move more to inside dev_resources

mattclifford1 · Oct 9, 2024 · b527760 · b527760
1 parent 35ca1dd
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Showing 225 changed files with 48 additions and 48 deletions.
diff --git a/.github/workflows/deploy-package-to-PyPi.yml b/.github/workflows/deploy-package-to-PyPi.yml
@@ -21,8 +21,8 @@ jobs:
     - uses: actions/checkout@v3
     - name: Get Version numbers
       run: |
-        echo "code_version=$(./scripts/get_local_version.py)" >> $GITHUB_ENV
-        echo "pypi_version=$(./scripts/get_latest_pypi_version.py)" >> $GITHUB_ENV
+        echo "code_version=$(./dev_resources/scripts/get_local_version.py)" >> $GITHUB_ENV
+        echo "pypi_version=$(./dev_resources/scripts/get_latest_pypi_version.py)" >> $GITHUB_ENV
 
     - name: Set up Python
       if: env.code_version != env.pypi_version

diff --git a/.github/workflows/publish-documentation.yml b/.github/workflows/publish-documentation.yml
@@ -1,6 +1,6 @@
 # Deploy documentation when a new VERSION is release to the main branch
-# N.B. currently doesn't build the docs: need to do that locally with
-# ./scrips/make_docs.sh
+# N.B. currently doesn't build the dev_resources/docs: need to do that locally with
+# ./scrips/make_dev_resources/docs.sh
 # Author: Matt Clifford <[email protected]>
 # License: BSD 3-Clause License
 
@@ -16,14 +16,14 @@ permissions:
     contents: write
 
 jobs:
-  docs:
+  dev_resources/docs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
       - name: Get Version numbers
         run: |
           echo "code_version=$(cat VERSION)" >> $GITHUB_ENV
-          echo "pypi_version=$(./scripts/get_latest_pypi_version.py)" >> $GITHUB_ENV
+          echo "pypi_version=$(./dev_resources/scripts/get_latest_pypi_version.py)" >> $GITHUB_ENV
 
       # - name: Setup Python
       #   uses: actions/setup-python@v3
@@ -54,9 +54,9 @@ jobs:
       #
       # - name: Sphinx build
       #   run: |
-      #     rm docs/IQM_Vis.*
-      #     sphinx-apidoc -o docs IQM_Vis
-      #     cd docs
+      #     rm dev_resources/docs/IQM_Vis.*
+      #     sphinx-apidoc -o dev_resources/docs IQM_Vis
+      #     cd dev_resources/docs
       #     make clean html
       #     make html
 
@@ -66,4 +66,4 @@ jobs:
         with:
           publish_branch: gh-pages
           github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: docs/_build/html
+          publish_dir: dev_resources/docs/_build/html
diff --git a/.gitignore b/.gitignore
@@ -81,7 +81,7 @@ instance/
 .scrapy
 
 # Sphinx documentation
-# docs/_build/
+# dev_resources/docs/_build/
 
 # PyBuilder
 target/
@@ -129,7 +129,7 @@ venv.bak/
 # Rope project settings
 .ropeproject
 
-# mkdocs documentation
+# mkdev_resources/docs documentation
 /site
 
 # mypy

diff --git a/IQM_Vis/transforms/effects.py b/IQM_Vis/transforms/effects.py
@@ -69,8 +69,8 @@ def jpeg_compression(image, compression=101):
 def _encode_compression(image, encoder, encode_param, uint=True):
     '''
         generic image encoder for jpeg, png etc
-        using https://docs.opencv.org/3.4/d4/da8/group__imgcodecs.html to encode/decode
-        for encode types: https://docs.opencv.org/3.4/d6/d87/imgcodecs_8hpp.html
+        using https://dev_resources/docs.opencv.org/3.4/d4/da8/group__imgcodecs.html to encode/decode
+        for encode types: https://dev_resources/docs.opencv.org/3.4/d6/d87/imgcodecs_8hpp.html
     '''
     original_size = image.shape
     if uint == True:

diff --git a/IQM_Vis/ui_wrapper.py b/IQM_Vis/ui_wrapper.py
@@ -1,6 +1,6 @@
 '''
 API to access making the PyQt6 UI for IQM-Vis
-TODO: write docs on example usage/ what inputs etc. and what attributes that the data_store class needs
+TODO: write dev_resources/docs on example usage/ what inputs etc. and what attributes that the data_store class needs
 '''
 # Author: Matt Clifford <[email protected]>
 # License: BSD 3-Clause License

diff --git a/IQM_Vis/utils/plot_utils.py b/IQM_Vis/utils/plot_utils.py
@@ -1,6 +1,6 @@
 '''
 matplotlib plotting helpers
-TODO: write docs how to use these (currently just have to look at the UI code)
+TODO: write dev_resources/docs how to use these (currently just have to look at the UI code)
 '''
 # Author: Matt Clifford <[email protected]>
 # License: BSD 3-Clause License

diff --git a/README.md b/README.md
@@ -12,7 +12,7 @@
 # IQM-Vis
 Image Quality Metric Visualision. An extendable user interface for the assessment of transformations on image metrics.
 
-Head over to the [DOCUMENTATION](https://mattclifford1.github.io/IQM-Vis/) for tutorials and package reference. Read our [PAPER](https://github.com/mattclifford1/IQM-Vis/blob/main/docs/resources/Software_paper.pdf) for in depth details of the software.
+Head over to the [DOCUMENTATION](https://mattclifford1.github.io/IQM-Vis/) for tutorials and package reference. Read our [PAPER](https://github.com/mattclifford1/IQM-Vis/blob/main/dev_resources/docs/resources/Software_paper.pdf) for in depth details of the software.
 
 ### IQM's average sensitivity to tranforms
 ![Alt text](https://github.com/mattclifford1/IQM-Vis/blob/main/dev_resources/pics/data_graphs.gif?raw=true "Dataset UI") 

