User Tools

Site Tools


analysis:nsb2019:week1

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
analysis:nsb2019:week1 [2021/06/14 11:51]
mvdm
analysis:nsb2019:week1 [2022/06/24 11:25] (current)
mvdm
Line 1: Line 1:
-~~DISCUSSION~~ 
- 
 ==== Module 1: Setting up ==== ==== Module 1: Setting up ====
  
Line 24: Line 22:
 At MBL, MATLAB should already be installed on lab computers. Verify it starts correctly; you should see its main window open up, including a panel called "​Command Window"​ greeting you with a prompt (''>>''​). At Dartmouth, follow [[https://​tech.dartmouth.edu/​itc/​services-support/​help-yourself/​knowledge-base/​matlab|these instructions]] to install MATLAB. Release 2018a seems to work. At MBL, MATLAB should already be installed on lab computers. Verify it starts correctly; you should see its main window open up, including a panel called "​Command Window"​ greeting you with a prompt (''>>''​). At Dartmouth, follow [[https://​tech.dartmouth.edu/​itc/​services-support/​help-yourself/​knowledge-base/​matlab|these instructions]] to install MATLAB. Release 2018a seems to work.
  
-=== Setting up GitHub ​===+=== Setting up Git ===
  
 Next, we need to obtain some existing MATLAB code that we will build on in this module. To do this, we will use [[http://​www.github.com|GitHub]]. Next, we need to obtain some existing MATLAB code that we will build on in this module. To do this, we will use [[http://​www.github.com|GitHub]].
Line 30: Line 28:
 %%GitHub%% is a system for "​distributed version control":​ it keeps track of changes to a set of files, such as pieces of MATLAB code, with one or more contributors. This system makes it easy to keep track of evolving code, and to share improvements between collaborators. Typical scenarios in which such version control is useful include, for instance, if you want to run the exact code that you used to generate some figure a while ago, but you've since made changes to the code; or the same analysis suddenly gives a different result and you want to track down what change caused it. If you are new to %%GitHub%%, you can watch the video under Resources above to get an overall idea of how it works and why it is useful. %%GitHub%% is a system for "​distributed version control":​ it keeps track of changes to a set of files, such as pieces of MATLAB code, with one or more contributors. This system makes it easy to keep track of evolving code, and to share improvements between collaborators. Typical scenarios in which such version control is useful include, for instance, if you want to run the exact code that you used to generate some figure a while ago, but you've since made changes to the code; or the same analysis suddenly gives a different result and you want to track down what change caused it. If you are new to %%GitHub%%, you can watch the video under Resources above to get an overall idea of how it works and why it is useful.
  
-Meanwhile, download and install the Git client of your choice if you don't already have one installed. This is a piece of software that will allow you to talk to %%GitHub%%, which is where the code is actually stored. For Windows, you can get git [[https://​git-scm.com/​download/​win | here]]. For more detailed info on different Git clients and setting up Git on other operating systems, see [[https://​help.github.com/​articles/​set-up-git|GitHub:​ Set Up Git]]. At some point in  +Meanwhile, download and install the Git client of your choice if you don't already have one installed. This is a piece of software that will allow you to talk to %%GitHub%%, which is where the code is actually stored. For Windows, you can get git [[https://​git-scm.com/​download/​win | here]]. For more detailed info on different Git clients and setting up Git on other operating systems, see [[https://​help.github.com/​articles/​set-up-git|GitHub:​ Set Up Git]].
-the installation process you will be asked for your account information;​ sign up for a [[http://​www.github.com|GitHub account]] if you don't already have one, and post your username in the module Slack channel.+
  
 === Cloning the module codebase === === Cloning the module codebase ===
  
-Now we are ready to use Git to create a local copy ("​clone"​) of the module codebase. On Windows, open a Git Shell, which you can do by typing ''​Git Shell''​ in the search box of the Start menu. Once open, note your working directory (displayed at the prompt of your now opened shell), and change it to a different location if you prefer, using the ``cd`` command. Once you are in an appropriate location, such as a new folder named ''​GitHub''​ on your local machine, type ''​git clone https://​github.com/​vandermeerlab/​nsb2021'',​ which will create a new folder ''​nsb2021''​ in your working directory.+Now we are ready to use Git to create a local copy ("​clone"​) of the module codebase. On Windows, open a PowerShell, which you can do by typing ''​PowerShell''​ in the search box of the Start menu. Once open, note your working directory (displayed at the prompt of your now opened shell), and change it to a different location if you prefer, using the ``cd`` command. Once you are in an appropriate location, such as a new folder named ''​GitHub''​ on your local machine, type ''​git clone https://​github.com/​vandermeerlab/​nsb2022'',​ which will create a new folder ''​nsb2022''​ in your working directory.
  
-Now, verify that the above steps have resulted in the creation of a ''​nsb2021''​ folder with various subfolders and files in it, indicating that you have a local copy of the codebase. Because Git is tracking the contents of this folder, it is now easy to "​pull"​ the latest version from %%GitHub%%:+Now, verify that the above steps have resulted in the creation of a ''​nsb2022''​ folder with various subfolders and files in it, indicating that you have a local copy of the codebase. Because Git is tracking the contents of this folder, it is now easy to "​pull"​ the latest version from %%GitHub%%:
  
 <​code>​ <​code>​
Line 46: Line 43:
  
 === A first commit and push ===  === A first commit and push === 
 +
 +To complete this part, sign up for a [[http://​www.github.com|GitHub account]] if you don't already have one, and post your username in the module Slack channel so I can give you permission to write to the code repository.
  
 First, if you haven'​t "done a pull" recently, do one now before starting the next step. First, if you haven'​t "done a pull" recently, do one now before starting the next step.
  
