Repository: iBridges-for-iRODS/iBridges (language: python)

Issue:
pypi release hook (#61)



Discussion / hints:

Fix patch:
diff --git a/.dockerignore b/.dockerignore
new file mode 100644
index 00000000..83a81467
--- /dev/null
+++ b/.dockerignore
@@ -0,0 +1,3 @@
+.github
+.dockerignore
+**/.dockerignore
\ No newline at end of file
diff --git a/LICENSE b/LICENSE
index f288702d..fe421d8b 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,674 +1,20 @@
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-THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
-PURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
-IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
-ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
-
-  16. Limitation of Liability.
-
-  IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
-WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
-THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
-GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
-USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
-DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
-PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
-EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
-SUCH DAMAGES.
-
-  17. Interpretation of Sections 15 and 16.
-
-  If the disclaimer of warranty and limitation of liability provided
-above cannot be given local legal effect according to their terms,
-reviewing courts shall apply local law that most closely approximates
-an absolute waiver of all civil liability in connection with the
-Program, unless a warranty or assumption of liability accompanies a
-copy of the Program in return for a fee.
-
-                     END OF TERMS AND CONDITIONS
-
-            How to Apply These Terms to Your New Programs
-
-  If you develop a new program, and you want it to be of the greatest
-possible use to the public, the best way to achieve this is to make it
-free software which everyone can redistribute and change under these terms.
-
-  To do so, attach the following notices to the program.  It is safest
-to attach them to the start of each source file to most effectively
-state the exclusion of warranty; and each file should have at least
-the "copyright" line and a pointer to where the full notice is found.
-
-    <one line to give the program's name and a brief idea of what it does.>
-    Copyright (C) <year>  <name of author>
-
-    This program is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    This program is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with this program.  If not, see <https://www.gnu.org/licenses/>.
-
-Also add information on how to contact you by electronic and paper mail.
-
-  If the program does terminal interaction, make it output a short
-notice like this when it starts in an interactive mode:
-
-    <program>  Copyright (C) <year>  <name of author>
-    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
-    This is free software, and you are welcome to redistribute it
-    under certain conditions; type `show c' for details.
-
-The hypothetical commands `show w' and `show c' should show the appropriate
-parts of the General Public License.  Of course, your program's commands
-might be different; for a GUI interface, you would use an "about box".
-
-  You should also get your employer (if you work as a programmer) or school,
-if any, to sign a "copyright disclaimer" for the program, if necessary.
-For more information on this, and how to apply and follow the GNU GPL, see
-<https://www.gnu.org/licenses/>.
-
-  The GNU General Public License does not permit incorporating your program
-into proprietary programs.  If your program is a subroutine library, you
-may consider it more useful to permit linking proprietary applications with
-the library.  If this is what you want to do, use the GNU Lesser General
-Public License instead of this License.  But first, please read
-<https://www.gnu.org/licenses/why-not-lgpl.html>.
+MIT License
+
+Copyright (c) 2024 Utrecht University
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/README.md b/README.md
index b11e1fb9..98688dae 100644
--- a/README.md
+++ b/README.md
@@ -1,60 +1,95 @@
 # iBridges
-## Development status
-[![Python package](https://github.com/UtrechtUniversity/iBridges/actions/workflows/main.yml/badge.svg?branch=develop)](https://github.com/UtrechtUniversity/iBridges/actions/workflows/main.yml) [![Run integration tests against Yoda](https://github.com/UtrechtUniversity/iBridges/actions/workflows/integration-tests-yoda.yml/badge.svg)](https://github.com/UtrechtUniversity/iBridges/actions/workflows/integration-tests-yoda.yml)
+[![](https://github.com/UtrechtUniversity/iBridges/actions/workflows/integration-tests-irods.yml/badge.svg?branch=develop)](https://github.com/UtrechtUniversity/iBridges/actions/workflows/integration-tests-irods.yml) [![](https://github.com/UtrechtUniversity/iBridges/actions/workflows/main.yml/badge.svg?branch=develop)](https://github.com/UtrechtUniversity/iBridges/actions/workflows/main.yml) 
+[![](https://github.com/UtrechtUniversity/iBridges/actions/workflows/integration-tests-yoda.yml/badge.svg)](https://github.com/UtrechtUniversity/iBridges/actions/workflows/integration-tests-yoda.yml) ![](https://readthedocs.org/projects/ibridges/badge/?version=latest&style=flat-default)
 
 ## About
 
-This git repo contains some wrapping classes and functions around the *python-irodsclient* 
-to ease the connection and meta/data handling in iRODS.
+iBridges is library for scientific programmers who are working with data in iRODS. We provide a wrapper around the [python-irodsclient](https://pypi.org/project/python-irodsclient/) to facilitate easy interaction with the iRODS server.
 
-We offer two main classes
+Since iBridges is solely based on python it works on all operating systems.
 
-- irodsConnector: basic iRODS functionality
-- ibridges: extra fuctionality and presets for scientific programmers to safely wirk with data on an iRODS server.
+- Runs on Python 3.8 or higher.
+- Supported iRODS server versions: 4.2.11 or higher and 4.3.0 or higher.
 
-## Authors
+ <p align="center">
+    <a href="https://github.com/UtrechtUniversity/iBridges/issues/new?assignees=&labels=&projects=&template=bug_report.md&title=%5BBUG%5D">Report Bug</a>
+    .
+    <a href="https://github.com/UtrechtUniversity/iBridges/issues/new?assignees=&labels=&projects=&template=feature_request.md&title=%5BFEATURE%5D">Request Feature</a>
+    .
+    <a href="https://github.com/UtrechtUniversity/iBridges/discussions/categories/ideas">Share an idea</a>
+    .
+    <a href="https://github.com/UtrechtUniversity/iBridges/discussions/categories/general">Leave some feedback</a>
+    .
+    <a href="https://github.com/UtrechtUniversity/iBridges/discussions/categories/q-a">Ask a question</a>
+  </p>
+</p>
 
-Tim van Daalen, Christine Staiger
+## Installation
+### From Github repository
+```
+git clone git@github.com:UtrechtUniversity/iBridges.git
+cd iBridges
+pip install .
+```
 
-Wageningen University & Research 2021
+### Pypi install
+```
+pip install ibridges
+```
 
-## Contributors
+## Usage
+```py
+# Create an iRODS session
+from ibridges import Session
 
-J.P. Mc Farland
+session = Session(irods_env_path="~/.irods/irods_environment.json", password="mypassword")
 
-University of Groningen, Center for Information Technology, 2022
+# Upload data
+from ibridges import upload
 
-Raoul Schram, Maarten Schermer
+upload(session, "/your/local/path", "/irods/path")
 
-Utrecht University, 2023
+# Download data
+from ibridges import download
 
-## Dependencies
+download(session, "/irods/path", "/other/local/path")
 
-### Supported iRODS versions
+```
 
-- 4.2.11, 4.2.12
-- 4.3.0
+## Tutorials
+### Documentation
+- **[ReadTheDocs](https://ibridges.readthedocs.io/en/latest/)**
 
-### Python
+### Guides
+- [QuickStart](Tutorials/QuickStart.ipynb)
+- [iRODS Paths](Tutorials/iRODS_paths.ipynb)
+- [Data synchronisation](Tutorials/Data_sync.ipynb)
 