diff --git a/docs/.nojekyll → dev_resources/docs/.nojekyll b/docs/.nojekyll → dev_resources/docs/.nojekyll
diff --git a/docs/IQM_Vis.UI.rst → dev_resources/docs/IQM_Vis.UI.rst b/docs/IQM_Vis.UI.rst → dev_resources/docs/IQM_Vis.UI.rst
diff --git a/docs/IQM_Vis.data_handlers.rst → dev_resources/docs/IQM_Vis.data_handlers.rst b/docs/IQM_Vis.data_handlers.rst → dev_resources/docs/IQM_Vis.data_handlers.rst
diff --git a/docs/IQM_Vis.examples.images.rst → ...esources/docs/IQM_Vis.examples.images.rst b/docs/IQM_Vis.examples.images.rst → ...esources/docs/IQM_Vis.examples.images.rst
diff --git a/docs/IQM_Vis.examples.rst → dev_resources/docs/IQM_Vis.examples.rst b/docs/IQM_Vis.examples.rst → dev_resources/docs/IQM_Vis.examples.rst
diff --git a/docs/IQM_Vis.metrics.SSIM.rst → dev_resources/docs/IQM_Vis.metrics.SSIM.rst b/docs/IQM_Vis.metrics.SSIM.rst → dev_resources/docs/IQM_Vis.metrics.SSIM.rst
diff --git a/docs/IQM_Vis.metrics.rst → dev_resources/docs/IQM_Vis.metrics.rst b/docs/IQM_Vis.metrics.rst → dev_resources/docs/IQM_Vis.metrics.rst
diff --git a/docs/IQM_Vis.rst → dev_resources/docs/IQM_Vis.rst b/docs/IQM_Vis.rst → dev_resources/docs/IQM_Vis.rst
diff --git a/docs/IQM_Vis.transforms.rst → dev_resources/docs/IQM_Vis.transforms.rst b/docs/IQM_Vis.transforms.rst → dev_resources/docs/IQM_Vis.transforms.rst
diff --git a/docs/IQM_Vis.utils.rst → dev_resources/docs/IQM_Vis.utils.rst b/docs/IQM_Vis.utils.rst → dev_resources/docs/IQM_Vis.utils.rst
diff --git a/docs/Makefile → dev_resources/docs/Makefile b/docs/Makefile → dev_resources/docs/Makefile
diff --git a/docs/Tutorials.rst → dev_resources/docs/Tutorials.rst b/docs/Tutorials.rst → dev_resources/docs/Tutorials.rst
diff --git a/docs/_build/doctrees/IQM_Vis.UI.doctree → ...s/docs/_build/doctrees/IQM_Vis.UI.doctree b/docs/_build/doctrees/IQM_Vis.UI.doctree → ...s/docs/_build/doctrees/IQM_Vis.UI.doctree
diff --git a/...ld/doctrees/IQM_Vis.data_handlers.doctree → ...ld/doctrees/IQM_Vis.data_handlers.doctree b/...ld/doctrees/IQM_Vis.data_handlers.doctree → ...ld/doctrees/IQM_Vis.data_handlers.doctree
diff --git a/docs/_build/doctrees/IQM_Vis.doctree → ...rces/docs/_build/doctrees/IQM_Vis.doctree b/docs/_build/doctrees/IQM_Vis.doctree → ...rces/docs/_build/doctrees/IQM_Vis.doctree
diff --git a/.../_build/doctrees/IQM_Vis.examples.doctree → .../_build/doctrees/IQM_Vis.examples.doctree b/.../_build/doctrees/IQM_Vis.examples.doctree → .../_build/doctrees/IQM_Vis.examples.doctree
diff --git a/.../doctrees/IQM_Vis.examples.images.doctree → .../doctrees/IQM_Vis.examples.images.doctree b/.../doctrees/IQM_Vis.examples.images.doctree → .../doctrees/IQM_Vis.examples.images.doctree
diff --git a/...ild/doctrees/IQM_Vis.metrics.SSIM.doctree → ...ild/doctrees/IQM_Vis.metrics.SSIM.doctree b/...ild/doctrees/IQM_Vis.metrics.SSIM.doctree → ...ild/doctrees/IQM_Vis.metrics.SSIM.doctree
diff --git a/docs/_build/doctrees/IQM_Vis.metrics.doctree → ...s/_build/doctrees/IQM_Vis.metrics.doctree b/docs/_build/doctrees/IQM_Vis.metrics.doctree → ...s/_build/doctrees/IQM_Vis.metrics.doctree
diff --git a/...build/doctrees/IQM_Vis.transforms.doctree → ...build/doctrees/IQM_Vis.transforms.doctree b/...build/doctrees/IQM_Vis.transforms.doctree → ...build/doctrees/IQM_Vis.transforms.doctree
diff --git a/docs/_build/doctrees/IQM_Vis.utils.doctree → ...ocs/_build/doctrees/IQM_Vis.utils.doctree b/docs/_build/doctrees/IQM_Vis.utils.doctree → ...ocs/_build/doctrees/IQM_Vis.utils.doctree
diff --git a/docs/_build/doctrees/Tutorials.doctree → ...es/docs/_build/doctrees/Tutorials.doctree b/docs/_build/doctrees/Tutorials.doctree → ...es/docs/_build/doctrees/Tutorials.doctree
diff --git a/docs/_build/doctrees/about.doctree → ...ources/docs/_build/doctrees/about.doctree b/docs/_build/doctrees/about.doctree → ...ources/docs/_build/doctrees/about.doctree
diff --git a/docs/_build/doctrees/environment.pickle → ...s/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle → ...s/docs/_build/doctrees/environment.pickle
diff --git a/docs/_build/doctrees/getting_started.doctree → ...s/_build/doctrees/getting_started.doctree b/docs/_build/doctrees/getting_started.doctree → ...s/_build/doctrees/getting_started.doctree
diff --git a/docs/_build/doctrees/index.doctree → ...ources/docs/_build/doctrees/index.doctree b/docs/_build/doctrees/index.doctree → ...ources/docs/_build/doctrees/index.doctree
diff --git a/docs/_build/doctrees/modules.doctree → ...rces/docs/_build/doctrees/modules.doctree b/docs/_build/doctrees/modules.doctree → ...rces/docs/_build/doctrees/modules.doctree
diff --git a/.../notebooks/Tutorial_1-making_the_UI.ipynb → .../notebooks/Tutorial_1-making_the_UI.ipynb b/.../notebooks/Tutorial_1-making_the_UI.ipynb → .../notebooks/Tutorial_1-making_the_UI.ipynb
diff --git a/.../notebooks/Tutorial_2-Customisation.ipynb → .../notebooks/Tutorial_2-Customisation.ipynb b/.../notebooks/Tutorial_2-Customisation.ipynb → .../notebooks/Tutorial_2-Customisation.ipynb
diff --git a/.../Tutorial_3-Advanced-Customisations.ipynb → .../Tutorial_3-Advanced-Customisations.ipynb b/.../Tutorial_3-Advanced-Customisations.ipynb → .../Tutorial_3-Advanced-Customisations.ipynb
diff --git a/...ks/Tutorial_4-running_an_experiment.ipynb → ...ks/Tutorial_4-running_an_experiment.ipynb b/...ks/Tutorial_4-running_an_experiment.ipynb → ...ks/Tutorial_4-running_an_experiment.ipynb
diff --git a/...otebooks/Tutorial_1-making_the_UI.doctree → ...otebooks/Tutorial_1-making_the_UI.doctree b/...otebooks/Tutorial_1-making_the_UI.doctree → ...otebooks/Tutorial_1-making_the_UI.doctree
diff --git a/...otebooks/Tutorial_2-Customisation.doctree → ...otebooks/Tutorial_2-Customisation.doctree b/...otebooks/Tutorial_2-Customisation.doctree → ...otebooks/Tutorial_2-Customisation.doctree
diff --git a/...utorial_3-Advanced-Customisations.doctree → ...utorial_3-Advanced-Customisations.doctree b/...utorial_3-Advanced-Customisations.doctree → ...utorial_3-Advanced-Customisations.doctree
diff --git a/.../Tutorial_4-running_an_experiment.doctree → .../Tutorial_4-running_an_experiment.doctree b/.../Tutorial_4-running_an_experiment.doctree → .../Tutorial_4-running_an_experiment.doctree
diff --git a/docs/_build/doctrees/what-are-IQMs.doctree → ...ocs/_build/doctrees/what-are-IQMs.doctree b/docs/_build/doctrees/what-are-IQMs.doctree → ...ocs/_build/doctrees/what-are-IQMs.doctree
diff --git a/docs/_build/html/.buildinfo → dev_resources/docs/_build/html/.buildinfo b/docs/_build/html/.buildinfo → dev_resources/docs/_build/html/.buildinfo
diff --git a/docs/_build/html/IQM_Vis.UI.html → ...esources/docs/_build/html/IQM_Vis.UI.html b/docs/_build/html/IQM_Vis.UI.html → ...esources/docs/_build/html/IQM_Vis.UI.html
diff --git a/docs/_build/html/IQM_Vis.data_handlers.html → ...cs/_build/html/IQM_Vis.data_handlers.html b/docs/_build/html/IQM_Vis.data_handlers.html → ...cs/_build/html/IQM_Vis.data_handlers.html
diff --git a/docs/_build/html/IQM_Vis.examples.html → ...es/docs/_build/html/IQM_Vis.examples.html b/docs/_build/html/IQM_Vis.examples.html → ...es/docs/_build/html/IQM_Vis.examples.html
diff --git a/.../_build/html/IQM_Vis.examples.images.html → .../_build/html/IQM_Vis.examples.images.html b/.../_build/html/IQM_Vis.examples.images.html → .../_build/html/IQM_Vis.examples.images.html
diff --git a/docs/_build/html/IQM_Vis.html → dev_resources/docs/_build/html/IQM_Vis.html b/docs/_build/html/IQM_Vis.html → dev_resources/docs/_build/html/IQM_Vis.html
@@ -555,7 +555,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 <section id="module-IQM_Vis.ui_wrapper">
 <span id="iqm-vis-ui-wrapper-module"></span><h2>IQM_Vis.ui_wrapper module<a class="headerlink" href="#module-IQM_Vis.ui_wrapper" title="Permalink to this heading"></a></h2>
 <p>API to access making the PyQt6 UI for IQM-Vis
-TODO: write docs on example usage/ what inputs etc. and what attributes that the data_store class needs</p>
+TODO: write dev_resources/docs on example usage/ what inputs etc. and what attributes that the data_store class needs</p>
 <dl class="py function">
 <dt class="sig sig-object py" id="IQM_Vis.ui_wrapper.check_pyqt_install_deps">
 <span class="sig-prename descclassname"><span class="pre">IQM_Vis.ui_wrapper.</span></span><span class="sig-name descname"><span class="pre">check_pyqt_install_deps</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/IQM_Vis/ui_wrapper.html#check_pyqt_install_deps"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#IQM_Vis.ui_wrapper.check_pyqt_install_deps" title="Permalink to this definition"></a></dt>

