Modernising Build Process#9010
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Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
…requirements Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
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Actionable comments posted: 9
🧹 Nitpick comments (3)
monai/_version.py (1)
47-640: 📐 Maintainability & Code Quality | 🔵 Trivial | ⚖️ Poor tradeoffMake generated definitions conform durably.
These modified definitions lack the required Google-style argument/return/exception documentation. Update the Versioneer template or exempt generated
monai/_version.py; hand edits will be overwritten. As per path instructions, definitions require Google-style variable, return, and exception documentation.🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the rest with a brief reason, keep changes minimal, and validate. In `@monai/_version.py` around lines 47 - 640, The generated Versioneer definitions lack the required Google-style variable, return, and exception documentation. Update the Versioneer template that generates symbols such as get_config, run_command, git_pieces_from_vcs, render, and get_versions, or add the generated monai/_version.py path to the documentation exemption; do not hand-edit the generated file because regeneration will overwrite it.Source: Path instructions
runtests.sh (1)
139-146: 📐 Maintainability & Code Quality | 🔵 Trivial | ⚡ Quick winQuote
$REQand clean up the temp file.Unquoted
$REQ(Lines 145-146) is unsafe ifTMPDIRcontains spaces/glob chars, and the temp requirements file is never removed after use.🧹 Proposed fix
REQ=$(mktemp --tmpdir XXX.txt) - ${cmdPrefix}"${PY_EXE}" monai/config/print_dependencies.py all testing > $REQ - ${cmdPrefix}"${PY_EXE}" -m pip install -r $REQ + ${cmdPrefix}"${PY_EXE}" monai/config/print_dependencies.py all testing > "$REQ" + ${cmdPrefix}"${PY_EXE}" -m pip install -r "$REQ" + rm -f "$REQ" }🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the rest with a brief reason, keep changes minimal, and validate. In `@runtests.sh` around lines 139 - 146, Update install_deps to quote "$REQ" wherever the temporary requirements file is passed to pip, and remove the temporary file after installation completes. Keep the existing dependency-generation and installation flow unchanged.Source: Linters/SAST tools
docs/source/installation.md (1)
54-56: 📐 Maintainability & Code Quality | 🔵 Trivial | 💤 Low valueAdd a language to the fenced code block.
Markdownlint flags this block for missing a fence language (MD040).
🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the rest with a brief reason, keep changes minimal, and validate. In `@docs/source/installation.md` around lines 54 - 56, Add a language identifier to the fenced code block containing the dependency list in the installation documentation, using an appropriate plain-text language such as text; leave the dependency contents unchanged.Source: Linters/SAST tools
🤖 Prompt for all review comments with AI agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
Inline comments:
In @.github/workflows/cicd_tests.yml:
- Around line 277-282: Update the dependency installation steps in the workflow
to install only `.[all,testing]`, then explicitly install `omegaconf` and
`nvsubquadratic>=0.1.1` with `--no-deps`. Remove the separate `python -m pip
install -e .[hyena]` step and keep the existing isolation strategy.
In @.github/workflows/cron.yml:
- Line 189: Update the artifact-install step in the workflow to install the
built package by its package name variable, using the extras all and testing,
instead of installing the current directory. Remove the python -m pip install
.[all,testing] command and the obsolete requirements*.txt copy from this step.
- Line 242: Update the dependency installation steps in the workflow to complete
the pip-only migration: replace both the existing pip install and BUILD_MONAI
setup.py develop commands with BUILD_MONAI=1 python -m pip install -e
.[all,testing].
In @.github/workflows/integration.yml:
- Line 40: Update the container image used by both integration jobs in
.github/workflows/integration.yml at lines 40-40 and 115-115 to the same image
providing Python 3.10 or newer, before the python -m pip install steps; no other
workflow behavior needs to change.
