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A collection of useful shell scripts for Linux, Windows & Mac

Home Page: https://miguelgfierro.com

License: Other

Shell 68.26% PowerShell 9.67% Python 20.83% Batchfile 1.24%

script useful useful-bash-scripts

scripts's Introduction

A collection of useful scripts for Linux, Windows & Mac.

Utilities for command line in Linux and Mac

git_configure.sh: Configure options in git such as alias, user name, email and credential helper.
git_update_repos.sh: It iteratively updates several git repositories for a user.
git_status_repos.sh: It iteratively finds the status of several git repositories for a user.
git_find_big.sh: List git objects ordered by size.
jupyter_configure.sh: Set up jupyter notebook environment in a Ubuntu server.
setup_bashrc.sh: Set up several functions to .bashrc like cs (a combination of cd+ls), ccat (cat with color) or reimplement evince to run in background.
setup_vim.sh: Set up functions for vim such as the line numbers

Utilities for Azure

adls_download_folder_with_files.ps1: Powershell script to download a folder with multiple files to ADLS.
adls_download_folder_with_files.py: Python script to download a folder with multiple files to ADLS.
alds_download_single_file.ps1: Powershell script to download a file to ADLS.
adls_download_single_file.sh: Bash script to download a file from Azure DataLake Storage (ADLS).
adls_upload_folder_with_files.ps1: Powershell script to upload a folder with multiple files to ADLS.
adls_upload_folder_with_files.py: Python script to upload a folder with multiple files to ADLS.
adls_upload_single_file.ps1: Powershell script to upload a file to ADLS.
azure_blob_download_folder_with_files.sh: Bash script to download a folder from Azure Storage Blob.
azure_blob_download_single_file.sh: Bash script to download a single file from Azure Storage Blob.
azure_blob_upload_folder_with_files.sh: Bash script to upload a folder to Azure Storage Blob.
azure_blob_upload_single_file.sh: Bash script to upload a single file to Azure Storage Blob.
mount_azure_fileshare.cmd: Windows executable to mount an Azure Fileshare.
mount_azure_fileshare.sh: Bash script to mount an Azure Fileshare.
mount_external_disk.sh: Bash script to automatically mount an external Azure disk.
vmss_deploy_with_public_ip.py: deploys Azure VMSS (Virtual Machine Scale Set), and run vm_user_env_setup.sh on each VM instance to clone a repository, install conda environment and create multiple JupyterHub users.

Utilities for installing software

header_creator.sh: A simple shell to add headers (like copyright statements) in files.
make_cmake_project.sh: A simple shell script for generating C++ projects with CMake. It generates the CMakeList.txt, Doxigen files, folder structure and initial filenames.
rstudio_server_install.sh: Installs RStudio Server in an Azure HDI cluster.
start_ubuntu.sh: Installation of many packages in a fresh Ubuntu.
start_gpu_ubuntu.sh: Installation of many packages for a GPU Ubuntu.

Misc

bing_images_downloader.py: A script to download images from Bing.

scripts's People

Contributors

Stargazers

Watchers

scripts's Issues

git autocompletion in bash profile Mac

Create cs N based on Gustav idea

Idea from #2

Fix error in gpu installation script with MKL

MXNet complains that
/datadrive/installer/mxnet/mshadow/mshadow/./base.h:139:24: fatal error: mkl_blas.h: No such file or directory.

Install MKL like in the previous version

add git autocompletion in mac and linux

https://git-scm.com/book/en/v1/Git-Basics-Tips-and-Tricks

Test script in Mac

Update adls script to force rewrite files

When I use the uploader to ADLS and the file is already in the cloud it returns an error. To solve it I have to force the writing operation

Solve issue when creating a disk partition bigger than 2Tb in linux

got this error:
The size of this disk is 4 TiB (4396972769280 bytes). DOS partition table format can not be used on drives for volumes larger than 2199023255040 bytes for 512-byte sectors. Use GUID partition table format (GPT).

