Minor README fix #882
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Minor README fix #882
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jscanvic
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Nov 2, 2025
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LGTM thanks Andrew
Happy to merge once CI passes
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #882 +/- ##
==========================================
+ Coverage 84.53% 84.60% +0.07%
==========================================
Files 208 208
Lines 21175 21281 +106
Branches 2883 2893 +10
==========================================
+ Hits 17900 18005 +105
- Misses 2358 2359 +1
Partials 917 917 ☔ View full report in Codecov by Sentry. |
Andrewwango
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Nov 14, 2025
* 3D Total variation priors (#745) * 3D denoising variational * comments * comments jeremy * Remove concurrency settings from gpu_docs.yml (#850) * Remove concurrency settings from gpu_docs.yml final CI fixes * Remove concurrency settings from test_gpu.yml Removed concurrency settings from the GPU test workflow. * Refine Codecov upload condition for Linux only * Update Codecov upload condition in workflow Restrict Codecov upload to Linux with Python 3.10 only. * Fix astra test failing on GPU (#841) * fix normalize threshold in astra tests * black * Fix test transform on GPU (#852) Co-authored-by: Andrew Wang <[email protected]> * Fix broken download Set14 (#845) * . * fix * adapt docs & use utils * changelog * Fix py3.9 not supported by recent coverage version (#856) * . * . * Follow up to #856 (#857) * Robustify CI for Python 3.9 (#858) * Robustify CI for Python 3.9 * Update test_pr.yml * Fix pip install command for Python 3.9 * Update test_pr.yml * Update CI workflow for deepinv installation Refactor installation steps for deepinv in CI workflow to handle Python 3.9 compatibility. * Add compatibility step for Python 3.9 in workflow Add step to modify pyproject.toml for Python 3.9 compatibility. * Refactor deepinv installation steps in workflow Removed conditional installation for Python 3.9 and adjusted the installation step for deepinv dependencies. * Support 3D patches datasets (#806) * Nibabel test hotfix (#863) * Nibabel test hotfix * Require 'blosc2' for the test dataset Added a dependency check for 'blosc2' in the test. * Typing optim (#827) * distance typed * dpir * data fidelity * fix callable * bregman * fix callable distance * epll * start optimizers.py * phase retrieval * start utils * utils fixes * fix circular import from physics * bregman returns * data fid phsycis & return * distance returns * epll returns * opt & phase retrieval * return spectral wrapper * future annotations * _reconstruction_step * utils * add suggestions * finish optimizers.py * Gentler loader check (#871) * Gentler loader check * remove codecov from test * black * add wee comment * Fix error handling for CBSD68 dataset (#868) * fix error handling * fix * suggestions * add PR #723 in CHANGELOG; fix some minor typos (#860) * add PR #723 in CHANGELOG; fix some minor typos * update CHANGELOG * Fix DDRM citation to reference Kawar et al. 2022 (#876) * Initial plan * Fix DDRM reference to cite Kawar et al. 2022 Co-authored-by: tachella <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: tachella <[email protected]> * Allow for complex data inside Wavelets (#738) * Update mri.py * Update mri.py * Added Complex support * Added support for complex data * reformat * Undo MRI change * More fixes * More fixes * yet more fixes, gosh why am i like this * Finally done * Take in comments * fix psnr and add performance checks --------- Co-authored-by: German Shâma Wache <[email protected]> Co-authored-by: Jérémy Scanvic <[email protected]> * add self-sup eval + history fixes (#777) * add self-sup eval + history fixes * changelog * avoid using losses as metrics + add explicit model inference with .eval + trainer tests * add docs warning * remove loss docstring from metric * add missing docstrings * small fix * doc fixes * doc fixes * fixes * fix adversarial * fixes * fix bugs * black * reblack * jeremy's comments * improve docs explanation * unsure + community + generate_datasets fix * early_stop int + fix doc typo * fix docs * add pragma * andrew's comments * docstring compute_metrics * change names + test * still some fixes to go * black * add train_metrics_history * fix wandb bug * black + docs fixes * black + docs