-- Python 3 (>= 3.9)
-  - Tested with python versions 3.11 on Windows, Ubuntu20.22 and MacOs
-- pip-22.2.2
-- Python packages (see install via `requirements.txt` below)
+### Beginners tutorials
+- [Setup client configuration](Tutorials/01-Setup-and-connect.ipynb)
+- [Working with data](Tutorials/02-Working-with-data.ipynb)
+- [iRODS and local Paths](Tutorials/03-iRODS-Paths.ipynb)
+- [Metadata](Tutorials/04-Metadata.ipynb)
+- [Sharing data](Tutorials/05-Data-Sharing.ipynb)
 
-Install dependencies with, for example:
+## Authors
 
-```sh
-python3.11 -m pip install -r requirements.txt
-```
-### icommands (optional)
-If the icommands are installed, the users can choose them as backend for up and downloads.
+**Christine Staiger (Maintainer) [ORCID](https://orcid.org/0000-0002-6754-7647)**
 
-## Usage
+- *Wageningen University & Research* 2021 - 2022
+- *Utrecht University* 2022
+
+**Tim van Daalen**, *Wageningen University & Research* 2021
 
-[irodsConnector](Tutorial_irodsConnector.ipynb)
+**Maarten Schermer (Maintainer) [ORCID](https://orcid.org/my-orcid?orcid=0000-0001-6770-3155)**, *Utrecht University* 2023
+
+**Raoul Schram (Maintainer) [ORCID](https://orcid.org/my-orcid?orcid=0000-0001-6616-230X)**. 
+*Utrecht University* 2023
+
+## Contributors
 
-[iRODS paths](Tutorial_iRODS_paths.ipynb)
+**J.P. Mc Farland**,
+*University of Groningen, Center for Information Technology*, 2022
 
 ## License
 This project is licensed under the GPL-v3 license.
diff --git a/docker-compose.yml b/docker-compose.yml
index d9e8c479..023e6c12 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -2,6 +2,7 @@ version: '3'
 
 services:
     irods-catalog:
+        image: irods-catalog
         build:
             context: ./docker/irods_catalog
         # 5432 is exposed by default and can conflict with other postgres containers.
@@ -12,15 +13,19 @@ services:
             - POSTGRES_PASSWORD=testpassword
 
     irods-catalog-provider:
+        image: irods-catalog-provider
         build:
             context: ./docker/irods_catalog_provider
         depends_on:
             - irods-catalog
 
     irods-client:
+        image: irods-client
         build:
             context: .
             dockerfile: ./docker/irods_client/Dockerfile
         depends_on:
             - irods-catalog-provider
         tty: true
+        environment:
+          - CI=${CI}
diff --git a/docker/irods_catalog_provider/Dockerfile_4.2.12 b/docker/irods_catalog_provider/Dockerfile_4.2.12
deleted file mode 100644
index faf62c55..00000000
--- a/docker/irods_catalog_provider/Dockerfile_4.2.12
+++ /dev/null
@@ -1,54 +0,0 @@
-FROM ubuntu:18.04
-
-ENV DEBIAN_FRONTEND=noninteractive
-
-RUN apt-get update && \
-    apt-get install -y \
-        apt-transport-https \
-        gnupg \
-        wget \
-    && \
-    apt-get clean && \
-    rm -rf /var/lib/apt/lists/* /tmp/*
-
-RUN wget -qO - https://packages.irods.org/irods-signing-key.asc | apt-key add - && \
-    echo "deb [arch=amd64] https://packages.irods.org/apt/ bionic main" | tee /etc/apt/sources.list.d/renci-irods.list
-
-RUN apt-get update && \
-    apt-get install -y \
-        libcurl4-gnutls-dev \
-        python3 \
-        python3-distro \
-        python3-jsonschema \
-        python3-pip \
-        python3-psutil \
-        python3-requests \
-        rsyslog \
-        unixodbc \
-    && \
-    apt-get clean && \
-    rm -rf /var/lib/apt/lists/* /tmp/*
-
-ARG irods_version=4.2.12
-ARG irods_package_version_suffix=-1~bionic
-ARG irods_package_version=${irods_version}${irods_package_version_suffix}
-ARG irods_resource_plugin_version=${irods_version}.0${irods_package_version_suffix}
-
-RUN apt-get update && \
-    apt-get install -y \
-        irods-database-plugin-postgres=${irods_package_version} \
-        irods-runtime=${irods_package_version} \
-        irods-icommands=${irods_package_version} \
-	irods-server=${irods_package_version} \
-        irods-resource-plugin-s3=${irods_resource_plugin_version} \
-    && \
-    apt-get clean && \
-    rm -rf /var/lib/apt/lists/* /tmp/*
-
-COPY setup-${irods_version}.input /
-RUN mv /setup-${irods_version}.input /irods_setup.input
-
-WORKDIR /
-COPY entrypoint.sh .
-RUN chmod u+x ./entrypoint.sh
-ENTRYPOINT ["./entrypoint.sh"]
diff --git a/docker/irods_client/entrypoint.sh b/docker/irods_client/entrypoint.sh
index 0d0fd7be..d236b73e 100644
--- a/docker/irods_client/entrypoint.sh
+++ b/docker/irods_client/entrypoint.sh
@@ -31,4 +31,9 @@ echo $(iadmin lu testuser)
 
 cd /ibridges/integration_test
 pytest .
-/bin/bash
+result=$?
+if [[ -z "$CI" ]]; then
+  /bin/bash
+else
+  exit $result
+fi
\ No newline at end of file
diff --git a/ibridges/keywords.py b/ibridges/keywords.py
index 20b220ac..9fac1180 100644
--- a/ibridges/keywords.py
+++ b/ibridges/keywords.py
@@ -18,6 +18,7 @@
 COLL_NAME = imodels.Collection.name
 COLL_ID = imodels.Collection.id
 DATA_NAME = imodels.DataObject.name
+DATA_PATH = imodels.DataObject.path
 DATA_ID = imodels.DataObject.id
 DATA_CHECKSUM = imodels.DataObject.checksum
 META_COLL_ATTR_NAME = imodels.CollectionMeta.name
diff --git a/ibridges/search.py b/ibridges/search.py
index 350d6e15..d5a46841 100644
--- a/ibridges/search.py
+++ b/ibridges/search.py
@@ -61,9 +61,9 @@ def search_data(session: Session, path: Optional[Union[str, IrodsPath]] = None,
     # gather results
     results = list(data_query.get_results())
     if checksum is None:
-        coll_res = coll_query.get_results()
-        if len(list(coll_res)) > 0:
-            results.append(coll_res)
+        coll_res = list(coll_query.get_results())
+        if len(coll_res) > 0:
+            results.extend(coll_res)
 
     for item in results:
         if isinstance(item, dict):
diff --git a/pyproject.toml b/pyproject.toml
index 87db7330..4e2a27a5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -24,7 +24,6 @@ classifiers = [
 
 dependencies = [
     "python-irodsclient==1.1.6",
-    "setproctitle==1.3.2",
     "tqdm",
 ]
 