diff --git a/docs/_build/html/IQM_Vis.metrics.SSIM.html → ...ocs/_build/html/IQM_Vis.metrics.SSIM.html b/docs/_build/html/IQM_Vis.metrics.SSIM.html → ...ocs/_build/html/IQM_Vis.metrics.SSIM.html
diff --git a/docs/_build/html/IQM_Vis.metrics.html → ...ces/docs/_build/html/IQM_Vis.metrics.html b/docs/_build/html/IQM_Vis.metrics.html → ...ces/docs/_build/html/IQM_Vis.metrics.html
diff --git a/docs/_build/html/IQM_Vis.transforms.html → .../docs/_build/html/IQM_Vis.transforms.html b/docs/_build/html/IQM_Vis.transforms.html → .../docs/_build/html/IQM_Vis.transforms.html
diff --git a/docs/_build/html/IQM_Vis.utils.html → ...urces/docs/_build/html/IQM_Vis.utils.html b/docs/_build/html/IQM_Vis.utils.html → ...urces/docs/_build/html/IQM_Vis.utils.html
@@ -223,7 +223,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 <section id="module-IQM_Vis.utils.plot_utils">
 <span id="iqm-vis-utils-plot-utils-module"></span><h2>IQM_Vis.utils.plot_utils module<a class="headerlink" href="#module-IQM_Vis.utils.plot_utils" title="Permalink to this heading"></a></h2>
 <p>matplotlib plotting helpers
-TODO: write docs how to use these (currently just have to look at the UI code)</p>
+TODO: write dev_resources/docs how to use these (currently just have to look at the UI code)</p>
 <dl class="py class">
 <dt class="sig sig-object py" id="IQM_Vis.utils.plot_utils.bar_plotter">
 <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">IQM_Vis.utils.plot_utils.</span></span><span class="sig-name descname"><span class="pre">bar_plotter</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">bar_names</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">var_names</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ax</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lim</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/IQM_Vis/utils/plot_utils.html#bar_plotter"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#IQM_Vis.utils.plot_utils.bar_plotter" title="Permalink to this definition"></a></dt>

