Install Miniconda on Mac

This post introduces how to install Miniconda on Mac.

(For installing Miniconda on Linux OS, check out this post.)

(For commonly used conda commands check this post.)

(For the comparison among Anaconda, Miniconda, and Virtualenv with pip, check this post.)

Step 1: download  Miniconda (bash installer) from

https://docs.conda.io/en/latest/miniconda.html 

see the highlighted in the pic below.

A file called Miniconda3-latest-MacOSX-x86_64.sh will be shown in your Downloads folder.

Step 2: Open a Terminal window.

(If you don’t know how to open a terminal window,  through lauchpad type in Terminal, you will see the application.)

In the terminal window, type in

$ cd Downloads

Step 3: run the bash “shell” script to install Miniconda

In the terminal window, type in the following.

$ bash Miniconda3-latest-MacOSX-x86_64.sh

Scroll through the license (press the Space bar or Enter to move through quickly), type ‘yes’ to approve the terms, and then accept all the installation defaults.

Step 4: Close the Terminal window, and open a new Terminal window.

in the newly opened Terminal window.

Type the following:

$ conda -V

If you see something like the following, it means you have successfully installed conda via miniconda on your Mac.

conda 4.5.11

Step 5: Uninstalling Miniconda

To uninstall Python Anconda/Miniconda, we just simply remove the installation folder and remove the environment variables set in the hidden file .bash_profile in your home directory. For my installation, it will be just like this.

$ rm -rf /users/my-user-name/miniconda/
$ rm -rf /users/my-user-name/anaconda/

Then, you can edit the .bash_profile file and remove the following entries added for Anaconda/Miniconda directory from your PATH environment variable.

# added by Miniconda3 installer
$ export PATH="/Users/my-user-name/miniconda3/bin:$PATH"
# added by Anaconda3 installer
$ export PATH="/Users/my-user-name/anaconda3/bin:$PATH"

If you do not know where the hidden .bash_profile is located and how to edit it, see below for detailed instructions.

(1) Open a new terminal and go to your home directory. You can do this by using the command below.

$ cd

(2) use the following command to list all files, including hidden files in your home directory.

$ ls -a 
# you should see there is a file called .bash_profile.

(3) Use the cat command to see the contents of the hidden file .bash_profile. Type the following command into your terminal.

$ cat .bash_profile

You will see something like the following (depends on what you installed, if you installed Miniconda3, you will only see the first two lines. If you installed Anaconda3, you will see the bottom two lines.

# added by Miniconda3 installer 
$ export PATH="/Users/my-user-name/miniconda3/bin:$PATH" 

# added by Anaconda3 installer 
$ export PATH="/Users/my-user-name/anaconda3/bin:$PATH"

(4) To remove installed Miniconda/Anaconda from your .bash_profile use the command below to edit the file using the nano editor.

$ nano .bash_profile

Remove the Miniconda /Anoconda path in your .bash_profile hidden file.

Then Type control + X to exit out of nano

Save changes by typing Y.

Close the terminal, and now Miniconda/Anaconda should be successfully uninstalled from your Mac.

 

(Tested on macOS Mojave. Note that you can install Miniconda onto your Mac even when you are not an admin user.)

For commonly used conda commands check this post.

For the comparison among Anaconda, Miniconda, and Virtualenv with pip, check this post.

 

 

 

 

 

 

Anaconda vs. Miniconda vs. Virtualenv

This post briefly introduces which to choose among Anaconda, Miniconda, and Virtualenv.

If you have used pip and virtualenv in the past, you can use conda to perform all of the same operations. Pip is a package manager, and virtualenv is an environment manager; and conda is both.

Specifically, conda is a packaging tool and installer that aims to do more than what pip does; it handles library dependencies outside of the Python packages as well as the Python packages themselves. Conda also creates a virtual environment, like virtualenv does.

Both Anaconda and Miniconda uses Conda as the package manager. The difference among Anaconda and Miniconda is that Miniconda only comes the package management system. So when you install it, there is just the management system and not coming with a bundle of pre-installed packages like Anaconda does. Once Conda is installed, you can then install whatever package you need from scratch along with any desired version of Python.

Choose Anaconda if you:

  • Are new to conda or Python
  • Prefer having Python and 720+ open source certified packages automatically installed at once
  • Have the time and disk space (a few minutes and 3 GB), and/or
  • Don’t want to install each of the packages you want to use individually.

Choose Miniconda if you:

  • Know what package(s) you need to install
  • Do not have time or disk space (about 3 GB) to install over 720+ packages (many of the packages are never used and could be easily installed when needed), and/or
  • Just want fast access to Python and the conda commands, and prefer to sorting out the other packages later.