diff --git a/tutorials/01-Setup-and-connect.ipynb b/tutorials/01-Setup-and-connect.ipynb
new file mode 100644
index 00000000..ca405f21
--- /dev/null
+++ b/tutorials/01-Setup-and-connect.ipynb
@@ -0,0 +1,431 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "b37a773f",
+   "metadata": {},
+   "source": [
+    "# Setup and connect to iRODS"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "610d2838",
+   "metadata": {},
+   "source": [
+    "## The iRODS environment file"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "466e791e",
+   "metadata": {},
+   "source": [
+    "To connect to a specific iRODS instance you will need a so-called `irods_environment.json` file. This file contains all parameters to establish the connection. Your iRODS sysadmin or service provider will give you such an environment file."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "c0dec8b5",
+   "metadata": {},
+   "source": [
+    "When you are working with Yoda, you can find the information by clicking on the Yoda version label on the bottom of the Yoda portal **after you logged into the portal**.\n",
+    "\n",
+    "<img src=\"img/Yoda_environment.png\" align=\"center\" width=\"200\"/>"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "1fecf346",
+   "metadata": {},
+   "source": [
+    "## Required information to connect to iRODS"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "0763be04",
+   "metadata": {},
+   "source": [
+    "The `irods_envirnment.json` needs to contain the following information:\n",
+    "\n",
+    "```\n",
+    "{\n",
+    "\"irods_host\": \"<SERVER ADDRESS>\",\n",
+    "\"irods_port\": 1247,\n",
+    "\"irods_home\": \"<YOUR CURRENT WORKING DIRECTORY>\",\n",
+    "\"irods_user_name\": \"<YOUR USERNAME>\",\n",
+    "\"irods_zone_name\": \"<ZONE NAME>\",\n",
+    "\"irods_authentication_scheme\": \"pam\",\n",
+    "\"irods_encryption_algorithm\": \"AES-256-CBC\",\n",
+    "\"irods_encryption_key_size\": 32,\n",
+    "\"irods_encryption_num_hash_rounds\": 16,\n",
+    "\"irods_encryption_salt_size\": 8,\n",
+    "\"irods_client_server_policy\": \"CS_NEG_REQUIRE\",\n",
+    "\"irods_client_server_negotiation\": \"request_server_negotiation\"\n",
+    "}\n",
+    "```\n",
+    "Apart from your user name all settings should be given by your iRODS service provider.\n",
+    "\n",
+    "**Important**: please make sure that the parameter `\"irods_client_server_policy\": \"CS_NEG_REQUIRE\",` is there!"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "b9ce1bf1",
+   "metadata": {},
+   "source": [
+    "## Additional information"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "57f676d6",
+   "metadata": {},
+   "source": [
+    "- The `\"irods_home\"` functions similarly to a \"current working directory\" and you will be be guided to that location automatically. So we encourage you to set it to a valid location for your project.\n",
+    "\n",
+    "    - Plain iRODS: `\"irods_home\": \"/<ZONE NAME>/home/<YOUR USERNAME>\"`.\n",
+    "\n",
+    "    - Yoda: `\"irods_home\": \"/<ZONE NAME>/home/research-<YOUR GROUP>\"`\n",
+    "    \n",
+    "\n",
+    "- We also encourage you to ask your iRODS provider about the `\"irods_default_resource\"`. \n",
+    "    In most Yoda instances this is `\"irods_default_resource\": \"irodsResc\"`.\n",
+    "\n",
+    "Both of the settings are not essential but will make it easier and less error-prone when working with data in iRODS. The `\"irods_home\"` can also be changed later."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "a1e82b29",
+   "metadata": {},
+   "source": [
+    "## Where to put the irods_environment.json?"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "1ba9bf4c",
+   "metadata": {},
+   "source": [
+    "All iRODS clients (icommands and APIs) expect the above parameters to be stored in a special folder. This folder is called `.irods` and it lies in your home directory:\n",
+    "- Mac: `/Users/<user>/.irods`\n",
+    "- Linux: `/home/<user>/.irods`\n",
+    "- Windows: `C:\\Users\\<user>\\.irods`\n",
+    "\n",
+    "In Mac and Linux you can simply create the folder manually in the file browser.\n",
+    "The `.` shows that it is a hidden folder, which can be quite difficult to create in Windows. Below we provide a python cde snippet which creates the folder:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5196436f",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "Path.mkdir"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e9c74026",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from pathlib import Path\n",
+    "\n",
+    "loc = Path.expanduser(Path('~')).joinpath(\".irods\")\n",
+    "if not loc.exists():\n",
+    "    loc.mkdir()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "d404e8d0",
+   "metadata": {},
+   "source": [
+    "Please store your `irods_environment.json` in that folder and make sure that its extension is `json`. \n",
+    "\n",
+    "Again under Windows the text editors usually safe files with the `.txt` extension. So please watch out for this.\n",
+    "Below we provide a code snippet which saves your personal iRODS/Yoda information in the right place. Please adjust:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "d8ac6622",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import json\n",
+    "env = {\n",
+    "    \"irods_host\": \"<FILL_IN>\",\n",
+    "    \"irods_port\": 1247,\n",
+    "    \"irods_home\": \"<FILL_IN>\",\n",
+    "    \"irods_user_name\": \"<FILL_IN>\",\n",
+    "    \"irods_zone_name\": \"<FILL_IN>\",\n",
+    "    \"irods_default_resource\": \"<FILL_IN>\",\n",
+    "    \"irods_authentication_scheme\": \"pam\",\n",
+    "    \"irods_client_server_policy\": \"CS_NEG_REQUIRE\",\n",
+    "    \"irods_client_server_negotiation\": \"request_server_negotiation\",\n",
+    "    \"irods_encryption_algorithm\": \"AES-256-CBC\",\n",
+    "    \"irods_encryption_key_size\": 32,\n",
+    "    \"irods_encryption_num_hash_rounds\": 16,\n",
+    "    \"irods_encryption_salt_size\": 8\n",
+    "}\n",
+    "loc = Path.expanduser(Path('~')).joinpath(\".irods\", \"irods_environment.json\")\n",
+    "with open(loc, 'w') as write_json:\n",
+    "    json.dump(env, write_json)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "da3ea9e2",
+   "metadata": {},
+   "source": [
+    "If your settings are saved correctly under Windows, you should see this file in `C:\\Users\\<user>\\.irods`.\n",
+    "\n",
+    "<img src=\"img/Save_json.png\">\n",
+    "\n",
+    "Some last check, if the output is `True` all is setup correctly:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f01e88f2",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "loc = Path.expanduser(Path('~')).joinpath(\".irods\", \"irods_environment.json\")\n",
+    "Path.is_file(loc)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "a1648345",
+   "metadata": {},
+   "source": [
+    "## Connecting to iRODS"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "460db0d9",
+   "metadata": {},
+   "source": [
+    "### Interactively creating an  iRODS session"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "acede9da",
+   "metadata": {},
+   "source": [
+    "When you are working interactively in a jupyter notebook or another environment, we can use the following way of connecting:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "c047bf20",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from ibridges.interactive import interactive_auth\n",
+    "session = interactive_auth()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "8837188d",
+   "metadata": {},
+   "source": [
+    "This command reads in the information from your `irods_environment.json`; it tries to find a cached password in the `.irods` folder and asks you for your password, in case there is no cached password. \n",
+    "Upon successful login, the command/function stores your password in a scrambled way so that the next time you will not be bothered with typing in the password again.\n",
+    "\n",
+    "Let's see what happens if we rerun this command. We will first delete the current session and login again:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "cb564f71",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "del session\n",
+    "session = interactive_auth()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "7f9dd9b3",
+   "metadata": {},
+   "source": [
+    "You see, that `interactive_auth` still remembers the password from the last time you logged in. **NOTE, that the cached password will expire at some point!**"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "29aa5a45",
+   "metadata": {},
+   "source": [
+    "### Connecting by passing a password"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "20a3b231",
+   "metadata": {},
+   "source": [
+    "In some programming situations you cannot interactively pass a password. For these cases `iBridges` provides you with another function to connect:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "cd07d90f",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from ibridges import Session\n",
+    "env_file = Path.expanduser(Path('~')).joinpath(\".irods\", \"irods_environment.json\")\n",
+    "password = <YOUR PASSWORD>\n",
+    "\n",
+    "session = Session(irods_env=ienv, password=password)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "ac22dfc7",
+   "metadata": {},
+   "source": [
+    "## What is this session thing?"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "71376db2",
+   "metadata": {},
+   "source": [
+    "The `session` stores all information from your `irods_environment.json`, it provides you with even more information about the iRODS you are connected to and it is needed for all interactions with iRODS.\n",
+    "\n",
+    "Let's ave a look:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "d4d14991",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "print(session.username)\n",
+    "print(session.default_resc) # the resource to which data will be uploaded\n",
+    "print(session.zone) \n",
+    "print(session.server_version)\n",
+    "print(session.home) # default home for iRODS /zone/home/username"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "0a34d792",
+   "metadata": {},
+   "source": [
+    "You will see some information about you as a user on iRODS. The last statement shows your current working location on iRODS.\n",
+    "**Note that it is not verified that this location exists!**. Let's have a closer look."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "64d1e7c7",
+   "metadata": {},
+   "source": [
+    "## The iRODS home"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "33bffc91",
+   "metadata": {},
+   "source": [
+    "Let us verify that the current working location ineed exists:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6d06932a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from ibridges.utils.path import IrodsPath\n",
+    "irods_path = IrodsPath(session, session.home)\n",
+    "irods_path.collection_exists()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "a06f0c7d",
+   "metadata": {},
