From 9f6d4a8ccd90de4f497cb3e459dd67f070fe5618 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <14138589+paskino@users.noreply.github.com>
Date: Tue, 8 Jul 2025 12:17:13 +0100
Subject: [PATCH 01/14] added Table of dependencies versions

Signed-off-by: Edoardo Pasca <14138589+paskino@users.noreply.github.com>
---
 README.md | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/README.md b/README.md
index 75e80d2e23..034a505294 100644
--- a/README.md
+++ b/README.md
@@ -47,6 +47,21 @@ CIL's [optimised FDK/FBP](https://github.com/TomographicImaging/CIL/discussions/
 1. the Intel [Integrated Performance Primitives](https://www.intel.com/content/www/us/en/developer/tools/oneapi/ipp.html#gs.gxwq5p) Library ([license](https://www.intel.com/content/dam/develop/external/us/en/documents/pdf/intel-simplified-software-license-version-august-2021.pdf)) which can be installed via conda from the `https://software.repos.intel.com/python/conda` channel.
 2. [TIGRE](https://github.com/CERN/TIGRE), which can be installed via conda from the `ccpi` channel.
 
+#### Binary packages and dependencies
+
+While building the CIL package we test with specific versions of dependencies. These are listed in the [build.yml](https://github.com/TomographicImaging/CIL/blob/master/.github/workflows/build.yml) GitHub workflow and [environment-test.yml](https://github.com/TomographicImaging/CIL/blob/master/scripts/requirements-test.yml). The following table tries to resume the tested versions of CIL and its dependencies.
+
+| Package | Tested Version |  Recommended conda channel | Compatible Version |
+|----------|----------|----------|----|
+| Python | 3.10, 3.11, 3.12 |  conda-forge | [PSLF](https://docs.python.org/3/license.html) |
+| Numpy |  >1.23 and <2.0.0 |  conda-forge | [BSD](https://numpy.org/doc/stable/license.html)|
+| Optional | | | | 
+| IPP | 2021.12 | https://software.repos.intel.com/python/conda| [Intel Simplified Software License](http://www.intel.com/content/www/us/en/developer/articles/license/end-user-license-agreement.html) |
+| ASTRA | 2.1 |  astra-toolbox | [GPLv3](https://github.com/astra-toolbox/astra-toolbox?tab=GPL-3.0-1-ov-file#readme) |
+| TIGRE | 2.6 |  ccpi | [BSD](https://github.com/CERN/TIGRE?tab=BSD-3-Clause-1-ov-file#readme) |
+| CCPi-Regularisation |  24.0.1 | ccpi | [Apache v2](https://github.com/TomographicImaging/CCPi-Regularisation-Toolkit?tab=Apache-2.0-1-ov-file#readme) |
+| TomoPhantom | 22.0.0 | ccpi | [Apache v2](https://github.com/dkazanc/TomoPhantom?tab=Apache-2.0-1-ov-file#readme) |
+
 ### Docker
 
 Finally, CIL can be run via a Jupyter Notebook enabled Docker container:

From fdd6143fa664ba39488c0307dd8c05ef3e942720 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <14138589+paskino@users.noreply.github.com>
Date: Wed, 30 Jul 2025 15:00:14 +0200
Subject: [PATCH 02/14] Update to matrix: added optional changes

Signed-off-by: Edoardo Pasca <14138589+paskino@users.noreply.github.com>
---
 README.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index 034a505294..9f49655609 100644
--- a/README.md
+++ b/README.md
@@ -49,13 +49,13 @@ CIL's [optimised FDK/FBP](https://github.com/TomographicImaging/CIL/discussions/
 
 #### Binary packages and dependencies
 
-While building the CIL package we test with specific versions of dependencies. These are listed in the [build.yml](https://github.com/TomographicImaging/CIL/blob/master/.github/workflows/build.yml) GitHub workflow and [environment-test.yml](https://github.com/TomographicImaging/CIL/blob/master/scripts/requirements-test.yml). The following table tries to resume the tested versions of CIL and its dependencies.
+While building the CIL package we test with specific versions of dependencies. These are listed in the [build.yml](https://github.com/TomographicImaging/CIL/blob/master/.github/workflows/build.yml) GitHub workflow and [environment-test.yml](https://github.com/TomographicImaging/CIL/blob/master/scripts/requirements-test.yml). The following table tries to resume the tested versions of CIL and its required and optional dependencies.
 
-| Package | Tested Version |  Recommended conda channel | Compatible Version |
+| Package | Tested Version |  Recommended conda channel | License |
 |----------|----------|----------|----|
 | Python | 3.10, 3.11, 3.12 |  conda-forge | [PSLF](https://docs.python.org/3/license.html) |
-| Numpy |  >1.23 and <2.0.0 |  conda-forge | [BSD](https://numpy.org/doc/stable/license.html)|
-| Optional | | | | 
+| Numpy |  >=1.23 and <2.0.0 |  conda-forge | [BSD](https://numpy.org/doc/stable/license.html)|
+| **Optional dependencies** ||| 
 | IPP | 2021.12 | https://software.repos.intel.com/python/conda| [Intel Simplified Software License](http://www.intel.com/content/www/us/en/developer/articles/license/end-user-license-agreement.html) |
 | ASTRA | 2.1 |  astra-toolbox | [GPLv3](https://github.com/astra-toolbox/astra-toolbox?tab=GPL-3.0-1-ov-file#readme) |
 | TIGRE | 2.6 |  ccpi | [BSD](https://github.com/CERN/TIGRE?tab=BSD-3-Clause-1-ov-file#readme) |

From d5c98bf0b6092b55afa637f325f21dd738dd8a58 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <14138589+paskino@users.noreply.github.com>
Date: Wed, 30 Jul 2025 15:01:29 +0200
Subject: [PATCH 03/14] modified conda install command