Choose Virtualenv only when you have sudo access to the machine you are working on. It is much easier to setup conda rather than virtualenv for a regular (i.e., non sudo/root) user on a linux/Mac machine.

I use Miniconda myself (because it is much more light weight than Anaconda) when I need to setup python programming environment and when I do not have sudo privilege, and I use Virtualenv when I have sudo access on the machine.

(Thanks to  Dr. Brendt Wohlberg  for introducing Miniconda — Miniconda makes me switching from pip & virtualenv to conda.)

References

 

Setting up Python and Jupyter Notebook on Mac

This page provides the instructions for how to install and run IPython and  Jupyter Notebook in a virtualenv  on Mac.

Most probably your Mac has already come with Python installed (see step 1 and step 2 below to check whether Python and Python 3 is installed on your mac, because my Mac book air has both Python and Python3.6 installed, I will go ahead to step 3 to install virtualenv).  

Open a terminal on your mac and type in Python and Python3 to see whether Python and Python3 installed on your mac. See below for example.

Follow the steps below for detailed instructions.

Step 1: Check whether Python is installed on your Mac

To test whether your Mac has Python 2.x or 3.x, look at the instructions below.

Open a terminal  (in your launchpad, type in terminal, and then click and open it.)

Type in python, if you see similar thing as the pic shown below, it means python 2.7 was installed on your Mac

type exit() to exit from the Python 2.7 environment

Type python3 in your terminal, if you see similar warning as the pic shown below, it means you will need to install Python 3 (see the steps below for installation). If you see older version (< 3.5) of python 3 installed on your mac, follow step 2 to install Python 3.5

Step 2: Install Python 3.5

I recommend you download Python 3.5.4 from here, if you do not have Python 3.x pre-installed on your mac.

https://www.python.org/downloads/mac-osx/ 

Click the installer and install it following the wizard.

When you finish the installation, type python3 in your terminal, if you see similar stuff in the pic below, Python 3.5 is installed successfully and you are ready to proceed to step 3.

Step 3: Install virtualenv 

Note: the command text in blue is the exact command you should type into your terminal, the same through this whole instruction.

Lipings-MacBook-Pro:~ Liping$ pip3 install virtualenv

Step 4: Setup virtualenv environment

Issue the command below to set up a virtualenv environment that we will use later, using the vitualenvwe installed in step 3 above.

$ virtualenv --system-site-packages -p python3 ~/ipy-jupyter-venv3

Step 5: Install IPython

Before installing IPython and Jupyter Notebook, be sure to activate your python virtual environment first.

$ source ~/ipy-jupyter-venv3/bin/activate 
(ipy-jupyter-venv3)$  # Your prompt should change

Type the following command to install IPython

(ipy-jupyter-venv3) liping:~pip3 install ipython

Step 6: Install Jupyter Notebook

Use the following command to install Jupyter Notebook

(ipy-jupyter-venv3) liping:~$ pip3 install jupyter

Step 7: Test jupypter notebook installation

(ipy-jupyter-venv3) liping:~$ which python3

/Users/Liping/ipy-jupyter-venv3/bin/python3
#for python 3.x
(ipy-jupyter-venv3) liping:~$ which ipython3

/Users/Liping/ipy-jupyter-venv3/bin/ipython3
#for python 3.x
(ipy-jupyter-venv3) liping:~$ which jupyter-notebook

/Users/Liping/ipy-jupyter-venv3/bin/jupyter-notebook

Step 8: Add Kernel

The Jupyter Notebook and other frontends automatically ensure that the IPython kernel is available. However, if you want to use a kernel with a different version of Python, or in a virtualenv environment, you’ll need to install that manually. 

We are using virutalenv, so we need to install IPython kernel in the virtualenv we created in Step 4 above.

(ipy-jupyter-venv3) liping:~$  python3 -m ipykernel install --user --name myipy_jupter_env3 --display-name "ipy-jupyter-venv3"

Installed kernelspec myipy_jupter_env3 in /Users/Liping/Library/Jupyter/kernels/myipy_jupter_env3

 

Step 9: Before we are running our jupyter Notebook, let us create a folder from which we will start our jupyter notebook.

The following command will change our directory to Desktop (cd refers to change directory)

(ipy-jupyter-venv3) Lipings-MacBook-Pro:~ Liping$ cd Desktop 

the following command will help us create a folder named Geog597_ML_session under our Desktop folder

(ipy-jupyter-venv3) Lipings-MacBook-Pro:Desktop Liping$ mkdir test_jupyter

the following command will change our directory into the folder we just created.

