Update documentation (#64)

* Fix typos
* Remove outdated license 
* merge data preparation and usage guide
* fix rst

README.md

@@ -5,51 +5,57 @@
 The data analyzed by C-COMPASS typically derives from proteomics fractionation samples that result in compartment-specific protein profiles. Our tool can be used to analyze datasets derived from various experimental techniques.
 
 ## Key Features
+
 - **Protein Localization Prediction**: Use a neural network to predict the spatial distribution of proteins within cellular compartments.
 - **Dynamic Compartment Composition Analysis**: Model changes in compartment composition based on protein abundance data under various conditions.
 - **Comparison of Biological Conditions**: Compare different biological conditions to identify and quantify relocalization of proteins and re-organization of cellular compartments.
 - **Multi-Omics Support**: Combine your proteomics experiment with different omics measurements such as lipidomics to bring your project to the spacial multi-omics level.
 - **User-Friendly Interface**: No coding skills required; the tool features a simple GUI for conducting analysis.
 
-## System Requirements
-- 64-bit Windows Operating System
-- **No** Python Installation Required
+## Documentation
+
+Further documentation is available at https://c-compass.readthedocs.io/en/latest/.
 
 ## Installation
 
 ### Single-file executables
 
-Single-file executables that don't require a Python installation are available on the release page.
+Single-file executables that don't require a Python installation are available
+on the release page for Linux, Windows, and MacOS. Download the appropriate
+file for your operating system and run it.
 
-On Windows, make sure to install the Microsoft C and C++ (MSVC) runtime libraries before ([further information](ttps://learn.microsoft.com/en-us/cpp/windows/latest-supported-vc-redist?view=msvc-170), [direct download](https://aka.ms/vs/17/release/vc_redist.x64.exe)).
+On Windows, make sure to install the Microsoft C and C++ (MSVC) runtime
+libraries before ([further information](ttps://learn.microsoft.com/en-us/cpp/windows/latest-supported-vc-redist?view=msvc-170),
+[direct download](https://aka.ms/vs/17/release/vc_redist.x64.exe)).
 
 ### Via pip
 
 ```bash
+# install
 pip install ccompass
+# launch the GUI
+ccompass
 ```
 
-### Prerequisites
-C-COMPASS requires Python>=3.10, and due to its `tensorflow` dependency Python<=3.12.
+Note that C-COMPASS currently requires Python>=3.10, and due to its
+`tensorflow` dependency Python<=3.12.
 
-#### Ubuntu
+On Ubuntu linux, installing the `python3-tk` package is required:
 
 ```bash
 sudo apt-get install python3-tk
 ```
 
 ## Usage
 
-To launch the GUI, run the following command:
-
-```bash
-ccompass
-```
+See also https://c-compass.readthedocs.io/en/latest/usage.html.
 
 ### Graphical User Interface (GUI)
-- The GUI will guide you through the process of loading and analyzing your proteomics dataset, including fractionation samples and Total Proteome samples.
-- Follow the on-screen instructions to perform the analysis and configure settings only if required
-- Standard parameters should fit for the majority of experiments. You **don't need to change the default settings!**
+
+* The GUI will guide you through the process of loading and analyzing your proteomics dataset, including fractionation samples and Total Proteome samples.
+*Follow the on-screen instructions to perform the analysis and configure settings only if required
+* Standard parameters should fit for the majority of experiments.
+  You **don't need to change the default settings!**
 
 ### Command-Line Usage (Optional)
 You can also run the software via the command line:
@@ -68,23 +74,24 @@ You can also run the software via the command line:
 - Principal analysis steps and calculations will be kept as they are in version 1.0 unless changes are suggested by the reviewers.
 
 ### Contributing
+
 Contributions to C-COMPASS are welcome! To contribute:
+
 1. **Fork the repository** on GitHub.
 2. **Create a new branch** for your changes.
 3. **Commit your changes**.
 4. **Submit a pull request**.
 
 ### License
+
 C-COMPASS is licensed under the BSD 3-Clause License.
 
 ### Trouble-Shooting
-- **SmartScreen Warning**: If Windows blocks the application via SmartScreen, this is due to the software being unsigned. Please consult your IT department to bypass this restriction if necessary.
-- **Long Path Issues on Windows**: If your system encounters long path errors, you can activate them in your registry under 'HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\FileSystem' by setting the value for **LongPathsEnabled* from 0 to 1.
+
+* **SmartScreen Warning**: If Windows blocks the application via SmartScreen, this is due to the software being unsigned. Please consult your IT department to bypass this restriction if necessary.
+* **Long Path Issues on Windows**: If your system encounters long path errors, you can activate them in your registry under 'HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\FileSystem' by setting the value for **LongPathsEnabled* from 0 to 1.
 