In `@Dockerfile.slim`:
- Around line 49-56: Update the editable install command after the BUILD_MONAI
and FORCE_CUDA environment settings to include pip’s --no-build-isolation
option, matching the established Dockerfile installation pattern and ensuring
extensions build against the preinstalled runtime dependencies.
In `@docs/source/installation.md`:
- Around line 52-58: Update the corresponding packages list in the installation
documentation by adding cucim-cu12 and cucim-cu13 immediately after clearml and
before cupy, preserving the extras list order so cucim has a 1:1 mapping with
its Pip dependencies.
In `@monai/__init__.py`:
- Around line 65-66: Update the __revision_id__ assignment to preserve an absent
full-revisionid as an empty string instead of converting None to "None", while
leaving the existing version fallback unchanged.
In `@monai/config/print_dependencies.py`:
- Around line 29-57: The parse_dependencies function mutates the caller-owned
sections collection via sections.remove and uses a mutable default. Change
sections to default to None, create a local set from the provided sections, and
perform BUILD_SYSTEM_KEY removal and subsequent membership/iteration operations
on that local copy.
In `@pyproject.toml`:
- Around line 72-73: Update the MetricsReloaded dependency entries for both the
all and metrics_reloaded extras to use the same immutable commit reference
instead of the differing mutable branches. Remove the branch-based URLs and
ensure both entries resolve to that identical pinned commit.
---
Nitpick comments:
In `@docs/source/installation.md`:
- Around line 54-56: Add a language identifier to the fenced code block
containing the dependency list in the installation documentation, using an
appropriate plain-text language such as text; leave the dependency contents
unchanged.
In `@monai/_version.py`:
- Around line 47-640: The generated Versioneer definitions lack the required
Google-style variable, return, and exception documentation. Update the
Versioneer template that generates symbols such as get_config, run_command,
git_pieces_from_vcs, render, and get_versions, or add the generated
monai/_version.py path to the documentation exemption; do not hand-edit the
generated file because regeneration will overwrite it.
In `@runtests.sh`:
- Around line 139-146: Update install_deps to quote "$REQ" wherever the
temporary requirements file is passed to pip, and remove the temporary file
after installation completes. Keep the existing dependency-generation and
installation flow unchanged.
🪄 Autofix (Beta)
Fix all unresolved CodeRabbit comments on this PR:
- Push a commit to this branch (recommended)
- Create a new PR with the fixes
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Plan: Pro Plus
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📒 Files selected for processing (27)
.github/workflows/build_docs.yml.github/workflows/cicd_tests.yml.github/workflows/codeql-analysis.yml.github/workflows/cron-ngc-bundle.yml.github/workflows/cron.yml.github/workflows/docker.yml.github/workflows/integration.yml.github/workflows/pythonapp-gpu.yml.github/workflows/pythonapp-hyena-gpu.yml.github/workflows/release.yml.github/workflows/weekly-preview.ymlDockerfileDockerfile.slimdocs/requirements.txtdocs/source/installation.mdenvironment-dev.ymlmonai/__init__.pymonai/_version.pymonai/config/print_dependencies.pypyproject.tomlrequirements-dev.txtrequirements-min.txtrequirements.txtruntests.shsetup.cfgsetup.pyversioneer.py
💤 Files with no reviewable changes (6)
- requirements-dev.txt
- setup.cfg
- .github/workflows/docker.yml
- requirements-min.txt
- requirements.txt
- .github/workflows/release.yml
| python -m pip install -e .[all,hyena,testing] | ||
| # # nvsubquadratic runtime imports need only torch + einops + omegaconf; install | ||
| # # the package itself without its core dependency tree (see job comment above). | ||
| # python -m pip install omegaconf | ||
| # python -m pip install --no-deps 'nvsubquadratic>=0.1.1' | ||
| python -m pip install -e .[hyena] |
There was a problem hiding this comment.
🩺 Stability & Availability | 🟠 Major | ⚡ Quick win
Keep the Hyena dependency install --no-deps.