fixes * fix * fix class link * re-order * Update deepinv/training/trainer.py Co-authored-by: Andrew Wang <[email protected]> * andrew's comments * andrew's comments * fix julian issue * docstring fixes --------- Co-authored-by: Andrew Wang <[email protected]> * Add 3D variants of CNN networks (#869) * dncnn * gan * . * ruff check * fix ordering test_pad * maxpool unet nd * icnn * dsccp * PDNet * fix icnn * fix dim drunet * pragma * fix dip * test dsccp 3D * icnn 3D test * more tests * test PDNet * tests GAN * . * test all modes drunet + fix bug from main * changelog * clean dummy * remove c variable * fix doc rician noise * 3d models -> denoisers * warnings * fixdim doc * userguide * syntax * Fix LsdirHR download (#866) * . * ruff + fix docs * add proposed train glob * changelog * fix docstring randompatchsampler * fix sphynx? * pragma * pragma * fix denoiser docs * `dinv.io` module and clean up utils (#768) * start develpoing io submodule + modify examples * add scipy load mat * fix doc * add references to DIP demo (idk why this hasn't been added before) * add raster * io -> io_utils, signal -> signals * checks * ISMRMD loading * add all tests * fix optional deps * add new example * fix example * changelog * fix docs * oops * fix doc * update typing * remove load_np and load_nifit in preparation for merge from vicky PR * black * test assert in doctest * add nifti vicky comment + io_utils -> io * pydicom rescale + lidc uses load_dicom * fix test * fix typing in io and add kwargs * fix sphinx typing * fix test * fix doc * vicky comments * vicky comment * fix doc * blosc2 test * PET comment * Minor README fix (#882) * fix (#885) Co-authored-by: mh-nguyen712 <[email protected]> * Minor trainer docstring fixes (#884) * io -> utils.io * improve docstring * very minor fix * Fix formatting in contributing section of README (#888) * Fix #887 (#890) * Move changelog.rst to docs (#889) * init * fix links * fix links * fix double changelog * change pytorch link * remove llm bs * black * fix docs * Update .github/workflows/release.yml Co-authored-by: Minh Hai Nguyen <[email protected]> * fix ghs * fix ghs --------- Co-authored-by: Minh Hai Nguyen <[email protected]> * Enable ruff rule N805 (#892) * enable ruff rule N805 Co-authored-by: Jérémy Scanvic <[email protected]> * ruff check --fix --unsafe-fixes Co-authored-by: Jérémy Scanvic <[email protected]> --------- Co-authored-by: Andrewwango <[email protected]> * Fix announcement text in conf.py (#901) * Update link to changelog in PR template (#903) * Fix docstring formatting in BaseSDE class (#902) * Refactor release workflow (#914) * Refactor release workflow by removing CI checks Remove CI status check step from release workflow * fixes * fixes * black * Release v0.3.6 (#917) Co-authored-by: tachella <[email protected]> * Fix license formatting in CITATION.cff (#920) * Fix license formatting in CITATION.cff * Create workflow to validate CITATION.cff Add GitHub Actions workflow to validate CITATION.cff file * Add check_citation.yml workflow file * Fix license format in CITATION.cff * Add DOI and version to CITATION.cff * Warn inconsistent upsampling parameters in SwinIR (#909) * add a warning to SwinIR * update the changelog * let test be skipped when timm is absent (#922) * Enable ruff rule E402 (#910) * enable rule E402 Co-authored-by: Jérémy Scanvic <[email protected]> * ignore E402 in the examples Co-authored-by: Jérémy Scanvic <[email protected]> * disable E402 in deepinv/__init__.py Co-authored-by: Jérémy Scanvic <[email protected]> * pull changes from original PR * fix the import location * put back the weird named import --------- Co-authored-by: Thibaut Modrzyk <[email protected]> * Add demo to connect spyrit and deepinv (#865) * Add demo to connect spyrit and deepinv * implement changes * lint * add spyrit optional dependency * fix toml file * fix attribute to /images/ * Update examples/external-libraries/demo_connect_spyrit.py Co-authored-by: Jérémy Scanvic <[email protected]> * Update examples/external-libraries/demo_connect_spyrit.py Co-authored-by: Jérémy Scanvic <[email protected]> * Update examples/external-libraries/demo_connect_spyrit.py Co-authored-by: Jérémy Scanvic <[email protected]> * Update examples/external-libraries/demo_connect_spyrit.py Co-authored-by: Jérémy Scanvic <[email protected]> * Update examples/external-libraries/demo_connect_spyrit.py Co-authored-by: Jérémy Scanvic <[email protected]> * Update