 ### Contact
-For any questions, contact [email protected]
 
-### Pre-Publication Information
-The software documentation to C-COMPASS is accessible under
-**/docs/build/html/index.html**
-and will be publicly available by the official release of C-COMPASS.
+For any questions, contact `[email protected]` or post an
+issue at https://github.com/ICB-DCM/C-COMPASS/issues/.

doc/changelog.rst

@@ -1,5 +1,5 @@
-VII. Changelog
-==============================
+Changelog
+=========
 
 Version 1.0.0
 -------------

doc/contributing.rst

@@ -1,5 +1,5 @@
-V. Contributions
-=========================
+Contributing
+============
 
 We welcome contributions to C-COMPASS and encourage the community to participate in its development. Whether you are fixing bugs, adding new features, or improving documentation, your help is greatly appreciated.
 
@@ -14,8 +14,8 @@ Before starting major changes, it's a good idea to open an issue to discuss the
 
 We appreciate your time and effort in making C-COMPASS even better!
 
-VI. Pre-commit Hooks
---------------------
+Pre-commit Hooks
+----------------
 
 We use `pre-commit <https://github.com/pre-commit/pre-commit>`__ hooks to
 ensure code quality and consistency. Pre-commit hooks automatically run checks

doc/faq.rst

@@ -1,12 +1,6 @@
-IV. Help
-================
+FAQ
+====
 
-1. FAQ
--------------------------------------
+**What if one or more of my gradients are missing some fractions?**
 
-   a. What if one or more of my gradients are missing some fractions?
-
-   A. By default, C-COMPASS analyses each replicate secparately which means it is not necessary that all fractionations are complete. However, if the number of remaining fractions is decreased, the prediction accuracy is affected. Furthermore, it can happen that the missing fraction is an important feature for a distinct compartment. You can check the correlation matrix for marker proteins and their median profile to evaluate how distinguishable your profiles still are.
-
-2. Trouble Shooting
--------------------
+A. By default, C-COMPASS analyses each replicate separately which means it is not necessary that all fractionations are complete. However, if the number of remaining fractions is decreased, the prediction accuracy is affected. Furthermore, it can happen that the missing fraction is an important feature for a distinct compartment. You can check the correlation matrix for marker proteins and their median profile to evaluate how distinguishable your profiles still are.

doc/index.rst

@@ -1,5 +1,5 @@
-Welcome to CCMPS Documentation
-==============================
+Welcome to C-COMPASS Documentation
+==================================
 
 Introduction
 ------------
@@ -18,7 +18,6 @@ With C-COMPASS, users can perform comprehensive quantitative analyses of compart
    :caption: Contents:
 
    installation.rst
-   preparation.rst
    usage.rst
    faq.rst
    contributing.rst

doc/installation.rst

@@ -1,29 +1,7 @@
-I. Installation
-==============================
-
-System Requirements
---------------------
-
-- 64-bit Windows Operating System
-
-
-Running the Software
---------------------
-
-- Download the ZIP file from the repository or release section.
-- Extract the ZIP file to any location on your machine.
-- Navigate to the extracted folder.
-- Double-click `C-CMPS.bat` to start the application.
-- The software will initialize the portable Python environment and launch the GUI (this may take a few minutes).
-
-
-Command-Line Usage (optional)
------------------------------
-
-You can also run the software via the command line:
-
-> python CCMPS.py
+Installation
+============
 
+See `https://github.com/ICB-DCM/C-COMPASS?tab=readme-ov-file#installation <https://github.com/ICB-DCM/C-COMPASS?tab=readme-ov-file#installation>`__ for the latest installation instructions.
 
 Trouble-Shooting
 ----------------

doc/license.rst

@@ -1,41 +1,5 @@
-VI. License
-===========
-
-**Note**
-
-WinPython components are distributed as they were received from
-their copyright holder, under their own copyright and/or license,
-and without any linking with each other.
-
-WinPython software collection (i.e., the collection of software,
-libraries, and documents) is licensed under the terms of the
-following license agreement.
-
-**WinPython License Agreement (MIT License)**
-
-Copyright (c) 2012 Pierre Raybaut, 2016+ WinPython team
-
-Permission is hereby granted, free of charge, to any person
-obtaining a copy of this software and associated documentation
-files (the "Software"), to deal in the Software without
-restriction, including without limitation the rights to use,
-copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the
-Software is furnished to do so, subject to the following
-conditions:
-
-The above copyright notice and this permission notice shall be
-included in all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
-OTHER DEALINGS IN THE SOFTWARE.
-
+License
+=======
 
 **C-COMPASS (BSD 3-Clause License)**