diff --git a/docs/_build/html/Tutorials.html → ...resources/docs/_build/html/Tutorials.html b/docs/_build/html/Tutorials.html → ...resources/docs/_build/html/Tutorials.html
diff --git a/docs/_build/html/_images/UI-blank.png → ...ces/docs/_build/html/_images/UI-blank.png b/docs/_build/html/_images/UI-blank.png → ...ces/docs/_build/html/_images/UI-blank.png
diff --git a/docs/_build/html/_images/UI-checked.png → ...s/docs/_build/html/_images/UI-checked.png b/docs/_build/html/_images/UI-checked.png → ...s/docs/_build/html/_images/UI-checked.png
diff --git a/docs/_build/html/_images/correlation.gif → .../docs/_build/html/_images/correlation.gif b/docs/_build/html/_images/correlation.gif → .../docs/_build/html/_images/correlation.gif
diff --git a/.../_build/html/_images/correlation_plot.png → .../_build/html/_images/correlation_plot.png b/.../_build/html/_images/correlation_plot.png → .../_build/html/_images/correlation_plot.png
diff --git a/docs/_build/html/_images/custom_UI.png → ...es/docs/_build/html/_images/custom_UI.png b/docs/_build/html/_images/custom_UI.png → ...es/docs/_build/html/_images/custom_UI.png
diff --git a/docs/_build/html/_images/custom_UI_2.png → .../docs/_build/html/_images/custom_UI_2.png b/docs/_build/html/_images/custom_UI_2.png → .../docs/_build/html/_images/custom_UI_2.png
diff --git a/docs/_build/html/_images/data_graphs.gif → .../docs/_build/html/_images/data_graphs.gif b/docs/_build/html/_images/data_graphs.gif → .../docs/_build/html/_images/data_graphs.gif
diff --git a/docs/_build/html/_images/experiment_1.png → ...docs/_build/html/_images/experiment_1.png b/docs/_build/html/_images/experiment_1.png → ...docs/_build/html/_images/experiment_1.png
diff --git a/docs/_build/html/_images/experiment_2.png → ...docs/_build/html/_images/experiment_2.png b/docs/_build/html/_images/experiment_2.png → ...docs/_build/html/_images/experiment_2.png
diff --git a/docs/_build/html/_images/experiment_3.png → ...docs/_build/html/_images/experiment_3.png b/docs/_build/html/_images/experiment_3.png → ...docs/_build/html/_images/experiment_3.png
diff --git a/docs/_build/html/_images/experiment_4.png → ...docs/_build/html/_images/experiment_4.png b/docs/_build/html/_images/experiment_4.png → ...docs/_build/html/_images/experiment_4.png
diff --git a/.../_build/html/_images/experiment_setup.png → .../_build/html/_images/experiment_setup.png b/.../_build/html/_images/experiment_setup.png → .../_build/html/_images/experiment_setup.png
diff --git a/docs/_build/html/_images/params.gif → ...urces/docs/_build/html/_images/params.gif b/docs/_build/html/_images/params.gif → ...urces/docs/_build/html/_images/params.gif
diff --git a/docs/_build/html/_images/settings.png → ...ces/docs/_build/html/_images/settings.png b/docs/_build/html/_images/settings.png → ...ces/docs/_build/html/_images/settings.png
diff --git a/...l/_modules/IQM_Vis/UI/custom_widgets.html → ...l/_modules/IQM_Vis/UI/custom_widgets.html b/...l/_modules/IQM_Vis/UI/custom_widgets.html → ...l/_modules/IQM_Vis/UI/custom_widgets.html
diff --git a/.../_modules/IQM_Vis/UI/experiment_mode.html → .../_modules/IQM_Vis/UI/experiment_mode.html b/.../_modules/IQM_Vis/UI/experiment_mode.html → .../_modules/IQM_Vis/UI/experiment_mode.html
diff --git a/...uild/html/_modules/IQM_Vis/UI/images.html → ...uild/html/_modules/IQM_Vis/UI/images.html b/...uild/html/_modules/IQM_Vis/UI/images.html → ...uild/html/_modules/IQM_Vis/UI/images.html
diff --git a/...uild/html/_modules/IQM_Vis/UI/layout.html → ...uild/html/_modules/IQM_Vis/UI/layout.html b/...uild/html/_modules/IQM_Vis/UI/layout.html → ...uild/html/_modules/IQM_Vis/UI/layout.html
diff --git a/..._build/html/_modules/IQM_Vis/UI/main.html → ..._build/html/_modules/IQM_Vis/UI/main.html b/..._build/html/_modules/IQM_Vis/UI/main.html → ..._build/html/_modules/IQM_Vis/UI/main.html
diff --git a/...ild/html/_modules/IQM_Vis/UI/threads.html → ...ild/html/_modules/IQM_Vis/UI/threads.html b/...ild/html/_modules/IQM_Vis/UI/threads.html → ...ild/html/_modules/IQM_Vis/UI/threads.html
diff --git a/...build/html/_modules/IQM_Vis/UI/utils.html → ...build/html/_modules/IQM_Vis/UI/utils.html b/...build/html/_modules/IQM_Vis/UI/utils.html → ...build/html/_modules/IQM_Vis/UI/utils.html
diff --git a/...ild/html/_modules/IQM_Vis/UI/widgets.html → ...ild/html/_modules/IQM_Vis/UI/widgets.html b/...ild/html/_modules/IQM_Vis/UI/widgets.html → ...ild/html/_modules/IQM_Vis/UI/widgets.html
diff --git a/...dules/IQM_Vis/data_handlers/data_api.html → ...dules/IQM_Vis/data_handlers/data_api.html b/...dules/IQM_Vis/data_handlers/data_api.html → ...dules/IQM_Vis/data_handlers/data_api.html
diff --git a/..._Vis/data_handlers/data_api_abstract.html → ..._Vis/data_handlers/data_api_abstract.html b/..._Vis/data_handlers/data_api_abstract.html → ..._Vis/data_handlers/data_api_abstract.html
diff --git a/...d/html/_modules/IQM_Vis/examples/all.html → ...d/html/_modules/IQM_Vis/examples/all.html b/...d/html/_modules/IQM_Vis/examples/all.html → ...d/html/_modules/IQM_Vis/examples/all.html
diff --git a/...ml/_modules/IQM_Vis/examples/dataset.html → ...ml/_modules/IQM_Vis/examples/dataset.html b/...ml/_modules/IQM_Vis/examples/dataset.html → ...ml/_modules/IQM_Vis/examples/dataset.html
diff --git a/...html/_modules/IQM_Vis/examples/dists.html → ...html/_modules/IQM_Vis/examples/dists.html b/...html/_modules/IQM_Vis/examples/dists.html → ...html/_modules/IQM_Vis/examples/dists.html
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diff --git a/...html/_modules/IQM_Vis/examples/kodak.html → ...html/_modules/IQM_Vis/examples/kodak.html b/...html/_modules/IQM_Vis/examples/kodak.html → ...html/_modules/IQM_Vis/examples/kodak.html
diff --git a/...l/_modules/IQM_Vis/examples/multiple.html → ...l/_modules/IQM_Vis/examples/multiple.html b/...l/_modules/IQM_Vis/examples/multiple.html → ...l/_modules/IQM_Vis/examples/multiple.html
diff --git a/...ml/_modules/IQM_Vis/examples/new_api.html → ...ml/_modules/IQM_Vis/examples/new_api.html b/...ml/_modules/IQM_Vis/examples/new_api.html → ...ml/_modules/IQM_Vis/examples/new_api.html
diff --git a/...tml/_modules/IQM_Vis/examples/simple.html → ...tml/_modules/IQM_Vis/examples/simple.html b/...tml/_modules/IQM_Vis/examples/simple.html → ...tml/_modules/IQM_Vis/examples/simple.html
diff --git a/..._build/html/_modules/IQM_Vis/metrics.html → ..._build/html/_modules/IQM_Vis/metrics.html b/..._build/html/_modules/IQM_Vis/metrics.html → ..._build/html/_modules/IQM_Vis/metrics.html
diff --git a/...l/_modules/IQM_Vis/metrics/SSIM/ssim.html → ...l/_modules/IQM_Vis/metrics/SSIM/ssim.html b/...l/_modules/IQM_Vis/metrics/SSIM/ssim.html → ...l/_modules/IQM_Vis/metrics/SSIM/ssim.html
diff --git a/...dules/IQM_Vis/metrics/non_perceptual.html → ...dules/IQM_Vis/metrics/non_perceptual.html b/...dules/IQM_Vis/metrics/non_perceptual.html → ...dules/IQM_Vis/metrics/non_perceptual.html
diff --git a/...odules/IQM_Vis/metrics/perceptual_DL.html → ...odules/IQM_Vis/metrics/perceptual_DL.html b/...odules/IQM_Vis/metrics/perceptual_DL.html → ...odules/IQM_Vis/metrics/perceptual_DL.html
diff --git a/...ules/IQM_Vis/metrics/perceptual_trad.html → ...ules/IQM_Vis/metrics/perceptual_trad.html b/...ules/IQM_Vis/metrics/perceptual_trad.html → ...ules/IQM_Vis/metrics/perceptual_trad.html
diff --git a/...ild/html/_modules/IQM_Vis/transforms.html → ...ild/html/_modules/IQM_Vis/transforms.html b/...ild/html/_modules/IQM_Vis/transforms.html → ...ild/html/_modules/IQM_Vis/transforms.html
diff --git a/...es/IQM_Vis/transforms/additive_noise.html → ...es/IQM_Vis/transforms/additive_noise.html b/...es/IQM_Vis/transforms/additive_noise.html → ...es/IQM_Vis/transforms/additive_noise.html
diff --git a/...l/_modules/IQM_Vis/transforms/affine.html → ...l/_modules/IQM_Vis/transforms/affine.html b/...l/_modules/IQM_Vis/transforms/affine.html → ...l/_modules/IQM_Vis/transforms/affine.html
diff --git a/.../_modules/IQM_Vis/transforms/effects.html → .../_modules/IQM_Vis/transforms/effects.html b/.../_modules/IQM_Vis/transforms/effects.html → .../_modules/IQM_Vis/transforms/effects.html
@@ -158,8 +158,8 @@ <h1>Source code for IQM_Vis.transforms.effects</h1><div class="highlight"><pre>
 <span class="k">def</span> <span class="nf">_encode_compression</span><span class="p">(</span><span class="n">image</span><span class="p">,</span> <span class="n">encoder</span><span class="p">,</span> <span class="n">encode_param</span><span class="p">,</span> <span class="n">uint</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
     <span class="sd">&#39;&#39;&#39;</span>
 <span class="sd">        generic image encoder for jpeg, png etc</span>
-<span class="sd">        using https://docs.opencv.org/3.4/d4/da8/group__imgcodecs.html to encode/decode</span>
-<span class="sd">        for encode types: https://docs.opencv.org/3.4/d6/d87/imgcodecs_8hpp.html</span>
+<span class="sd">        using https://dev_resources/docs.opencv.org/3.4/d4/da8/group__imgcodecs.html to encode/decode</span>
+<span class="sd">        for encode types: https://dev_resources/docs.opencv.org/3.4/d6/d87/imgcodecs_8hpp.html</span>
 <span class="sd">    &#39;&#39;&#39;</span>
     <span class="n">original_size</span> <span class="o">=</span> <span class="n">image</span><span class="o">.</span><span class="n">shape</span>
     <span class="k">if</span> <span class="n">uint</span> <span class="o">==</span> <span class="kc">True</span><span class="p">:</span>