.[hyena] resolves nvsubquadratic and its Torch constraint, contradicting the job’s stated isolation strategy. Install .[all,testing], then explicitly install omegaconf and nvsubquadratic with --no-deps; remove the second editable install.
🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
In @.github/workflows/cicd_tests.yml around lines 277 - 282, Update the
dependency installation steps in the workflow to install only `.[all,testing]`,
then explicitly install `omegaconf` and `nvsubquadratic>=0.1.1` with
`--no-deps`. Remove the separate `python -m pip install -e .[hyena]` step and
keep the existing isolation strategy.
| python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))" | ||
|
|
||
| python -m pip install -r requirements-dev.txt | ||
| python -m pip install .[all,testing] |
There was a problem hiding this comment.
🩺 Stability & Availability | 🟠 Major | ⚡ Quick win
Do not install . from the artifact directory.
At this point $tmp_dir contains the sdist and tests, not pyproject.toml or setup.py, so this fails. Install "${name}[all,testing]" at the artifact-install step and remove this command and the obsolete requirements*.txt copy.
🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
In @.github/workflows/cron.yml at line 189, Update the artifact-install step in
the workflow to install the built package by its package name variable, using
the extras all and testing, instead of installing the current directory. Remove
the python -m pip install .[all,testing] command and the obsolete
requirements*.txt copy from this step.
| which python | ||
| python -m pip install --upgrade pip wheel | ||
| python -m pip install -r requirements-dev.txt | ||
| python -m pip install .[all,testing] |
There was a problem hiding this comment.
📐 Maintainability & Code Quality | 🟠 Major | ⚡ Quick win
🧩 Analysis chain
🏁 Script executed:
#!/bin/bash
set -euo pipefail
echo "== workflow matching files =="
fd -a 'cron\.yml$|cron\.yaml$' .github/workflows 2>/dev/null || true
echo "== target lines =="
if [ -f .github/workflows/cron.yml ]; then
nl -ba .github/workflows/cron.yml | sed -n '228,250p'
fi
echo "== pip install / setup.py occurrences =="
rg -n "pip install|setup\.py develop|\[all,testing\]|BUILD_MONAI" .github/workflows/cron.yml .github/workflows 2>/dev/null || true
echo "== repository references to install commands =="
rg -n "pip install.*\[all,testing\]|setup\.py develop|BUILD_MONAI|editable|develop" .github workflows setup.py pyproject.toml 2>/dev/null | head -120 || trueRepository: Project-MONAI/MONAI
Length of output: 292
🏁 Script executed:
#!/bin/bash
set -euo pipefail
echo "== target lines =="
awk 'NR>=228 && NR<=252 { printf "%s\t%s\n", NR, $0 }' .github/workflows/cron.yml
echo "== install-related occurrences in cron workflow =="
awk '
/pip install|setup\.py develop|\[all,testing\]|BUILD_MONAI|develop|editable|editable_install/ {
printf "%s\t%s\n", NR, $0
}
' .github/workflows/cron.yml
echo "== repository installs mentioning all/testing/build_monai/develop =="
git grep -n "pip install.*\[all,testing\]\|setup\.py develop\|BUILD_MONAI\|\[all,testing\]\|\[testing\]" .github setup.py pyproject.toml README.md 2>/dev/null | head -200 || trueRepository: Project-MONAI/MONAI
Length of output: 7270
Finish the pip-only migration.
Line 243 still runs BUILD_MONAI=1 python setup.py develop. Replace both install commands with BUILD_MONAI=1 python -m pip install -e .[all,testing].
🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
In @.github/workflows/cron.yml at line 242, Update the dependency installation
steps in the workflow to complete the pip-only migration: replace both the
existing pip install and BUILD_MONAI setup.py develop commands with
BUILD_MONAI=1 python -m pip install -e .[all,testing].
| pip uninstall -y monai-weekly | ||
| python -m pip install --upgrade torch torchvision torchaudio torchtext | ||
| python -m pip install -r requirements-dev.txt | ||
| python -m pip install .[all,testing] |
There was a problem hiding this comment.
