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Change all the links to the new organization #272

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Oct 10, 2024
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Change all the links to the new organization #272

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55b7756
Change all the links to the new organization
qubixes Oct 9, 2024
a0164ff
Fix yoda integration test
qubixes Oct 9, 2024
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2 changes: 1 addition & 1 deletion docker/README.md
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Expand Up @@ -10,7 +10,7 @@ Dockerised integration tests of iBridges with iRODS
1. Clone iBridges

```sh
git clone --branch develop https://github.com/UtrechtUniversity/iBridges.git
git clone --branch develop https://github.com/iBridges-for-iRODS/iBridges.git
```

Execute the following commands in the root ibridges directory:
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2 changes: 1 addition & 1 deletion docs/source/cli.rst
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Expand Up @@ -36,7 +36,7 @@ create the environment file for you. Below are the currently (known) plugins, se
* - Organization
- Link
* - Utrecht University
- https://github.com/UtrechtUniversity/ibridges-servers-uu
- https://github.com/iBridges-for-iRODS/ibridges-servers-uu
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Do you want to move them here too, or shall they stay under the UU organisation?

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I guess it makes more sense to have in under UtrechtUniversity, though I just like the idea of having everything under the same organization.


After installation, you will be able to create an `irods_environment.json` by simply answering questions such as which email-address
you have. First find the server name with:
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6 changes: 3 additions & 3 deletions docs/source/faq.rst
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Expand Up @@ -18,15 +18,15 @@ An advantage compared to the iCommands is that iBridges also works on Mac OS and

**I found a bug or have a feature request, where do I go?**
------------------------------------------------------------------------
Our development is done on `GitHub <https://github.com/UtrechtUniversity/iBridges>`__ Look under the `Issues` section
Our development is done on `GitHub <https://github.com/iBridges-for-iRODS/iBridges>`__ Look under the `Issues` section
whether the bug or feature request has already been reported. If not, we heartily welcome creating a new issue. We
try to get back to you as soon as possible, at least within a few days.


**I want to contribute to iBridges, where do I go?**
----------------------------------------------------

Our development is done on `GitHub <https://github.com/UtrechtUniversity/iBridges>`__ We are welcoming contributions
Our development is done on `GitHub <https://github.com/iBridges-for-iRODS/iBridges>`__ We are welcoming contributions
by pull requests. You can also ask for new features/ideas in our issue tracker.


Expand Down Expand Up @@ -91,4 +91,4 @@ Warnings can also be switched off through python's `warnings` package:
**My metadata with keys starting with `org_` do not show up in the iBridges metadata.**
---------------------------------------------------------------------------------------

iBridges **does not show** metadata that contain a key starting with the prefix `org_`. This is due to data security reasons on `Yoda systems <https://github.com/UtrechtUniversity/yoda>`__.
iBridges **does not show** metadata that contain a key starting with the prefix `org_`. This is due to data security reasons on `Yoda systems <https://github.com/iBridges-for-iRODS/yoda>`__.
6 changes: 3 additions & 3 deletions docs/source/index.rst
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Expand Up @@ -6,20 +6,20 @@
Welcome to the iBridges documentation!
======================================

`iBridges <https://github.com/UtrechtUniversity/iBridges>`__ is a Python library to connect to iRODS servers in a simplified and safe manner.
`iBridges <https://github.com/iBridges-for-iRODS/iBridges>`__ is a Python library to connect to iRODS servers in a simplified and safe manner.
iBridges consists of three major components: a Python API for Python programmers, a Command Line Interface and a Graphical user interface.
The documentation presented here is for the Python API and Command Line Interface. The documentation for the Graphical User Interface is
located on a separate `page <https://chstaiger.github.io/iBridges-Gui/>`__.

.. note::
The project is in active development, current features are stable and the documentation is complete. However, we are still actively developing new features and improving the existing ones. We appreciate help, suggestions, issues and bug reports in our issue tracker on `GitHub <https://github.com/UtrechtUniversity/iBridges>`__.
The project is in active development, current features are stable and the documentation is complete. However, we are still actively developing new features and improving the existing ones. We appreciate help, suggestions, issues and bug reports in our issue tracker on `GitHub <https://github.com/iBridges-for-iRODS/iBridges>`__.


iBridges is a wrapper around the `python-irodsclient <https://github.com/irods/python-irodsclient>`__. While the
python-irodsclient is very powerful and feature rich, we aim to provide an easier API for users (mainly researchers)
that do not have any technical knowledge of iRods.

We provide extensive tutorials on how to work with data in iRODS. Please consult our `tutorials <https://github.com/UtrechtUniversity/iBridges/tree/main/tutorials>`__ page.
We provide extensive tutorials on how to work with data in iRODS. Please consult our `tutorials <https://github.com/iBridges-for-iRODS/iBridges/tree/main/tutorials>`__ page.

.. toctree::
:hidden:
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2 changes: 1 addition & 1 deletion docs/source/ipath.rst
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Expand Up @@ -14,7 +14,7 @@ We strongly recommend using :class:`IrodsPath` over using strings for the follow
- :class:`IrodsPath` is **more convenient** since there are many methods and attributes available such as: the name, size and parent of the iRODS path.
- The string representation of the :class:`IrodsPath` is available through :code:`str(ipath)`.

A complete tutorial on iRODS paths can be followed `here <https://github.com/UtrechtUniversity/iBridges/tree/main/tutorials>`__. For an overview of
A complete tutorial on iRODS paths can be followed `here <https://github.com/iBridges-for-iRODS/iBridges/tree/main/tutorials>`__. For an overview of
all functionality connected to the :class:`IrodsPath`, see the :doc:`API documentation <api/generated/ibridges.path.IrodsPath>`.

IrodsPath
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2 changes: 1 addition & 1 deletion ibridges/__main__.py
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Expand Up @@ -278,7 +278,7 @@ def ibridges_setup():
if len(env_providers) == 0:
print(
"No server information was found. To use this function, please install a plugin"
" such as:\n\nhttps://github.com/UtrechtUniversity/ibridges-servers-uu"
" such as:\n\nhttps://github.com/iBridges-for-iRODS/ibridges-servers-uu"
"\n\nAlternatively create an irods_environment.json by yourself or with the help "
"of your iRODS administrator."
)
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4 changes: 2 additions & 2 deletions pyproject.toml
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Expand Up @@ -34,8 +34,8 @@ dependencies = [
dynamic = ["version"]

[project.urls]
GitHub = "https://github.com/UtrechtUniversity/iBridges"
documentation = "https://github.com/UtrechtUniversity/iBridges"
GitHub = "https://github.com/iBridges-for-iRODS/iBridges"
documentation = "https://github.com/iBridges-for-iRODS/iBridges"

[project.optional-dependencies]
test = [
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