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fix(tutorial): add pip install
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@jjjermiah
jjjermiah committed Dec 16, 2023
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6 changes: 3 additions & 3 deletions README.md
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Expand Up @@ -24,11 +24,11 @@ See the [Wiki](https://github.com/jjjermiah/NBIA-toolkit/wiki) for more informat

## Installation

`nbiatoolkit` will be made available on PyPI and Conda Forge soon. Until then, you can install the latest development version from GitHub by cloning the repository and running the following commands in the root directory:
`nbiatoolkit` is currently under development.
It is made available via PyPI and can be installed using pip:

```bash
pip install poetry
poetry install
pip install nbiatoolkit
```


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23 changes: 23 additions & 0 deletions docs/Tutorial.ipynb
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" `NBIAClient(username=\"YOUR_USERNAME\", password=\"YOUR_PASSWORD\")`"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Requirement already satisfied: nbiatoolkit in /opt/homebrew/Caskroom/miniconda/base/envs/nbia/lib/python3.12/site-packages (0.1.0)\n",
"Requirement already satisfied: pydicom<3.0.0,>=2.4.3 in /opt/homebrew/Caskroom/miniconda/base/envs/nbia/lib/python3.12/site-packages (from nbiatoolkit) (2.4.3)\n",
"Requirement already satisfied: requests==2.31.0 in /opt/homebrew/Caskroom/miniconda/base/envs/nbia/lib/python3.12/site-packages (from nbiatoolkit) (2.31.0)\n",
"Requirement already satisfied: charset-normalizer<4,>=2 in /opt/homebrew/Caskroom/miniconda/base/envs/nbia/lib/python3.12/site-packages (from requests==2.31.0->nbiatoolkit) (3.3.2)\n",
"Requirement already satisfied: idna<4,>=2.5 in /opt/homebrew/Caskroom/miniconda/base/envs/nbia/lib/python3.12/site-packages (from requests==2.31.0->nbiatoolkit) (3.4)\n",
"Requirement already satisfied: urllib3<3,>=1.21.1 in /opt/homebrew/Caskroom/miniconda/base/envs/nbia/lib/python3.12/site-packages (from requests==2.31.0->nbiatoolkit) (2.1.0)\n",
"Requirement already satisfied: certifi>=2017.4.17 in /opt/homebrew/Caskroom/miniconda/base/envs/nbia/lib/python3.12/site-packages (from requests==2.31.0->nbiatoolkit) (2023.11.17)\n"
]
}
],
"source": [
"!pip install nbiatoolkit"
]
},
{
"cell_type": "code",
"execution_count": 1,
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207 changes: 205 additions & 2 deletions docs/changelog.md
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```{include} ../CHANGELOG.md
```
# CHANGELOG



## v0.0.0 (2023-12-16)

### Documentation

* docs: add package for version bumping ([`efbed0f`](https://github.com/jjjermiah/NBIA-toolkit/commit/efbed0fb7c91df8991135ed4800c60a49f0d7905))

### Unknown

* Update example notebook and package initialization ([`b940a6f`](https://github.com/jjjermiah/NBIA-toolkit/commit/b940a6fa1a157b5e2466b78dcc0d32553d2ca4ce))

* convert readme into issues ([`0fe7583`](https://github.com/jjjermiah/NBIA-toolkit/commit/0fe7583d359c5e4f127f5d2b8d8cbf91321a4a8e))

* Update README.md to include TCIA database access ([`973590a`](https://github.com/jjjermiah/NBIA-toolkit/commit/973590a2737ef6a9174483b160e0cabba5f3ab0b))

* Update logging setup ([`09d323a`](https://github.com/jjjermiah/NBIA-toolkit/commit/09d323af39974dbc9d41b701d95bd1306e0c69d0))

* Update GitHub Actions workflow and README.md ([`1c80e8d`](https://github.com/jjjermiah/NBIA-toolkit/commit/1c80e8dcc628e364a323b242f81db1f4036ad4f5))

* Fix capitalization of parameters in
nbia_client.getPatients() and
