BUG: Use link to new repository

Closes #11

Author: ghisvail

CONTRIBUTING.md

@@ -13,11 +13,11 @@ Once tested, reviewed and approved, they will be merged back into `main`.
 The medkit contributing process is as follows:
 
 - fork the project into your personal space
-- before creating a new branch, open an [issue](https://github.com/TeamHeka/medkit/issues/new) describing the bug or the feature you will be working on, unless there is already an existing issue.
+- before creating a new branch, open an [issue](https://github.com/medkit-lib/medkit/issues/new) describing the bug or the feature you will be working on, unless there is already an existing issue.
 - in your fork, create a branch from `main` and name it with a short description: `<issue-id>-<short-description>` (without the `#` character).
 - start working by adding commits to this branch. Try to have clear [commit messages](https://cbea.ms/git-commit/). Do not forget to also write tests in the `tests/`directory if applicable (cf [Tests](#tests)).
 - once you are done, check that your code follows our coding standards with `black`and `flake8` (cf [Linting and formatting](#linting-and-formatting)) and that all the tests pass with `pytest` (cf [Tests](#tests))
-- open a [pull request](https://github.com/TeamHeka/medkit/compare) (PR). Unit tests and linting/formatting checks will automatically be run on the PR and prevent it from being merged if they fail.
+- open a [pull request](https://github.com/medkit-lib/medkit/compare) (PR). Unit tests and linting/formatting checks will automatically be run on the PR and prevent it from being merged if they fail.
 - once all CI checks passed, wait for the review of the medkit maintainers. They will make sure it aligns with the project goals and may ask for some changes.
 
 Once this reviewing phase is over, the pull request will be integrated into `main`, either with a merge, a squash & merge or a rebase, depending on the impact of the merge request and the state of its git history.

docs/api/text.md

@@ -260,7 +260,7 @@ reference of the file.
 :::{note}
 You may test French default rules using `section_tokenizer = SectionTokenizer()`.
 The corresponding file content is available
-[here](https://raw.githubusercontent.com/TeamHeka/medkit/develop/medkit/text/segmentation/default_section_definition.yml).
+[here](https://raw.githubusercontent.com/medkit-lib/medkit/develop/medkit/text/segmentation/default_section_definition.yml).
 :::
 
 For {class}`~.text.segmentation.SyntagmaTokenizer`, here is the yaml schema 
@@ -272,7 +272,7 @@ start of a new syntagma.
 :::{note}
 You may test default French rules using `syntagma_tokenizer = SyntagmaTokenizer()`.
 The corresponding file content is available
-[here](https://raw.githubusercontent.com/TeamHeka/medkit/develop/medkit/text/segmentation/default_syntagma_definition.yml).
+[here](https://raw.githubusercontent.com/medkit-lib/medkit/develop/medkit/text/segmentation/default_syntagma_definition.yml).
 :::
 
 

docs/examples/brat_io.md

@@ -30,7 +30,7 @@ Consider this text file:
 +++
 ```{code-cell} ipython3
 # You can download the file available in source code
-# !wget https://raw.githubusercontent.com/TeamHeka/medkit/main/docs/examples/input/brat/doc_01.txt
+# !wget https://raw.githubusercontent.com/medkit-lib/medkit/main/docs/examples/input/brat/doc_01.txt
 
 from pathlib import Path
 
@@ -43,7 +43,7 @@ It has the following brat annotation file:
 
 ```{code-cell} ipython3
 # You can download the file available in source code
-# !wget https://raw.githubusercontent.com/TeamHeka/medkit/main/docs/examples/input/brat/doc_01.ann
+# !wget https://raw.githubusercontent.com/medkit-lib/medkit/main/docs/examples/input/brat/doc_01.ann
 
 print(Path("./input/brat/doc_01.ann").read_text(encoding="utf-8"))
 ```

docs/examples/cleaning_text.md

@@ -25,7 +25,7 @@ Consider the following document:
 