Signed-off-by: Edoardo Pasca <14138589+paskino@users.noreply.github.com>
---
 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 9f49655609..14b8861c36 100644
--- a/README.md
+++ b/README.md
@@ -21,13 +21,13 @@ We recommend using either [`miniconda`](https://docs.conda.io/projects/miniconda
 Install a new environment using:
 
 ```sh
-conda create --name cil -c conda-forge -c https://software.repos.intel.com/python/conda -c ccpi cil=24.3.0 ipp=2021.12
+conda env create -f https://raw.githubusercontent.com/TomographicImaging/Build-scripts/refs/heads/main/env_files/cil_env.yml
 ```
 
 To install CIL and the additional packages and plugins needed to run the [CIL demos](https://github.com/TomographicImaging/CIL-Demos) install the environment with:
 
 ```sh
-conda create --name cil -c conda-forge -c https://software.repos.intel.com/python/conda -c ccpi cil=24.3.0 ipp=2021.12 astra-toolbox=*=cuda* tigre ccpi-regulariser tomophantom ipykernel ipywidgets scikit-image
+conda env create -f https://raw.githubusercontent.com/TomographicImaging/Build-scripts/refs/heads/main/env_files/cil_demos_env.yml
 ```
 
 where:

From fcbaf5f8fb5122f147b40dae0ea395252cfa9cad Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <14138589+paskino@users.noreply.github.com>
Date: Wed, 30 Jul 2025 15:18:21 +0200
Subject: [PATCH 04/14] Update install commands

Signed-off-by: Edoardo Pasca <14138589+paskino@users.noreply.github.com>
---
 README.md | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index 14b8861c36..9d25727ac7 100644
--- a/README.md
+++ b/README.md
@@ -18,16 +18,16 @@ Binary installation of CIL can be achieved with `conda`.
 
 We recommend using either [`miniconda`](https://docs.conda.io/projects/miniconda/en/latest) or [`miniforge`](https://github.com/conda-forge/miniforge), which are both minimal installers for `conda`. We also recommend a `conda` version of at least `23.10` for quicker installation.
 
-Install a new environment using:
+Install a new minimal environment with CIL using:
 
 ```sh
-conda env create -f https://raw.githubusercontent.com/TomographicImaging/Build-scripts/refs/heads/main/env_files/cil_env.yml
+conda create --name cil -c conda-forge -c ccpi cil=24.3.0 
 ```
 
-To install CIL and the additional packages and plugins needed to run the [CIL demos](https://github.com/TomographicImaging/CIL-Demos) install the environment with:
+To install CIL and the additional packages and plugins needed to run the [CIL demos](https://github.com/TomographicImaging/CIL-Demos) and do X-Ray CT reconstructions, install the environment with:
 
 ```sh
-conda env create -f https://raw.githubusercontent.com/TomographicImaging/Build-scripts/refs/heads/main/env_files/cil_demos_env.yml
+conda create --name cil -c conda-forge -c https://software.repos.intel.com/python/conda -c ccpi cil=24.3.0 ipp=2021.12 astra-toolbox=*=cuda* tigre ccpi-regulariser tomophantom ipykernel ipywidgets scikit-image
 ```
 
 where:
@@ -40,6 +40,14 @@ where:
 - `ipykernel`  provides the IPython kernel for Jupyter (allowing jupyter notebooks to be run)
 - `ipywidgets` enables visulisation tools within jupyter noteboooks
 
+Users may chose to omit any of the optional dependencies in the above command.
+
+We maintain an environment file with the required packages to run the [CIL demos](https://github.com/TomographicImaging/CIL-Demos) which you can use to create a new environment. This will have specific and tested versions of all dependencies, see table below: 
+
+```sh
+conda env create -f https://raw.githubusercontent.com/TomographicImaging/Build-scripts/refs/heads/main/env_files/cil_demos_env.yml
+```
+
 ### Dependencies
 
 CIL's [optimised FDK/FBP](https://github.com/TomographicImaging/CIL/discussions/1070) `recon` module requires:

From ba7734e01936d989ed2c90104f363beabe495de4 Mon Sep 17 00:00:00 2001
From: Hannah Robarts <77114597+hrobarts@users.noreply.github.com>
Date: Tue, 5 Aug 2025 11:00:33 +0100
Subject: [PATCH 05/14] Update README.md

Co-authored-by: Casper da Costa-Luis <casper.dcl@physics.org>
Signed-off-by: Hannah Robarts <77114597+hrobarts@users.noreply.github.com>
---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 9d25727ac7..0abccda20f 100644
--- a/README.md
+++ b/README.md
@@ -45,7 +45,7 @@ Users may chose to omit any of the optional dependencies in the above command.
 We maintain an environment file with the required packages to run the [CIL demos](https://github.com/TomographicImaging/CIL-Demos) which you can use to create a new environment. This will have specific and tested versions of all dependencies, see table below: 
 
 ```sh
-conda env create -f https://raw.githubusercontent.com/TomographicImaging/Build-scripts/refs/heads/main/env_files/cil_demos_env.yml
+conda env create -f https://tomographicimaging.github.io/scripts/env/cil_demos.yml
 ```
 
 ### Dependencies

From c82e7294dac37621741b6bcfbce8500522bd7bfb Mon Sep 17 00:00:00 2001
From: Hannah Robarts <77114597+hrobarts@users.noreply.github.com>
Date: Tue, 5 Aug 2025 17:28:28 +0100
Subject: [PATCH 06/14] Move package descriptions into dependency table

Signed-off-by: Hannah Robarts <77114597+hrobarts@users.noreply.github.com>
---
 README.md | 60 ++++++++++++++++++-------------------------------------
 1 file changed, 19 insertions(+), 41 deletions(-)

diff --git a/README.md b/README.md
index 0abccda20f..2b8779b3bb 100644
--- a/README.md
+++ b/README.md
@@ -21,55 +21,33 @@ We recommend using either [`miniconda`](https://docs.conda.io/projects/miniconda
 Install a new minimal environment with CIL using:
 
 ```sh
-conda create --name cil -c conda-forge -c ccpi cil=24.3.0 
+conda create --name cil - c https://software.repos.intel.com/python/conda -c conda-forge -c ccpi cil=24.3.0 
 ```
+A number of additional dependencies are required for specific functionality in CIL, these should be added to your environment as necessary. See the dependency table below for details.
 