http://www.thegeekstuff.com/2012/08/2tb-gtp-parted/

update script with new cuda

# install CUDA 9

CUDA_REPO_PKG="cuda-repo-ubuntu1604_9.0.176-1_amd64.deb"
wget http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1604/x86_64/${CUDA_REPO_PKG}
sudo dpkg -i ${CUDA_REPO_PKG}
sudo apt-get update
sudo apt-get -y install cuda

# install cuDNN v7.0.5.15

wget https://ikpublictutorial.blob.core.windows.net/deeplearningframeworks/libcudnn7_7.0.5.15-1%2Bcuda9.0_amd64.deb
wget https://ikpublictutorial.blob.core.windows.net/deeplearningframeworks/libcudnn7-dev_7.0.5.15-1%2Bcuda9.0_amd64.deb
wget https://ikpublictutorial.blob.core.windows.net/deeplearningframeworks/libcudnn7-doc_7.0.5.15-1%2Bcuda9.0_amd64.deb

CUDNN_RUNTIME_PKG="libcudnn7_7.0.5.15-1+cuda9.0_amd64.deb"
CUDNN_DEV_PKG="libcudnn7-dev_7.0.5.15-1+cuda9.0_amd64.deb"
CUDNN_SAMPLES_PKG="libcudnn7-doc_7.0.5.15-1+cuda9.0_amd64.deb"

sudo dpkg -i ${CUDNN_RUNTIME_PKG}
sudo dpkg -i ${CUDNN_DEV_PKG}
sudo dpkg -i ${CUDNN_SAMPLES_PKG}

mount fileshare for windows

take a look at mat's gists

https://gist.github.com/msalvaris

in Mac scripts are not permanent when using bashrc

I have to add the content of bashrc and add autocomplete git #26 also

Timer for ADLS powershell

Update license

MIT: https://tldrlegal.com/license/mit-license Basically it means that anybody can use my code but I won't be liable/responsible for it.

Apache 2: https://tldrlegal.com/license/apache-license-2.0-(apache-2.0). Anybody can use my code. I won't be liable for it and nobody can use my name/trademark to promote their code. You have to maintain license, contributors and state changes.

BSD-0: https://tldrlegal.com/license/bsd-0-clause-license. Anybody can use my code. I won't be liable for it and you don't need to add the license

BSD-2: https://tldrlegal.com/license/bsd-2-clause-license-(freebsd). Identical to MIT

BSD-3: https://tldrlegal.com/license/bsd-3-clause-license-(revised). Code free to use. No liable and no trademark. Maintain copyright and license.

BSD-4: https://tldrlegal.com/license/4-clause-bsd. Idem to BSD-3 but you have to give credit to the author.

reorg README

when creating the ssh for git, fix it when a person uses a non default rsa file

https://github.com/miguelgfierro/scripts/blob/master/git_configure.sh#L35

fix bashrc and automatically add bash profile

# include .bashrc if it exists
if [ -f "$HOME/.bashrc" ]; then
    . "$HOME/.bashrc"
fi

automatically mount an attached disk created in azure

https://docs.microsoft.com/en-us/azure/virtual-machines/linux/classic/attach-disk

fix timer in adls python scripts

Check if Import-AzureRmDataLakeStoreItem is faster with -Recurse

https://docs.microsoft.com/en-us/powershell/resourcemanager/azurerm.datalakestore/v2.1.0/import-azurermdatalakestoreitem

azcopy download in linux

https://docs.microsoft.com/en-us/azure/storage/common/storage-use-azcopy-linux?toc=%2fazure%2fstorage%2fblobs%2ftoc.json

script to automatically mount a fileshare in Azure

Azure blob upload and download

move data between Azure Data Lake and Azure Storage

Data factory:

https://docs.microsoft.com/en-us/azure/data-factory/data-factory-azure-datalake-connector

In adls python I/O take automatically the number of threads

    multithread.ADLDownloader(adls_client, lpath=args.local_folder, rpath=args.adls_folder, nthreads=16,
                              overwrite=True, buffersize=4194304, blocksize=4194304)

Add private email as default option in github config

git config --global user.email "[email protected]"

add bing image downloader

Source and cygwin check can be made by bash

Hi! Nice script. I added some code if you feel like automating the instructions.

