[python] Do not copy `libtiledbsoma.so` into `package_data` if it already exists #1937

nguyenv · 2023-11-30T21:14:30Z

Issue and/or context:

The copying issue was reported in internal channel by @jdblischak: https://tiledb.slack.com/archives/C052CFC4D2Q/p1700678097748879
This PR also includes a fix for [python] pip install directly from GitHub not working #1991

Changes:

TileDB Exists	TileDB SOMA Exists	Action
No	No	Both TileDB and TileDB-SOMA get copied
No	Yes	Error: The TileDB shared object that is linked to TileDB-SOMA shared object needs to exist somewhere
Yes	No	Copy TileDB-SOMA only
Yes	Yes	No copies

codecov-commenter · 2023-12-01T00:55:35Z

Codecov Report

Merging #1937 (453d03b) into main (3f021c4) will decrease coverage by 5.08%.
Report is 17 commits behind head on main.
The diff coverage is n/a.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1937      +/-   ##
==========================================
- Coverage   76.84%   71.77%   -5.08%     
==========================================
  Files         136      101      -35     
  Lines       10689     6926    -3763     
  Branches      207      211       +4     
==========================================
- Hits         8214     4971    -3243     
+ Misses       2375     1853     -522     
- Partials      100      102       +2

Flag	Coverage Δ
libtiledbsoma	`66.97% <ø> (-1.25%)`	⬇️
python	`?`
r	`74.62% <ø> (+4.64%)`	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Components	Coverage Δ
python_api	`∅ <ø> (∅)`
libtiledbsoma	`48.27% <ø> (-3.29%)`	⬇️

jdblischak · 2023-12-01T16:04:26Z

I tested to confirm that the libtiledbsoma.so is still copied into the wheel when it is built as part of the package build:

git clone https://github.com/single-cell-data/TileDB-SOMA.git test-soma-copying
cd test-soma-copying
git checkout viviannguyen/do-not-cp-in-edit-mode
python -m venv ./venv-soma
source ./venv-soma/bin/activate
pip install --prefer-binary tiledb wheel
## tiledb-0.24.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
pip install --prefer-binary apis/python/requirements_dev.txt
python -c "import tiledb; print(tiledb.version())"
## (0, 24, 0)
python -c "import tiledb; print(tiledb.libtiledb.version())"
## (2, 18, 2)
cd apis/python/
python setup.py bdist_wheel
unzip -l dist/tiledbsoma-1.5.0rc0.post82.dev2249632267-cp310-cp310-linux_x86_64.whl | grep '\.so'
##  1417912  2023-12-01 15:32   tiledbsoma/libtiledbsoma.so
##   839072  2023-12-01 15:32   tiledbsoma/pytiledbsoma.cpython-310-x86_64-linux-gnu.so
ldd build/lib.linux-x86_64-cpython-310/tiledbsoma/libtiledbsoma.so | grep libtiledb
##        libtiledb.so.2.18 => /home/jdblischak/test-soma-copying/dist/lib/libtiledb.so.2.18 (0x00007fdad1642000)

Note however that libtiledb.so wasn't copied into the wheel. Maybe because I ran pip install tiledb beforehand? The PyPI wheel vendors both libtiledb.so and libtiledbsoma.so

wget https://files.pythonhosted.org/packages/6e/2b/22cbf22a6e24d1b876ddea3bae6ef730ce97a6c38ddf017b6040436f7594/tiledbsoma-1.5.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
unzip -l tiledbsoma-1.5.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl | grep '\.so'
## 42973497  2023-11-13 15:17   tiledbsoma.libs/libtiledb-9844ae44.so.2.17
##  2089017  2023-11-13 15:17   tiledbsoma.libs/libtiledbsoma-a235b3e5.so
##   785249  2023-11-13 15:17   tiledbsoma/pytiledbsoma.cpython-310-x86_64-linux-gnu.so
##  1909369  2023-11-13 15:17   tiledbsoma/libtiledbsoma.so

Please let me know if I need to investigate further. For now, I've confirmed that libtiledbsoma.so isn't copied into the package when it already exists when I run pip install -e, and it is copied into the package when it is built during the Python package to create a wheel. There are various other permutations I could test if needed (eg build a wheel against an existing shared object, pip install without an existing shared object)

nguyenv · 2023-12-04T14:28:58Z

I tested with pip install -e and pip install with and without an existing shared object, and it looked ok to me, but please double check my work!

