216 lines
11 KiB
Plaintext
Executable File
216 lines
11 KiB
Plaintext
Executable File
This worked for me to set up Matt's ResouceNotebook. I did have python already installed.
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Quickest start:
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Go to the directory where you'd like to install the repository. Make sure that there is not already a directory called AvidaResourceNotebook present. Then paste and run this in the terminal:
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git clone https://github.com/ruppmatt/AvidaResourceNotebook && cd AvidaResourceNotebook && git clone https://github.com/devosoft/avida && cd avida && ./build_avida && cd .. && virtualenv -p `which python3` venv && . venv/bin/activate && pip install -r requirements.txt && ln -s ../avida/cbuild/work/avida default_config/avida && cd default_config && ./avida && cd ..
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At that point you can launch the notebook by:
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jupyter notebook
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————————————————————————————————————————————————————————————————————————————————————————————
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Avida resources animations
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————————————————————————————————————————————————————————————————————————————————————————————
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To build avida go to avida-projects/avida and run
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./build_avida
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folder structure for this project
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avida-projects/
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resources/
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avida/ soft link to avida under work in avida folder below
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venv/
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avida/
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cbuiid/
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work/
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avida
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*.cfg
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*.org
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to set up softlink go to the resources/avida folder
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ln -s ../../avida/cbuild/work/avida .
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cp ../../avida/cbuild/work/*.cfg .
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cp ../../avida/cbuild/work/default-heads.org .
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——————————————————————————
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Files: in general
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——————————————————————————
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analyze.cfg - for analyze mode (avdia -a) can be blank, but needs to exist
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utility to analyze after the fact. can be blank, but must exist.
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avida.cfg - global configuration
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environment.cfg
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eventts.cfg
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instset-heads.cfg - instruction set list
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default-head.org default ancestor
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not using the following so we removed them
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>rm instset-heads-sex.cfg instset-transsmt.cfg
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————————————————————————————————————————————————————————————————————————————————————————————
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Getting Jupyter on Computer
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————————————————————————————————————————————————————————————————————————————————————————————
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I’m putting this in a folder called avida-projects
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Create virtual environment by going to the folder where the virtual environment will be crated and running:
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>virtualenv -p /Library/Frameworks/Python.framework/Versions/3.6/bin/python3 venv
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Then activate the virtual environment
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>source venv/bin/activate
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path for python3 might be different on a different computer.
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Matt then supplied requirements.txt file that goes in the avida-stuff folder
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So then in the same folder run
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>pip install -r requirements.txt
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Matt also provided Animate Spatial Resources.ipynb
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————————————————————————————————————————————————————————————————————————————————————————————
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to run jupyter python notebook
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————————————————————————————————————————————————————————————————————————————————————————————
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activate the virtual environment if that has not been done already
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>source venv/bin/activate
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python -m jupyter notebook
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————————————————————————————————————————————————————————————————————————————————————————————
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In the Notebook
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————————————————————————————————————————————————————————————————————————————————————————————
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TO run: In the Cells dropdown menu, Click “Run Cells”
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or <control><enter> to run the cell that one is currently in
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In [ ] beside the cell gives some status information
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empty = never executed
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[#] what order it was executed (such as [1]
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[*} executing or about to be executed
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To start clean use the Kernel menu
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python is single threaded
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- interupt will stop the kernel (stop running)
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-
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——————————————————————————
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Command Mode:
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——————————————————————————
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When the vertical line on the left is blue, it is in command mode
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h: gives some command listings
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<esc> got me into command mode
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——————————————————————————
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Typing Mode
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——————————————————————————
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The vertical line on the left is green
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clicking in the cell put it in this mode.
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————————————————————————————————————————————————————————————————————————————————————————————
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Test to see that avida runs
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————————————————————————————————————————————————————————————————————————————————————————————
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go to avida-projects/resources/avida
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>./avida
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to clear the data folder (output created when running avida)
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>rm -rf data
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————————————————————————————————————————————————————————————————————————————————————————————
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First Experiment with one non-reproducing organism and let resources flow
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————————————————————————————————————————————————————————————————————————————————————————————
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Files
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analyze.cfg - for analyze mode (avdia -a) can be blank, but needs to exist
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avida.cfg -
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disable mutations
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disable death
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environment.cfg
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eventts.cfg
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only inject
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printSpatial Resources
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Exit
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instset-heads.cfg - (add nop-x to end)
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default-head.org default ancestor
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replace
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h-divide w/ nop-x
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————————————————————————————————————————————————————————————————————————————————————————————
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vim notes
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————————————————————————————————————————————————————————————————————————————————————————————
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vim cheatsheet on line to find more help on vim
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vim filename
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<esc> put in command mode
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in commmand mode
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G - puts at end of file
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gg - goes to the top
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o - opens an new line below and goes into insert mode
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O - opens a new line above the current line and goes into insert mode
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i - goes into insert mode
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:wq - write quit the colon is important
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R - replace mode
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0 - go to the start of the line
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$ - go to the end of the line
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/ - begin search process
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:nohls to get rid of highlighting from search
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:19 jumps to line 19 for example
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————————————————————————————————————————————————————————————————————————————————————————————
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https://docs.google.com/spreadsheets/d/1ZS9OT1Om0PYd_ePamXXgr1MhGPrC7ZcvP-7rUCqq7Gs/edit#gid=0
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————————————————————————————————————————————————————————————————————————————————————————————
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Asking Students about Nature of Science
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“Science and the Citezin”
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Nature and Process of Science”
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General Education at the college level - Utah State regional campus (20 students)
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Mike will interview over Zoom in December
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how does this fit into experimental design.
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Nature and Practice of Science.
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————————————————————————————————————————————————————————————————————————————————————————————
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git reset --hard to revert back to last clone commit or pull or clone
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git reset --hard origin/master to pull to latest and erase local changes.
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origin is the name of the remote (git hub) branch
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start virtual environment
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. venv/bin/activate
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————————————————————————————————————————————————————————————————————————————————————————————
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Info about how the python notebook works.
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Currently developing on avidares
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this is a package because it has a file called __init__.py
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not full, because there is no setup.py file that would let .pip install it (part of the Easy_setup)
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avidares.SingleExperiment is getting SingleExperiment is module (file) withing the package avidares
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classes in SingleExperiment that mostly use
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ResourceExperiment.
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ResourceExperimentAnimation
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classes in FactoredExperiment that mostly use
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ResourceFactoredExperiment
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ResourceFactoredExperimentIterator
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ResourceFactoredExperimentAnimation
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