Have a nice day!

ADLS management in python

https://docs.microsoft.com/en-us/azure/data-lake-store/data-lake-store-get-started-python

http://azure-datalake-store.readthedocs.io/en/latest/

API: http://azure-datalake-store.readthedocs.io/en/latest/api.html

Azure blob download and upload in batch

https://docs.microsoft.com/en-us/cli/azure/storage/blob?view=azure-cli-latest#az_storage_blob_download_batch

Error when uploading a folder with files in a premium blob

I got this error:

HTTPSConnectionPool(host='datasets.blob.core.windows.net', port=443): Max retries exceeded with url: /datasets?restype=container (Caused by NewConnectionError('<urllib3.connection.VerifiedHTTPSConnection object at 0x7f4a75c11550>: Failed to establish a new connection: [Errno -2] Name or service not known',))
Traceback (most recent call last):
  File "/opt/az/lib/python3.6/site-packages/urllib3/connection.py", line 171, in _new_conn
    (self._dns_host, self.port), self.timeout, **extra_kw)
  File "/opt/az/lib/python3.6/site-packages/urllib3/util/connection.py", line 56, in create_connection
    for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM):
  File "/opt/az/lib/python3.6/socket.py", line 745, in getaddrinfo
    for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
socket.gaierror: [Errno -2] Name or service not known

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/az/lib/python3.6/site-packages/urllib3/connectionpool.py", line 600, in urlopen
    chunked=chunked)
  File "/opt/az/lib/python3.6/site-packages/urllib3/connectionpool.py", line 343, in _make_request
    self._validate_conn(conn)
  File "/opt/az/lib/python3.6/site-packages/urllib3/connectionpool.py", line 849, in _validate_conn
    conn.connect()
  File "/opt/az/lib/python3.6/site-packages/urllib3/connection.py", line 314, in connect
    conn = self._new_conn()
  File "/opt/az/lib/python3.6/site-packages/urllib3/connection.py", line 180, in _new_conn
    self, "Failed to establish a new connection: %s" % e)
urllib3.exceptions.NewConnectionError: <urllib3.connection.VerifiedHTTPSConnection object at 0x7f4a75c11550>: Failed to establish a new connection: [Errno -2] Name or service not known

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/az/lib/python3.6/site-packages/requests/adapters.py", line 445, in send
    timeout=timeout
  File "/opt/az/lib/python3.6/site-packages/urllib3/connectionpool.py", line 638, in urlopen
    _stacktrace=sys.exc_info()[2])
  File "/opt/az/lib/python3.6/site-packages/urllib3/util/retry.py", line 398, in increment
    raise MaxRetryError(_pool, url, error or ResponseError(cause))
urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='datasets.blob.core.windows.net', port=443): Max retries exceeded with url: /datasets?restype=container (Caused by NewConnectionError('<urllib3.connection.VerifiedHTTPSConnection object at 0x7f4a75c11550>: Failed to establish a new connection: [Errno -2] Name or service not known',))

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/az/lib/python3.6/site-packages/azure/multiapi/storage/v2018_03_28/common/storageclient.py", line 269, in _perform_request
    response = self._httpclient.perform_request(request)
  File "/opt/az/lib/python3.6/site-packages/azure/multiapi/storage/v2018_03_28/common/_http/httpclient.py", line 92, in perform_request
    proxies=self.proxies)
  File "/opt/az/lib/python3.6/site-packages/requests/sessions.py", line 512, in request
    resp = self.send(prep, **send_kwargs)
  File "/opt/az/lib/python3.6/site-packages/requests/sessions.py", line 622, in send
    r = adapter.send(request, **kwargs)
  File "/opt/az/lib/python3.6/site-packages/requests/adapters.py", line 513, in send
    raise ConnectionError(e, request=request)
requests.exceptions.ConnectionError: HTTPSConnectionPool(host='datasets.blob.core.windows.net', port=443): Max retries exceeded with url: /datasets?restype=container (Caused by NewConnectionError('<urllib3.connection.VerifiedHTTPSConnection object at 0x7f4a75c11550>: Failed to establish a new connection: [Errno -2] Name or service not known',))