-To install CIL and the additional packages and plugins needed to run the [CIL demos](https://github.com/TomographicImaging/CIL-Demos) and do X-Ray CT reconstructions, install the environment with:
 
-```sh
-conda create --name cil -c conda-forge -c https://software.repos.intel.com/python/conda -c ccpi cil=24.3.0 ipp=2021.12 astra-toolbox=*=cuda* tigre ccpi-regulariser tomophantom ipykernel ipywidgets scikit-image
-```
-
-where:
-
-- `astra-toolbox=*=py*` enables CIL support for [ASTRA toolbox](http://www.astra-toolbox.com) CPU projector (2D Parallel beam only) (GPLv3 license)
-- `astra-toolbox=*=cuda*` (requires an NVIDIA GPU) enables CIL support for [ASTRA toolbox](http://www.astra-toolbox.com) GPU projectors (GPLv3 license)
-- `tigre` (requires an NVIDIA GPU) enables support for [TIGRE](https://github.com/CERN/TIGRE) toolbox projectors (BSD license)
-- `ccpi-regulariser` is the [CCPi Regularisation Toolkit](https://github.com/TomographicImaging/CCPi-Regularisation-Toolkit)
-- `tomophantom` can generate phantoms to use as test data [Tomophantom](https://github.com/dkazanc/TomoPhantom)
-- `ipykernel`  provides the IPython kernel for Jupyter (allowing jupyter notebooks to be run)
-- `ipywidgets` enables visulisation tools within jupyter noteboooks
-
-Users may chose to omit any of the optional dependencies in the above command.
-
-We maintain an environment file with the required packages to run the [CIL demos](https://github.com/TomographicImaging/CIL-Demos) which you can use to create a new environment. This will have specific and tested versions of all dependencies, see table below: 
+#### Binary packages and dependencies
+While building the CIL package we test with specific versions of dependencies. These are listed in the [build.yml](https://github.com/TomographicImaging/CIL/blob/master/.github/workflows/build.yml) GitHub workflow and [environment-test.yml](https://github.com/TomographicImaging/CIL/blob/master/scripts/requirements-test.yml). The following table tries to resume the tested versions of CIL and its required and optional dependencies. If you use these packages as a backend please remember to cite them in addition to CIL.
+
+| Package | Tested Version |  Conda install command | Description | License |
+|----|----|--------|--------|----|
+| [Python](https://www.python.org/) | >=3.10,<=3.12 |  `conda-forge::python>=3.10,<=3.12` | | [PSLF](https://docs.python.org/3/license.html) |
+| [Numpy](https://github.com/numpy/numpy) |  >=1.23,<2.0.0 |  `conda-forge::numpy>=1.23,<2.0.0` | | [BSD](https://numpy.org/doc/stable/license.html)|
+| **Optional dependencies** |||| 
+| [IPP](https://www.intel.com/content/www/us/en/developer/tools/oneapi/ipp.html#gs.gxwq5p) | 2021.12 | `conda install -c https://software.repos.intel.com/python/conda ipp=2021.12`| The Intel Integrated Performance Primitives Library (required for the CIL recon class) |[Intel Simplified Software License](http://www.intel.com/content/www/us/en/developer/articles/license/end-user-license-agreement.html) |
+| [ASTRA toolbox](http://www.astra-toolbox.com) | 2.1 |  CPU: `conda-forge::astra-toolbox=2.1=py*` <br> GPU: `conda-forge::astra-toolbox=2.1=cuda*` | CT projectors, FBP and FDK. |[GPLv3](https://github.com/astra-toolbox/astra-toolbox?tab=GPL-3.0-1-ov-file#readme) |
+| [TIGRE](https://github.com/CERN/TIGRE) | 2.6 |  `ccpi::tigre=2.6` | CT projectors, FBP and FDK. |[BSD](https://github.com/CERN/TIGRE?tab=BSD-3-Clause-1-ov-file#readme) |
+| [CCPi Regularisation Toolkit](https://github.com/TomographicImaging/CCPi-Regularisation-Toolkit) |  24.0.1 | `ccpi::ccpi-regulariser=24.0.1` | Toolbox of regularisation methods. |[Apache v2](https://github.com/TomographicImaging/CCPi-Regularisation-Toolkit?tab=Apache-2.0-1-ov-file#readme) |
+| [TomoPhantom](https://github.com/dkazanc/TomoPhantom) | 22.0.0 | `ccpi::tomophantom=22.0.0` |  Generates phantoms to use as test data. |[Apache v2](https://github.com/dkazanc/TomoPhantom?tab=Apache-2.0-1-ov-file#readme) |
+| [ipykernel](https://github.com/ipython/ipykernel) |    |  `conda-forge::ipykernel` | Provides the IPython kernel to run Jupyter notebooks | [BSD](https://github.com/ipython/ipykernel?tab=BSD-3-Clause-1-ov-file) |
+| [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) |    |  `conda-forge::ipywidgets` | Enables visulisation tools within jupyter noteboooks | [BSD](https://github.com/jupyter-widgets/ipywidgets?tab=BSD-3-Clause-1-ov-file) |
+
+We maintain an environment file with the required packages to run the [CIL demos](https://github.com/TomographicImaging/CIL-Demos) which you can use to create a new environment. This will have specific and tested versions of all dependencies that are outlined in the table above: 
 
 ```sh
 conda env create -f https://tomographicimaging.github.io/scripts/env/cil_demos.yml
 ```
 