+   "source": [
+    "We create an `IrodsPath` which is not a simple text or string, but which is actually connected to iRODS through the `session`. With that we can ask iRODS wether the path indeed is a collection (similar to folder, see chapter about Data).\n",
+    "\n",
+    "In case the last command gave you a `False`, do not despair. You can set this parameter with."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "619e1f5b",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "session.home = \"<YOUR NEW iRODS PATH>\""
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "efa0b4b5",
+   "metadata": {},
+   "source": [
+    "Another way to access the current iRODS home is the `~`. Linux and Mac users might know this notation:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5590a92d",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "print(IrodsPath(session, \"~\"))"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/tutorials/02-Working-with-data.ipynb b/tutorials/02-Working-with-data.ipynb
new file mode 100644
index 00000000..a0dff0f6
--- /dev/null
+++ b/tutorials/02-Working-with-data.ipynb
@@ -0,0 +1,445 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "d3598e82",
+   "metadata": {},
+   "source": [
+    "# Working with data"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "26ff36c3",
+   "metadata": {},
+   "source": [
+    "On your computer you can open an Explorer which will show you all the files and the directories. In iRODS we have something similar: we have data objects which you can see for the moment as a file and we have collections which are similar to directories.\n",
+    "\n",
+    "In the course of this and the next tutorials it will become clear that this is only an analogy and that there is more to data objects and collections."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "458b2f0f",
+   "metadata": {},
+   "source": [
+    "## Create an iRODS session"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "ed555077",
+   "metadata": {},
+   "source": [
+    "Again, to work from your Laptop with data in iRODS you will need a `session` as describes in [01-Setup-and-connect](01-Setup-and-connect.ipynb)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e5ef4e10",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from ibridges.interactive import interactive_auth\n",
+    "session = interactive_auth()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "172e153a",
+   "metadata": {},
+   "source": [
+    "## Create a collection and upload a file"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "9645865a",
+   "metadata": {},
+   "source": [
+    "We will now create a new collection on iRODS in your current iRODS working location:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "716769b9",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from ibridges.path import IrodsPath\n",
+    "from ibridges.data_operations import create_collection\n",
+    "irods_path = IrodsPath(session, '~')\n",
+    "print(\"Current working location:\", irods_path)\n",
+    "irods_coll_path = irods_path.joinpath('demo')\n",
+    "print(\"New collection name:\", irods_coll_path)\n",
+    "coll = create_collection(session, irods_coll_path)\n",
+    "print(\"New collection is created:\", irods_coll_path.collection_exists())"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "2ef9c2fd",
+   "metadata": {},
+   "source": [
+    "Now we will upload a file to that new iRODS collection. In this tutorial we assume that you have a file called `demofile.txt` in your home:\n",
+    "- Linux: `/home/<user>/demofile.txt`\n",
+    "- Mac: `/Users/<user>/demofile.txt`\n",
+    "- Windows: `C:\\Users\\<user>\\demofile.txt`\n",
+    "\n",
+    "Let's check that first."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "cbe34a24",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from pathlib import Path\n",
+    "local_file = Path.expanduser(Path('~')).joinpath('demofile.txt')\n",
+    "if local_file.is_file():\n",
+    "    print('You are good to follow the next steps!')\n",
+    "else:\n",
+    "    print(f'Please create a file {local_file} before you continue')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "eaf9182b",
+   "metadata": {},
+   "source": [
+    "Now we can upload that file:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f6be04e0",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from ibridges import upload\n",
+    "upload(session, local_file, irods_coll_path)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "94ace2c2",
+   "metadata": {},
+   "source": [
+    "We now created a new data object in iRODS:\n",
+    "\n",
+    "<img src=\"img/DataObject1.png\" width=\"400\">\n",
+    "\n",
+    "How can we now be sure that the file is uploaded? Remember, when we created the new collection `demo`, we created a python object called `coll`. Let's inspect that:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "91b73ddd",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "print(coll.name)\n",
+    "print(coll.path)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "e41763a3",
+   "metadata": {},
+   "source": [
+    "Apart from information about its name and its path, a collection also carries a list of `subcollections` and `data_objects`."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "48777591",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "print(f'Current subcollections in {coll.path}:', coll.subcollections)\n",
+    "print(f'Current data objects in {coll.path}:', coll.data_objects)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "2e3380dc",
+   "metadata": {},
+   "source": [
+    "## Download the file and the collection"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "ef68a87a",
+   "metadata": {},
+   "source": [
+    "Of course we can also download the data object we have just created. We will download it to your `Downloads` directory on you computer:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e7e770d3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "local_path = Path.expanduser(Path('~')).joinpath('Downloads')\n",
+    "assert local_path.is_dir()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "3d4a6914",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from ibridges import download\n",
+    "download(session, irods_coll_path.joinpath('demofile.txt'), local_path)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "32a53bfc",
+   "metadata": {},
+   "source": [
+    "You can verify taht the file is downloaded.\n",
+    "Now, what happens if we download the file again?"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2d67068c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "download(session, irods_coll_path.joinpath('demofile.txt'), local_path)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "13e5c96d",
+   "metadata": {},
+   "source": [
+    "You will receive an Exception `OVERWRITE_WITHOUT_FORCE_FLAG`. This means that the file is already there.  \n",
+    "\n",
+    "**Note, both the upload and the download function do not overwrite existing data by default.** \n",
+    "\n",
+    "You can force to overwrite the existing data by setting the flag `overwrite`:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "22496425",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "download(session, irods_coll_path.joinpath('demofile.txt'), local_path, overwrite=True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "bff8110e",
+   "metadata": {},
+   "source": [
+    "## System metadata"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "74c72c43",
+   "metadata": {},
+   "source": [
+    "Both, collections and data objects in iRODS are labeled automatically with some extra information. This information is called *system metadata*. We already saw the `name` and the `path` for the collection. But there is more!"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "70f3e9a4",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "print(f'Collection {coll.name} was created on {coll.create_time}')\n",
+    "print(f'The collection was last modified on {coll.modify_time}')\n",
+    "print(f'The collection was uploaded by and is owned by {coll.owner_name}')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "19779512",
+   "metadata": {},
+   "source": [
+    "We can also get some system information about the data object we created by uploading the demo file. To insoect a data object (and also a collection) we have to retrieve it from iRODS. We will use the function `get_dataobject` to do so. Note, for collections the function is called `get_collection`."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "bd40cf7c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from ibridges import get_dataobject, get_collection\n",
+    "obj = get_dataobject(session, irods_coll_path.joinpath('demofile.txt'))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "58906168",
+   "metadata": {},
+   "source": [
+    "Now we can inspect the object:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "908b0f87",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "print(f'Data object {obj.name} was created on {obj.create_time}')\n",
+    "print(f'Data object {obj.name} full path in iRODS is {obj.path}')\n",
+    "print(f'The data object was created on {obj.create_time}')\n",
+    "print(f'The data object was last modified on {obj.modify_time}')\n",
+    "print(f'The data object was uploaded by and is owned by {obj.owner_name}')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "007b5097",
+   "metadata": {},
+   "source": [
+    "**Data objects also carry a `size` and a `checksum`**, with which you can check whether the data reached iRODS completely. Checksums are particularly useful. With the size you can only check whether the length of your local file matches the on in iRODS. However, you cannot see if the contents is really the same. E.g. the length of 'Hello' and 'Hallo' are the same, but they do differ. With a checksum you can detect this. A checksum is a digest of the contents of a file.\n",
+    "\n",
+    "**Note, both functions, `upload` and `download`, will always calculate and compare the checksums between your computer and iRODS**, to make sure that the data is tranferred correctly. "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "73727623",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "print('Data object size', obj.size)\n",
+    "print('Data object checksum', obj.checksum)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "c0d605fa",
+   "metadata": {},
+   "source": [
+    "The iRODS full path `obj.path` is the address with which you can get the full data object. Currently, this is the uploaded file and its system metadata\n",
+    "\n",
+    "<img src=\"img/DataObject2.png\" width=\"400\">"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "d3614078",
+   "metadata": {},
+   "source": [
+    "## Data object replicas"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "98a206e8",
+   "metadata": {},
+   "source": [
+    "Usually when we upload a file to another computer we create one new item which can be found under the path that we used to upload the data. \n",