nbia_client.getBodyPartCounts() ([`773955e`](https://github.com/jjjermiah/NBIA-toolkit/commit/773955e7591eee2418e940784a41548a489f9485))

* Merge pull request #17 from jjjermiah/jjjermiah-patch-1

Update README.md ([`8fb1c95`](https://github.com/jjjermiah/NBIA-toolkit/commit/8fb1c95c46f5b26bbb0d8911bcc2e67e58c92768))

* Update README.md ([`792f287`](https://github.com/jjjermiah/NBIA-toolkit/commit/792f287aa02d269651192eba0f6318706a7d2e3b))

* Merge branch &#39;main&#39; of https://github.com/jjjermiah/NBIA-toolkit into main ([`f909a44`](https://github.com/jjjermiah/NBIA-toolkit/commit/f909a444f7a60c0b0dc279deaed32ef2584d8c05))

* add to gitignore ([`9cc6722`](https://github.com/jjjermiah/NBIA-toolkit/commit/9cc6722e890440449553d2d9343633152abfe0ee))

* Merge pull request #16 from jjjermiah/development

Development ([`f68181a`](https://github.com/jjjermiah/NBIA-toolkit/commit/f68181a78ee38d6e2dc1efc2bb2e2ef35f8e6c74))

* Add pydicom package and update dependencies ([`3f15108`](https://github.com/jjjermiah/NBIA-toolkit/commit/3f1510865dc62a13e9310079b939f3a97e045606))

* Delete unnecessary code for downloading series
from NBIA ([`afb0cef`](https://github.com/jjjermiah/NBIA-toolkit/commit/afb0cef2413f66ed2ef104ba2ec665deb98ced81))

* add dicomsort back ([`d512b0b`](https://github.com/jjjermiah/NBIA-toolkit/commit/d512b0bc1b656ef22220622b58ba2e35eeeedc4c))

* Merge pull request #14 from jjjermiah/jjjermiah-patch-1

Delete driver.py ([`66705e6`](https://github.com/jjjermiah/NBIA-toolkit/commit/66705e621d9290b4745a95f11c206a064beacd40))

* lint nbia class and add baseURL to nbiaEndpoints ([`9d85950`](https://github.com/jjjermiah/NBIA-toolkit/commit/9d859506766faec5c92fede916d9ba3e2177acaf))

* added dicomSort functionality to downloadSeries ([`a229025`](https://github.com/jjjermiah/NBIA-toolkit/commit/a2290253bc13236c33e8541e9301d74cd9ae9eba))

* Delete driver.py ([`2c51fba`](https://github.com/jjjermiah/NBIA-toolkit/commit/2c51fba68b752acd39e19ab3b218036f9f273fe5))

* Merge pull request #13 from jjjermiah/development

refactor dicomsorter class and add some tests ([`7e51e20`](https://github.com/jjjermiah/NBIA-toolkit/commit/7e51e203c981120deb06114cfec1e61cd2cf0816))

* refactor dicomsorter class and add some tests ([`b5cf783`](https://github.com/jjjermiah/NBIA-toolkit/commit/b5cf7830e4e21d63b81da561f12584a8169a83c5))

* Merge pull request #12 from jjjermiah/development

Development ([`931eb4a`](https://github.com/jjjermiah/NBIA-toolkit/commit/931eb4ad7879ac3b8da3e1c5eff0dd37dc54a9a8))

* refactor nbia client and add tests ([`b199a83`](https://github.com/jjjermiah/NBIA-toolkit/commit/b199a83897ac1211d0e3727d574e8abe7d5f02a0))

* Merge branch &#39;main&#39; of https://github.com/jjjermiah/NBIA-toolkit into development ([`709551d`](https://github.com/jjjermiah/NBIA-toolkit/commit/709551da563cf7ea282a149020dce55fdaa48d2d))

* added more examples ([`3a2fca2`](https://github.com/jjjermiah/NBIA-toolkit/commit/3a2fca27a772bc97079b26440fc97a36f1921825))

* add mac-OS ([`eb038d4`](https://github.com/jjjermiah/NBIA-toolkit/commit/eb038d42c099eaa3091f2a10eb4cb9ade798db37))

* Add validateMD5 function and update NBIA_ENDPOINTS ([`2a16f72`](https://github.com/jjjermiah/NBIA-toolkit/commit/2a16f72aca01cbcd312b53d206ba97763f433f91))

* Merge pull request #11 from jjjermiah/development

add todos and rearrange md5 function ([`0d638cb`](https://github.com/jjjermiah/NBIA-toolkit/commit/0d638cb01a604d87f96bb18d93810d8b8811fac8))

* add todos and rearrange md5 function ([`2c70522`](https://github.com/jjjermiah/NBIA-toolkit/commit/2c70522432eba308ad0749e52ba9caa66a66cba2))

* Merge pull request #10 from jjjermiah/development