🩺 Stability & Availability | 🟠 Major | ⚡ Quick win
Use a Python 3.10+ integration image. Both jobs run nvcr.io/nvidia/pytorch:22.04-py3 (Python 3.8), while pyproject.toml requires Python >=3.10; pip will reject these installs.
.github/workflows/integration.yml#L40-L40: update the container to a Python 3.10+ image before installing extras..github/workflows/integration.yml#L115-L115: update the container to the same compatible Python version.
📍 Affects 1 file
.github/workflows/integration.yml#L40-L40(this comment).github/workflows/integration.yml#L115-L115
🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
In @.github/workflows/integration.yml at line 40, Update the container image
used by both integration jobs in .github/workflows/integration.yml at lines
40-40 and 115-115 to the same image providing Python 3.10 or newer, before the
python -m pip install steps; no other workflow behavior needs to change.
| # TODO: remark for issue [revise the dockerfile #1276](https://github.com/Project-MONAI/MONAI/issues/1276) | ||
| # please specify exact files and folders to be copied -- else, basically always, the Docker build process cannot cache | ||
| # this or anything below it and always will build from at most here; one file change leads to no caching from here on... | ||
| COPY LICENSE CHANGELOG.md CODE_OF_CONDUCT.md CONTRIBUTING.md README.md versioneer.py setup.py pyproject.toml runtests.sh MANIFEST.in ./ | ||
| COPY tests ./tests | ||
| COPY monai ./monai | ||
|
|
||
| # install full deps | ||
| RUN python -m pip install --no-cache-dir --no-build-isolation -U wheel wheel-stub | ||
| RUN python -m pip install --no-cache-dir --no-build-isolation "torch>=2.8.0,<2.11" -r requirements-dev.txt | ||
|
|
||
| # compile ext | ||
| RUN CUDA_HOME=/usr/local/cuda FORCE_CUDA=1 USE_COMPILED=1 BUILD_MONAI=1 python setup.py develop | ||
| RUN BUILD_MONAI=1 FORCE_CUDA=1 pip install --no-cache-dir -e .[all,testing] |
There was a problem hiding this comment.
🩺 Stability & Availability | 🟠 Major | ⚡ Quick win
Missing --no-build-isolation risks ABI-mismatched compiled extensions.
Unlike Dockerfile (which pre-installs build-system deps and uses --no-build-isolation), this editable install with BUILD_MONAI=1 uses pip's default build isolation. Per this PR's own new warning in docs/source/installation.md, build isolation may resolve a different PyTorch than the one that ends up installed at runtime, producing a compiled extension that's ABI-incompatible and won't load. Apply the same pattern as Dockerfile.
🔧 Proposed fix mirroring Dockerfile's approach
-RUN BUILD_MONAI=1 FORCE_CUDA=1 pip install --no-cache-dir -e .[all,testing]
+RUN python monai/config/print_dependencies.py build-system | xargs pip install --no-cache-dir --no-build-isolation \
+ && BUILD_MONAI=1 FORCE_CUDA=1 pip install --no-cache-dir --no-build-isolation -e .[all,testing]📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| # TODO: remark for issue [revise the dockerfile #1276](https://github.com/Project-MONAI/MONAI/issues/1276) | |
| # please specify exact files and folders to be copied -- else, basically always, the Docker build process cannot cache | |
| # this or anything below it and always will build from at most here; one file change leads to no caching from here on... | |
| COPY LICENSE CHANGELOG.md CODE_OF_CONDUCT.md CONTRIBUTING.md README.md versioneer.py setup.py pyproject.toml runtests.sh MANIFEST.in ./ | |
| COPY tests ./tests | |
| COPY monai ./monai | |
| # install full deps | |
| RUN python -m pip install --no-cache-dir --no-build-isolation -U wheel wheel-stub | |
| RUN python -m pip install --no-cache-dir --no-build-isolation "torch>=2.8.0,<2.11" -r requirements-dev.txt | |
| # compile ext | |
| RUN CUDA_HOME=/usr/local/cuda FORCE_CUDA=1 USE_COMPILED=1 BUILD_MONAI=1 python setup.py develop | |
| RUN BUILD_MONAI=1 FORCE_CUDA=1 pip install --no-cache-dir -e .[all,testing] | |
