Update dev instructions by paskino · Pull Request #2286 · TomographicImaging/CIL

paskino · 2026-02-02T13:53:20Z

Description

Updates instructions on local build of CIL.
- README
- Developer's guide
Updates to FindIPP.cmake to find IPP libraries on Windows

Example Usage

Contribution Notes

The content of this Pull Request (the Contribution) is intentionally submitted for inclusion in CIL (the Work) under the terms and conditions of the Apache-2.0 License
I confirm that the contribution does not violate any intellectual property rights of third parties

Changes

README.md
Updates the build script as locally I noticed that IPP was not found unless -Ccmake.define.IPP_ROOT=$CONDA_PREFIX was passed
Created environment files:
- Development envs scripts#9

Testing you performed

Please add any demo scripts to https://github.com/TomographicImaging/CIL-Demos/tree/main/misc

Local build on:

Linux
mac ARM
Windows

Checked the artifact documentation produced by GHA.

Linux

On Linux a total of 43 tests are skipped:

test_aqdata_full_tigre (test_DataProcessor.TestBinner.test_aqdata_full_tigre) 
test_pad_id_full_tigre (test_DataProcessor.TestPadder.test_pad_id_full_tigre) 
test_aqdata_full_tigre (test_DataProcessor.TestSlicer.test_aqdata_full_tigre) 
test_linearity (test_PluginsTigre_Siddon.Test_Parallel2D_Projectors_toy_tigre.test_linearity) TIGRE backprojector weights bug
test_norm (test_PluginsTigre_Siddon.Test_Parallel2D_Projectors_toy_tigre.test_norm) TIGRE backprojector weights bug
test_linearity (test_PluginsTigre_Siddon.Test_Parallel3D_Projectors_toy_tigre.test_linearity) TIGRE backprojector weights bug
test_norm (test_PluginsTigre_Siddon.Test_Parallel3D_Projectors_toy_tigre.test_norm) TIGRE backprojector weights bug
test_linearity (test_PluginsTigre_interpolated.Test_Parallel2D_Projectors_toy_tigre.test_linearity) TIGRE backprojector weights bug
test_norm (test_PluginsTigre_interpolated.Test_Parallel2D_Projectors_toy_tigre.test_norm) TIGRE backprojector weights bug
test_linearity (test_PluginsTigre_interpolated.Test_Parallel3D_Projectors_toy_tigre.test_linearity) TIGRE backprojector weights bug
test_norm (test_PluginsTigre_interpolated.Test_Parallel3D_Projectors_toy_tigre.test_norm) TIGRE backprojector weights bug
test_geometry_gpu (test_io.TestZeissDataReader.test_geometry_gpu) Missing prerequisites: has_file False, has_olefile True has_dxchange True
test_import_error (test_io.TestZeissDataReader.test_import_error) This unit test runs only if dxchange is not installed: has_dxchange True
test_read_and_reconstruct_2D_gpu (test_io.TestZeissDataReader.test_read_and_reconstruct_2D_gpu) Missing prerequisites: has_file False, has_olefile True has_dxchange True, has_astra True has_wget True
test_read_txm_recon_file_gpu (test_io.TestZeissDataReader.test_read_txm_recon_file_gpu) Missing prerequisites: has_file False, has_recon_file False has_olefile True has_dxchange True, has_astra True has_wget True

Plus these which test compatibility with SIRF (which is not installed)