diff --git a/...ild/html/_modules/IQM_Vis/ui_wrapper.html → ...ild/html/_modules/IQM_Vis/ui_wrapper.html b/...ild/html/_modules/IQM_Vis/ui_wrapper.html → ...ild/html/_modules/IQM_Vis/ui_wrapper.html
@@ -88,7 +88,7 @@
   <h1>Source code for IQM_Vis.ui_wrapper</h1><div class="highlight"><pre>
 <span></span><span class="sd">&#39;&#39;&#39;</span>
 <span class="sd">API to access making the PyQt6 UI for IQM-Vis</span>
-<span class="sd">TODO: write docs on example usage/ what inputs etc. and what attributes that the data_store class needs</span>
+<span class="sd">TODO: write dev_resources/docs on example usage/ what inputs etc. and what attributes that the data_store class needs</span>
 <span class="sd">&#39;&#39;&#39;</span>
 <span class="c1"># Author: Matt Clifford &lt;[email protected]&gt;</span>
 <span class="c1"># License: BSD 3-Clause License</span>

diff --git a/...tml/_modules/IQM_Vis/utils/gui_utils.html → ...tml/_modules/IQM_Vis/utils/gui_utils.html b/...tml/_modules/IQM_Vis/utils/gui_utils.html → ...tml/_modules/IQM_Vis/utils/gui_utils.html
diff --git a/...l/_modules/IQM_Vis/utils/image_utils.html → ...l/_modules/IQM_Vis/utils/image_utils.html b/...l/_modules/IQM_Vis/utils/image_utils.html → ...l/_modules/IQM_Vis/utils/image_utils.html
diff --git a/...ml/_modules/IQM_Vis/utils/plot_utils.html → ...ml/_modules/IQM_Vis/utils/plot_utils.html b/...ml/_modules/IQM_Vis/utils/plot_utils.html → ...ml/_modules/IQM_Vis/utils/plot_utils.html
@@ -88,7 +88,7 @@
   <h1>Source code for IQM_Vis.utils.plot_utils</h1><div class="highlight"><pre>
 <span></span><span class="sd">&#39;&#39;&#39;</span>
 <span class="sd">matplotlib plotting helpers</span>
-<span class="sd">TODO: write docs how to use these (currently just have to look at the UI code)</span>
+<span class="sd">TODO: write dev_resources/docs how to use these (currently just have to look at the UI code)</span>
 <span class="sd">&#39;&#39;&#39;</span>
 <span class="c1"># Author: Matt Clifford &lt;[email protected]&gt;</span>
 <span class="c1"># License: BSD 3-Clause License</span>

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diff --git a/docs/_build/html/_modules/index.html → ...rces/docs/_build/html/_modules/index.html b/docs/_build/html/_modules/index.html → ...rces/docs/_build/html/_modules/index.html
diff --git a/docs/_build/html/_sources/IQM_Vis.UI.rst.txt → ...s/_build/html/_sources/IQM_Vis.UI.rst.txt b/docs/_build/html/_sources/IQM_Vis.UI.rst.txt → ...s/_build/html/_sources/IQM_Vis.UI.rst.txt
diff --git a/...ml/_sources/IQM_Vis.data_handlers.rst.txt → ...ml/_sources/IQM_Vis.data_handlers.rst.txt b/...ml/_sources/IQM_Vis.data_handlers.rst.txt → ...ml/_sources/IQM_Vis.data_handlers.rst.txt
diff --git a/.../_sources/IQM_Vis.examples.images.rst.txt → .../_sources/IQM_Vis.examples.images.rst.txt b/.../_sources/IQM_Vis.examples.images.rst.txt → .../_sources/IQM_Vis.examples.images.rst.txt
diff --git a/...ld/html/_sources/IQM_Vis.examples.rst.txt → ...ld/html/_sources/IQM_Vis.examples.rst.txt b/...ld/html/_sources/IQM_Vis.examples.rst.txt → ...ld/html/_sources/IQM_Vis.examples.rst.txt
diff --git a/...tml/_sources/IQM_Vis.metrics.SSIM.rst.txt → ...tml/_sources/IQM_Vis.metrics.SSIM.rst.txt b/...tml/_sources/IQM_Vis.metrics.SSIM.rst.txt → ...tml/_sources/IQM_Vis.metrics.SSIM.rst.txt
diff --git a/...ild/html/_sources/IQM_Vis.metrics.rst.txt → ...ild/html/_sources/IQM_Vis.metrics.rst.txt b/...ild/html/_sources/IQM_Vis.metrics.rst.txt → ...ild/html/_sources/IQM_Vis.metrics.rst.txt
diff --git a/docs/_build/html/_sources/IQM_Vis.rst.txt → ...docs/_build/html/_sources/IQM_Vis.rst.txt b/docs/_build/html/_sources/IQM_Vis.rst.txt → ...docs/_build/html/_sources/IQM_Vis.rst.txt
diff --git a/.../html/_sources/IQM_Vis.transforms.rst.txt → .../html/_sources/IQM_Vis.transforms.rst.txt b/.../html/_sources/IQM_Vis.transforms.rst.txt → .../html/_sources/IQM_Vis.transforms.rst.txt
diff --git a/...build/html/_sources/IQM_Vis.utils.rst.txt → ...build/html/_sources/IQM_Vis.utils.rst.txt b/...build/html/_sources/IQM_Vis.utils.rst.txt → ...build/html/_sources/IQM_Vis.utils.rst.txt
diff --git a/docs/_build/html/_sources/Tutorials.rst.txt → ...cs/_build/html/_sources/Tutorials.rst.txt b/docs/_build/html/_sources/Tutorials.rst.txt → ...cs/_build/html/_sources/Tutorials.rst.txt
diff --git a/docs/_build/html/_sources/about.rst.txt → ...s/docs/_build/html/_sources/about.rst.txt b/docs/_build/html/_sources/about.rst.txt → ...s/docs/_build/html/_sources/about.rst.txt
diff --git a/...ild/html/_sources/getting_started.rst.txt → ...ild/html/_sources/getting_started.rst.txt b/...ild/html/_sources/getting_started.rst.txt → ...ild/html/_sources/getting_started.rst.txt
diff --git a/docs/_build/html/_sources/index.rst.txt → ...s/docs/_build/html/_sources/index.rst.txt b/docs/_build/html/_sources/index.rst.txt → ...s/docs/_build/html/_sources/index.rst.txt
@@ -9,7 +9,7 @@ IQM-Vis is an image quality metric visualisation toolbox to facilitate visualisi
 View our demonstration `video <https://youtu.be/C6x_E0JvKqI>`_ which illustrates the features and how to use IQM-Vis.
 
 
-Read our `PAPER <https://github.com/mattclifford1/IQM-Vis/blob/main/docs/resources/Software_paper.pdf>`_ for in depth details of the software.
+Read our `PAPER <https://github.com/mattclifford1/IQM-Vis/blob/main/dev_resources/docs/resources/Software_paper.pdf>`_ for in depth details of the software.
 