examples/external-libraries/demo_connect_spyrit.py Co-authored-by: Jérémy Scanvic <[email protected]> * Update examples/external-libraries/demo_connect_spyrit.py Co-authored-by: Jérémy Scanvic <[email protected]> * Update examples/external-libraries/demo_connect_spyrit.py Co-authored-by: Jérémy Scanvic <[email protected]> * Update examples/external-libraries/demo_connect_spyrit.py Co-authored-by: Jérémy Scanvic <[email protected]> * Update examples/external-libraries/demo_connect_spyrit.py Co-authored-by: Jérémy Scanvic <[email protected]> --------- Co-authored-by: Thibaut Modrzyk <[email protected]> Co-authored-by: Jérémy Scanvic <[email protected]> * add youtube (#926) * Add center_crop parameter to Metric class (#913) * Initial plan * Add center_crop functionality to Metric class and update all child classes Co-authored-by: tachella <[email protected]> * fix metric docs + black + test for mixed signs * fix docstrings --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: tachella <[email protected]> Co-authored-by: Julián Tachella <[email protected]> * fix contributing doc * remove auto labeller --------- Co-authored-by: Matthieu Terris <[email protected]> Co-authored-by: Julián Tachella <[email protected]> Co-authored-by: romainvo <[email protected]> Co-authored-by: Andrew Wang <[email protected]> Co-authored-by: Vicky De Ridder <[email protected]> Co-authored-by: Jérémy Scanvic <[email protected]> Co-authored-by: Johannes Hertrich <[email protected]> Co-authored-by: Brayan Monroy <[email protected]> Co-authored-by: Copilot <[email protected]> Co-authored-by: Chaithya G R <[email protected]> Co-authored-by: German Shâma Wache <[email protected]> Co-authored-by: Jérémy Scanvic <[email protected]> Co-authored-by: Minh Hai Nguyen <[email protected]> Co-authored-by: mh-nguyen712 <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Thibaut Modrzyk <[email protected]> Co-authored-by: tbaudier <[email protected]> Co-authored-by: Julián Tachella <[email protected]>
Andrewwango
added a commit
that referenced
this pull request
Nov 14, 2025
* enable blank issues * PR status labels * readme/index/community references contributing * add label system * Labelling (#931) * 3D Total variation priors (#745) * 3D denoising variational * comments * comments jeremy * Remove concurrency settings from gpu_docs.yml (#850) * Remove concurrency settings from gpu_docs.yml final CI fixes * Remove concurrency settings from test_gpu.yml Removed concurrency settings from the GPU test workflow. * Refine Codecov upload condition for Linux only * Update Codecov upload condition in workflow Restrict Codecov upload to Linux with Python 3.10 only. * Fix astra test failing on GPU (#841) * fix normalize threshold in astra tests * black * Fix test transform on GPU (#852) Co-authored-by: Andrew Wang <[email protected]> * Fix broken download Set14 (#845) * . * fix * adapt docs & use utils * changelog * Fix py3.9 not supported by recent coverage version (#856) * . * . * Follow up to #856 (#857) * Robustify CI for Python 3.9 (#858) * Robustify CI for Python 3.9 * Update test_pr.yml * Fix pip install command for Python 3.9 * Update test_pr.yml * Update CI workflow for deepinv installation Refactor installation steps for deepinv in CI workflow to handle Python 3.9 compatibility. * Add compatibility step for Python 3.9 in workflow Add step to modify pyproject.toml for Python 3.9 compatibility. * Refactor deepinv installation steps in workflow Removed conditional installation for Python 3.9 and adjusted the installation step for deepinv dependencies. * Support 3D patches datasets (#806) * Nibabel test hotfix (#863) * Nibabel test hotfix * Require 'blosc2' for the test dataset Added a dependency check for 'blosc2' in the test. * Typing optim (#827) * distance typed * dpir * data fidelity * fix callable * bregman * fix callable distance * epll * start optimizers.py * phase retrieval * start utils * utils fixes * fix circular import from physics * bregman returns * data fid phsycis & return * distance returns * epll returns * opt & phase retrieval * return spectral wrapper * future annotations * _reconstruction_step * utils * add suggestions * finish optimizers.py * Gentler loader check (#871) * Gentler loader check * remove codecov from test * black * add wee comment * Fix error handling for CBSD68 dataset (#868) * fix error handling * fix * suggestions * add PR #723 in CHANGELOG; fix some minor typos (#860) * add PR #723 in CHANGELOG; fix some minor typos * update CHANGELOG * Fix DDRM citation to reference Kawar et al. 2022 (#876) * Initial plan * Fix DDRM reference to cite Kawar et al. 2022 Co-authored-by: tachella <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: tachella <[email protected]> * Allow for complex data inside Wavelets (#738) * Update mri.py * Update mri.py * Added Complex support * Added support for complex data * reformat * Undo MRI change * More fixes * More fixes * yet more fixes, gosh why am i like this * Finally done * Take in comments * fix psnr and add performance checks --------- Co-authored-by: German Shâma Wache <[email protected]> Co-authored-by: Jérémy Scanvic <[email protected]> * add self-sup eval + history fixes (#777) * add self-sup eval + history fixes * changelog * avoid using losses as metrics + add explicit model inference with .eval + trainer tests * add docs warning * remove loss docstring from metric * add missing docstrings * small fix * doc fixes * doc fixes * fixes * fix adversarial * fixes * fix bugs * black * reblack * jeremy's comments * improve docs explanation * unsure + community + generate_datasets fix * early_stop int + fix doc typo * fix docs * add pragma * andrew's comments * docstring compute_metrics * change names + test * still some fixes to go * black * add train_metrics_history * fix wandb bug * black + docs fixes * black + docs fixes * fix * fix class link * re-order * Update deepinv/training/trainer.py Co-authored-by: Andrew Wang <[email protected]> * andrew's comments * andrew's comments * fix julian issue * docstring fixes --------- Co-authored-by: Andrew Wang <[email protected]> * Add 3D variants of CNN networks (#869) * dncnn * gan * . * ruff check * fix ordering test_pad * maxpool unet nd * icnn * dsccp * PDNet * fix icnn * fix dim drunet * pragma * fix dip * test dsccp 3D * icnn 3D test * more tests * test PDNet * tests GAN * . * test all modes drunet + fix bug from main * changelog * clean dummy * remove c variable * fix doc rician noise * 3d models -> denoisers * warnings * fixdim doc * userguide * syntax * Fix LsdirHR download (#866) * . * ruff + fix docs * add proposed train glob * changelog * fix docstring randompatchsampler * fix sphynx? * pragma * pragma * fix denoiser docs * `dinv.io` module and clean up utils (#768) * start develpoing io submodule + modify examples * add scipy load mat * fix doc * add references to DIP demo (idk why this hasn't been added before) * add raster * io -> io_utils, signal -> signals * checks * ISMRMD loading * add all tests * fix optional deps * add new example * fix example * changelog * fix docs * oops * fix doc * update typing * remove load_np and load_nifit in preparation for merge from vicky PR * black * test assert in doctest * add nifti vicky comment + io_utils -> io * pydicom rescale + lidc uses load_dicom * fix test * fix typing in io and add kwargs * fix sphinx typing * fix test * fix doc * vicky comments * vicky comment * fix doc * blosc2 test * PET comment * Minor README fix (#882) * fix (#885) Co-authored-by: mh-nguyen712 <[email protected]> * Minor trainer docstring fixes (#884) * io -> utils.io * improve docstring * very minor fix * Fix formatting in contributing section of README (#888) * Fix #887 (#890) * Move changelog.rst to docs (#889) * init * fix links * fix links * fix double changelog * change pytorch link * remove llm bs * black * fix docs * Update .github/workflows/release.yml Co-authored-by: Minh Hai Nguyen <[email protected]> * fix ghs * fix ghs --------- Co-authored-by: Minh Hai Nguyen <[email protected]> * Enable ruff rule N805 (#892) * enable ruff rule N805 Co-authored-by: Jérémy Scanvic <[email protected]> * ruff check --fix --unsafe-fixes Co-authored-by: Jérémy Scanvic <[email protected]> --------- Co-authored-by: Andrewwango <[email protected]> * Fix announcement text in conf.py (#901) * Update link to changelog in PR template (#903) * Fix docstring formatting in BaseSDE class (#902) * Refactor release workflow (#914) * Refactor release workflow by removing CI checks Remove CI status check step from release workflow * fixes * fixes * black * Release v0.3.6 (#917) Co-authored-by: tachella <[email protected]> * Fix license formatting in CITATION.cff (#920) * Fix license formatting in CITATION.cff * Create workflow to validate CITATION.cff Add GitHub Actions workflow to validate CITATION.cff file * Add check_citation.yml workflow file * Fix license