test_TNV_call_works (test_SIRF.TestPETRegularisation.test_TNV_call_works) TNV not implemented for 2D
test_TNV_proximal_works (test_SIRF.TestPETRegularisation.test_TNV_proximal_works) TNV not implemented for 2D
test_SIRF_CIL_MLEM (test_SIRF.TestCILSIRFPrecond.test_SIRF_CIL_MLEM) Skipping as SIRF is not available
test_Gradient (test_SIRF.TestGradientMR_2D.test_Gradient) Skipping as SIRF is not available
test_TVdenoisingMR (test_SIRF.TestGradientMR_2D.test_TVdenoisingMR) Has SIRF
test_Gradient (test_SIRF.TestGradientPET_2D.test_Gradient) Skipping as SIRF is not available
test_Gradient (test_SIRF.TestGradientPET_3D.test_Gradient) Skipping as SIRF is not available
test_FGP_TV_call_works (test_SIRF.TestMRRegularisation.test_FGP_TV_call_works) Has SIRF and CCPi Regularisation
test_FGP_TV_proximal_works (test_SIRF.TestMRRegularisation.test_FGP_TV_proximal_works) Has SIRF and CCPi Regularisation
test_TGV_call_works (test_SIRF.TestMRRegularisation.test_TGV_call_works) Has SIRF and CCPi Regularisation
test_TGV_proximal_works (test_SIRF.TestMRRegularisation.test_TGV_proximal_works) Has SIRF and CCPi Regularisation
test_TNV_call_works (test_SIRF.TestMRRegularisation.test_TNV_call_works) Has SIRF and CCPi Regularisation
test_TNV_proximal_works (test_SIRF.TestMRRegularisation.test_TNV_proximal_works) Has SIRF and CCPi Regularisation
test_FGP_TV_call_works (test_SIRF.TestPETRegularisation.test_FGP_TV_call_works) Has SIRF and CCPi Regularisation
test_FGP_TV_proximal_works (test_SIRF.TestPETRegularisation.test_FGP_TV_proximal_works) Has SIRF and CCPi Regularisation
test_TGV_call_works (test_SIRF.TestPETRegularisation.test_TGV_call_works) Has SIRF and CCPi Regularisation
test_TGV_proximal_works (test_SIRF.TestPETRegularisation.test_TGV_proximal_works) Has SIRF and CCPi Regularisation
test_FGP_TV_call_works (test_SIRF.TestRegRegularisation.test_FGP_TV_call_works) Has SIRF and CCPi Regularisation
test_FGP_TV_proximal_works (test_SIRF.TestRegRegularisation.test_FGP_TV_proximal_works) Has SIRF and CCPi Regularisation
test_TGV_call_works (test_SIRF.TestRegRegularisation.test_TGV_call_works) Has SIRF and CCPi Regularisation
test_TGV_proximal_works (test_SIRF.TestRegRegularisation.test_TGV_proximal_works) Has SIRF and CCPi Regularisation
test_TNV_call_works (test_SIRF.TestRegRegularisation.test_TNV_call_works) Has SIRF and CCPi Regularisation
test_TNV_proximal_works (test_SIRF.TestRegRegularisation.test_TNV_proximal_works) Has SIRF and CCPi Regularisation
test_BlockDataContainer_with_SIRF_DataContainer_add (test_SIRF.TestSIRFCILIntegration.test_BlockDataContainer_with_SIRF_DataContainer_add) Has SIRF
test_BlockDataContainer_with_SIRF_DataContainer_divide (test_SIRF.TestSIRFCILIntegration.test_BlockDataContainer_with_SIRF_DataContainer_divide) Has SIRF
test_BlockDataContainer_with_SIRF_DataContainer_multiply (test_SIRF.TestSIRFCILIntegration.test_BlockDataContainer_with_SIRF_DataContainer_multiply) Has SIRF
test_BlockDataContainer_with_SIRF_DataContainer_subtract (test_SIRF.TestSIRFCILIntegration.test_BlockDataContainer_with_SIRF_DataContainer_subtract) Has SIRF

Windows

======================================================================
FAIL: test_set_up (test_algorithms.TestLSQR.test_set_up)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "C:\Users\ofn77899\Dev\CIL\Wrappers\Python\test\test_algorithms.py", line 2059, in test_set_up
    self.assertAlmostEqual(lsqr.beta,  beta, 5 )
AssertionError: 96.19578 != 96.19578622941998 within 5 places (8.33635357366802e-06 difference)

----------------------------------------------------------------------
Ran 1125 tests in 226.381s

FAILED (failures=1, skipped=43)

Related issues/links

Checklist

I have performed a self-review of my code
I have added docstrings in line with the guidance in the developer guide
I have updated the relevant documentation
I have implemented unit tests that cover any new or modified functionality
CHANGELOG.md has been updated with any functionality change
Request review from all relevant developers

data is not installed by the pip command so it is not useful to clone the repo recursively

Added information about creating a shallow clone with --depth parameter.

lauramurgatroyd · 2026-02-10T15:33:40Z

+     - Command
+     - Status
+   * - Linux
+     - ``conda env create -f https://tomographicimaging.github.io/scripts/env/cil_development.yml``


conda env create -f https://tomographicimaging.github.io/scripts/env/cil_development.yml

CondaHTTPError: HTTP 404 NOT FOUND for url https://tomographicimaging.github.io/scripts/env/cil_development.yml

For anyone else who is testing the files are here and you need to use them instead of the url:

https://github.com/TomographicImaging/scripts/pull/9/changes

That's right, I didn't want to link to a PR, so I wrote the link as it will be once #9 is merged

casperdcl

a bit concerned about:

repetition in README.md & developer_guide.rst (would prefer one to link to the other)
lack of mention of conda env names (create --name <env_name> && activate <env_name)

Signed-off-by: Casper da Costa-Luis <casper.dcl@physics.org>

Co-authored-by: Nalin Gupta <nalin.gupta3142@gmail.com> Signed-off-by: Laura Murgatroyd <60604372+lauramurgatroyd@users.noreply.github.com>

lauramurgatroyd · 2026-04-09T14:49:23Z

-bash ./scripts/create_local_env_for_cil_development.sh
-```
-
-Or with the CIL build and test dependencies:


Should we remove the batch script file itself if we no longer recommend to use it?