-### Dependencies
-
-CIL's [optimised FDK/FBP](https://github.com/TomographicImaging/CIL/discussions/1070) `recon` module requires:
-
-1. the Intel [Integrated Performance Primitives](https://www.intel.com/content/www/us/en/developer/tools/oneapi/ipp.html#gs.gxwq5p) Library ([license](https://www.intel.com/content/dam/develop/external/us/en/documents/pdf/intel-simplified-software-license-version-august-2021.pdf)) which can be installed via conda from the `https://software.repos.intel.com/python/conda` channel.
-2. [TIGRE](https://github.com/CERN/TIGRE), which can be installed via conda from the `ccpi` channel.
-
-#### Binary packages and dependencies
-
-While building the CIL package we test with specific versions of dependencies. These are listed in the [build.yml](https://github.com/TomographicImaging/CIL/blob/master/.github/workflows/build.yml) GitHub workflow and [environment-test.yml](https://github.com/TomographicImaging/CIL/blob/master/scripts/requirements-test.yml). The following table tries to resume the tested versions of CIL and its required and optional dependencies.
-
-| Package | Tested Version |  Recommended conda channel | License |
-|----------|----------|----------|----|
-| Python | 3.10, 3.11, 3.12 |  conda-forge | [PSLF](https://docs.python.org/3/license.html) |
-| Numpy |  >=1.23 and <2.0.0 |  conda-forge | [BSD](https://numpy.org/doc/stable/license.html)|
-| **Optional dependencies** ||| 
-| IPP | 2021.12 | https://software.repos.intel.com/python/conda| [Intel Simplified Software License](http://www.intel.com/content/www/us/en/developer/articles/license/end-user-license-agreement.html) |
-| ASTRA | 2.1 |  astra-toolbox | [GPLv3](https://github.com/astra-toolbox/astra-toolbox?tab=GPL-3.0-1-ov-file#readme) |
-| TIGRE | 2.6 |  ccpi | [BSD](https://github.com/CERN/TIGRE?tab=BSD-3-Clause-1-ov-file#readme) |
-| CCPi-Regularisation |  24.0.1 | ccpi | [Apache v2](https://github.com/TomographicImaging/CCPi-Regularisation-Toolkit?tab=Apache-2.0-1-ov-file#readme) |
-| TomoPhantom | 22.0.0 | ccpi | [Apache v2](https://github.com/dkazanc/TomoPhantom?tab=Apache-2.0-1-ov-file#readme) |
-
 ### Docker
 
 Finally, CIL can be run via a Jupyter Notebook enabled Docker container:

From deddd3ad2df9d5f67a434ede01943360b1ed2135 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Tue, 5 Aug 2025 23:51:47 +0100
Subject: [PATCH 07/14] tidy table

Signed-off-by: Casper da Costa-Luis <casper.dcl@physics.org>
---
 README.md | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/README.md b/README.md
index 2b8779b3bb..692dc2f329 100644
--- a/README.md
+++ b/README.md
@@ -31,16 +31,16 @@ While building the CIL package we test with specific versions of dependencies. T
 