+    "\n",
+    "Some iRODS systems distribute the uploaded data to different storage systems. That means, that the file is stored on several storage systems, but you have one path under which you can find the data and address the data. This is called in iRODS a data object `relpica`. When you download data the system decides for you, which is the most advantageous replica to give to you in terms of speed and integrity.\n",
+    "\n",
+    "<img src=\"img/DataObject3.png\" width=\"400\">\n",
+    "\n",
+    "Let us inspect how many replicas of our file we have in iRODS:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f4ce4f52",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from ibridges.data_operations import obj_replicas\n",
+    "obj_replicas(obj)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "9438ebba",
+   "metadata": {},
+   "source": [
+    "In Yoda you might have to wait for some time until the data is replicated.\n",
+    "\n",
+    "The structure of the answer is a list, where each element of this list is structured like this:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4b33598a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "item = obj_replicas(obj)[0]\n",
+    "print('Relplica index:', item[0])\n",
+    "print('Storage system:', item[1])\n",
+    "print('Replica cecksum', item[2])\n",
+    "print('Replica size', item[3])\n",
+    "print('Replica status', item[4])"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "0e94ef61",
+   "metadata": {},
+   "source": [
+    "The replica status tells you of this particular copy of the data is verified and ok. It should say `good`. In all other cases please send the whole replica information including the path to your iRODS help."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1143fc1f",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/tutorials/03-iRODS-Paths.ipynb b/tutorials/03-iRODS-Paths.ipynb
new file mode 100644
index 00000000..e65cedfa
--- /dev/null
+++ b/tutorials/03-iRODS-Paths.ipynb
@@ -0,0 +1,290 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "b814e80d",
+   "metadata": {},
+   "source": [
+    "# A word on local paths and iRODS paths"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "18b446f3",
+   "metadata": {},
+   "source": [
+    "## Local paths on your computer and `pathlib`"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "2fdd6100",
+   "metadata": {},
+   "source": [
+    "You might have wondered in the previous tutorials why we do not simply note down the location of data like a string `/home/user/folder/datafile.txt`.\n",
+    "\n",
+    "- Operating systems use different standard locations. For example your user folder lies in different locations for Linux, MacOS and Windows\n",
+    "- The separator between parts of the path differs, Linux and MacOS use `/` while Windows uses `\\`.\n",
+    "\n",
+    "To be sure we are in your home directory independent from the operating system, we use:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "dd8f03ec",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from pathlib import Path\n",
+    "Path.expanduser(Path('~'))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "96578ae7",
+   "metadata": {},
+   "source": [
+    "Another way to retrieve this location is:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8b91ca62",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "Path.home()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "d05ac550",
+   "metadata": {},
+   "source": [
+    "Moreover, when we want to extend a path with a new subdirectory, we can conveniently use:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6cdf6780",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "Path.home().joinpath('new_dir')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "7f3afd10",
+   "metadata": {},
+   "source": [
+    "The command will take care that the correct separator is used and it provides you with functions to test whether the location already exist, to create the location etc:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "3f8f2645",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "path = Path.home().joinpath('new_dir')\n",
+    "print(f'{path} exists: {path.exists()}')\n",
+    "print(f'{path} has parts: {path.parts}')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "014692ed",
+   "metadata": {},
+   "source": [
+    "## iRODS paths and `IrodsPath`"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "d77ce9cc",
+   "metadata": {},
+   "source": [
+    "iRODS also uses `/` as the separator.\n",
+    "\n",
+    "To determine the default home location in iRODS is dependent on how the iRODS instance is setup. In a default iRODS instance you have a personal home collection:\n",
+    "`/<zonename>/home/<username>`\n",
+    "\n",
+    "On Yoda instances you have a group collection:\n",
+    "`/<yodazone>/home/research-<groupname>`\n",
+    "\n",
+    "You can set this home collection in your `irods_environment.json`.\n",
+    "\n",
+    "iBridges offers the `IrodsPath` which has similar functions as the `pathlib.Path`. We will always need a valis iRODS session to create those paths:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "06846322",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from ibridges.interactive import interactive_auth\n",
+    "session = interactive_auth()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "808df0e1",
+   "metadata": {},
+   "source": [
+    "Now we can retrieve our configured home collection:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e1557bf6",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from ibridges.path import IrodsPath\n",
+    "print(IrodsPath(session, '~'))\n",
+    "# or \n",
+    "print(IrodsPath(session, session.home))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "19a4bf31",
+   "metadata": {},
+   "source": [
+    "Here a list of some functionality:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2b7df9dc",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "irods_path = IrodsPath(session, session.home)\n",
+    "print(f'Extend {irods_path}:', irods_path.joinpath('new_collection'))\n",
+    "print(f'{irods_path} exists:', irods_path.exists())\n",
+    "print(f'{irods_path} is collection:', irods_path.collection_exists())\n",
+    "print(f'{irods_path} is data object:', irods_path.dataobject_exists())\n",
+    "print(f'{irods_path} has parts: {irods_path.parts}')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "82ea884f",
+   "metadata": {},
+   "source": [
+    "## Concatenating iRODS paths  and local paths"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "fe0e20ed",
+   "metadata": {},
+   "source": [
+    "Assume we would like to create a counter part collection to our local path:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "a1dd79a2",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "path"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "5d89637e",
+   "metadata": {},
+   "source": [
+    "We know that we would have to create `new_dir` in our iRODS home collection:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4aee24f6",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "name = path.name\n",
+    "new_irods_coll_path = irods_path.joinpath(name)\n",
+    "print(new_irods_coll_path)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "c0482bab",
+   "metadata": {},
+   "source": [
+    "You see, that `path.name` gives us the name of the last part of the path. We join that name to the iRODS path and now we can create the new collection:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e590f4d7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "coll = IrodsPath.create_collection(session, new_irods_coll_path)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "1da30ba5",
+   "metadata": {},
+   "source": [
+    "## Summary"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "e7dc79ec",
+   "metadata": {},
+   "source": [
+    "To work with `pathlib` and `IrodsPath` is safer since it takes care of the correct concatenation of parts of the path according to the operating system and their specific setup."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "20f547d9",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/tutorials/04-Metadata.ipynb b/tutorials/04-Metadata.ipynb
new file mode 100644
index 00000000..d7784a3e
--- /dev/null
+++ b/tutorials/04-Metadata.ipynb
@@ -0,0 +1,463 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "f9e6811a",
+   "metadata": {},
+   "source": [
+    "# User-defined metadata"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "8564525b",
+   "metadata": {},
+   "source": [
+    "Next to system metadata, iRODS allows you to create own metadata with data objects and collections.\n",
+    "\n",
+    "You can use that metadata to describe your data andlater search for this data; and it can help you keeping the overview of what was the input for an analysis and what is the outcome.\n",
+    "\n",
+    "<img src=\"img/DataObject5.png\" width=\"400\">\n",
+    "\n",
+    "Technically, iRODS offers metadata as key-value-units triple. Let's investigate this:"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "bde731e4",
+   "metadata": {},
+   "source": [
+    "## Add metadata to data objects"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "784fdac1",
+   "metadata": {},
+   "source": [
+    "As always: first we have to create an iRODS session:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "277459df",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from ibridges.interactive import interactive_auth\n",
+    "session = interactive_auth()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "81094d42",
+   "metadata": {},
+   "source": [
+    "Now we can retrieve a data object and insect its metadata."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "69066865",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from ibridges import get_dataobject\n",
+    "from ibridges.path import IrodsPath\n",
+    "from ibridges.meta import MetaData\n",
+    "\n",
+    "irods_coll_path = IrodsPath(session, '~').joinpath('demo')\n",
+    "obj = get_dataobject(session, irods_coll_path.joinpath('demofile.txt'))\n",
+    "\n",
+    "obj_metadata = MetaData(obj)\n",
+    "print(obj_metadata)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "7d9a578b",
+   "metadata": {},
+   "source": [
+    "Most probably you will see no metadata in the above cell. **Note, that system metadata and user-defined metadata are two different entities in a data object!**\n",
+    "With the command `MetaData(obj)` we only retrieve the user-defined metadata.\n",
+    "\n",
+    "<img src=\"img/DataObject4.png\" width=\"400\">"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "1fb67574",
+   "metadata": {},
+   "source": [
+    "Now we can add some own metadata. The metadata comes as key-value-units triple:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "79a1bb89",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "obj_metadata.add('Key', 'Value', 'Units')\n",