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/az/lib/python3.6/site-packages/knack/cli.py", line 197, in invoke
    cmd_result = self.invocation.execute(args)
  File "/opt/az/lib/python3.6/site-packages/azure/cli/core/commands/__init__.py", line 369, in execute
    six.reraise(*sys.exc_info())
  File "/opt/az/lib/python3.6/site-packages/six.py", line 693, in reraise
    raise value
  File "/opt/az/lib/python3.6/site-packages/azure/cli/core/commands/__init__.py", line 343, in execute
    result = cmd(params)
  File "/opt/az/lib/python3.6/site-packages/azure/cli/core/commands/__init__.py", line 182, in __call__
    return self.handler(*args, **kwargs)
  File "/opt/az/lib/python3.6/site-packages/azure/cli/core/__init__.py", line 436, in default_command_handler
    result = op(**command_args)
  File "/opt/az/lib/python3.6/site-packages/azure/multiapi/storage/v2018_03_28/blob/baseblobservice.py", line 630, in create_container
    self._perform_request(request, expected_errors=[_CONTAINER_ALREADY_EXISTS_ERROR_CODE])
  File "/opt/az/lib/python3.6/site-packages/azure/multiapi/storage/v2018_03_28/common/storageclient.py", line 381, in _perform_request
    raise ex
  File "/opt/az/lib/python3.6/site-packages/azure/multiapi/storage/v2018_03_28/common/storageclient.py", line 311, in _perform_request
    raise AzureException(ex.args[0])
azure.common.AzureException: HTTPSConnectionPool(host='datasets.blob.core.windows.net', port=443): Max retries exceeded with url: /datasets?restype=container (Caused by NewConnectionError('<urllib3.connection.VerifiedHTTPSConnection object at 0x7f4a75c11550>: Failed to establish a new connection: [Errno -2] Name or service not known',))
uploading /data1/imagenet/ILSVRC2012_devkit_t12.tar.gz
HTTPSConnectionPool(host='datasets.blob.core.windows.net', port=443): Max retries exceeded with url: /datasets/imagenet/ILSVRC2012_devkit_t12.tar.gz (Caused by NewConnectionError('<urllib3.connection.VerifiedHTTPSConnection object at 0x7f777f7b15f8>: Failed to establish a new connection: [Errno -2] Name or service not known',))
Traceback (most recent call last):
  File "/opt/az/lib/python3.6/site-packages/urllib3/connection.py", line 171, in _new_conn
    (self._dns_host, self.port), self.timeout, **extra_kw)
  File "/opt/az/lib/python3.6/site-packages/urllib3/util/connection.py", line 56, in create_connection
    for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM):
  File "/opt/az/lib/python3.6/socket.py", line 745, in getaddrinfo
    for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
socket.gaierror: [Errno -2] Name or service not known

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/az/lib/python3.6/site-packages/urllib3/connectionpool.py", line 600, in urlopen
    chunked=chunked)
  File "/opt/az/lib/python3.6/site-packages/urllib3/connectionpool.py", line 343, in _make_request
    self._validate_conn(conn)
  File "/opt/az/lib/python3.6/site-packages/urllib3/connectionpool.py", line 849, in _validate_conn
    conn.connect()
  File "/opt/az/lib/python3.6/site-packages/urllib3/connection.py", line 314, in connect
    conn = self._new_conn()
  File "/opt/az/lib/python3.6/site-packages/urllib3/connection.py", line 180, in _new_conn
    self, "Failed to establish a new connection: %s" % e)
urllib3.exceptions.NewConnectionError: <urllib3.connection.VerifiedHTTPSConnection object at 0x7f777f7b15f8>: Failed to establish a new connection: [Errno -2] Name or service not known