| # TODO: remark for issue [revise the dockerfile `#1276`](https://github.com/Project-MONAI/MONAI/issues/1276) | |
| # please specify exact files and folders to be copied -- else, basically always, the Docker build process cannot cache | |
| # this or anything below it and always will build from at most here; one file change leads to no caching from here on... | |
| COPY LICENSE CHANGELOG.md CODE_OF_CONDUCT.md CONTRIBUTING.md README.md versioneer.py setup.py pyproject.toml runtests.sh MANIFEST.in ./ | |
| COPY tests ./tests | |
| COPY monai ./monai | |
| RUN python monai/config/print_dependencies.py build-system | xargs pip install --no-cache-dir --no-build-isolation \ | |
| && BUILD_MONAI=1 FORCE_CUDA=1 pip install --no-cache-dir --no-build-isolation -e .[all,testing] |
🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
In `@Dockerfile.slim` around lines 49 - 56, Update the editable install command
after the BUILD_MONAI and FORCE_CUDA environment settings to include pip’s
--no-build-isolation option, matching the established Dockerfile installation
pattern and ensuring extensions build against the preinstalled runtime
dependencies.
| MONAI supports the extras syntax such as `pip install 'monai[nibabel]'`. The options are | ||
|
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||
| ``` | ||
| clearml, cucim, cupy, einops, fire, gdown, h5py, huggingface_hub, hyena, ignite, imagecodecs, itk, jsonschema, lmdb, lpips, matplotlib, mccabe, metrics_reloaded, mlflow, mypy, nibabel, nni, onnx, openslide, optuna, pandas, pillow, polygraphy, psutil, pyamg, pybind11, pydicom, pynrrd, pytest, pynvml, pyyaml, requests, segment_anything, scipy, skimage, tensorboard, tensorboardX, tifffile, torchio, torchvision, tqdm, transformers, zarr | ||
| ``` | ||
|
|
||
| which correspond to the packages: `clearml`, `cupy`, `einops`, `fire`, `gdown`, `h5py`, `huggingface_hub`, `nvsubquadratic`, `omegaconf`, `pytorch-ignite`, `imagecodecs`, `itk`, `jsonschema`, `lmdb`, `lpips`, `matplotlib`, `mccabe`, `MetricsReloaded`, `mlflow`, `mypy`, `nibabel`, `nni`, `filelock`, `onnx`, `onnxruntime`, `onnx_graphsurgeon`, `onnxscript`, `openslide-python`, `openslide-bin`, `optuna`, `pandas`, `pillow`, `polygraphy`, `psutil`, `pyamg`, `pybind11`, `pydicom`, `pynrrd`, `pytest`, `nvidia-ml-py`, `pyyaml`, `requests`, `segment_anything`, `scipy`, `scikit-image`, `tensorboard`, `tensorboardX`, `tifffile`, `torchio`, `torchvision`, `tqdm`, `transformers`, `zarr`. |
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📐 Maintainability & Code Quality | 🟡 Minor | ⚡ Quick win
🧩 Analysis chain
🏁 Script executed:
#!/bin/bash
set -euo pipefail
echo "== file exists and relevant section =="
if [ -f docs/source/installation.md ]; then
sed -n '45,65p' docs/source/installation.md | cat -n -v
else
echo "docs/source/installation.md not found"
fi
echo
echo "== search for cucim in repo =="
rg -n "\bcucim\b|clearml|cupy|openslide-python|pip install" docs/source/installation.md setup.py setup.cfg pyproject.toml 2>/dev/null || true
echo
echo "== deterministic list comparison for sections around lines 54-58 =="
python3 - <<'PY'
from pathlib import Path
import re
p = Path("docs/source/installation.md")
if not p.exists():
print("source missing")
raise SystemExit(0)
text = p.read_text()
m = re.search(r"```(?P<l>\w*)\n(?P<body>.*?)\n```", text)
if not m:
print("no fenced block found")
raise SystemExit(0)
print("fence language:", repr(m.group("l")))
block = m.group("body").strip().splitlines()
print("extras block lines:", len(block))
matches = [re.sub(r"[,\s]+", " ", line).split() for line in block if line.strip()]
extras = [x for entry in matches for x in entry]
next_sentence = []
for line in text[m.end():].splitlines():
if line.strip():
next_sentence.append(line)
break
print("next sentence:", next_sentence)
all_text = "\n".join(matches[-6:])
