VS Build tools required to install

[andreped]

This is probably more of a feature request than a bug.

Whenever I wish to install this solution on Windows it requires that I have VS build tools installed as it seems like it needs to build maxflow. This becomes a challenge as some of the users of a software I am using find it challenging to install this.

What I was thinking is why this is not just built on the cloud, for instance using GitHub Actions, and then when installing you are just catching the pre-built wheel and using that to install. I guess this would be of interest to the MONAI-Label team (@diazandr3s) as well.

I can assist in setting up the Actions workflow and submit a PR, if that would be of interest.

I could attempt to setup builds for the operating systems: Windows, macOSX, and Ubuntu Linux.

Shall I make a try?

[diazandr3s]

Hi @andreped,

Thanks for pinging me. I think this will be great.
Recently, a Windows user (@ralkalay) trying to install MONAI Label on his computer had a VS-related problem. See this issue: Project-MONAI/MONAILabel#363

I'm sure @masadcv and @SachidanandAlle can provide more information about the use of simpleCRF in MONAI Label.

[masadcv]

Thanks @diazandr3s for tagging me here.
Currently SimpleCRF is used for scribbles-based methods within MONAI Label.

As @andreped mentioned, SimpleCRF requires compiling, i.e. pip install simplecrf compiles the code during installation. This is only needed once, and is just like any other pip installation you would do. The problem with Windows is that it requires installation of VS build tools to compile as Windows does not come with these pre-installed, where the error message points to the link for downloading and installing the tools (see Project-MONAI/MONAILabel#363 (comment)).

It would be good to have pre-compiled binaries for this if possible, however I am unsure how much work this would be as compilation is required for all systems and for each python version. Some functions depend on numpy for compilation – I am unsure how this can be handled to make pre-compiled binaries that work across platforms but also with different versions of numpy.

Lets wait for someone from HiLab to comment on this.

cc: @taigw

[andreped]

@masadcv I will make an attempt and we will see how easy it is :P Will let you know when the workflow from making pre-compiled binaries is running and I can make a PR and we can co-develop from there?

I can setup builds for various Python versions. However, from the setup.py, I see that there is no limitations on Python version used. Is that so? Have you tested installing SimpleCRF on different versions?

[andreped]

I have gotten quite far. What remains is setting up such that python limited api is used and creating a wheel for each operating system. However, I see that classifiers and python_requires in setup.py are contradicting.

Do you only support Python 3.6 and above, or do you want to support Python 2 as well? See here. If only Python >=3.6, then it is easy.

See my fork for my proposed workflow:
https://github.com/andreped/SimpleCRF/tree/workflow/.github/workflows

It is still a work in progress, but at least the wheels are produced. As the software include C++ code, I will have to make a wheel for each operating system. I can set that up now.

[SachidanandAlle]

We don't want to go back.. we don't want to worry about python 2.x

[andreped]

We don't want to go back.. we don't want to worry about python 2.x

Understandable. Will let you know when I have the wheels ready for you to test.

Also, I played a lot around with getting the demos to run on the cloud, but it failed on Windows and macOS. On the latter it failed due to some graphics-related issue, which makes sense as I believe it runs headless? Also OpenGL is not supported on macOS any longer, so it complained about that as well. For Windows it froze on plt.show(). Perhaps having a simple way to neglect that if not possible would be better. I tested the maxflow demo.

[andreped]

Forward-compatible python wheels with abi3 for windows, ubuntu, and macos are now being created:
https://github.com/andreped/SimpleCRF/actions

These wheels are compatible with Python >=3.6 as discussed.

It is also possible to push these directly to PyPI in the workflow. However, AFAIK this would require permissions to your PyPI repo which I doubt I have nor need. A separate workflow to release could be a good idea, for instance to only make the release when a new tag is made.

Feel free to test the workflow and produced binaries on different operating systems, different python versions, and different setups. Or even better, make unit tests which can be deployed as workflows instead.

The final part has to be done by the developing team, and then I guess the MONAI-Label team and @diazandr3s could test if the new pre-compiled binaries can be used directly when installing through pip. Especially relevant for windows which previously required VS and Visual C++ build tools to be able to install SimpleCRF.

[SachidanandAlle]

@masadcv can we try and test the precompiled version of crf.. this will bring more convenience for MONAILabel users while installing the package

[andreped]

@masadcv can we try and test the precompiled version of crf.. this will bring more convenience for MONAILabel users while installing the package

Definitely. With GitHub Actions these are compiled on the fly and made available as artifacts. For instance for ubuntu, see here, under Artifacts there should be a file called "Python wheel". Download and extract and you should have the python wheel. Similar wheels are produced for all operating systems - see here to access wheels for different builds.