 | Package | Tested Version |  Conda install command | Description | License |
 |----|----|--------|--------|----|
-| [Python](https://www.python.org/) | >=3.10,<=3.12 |  `conda-forge::python>=3.10,<=3.12` | | [PSLF](https://docs.python.org/3/license.html) |
-| [Numpy](https://github.com/numpy/numpy) |  >=1.23,<2.0.0 |  `conda-forge::numpy>=1.23,<2.0.0` | | [BSD](https://numpy.org/doc/stable/license.html)|
-| **Optional dependencies** |||| 
-| [IPP](https://www.intel.com/content/www/us/en/developer/tools/oneapi/ipp.html#gs.gxwq5p) | 2021.12 | `conda install -c https://software.repos.intel.com/python/conda ipp=2021.12`| The Intel Integrated Performance Primitives Library (required for the CIL recon class) |[Intel Simplified Software License](http://www.intel.com/content/www/us/en/developer/articles/license/end-user-license-agreement.html) |
-| [ASTRA toolbox](http://www.astra-toolbox.com) | 2.1 |  CPU: `conda-forge::astra-toolbox=2.1=py*` <br> GPU: `conda-forge::astra-toolbox=2.1=cuda*` | CT projectors, FBP and FDK. |[GPLv3](https://github.com/astra-toolbox/astra-toolbox?tab=GPL-3.0-1-ov-file#readme) |
-| [TIGRE](https://github.com/CERN/TIGRE) | 2.6 |  `ccpi::tigre=2.6` | CT projectors, FBP and FDK. |[BSD](https://github.com/CERN/TIGRE?tab=BSD-3-Clause-1-ov-file#readme) |
-| [CCPi Regularisation Toolkit](https://github.com/TomographicImaging/CCPi-Regularisation-Toolkit) |  24.0.1 | `ccpi::ccpi-regulariser=24.0.1` | Toolbox of regularisation methods. |[Apache v2](https://github.com/TomographicImaging/CCPi-Regularisation-Toolkit?tab=Apache-2.0-1-ov-file#readme) |
-| [TomoPhantom](https://github.com/dkazanc/TomoPhantom) | 22.0.0 | `ccpi::tomophantom=22.0.0` |  Generates phantoms to use as test data. |[Apache v2](https://github.com/dkazanc/TomoPhantom?tab=Apache-2.0-1-ov-file#readme) |
-| [ipykernel](https://github.com/ipython/ipykernel) |    |  `conda-forge::ipykernel` | Provides the IPython kernel to run Jupyter notebooks | [BSD](https://github.com/ipython/ipykernel?tab=BSD-3-Clause-1-ov-file) |
-| [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) |    |  `conda-forge::ipywidgets` | Enables visulisation tools within jupyter noteboooks | [BSD](https://github.com/jupyter-widgets/ipywidgets?tab=BSD-3-Clause-1-ov-file) |
+| [Python](https://www.python.org/) | 3.10 - 3.12 | `"python>=3.10,<=3.12"` || [PSLF](https://docs.python.org/3/license.html) |
+| [Numpy](https://github.com/numpy/numpy) | 1.23 - 1.26 | `"numpy>=1.23,<2"` || [BSD](https://numpy.org/doc/stable/license.html) |
+| **Optional dependencies** ||||
+| [IPP](https://www.intel.com/content/www/us/en/developer/tools/oneapi/ipp.html#gs.gxwq5p) | 2021.12 | `-c https://software.repos.intel.com/python/conda ipp=2021.12` | The Intel Integrated Performance Primitives Library (required for the CIL recon class) | [Intel Simplified Software License](http://www.intel.com/content/www/us/en/developer/articles/license/end-user-license-agreement.html) |
+| [ASTRA toolbox](http://www.astra-toolbox.com) | 2.1 | CPU: `conda-forge::astra-toolbox=2.1=py*` <br> GPU: `conda-forge::astra-toolbox=2.1=cuda*` | CT projectors, FBP and FDK. | [GPLv3](https://github.com/astra-toolbox/astra-toolbox/blob/master/COPYING) |
+| [TIGRE](https://github.com/CERN/TIGRE) | 2.6 | `ccpi::tigre=2.6` | CT projectors, FBP and FDK. | [BSD](https://github.com/CERN/TIGRE/blob/master/LICENSE.txt) |
+| [CCPi Regularisation Toolkit](https://github.com/TomographicImaging/CCPi-Regularisation-Toolkit) | 24.0.1 | `ccpi::ccpi-regulariser=24.0.1` | Toolbox of regularisation methods. | [Apache-2.0](https://github.com/TomographicImaging/CCPi-Regularisation-Toolkit/blob/master/LICENSE) |
+| [TomoPhantom](https://github.com/dkazanc/TomoPhantom) | 22 | `ccpi::tomophantom=22` | Generates phantoms to use as test data. | [Apache v2](https://github.com/dkazanc/TomoPhantom/blob/master/LICENSE) |
+| [ipykernel](https://github.com/ipython/ipykernel) || `ipykernel` | Provides the IPython kernel to run Jupyter notebooks | [BSD](https://github.com/ipython/ipykernel/blob/main/LICENSE) |
+| [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) || `ipywidgets` | Enables visualisation tools within jupyter noteboooks | [BSD](https://github.com/jupyter-widgets/ipywidgets/blob/main/LICENSE) |
 
 We maintain an environment file with the required packages to run the [CIL demos](https://github.com/TomographicImaging/CIL-Demos) which you can use to create a new environment. This will have specific and tested versions of all dependencies that are outlined in the table above: 
 

From 572c0d863ad716bcb677bf525db1b6c119dce0d6 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Wed, 6 Aug 2025 00:03:29 +0100
Subject: [PATCH 08/14] normalise licences

Signed-off-by: Casper da Costa-Luis <casper.dcl@physics.org>
---
 README.md | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/README.md b/README.md
index 692dc2f329..23e53d0e9f 100644
--- a/README.md
+++ b/README.md
@@ -31,16 +31,16 @@ While building the CIL package we test with specific versions of dependencies. T
 