 Quantitive Analysis
 ===================

diff --git a/docs/_build/html/_sources/modules.rst.txt → ...docs/_build/html/_sources/modules.rst.txt b/docs/_build/html/_sources/modules.rst.txt → ...docs/_build/html/_sources/modules.rst.txt
diff --git a/...ebooks/Tutorial_1-making_the_UI.ipynb.txt → ...ebooks/Tutorial_1-making_the_UI.ipynb.txt b/...ebooks/Tutorial_1-making_the_UI.ipynb.txt → ...ebooks/Tutorial_1-making_the_UI.ipynb.txt
diff --git a/...ebooks/Tutorial_2-Customisation.ipynb.txt → ...ebooks/Tutorial_2-Customisation.ipynb.txt b/...ebooks/Tutorial_2-Customisation.ipynb.txt → ...ebooks/Tutorial_2-Customisation.ipynb.txt
diff --git a/...orial_3-Advanced-Customisations.ipynb.txt → ...orial_3-Advanced-Customisations.ipynb.txt b/...orial_3-Advanced-Customisations.ipynb.txt → ...orial_3-Advanced-Customisations.ipynb.txt
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diff --git a/...build/html/_sources/what-are-IQMs.rst.txt → ...build/html/_sources/what-are-IQMs.rst.txt b/...build/html/_sources/what-are-IQMs.rst.txt → ...build/html/_sources/what-are-IQMs.rst.txt
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diff --git a/docs/_build/html/_static/sg_gallery.css → ...s/docs/_build/html/_static/sg_gallery.css b/docs/_build/html/_static/sg_gallery.css → ...s/docs/_build/html/_static/sg_gallery.css
diff --git a/docs/_build/html/_static/sphinx_highlight.js → ...s/_build/html/_static/sphinx_highlight.js b/docs/_build/html/_static/sphinx_highlight.js → ...s/_build/html/_static/sphinx_highlight.js
diff --git a/docs/_build/html/about.html → dev_resources/docs/_build/html/about.html b/docs/_build/html/about.html → dev_resources/docs/_build/html/about.html
diff --git a/docs/_build/html/genindex.html → dev_resources/docs/_build/html/genindex.html b/docs/_build/html/genindex.html → dev_resources/docs/_build/html/genindex.html
diff --git a/docs/_build/html/getting_started.html → ...ces/docs/_build/html/getting_started.html b/docs/_build/html/getting_started.html → ...ces/docs/_build/html/getting_started.html
diff --git a/docs/_build/html/index.html → dev_resources/docs/_build/html/index.html b/docs/_build/html/index.html → dev_resources/docs/_build/html/index.html
@@ -91,7 +91,7 @@
 <h1>IQM-Vis documentation<a class="headerlink" href="#iqm-vis-documentation" title="Permalink to this heading"></a></h1>
 <p>IQM-Vis is an image quality metric visualisation toolbox to facilitate visualising and evaluating image quality metrics (IQMs).
 View our demonstration <a class="reference external" href="https://youtu.be/C6x_E0JvKqI">video</a> which illustrates the features and how to use IQM-Vis.</p>
-<p>Read our <a class="reference external" href="https://github.com/mattclifford1/IQM-Vis/blob/main/docs/resources/Software_paper.pdf">PAPER</a> for in depth details of the software.</p>
+<p>Read our <a class="reference external" href="https://github.com/mattclifford1/IQM-Vis/blob/main/dev_resources/docs/resources/Software_paper.pdf">PAPER</a> for in depth details of the software.</p>
 <section id="quantitive-analysis">
 <h2>Quantitive Analysis<a class="headerlink" href="#quantitive-analysis" title="Permalink to this heading"></a></h2>
 <p>IQM-Vis is able to provide a comprehensive analysis of IQMs through various quantitative graphs. These graphs offer practitioners a well-rounded understanding of how different IQMs perform under different scenarios without having to write any code to set up the testing procedure.</p>

diff --git a/docs/_build/html/modules.html → dev_resources/docs/_build/html/modules.html b/docs/_build/html/modules.html → dev_resources/docs/_build/html/modules.html
diff --git a/...l/notebooks/Tutorial_1-making_the_UI.html → ...l/notebooks/Tutorial_1-making_the_UI.html b/...l/notebooks/Tutorial_1-making_the_UI.html → ...l/notebooks/Tutorial_1-making_the_UI.html
@@ -113,7 +113,7 @@
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
 
-  <p>View the whole notebook: <a class="reference external" href="https://github.com/mattclifford1/IQM-Vis/tree/main/docs/notebooks/Tutorial_1-making_the_UI.ipynb">https://github.com/mattclifford1/IQM-Vis/tree/main/docs/notebooks/Tutorial_1-making_the_UI.ipynb</a></p>
+  <p>View the whole notebook: <a class="reference external" href="https://github.com/mattclifford1/IQM-Vis/tree/main/dev_resources/docs/notebooks/Tutorial_1-making_the_UI.ipynb">https://github.com/mattclifford1/IQM-Vis/tree/main/dev_resources/docs/notebooks/Tutorial_1-making_the_UI.ipynb</a></p>
 <hr class="docutils" />
 <section id="Tutorial-1:-Making-the-UI">
 <h1>Tutorial 1: Making the UI<a class="headerlink" href="#Tutorial-1:-Making-the-UI" title="Permalink to this heading"></a></h1>

diff --git a/.../notebooks/Tutorial_1-making_the_UI.ipynb → .../notebooks/Tutorial_1-making_the_UI.ipynb b/.../notebooks/Tutorial_1-making_the_UI.ipynb → .../notebooks/Tutorial_1-making_the_UI.ipynb
diff --git a/...l/notebooks/Tutorial_2-Customisation.html → ...l/notebooks/Tutorial_2-Customisation.html b/...l/notebooks/Tutorial_2-Customisation.html → ...l/notebooks/Tutorial_2-Customisation.html
@@ -108,7 +108,7 @@
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
 
-  <p>View the whole notebook: <a class="reference external" href="https://github.com/mattclifford1/IQM-Vis/tree/main/docs/notebooks/Tutorial_2-Customisation.ipynb">https://github.com/mattclifford1/IQM-Vis/tree/main/docs/notebooks/Tutorial_2-Customisation.ipynb</a></p>
+  <p>View the whole notebook: <a class="reference external" href="https://github.com/mattclifford1/IQM-Vis/tree/main/dev_resources/docs/notebooks/Tutorial_2-Customisation.ipynb">https://github.com/mattclifford1/IQM-Vis/tree/main/dev_resources/docs/notebooks/Tutorial_2-Customisation.ipynb</a></p>
 <hr class="docutils" />
 <section id="Tutorial-2:-Simple-Customisation">
 <h1>Tutorial 2: Simple Customisation<a class="headerlink" href="#Tutorial-2:-Simple-Customisation" title="Permalink to this heading"></a></h1>

diff --git a/.../notebooks/Tutorial_2-Customisation.ipynb → .../notebooks/Tutorial_2-Customisation.ipynb b/.../notebooks/Tutorial_2-Customisation.ipynb → .../notebooks/Tutorial_2-Customisation.ipynb
diff --git a/...s/Tutorial_3-Advanced-Customisations.html → ...s/Tutorial_3-Advanced-Customisations.html b/...s/Tutorial_3-Advanced-Customisations.html → ...s/Tutorial_3-Advanced-Customisations.html
@@ -104,7 +104,7 @@
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
 
-  <p>View the whole notebook: <a class="reference external" href="https://github.com/mattclifford1/IQM-Vis/tree/main/docs/notebooks/Tutorial_3-Advanced-Customisations.ipynb">https://github.com/mattclifford1/IQM-Vis/tree/main/docs/notebooks/Tutorial_3-Advanced-Customisations.ipynb</a></p>
+  <p>View the whole notebook: <a class="reference external" href="https://github.com/mattclifford1/IQM-Vis/tree/main/dev_resources/docs/notebooks/Tutorial_3-Advanced-Customisations.ipynb">https://github.com/mattclifford1/IQM-Vis/tree/main/dev_resources/docs/notebooks/Tutorial_3-Advanced-Customisations.ipynb</a></p>
 <hr class="docutils" />
 <section id="Tutorial-3:-Customisation-Details">
 <h1>Tutorial 3: Customisation Details<a class="headerlink" href="#Tutorial-3:-Customisation-Details" title="Permalink to this heading"></a></h1>

diff --git a/.../Tutorial_3-Advanced-Customisations.ipynb → .../Tutorial_3-Advanced-Customisations.ipynb b/.../Tutorial_3-Advanced-Customisations.ipynb → .../Tutorial_3-Advanced-Customisations.ipynb
diff --git a/...oks/Tutorial_4-running_an_experiment.html → ...oks/Tutorial_4-running_an_experiment.html b/...oks/Tutorial_4-running_an_experiment.html → ...oks/Tutorial_4-running_an_experiment.html
@@ -106,7 +106,7 @@
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
 