---

EDIT: Might seem like there is a minor DLL issue. When testing on my personal, local windows desktop, I got ImportError: DLL load filed while importing denseCRF. Might be that there is something missing in the setup.py? Any ideas?

[masadcv]

@SachidanandAlle sure, I will do some tests locally. I only have access to Ubuntu machine at the moment. Can someone help verify Windows and Mac OS MONAI Label setups for this? In the meantime I will try to find a Windows machine to verify this.

Nice work @andreped !! What's the best way to access the compiled wheels? Would something like pip install git+https://github.com/andreped/SimpleCRF work for this? Or do I need to manually download them?
In the long- term, it would be good to release these as PyPI packages so we won't need changes on MONAI Label side...

[andreped]

You cannot do the proposed "pip install" solution as this will not download the binaries, but rather run the setup.py install as you previously did for SimpleCRF, and then we are back to square one.

I can publish the binaries as releases on my fork and you can access them there if you'd like. Otherwise, the binaries are found as Artifacts for each build. Currently, there seems to be a bug, so no point publishing as a release just yet.

When the solution is working as it should, the ideal solution would be to put these in the releases on PyPI, but as of now, we should verify that this actually works first :]

[ralkalay]

Hi, so I am not a technical programmer. I did install Microsoft C++2015-2019 and Visual studio installer. Not sure what I need to do. I have with Andres through teams in which we shared the workstation screen to help me set it up. I wonder if this could be a way to help me set up the system. The only thing is that I don't have a camera and a mike on the workstation, so I talked to Andres via the laptop. Alternatively, if you don't mind let me know what should I install in preparation or to be able to work with Andres to solve this thanks Ron

…

On Mon, Jan 31, 2022 at 8:25 PM Andres Diaz-Pinto ***@***.***> wrote: Hi @andreped <https://github.com/andreped>, Thanks for pinging me. I think this will be great. Recently, a Windows user ***@***.*** <https://github.com/ralkalay>) trying to install MONAI Label on his computer had a VS-related problem. See this issue: Project-MONAI/MONAILabel#363 <Project-MONAI/MONAILabel#363> I'm sure @masadcv <https://github.com/masadcv> and @SachidanandAlle <https://github.com/SachidanandAlle> can provide more information about the use of simpleCRF in MONAI Label. — Reply to this email directly, view it on GitHub <#7 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALXEEN5OAZY4Q7DZMQBOEVDUY4Y6ZANCNFSM5NGANCVQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[andreped]

@ralkalay the whole idea with this solution is that you should not need VS and C++ build tools to use SimpleCRF and AFAIK MONAI-Label for that manner. Simply pip install SimpleCRF and pip install monailabel

Are there any other reasons why VS and C++ build tools would be needed for just using the binary of MONAI-Label, @diazandr3s ? I am not talking about building anything just using the plugin with slicer.

[ralkalay]

Andres and I were installing via pip install -r requirements.txt should I do it differently? thanks

On Tue, Feb 1, 2022 at 10:27 AM André Pedersen ***@***.***> wrote: @ralkalay <https://github.com/ralkalay> the whole idea with this solution is that you should not need VS and C++ build tools to use SimpleCRF and AFAIK MONAI-Label for that manner. Simply pip install SimpleCRF and pip install monailabel Are there any other reasons why VS and C++ build tools would be needed for just using the binary of MONAI-Label, @diazandr3s <https://github.com/diazandr3s> ? I am not talking about building anything just using the plugin with slicer. — Reply to this email directly, view it on GitHub <#7 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALXEEN5FLEIIHLB7NOBHR4TUY73VLANCNFSM5NGANCVQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you were mentioned.Message ID: ***@***.***>

aiofiles==0.6.0 fastapi==0.65.2 monai[nibabel, skimage, pillow, tensorboard, gdown, ignite, torchvision, itk, tqdm, lmdb, psutil, openslide]==0.8.* pyyaml==5.4.1 python-multipart==0.0.5 requests-toolbelt==0.9.1 uvicorn==0.13.4 watchdog==2.0.2 pydantic==1.8.2 python-dotenv==0.17.1 filelock==3.0.12 httpx==0.18.2 dicomweb-client==0.52.0 pydicom==2.1.2 pydicom-seg==0.2.3 pynetdicom==1.5.7 expiringdict==1.2.1 schedule==1.1.0 timeloop==1.0.2 simplecrf==0.2.1.1 einops==0.3.2