+    "print(obj_metadata)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "dafbeaff",
+   "metadata": {},
+   "source": [
+    "Sometimes we do not really have `units`, so we can leave this part empty:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "fb439f38",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "obj_metadata.add('Author', 'Christine')\n",
+    "print(obj_metadata)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "3bfbfa71",
+   "metadata": {},
+   "source": [
+    "We can also add a second author:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "bb35166a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "obj_metadata.add('Author', 'Raoul')\n",
+    "print(obj_metadata)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "116c0f10",
+   "metadata": {},
+   "source": [
+    "You see, that keys in **iRODS metadata keys can have different values**. That is different from python dictionaries where one key can only have one value. **How then to overwrite a value?**"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "cf6d7f93",
+   "metadata": {},
+   "source": [
+    "## Overwrite metadata"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "cb5b7fef",
+   "metadata": {},
+   "source": [
+    "If youw wish to *overwrite* a value, you can first add the new metadata key-value-units triple as above and subsequently remove the old one, you need to specify the whole triple if the metadata contains a units part. As you see the follwing command will fail:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "d0cbd9bf",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "obj_metadata.delete('Key', 'Value')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "77993416",
+   "metadata": {},
+   "source": [
+    "While this one will succeed:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ce98d47c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "obj_metadata.delete('Key', 'Value', 'Units')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "e7f47a59",
+   "metadata": {},
+   "source": [
+    "You can also set all existing values to **one** new value:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "c9f0a95b",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "print(obj_metadata)\n",
+    "obj_metadata.set('Author', 'Maarten')\n",
+    "print(obj_metadata)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "c3f54857",
+   "metadata": {},
+   "source": [
+    "## Add metadata to collections"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "51438d57",
+   "metadata": {},
+   "source": [
+    "The same functionality we saw above, we can use for collections:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "65fb35a5",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from ibridges import get_collection\n",
+    "coll = get_collection(session, irods_coll_path)\n",
+    "coll_metadata = MetaData(coll)\n",
+    "print(coll_metadata)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2af31459",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "coll_metadata.add('TypeOfCollection', 'Results')\n",
+    "print(coll_metadata)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "d7eacaba",
+   "metadata": {},
+   "source": [
+    "## Which metadata can help you keeping an overview?"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "cb48bb74",
+   "metadata": {},
+   "source": [
+    "iRODS metadata can help you keeping an overview while youare working with data and maybe many files which have relations to each other. There are ontologies which define keywords and links between keywords like the **[prov-o Ontology](https://www.w3.org/TR/prov-o/#prov-o-at-a-glance)**.\n",
+    "\n",
+    "Let's see how we can annotate our test data, so that we know that it is test data."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "bbadefc7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from datetime import datetime\n",
+    "coll_metadata.add('prov:wasGeneratedBy', 'Christine')\n",
+    "coll_metadata.add('CollectionType', 'testcollection')\n",
+    "obj_metadata.add('prov:SoftwareAgent', 'iRODS jupyter Tutorial')\n",
+    "obj_metadata.add('prov:wasGeneratedBy', 'Maarten')\n",
+    "obj_metadata.add('DataType', 'testdata')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "5be8180b",
+   "metadata": {},
+   "source": [
+    "Now we have some more descriptive metadata that gives us hints, in which context the data was created:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "a0b8e2d4",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "print(coll_metadata)\n",
+    "print(obj_metadata)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "7f721760",
+   "metadata": {},
+   "source": [
+    "## Finding data by their metadata"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "59518813",
+   "metadata": {},
+   "source": [
+    "Metadata does not only help you to. keep an overview over your data, but can also be used to select and retrieve data. In iBridges you can use the user-defined metadata and some system metadata fields to search for data.\n",
+    "\n",
+    "In our first example we list all collections and data objects in our iRODS home."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e6918fe7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from ibridges.search import search_data\n",
+    "result = search_data(session, path=session.home)\n",
+    "print(result)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "31c88425",
+   "metadata": {},
+   "source": [
+    "The output is a list of Python dictionaries, where each dictionary contains\n",
+    "\n",
+    "1) Collections: `'COLL_NAME': '/<ZONE>/home/<YOUR PATH>'}`\n",
+    "2) Data Objects: \n",
+    "    ```\n",
+    "    {'COLL_NAME': '/<ZONE>/home/<YOUR PATH>', \n",
+    "     'DATA_NAME': '<OBJECT NAME>', \n",
+    "     'D_DATA_CHECKSUM': '<CHECKSUM>'}\n",
+    "    ```\n",
+    "\n",
+    "Now let's try to find data by its metadata. We will have to create a Python dictionary with the metadata keys and the metadata values as search criterion:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5b054794",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "key_vals = {'prov:wasGeneratedBy': 'Christine'}\n",
+    "result = search_data(session, key_vals=key_vals)\n",
+    "print(result)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "81d73352",
+   "metadata": {},
+   "source": [
+    "If we do not want to specify the particular value of the key, we can use a *wildcard*. In iRODS the wildcard is `%`."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "49a9f17e",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "key_vals = {'prov:wasGeneratedBy': '%'}\n",
+    "result = search_data(session, key_vals=key_vals)\n",
+    "print(result)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "69a2e046",
+   "metadata": {},
+   "source": [
+    "Now we also receive the data object that was generated by *Maarten*.\n",
+    "\n",
+    "And of course we can combine information about the path and the metadata. they will be connected with `and`. The following search will retrieve all data objects and collections wich are labeled with a metadata key *'prov:wasGeneratedBy'* and whose path has the prefix */nluu12p/home/research-test-christine/demo/*."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e0d2fad9",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "key_vals = {'prov:wasGeneratedBy': '%'}\n",
+    "result = search_data(session, path='/nluu12p/home/research-test-christine/%', key_vals=key_vals)\n",
+    "print(result)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "14bc70b0",
+   "metadata": {},
+   "source": [
+    "## Retrieving data"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "946e355c",
+   "metadata": {},
+   "source": [
+    "Now that we have the search results in a list of Python dictionaries, we can use the information to create the full iRODS paths and continue working with them e.g. download them."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ff72b0ca",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from ibridges.path import IrodsPath\n",
+    "\n",
+    "paths = [IrodsPath(session, r.get('COLL_NAME', '')).joinpath(r.get('DATA_NAME', '')) for r in result]\n",
+    "print(paths)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/tutorials/05-Data-Sharing.ipynb b/tutorials/05-Data-Sharing.ipynb
new file mode 100644
index 00000000..466e78ec
--- /dev/null
+++ b/tutorials/05-Data-Sharing.ipynb
@@ -0,0 +1,360 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "b34804ad",
+   "metadata": {},
+   "source": [
+    "# Data sharing - iRODS permissions"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "ea97cc95",
+   "metadata": {},
+   "source": [
+    "In this tutorial we will show you how to share your data with other users in the iRODS system. To see the effects it is helpful to team up with a colleague!!!"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "d81b1269",
+   "metadata": {},
+   "source": [
+    "## What are permissions"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "48815ec5",
+   "metadata": {},
+   "source": [
+    "Permissions in iRODS are part of the data objects and collections. They give information and they allow other users of the same iRODS system to read and edit your data.\n",
+    "\n",
+    "<img src=\"img/DataObject6.png\" width=\"400\">\n",
+    "\n",
+    "In iRODS there are four types of permissions:\n",
+    "\n",
+    "| Access | Meaning|\n",
+    "|:---:|:---|\n",
+    "|read| The user or the group can **read and download** the data.|\n",
+    "|write| The user or group can **modify data objects and upload data to collections**, but can not delete the data or collection.|\n",
+    "|own| The user or group can **share and delete** the data.|"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "dee1520f",
+   "metadata": {},
+   "source": [
+    "## Give access to data objects and collections"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ed6a8a46",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from ibridges.interactive import interactive_auth\n",
+    "session = interactive_auth()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "76f3ab74",
+   "metadata": {},
+   "source": [
+    "Let us have a look at the permissions of our demo data:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "df8697e4",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from ibridges import get_collection, get_dataobject\n",
+    "from ibridges.path import IrodsPath\n",
+    "\n",
+    "irods_coll_path = IrodsPath(session, '~').joinpath('demo')\n",
+    "coll = get_collection(session, irods_coll_path)\n",
+    "obj = get_dataobject(session, irods_coll_path.joinpath('demofile.txt'))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "785383c9",
+   "metadata": {},
+   "source": [
+    "Like for the metadata we need to load the permissions."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "3b3fc2d5",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from ibridges.permissions import Permissions\n",