-  <p>View the whole notebook: <a class="reference external" href="https://github.com/mattclifford1/IQM-Vis/tree/main/docs/notebooks/Tutorial_4-running_an_experiment.ipynb">https://github.com/mattclifford1/IQM-Vis/tree/main/docs/notebooks/Tutorial_4-running_an_experiment.ipynb</a></p>
+  <p>View the whole notebook: <a class="reference external" href="https://github.com/mattclifford1/IQM-Vis/tree/main/dev_resources/docs/notebooks/Tutorial_4-running_an_experiment.ipynb">https://github.com/mattclifford1/IQM-Vis/tree/main/dev_resources/docs/notebooks/Tutorial_4-running_an_experiment.ipynb</a></p>
 <hr class="docutils" />
 <section id="Tutorial-4:-Running-an-Experiment">
 <h1>Tutorial 4: Running an Experiment<a class="headerlink" href="#Tutorial-4:-Running-an-Experiment" title="Permalink to this heading"></a></h1>

diff --git a/...ks/Tutorial_4-running_an_experiment.ipynb → ...ks/Tutorial_4-running_an_experiment.ipynb b/...ks/Tutorial_4-running_an_experiment.ipynb → ...ks/Tutorial_4-running_an_experiment.ipynb
diff --git a/docs/_build/html/objects.inv → dev_resources/docs/_build/html/objects.inv b/docs/_build/html/objects.inv → dev_resources/docs/_build/html/objects.inv
diff --git a/docs/_build/html/py-modindex.html → ...sources/docs/_build/html/py-modindex.html b/docs/_build/html/py-modindex.html → ...sources/docs/_build/html/py-modindex.html
diff --git a/docs/_build/html/search.html → dev_resources/docs/_build/html/search.html b/docs/_build/html/search.html → dev_resources/docs/_build/html/search.html
diff --git a/dev_resources/docs/_build/html/searchindex.js b/dev_resources/docs/_build/html/searchindex.js
diff --git a/docs/_build/html/what-are-IQMs.html → ...urces/docs/_build/html/what-are-IQMs.html b/docs/_build/html/what-are-IQMs.html → ...urces/docs/_build/html/what-are-IQMs.html
diff --git a/docs/about.rst → dev_resources/docs/about.rst b/docs/about.rst → dev_resources/docs/about.rst
diff --git a/docs/conf.py → dev_resources/docs/conf.py b/docs/conf.py → dev_resources/docs/conf.py
@@ -65,7 +65,7 @@
 
 # notebook links
 nbsphinx_prolog = """
-View the whole notebook: https://github.com/mattclifford1/IQM-Vis/tree/main/docs/{{ env.doc2path(env.docname, base=None) }}
+View the whole notebook: https://github.com/mattclifford1/IQM-Vis/tree/main/dev_resources/docs/{{ env.doc2path(env.docname, base=None) }}
 
 ----
 """

diff --git a/docs/getting_started.rst → dev_resources/docs/getting_started.rst b/docs/getting_started.rst → dev_resources/docs/getting_started.rst
diff --git a/docs/images/correlation.gif → dev_resources/docs/images/correlation.gif b/docs/images/correlation.gif → dev_resources/docs/images/correlation.gif
diff --git a/docs/images/data_graphs.gif → dev_resources/docs/images/data_graphs.gif b/docs/images/data_graphs.gif → dev_resources/docs/images/data_graphs.gif
diff --git a/docs/images/jupyter_logo.png → dev_resources/docs/images/jupyter_logo.png b/docs/images/jupyter_logo.png → dev_resources/docs/images/jupyter_logo.png
diff --git a/docs/images/notebook_icon.png → dev_resources/docs/images/notebook_icon.png b/docs/images/notebook_icon.png → dev_resources/docs/images/notebook_icon.png
diff --git a/docs/images/params.gif → dev_resources/docs/images/params.gif b/docs/images/params.gif → dev_resources/docs/images/params.gif
diff --git a/docs/index.rst → dev_resources/docs/index.rst b/docs/index.rst → dev_resources/docs/index.rst
@@ -9,7 +9,7 @@ IQM-Vis is an image quality metric visualisation toolbox to facilitate visualisi
 View our demonstration `video <https://youtu.be/C6x_E0JvKqI>`_ which illustrates the features and how to use IQM-Vis.
 
 
-Read our `PAPER <https://github.com/mattclifford1/IQM-Vis/blob/main/docs/resources/Software_paper.pdf>`_ for in depth details of the software.
+Read our `PAPER <https://github.com/mattclifford1/IQM-Vis/blob/main/dev_resources/docs/resources/Software_paper.pdf>`_ for in depth details of the software.
 
 Quantitive Analysis
 ===================

diff --git a/docs/make.bat → dev_resources/docs/make.bat b/docs/make.bat → dev_resources/docs/make.bat
diff --git a/docs/modules.rst → dev_resources/docs/modules.rst b/docs/modules.rst → dev_resources/docs/modules.rst
diff --git a/.../notebooks/Tutorial_1-making_the_UI.ipynb → .../notebooks/Tutorial_1-making_the_UI.ipynb b/.../notebooks/Tutorial_1-making_the_UI.ipynb → .../notebooks/Tutorial_1-making_the_UI.ipynb
diff --git a/.../notebooks/Tutorial_2-Customisation.ipynb → .../notebooks/Tutorial_2-Customisation.ipynb b/.../notebooks/Tutorial_2-Customisation.ipynb → .../notebooks/Tutorial_2-Customisation.ipynb
diff --git a/.../Tutorial_3-Advanced-Customisations.ipynb → .../Tutorial_3-Advanced-Customisations.ipynb b/.../Tutorial_3-Advanced-Customisations.ipynb → .../Tutorial_3-Advanced-Customisations.ipynb
diff --git a/...ks/Tutorial_4-running_an_experiment.ipynb → ...ks/Tutorial_4-running_an_experiment.ipynb b/...ks/Tutorial_4-running_an_experiment.ipynb → ...ks/Tutorial_4-running_an_experiment.ipynb
diff --git a/docs/notebooks/resources/UI-blank.png → ...ces/docs/notebooks/resources/UI-blank.png b/docs/notebooks/resources/UI-blank.png → ...ces/docs/notebooks/resources/UI-blank.png
diff --git a/docs/notebooks/resources/UI-checked.png → ...s/docs/notebooks/resources/UI-checked.png b/docs/notebooks/resources/UI-checked.png → ...s/docs/notebooks/resources/UI-checked.png
diff --git a/.../notebooks/resources/correlation_plot.png → .../notebooks/resources/correlation_plot.png b/.../notebooks/resources/correlation_plot.png → .../notebooks/resources/correlation_plot.png
diff --git a/docs/notebooks/resources/custom_UI.png → ...es/docs/notebooks/resources/custom_UI.png b/docs/notebooks/resources/custom_UI.png → ...es/docs/notebooks/resources/custom_UI.png
diff --git a/docs/notebooks/resources/custom_UI_2.png → .../docs/notebooks/resources/custom_UI_2.png b/docs/notebooks/resources/custom_UI_2.png → .../docs/notebooks/resources/custom_UI_2.png
diff --git a/docs/notebooks/resources/experiment_1.png → ...docs/notebooks/resources/experiment_1.png b/docs/notebooks/resources/experiment_1.png → ...docs/notebooks/resources/experiment_1.png
diff --git a/docs/notebooks/resources/experiment_2.png → ...docs/notebooks/resources/experiment_2.png b/docs/notebooks/resources/experiment_2.png → ...docs/notebooks/resources/experiment_2.png
diff --git a/docs/notebooks/resources/experiment_3.png → ...docs/notebooks/resources/experiment_3.png b/docs/notebooks/resources/experiment_3.png → ...docs/notebooks/resources/experiment_3.png
diff --git a/docs/notebooks/resources/experiment_4.png → ...docs/notebooks/resources/experiment_4.png b/docs/notebooks/resources/experiment_4.png → ...docs/notebooks/resources/experiment_4.png
diff --git a/.../notebooks/resources/experiment_setup.png → .../notebooks/resources/experiment_setup.png b/.../notebooks/resources/experiment_setup.png → .../notebooks/resources/experiment_setup.png
diff --git a/docs/notebooks/resources/settings.png → ...ces/docs/notebooks/resources/settings.png b/docs/notebooks/resources/settings.png → ...ces/docs/notebooks/resources/settings.png
diff --git a/docs/readme.md → dev_resources/docs/readme.md b/docs/readme.md → dev_resources/docs/readme.md
diff --git a/docs/requirements.txt → dev_resources/docs/requirements.txt b/docs/requirements.txt → dev_resources/docs/requirements.txt
diff --git a/docs/resources/Software_paper.pdf → ...sources/docs/resources/Software_paper.pdf b/docs/resources/Software_paper.pdf → ...sources/docs/resources/Software_paper.pdf
diff --git a/docs/what-are-IQMs.rst → dev_resources/docs/what-are-IQMs.rst b/docs/what-are-IQMs.rst → dev_resources/docs/what-are-IQMs.rst
diff --git a/dev_resources/pics/ffmpeg-cmd.txt b/dev_resources/pics/ffmpeg-cmd.txt
@@ -1,3 +1,3 @@
-# convert webm screenshot to gif for docs
+# convert webm screenshot to gif for dev_resources/docs
 