 | Package | Tested Version |  Conda install command | Description | License |
 |----|----|--------|--------|----|
-| [Python](https://www.python.org/) | 3.10 - 3.12 | `"python>=3.10,<=3.12"` || [PSLF](https://docs.python.org/3/license.html) |
-| [Numpy](https://github.com/numpy/numpy) | 1.23 - 1.26 | `"numpy>=1.23,<2"` || [BSD](https://numpy.org/doc/stable/license.html) |
+| [Python](https://www.python.org/) | 3.10 - 3.12 | `"python>=3.10,<=3.12"` || [PSF-2.0](https://docs.python.org/3/license.html) |
+| [Numpy](https://github.com/numpy/numpy) | 1.23 - 1.26 | `"numpy>=1.23,<2"` || [BSD-3-Clause](https://numpy.org/doc/stable/license.html) |
 | **Optional dependencies** ||||
-| [IPP](https://www.intel.com/content/www/us/en/developer/tools/oneapi/ipp.html#gs.gxwq5p) | 2021.12 | `-c https://software.repos.intel.com/python/conda ipp=2021.12` | The Intel Integrated Performance Primitives Library (required for the CIL recon class) | [Intel Simplified Software License](http://www.intel.com/content/www/us/en/developer/articles/license/end-user-license-agreement.html) |
-| [ASTRA toolbox](http://www.astra-toolbox.com) | 2.1 | CPU: `conda-forge::astra-toolbox=2.1=py*` <br> GPU: `conda-forge::astra-toolbox=2.1=cuda*` | CT projectors, FBP and FDK. | [GPLv3](https://github.com/astra-toolbox/astra-toolbox/blob/master/COPYING) |
-| [TIGRE](https://github.com/CERN/TIGRE) | 2.6 | `ccpi::tigre=2.6` | CT projectors, FBP and FDK. | [BSD](https://github.com/CERN/TIGRE/blob/master/LICENSE.txt) |
+| [IPP](https://www.intel.com/content/www/us/en/developer/tools/oneapi/ipp.html#gs.gxwq5p) | 2021.12 | `-c https://software.repos.intel.com/python/conda ipp=2021.12` | The Intel Integrated Performance Primitives Library (required for the CIL recon class) | [ISSL](http://www.intel.com/content/www/us/en/developer/articles/license/end-user-license-agreement.html) |
+| [ASTRA toolbox](http://www.astra-toolbox.com) | 2.1 | CPU: `conda-forge::astra-toolbox=2.1=py*` <br> GPU: `conda-forge::astra-toolbox=2.1=cuda*` | CT projectors, FBP and FDK. | [GPL-3.0](https://github.com/astra-toolbox/astra-toolbox/blob/master/COPYING) |
+| [TIGRE](https://github.com/CERN/TIGRE) | 2.6 | `ccpi::tigre=2.6` | CT projectors, FBP and FDK. | [BSD-3-Clause](https://github.com/CERN/TIGRE/blob/master/LICENSE.txt) |
 | [CCPi Regularisation Toolkit](https://github.com/TomographicImaging/CCPi-Regularisation-Toolkit) | 24.0.1 | `ccpi::ccpi-regulariser=24.0.1` | Toolbox of regularisation methods. | [Apache-2.0](https://github.com/TomographicImaging/CCPi-Regularisation-Toolkit/blob/master/LICENSE) |
-| [TomoPhantom](https://github.com/dkazanc/TomoPhantom) | 22 | `ccpi::tomophantom=22` | Generates phantoms to use as test data. | [Apache v2](https://github.com/dkazanc/TomoPhantom/blob/master/LICENSE) |
-| [ipykernel](https://github.com/ipython/ipykernel) || `ipykernel` | Provides the IPython kernel to run Jupyter notebooks | [BSD](https://github.com/ipython/ipykernel/blob/main/LICENSE) |
-| [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) || `ipywidgets` | Enables visualisation tools within jupyter noteboooks | [BSD](https://github.com/jupyter-widgets/ipywidgets/blob/main/LICENSE) |
+| [TomoPhantom](https://github.com/dkazanc/TomoPhantom) | 22 | `ccpi::tomophantom=22` | Generates phantoms to use as test data. | [Apache-2.0](https://github.com/dkazanc/TomoPhantom/blob/master/LICENSE) |
+| [ipykernel](https://github.com/ipython/ipykernel) || `ipykernel` | Provides the IPython kernel to run Jupyter notebooks | [BSD-3-Clause](https://github.com/ipython/ipykernel/blob/main/LICENSE) |
+| [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) || `ipywidgets` | Enables visualisation tools within jupyter noteboooks | [BSD-3-Clause](https://github.com/jupyter-widgets/ipywidgets/blob/main/LICENSE) |
 
 We maintain an environment file with the required packages to run the [CIL demos](https://github.com/TomographicImaging/CIL-Demos) which you can use to create a new environment. This will have specific and tested versions of all dependencies that are outlined in the table above: 
 

From e267ddc10c57106c7f3fdf2c464d1141f80afbbc Mon Sep 17 00:00:00 2001
From: Hannah Robarts <77114597+hrobarts@users.noreply.github.com>
Date: Thu, 7 Aug 2025 08:30:25 +0100
Subject: [PATCH 09/14] Apply suggestions from code review

Co-authored-by: Casper da Costa-Luis <casper.dcl@physics.org>
Signed-off-by: Hannah Robarts <77114597+hrobarts@users.noreply.github.com>
---
 README.md | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/README.md b/README.md
index 23e53d0e9f..c4ee418caf 100644
--- a/README.md
+++ b/README.md
@@ -21,7 +21,7 @@ We recommend using either [`miniconda`](https://docs.conda.io/projects/miniconda
 Install a new minimal environment with CIL using:
 
 ```sh
-conda create --name cil - c https://software.repos.intel.com/python/conda -c conda-forge -c ccpi cil=24.3.0 
+conda create --name cil -c https://software.repos.intel.com/python/conda -c conda-forge -c ccpi cil=24.3.0
 ```
 A number of additional dependencies are required for specific functionality in CIL, these should be added to your environment as necessary. See the dependency table below for details.
 
@@ -33,14 +33,14 @@ While building the CIL package we test with specific versions of dependencies. T
 |----|----|--------|--------|----|
 | [Python](https://www.python.org/) | 3.10 - 3.12 | `"python>=3.10,<=3.12"` || [PSF-2.0](https://docs.python.org/3/license.html) |
 | [Numpy](https://github.com/numpy/numpy) | 1.23 - 1.26 | `"numpy>=1.23,<2"` || [BSD-3-Clause](https://numpy.org/doc/stable/license.html) |
-| **Optional dependencies** ||||
-| [IPP](https://www.intel.com/content/www/us/en/developer/tools/oneapi/ipp.html#gs.gxwq5p) | 2021.12 | `-c https://software.repos.intel.com/python/conda ipp=2021.12` | The Intel Integrated Performance Primitives Library (required for the CIL recon class) | [ISSL](http://www.intel.com/content/www/us/en/developer/articles/license/end-user-license-agreement.html) |
+|--|--| **Optional dependencies** |--|--|
+| [IPP](https://www.intel.com/content/www/us/en/developer/tools/oneapi/ipp.html#gs.gxwq5p) | 2021.12 | `-c https://software.repos.intel.com/python/conda ipp=2021.12` | The Intel Integrated Performance Primitives Library (required for the CIL recon class). | [ISSL](http://www.intel.com/content/www/us/en/developer/articles/license/end-user-license-agreement.html) |
 | [ASTRA toolbox](http://www.astra-toolbox.com) | 2.1 | CPU: `conda-forge::astra-toolbox=2.1=py*` <br> GPU: `conda-forge::astra-toolbox=2.1=cuda*` | CT projectors, FBP and FDK. | [GPL-3.0](https://github.com/astra-toolbox/astra-toolbox/blob/master/COPYING) |
 | [TIGRE](https://github.com/CERN/TIGRE) | 2.6 | `ccpi::tigre=2.6` | CT projectors, FBP and FDK. | [BSD-3-Clause](https://github.com/CERN/TIGRE/blob/master/LICENSE.txt) |
 | [CCPi Regularisation Toolkit](https://github.com/TomographicImaging/CCPi-Regularisation-Toolkit) | 24.0.1 | `ccpi::ccpi-regulariser=24.0.1` | Toolbox of regularisation methods. | [Apache-2.0](https://github.com/TomographicImaging/CCPi-Regularisation-Toolkit/blob/master/LICENSE) |
 | [TomoPhantom](https://github.com/dkazanc/TomoPhantom) | 22 | `ccpi::tomophantom=22` | Generates phantoms to use as test data. | [Apache-2.0](https://github.com/dkazanc/TomoPhantom/blob/master/LICENSE) |
-| [ipykernel](https://github.com/ipython/ipykernel) || `ipykernel` | Provides the IPython kernel to run Jupyter notebooks | [BSD-3-Clause](https://github.com/ipython/ipykernel/blob/main/LICENSE) |
-| [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) || `ipywidgets` | Enables visualisation tools within jupyter noteboooks | [BSD-3-Clause](https://github.com/jupyter-widgets/ipywidgets/blob/main/LICENSE) |
+| [ipykernel](https://github.com/ipython/ipykernel) || `ipykernel` | Provides the IPython kernel to run Jupyter notebooks. | [BSD-3-Clause](https://github.com/ipython/ipykernel/blob/main/LICENSE) |
+| [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) || `ipywidgets` | Enables visualisation tools within jupyter noteboooks. | [BSD-3-Clause](https://github.com/jupyter-widgets/ipywidgets/blob/main/LICENSE) |
 
