Collection of smaller changes in the documentation (#16)

* Update README.md * Update setup.cfg * Update README.md * Update README.md * upload illustrations * Update README.md * update images of doc * Update README.md
fish-quant · Nov 14, 2024 · befa0e3 · befa0e3
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diff --git a/README.md b/README.md
@@ -5,16 +5,24 @@
 
 Python library to control an automated fluidics system and perform acquisition on a microscope for sequential FISH experiments.
 
-**TESTED FOR WIN 10 only**: micromanager and most microscope controls work only under Windows.
+> :warning: **TESTED FOR WINDOWS only**: micromanager and most microscope controls work only under Windows.
+
+<img src="docs/instrumentation-control.png" width="400">
+
+## Protocols for smFISH experiments
+
+We provide detailed protocols for single molecule FISH adapated to autoFISH [**here**](https://drive.google.com/drive/folders/1m4SFZFpOHzQbgO7dFY38xFbccV2XqMKH?usp=sharing).
+
+<img src="docs/experimental-protocols.png" width="800">
 
 ## Documentation
 
 We provide details documentation for the fluidics system and the experimental workflows with the links below:
 
 ### Fluidics system and software usage
 
-- Documentation of this **package**: 
-  [**PDF**](https://drive.google.com/open?id=1-Fr_Dbg0eQDSbhBmq2gmJ1FDb4Uy_ToI&usp=drive_fs)  or 
+- Documentation to use Python **control software**: 
+  [**PDF**](https://drive.google.com/open?id=1-Fr_Dbg0eQDSbhBmq2gmJ1FDb4Uy_ToI&usp=drive_fs) or 
   [**WORD**](https://docs.google.com/document/d/1-IA6f02elFrF7JSLvXx199cNjnm8ciBB?rtpof=true&usp=drive_fs)
 
 - Documentation to **build the fluidics system**:
@@ -25,17 +33,19 @@ We provide details documentation for the fluidics system and the experimental wo
   [**PDF**](https://drive.google.com/open?id=1-bkihEoPfgZdNXIDN6bbxiwU0kXM9xOt&usp=drive_fs) or 
   [**WORD**](https://docs.google.com/document/d/1-ZXZ6kcjAJHre7fJ8rNfXpDT03TYYEI-?rtpof=true&usp=drive_fs)
 
+<img src="docs/fluidic-system.png" width="800">
+
 ## Getting started
 
 ### Installation
 
 We recommend using a package manager (conda) to maintain a clean Python installation. This nees to be done only once.
 
 1. Download latest version of miniconda from [**here**](https://docs.conda.io/en/latest/miniconda.html).
-2. Open Anaconda terminal and create dedicated environment: `conda create --name autofish python=3.9`
+2. Open Anaconda terminal and create dedicated environment: `conda create --name autofish python=3.10`
 3. Activate environment: `conda activate autofish`
 4. Pip install **autofish** (as an alternative see development installation below)
-   - Base version (without pycromanager) : `pip install -i https://test.pypi.org/simple/autofish`
+   - Base version (without pycromanager) : `pip install autofish`
    - [Optional] Install pycromanager : `pip install pycromanager`
 
 ### Starting autofish
@@ -46,7 +56,7 @@ We recommend using a package manager (conda) to maintain a clean Python installa
 ### Upgrading to a new version
 
 1. Open Anaconda terminal and activate environment: `conda activate autofish`
-2. Upgrade autoFISH `pip install --upgrade https://test.pypi.org/simple/autofish`
+2. Upgrade autoFISH `pip install --upgrade autofish`
 
 ### Development installation
 

diff --git a/docs/experimental-protocols.png b/docs/experimental-protocols.png
diff --git a/docs/fluidic-system.png b/docs/fluidic-system.png
diff --git a/docs/fluidics-overview.png b/docs/fluidics-overview.png
diff --git a/docs/instrumentation-control.png b/docs/instrumentation-control.png
diff --git a/setup.cfg b/setup.cfg
@@ -1,6 +1,6 @@
 [metadata]
 name = autofish
-version = 0.0.6
+version = 0.0.7
 author = Florian Mueller
 author_email = fmueller@pasteur.fr
 url = https://github.com/fish-quant/autofish
@@ -16,7 +16,7 @@ classifiers =
 packages = find:
 zip_safe = True
 include_package_data = True
-python_requires = >=3.9
+python_requires = >=3.10
 install_requires =
     pyserial
     PySimpleGUI==4.60.5