chore: Fixed all build errors

Author: Joachim

conf.py

@@ -41,7 +41,7 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', 'old', 'README.md']
 
 
 # -- Options for HTML output -------------------------------------------------

docs/intro/about.md

@@ -21,4 +21,4 @@ Features include:
 - Side by side image comparison                            
 
 
-To find out more, check out the [original publication introducing ImageC](https://pubmed.ncbi.nlm.nih.gov/36437554/) or {doc}`dive into the tutorials <../tutorials/index>` to see some of what it can do.
+To find out more, check out the [original publication introducing ImageC](https://pubmed.ncbi.nlm.nih.gov/36437554/).

docs/intro/installation.md

@@ -2,14 +2,21 @@
 
 ## Which ImageC download do I need?
 
+:::{hint}
 It is recommended to use ImageC under Linux for best stability and performance.
+:::
+
+:::{note}
 Because of licensing issues, ImageC is not available for Mac yet.
+:::
+
 
 On **Linux** use `imagec-x64-linux-bundle.zip` from the [GithHub release](https://github.com/joda01/imagec/releases) page.
 
 On **Windows** use `imagec-x64-win-bundle.zip` form the [GithHub release](https://github.com/joda01/imagec/releases) page. 
 
 
+
 ## Download & install
 
 There are signed and unsigned versions available for ImageC.
@@ -24,9 +31,7 @@ If you use an unsigned version you may need to take a few extra steps to get it
 - On **Windows**, if you want to use a signed version, download the {program}`imagec-x64-win-signed.exe` from a release with title `[signed]`.
   - Copy the downloaded `exe` into the folder beside the `imagec.exe`.
   - Double-click on the {program}`imagec-x64-win-signed.exe` to launch the application
-- On **macOS**, right-click the `.pkg` file, then choose 'Open' (you might need to do this twice)
-  - If you're using an M1/M2/M3 Mac, please check out the [notes on Apple silicon](apple-silicon)
 
-See {ref}`Troubleshooting` for more information.
+
 
 

docs/starting/export.md

@@ -7,7 +7,7 @@ If the resulting data should be further processed outside ImageC the export func
 Clicking on {guilabel}`Export` exports the current view (plate, well or image) to an XLSX formatted file which can be opened with e.g. Excel or R.
 
 :::{figure} images/screenshot_export.png
-:class: full-image
+:class: medium-image
 
 Export dialog
 :::

docs/starting/first_steps.md

@@ -12,7 +12,7 @@ The tutorial will demonstrate the following:
 - Export results
 
 
-## Getting started
+## Analyze images
 
 :::{note}
 If you have problems running ImageC see {doc}`here <../intro/installation>`.
@@ -35,7 +35,7 @@ Enter basic information on your project and group your images.
 
 
 :::{figure} images/screenshot_start_wizard.png
-:class: full-image
+:class: small-image
 
 ImageC new project wizard
 :::
@@ -170,7 +170,7 @@ With the back button on the top left the overview panel is displayed again.
 After all channels are added and all needed channel settings are done, the analysis can be started by pressing the {guilabel}`Run` button on the top.
 
 :::{figure} images/screenshot_running.png
-:class: full-image
+:class: small-image
 
 Analysis running
 :::

index.md

@@ -15,7 +15,7 @@ This page hosts the documentation for **ImageC {{ env.config.version }}.x**.
 
 
 ```{toctree}
-:caption: 'Full contents:'
+:caption: 'Contents:'
 :maxdepth: 2
 
 docs/intro/index

old/mac.md

@@ -0,0 +1,2 @@
+- On **macOS**, right-click the `.pkg` file, then choose 'Open' (you might need to do this twice)
+  - If you're using an M1/M2/M3 Mac, please check out the [notes on Apple silicon](apple-silicon)