 We maintain an environment file with the required packages to run the [CIL demos](https://github.com/TomographicImaging/CIL-Demos) which you can use to create a new environment. This will have specific and tested versions of all dependencies that are outlined in the table above: 
 

From b50e56e3f44492876eb9b61ae41a76c835f64e7c Mon Sep 17 00:00:00 2001
From: Hannah Robarts <77114597+hrobarts@users.noreply.github.com>
Date: Mon, 11 Aug 2025 13:45:37 +0100
Subject: [PATCH 10/14] Add instructions for cpu env

Signed-off-by: Hannah Robarts <77114597+hrobarts@users.noreply.github.com>
---
 README.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/README.md b/README.md
index 82d3b952f0..95c9194ce8 100644
--- a/README.md
+++ b/README.md
@@ -46,6 +46,10 @@ We maintain an environment file with the required packages to run the [CIL demos
 
 ```sh
 conda env create -f https://tomographicimaging.github.io/scripts/env/cil_demos.yml
+
+Or for a CPU-only environment which will work for a limited number of [CIL demos](https://github.com/TomographicImaging/CIL-Demos)
+```sh
+conda env create -f https://tomographicimaging.github.io/scripts/env/cil_demos_cpu.yml
 ```
 
 ### Docker

From 5fce886ef39b4a3c64ce0ede4024768285b11590 Mon Sep 17 00:00:00 2001
From: Hannah Robarts <77114597+hrobarts@users.noreply.github.com>
Date: Mon, 11 Aug 2025 13:47:20 +0100
Subject: [PATCH 11/14] Update README.md

Signed-off-by: Hannah Robarts <77114597+hrobarts@users.noreply.github.com>
---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 95c9194ce8..bed04ed5e5 100644
--- a/README.md
+++ b/README.md
@@ -46,7 +46,7 @@ We maintain an environment file with the required packages to run the [CIL demos
 
 ```sh
 conda env create -f https://tomographicimaging.github.io/scripts/env/cil_demos.yml
-
+```
 Or for a CPU-only environment which will work for a limited number of [CIL demos](https://github.com/TomographicImaging/CIL-Demos)
 ```sh
 conda env create -f https://tomographicimaging.github.io/scripts/env/cil_demos_cpu.yml

From 384fff4f45b3c04574b55ac3dd1cbc61fe7060ed Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <14138589+paskino@users.noreply.github.com>
Date: Tue, 12 Aug 2025 14:12:23 +0200
Subject: [PATCH 12/14] move IPP to required packages

Signed-off-by: Edoardo Pasca <14138589+paskino@users.noreply.github.com>
---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index bed04ed5e5..eabf1c7faa 100644
--- a/README.md
+++ b/README.md
@@ -33,8 +33,8 @@ While building the CIL package we test with specific versions of dependencies. T
 |----|----|--------|--------|----|
 | [Python](https://www.python.org/) | 3.10 - 3.12 | `"python>=3.10,<=3.12"` || [PSF-2.0](https://docs.python.org/3/license.html) |
 | [Numpy](https://github.com/numpy/numpy) | 1.23 - 1.26 | `"numpy>=1.23,<2"` || [BSD-3-Clause](https://numpy.org/doc/stable/license.html) |
-|--|--| **Optional dependencies** |--|--|
 | [IPP](https://www.intel.com/content/www/us/en/developer/tools/oneapi/ipp.html#gs.gxwq5p) | 2021.12 | `-c https://software.repos.intel.com/python/conda ipp=2021.12` | The Intel Integrated Performance Primitives Library (required for the CIL recon class). | [ISSL](http://www.intel.com/content/www/us/en/developer/articles/license/end-user-license-agreement.html) |
+|--|--| **Optional dependencies** |--|--|
 | [ASTRA toolbox](http://www.astra-toolbox.com) | 2.1 | CPU: `conda-forge::astra-toolbox=2.1=py*` <br> GPU: `conda-forge::astra-toolbox=2.1=cuda*` | CT projectors, FBP and FDK. | [GPL-3.0](https://github.com/astra-toolbox/astra-toolbox/blob/master/COPYING) |
 | [TIGRE](https://github.com/CERN/TIGRE) | 2.6 | `ccpi::tigre=2.6` | CT projectors, FBP and FDK. | [BSD-3-Clause](https://github.com/CERN/TIGRE/blob/master/LICENSE.txt) |
 | [CCPi Regularisation Toolkit](https://github.com/TomographicImaging/CCPi-Regularisation-Toolkit) | 24.0.1 | `ccpi::ccpi-regulariser=24.0.1` | Toolbox of regularisation methods. | [Apache-2.0](https://github.com/TomographicImaging/CCPi-Regularisation-Toolkit/blob/master/LICENSE) |