 ffmpeg -i qual.webm -vf "fps=5,scale=1080:-1:flags=lanczos,palettegen" -y 'qual-palette.png' && ffmpeg -i qual.webm -i qual-palette.png -lavfi "fps=5,scale=1080:-1:flags=lanczos [x]; [x][1:v] paletteuse" -y qual-red.gif
diff --git a/scripts/create_conda_dev_env.sh → ...resources/scripts/create_conda_dev_env.sh b/scripts/create_conda_dev_env.sh → ...resources/scripts/create_conda_dev_env.sh
diff --git a/scripts/get_latest_pypi_version.py → ...ources/scripts/get_latest_pypi_version.py b/scripts/get_latest_pypi_version.py → ...ources/scripts/get_latest_pypi_version.py
diff --git a/scripts/get_local_version.py → dev_resources/scripts/get_local_version.py b/scripts/get_local_version.py → dev_resources/scripts/get_local_version.py
diff --git a/dev_resources/scripts/make_docs.sh b/dev_resources/scripts/make_docs.sh
@@ -0,0 +1,11 @@
+#!/usr/bin/bash
+# Author: Matt Clifford <[email protected]>
+# License: BSD 3-Clause License
+
+
+rm dev_resources/docs/IQM_Vis.*
+# sphinx-build -o dev_resources/docs IQM_Vis
+sphinx-apidoc -o dev_resources/docs IQM_Vis IQM_Vis/metrics/NLPD_torch/*
+cd dev_resources/docs
+make clean html
+make html
diff --git a/scripts/push_to_pypi.sh → dev_resources/scripts/push_to_pypi.sh b/scripts/push_to_pypi.sh → dev_resources/scripts/push_to_pypi.sh
diff --git a/scripts/pytest_and_badges.sh → dev_resources/scripts/pytest_and_badges.sh b/scripts/pytest_and_badges.sh → dev_resources/scripts/pytest_and_badges.sh
diff --git a/dev_resources/todo.md b/dev_resources/todo.md
@@ -1,6 +1,6 @@
-write docs / guided examples
+write dev_resources/docs / guided examples
 
-## docs:
+## dev_resources/docs:
 Deatils of the data API
   (advanced - how to modify it)
   (how to make your own handler that conforms to the API)

diff --git a/docs/_build/html/searchindex.js b/docs/_build/html/searchindex.js
diff --git a/scripts/make_docs.sh b/scripts/make_docs.sh
diff --git a/tests/readme.md b/tests/readme.md
@@ -5,7 +5,7 @@ Tests cannot be run as part of a CI pipeline as a display is required to launch
 
 To run all tests and make badges automatically use the bash script
 ```
-./scripts/pytest_and_badges.sh 
+./dev_resources/scripts/pytest_and_badges.sh 
 ```
 Other wise refer below for running the individual steps
 

diff --git a/tests/reports/junit/junit.xml b/tests/reports/junit/junit.xml
@@ -1 +1 @@
-<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="0" time="2.527" timestamp="2024-10-09T11:47:32.525018" hostname="Dell-5320" /></testsuites>
+<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="13" time="19.587" timestamp="2024-10-09T12:08:16.360052" hostname="Dell-5320"><testcase classname="tests.test_metrics" name="test_all_metrics_initialise" time="0.238" /><testcase classname="tests.test_metrics" name="test_all_metrics_images_initialise" time="0.225" /><testcase classname="tests.test_metrics" name="test_all_metrics_process_image" time="2.064" /><testcase classname="tests.test_metrics" name="test_all_metric_images_process_image" time="0.253" /><testcase classname="tests.test_transforms" name="test_all_transforms_init_value_no_change_image" time="0.259" /><testcase classname="tests.test_transforms" name="test_all_transforms_min_max_specified" time="0.236" /><testcase classname="tests.test_transforms" name="test_all_transforms_min_change_image" time="0.279" /><testcase classname="tests.test_transforms" name="test_all_transforms_max_change_image" time="0.316" /><testcase classname="tests.UI.test_sliders" name="test_sliders" time="1.173" /><testcase classname="tests.notebook_examples.test_1_making_the_UI" name="test_build_1" time="1.011" /><testcase classname="tests.notebook_examples.test_2_simple_customisation" name="test_build_2" time="1.299" /><testcase classname="tests.notebook_examples.test_3_customisation_details" name="test_3" time="3.005" /><testcase classname="tests.notebook_examples.test_4_experiment" name="test_experiment_runs" time="6.290" /></testsuite></testsuites>
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="0" time="2.527" timestamp="2024-10-09T11:47:32.525018" hostname="Dell-5320" /></testsuites>
		<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="13" time="19.587" timestamp="2024-10-09T12:08:16.360052" hostname="Dell-5320"><testcase classname="tests.test_metrics" name="test_all_metrics_initialise" time="0.238" /><testcase classname="tests.test_metrics" name="test_all_metrics_images_initialise" time="0.225" /><testcase classname="tests.test_metrics" name="test_all_metrics_process_image" time="2.064" /><testcase classname="tests.test_metrics" name="test_all_metric_images_process_image" time="0.253" /><testcase classname="tests.test_transforms" name="test_all_transforms_init_value_no_change_image" time="0.259" /><testcase classname="tests.test_transforms" name="test_all_transforms_min_max_specified" time="0.236" /><testcase classname="tests.test_transforms" name="test_all_transforms_min_change_image" time="0.279" /><testcase classname="tests.test_transforms" name="test_all_transforms_max_change_image" time="0.316" /><testcase classname="tests.UI.test_sliders" name="test_sliders" time="1.173" /><testcase classname="tests.notebook_examples.test_1_making_the_UI" name="test_build_1" time="1.011" /><testcase classname="tests.notebook_examples.test_2_simple_customisation" name="test_build_2" time="1.299" /><testcase classname="tests.notebook_examples.test_3_customisation_details" name="test_3" time="3.005" /><testcase classname="tests.notebook_examples.test_4_experiment" name="test_experiment_runs" time="6.290" /></testsuite></testsuites>