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/az/lib/python3.6/site-packages/requests/adapters.py", line 445, in send
    timeout=timeout
  File "/opt/az/lib/python3.6/site-packages/urllib3/connectionpool.py", line 638, in urlopen
    _stacktrace=sys.exc_info()[2])
  File "/opt/az/lib/python3.6/site-packages/urllib3/util/retry.py", line 398, in increment
    raise MaxRetryError(_pool, url, error or ResponseError(cause))
urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='datasets.blob.core.windows.net', port=443): Max retries exceeded with url: /datasets/imagenet/ILSVRC2012_devkit_t12.tar.gz (Caused by NewConnectionError('<urllib3.connection.VerifiedHTTPSConnection object at 0x7f777f7b15f8>: Failed to establish a new connection: [Errno -2] Name or service not known',))

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/az/lib/python3.6/site-packages/azure/multiapi/storage/v2018_03_28/common/storageclient.py", line 269, in _perform_request
    response = self._httpclient.perform_request(request)
  File "/opt/az/lib/python3.6/site-packages/azure/multiapi/storage/v2018_03_28/common/_http/httpclient.py", line 92, in perform_request
    proxies=self.proxies)
  File "/opt/az/lib/python3.6/site-packages/requests/sessions.py", line 512, in request
    resp = self.send(prep, **send_kwargs)
  File "/opt/az/lib/python3.6/site-packages/requests/sessions.py", line 622, in send
    r = adapter.send(request, **kwargs)
  File "/opt/az/lib/python3.6/site-packages/requests/adapters.py", line 513, in send
    raise ConnectionError(e, request=request)
requests.exceptions.ConnectionError: HTTPSConnectionPool(host='datasets.blob.core.windows.net', port=443): Max retries exceeded with url: /datasets/imagenet/ILSVRC2012_devkit_t12.tar.gz (Caused by NewConnectionError('<urllib3.connection.VerifiedHTTPSConnection object at 0x7f777f7b15f8>: Failed to establish a new connection: [Errno -2] Name or service not known',))

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/az/lib/python3.6/site-packages/knack/cli.py", line 197, in invoke
    cmd_result = self.invocation.execute(args)
  File "/opt/az/lib/python3.6/site-packages/azure/cli/core/commands/__init__.py", line 369, in execute
    six.reraise(*sys.exc_info())
  File "/opt/az/lib/python3.6/site-packages/six.py", line 693, in reraise
    raise value
  File "/opt/az/lib/python3.6/site-packages/azure/cli/core/commands/__init__.py", line 343, in execute
    result = cmd(params)
  File "/opt/az/lib/python3.6/site-packages/azure/cli/core/commands/__init__.py", line 182, in __call__
    return self.handler(*args, **kwargs)
  File "/opt/az/lib/python3.6/site-packages/azure/cli/core/__init__.py", line 436, in default_command_handler
    result = op(**command_args)
  File "/opt/az/lib/python3.6/site-packages/azure/cli/command_modules/storage/operations/blob.py", line 199, in storage_blob_upload_batch
    if_none_match=if_none_match, timeout=timeout)
  File "/opt/az/lib/python3.6/site-packages/azure/cli/command_modules/storage/util.py", line 218, in wrapper
    return True, func(*args, **kwargs)
  File "/opt/az/lib/python3.6/site-packages/azure/cli/command_modules/storage/operations/blob.py", line 185, in _upload_blob
    return upload_blob(*args, **kwargs)
  File "/opt/az/lib/python3.6/site-packages/azure/cli/command_modules/storage/operations/blob.py", line 286, in upload_blob
    return type_func[blob_type]()
  File "/opt/az/lib/python3.6/site-packages/azure/cli/command_modules/storage/operations/blob.py", line 279, in upload_block_blob
    return client.create_blob_from_path(**create_blob_args)
  File "/opt/az/lib/python3.6/site-packages/azure/multiapi/storage/v2018_03_28/blob/blockblobservice.py", line 463, in create_blob_from_path
    timeout=timeout)
  File "/opt/az/lib/python3.6/site-packages/azure/multiapi/storage/v2018_03_28/blob/blockblobservice.py", line 582, in create_blob_from_stream
    timeout=timeout)
  File "/opt/az/lib/python3.6/site-packages/azure/multiapi/storage/v2018_03_28/blob/blockblobservice.py", line 971, in _put_blob
    return self._perform_request(request, _parse_base_properties)
  File "/opt/az/lib/python3.6/site-packages/azure/multiapi/storage/v2018_03_28/common/storageclient.py", line 381, in _perform_request
    raise ex
  File "/opt/az/lib/python3.6/site-packages/azure/multiapi/storage/v2018_03_28/common/storageclient.py", line 311, in _perform_request
    raise AzureException(ex.args[0])
azure.common.AzureException: HTTPSConnectionPool(host='datasets.blob.core.windows.net', port=443): Max retries exceeded with url: /datasets/imagenet/ILSVRC2012_devkit_t12.tar.gz (Caused by NewConnectionError('<urllib3.connection.VerifiedHTTPSConnection object at 0x7f777f7b15f8>: Failed to establish a new connection: [Errno -2] Name or service not known',))