Refactor code and implement TODOs ([`32fe6ee`](https://github.com/jjjermiah/NBIA-toolkit/commit/32fe6eeba7e6802fd4f5e1c0dcd7de95436a7fc4))

* Refactor code and implement TODOs ([`4aac4e4`](https://github.com/jjjermiah/NBIA-toolkit/commit/4aac4e469d5bb2c0574a11fcec86d1cab50d60bf))

* Merge pull request #9 from jjjermiah/development

Development ([`442d675`](https://github.com/jjjermiah/NBIA-toolkit/commit/442d6759a9dd12f80320b7db0b6b5a61c6d7b559))

* Merge pull request #8 from jjjermiah/main

merge from main ([`201dda7`](https://github.com/jjjermiah/NBIA-toolkit/commit/201dda7ca48ee7c2ca6e30c98f290688210491da))

* Add documentation status badge ([`f7474f0`](https://github.com/jjjermiah/NBIA-toolkit/commit/f7474f097accf5a091500717d7423b13f2816665))

* add wiki page on NBIA ([`ccb6bb1`](https://github.com/jjjermiah/NBIA-toolkit/commit/ccb6bb19ce3298a2c2012036634fe837eb6e1105))

* Merge pull request #7 from jjjermiah/development

Update GitHub Actions workflow and add documentation generation ([`05965e3`](https://github.com/jjjermiah/NBIA-toolkit/commit/05965e3b827b5a3fedf0dfc19350093c135855e2))

* Update GitHub Actions workflow and add
documentation generation ([`5a285e8`](https://github.com/jjjermiah/NBIA-toolkit/commit/5a285e894d7611a390604582249ce6874ddc8c6e))

* Merge pull request #6 from jjjermiah/development

Update ReadTheDocs ([`4d08cc7`](https://github.com/jjjermiah/NBIA-toolkit/commit/4d08cc7891362c1edf46fd361bb58139a8ac05ff))

* Update .readthedocs.yml configuration ([`e372b3a`](https://github.com/jjjermiah/NBIA-toolkit/commit/e372b3a4e24b72973f11d0e5691dcf71259baf52))

* add build os ([`fd5dbc1`](https://github.com/jjjermiah/NBIA-toolkit/commit/fd5dbc118d9a4ea50f036724adb613854d1a8548))

* Remove unnecessary Sphinx configuration ([`3ebe543`](https://github.com/jjjermiah/NBIA-toolkit/commit/3ebe5431bcba48e3f40b96581af1f223b4cfb45b))

* update read the docs yaml ([`0f2d01b`](https://github.com/jjjermiah/NBIA-toolkit/commit/0f2d01bbb8a891beeb8c916bcfc7f6e335dd6d2d))

* Merge pull request #5 from jjjermiah/development

Development ([`95afa63`](https://github.com/jjjermiah/NBIA-toolkit/commit/95afa63e7f9655124e89547ed001d0d5b04d5e01))

* update docs ([`65ba441`](https://github.com/jjjermiah/NBIA-toolkit/commit/65ba441f548d8da6681f0c4eb6e63ebf8440cdb6))

* Merge pull request #4 from jjjermiah/main

merge with main ([`e591acd`](https://github.com/jjjermiah/NBIA-toolkit/commit/e591acd5cd10fb3463cf976d6530fc620cdc21a9))

* add download Image ([`f6860b8`](https://github.com/jjjermiah/NBIA-toolkit/commit/f6860b85bd4ac49ec490ff8b8416d1a3ac6d76b9))

* started sphinx documentation. doesnt work yet ([`fd36a2d`](https://github.com/jjjermiah/NBIA-toolkit/commit/fd36a2d96f895cfa3a0f555cef4063b3d6a834c0))

* improve auth documentation ([`ebc3d3b`](https://github.com/jjjermiah/NBIA-toolkit/commit/ebc3d3be78e8652c55748be54aa593ee77db5e10))

* Merge pull request #3 from jjjermiah/development

Development ([`d9386db`](https://github.com/jjjermiah/NBIA-toolkit/commit/d9386dbb721ab0f0bf514fa0dd78f8c44fa04375))

* poetry add --group dev pytest ([`71f6960`](https://github.com/jjjermiah/NBIA-toolkit/commit/71f69604708e99c011016218775128b53b882d85))

* test ([`fdc7cd5`](https://github.com/jjjermiah/NBIA-toolkit/commit/fdc7cd54ed2c5135dc399aedd5a593f877eef8ad))

* add dependencies ([`eba1556`](https://github.com/jjjermiah/NBIA-toolkit/commit/eba155685a937bf3bd443dc58ddba1c08c1f0a2c))

* test cicd ([`7ba0324`](https://github.com/jjjermiah/NBIA-toolkit/commit/7ba0324bb9b35342b40d58ab0c9277a4515ea824))

* pytest only auth ([`74aa4ad`](https://github.com/jjjermiah/NBIA-toolkit/commit/74aa4ad01db3609c375185ab730983a42d3ed1b2))

