Do not depends on unused libraries for libtiff

[gigony]

Libraries such as jbig, libwebp-base, and zlib are not used for the functionality of cuCIM.
These codec libraries are linked to libtiff only when available at build time.

This patch explicitly disables external codecs and removes unnecessary dependencies from the dependencies.yaml.

With this patch, I can confirm that they are not requested at all.

--  Support for external codecs:
--   ZLIB support:                       OFF (requested)  (availability)
--   Pixar log-format algorithm:         OFF (requested) FALSE (availability)
--   JPEG support:                       OFF (requested) TRUE (availability)
--   Old JPEG support:                   OFF (requested) TRUE (availability)
--   JPEG 8/12 bit dual mode:            OFF (requested) FALSE (availability)
--   ISO JBIG support:                   OFF (requested) FALSE (availability)
--   LZMA2 support:                      OFF (requested)  (availability)
--   ZSTD support:                       OFF (requested)  (availability)
--   WEBP support:                       OFF (requested) FALSE (availability)

[jakirkham]

Thanks Gigon! 🙏

Can we please drop these as well?

cucim/conda/recipes/libcucim/meta.yaml

Lines 77 to 78 in 6e3fd31

	- jbig
	- libwebp-base

cucim/conda/recipes/libcucim/meta.yaml

Lines 95 to 98 in 6e3fd31

	- jbig
	- xz
	- zlib
	- zstd

cucim/conda/recipes/libcucim/meta.yaml

Lines 81 to 83 in 6e3fd31

	- xz
	- zlib
	- zstd

[gigony]

Thanks Gigon! 🙏

Can we please drop these as well?

cucim/conda/recipes/libcucim/meta.yaml

Lines 77 to 78 in 6e3fd31

	- jbig
	- libwebp-base

cucim/conda/recipes/libcucim/meta.yaml

Lines 95 to 98 in 6e3fd31

	- jbig
	- xz
	- zlib
	- zstd

cucim/conda/recipes/libcucim/meta.yaml

Lines 81 to 83 in 6e3fd31

	- xz
	- zlib
	- zstd

Thanks @jakirkham!
I missed those. Appreciate the reminder!

[jakirkham]

As we dropped libwebp-base above, this can also be dropped

Suggested change

- {{ pin_compatible('libwebp-base', max_pin='x.x') }}

[gigony]

Thanks @jakirkham !
Also removed the other line containing libwebp-base in the same file.

[jakirkham]

Thanks Gigon! 🙏

Are we able to use the Conda libtiff package? If so, we could drop this build step altogether (simplifying this further)

[jameslamb]

I found one reference in docs that should be updated (xz and zlib should be removed from it):

cucim/CONTRIBUTING.md

Line 126 in 6e3fd31

Otherwise, you may need to install dependencies (such as zlib, xz, yasm) through your OS's package manager (`apt`, `yum`, and so on).

Otherwise, this looks good to me!

I won't merge this until you and @jakirkham come to some agreement on whether to go further and directly depend on conda-forge's libtiff (#785 (comment)). My perspective on that... it should be documented in an issue as a potential follow-up and not done here. I expect it'd take some fairly-involved design work to answer questions like:

• what is the ongoing amount of effort to require the source build of libtiff?
• how do wheels get their libtiff dependency?
• does the set of codecs supported by the conda-forge package include everything cucim needs? Are we ok with it pulling in more, unnecessary things (for example, it does depend on libwebp, xz, and zstd)

[jakirkham]

@jameslamb could you please take another look? 🙂

[jakirkham]

Are we able to use the Conda libtiff package? If so, we could drop this build step altogether (simplifying this further)

Discussed this point with Gigon earlier, we decided to leave this task for PR ( #753 ), which is already doing that work

[gigony]

I found one reference in docs that should be updated (xz and zlib should be removed from it):

cucim/CONTRIBUTING.md

Line 126 in 6e3fd31

Otherwise, you may need to install dependencies (such as zlib, xz, yasm) through your OS's package manager (`apt`, `yum`, and so on).

Otherwise, this looks good to me!

I won't merge this until you and @jakirkham come to some agreement on whether to go further and directly depend on conda-forge's libtiff (#785 (comment)). My perspective on that... it should be documented in an issue as a potential follow-up and not done here. I expect it'd take some fairly-involved design work to answer questions like:

• what is the ongoing amount of effort to require the source build of libtiff?
• how do wheels get their libtiff dependency?
• does the set of codecs supported by the conda-forge package include everything cucim needs? Are we ok with it pulling in more, unnecessary things (for example, it does depend on libwebp, xz, and zstd)

Thanks @jameslamb for your thoughtful comments!

Removed the wording 'xz' and 'zlib' in CONTRIBUTING.md file.

Regarding 'directly depend on conda-forge's libtiff, there is one-going work for Devendering CMake dependencies (#686, #753)

• Devendor CMake dependencies #686
• De-vendor CMake dependencies and use shared libraries #753

• what is the ongoing amount of effort to require the source build of libtiff?

I will continue working on it to use conda-forge's libraries, including libtiff.

• how do wheels get their libtiff dependency?

In the current implementation, the source code of libtiff is built as a static library and linked to cucim.kit.cuslide@24.xx.00.so, so no additional third-party library dependencies are required from the shared library in the Python wheel.

• does the set of codecs supported by the conda-forge package include everything cuCIM needs? Are we ok with it pulling in more, unnecessary things (for example, it does depend on libwebp, xz, and zstd)

I'm not entirely sure about that.
I can see that conda-forge's libtiff package (https://anaconda.org/conda-forge/libtiff/files) includes a static library (libtiff.a).
I may end up static linking all the dependent static libraries (https://github.com/conda-forge/libtiff-feedstock/blob/main/recipe/meta.yaml#L39C3-L46C37), or vendoring those dependent libraries in the wheel file, which might increase the size of the wheel.

Let me consider those aspects as I continue to work on #753.

Thanks!

[jameslamb]

Re-reviewed, this looks good to me and I supported merging it. Thanks for considering my questions about libtiff, I'm glad that won't be part of the scope for this PR.

[jakirkham]

/merge

[jakirkham]

Thanks Gigon and James! 🙏