 ```{code-cell} ipython3
 # You can download the file available in source code
-# !wget https://raw.githubusercontent.com/TeamHeka/medkit/main/docs/examples/input/text/text_to_clean.txt
+# !wget https://raw.githubusercontent.com/medkit-lib/medkit/main/docs/examples/input/text/text_to_clean.txt
 
 from pathlib import Path
 from medkit.core.text import TextDocument

docs/examples/text_segmentation/document.md

@@ -29,7 +29,7 @@ Let's detect the sections and add some annotations using medkit operations.
 
 ```{code-cell} ipython3
 # You can download the file available in source code
-# !wget https://raw.githubusercontent.com/TeamHeka/medkit/main/docs/data/text/1.txt
+# !wget https://raw.githubusercontent.com/medkit-lib/medkit/main/docs/data/text/1.txt
 
 from pathlib import Path
 from medkit.core.text import TextDocument

docs/examples/text_segmentation/section.md

@@ -27,7 +27,7 @@ For beginners, let's load a text file using the {class}`~medkit.core.text.TextDo
 
 ```{code-cell} ipython3
 # You can download the file available in source code
-# !wget https://raw.githubusercontent.com/TeamHeka/medkit/main/docs/data/text/1.txt
+# !wget https://raw.githubusercontent.com/medkit-lib/medkit/main/docs/data/text/1.txt
 
 from pathlib import Path
 from medkit.core.text import TextDocument

docs/examples/text_segmentation/syntagma.md

@@ -25,7 +25,7 @@ For beginners, let's load a text file using the {class}`~medkit.core.text.TextDo
 
 ```{code-cell} ipython3
 # You can download the file available in source code
-# !wget https://raw.githubusercontent.com/TeamHeka/medkit/main/docs/data/text/1.txt
+# !wget https://raw.githubusercontent.com/medkit-lib/medkit/main/docs/data/text/1.txt
 
 from pathlib import Path
 from medkit.core.text import TextDocument

docs/user_guide/context_detection.md

@@ -194,7 +194,7 @@ for syntagma_seg in syntagma_segs:
 
 As you can see, a few sentences where split into smaller parts. We can now run a
 {class}`~medkit.text.context.NegationDetector` instance on the syntagmas (using
-the [default rules file](https://github.com/TeamHeka/medkit/blob/main/medkit/text/context/negation_detector_default_rules.yml)).
+the [default rules file](https://github.com/medkit-lib/medkit/blob/main/medkit/text/context/negation_detector_default_rules.yml)).
 
 ```{code-cell} ipython3
 from medkit.text.context import NegationDetector, NegationDetectorRule

docs/user_guide/first_steps.md

@@ -24,7 +24,7 @@ For starters, let's load a text file using the
 
 ```{code-cell} ipython3
 # You can download the file available in source code
-# !wget https://raw.githubusercontent.com/TeamHeka/medkit/main/docs/data/text/1.txt
+# !wget https://raw.githubusercontent.com/medkit-lib/medkit/main/docs/data/text/1.txt
 
 from pathlib import Path
 from medkit.core.text import TextDocument

docs/user_guide/install.md

@@ -9,7 +9,7 @@ From 0.4.1 version, medkit package (named **medkit-lib**) is available on
 [PyPi](https://pypi.org/project/medkit-lib/).
 :::
 
-Releases are published on <https://github.com/TeamHeka/medkit/releases>.
+Releases are published on <https://github.com/medkit-lib/medkit/releases>.
 
 To install medkit :
 
@@ -35,8 +35,8 @@ pip install 'medkit-lib[all]'
 ## Install a development version
 
 If you want to contribute, clone the `medkit` repository locally:
-  - SSH: `git clone  git@github.com:TeamHeka/medkit.git`
-  - HTTPS: `git clone https://github.com/TeamHeka/medkit.git`
+  - SSH: `git clone  git@github.com:medkit-lib/medkit.git`
+  - HTTPS: `git clone https://github.com/medkit-lib/medkit.git`
 
 [Poetry](https://python-poetry.org) is used for managing dependencies and
 packaging medkit.