# take comma-separated package names while preserving dashes/underscores, and strip package names from quotes if any.
pkgs = re.findall(r"(?:^|,\s*|:\s*|)`?([A-Za-z0-9_\-\.]+)`?", "\n".join(matches))
pkgs_normalized = []
for pkg in pkgs:
# Strip quote-surrounded entries if any
pkg = pkg.strip("'`").strip()
if pkg:
pkgs_normalized.append(pkg)
print("extras:", "\n".join(f"{i}: {e}" for i,e in enumerate(extras)))
print("packages:", "\n".join(f"{i}: {pe}" for i,pe in enumerate(pkgs_normalized)))
print("counts:", len(extras), len(pkgs_normalized))
print("same extras==packages?", extras == pkgs_normalized)
for i, (e, pe) in enumerate(zip(extras, pkgs_normalized)):
if e != pe:
print("first mismatch:", i, repr(e), repr(pe))
PYRepository: Project-MONAI/MONAI
Length of output: 6440
🌐 Web query:
MONAI installation documentation cucumber cucim extras pip install cucim correspondence list
💡 Result:
In the MONAI ecosystem, the cucim extra is a dependency option that facilitates GPU-accelerated image processing [1][2]. ### Installation and Correspondence When installing MONAI via pip, you can include cucim as an optional dependency using the extras syntax [1][3]. For example: pip install 'monai[cucim]' This command specifically triggers the installation of the corresponding cucim packages [2]. According to the project's configuration, the cucim extra maps to cucim-cu12 (for Python versions 3.9–3.10) or cucim-cu13 (for Python 3.11 and newer) on Linux platforms [2]. ### Important Compatibility Notes * Platform Limitation: The cucim packages currently provided through MONAI's extras are primarily intended for Linux environments [2]. Users on Windows may encounter errors if they attempt to install the all extras bundle—which includes cucim—because cucim does not currently provide native Windows wheels [4]. * Scope: Including cucim via pip install 'monai[cucim]' provides the necessary libraries to enable specific GPU-accelerated features within MONAI, such as those found in cucim.skimage [5][6]. * Full Installation: If you wish to install all optional dependencies, including cucim, you can use pip install 'monai[all]' [1][7]. However, users on unsupported platforms (like Windows) should install dependencies selectively to avoid dependency resolution or wheel availability issues [4].
Citations:
- 1: https://monai.readthedocs.io/en/stable/installation.html
- 2: https://github.com/Project-MONAI/MONAI/blob/dev/setup.cfg
- 3: https://monai.readthedocs.io/en/1.5.1/installation.html
- 4: pip install monai[all] -> cucim error #8258
- 5: https://pypi.org/project/cucim/
- 6: Documentation is not entirely clear about CUDA/
cupyinstallation requirements #8106 - 7: https://monai.readthedocs.io/en/1.4.0/installation.html
Align the extras and corresponding packages list for the cucim entry.
docs/source/installation.md:55 lists cucim, but line 58 jumps from clearml to cupy, so packages after cupy no longer match their extras. For cucim, the corresponding Pip dependencies are cucim-cu12 and cucim-cu13; add those to the package list before cupy to keep the 1:1 mapping accurate.