ADLS download folder

See fi I can check if you are already logged in Azure

For the scripts of ADLS I always log: Login-AzureRmAccount. Check if it is possible to know if the user is already logged and skip that step

list git files by size

https://confluence.atlassian.com/bitbucket/reduce-repository-size-321848262.html

unlimited WiFi at airports

https://twitter.com/mgechev/status/1130441471105093632?s=19

ADLS download single file

See if we can automatically add a ssl certificate when seting up jupyter in VMs

I get this error:

Your connection is not secure

The owner of *****.southcentralus.cloudapp.azure.com has configured their web site improperly. To protect your information from being stolen, Firefox has not connected to this web site.

mount external disk windows

https://docs.microsoft.com/en-us/azure/virtual-machines/windows/attach-managed-disk-portal

https://docs.microsoft.com/en-us/azure/virtual-machines/windows/attach-disk-ps

mount fileshare in Mac

sudo mount_smbfs //[email protected]/share-name desired-mount-point

then it asks for the password and you add the key.

However, I don't have permissions to enter the drive unless I do sudo -s. It doesn't appear in the finder

Authentication without password using OpenSSH Key, certificates .pem and .pub

Based on this tutorial.

How to generate a Key Pair for authentication without password

ssh-keygen -t rsa -b 2048 -v

We have to add the keyname migonzagpup100_rsa:

Generating public/private rsa key pair.
Enter file in which to save the key (/Users/miguel/.ssh/id_rsa): /Users/miguel/.ssh/migonzagpup100_rsa
Enter passphrase (empty for no passphrase): 
Enter same passphrase again: 
Your identification has been saved in /Users/miguel/.ssh/migonzagpup100_rsa.
Your public key has been saved in /Users/miguel/.ssh/migonzagpup100_rsa.pub.
The key fingerprint is:
SHA256:2VVHKEfxyzrawPDUzrYvK/WbMLlvYK/6PzUBCKoWmW4 [email protected]
The key's randomart image is:

You get two files, migonzagpup100_rsa.pub and migonzagpup100_rsa.

Uploading the generated certificate from client computer to server

Then we need to copy the public key to the server

ssh-copy-id -i /Users/miguel/.ssh/migonzagpup100_rsa.pub [email protected]

Now we make sure that we can log in using the private key (without the password):

ssh -i /Users/miguel/.ssh/migonzagpup100_rsa [email protected]

Authenticating directly through hostname

You can create the file ~/.ssh/config and add the following lines:

Host migonzagpup100 migonzagpup100.westeurope.cloudapp.azure.com
Hostname migonzagpup100.westeurope.cloudapp.azure.com
User hoaphumanoid
IdentityFile /Users/miguel/.ssh/migonzagpup100_rsa

Host migonzagpup100london migonzagpup100london.westeurope.cloudapp.azure.com
Hostname migonzagpup100london.westeurope.cloudapp.azure.com
User hoaphumanoid
IdentityFile /Users/miguel/.ssh/migonzagpup100london

Now you can ssh to the machine directly by using the hostname: ssh migonzagpup100.

Automatically register conda environments when configuring jupyter

conda install ipykernel
source activate myenv
python -m ipykernel install --user --name myenv --display-name "Python (myenv)"
source activate other-env
python -m ipykernel install --user --name other-env --display-name "Python (other-env)"

with ipython >= 6.1.0

Source