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cr_mech_coli

License: GPL 2.0 Test CI Docs PyPI - Version

Find the documentation of this package under jonaspleyer.github.io/cr_mech_coli/.

Example

import cr_mech_coli as crm

# Contains settings regarding simulation domain, time increments etc.
config = crm.Configuration()

# Use predefined values for agents
agent_settings = crm.AgentSettings()

# Automatically generate agents
agents = crm.generate_agents(
    4,
    agent_settings,
    config
)

# Run simulation and return container
cell_container = crm.run_simulation_with_agents(agents, config)

# Plot individual results
crm.store_all_images(cell_container, config.domain_size)

The generated images will be stored (by default) in out.

out
├── images
│   ├── 000000100.png
│   ...
│   └── 000001000.png
├── masks
│   ├── 000000100.png
│   ...
│   └── 000001000.png

Installation

Use maturin to build the project. The following instructions are for nix-like operating systems. Please use the resources at python.org to adjust them for your needs. First we create a virtual environment and activate it.

python3 -m venv .venv
source .venv/bin/activate

If you have not yet used maturin, install it. We recommend that you use the uv package manager for dependency management.

uv pip install maturin
maturin develop -r --uv

Now you are ready to use cr_mech_coli. If you modify the source code, you have rerun the last command in order to install the updated version.

Project details


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SHA256 754f09a96a812b94493578963f3d24a21876afa73ed931393911df877806dee3
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MD5 82a6b46c03bbe9067d2c32b4c494aca5
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SHA256 2fbc964e228192baf7c8eb5054050224413973d0f1e8840de99f375a0078db29
MD5 520022bf8852767ea6496bade0919187
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MD5 29a56c6cd64b59305363a84b92f4569e
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SHA256 0a389600cce76da871953c2d66acc6982d70f9fef9eeb91ac24192d72eb4b70c
MD5 782fae499485b964ea968d674cfb18c4
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SHA256 49d940cbd2acf689255f09cf4fd1642aec89694d5705bb61f19a115c57bfb6be
MD5 8e826d2b823d76d1050a07a3e91ab072
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SHA256 0621d95ebc4c6ea553da679efbcf1070aa24e2247585c0e7f4ec4736cac5d868
MD5 a27517e8ad26f39331faefeca258e9aa
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SHA256 0983ab7f06e62cc9f7e6d4a845cd81ab3b2f36bd07f9b317a4ead9c98cb2b3a3
MD5 d0081e1b1daff8e3fdf3fd10e998c325
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SHA256 2a2d154cdab9318b29c73c63581bd825c5d57b75e45127f71ac0db74f10653b6
MD5 320b52770955291d7aef6a4171ee11a7
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SHA256 6b6dc353a815e14b53378d82ad36d24e3cf2b078046d4b4ada833879845b3835
MD5 1b7994f679ce8528e6423943aae79205
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SHA256 9fbfb8d3d1a53ab2feeecd06ce5aa3e097fc217bf830e59e34fd96098aab2019
MD5 412a4862f41eb82daedda6a4b8f31222
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SHA256 5f280ec9940eb5aa52dfec1292ba89f2b1c4818e71867c87bbb80ab9d439cdbe
MD5 c986410c799bf7d07c110fcffc3a4859
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SHA256 358207b76c36e1da0430f8feda03c86263dfd0730dd056f8fbbd45241ca16b36
MD5 68b64434a1947e35d6ba3d08d4a734ae
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SHA256 a300a3af90c0d2cfddee0371a3729f4e97321656e565e58f282b4e3880ac997c
MD5 c503e65ad4e6353c57daf3141e2af8b8
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SHA256 24df41170557e23bbb6a98a4a20403538c12f5b7b4f37e41f0e6eb8cecbba8ed
MD5 43314b08e9c944b4b60ca7d72ba726c1
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SHA256 f739b677c503ef7ba21df7cd24248d588e35544216e6db1bde3831bb74bca9fb
MD5 825adbab4969e3c7bd4e65a01dce8166
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SHA256 26e15753e27d632be201c30d39b67f8c813d564405dec32767be9892c27a93a7
MD5 dfda41932ceff57bc6504131aaa3177f
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SHA256 cd16f6122b91160d549cb83081a8557276ec445b7961d35cc8a44cb803bb8714
MD5 8e8b6999a1a0baa331bc0373b2e81b7f
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SHA256 8d875300849fc5fd0190a07ea6d1cb6ffd48b79efd18e9b6e730a4dfde26adfe
MD5 377af4f08474e3936502963a54129405
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SHA256 23197975f63a453b7da09a6b1150b2c43a249d72cec8eec01ee2560db8c1e8c6
MD5 ce3c029310c4cad1835d08418332546a
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SHA256 2ff724c4812a9c20ce93381189bbcb493360f4d662e97f7d8c09718bd85e72c8
MD5 ae65990aa3d0918ffe28f7c72caf8f02
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SHA256 09b30774ec2ddd824ac883e043cfab4a8816bfe4b5118edc1599c2fef2896537
MD5 60f3837e6d8f1d939073f76f50f8d84b
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SHA256 55ba14aeb5ded4bf41bed73916e4f1497170971b0abfc139e9129d6d25600c7f
MD5 8588313d072225c52384c3ebf0201b12
BLAKE2b-256 94c70c3e9ab69e5e036cb8c5d18ef84cdfa122169b6b9a96d934182ab931b8ab

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SHA256 78371b6a18e244e323d2a2e21c13e07a1a9b9939cd13025f167519acc4d80dd2
MD5 d2664c552e5651ce5cba4dd3ae969111
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SHA256 af0155f3a27feeddad97bd6cabcb6da008e62af52b60af9d4926316e5165d76b
MD5 55c3eaa2439cb249423e5e25bc16bfd9
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SHA256 282b16dd7b5cd0bda04a4c6ffb830565069c29bccfe7204a9bca32436936a2ce
MD5 d68f42ad649c0e0509ec59bf5ccfdea9
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SHA256 8659fb9f9ebf64df157c1994ee3702a89881966e46fda0984c366bf363c19faf
MD5 55a282b69ec972340bb55b3a2c3b6dd1
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SHA256 4a76d45d9ba2a47d46475835f1b305c4137d06aa9f09f4329e86d9e48116f097
MD5 2270e8dd9482caf2f1c31813a726c9d2
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SHA256 358b66de625c6abbec96c1d8f2edca74e4ce3c34e3846d764f50d156357b8273
MD5 69494eb8cf21aff0a83eb80e717e719b
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