I have done this, please let me know if ok

lauramurgatroyd · 2026-04-09T15:07:17Z

+
+You can achieve this in two ways:
+
+1. by opening a "Developer Command Prompt for Visual Studio" and activating the conda environment from there. This requires you 


Suggested change

1. by opening a "Developer Command Prompt for Visual Studio" and activating the conda environment from there. This requires you

1. by opening a "Developer Command Prompt for VS" and activating the conda environment from there. This requires you

I do not have anything called "Developer Command Prompt for Visual Studio"

Please can you check the name of yours @paskino , I wonder if its a typo or if the name of the program is different in different versions

x64 Native Tools Command Prompt for VS
might be the better option here?

yes that's what mine is called, and was in my original instructions

lauramurgatroyd · 2026-04-09T16:33:19Z

+
+If you are developing on Windows with conda, you need to have access to both the Visual Studio compiler and the conda environment. 
+
+You can achieve this in two ways:


I just retested and found the instructions below worked for me, so I am happy that they are correct provided we state versions we tested with. I added the version of Visual Studio I had, as a suggested change Any other versions we should include a note of?

lauramurgatroyd · 2026-04-10T10:31:40Z

Hi @paskino I am going to take over your branch. I will merge in my suggestions from yesterday, just leaving the questions I had.

In stand-up today we agreed to remove duplication and have all of the content in the developer guide, and the README linking to the developer guide. I will make this change.

Co-authored-by: Casper da Costa-Luis <casper.dcl@physics.org> Co-authored-by: Laura Murgatroyd <60604372+lauramurgatroyd@users.noreply.github.com> Co-authored-by: Edoardo Pasca <14138589+paskino@users.noreply.github.com> Signed-off-by: Laura Murgatroyd <60604372+lauramurgatroyd@users.noreply.github.com>

lauramurgatroyd · 2026-04-14T11:10:14Z

Some screenshots of the rendered developer guide:

lauramurgatroyd · 2026-04-14T11:11:17Z

Hi, this PR is now ready for review again. I actioned the changes I suggested. Please see the unresolved threads for open questions.

gfardell

I'm confused by the environment file links not working, maybe they are in an unmerged PR?

However, I would have thought that using the environment files that ship with CIL is good enough as users will need to clone the repositories by default. Was there a reason to move away from that?

gfardell · 2026-04-16T14:22:32Z

    - cvxpy maximum version set to 1.7.5 to fix #2303 (#2304)
  - Documentation:
    - Render the user showcase notebooks in the documentation (#2189)
+    - Update on build instructions in README and developer guide for all OS


Also find IPP change?

Adds conda environment paths to find IPP command in cmake?

gfardell · 2026-04-16T14:33:48Z

+
+You can achieve this in two ways:
+
+1. by opening a "Developer Command Prompt for Visual Studio" and activating the conda environment from there. This requires you 


x64 Native Tools Command Prompt for VS
might be the better option here?

Co-authored-by: Gemma Fardell <47746591+gfardell@users.noreply.github.com> Signed-off-by: Laura Murgatroyd <60604372+lauramurgatroyd@users.noreply.github.com>

lauramurgatroyd · 2026-04-16T14:53:21Z

I'm confused by the environment file links not working, maybe they are in an unmerged PR?

However, I would have thought that using the environment files that ship with CIL is good enough as users will need to clone the repositories by default. Was there a reason to move away from that?

This PR in scripts has the env file: https://github.com/TomographicImaging/scripts/pull/9/changes

I am not sure where they should live - we need to discuss what the purpose of https://github.com/TomographicImaging/scripts is

Signed-off-by: Casper da Costa-Luis <casper.dcl@physics.org>

casperdcl

We could also move scripts/requirements-test.yml to just environment.yml in the root.

lauramurgatroyd · 2026-04-17T16:37:36Z

We will move the dev environment files into CIL, not host them in scripts, see: TomographicImaging/scripts#9 (review)