-Open the ''​README.md''​ file in the ''​nsb2021''​ folder. The ''​.md''​ extension is for %%Markdown%%,​ a lightweight set of commands to format text (syntax reference is [[https://​help.github.com/​articles/​markdown-basics | here]]).+Open the ''​README.md''​ file in the ''​nsb2022''​ folder. The ''​.md''​ extension is for %%Markdown%%,​ a lightweight set of commands to format text (syntax reference is [[https://​help.github.com/​articles/​markdown-basics | here]]).
  
-Add your name to the list, and save the file. Then navigate to the ''​nsb2021''​ repository in a shell and type ''​git status''​. Git should notice the change, but it says that this change is not yet "​staged for commit"​. In other words, git is not tracking this file. Let's fix this:+Add your name to the list, and save the file. Then navigate to the ''​nsb2022''​ repository in a shell and type ''​git status''​. Git should notice the change, but it says that this change is not yet "​staged for commit"​. In other words, git is not tracking this file. Let's fix this:
  
 <​code>​ <​code>​
Line 58: Line 57:
 </​code>​ </​code>​
  
-If you now do a ''​git status''​ you will see that you are ahead of the origin (the online repository) by 1 commit. This makes sense because you just made a change. Let's push this by doing ''​git push''​. If you get an "​access denied"​ type error, let me (mvdm) know and I will give you permission. If everything goes to plan you should now be able to see the updated README file [[https://​github.com/​vandermeerlab/​nsb2021| on GitHub]].+If you now do a ''​git status''​ you will see that you are ahead of the origin (the online repository) by 1 commit. This makes sense because you just made a change. Let's push this by doing ''​git push''​. If you get an "​access denied"​ type error, let me (mvdm) know and I will give you permission. If everything goes to plan you should now be able to see the updated README file [[https://​github.com/​vandermeerlab/​nsb2022| on GitHub]].
  
 A schematic of these basic operations (pull, commit, push) is shown below, using the amazing [[https://​www.dokuwiki.org/​plugin:​graphviz|DokuWiki plugin]] for [[http://​www.graphviz.org/​|GraphViz]]:​ A schematic of these basic operations (pull, commit, push) is shown below, using the amazing [[https://​www.dokuwiki.org/​plugin:​graphviz|DokuWiki plugin]] for [[http://​www.graphviz.org/​|GraphViz]]:​
Line 74: Line 73:
 === Using GitHub to acquire the FieldTrip toolbox === === Using GitHub to acquire the FieldTrip toolbox ===
  
-Using your experience from the previous section, create a local clone of the [[https://​github.com/​fieldtrip/​fieldtrip|FieldTrip toolbox]]. If you are using the command line (shell), make sure that you ''​cd''​ to your %%GitHub%% folder, i.e. that you are not within some other project such as ''​nsb2021'',​ before cloning. If things worked correctly you should have ''​fieldtrip''​ and ''​nsb2021''​ folders within your %%GitHub%% folder; **not** a ''​fieldtrip''​ folder within your ''​nsb2021''​ folder!+Using your experience from the previous section, create a local clone of the [[https://​github.com/​fieldtrip/​fieldtrip|FieldTrip toolbox]]. If you are using the command line (shell), make sure that you ''​cd''​ to your %%GitHub%% folder, i.e. that you are not within some other project such as ''​nsb2022'',​ before cloning. If things worked correctly you should have ''​fieldtrip''​ and ''​nsb2022''​ folders within your %%GitHub%% folder; **not** a ''​fieldtrip''​ folder within your ''​nsb2022''​ folder!
  
 This toolbox is useful for the analysis of local field potential (LFP) data. Be aware that it is about 1.2GB in size! This toolbox is useful for the analysis of local field potential (LFP) data. Be aware that it is about 1.2GB in size!
Line 87: Line 86:
 restoredefaultpath;​ clear classes; % start with a clean slate restoredefaultpath;​ clear classes; % start with a clean slate
  
-cd('​D:​\My_Documents\GitHub\nsb2021\code-matlab\shared'​);​ % or, wherever your code is located -- NOTE \shared subfolder!+cd('​D:​\My_Documents\GitHub\nsb2022\code-matlab\shared'​);​ % or, wherever your code is located -- NOTE \shared subfolder!
 p = genpath(pwd);​ % create list of all folders from here p = genpath(pwd);​ % create list of all folders from here
 addpath(p); addpath(p);
Line 99: Line 98:
 This ensures that whenever you click this button, you have a clean **path** (the set of folders, other than the current working directory, whose contents MATLAB can access) of only the MATLAB default plus your local versions of the two %%GitHub%% repositories. This ensures that whenever you click this button, you have a clean **path** (the set of folders, other than the current working directory, whose contents MATLAB can access) of only the MATLAB default plus your local versions of the two %%GitHub%% repositories.
  
-:!: When setting your path in MATLAB to add the ''​shared''​ folder only and //not// a parent folder such as ''​nsb2019''​. Adding the entire ''​nsb2019''​ folder will result in an error when you try to run the LoadCSC command later in the module!+:!: When setting your path in MATLAB to add the ''​shared''​ folder only and //not// a parent folder such as ''​nsb2022''​. Adding the entire ''​nsb2022''​ folder will result in an error when you try to run the LoadCSC command later in the module!
  
 Optional: if you don't like the ''​.git''​ folders in your path, you can get clever with [[http://​www.mathworks.com/​help/​matlab/​matlab_prog/​regular-expressions.html|regular expressions]] to remove these: Optional: if you don't like the ''​.git''​ folders in your path, you can get clever with [[http://​www.mathworks.com/​help/​matlab/​matlab_prog/​regular-expressions.html|regular expressions]] to remove these:
analysis/nsb2019/week1.1623685908.txt.gz · Last modified: 2021/06/14 11:51 by mvdm