* add pytest ([`ff55df7`](https://github.com/jjjermiah/NBIA-toolkit/commit/ff55df7aa7a1a62c2d09535931ea731e5d9d6947))

* enforce python 3.12 only ([`bf6ea55`](https://github.com/jjjermiah/NBIA-toolkit/commit/bf6ea55c5fd23b2d0b5c1a1b36bffbdea4fcf58b))

* testing GHA fix ([`b776c53`](https://github.com/jjjermiah/NBIA-toolkit/commit/b776c53fb84a274d7fd437fd2aee91ced0020981))

* rearrange and add better intra-package references ([`f861774`](https://github.com/jjjermiah/NBIA-toolkit/commit/f861774407dd2ddcb26e4db738639b00e9fc4ca2))

* add pypackage stuff ([`1c3e285`](https://github.com/jjjermiah/NBIA-toolkit/commit/1c3e2856a55b116ca70fb87018c1e0bfe3cfddeb))

* Merge pull request #2 from jjjermiah/development

modify auth ([`5181e17`](https://github.com/jjjermiah/NBIA-toolkit/commit/5181e17e6be3b6bd4d099af976435706792ce821))

* modify auth ([`04b0c30`](https://github.com/jjjermiah/NBIA-toolkit/commit/04b0c301978bf2381c8d7103ab041ac54c393914))

* Merge branch &#39;main&#39; of https://github.com/jjjermiah/NBIA-toolkit into main ([`c2b0119`](https://github.com/jjjermiah/NBIA-toolkit/commit/c2b011910668ceeb56ea97a45917cd9622af6a3a))

* basic linting ([`8525b23`](https://github.com/jjjermiah/NBIA-toolkit/commit/8525b236b09be635c1393b1f4975362c85015b71))

* Update main.yml ([`2065a3d`](https://github.com/jjjermiah/NBIA-toolkit/commit/2065a3df04b9fe5e69242f766076728012da6fa8))

* testing only with 3.10 onwards ([`0a50629`](https://github.com/jjjermiah/NBIA-toolkit/commit/0a5062949260dbeeeb36ea610b01bae339ae9eac))

* modify tests for mac windows python versions ([`f1c2364`](https://github.com/jjjermiah/NBIA-toolkit/commit/f1c2364607b4b7392bdc043e146aac9eb7952983))

* fix badge ([`c60a1e6`](https://github.com/jjjermiah/NBIA-toolkit/commit/c60a1e689a522baf81597569b7376783d3bd3a20))

* add gha badge ([`86f375c`](https://github.com/jjjermiah/NBIA-toolkit/commit/86f375cb5ea5c7fe3cd161a45cea0e8b489d7edf))

* add ruff linter ([`19edd29`](https://github.com/jjjermiah/NBIA-toolkit/commit/19edd291f38376632363ada6f6914fba42264014))

* add coverage test ([`f9afee3`](https://github.com/jjjermiah/NBIA-toolkit/commit/f9afee34fb2b627e246ecd70269b67801b8f6dee))

* add requirements.txt ([`ea4c4f9`](https://github.com/jjjermiah/NBIA-toolkit/commit/ea4c4f9049c493a87dd15c60fa59f44c8145a731))

* modify worflow ([`957ca1a`](https://github.com/jjjermiah/NBIA-toolkit/commit/957ca1aa3035f350b64902ca2f45d77540c9cd2b))

* add requirements.txt ([`2075f9e`](https://github.com/jjjermiah/NBIA-toolkit/commit/2075f9e6a26ed41eda084d9131159d7216ac93af))

* Update main.yml ([`58a75cf`](https://github.com/jjjermiah/NBIA-toolkit/commit/58a75cf63b424ad9804153bd7e23b75defefed00))

* Update main.yml ([`3809f3a`](https://github.com/jjjermiah/NBIA-toolkit/commit/3809f3ac6b3d2aff092443ea7579da9b73a0a426))

* Update main.yml ([`dea0182`](https://github.com/jjjermiah/NBIA-toolkit/commit/dea01826b128bf811383caebf6e561c05b249004))

* Create main.yml ([`bbd0660`](https://github.com/jjjermiah/NBIA-toolkit/commit/bbd06608c0844b7fc1a417608cd6de7501a6a547))

* added jsondecode Error Handling ([`b7a4cee`](https://github.com/jjjermiah/NBIA-toolkit/commit/b7a4cee1d9223e7ddcf357a4a3e35df2e1fe0142))

* added functions, created tests ([`3c1c031`](https://github.com/jjjermiah/NBIA-toolkit/commit/3c1c031d02736521eee39a8d19d322fa30f5bc7b))

* add README ([`68d67ad`](https://github.com/jjjermiah/NBIA-toolkit/commit/68d67ad56cd399311ff11191af00fdb5680abc5f))

* first commit ([`11f25c0`](https://github.com/jjjermiah/NBIA-toolkit/commit/11f25c074e85181a521de2b3ded4842f79e2a215))

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