(ipy-jupyter-venv3) Lipings-MacBook-Pro:Desktop Liping$ cd test_jupyter/

(ipy-jupyter-venv3) Lipings-MacBook-Pro:test_jupyter Liping$ 

Step 10: Run Jupyter Notebook

(ipy-jupyter-venv3) Lipings-MacBook-Pro:test_jupyter Liping$ jupyter-notebook

Then your default browser should automatically open a web page similar to the one shown below.

If the web page does not show up automatically, just type localhost:8888 into your browser, you should see the page shown above.

 

Step 11: Testing and Using Jupyter Notebook

By this point you should have Jupyter Notebook running, and you should be connected to it using a web browser. Jupyter Notebook is very powerful and has many features. Below I will outline a few of the basic features to get you started using the notebook. Automatically, Jupyter Notebook will show all of the files and folders in the directory it is run from (for our case, it is empty now, because we have not put anything in that folder Desktop/test_jupyter we just created in step 9 ).

To create a new notebook file, select New > ipy-jupyter-venv3 from the top right pull-down menu (Note: this is the so called kernel we installed in Step 8 above):

This will open a notebook. We can now run Python code in the cell or change the cell to markdown (markdown is for note, not for code). For example, change the first cell to accept Markdown by clicking Cell > Cell Type > Markdown from the top navigation bar, or by click the Markdown shown in the pic below. We can now write notes using Markdown,  for example, type the following into the cell after changing it to markdown:

# Testing

Hit Ctrl + Enter, you will see it the text changed into heading style.

          Then insert one cell by the menu shown below (insert Cell Below).

type in the following

a = 5
b = 10
print (a+b)

and then hit Ctrl + Enter.  You should see the following.

Step 12: Stop jupyter Notebook.

To stop the Jupyter Notebook process, press CTRL+C,

type Y, and hit ENTER to confirm. The following will be displayed:

Step 13: Exit virtualenv environment

Once you are done, remember to exit your virtualenv using the following command:

(ipy-jupyter-venv3) Lipings-MacBook-Pro:test_jupyter Liping$

deactivate

Note that your prompt changes back (see the pic below)

Step 14: Instructions for using Jupyter Notebook next time

Next time when you need to use you jupyther notebook, following the steps summarized below.

Lipings-MacBook-Pro:~ Liping$ source ~/ipy-jupyter-venv3/bin/activate  

(ipy-jupyter-venv3)$  # Your prompt should change

Change directory to where you would like to start your jupyter-notebook

(ipy-jupyter-venv3) Lipings-MacBook-Pro:~ Liping$ cd Desktop/test_jupyter

(ipy-jupyter-venv3) Lipings-MacBook-Pro:test_jupyter Liping$ 

Run jupyter notebook:

(ipy-jupyter-venv3) Lipings-MacBook-Pro:test_jupyter Liping$ jupyter-notebook

 

Congratulations, you have now set up ipython and jupyter notebook on your mac!

Timing how long a python script runs

This post introduces several ways to find out how long a python script takes to complete its execution.

  • If you are using Linux or Mac OS, in your terminal
$ time ./your_script.py
  • Several ways to do the task by adding a few lines of code in your py script.
import time
startTime = time.time()

your_func() #python3: print ("It took", time.time() - startTime, "seconds.")

See the following for an example in python 3. 

import time
import functools

startTime = time.time()

print(functools.reduce(lambda x,y: x+y, [47,11,42,13]))

#python3:
print ("It took", time.time() - startTime, "seconds.")

Another way to do the same thing:

from datetime import datetime
startTime = datetime.now()

#do something

#Python 2: 
print datetime.now() - startTime 

#Python 3: 
print(datetime.now() - startTime)

One more way to do the same thing with a nicely formatted output.

import sys
import timeit

startTime = timeit.default_timer()

#do some nice things...

stopTime = timeit.default_timer()
totalRunningTime = stopTime - startTime

# output running time in a nice format.
mins, secs = divmod(totalRunningTime, 60)
hours, mins = divmod(mins, 60)

sys.stdout.write("Total running time: %d:%d:%d.\n" % (hours, mins, secs))

If you want to compare two blocks of code / functions quickly you can do the following:

import timeit

startTime = timeit.default_timer()
your_func1()
#python3
print(timeit.default_timer() - startTime)

startTime2 = timeit.default_timer()
your_func2()
#python3
print(timeit.default_timer() - starTime2)

[django] Sending matplotlib generated figure(s) to django web app

This post introduces how to serve the figures generated by matplotlib to django web app without saving on the server.

