Installation Guide¶
The easises way to install InspectorCell is via conda, a package system that not only manages Python, but also binary dependencies. It comes as slim lightweight distribution miniconda or as full distribution plattform anaconda Installation via pip and python virtual environment is possible, but might invole extra steps not covered in this documentation.
As a very first step, checkout the InspectorCell repository and change dir into it
$> git clone https://gitlab.com/InspectorCell/inspectorcell.git
$> cd inspectorcell
There, on linux you can use the icell utility script, or install by hand
Bash install script icell¶
For your convenience, there is an automated installation script, which creates a local virtual environment to install InspectorCell with Orange3 and all dependencies
$> ./icell -h
Basic usage: icell -i {conda,mamba,venv}
icell -c <cmd>
icell -[hrv]
Options:
h This help
i <variant> Install into '/mnt/storage/phd/src/inspectorcell/icell_venv' using <env> = 'conda', 'mamba' or 'venv'
r remove installed environment, if exists
c <cmd> Activate environment and run <cmd>
d Build and open the HTML documentation (will install sphinx)
t Run unit and integration tests (will install pytest)
v Print version strings and exit
Installation of InspectorCell and all its dependencies can be done using conda or Python 3.7 Virtual environmen (If you want a Python venv, have Python 3.7 installed, but you have an error, check that there is a link from python3.7 to python)
Installing and running InspectorCell via conda:
$> ./icell -i conda # install
...
$> ./icell # run
Installing and running InspectorCell via pythone virtual environment
$> ./icell -i venv # install
...
$> ./icell # run
By hand using conda¶
You will need conda installed and added to your PATH environment.
$> conda env create -p icell_venv -f condaenv.yml
Now you can install InspectorCell via drag and drop as described in the Quick Guide Alternatively, you can now install InspectorCell and its dependencies via
$> pip install . --force-reinstall --no-deps
To start inspectorcell you can either use the icell script
$> ./icell
Or activate the conda environment and start Oragne3 by hand
$> conda activate icell_venv
$> python -m Orange.canvas
By hand using venv¶
You will need Python 3.7 installed and added to your PATH environment. Python version larger than 3.7 should also work, but aren’t tested. Expect dependency conflicts.
Create a python virtual environment
$> python -m venv icell_venv
activate the environment and install the dependencies
$> source icel_venv/bin/activate # activate venv
$> python -m pip install --upgrade pip # (optional, upgrade pip)
$> python -m pip install -r requirements.txt # install dependencies
$> python -m pip install . --force-reinstall --no-deps # install dependencies
To start inspectorcell you can either use the icell script
$> ./icell
Or activate the cirtual environment and start Oragne3 by hand
$> source icel_venv/bin/activate
$> python -m Orange.canvas
Now you can install InspectorCell via drag and drop as described in the Quick Guide Alternatively, you can now install InspectorCell and its dependencies via
$> pip install . --force-reinstall --no-deps
To start inspectorcell you can either use the icell script
$> ./icell
Or activate the conda environment and start Oragne3 by hand
$> conda activate icell_venv
$> python -m Orange.canvas
Troubleshoots¶
How to get a commandline?¶
Got to the folder/directory where you want to use the commandline. In Windows 7
and later, click into the address bar of the explorer. Type cmd and hit
enter. Windows cmd commandline will open.
On linux, just rightclick on into the window. Most distributions have an option
Open Terminal here...
Missing Libraries¶
The GUI elements in InspectorCell depend on the Qt Framework. If you get an error like
ImportError: Compiled libraries cannot be found.
the Qt libraries might be missing. We suggest to install PyQt5. Using conda you do:
$> conda install PyQt5
or similar via pip
$> pip install PyQt5