+    "coll_perm = Permissions(session, coll)\n",
+    "print(coll_perm)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "43e1409b",
+   "metadata": {},
+   "source": [
+    "In a native iRODS instance you will see your own username who is labeled with `own`. In Yoda you will see three groups: *research-\\<group\\>*, *read-\\<group\\>* and the *\\<datamanager\\>* group. Every user in these groups has the respective permissions on the data.\n",
+    "\n",
+    "Now we iwll give your colleague explicit access. **Note that if your colleague is also in one of the respective Yoda groups, the highest permission (the most powerful) will apply.**"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "c70d6b13",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "coll_perm.set('write', '<username>')\n",
+    "print(coll_perm)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "3d1dd8d4",
+   "metadata": {},
+   "source": [
+    "You will see a new entry with your colleague's iRODS name and *modify object*. We can get the default permission names like that:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "795dea7b",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "coll_perm.available_permissions"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "bbebfaca",
+   "metadata": {},
+   "source": [
+    "Note that some permission-types have synonyms:\n",
+    "\n",
+    "+ read object: 'read', 'read object', 'read_object'\n",
+    "+ modify object: 'write', 'modify object', 'modify_object'"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "63a89479",
+   "metadata": {},
+   "source": [
+    "## Remove access"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "b8713621",
+   "metadata": {},
+   "source": [
+    "To remove any permissions, we use the keyword *null*. Again, please note, if your colleague is still part of a group that has access to your data, this will have no effect."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "7c804ff3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "coll_perm.set('null', '<username>')\n",
+    "print(coll_perm)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "0e3f3562",
+   "metadata": {},
+   "source": [
+    "iBridges also prohibits that you lock yourself out of your data:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "144c2d96",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "coll_perm.set('write', session.username)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "f167ffae",
+   "metadata": {},
+   "source": [
+    "All the above functionality can also be used for objects"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b322bdb9",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "obj_perm = Permissions(session, obj)\n",
+    "print(obj_perm)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "b4cff4b3",
+   "metadata": {},
+   "source": [
+    "## Collections: Inheritance"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "6a4e0119",
+   "metadata": {},
+   "source": [
+    "You might have noticed that collections carry a special permissions keyword *inheritance* which can be `True` or `False`. If inheritance is switched on all new data objects and subcollections will receive the same permissions as the parent collection.\n",
+    "\n",
+    "Below we create a new collection, ans give access to your colleague and switch te inheritance on:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2073f3b5",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "new_coll_path = IrodsPath(session, '~').joinpath('demo1')\n",
+    "coll = IrodsPath.create_collection(session, new_coll_path)\n",
+    "coll_perm = Permissions(session, coll)\n",
+    "coll_perm.set('write', '<username>')\n",
+    "coll_perm.set('inherit')\n",
+    "print(coll_perm)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "8c462e8d",
+   "metadata": {},
+   "source": [
+    "Now we create a new subcollection:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "88b5fbd2",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "subcoll = IrodsPath.create_collection(session, new_coll_path.joinpath('subcoll'))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "7e00c83f",
+   "metadata": {},
+   "source": [
+    "And inspect the permissions. They should be the same as the ones above."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e38a779c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "subcoll_perm = Permissions(session, subcoll)\n",
+    "print(subcoll_perm)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "896e5f3d",
+   "metadata": {},
+   "source": [
+    "Now we will switch off the inheritance of the parent collection and create another subcollection:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f588a39c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "coll_perm.set('noinherit')\n",
+    "print(coll_perm)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5af70cf0",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "subcoll = IrodsPath.create_collection(session, new_coll_path.joinpath('subcoll1'))\n",
+    "subcoll_perm = Permissions(session, subcoll)\n",
+    "print(subcoll_perm)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "8838c6bd",
+   "metadata": {},
+   "source": [
+    "You will see now that you `own` *subcoll1*, that the inheritnace of this collection is also `False` and that you colleague has no permissions on the new subcollection."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "39fecb18",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/tutorials/Data_sync.ipynb b/tutorials/Data_sync.ipynb
index 69aba7e9..11b92e99 100644
--- a/tutorials/Data_sync.ipynb
+++ b/tutorials/Data_sync.ipynb
@@ -18,19 +18,6 @@
     "The command can be in one of the two modes: synchronization of data from the client's local file system to iRODS, or from iRODS to the local file system."
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "76bb5c37",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import os\n",
-    "print(os.getcwd())\n",
-    "os.chdir('..')\n",
-    "print(os.getcwd()) # needs to return ../iBridges"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -38,11 +25,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import os\n",
     "from pathlib import Path\n",
     "from ibridges import Session\n",
     "from ibridges.path import IrodsPath\n",
-    "from ibridges.sync import sync"
+    "from ibridges.sync import sync_data"
    ]
   },
   {
@@ -62,7 +48,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "session = Session(irods_env_path=Path(os.path.expanduser(\"~\")).joinpath(\".irods\", \"irods_environment.json\"))"
+    "session = Session(irods_env_path=Path.expanduser(Path('~')).joinpath(\".irods\", \"irods_environment.json\"))"
    ]
   },
   {
@@ -197,7 +183,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.18"
+   "version": "3.10.13"
   }
  },
  "nbformat": 4,
diff --git a/tutorials/QuickStart.ipynb b/tutorials/QuickStart.ipynb
index 28a07dfb..57ad9a0c 100644
--- a/tutorials/QuickStart.ipynb
+++ b/tutorials/QuickStart.ipynb
@@ -16,19 +16,6 @@
     "## Create an iRODS session (connection to iRODS server)"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "5026bbb9",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import os\n",
-    "print(os.getcwd())\n",
-    "os.chdir('..')\n",
-    "print(os.getcwd()) # needs to return ../iBridges"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -38,7 +25,8 @@
    "source": [
     "from ibridges import Session\n",
     "from ibridges.path import IrodsPath\n",
-    "import os, json\n",
+    "\n",
+    "import json\n",
     "from pathlib import Path\n",
     "from getpass import getpass"
    ]
@@ -263,7 +251,7 @@
    "outputs": [],
    "source": [
     "# create a local file\n",
-    "local_path = os.path.expanduser(\"~/demofile.txt\")\n",
+    "local_path = Path.expanduser(Path('~')).joinpath(\"demofile.txt\")\n",
     "f = open(local_path, \"a\")\n",
     "f.write(\"My content! Super important\")\n",
     "f.close()\n",
@@ -398,9 +386,7 @@
   {
    "cell_type": "markdown",
    "id": "4d4cff1c",
-   "metadata": {
-    "heading_collapsed": true
-   },
+   "metadata": {},
    "source": [
     "### Delete a data object or collection"
    ]
@@ -409,9 +395,7 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "efbef178",
-   "metadata": {
-    "hidden": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "obj.unlink()\n",
@@ -563,7 +547,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import ibridges.search\n",
     "from ibridges.search import search_data\n",
     "\n",
     "#all collections and objects with \n",
@@ -1017,7 +1000,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.18"
+   "version": "3.10.13"
   }
  },
  "nbformat": 4,
diff --git a/tutorials/iRODS_paths.ipynb b/tutorials/iRODS_paths.ipynb
index 2e3622fd..a6056e48 100644
--- a/tutorials/iRODS_paths.ipynb
+++ b/tutorials/iRODS_paths.ipynb
@@ -49,19 +49,6 @@
     "### Create a session"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "8f45d63d",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import os\n",
-    "print(os.getcwd())\n",
-    "os.chdir('..')\n",
-    "print(os.getcwd()) # needs to return ../iBridges"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -70,7 +57,7 @@
    "outputs": [],
    "source": [
     "from ibridges import Session\n",
-    "import os, json\n",
+    "import json\n",
     "from pathlib import Path\n",
     "from getpass import getpass"
    ]
@@ -303,7 +290,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.18"
+   "version": "3.10.13"
   }
  },
  "nbformat": 4,
diff --git a/tutorials/img/DataObject1.png b/tutorials/img/DataObject1.png
new file mode 100644
index 00000000..e8e2bcbf
Binary files /dev/null and b/tutorials/img/DataObject1.png differ
diff --git a/tutorials/img/DataObject2.png b/tutorials/img/DataObject2.png
new file mode 100644
index 00000000..ed114bd6
Binary files /dev/null and b/tutorials/img/DataObject2.png differ
diff --git a/tutorials/img/DataObject3.png b/tutorials/img/DataObject3.png
new file mode 100644
index 00000000..c9f5e409
Binary files /dev/null and b/tutorials/img/DataObject3.png differ
diff --git a/tutorials/img/DataObject4.png b/tutorials/img/DataObject4.png
new file mode 100644
index 00000000..fa259805
Binary files /dev/null and b/tutorials/img/DataObject4.png differ
diff --git a/tutorials/img/DataObject5.png b/tutorials/img/DataObject5.png
new file mode 100644
index 00000000..405ee89a
Binary files /dev/null and b/tutorials/img/DataObject5.png differ
diff --git a/tutorials/img/DataObject6.png b/tutorials/img/DataObject6.png
new file mode 100644
index 00000000..e9120c60
Binary files /dev/null and b/tutorials/img/DataObject6.png differ
diff --git a/tutorials/img/Save_json.png b/tutorials/img/Save_json.png
new file mode 100644
index 00000000..d8387e37
Binary files /dev/null and b/tutorials/img/Save_json.png differ
diff --git a/tutorials/img/Yoda_environment.png b/tutorials/img/Yoda_environment.png
new file mode 100644
index 00000000..e8f0eafe
Binary files /dev/null and b/tutorials/img/Yoda_environment.png differ