In your django views py file, import the following libraries

import matplotlib
matplotlib.use("Agg")
import matplotlib.pyplot as plt

from io import BytesIO
import base64

Note: the two lines of code above in blue need to be placed at the very beginning of the py script; otherwise, you would meet the following error: _tkinter.TclError: no display name and no $DISPLAY environment variable.

In the views py file, in the function that you defined to pass the image data to the front end template file, add the following code:

buf = BytesIO()
plt.savefig(buf, format='png', dpi=300)
image_base64 = base64.b64encode(buf.getvalue()).decode('utf-8').replace('\n', '')
buf.close()

Note: in the function that you defined to pass the image data to the front end template file in your views py file, remember to send the value of the variable image_base64 via, for example, json.

Now, in your front end template file, you can add the following image tag.

<img src="data:image/png;base64,{{image_base64}}" alt="some text to display to your users when the image does not show correctly" width=500 height=auto />

You now should be able to see the figure displayed on your web app page:)

For more details about using data url to pass image data to front end html file, check here (pdf).

 

 

Run Jupyter notebook from terminal with tmux

This post will walk you through how to run a Jupyter notebook script from terminal with tmux (check here for my post about tmux usage).

When you are running Jupyter on a remote server or on cluster/ cloud resources, there are situations where you would like the Jupyter on the remote server or cluster continue running without termination when you shut down your laptop or desktop that you used to access the remote server. tmux will help with this.

In this post, we cover how to let your jupyter notebook running on a remote server continue running without termination via tmux.

Step 1: connect to your remote server with port forwarding

check the Step 5-2 in my post here about setting up Jupyter notebook for how to access your remote server with port forwarding, if you are not familiar with it.

Step 2: install tmux 

 check here for my post about tmux installation and usage

Step 3: install runipy  python package

Check here for runipy installation and usage.

Step 4: in your terminal type the following command, then it will go into tmux window

$ tmux

Step 5: Start jupyter notebook within your tmux session with the following command

$ jupyter notebook --no-browser

The –no-browser option prevents Jupyter from automatically opening a browser window.

Let this terminal stay running.

Step 6: from your laptop, ssh to your remote server (does not need port forwarding this time)

Step 7: cd to where the jupyter notebook script located that you would like to run from terminal

If you do not know what does cd mean and do, check my post for a list of commonly used Linux commands.

Step 8:  use the following command to run your ipynb script (this will save the output of each cell back to the notebook file)

$ runipy -o MyNotebook.ipynb 

To save the notebook output as a new notebook, run:

$ runipy MyNotebook.ipynb OutputNotebook.ipynb

If your ipynb script without any error itself, it should be running on the server now.

Step 9:  Things to pay attention to:

Do not close the terminal where you run the ipynb script within tmux session on your computer that you used to connect to the remote server, that will cause the termination of running the ipynb. But you can make your laptop in sleep or even shut down the computer, the tmux session will keep the ipynb running on your remote server and save the output in the ipynb.

References:

https://www.datasciencebytes.com/bytes/2015/12/18/using-jupyter-notebooks-securely-on-remote-linux-machines/ 

http://forums.fast.ai/t/ipython-notebook-on-a-remote-server-with-tmux/10044/2

Checking from command line if Jupyter server is running and kill if needed

This post provides instructions on how to check whether a Jupyter server is running from command line and kill if needed.

Normally, you can kill a Jupyter server from the same terminal window where you launched your Jupyter notebook by hit CTRL + C, then type yes, to shut down the kernels of Your jupyter notebook.

But, there are situations where you want to know whether a Jupyter-notebook running on your remote server, but the Jupyter notebook was started on another desktop (e.g., your office desktop), (and now you are working at home from your laptop, and want to check whether the notebook is still running).

After you login to your Server where you Jupyter notebook was installed and running, you can use the following command to list runing notebooks.

$ jupyter notebook list

You will see a list of running notebooks in the terminal, if you have several running ones.

You can use the following command to kill specific notebook (identified by the port it runs the jupyter) that you would like to stop.

$ jupyter notebook stop 8888

P.S.:

Each server should start on a new port. jupyter notebook list is reading a set of data files – each notebook server you run writes a file when it starts up, and attempts to remove it when it shuts down. If you see different listed servers on the same port, that means some of them exited without successful removal of the file when it created (for example, unexpected shut down of the notebook would cause this happens).

