software packages and [virtual environments](https://docs.conda.io/projects/conda/en/latest/user-guide/concepts/environments.html). To get `conda`, download [Anaconda](https://www.anaconda.com/), which includes hundreds of the most useful Python packages, using 2GB disk space. Alternatively, [miniconda](https://docs.conda.io/en/latest/miniconda.html) uses 400MB, and packages can be added as needed.
 
 [Github](https://github.com/about) is powered by the version control system [git](https://git-scm.com/), which has many users and uses. In Github, it is used to track versions of code and other documents.
 
@@ -62,13 +61,44 @@ tiatoolbox supports various features through command line. For more information,
 ### Prepare for development
 
 Prepare a computer as a convenient platform for further development of the Python package `tiatoolbox` and related programs as follows.
-1. Open a `bash` terminal window<br/>
-`cd <future-home-of-tiatoolbox-directory>` <br/>
-2. Download a complete copy of the `tiatoolbox`.<br/>`git clone https://github.com/TissueImageAnalytics/tiatoolbox.git`<br/>
-3. `cd tiatoolbox`
-4. `conda env create -f requirements.conda.yml`<br/>
-creates the virtual environment `tiatoolbox`. Details in the text file `requirements.conda.yml`
-5. To use the packages installed in the environment, run the command:<br/>`conda activate tiatoolbox`
+1. Install [pre-requisite software](https://tia-toolbox.readthedocs.io/en/latest/installation.html)
+2. Open a terminal window<br/>
+
+```sh
+    $ cd <future-home-of-tiatoolbox-directory>
+```
+
+3. Download a complete copy of the `tiatoolbox`.
+
+```sh
+    $ git clone https://github.com/TissueImageAnalytics/tiatoolbox.git
+```
+
+4. Change directory to `tiatoolbox`
+
+```sh
+    $ cd tiatoolbox
+```
+
+5. Create virtual environment for TIAToolbox using
+
+```sh
+    $ conda env create -f requirements.dev.conda.yml # for linux/mac only.
+    $ conda activate tiatoolbox-dev
+```
+or
+
+```sh
+    $ conda create -n tiatoolbox-dev python=3.8 # select version of your choice
+    $ conda activate tiatoolbox-dev
+    $ pip install -r requirements_dev.txt
+```
+6. To use the packages installed in the environment, run the command:
+
+```sh
+    $ conda activate tiatoolbox-dev
+```
+
 
 ### License
 
@@ -80,7 +110,7 @@ The full text of the licence is included in [LICENSE.md](https://raw.githubuserc
 
 ### Auxiliary Files
 
-Auxiliary files, such as pre-trained model weights downloaded from the TIA Centre webpage (https://warwick.ac.uk/fac/cross_fac/tia/), are provided under the [Creative Commons Attribution-NonCommercial-ShareAlike Version 4 (CC BY-NC-SA 4.0) license](https://creativecommons.org/licenses/by-nc-sa/4.0/).
+Auxiliary files, such as pre-trained model weights downloaded from the TIA Centre webpage (https://warwick.ac.uk/tia/), are provided under the [Creative Commons Attribution-NonCommercial-ShareAlike Version 4 (CC BY-NC-SA 4.0) license](https://creativecommons.org/licenses/by-nc-sa/4.0/).
 
 ### Dual License
 

docs/Makefile

@@ -3,7 +3,7 @@
 
 # You can set these variables from the command line.
 SPHINXOPTS    =
-SPHINXBUILD   = python -msphinx
+SPHINXBUILD   = sphinx-build
 SPHINXPROJ    = tiatoolbox
 SOURCEDIR     = .
 BUILDDIR      = _build
@@ -17,4 +17,9 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
+	rm -rf _build
+	rm -rf _notebooks
+	rm -rf _autosummary
+	mkdir _autosummary
+	cp -r images _autosummary/images
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/_templates/custom-class-template.rst

@@ -0,0 +1,43 @@
+{{ fullname.split('.')[-1] | escape | underline}}
+
+{% for idx in range(fullname.split('.')[:-1]|length) %}
+   :py:mod:{{'`~'+ '.'.join(fullname.split('.')[:(idx+1)]) + '`'}} .
+{%- endfor %}
+   :py:mod:{{'`~'+ fullname + '`'}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+   :members:
+   :special-members: __call__, __add__, __mul__
+
+   {% block methods %}
+   {% if methods %}
+   .. rubric:: {{ _('Methods') }}
+
+   .. autosummary::
+      :nosignatures:
+   {% for item in methods %}
+      {%- if item not in inherited_members %}
+         {%- if not item.startswith('_') %}
+            ~{{ name }}.{{ item }}
+         {%- endif -%}
+      {%- endif %}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: {{ _('Attributes') }}
+
+   .. autosummary::
+   {% for item in attributes %}
+      {%- if item not in inherited_members %}
+         {%- if not item.startswith('_') %}
+            ~{{ name }}.{{ item }}
+         {%- endif -%}
+      {%- endif %}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}

docs/_templates/custom-function-template.rst

@@ -0,0 +1,10 @@
+{{ fullname.split('.')[-1] | escape | underline }}
+
+{% for idx in range(fullname.split('.')[:-1]|length) %}
+   :py:mod:{{'`~'+ '.'.join(fullname.split('.')[:(idx+1)]) + '`'}} .
+{%- endfor %}
+   :py:mod:{{'`~'+ fullname + '`'}}
+
+.. currentmodule:: {{ module }}
+
+.. auto{{ objtype }}:: {{ objname }}

docs/_templates/custom-module-template.rst

@@ -0,0 +1,72 @@
+{{ fullname.split('.')[-1] | escape | underline }}
+
+{% for idx in range(fullname.split('.')[:-1]|length) %}
+   :py:mod:{{'`~'+ '.'.join(fullname.split('.')[:(idx+1)]) + '`'}} .
+{%- endfor %}
+   :py:mod:{{'`~'+ fullname + '`'}}
+
+.. automodule:: {{ fullname }}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: Module attributes
+
+   .. autosummary::
+      :toctree:
+   {% for item in attributes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block functions %}
+   {% if functions %}
+   .. rubric:: {{ _('Functions') }}
+
+   .. autosummary::
+      :toctree:
+      :template: custom-function-template.rst
+      :nosignatures:
+   {% for item in functions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block classes %}
+   {% if classes %}
+   .. rubric:: {{ _('Classes') }}
+
+   .. autosummary::
+      :toctree:
+      :template: custom-class-template.rst
+      :nosignatures:
+   {% for item in classes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block exceptions %}
+   {% if exceptions %}
+   .. rubric:: {{ _('Exceptions') }}
+
+   .. autosummary::
+      :toctree:
+   {% for item in exceptions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+{% block modules %}
+{% if modules %}
+.. autosummary::
+   :toctree:
+   :template: custom-module-template.rst
+   :recursive:
+{% for item in modules %}
+   {{ item }}
+{%- endfor %}
+{% endif %}
+{% endblock %}