From 7093289cfd392f1afd4aa5a4e4288a0f81c84ce7 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <14138589+paskino@users.noreply.github.com>
Date: Tue, 12 Aug 2025 14:20:41 +0200
Subject: [PATCH 13/14] update the version of TomoPhantom

Signed-off-by: Edoardo Pasca <14138589+paskino@users.noreply.github.com>
---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index eabf1c7faa..d8f8fb5483 100644
--- a/README.md
+++ b/README.md
@@ -38,7 +38,7 @@ While building the CIL package we test with specific versions of dependencies. T
 | [ASTRA toolbox](http://www.astra-toolbox.com) | 2.1 | CPU: `conda-forge::astra-toolbox=2.1=py*` <br> GPU: `conda-forge::astra-toolbox=2.1=cuda*` | CT projectors, FBP and FDK. | [GPL-3.0](https://github.com/astra-toolbox/astra-toolbox/blob/master/COPYING) |
 | [TIGRE](https://github.com/CERN/TIGRE) | 2.6 | `ccpi::tigre=2.6` | CT projectors, FBP and FDK. | [BSD-3-Clause](https://github.com/CERN/TIGRE/blob/master/LICENSE.txt) |
 | [CCPi Regularisation Toolkit](https://github.com/TomographicImaging/CCPi-Regularisation-Toolkit) | 24.0.1 | `ccpi::ccpi-regulariser=24.0.1` | Toolbox of regularisation methods. | [Apache-2.0](https://github.com/TomographicImaging/CCPi-Regularisation-Toolkit/blob/master/LICENSE) |
-| [TomoPhantom](https://github.com/dkazanc/TomoPhantom) | 22 | `ccpi::tomophantom=22` | Generates phantoms to use as test data. | [Apache-2.0](https://github.com/dkazanc/TomoPhantom/blob/master/LICENSE) |
+| [TomoPhantom](https://github.com/dkazanc/TomoPhantom) | [2.0.0](https://github.com/dkazanc/TomoPhantom/releases/tag/v2.0.0) | `ccpi::tomophantom=22` | Generates phantoms to use as test data. | [Apache-2.0](https://github.com/dkazanc/TomoPhantom/blob/master/LICENSE) |
 | [ipykernel](https://github.com/ipython/ipykernel) || `ipykernel` | Provides the IPython kernel to run Jupyter notebooks. | [BSD-3-Clause](https://github.com/ipython/ipykernel/blob/main/LICENSE) |
 | [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) || `ipywidgets` | Enables visualisation tools within jupyter noteboooks. | [BSD-3-Clause](https://github.com/jupyter-widgets/ipywidgets/blob/main/LICENSE) |
 

From b96ac245e4c6a4f314d6727e956b8ae672245dc7 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <14138589+paskino@users.noreply.github.com>
Date: Tue, 12 Aug 2025 14:23:57 +0200
Subject: [PATCH 14/14] fix the tomophantom version

Signed-off-by: Edoardo Pasca <14138589+paskino@users.noreply.github.com>
---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index d8f8fb5483..38386ca373 100644
--- a/README.md
+++ b/README.md
@@ -38,7 +38,7 @@ While building the CIL package we test with specific versions of dependencies. T
 | [ASTRA toolbox](http://www.astra-toolbox.com) | 2.1 | CPU: `conda-forge::astra-toolbox=2.1=py*` <br> GPU: `conda-forge::astra-toolbox=2.1=cuda*` | CT projectors, FBP and FDK. | [GPL-3.0](https://github.com/astra-toolbox/astra-toolbox/blob/master/COPYING) |
 | [TIGRE](https://github.com/CERN/TIGRE) | 2.6 | `ccpi::tigre=2.6` | CT projectors, FBP and FDK. | [BSD-3-Clause](https://github.com/CERN/TIGRE/blob/master/LICENSE.txt) |
 | [CCPi Regularisation Toolkit](https://github.com/TomographicImaging/CCPi-Regularisation-Toolkit) | 24.0.1 | `ccpi::ccpi-regulariser=24.0.1` | Toolbox of regularisation methods. | [Apache-2.0](https://github.com/TomographicImaging/CCPi-Regularisation-Toolkit/blob/master/LICENSE) |
-| [TomoPhantom](https://github.com/dkazanc/TomoPhantom) | [2.0.0](https://github.com/dkazanc/TomoPhantom/releases/tag/v2.0.0) | `ccpi::tomophantom=22` | Generates phantoms to use as test data. | [Apache-2.0](https://github.com/dkazanc/TomoPhantom/blob/master/LICENSE) |
+| [TomoPhantom](https://github.com/dkazanc/TomoPhantom) | [2.0.0](https://github.com/dkazanc/TomoPhantom/releases/tag/v2.0.0) | `ccpi::tomophantom=2.0.0` | Generates phantoms to use as test data. | [Apache-2.0](https://github.com/dkazanc/TomoPhantom/blob/master/LICENSE) |
 | [ipykernel](https://github.com/ipython/ipykernel) || `ipykernel` | Provides the IPython kernel to run Jupyter notebooks. | [BSD-3-Clause](https://github.com/ipython/ipykernel/blob/main/LICENSE) |
 | [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) || `ipywidgets` | Enables visualisation tools within jupyter noteboooks. | [BSD-3-Clause](https://github.com/jupyter-widgets/ipywidgets/blob/main/LICENSE) |