 

References:

https://github.com/jupyter/notebook/issues/1950

https://github.com/jupyter/notebook/issues/2844

 

 

Run Jupyter Notebook script from terminal

Normally people run jupyter notebook via browser, but in some situation, we will need to run it from terminal, for example, when running the script takes long time.

This post introduces how to run a jupyter notebook script from terminal.

Solution  I:

runipy can do this. runipy will run all cells in a notebook. If an error occurs, the process will stop.

  • Install  runipy package
$ pip3 install runipy # for python 3.x 
$ pip install runipy  # for python 2.x
  • runipy command-line usages

 

  • To run a .ipynb file as a script, run:
$ runipy MyNotebook.ipynb
  • To save the output of each cell back to the notebook file, run:
$ runipy -o MyNotebook.ipynb
  • To save the notebook output as a new notebook, run:
$ runipy MyNotebook.ipynb OutputNotebook.ipynb
  • To run a .ipynb file and generate an HTML report, run:
$ runipy MyNotebook.ipynb --html report.html

 

Solution  II:

The latest versions of jupyter comes with  the nbconvert command tool for notebook conversion allows us  to do this without any extra packages.

Just go to your terminal and type:

$ jupyter nbconvert --to notebook --execute mynotebook.ipynb --output mynotebook.ipynb

This will open the notebook, execute it, capture new output, and save the result in mynotebook.nbconvert.ipynb. By default, nbconvert will abort conversion if any exceptions occur during execution of a cell. If you specify --allow-errors (in addition to the --execute flag) then conversion will continue and the output from any exception will be included in the cell output.

if you meet this error,

raise exception(“Cell execution timed out”)

$ jupyter nbconvert --to notebook --execute --allow-errors --ExecutePreprocessor.timeout=180 mynotebook.ipynb 

You can use the –inplace flag as well:

$ jupyter nbconvert --to notebook --execute --inplace mynotebook.ipynb

 

check here for more (updated) usages about nbconvert jupyter command tool.

 

References:

https://pypi.python.org/pypi/runipy

http://nbconvert.readthedocs.io/en/latest/usage.html#convert-notebook 

Can I run Jupyter notebook cells in commandline?

 

 

 

 

[Python] get a list of sorted directories and/or files

This posts provides a piece of Python code to sort files, folders, and the combination of files and folders in a given directory. It works for Python 3.x. (It should work for Python 2.x, if you change the syntax of print statement to that of Python 2.x.)

Return the oldest and newest file(s), folder(s), or file(s) +folder(s) in a given directory and sort them by modified time.

import os

# change this as the parent directory name of the files you would like to sort

path = 'parent_directory_name'

if (os.path.isdir(path) and (not os.path.exists(path))):

   print("the directory does not exist")
else:
   os.chdir(path)

   # files varialbe contains all files and folders under the path directory

   files = sorted(os.listdir(os.getcwd()), key=os.path.getmtime)

   if len(files) == 0:

      print("there are no regular files or folders in the given directory!")

   else:

      #folder list

      directory_list = []

      #regular file list

      file_list = []

      for f in files:

          if (os.path.isdir(f)):

              directory_list.append(f)

      elif (os.path.isfile(f)):

          file_list.append(f)

      if len(directory_list) == 0:

         print("there are no folders in the given directory!")

    else:

        oldest_folder = directory_list[0]

        newest_folder = directory_list[-1]

        print("Oldest folder:", oldest_folder)

        print("Newest folder:", newest_folder)

        print("All folders sorted by modified time -- oldest to newest:", directory_list) 

    if len(file_list) == 0:

        print("there are no (regular) files in the given directory!")

    else:

        oldest_file = file_list[0]

        newest_file = file_list[-1]

        print("Oldest file:", oldest_file)

        print("Newest file:", newest_file)

        print("All (regular) files sorted by modified time -- oldest to newest:", file_list)

    if len(file_list) > 0 and len(directory_list) > 0:

        oldest = files[0]

        newest = files[-1]

        print("Oldest (file/folder):", oldest)

        print("Newest (file/folder):", newest)

        print("All (file/folder) sorted by modified time -- oldest to newest:", files)

See below for a pic of the code.

Saving IPython/Jupyter notebook as PDF on Ubuntu

When you would like to save your Jupyter notebook as a PDF file, and you encouter the following problems on Ubuntu OS. This post is for you.

The solution:

XeLatex is a part of texlive-xetex package.

To install on Ubuntu, run the following command: 

$ sudo apt-get install texlive-xetex

Now you can download  your ipynb file as PDF!