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

Check Update documentation build instructions to include windows #2251

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

docs/source/developer_guide.rst

+     - 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

lauramurgatroyd · 2026-02-10T15:44:26Z

docs/source/developer_guide.rst

+   * - OS
+     - Build Command
+   * - Linux
+     - ``pip install --no-deps . -Ccmake.define.IPP_ROOT=$CONDA_PREFIX``


I followed the instructions for linux and got:

ModuleNotFoundError: No module named 'cil'

I take it all back, I made a fresh clone of CIL and it worked

Every time I make a code change I have to run:
pip install --no-deps . -Ccmake.define.IPP_ROOT=$CONDA_PREFIX

otherwise IPP doesn't work.
I didn't used to have to do this with the old instructions

Yes. However, I don't believe this has anything to do with this change, rather with #2145
@casperdcl told me that when issuing pip install a new temporary environment (handled by pip) is created where CMake and scikit-build are installed,

CIL/pyproject.toml

Lines 1 to 16 in f8f2e31

[build-system]

requires = [

"setuptools>=64",

"setuptools_scm>=8",

"scikit-build-core>=0.10",

#"ipp-devel==2021.12.*", # PyPI conflicts with conda package

]

build-backend = "scikit_build_core.build"

[tool.scikit-build]

minimum-version = "build-system.requires"

cmake.version = ">=3.16"

metadata.version.provider = "scikit_build_core.metadata.setuptools_scm"

sdist.include = ["Wrappers/Python/cil/version.py"]

sdist.exclude = ["scripts", "docs", "Wrappers/Python/data", "Wrappers/Python/test", ".*"]

[tool.scikit-build.wheel.packages]

For this reason the build cache is not preserved and you always recompile from scratch. Currently this is not a big problem, as the cilacc library is small but we should do something more about caching the build artifacts.

I just tested with an environment where I install cmake and scikit-build from conda rather than let it handle by pip and:

pip install --no-deps . is sufficient, i.e. IPP is found

cilacc seems to be built all the times you issue pip install

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

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Update dev instructions#2286

Update dev instructions#2286
paskino wants to merge 10 commits intoTomographicImaging:masterfrom
paskino:update_dev_instructions

paskino commented Feb 2, 2026 •

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	[build-system]
	requires = [
	"setuptools>=64",
	"setuptools_scm>=8",
	"scikit-build-core>=0.10",
	#"ipp-devel==2021.12.*", # PyPI conflicts with conda package
	]
	build-backend = "scikit_build_core.build"

	[tool.scikit-build]
	minimum-version = "build-system.requires"
	cmake.version = ">=3.16"
	metadata.version.provider = "scikit_build_core.metadata.setuptools_scm"
	sdist.include = ["Wrappers/Python/cil/version.py"]
	sdist.exclude = ["scripts", "docs", "Wrappers/Python/data", "Wrappers/Python/test", ".*"]
	[tool.scikit-build.wheel.packages]

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Description

Example Usage

Contribution Notes

Changes

Testing you performed

Linux

Windows

Related issues/links

Checklist

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paskino commented Feb 2, 2026 •

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