Test patch:
diff --git a/.github/workflows/integration-tests-irods.yml b/.github/workflows/integration-tests-irods.yml
new file mode 100644
index 00000000..7b80c353
--- /dev/null
+++ b/.github/workflows/integration-tests-irods.yml
@@ -0,0 +1,40 @@
+name: Run integration tests against iRODS
+
+on:
+  push:
+    branches:
+      - develop
+  pull_request:
+
+jobs:
+  build:
+    runs-on: ubuntu-22.04
+    if: |
+      ${{ ! contains(github.event.head_commit.message, '#nointegrationtests') &&
+            ( github.event_name == 'push' ||
+              github.event.pull_request.head.repo.full_name == github.event.pull_request.base.repo.full_name
+            )
+       }}
+    steps:
+      - uses: actions/checkout@v2
+      - name: Install dependencies
+        run: |
+          sudo apt install -y docker-compose
+      - uses: docker/setup-buildx-action@v3
+      - name: Build utilizing cache
+        uses: docker/bake-action@v4
+        with:
+          load: true
+          push: false
+          set: |
+            irods-catalog.cache-from=type=gha
+            irods-catalog.cache-to=type=gha
+            irods-catalog.tags=irods-catalog
+            irods-catalog-provider.cache-from=type=gha
+            irods-catalog-provider.cache-to=type=gha
+            irods-catalog-provider.tags=irods-catalog-provider
+            irods-client.cache-from=type=gha
+            irods-client.cache-to=type=gha
+            irods-client.tags=irods-client
+      - name: Run tests using docker-compose
+        run: docker-compose up --no-build --exit-code-from irods-client