Co-authored-by: Gemma Fardell <47746591+gfardell@users.noreply.github.com> Signed-off-by: Laura Murgatroyd <60604372+lauramurgatroyd@users.noreply.github.com>

paskino added 5 commits February 2, 2026 11:12

update readme

250cb03

updated clone and build command

42af679

data is not installed by the pip command so it is not useful to clone the repo recursively

update pip command to find IPP

3c1b642

fix recipe to find IPP

482a640

Merge branch 'master' into update_dev_instructions

d227e3c

paskino added this to UM 2026 Feb 2, 2026

github-project-automation bot moved this to Todo in UM 2026 Feb 2, 2026

paskino moved this from Todo to In Progress in UM 2026 Feb 2, 2026

update pip command

d37a157

paskino mentioned this pull request Feb 5, 2026

ctests fail on Windows due to module problem #2141

Closed

paskino added 3 commits February 6, 2026 09:35

add search CMake search path for WIN32 IPP

758f315

added instructions on developer guide

6a098d5

updated changelog

e597d53

paskino marked this pull request as ready for review February 6, 2026 20:43

paskino requested a review from a team as a code owner February 6, 2026 20:43

paskino requested review from casperdcl, gfardell and lauramurgatroyd and removed request for a team February 6, 2026 20:44

Update README with shallow clone instructions

8b3f51b

Added information about creating a shallow clone with --depth parameter.

paskino removed this from UM 2026 Feb 10, 2026

paskino added this to CIL work Feb 10, 2026

github-project-automation bot moved this to Todo in CIL work Feb 10, 2026

gfardell requested review from Neonbluestoplight and hrobarts February 10, 2026 14:08

lauramurgatroyd reviewed Feb 10, 2026

View reviewed changes

Comment thread docs/source/developer_guide.rst Outdated

casperdcl requested changes Feb 17, 2026

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lauramurgatroyd reviewed Feb 19, 2026

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Comment thread README.md Outdated

lauramurgatroyd reviewed Feb 19, 2026

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Comment thread README.md Outdated

paskino commented Feb 25, 2026

View reviewed changes

Comment thread docs/source/developer_guide.rst Outdated

fix FindIPP

c7e05ab

Signed-off-by: Casper da Costa-Luis <casper.dcl@physics.org>

gfardell assigned paskino Mar 10, 2026

gfardell added this to the v26.0 milestone Apr 1, 2026

Neonbluestoplight reviewed Apr 8, 2026

View reviewed changes

Comment thread docs/source/developer_guide.rst Outdated

gfardell assigned lauramurgatroyd Apr 9, 2026

Apply suggestion from @Neonbluestoplight

36179bc

Co-authored-by: Nalin Gupta <nalin.gupta3142@gmail.com> Signed-off-by: Laura Murgatroyd <60604372+lauramurgatroyd@users.noreply.github.com>

lauramurgatroyd requested changes Apr 9, 2026

View reviewed changes

Merge branch 'master' into update_dev_instructions

f794772

lauramurgatroyd and others added 7 commits April 10, 2026 12:02

Merge branch 'master' into update_dev_instructions

52e7808

Move instructions out of readme

7e84ee4

update doc instructions and remove old scripts

222e9e6

Fix formatting

b8e7ed2

Rearrange docs

f56203b

Fix titles

9010a29

lauramurgatroyd moved this from Blocked to Priority review in CIL work Apr 15, 2026

lauramurgatroyd removed the request for review from hrobarts April 15, 2026 10:07

Merge branch 'master' into update_dev_instructions

79d14b4

gfardell reviewed Apr 16, 2026

View reviewed changes

Comment thread docs/source/developer_guide.rst

Apply suggestions from code review

66f0461

Co-authored-by: Gemma Fardell <47746591+gfardell@users.noreply.github.com> Signed-off-by: Laura Murgatroyd <60604372+lauramurgatroyd@users.noreply.github.com>

fix syntax

a0db0ab

Signed-off-by: Casper da Costa-Luis <casper.dcl@physics.org>

casperdcl approved these changes Apr 17, 2026

View reviewed changes

Apply suggestions from code review

5b8eeaf

Co-authored-by: Gemma Fardell <47746591+gfardell@users.noreply.github.com> Signed-off-by: Laura Murgatroyd <60604372+lauramurgatroyd@users.noreply.github.com>


		You can achieve this in two ways:

		1. by opening a "Developer Command Prompt for Visual Studio" and activating the conda environment from there. This requires you


		If you are developing on Windows with conda, you need to have access to both the Visual Studio compiler and the conda environment.

		You can achieve this in two ways:

Conversation

paskino commented Feb 2, 2026 • edited by lauramurgatroyd Loading Uh oh! There was an error while loading. Please reload this page.

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Description

Example Usage

Contribution Notes

Changes

Testing you performed

Linux

Windows

Related issues/links

Checklist

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lauramurgatroyd Apr 9, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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paskino commented Feb 2, 2026 •

edited by lauramurgatroyd

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lauramurgatroyd Apr 9, 2026 •

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lauramurgatroyd commented Apr 10, 2026 •

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lauramurgatroyd commented Apr 16, 2026 •

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