jdblischak · 2023-12-04T20:15:28Z

I checked the various installation methods with and without an external libtiledbsoma.so. This PR is working as expected. When an existing libtiledbsoma.so is used, it is no longer copied into the Python package structure. My test code below:

mkdir -p /tmp/test-soma-copy
cd /tmp/test-soma-copy

# install python dependencies
python -m venv ./venv-soma
conda deactivate
source ./venv-soma/bin/activate
pip install --prefer-binary cmake pybind11-global typeguard sparse wheel

# `pip install` copies libtiledbsoma.so
git clone https://github.com/single-cell-data/TileDB-SOMA.git pip-install
cd pip-install
git checkout viviannguyen/do-not-cp-in-edit-mode
cd apis/python
pip install .
find $VIRTUAL_ENV -name 'libtiledbsoma.so'
## /tmp/test-soma-copy/venv-soma/lib/python3.10/site-packages/tiledbsoma/libtiledbsoma.so
find $VIRTUAL_ENV -name 'libtiledbsoma.so' | xargs ldd | grep libtiledb
## libtiledb.so.2.18 => /tmp/test-soma-copy/pip-install/dist/lib/libtiledb.so.2.18 (0x00007ff9e1d0b000)
python -c "import tiledbsoma; print(tiledbsoma.pytiledbsoma.version())"
## libtiledb=2.18.2
cd /tmp/test-soma-copy/
rm -rf pip-install/
python -c "import tiledbsoma; print(tiledbsoma.pytiledbsoma.version())"
## OSError: libtiledbsoma.so: cannot open shared object file: No such file or directory
pip uninstall --yes tiledbsoma

# `pip install -e` copies libtiledbsoma.so
git clone https://github.com/single-cell-data/TileDB-SOMA.git pip-install-e
cd pip-install-e
git checkout viviannguyen/do-not-cp-in-edit-mode
cd apis/python
pip install -e .
find . -name 'libtiledbsoma.so'
## ./src/tiledbsoma/libtiledbsoma.so
find . -name 'libtiledbsoma.so' | xargs ldd | grep libtiledb
## libtiledb.so.2.18 => /tmp/test-soma-copy/pip-install-e/dist/lib/libtiledb.so.2.18 (0x00007fb4308a0000)
pip uninstall --yes tiledbsoma
cd /tmp/test-soma-copy/
rm -rf pip-install-e/

# bdist_wheel copies libtiledbsoma.so
git clone https://github.com/single-cell-data/TileDB-SOMA.git wheel
cd wheel
git checkout viviannguyen/do-not-cp-in-edit-mode
cd apis/python
python setup.py bdist_wheel
unzip -l dist/tiledbsoma-1.5.0rc0.post83.dev3915525106-cp310-cp310-linux_x86_64.whl | grep '\.so'
## 1417912  2023-12-04 19:50   tiledbsoma/libtiledbsoma.so
##  839072  2023-12-04 19:51   tiledbsoma/pytiledbsoma.cpython-310-x86_64-linux-gnu.so
cd /tmp/test-soma-copy/
rm -rf wheel

# install pre-built libtiledb
mkdir -p external
wget --quiet https://github.com/jdblischak/centralized-tiledb-nightlies/releases/download/2023-12-03/libtiledb-2023-12-03.tar.gz
tar -C external -xzf libtiledb-2023-12-03.tar.gz
export TILEDB_PATH=$(pwd)/external
export LD_LIBRARY_PATH=$(pwd)/external/lib:$LD_LIBRARY_PATH

# install pre-built libtiledbsoma
wget --quiet https://github.com/jdblischak/centralized-tiledb-nightlies/releases/download/2023-12-03/libtiledbsoma-2023-12-03.tar.gz
tar -C external -xzf libtiledbsoma-2023-12-03.tar.gz
export TILEDBSOMA_PATH=$(pwd)/external

# `pip install` does not copy external libtiledbsoma.so
git clone https://github.com/single-cell-data/TileDB-SOMA.git pip-install-ext
cd pip-install-ext
git checkout viviannguyen/do-not-cp-in-edit-mode
cd apis/python
pip install .
find $VIRTUAL_ENV -name 'libtiledbsoma.so'
find $VIRTUAL_ENV -name 'pytiledbsoma*\.so' | xargs ldd | grep libtiledb
## libtiledbsoma.so => /tmp/test-soma-copy/external/lib/libtiledbsoma.so (0x00007fb8a1d3e000)
## libtiledb.so.2.18 => /tmp/test-soma-copy/external/lib/libtiledb.so.2.18 (0x00007fb89f782000)
python -c "import tiledbsoma; print(tiledbsoma.pytiledbsoma.version())"
## libtiledb=2.18.0
cd /tmp/test-soma-copy/
rm -rf pip-install-ext/
python -c "import tiledbsoma; print(tiledbsoma.pytiledbsoma.version())"
## libtiledb=2.18.0
pip uninstall --yes tiledbsoma

