teselagen 0.4.4

Teselagen Biotechnology API client

TeselaGen Python API Client

The TeselaGen Python API Client runs on Python 3.

NOTE : All the following commands are supposed to be run on the base directory, unless specified.

Library Installation

This library contains the TeselaGen Python API Client.

To install it locally,

1. Install it with pip

   pip3 install teselagen
   

Examples

To be able to run the examples, you need to (after installing the library)

1. Clone or download teselagen/examples

2. Open any notebook in the examples folder with Jupyter Notebook

Use the provided environment

You can use the provided docker environment that contains a ready to use installation of all required packages to run the notebooks. Here are the instructions according to your OS

Linux/MacOS

1. After clone/download, run the build script with bash build.sh

2. Run the container with bash run.sh

3. Open your browser and set the address: http://localhost:8888. From there you can explore all example notebooks

Development (Linux/MacOS)

Docker environment

1. Build the docker environment with command bash build.sh

2. Run the container as a developer with the command bash run_dev.sh. With this command the teselagen library will be installed in editable mode.

Dependencies

Install dependencies

If lock file exists (the lock file contains fixed versions of dependencies), the poetry install command will install all dependencies according to the lock file (lock file must be added to the repo). If the file does not exist, it will generate the lock file again.

Update dependencies

Use this command if you made changes on the dependencies at the pyproject.toml file:

poetry update

It is the equivalent to make an install after deleting the lock file.

Tests

1. Add your credentials

   To run the tests, you must create a .credentials file containing the test username and password, in the root folder.

   The content of .credentials file should look similar to the following:

       {
           "username" : "ReplaceWithYourUsername",
           "password" : "ReplaceWithYourPassword"
       }
   

   • NOTE: It should be a valid JSON file. JSON with Comments (JSONC ) format is not supported.

   - DO NOT COMMIT THIS FILE : .credentials
   

2. Modify configuration

   You may modify some test configuration parameters by creating a .test_configuration file. This is a JSON formatted file, where you can edit the server name used for tests. This file must be stored next to .credentials file. Here is an example

   {
     "host_url" : "https://platform.teselagen.com"
   }
   

   • NOTE: It should be a valid JSON file. JSON with Comments (JSONC ) format is not supported.

3. Run the tests

   cd /home && python3 setup.py test
   

   You may use the docker environment for testing. For that, first build the environment with bash build.sh. Then just run the container with bash run_dev.sh. Once inside (docker exec -ti tgclient bash), go to home/ and you are ready to run the test command shown above.

Publishing

Publishing is limited to administrators. PyPi publishing is made by using poetry.

To publish:

1. Run poetry build from the project's root folder (same directory as pyproject.toml)

2. Be sure you have set the credentials with the api token:

poetry config pypi-token.pypi <TOKEN>

Ask for a token to administrators if needed

1. Publish (check you have set a new version tag in pyproject.toml):

poetry publish

Notes

Default shell in Ubuntu is dash, to which /bin/sh is symlinked. But dash doesn't have the pipefail option. That's why some of our shell scripts have the following line:

# pipefail is necessary to propagate exit codes (but it may not be supported by your shell)
bash | set -o pipefail > /dev/null 2>&1

For example, the following commands will list all options supported by set in each of the respective shells:

sh -c 'set -o'
dash -c 'set -o'
bash -c 'set -o'
zsh -c 'set -o'

So, in Ubuntu it may be recommended to use bash instead of sh.

bash some_shell_script.sh

Or, as follows:

. some_shell_script.sh

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