🧰 Tools
🪛 markdownlint-cli2 (0.23.0)
[warning] 54-54: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
In `@docs/source/installation.md` around lines 52 - 58, Update the corresponding
packages list in the installation documentation by adding cucim-cu12 and
cucim-cu13 immediately after clearml and before cupy, preserving the extras list
order so cucim has a 1:1 mapping with its Pip dependencies.
Source: Path instructions
| def parse_dependencies(filename=TOML_FILE, sections=[]): | ||
| # these imports should be here to avoid attempting to import when MONAI is imported and both packages are missing | ||
| if sys.version_info.minor >= 11: | ||
| import tomllib | ||
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| load_func = tomllib.loads | ||
| else: | ||
| import tomli | ||
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| load_func = tomli.loads | ||
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| with open(filename) as o: | ||
| data = load_func(o.read()) | ||
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| proj = data[PROJ_KEY] | ||
| opts = proj[OPTS_KEY] | ||
| dependencies = list(proj[DEP_KEY]) | ||
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| if BUILD_SYSTEM_KEY in sections: | ||
| sections.remove(BUILD_SYSTEM_KEY) | ||
| dependencies += data[BUILD_SYSTEM_KEY][REQ_KEY] | ||
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| if "*" in sections: | ||
| dependencies += sum(opts.values(), []) | ||
| else: | ||
| for s in sections: | ||
| dependencies += opts[s] | ||
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| return sorted(set(dependencies)) |
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🎯 Functional Correctness | 🟡 Minor | ⚡ Quick win
Do not mutate a default/caller-owned collection.
sections.remove() changes the passed collection. Default to None and copy into a local set.
🧰 Tools
🪛 ast-grep (0.44.1)
[warning] 39-39: File path is request-/variable-derived; validate and normalize to prevent path traversal.
Context: open(filename)
Note: [CWE-22] Improper Limitation of a Pathname to a Restricted Directory ('Path Traversal').
(open-filename-from-request)
🪛 Ruff (0.15.21)
[warning] 29-29: Do not use mutable data structures for argument defaults
Replace with None; initialize within function
(B006)
[warning] 52-52: Avoid quadratic list summation
Replace with functools.reduce
(RUF017)
🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
In `@monai/config/print_dependencies.py` around lines 29 - 57, The
parse_dependencies function mutates the caller-owned sections collection via
sections.remove and uses a mutable default. Change sections to default to None,
create a local set from the provided sections, and perform BUILD_SYSTEM_KEY
removal and subsequent membership/iteration operations on that local copy.
Source: Linters/SAST tools
| # TODO: change URL to https://github.com/Project-MONAI/MetricsReloaded@monai-support before finalising | ||
| "MetricsReloaded @ git+https://github.com/ericspod/MetricsReloaded@monai-support-fix", |
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🔒 Security & Privacy | 🟠 Major | ⚡ Quick win
Pin and unify MetricsReloaded.
all uses monai-support-fix, while metrics_reloaded uses monai-support; both are mutable branches. Use one immutable commit reference in both extras.
🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
In `@pyproject.toml` around lines 72 - 73, Update the MetricsReloaded dependency
entries for both the all and metrics_reloaded extras to use the same immutable
commit reference instead of the differing mutable branches. Remove the
branch-based URLs and ensure both entries resolve to that identical pinned
commit.
1 participant
Fixes #8980.
Description
This updates the way MONAI is built to be more modern, relying on
pipfor everything with all information consolidated into thepyproject.tomlfile. This is still in progress and requires more testing, and needs to be double checked that the optional dependencies are correct. Highlights:pyproject.toml.setup.cfgfile.Types of changes
./runtests.sh -f -u --net --coverage../runtests.sh --quick --unittests --disttests.make htmlcommand in thedocs/folder.