format in CITATION.cff * Add DOI and version to CITATION.cff * Warn inconsistent upsampling parameters in SwinIR (#909) * add a warning to SwinIR * update the changelog * let test be skipped when timm is absent (#922) * Enable ruff rule E402 (#910) * enable rule E402 Co-authored-by: Jérémy Scanvic <[email protected]> * ignore E402 in the examples Co-authored-by: Jérémy Scanvic <[email protected]> * disable E402 in deepinv/__init__.py Co-authored-by: Jérémy Scanvic <[email protected]> * pull changes from original PR * fix the import location * put back the weird named import --------- Co-authored-by: Thibaut Modrzyk <[email protected]> * Add demo to connect spyrit and deepinv (#865) * Add demo to connect spyrit and deepinv * implement changes * lint * add spyrit optional dependency * fix toml file * fix attribute to /images/ * Update examples/external-libraries/demo_connect_spyrit.py Co-authored-by: Jérémy Scanvic <[email protected]> * Update examples/external-libraries/demo_connect_spyrit.py Co-authored-by: Jérémy Scanvic <[email protected]> * Update examples/external-libraries/demo_connect_spyrit.py Co-authored-by: Jérémy Scanvic <[email protected]> * Update examples/external-libraries/demo_connect_spyrit.py Co-authored-by: Jérémy Scanvic <[email protected]> * Update examples/external-libraries/demo_connect_spyrit.py Co-authored-by: Jérémy Scanvic <[email protected]> * Update examples/external-libraries/demo_connect_spyrit.py Co-authored-by: Jérémy Scanvic <[email protected]> * Update examples/external-libraries/demo_connect_spyrit.py Co-authored-by: Jérémy Scanvic <[email protected]> * Update examples/external-libraries/demo_connect_spyrit.py Co-authored-by: Jérémy Scanvic <[email protected]> * Update examples/external-libraries/demo_connect_spyrit.py Co-authored-by: Jérémy Scanvic <[email protected]> * Update examples/external-libraries/demo_connect_spyrit.py Co-authored-by: Jérémy Scanvic <[email protected]> --------- Co-authored-by: Thibaut Modrzyk <[email protected]> Co-authored-by: Jérémy Scanvic <[email protected]> * add youtube (#926) * Add center_crop parameter to Metric class (#913) * Initial plan * Add center_crop functionality to Metric class and update all child classes Co-authored-by: tachella <[email protected]> * fix metric docs + black + test for mixed signs * fix docstrings --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: tachella <[email protected]> Co-authored-by: Julián Tachella <[email protected]> * fix contributing doc * remove auto labeller --------- Co-authored-by: Matthieu Terris <[email protected]> Co-authored-by: Julián Tachella <[email protected]> Co-authored-by: romainvo <[email protected]> Co-authored-by: Andrew Wang <[email protected]> Co-authored-by: Vicky De Ridder <[email protected]> Co-authored-by: Jérémy Scanvic <[email protected]> Co-authored-by: Johannes Hertrich <[email protected]> Co-authored-by: Brayan Monroy <[email protected]> Co-authored-by: Copilot <[email protected]> Co-authored-by: Chaithya G R <[email protected]> Co-authored-by: German Shâma Wache <[email protected]> Co-authored-by: Jérémy Scanvic <[email protected]> Co-authored-by: Minh Hai Nguyen <[email protected]> Co-authored-by: mh-nguyen712 <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Thibaut Modrzyk <[email protected]> Co-authored-by: tbaudier <[email protected]> Co-authored-by: Julián Tachella <[email protected]> --------- Co-authored-by: Matthieu Terris <[email protected]> Co-authored-by: Julián Tachella <[email protected]> Co-authored-by: romainvo <[email protected]> Co-authored-by: Andrew Wang <[email protected]> Co-authored-by: Vicky De Ridder <[email protected]> Co-authored-by: Jérémy Scanvic <[email protected]> Co-authored-by: Johannes Hertrich <[email protected]> Co-authored-by: Brayan Monroy <[email protected]> Co-authored-by: Copilot <[email protected]> Co-authored-by: Chaithya G R <[email protected]> Co-authored-by: German Shâma Wache <[email protected]> Co-authored-by: Jérémy Scanvic <[email protected]> Co-authored-by: Minh Hai Nguyen <[email protected]> Co-authored-by: mh-nguyen712 <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Thibaut Modrzyk <[email protected]> Co-authored-by: tbaudier <[email protected]> Co-authored-by: Julián Tachella <[email protected]>
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python3 -m pytest deepinv/testsruns successfully.black .runs successfully.make htmlruns successfully (in thedocs/directory).