# `pip install -e` does not copy external libtiledbsoma.so
git clone https://github.com/single-cell-data/TileDB-SOMA.git pip-install-e-ext
cd pip-install-e-ext
git checkout viviannguyen/do-not-cp-in-edit-mode
cd apis/python
pip install -e .
find . -name 'libtiledbsoma.so'
find . -name 'pytiledbsoma*.so' | xargs ldd | grep libtiledb
## libtiledbsoma.so => /tmp/test-soma-copy/external/lib/libtiledbsoma.so (0x00007f3e88dbd000)
## libtiledb.so.2.18 => /tmp/test-soma-copy/external/lib/libtiledb.so.2.18 (0x00007f3e86801000)
pip uninstall --yes tiledbsoma
cd /tmp/test-soma-copy/
rm -rf pip-install-e-ext/

# bdist_wheel does not copy external libtiledbsoma.so
git clone https://github.com/single-cell-data/TileDB-SOMA.git wheel-ext
cd wheel-ext
git checkout viviannguyen/do-not-cp-in-edit-mode
cd apis/python
python setup.py bdist_wheel
unzip -l dist/tiledbsoma-1.5.0rc0.post83.dev3915525106-cp310-cp310-linux_x86_64.whl | grep '\.so'
## 839072  2023-12-04 20:05   tiledbsoma/pytiledbsoma.cpython-310-x86_64-linux-gnu.so
cd /tmp/test-soma-copy/
rm -rf wheel-ext

# `setup.py install --single-version-externally-managed` does not copy external libtiledbsoma.so
# https://github.com/TileDB-Inc/tiledbsoma-feedstock/blob/4175b10522b7f6e1ac8687b9ab729224b85896a4/recipe/build-tiledbsoma-py.sh#L8
git clone https://github.com/single-cell-data/TileDB-SOMA.git single-version
cd single-version
git checkout viviannguyen/do-not-cp-in-edit-mode
cd apis/python
python setup.py install --single-version-externally-managed --record record.txt
find $VIRTUAL_ENV -name 'libtiledbsoma.so'
find $VIRTUAL_ENV -name 'pytiledbsoma*\.so' | xargs ldd | grep libtiledb
## libtiledbsoma.so => /tmp/test-soma-copy/external/lib/libtiledbsoma.so (0x00007f12ef483000)
## libtiledb.so.2.18 => /tmp/test-soma-copy/external/lib/libtiledb.so.2.18 (0x00007f12ecec7000)
python -c "import tiledbsoma; print(tiledbsoma.pytiledbsoma.version())"
## libtiledb=2.18.0
cd /tmp/test-soma-copy/
rm -rf single-version
python -c "import tiledbsoma; print(tiledbsoma.pytiledbsoma.version())"
## libtiledb=2.18.0
pip uninstall --yes tiledbsoma

jdblischak · 2023-12-04T20:26:41Z

However, while we are on the subject of copying shared objects, I am confused by the behavior for copying libtiledb.so. When libtiledbsoma.so is built during the package build, it is copied into the Python package structure. However, it doesn't copy libtiledb.so as well. Thus it is broken if the source is deleted. I confirm below that this is the current behavior in main, so it's not related to the current PR.

# continuing from above

# `pip install` does not copy needed libtiledb.so
unset LD_LIBRARY_PATH
unset TILEDB_PATH
unset TILEDBSOMA_PATH
git clone https://github.com/single-cell-data/TileDB-SOMA.git main
cd main
cd apis/python
pip install .
find $VIRTUAL_ENV -name '*tile*.so'
## /tmp/test-soma-copy/venv-soma/lib/python3.10/site-packages/tiledbsoma/libtiledbsoma.so
## /tmp/test-soma-copy/venv-soma/lib/python3.10/site-packages/tiledbsoma/pytiledbsoma.cpython-310-x86_64-linux-gnu.so
## /tmp/test-soma-copy/venv-soma/lib/python3.10/site-packages/tiledb/libtiledb.cpython-310-x86_64-linux-gnu.so
find $VIRTUAL_ENV -name 'libtiledbsoma.so' | xargs ldd | grep libtiledb
## libtiledb.so.2.18 => /tmp/test-soma-copy/main/dist/lib/libtiledb.so.2.18 (0x00007f682fa5a000)
python -c "import tiledbsoma; print(tiledbsoma.pytiledbsoma.version())"
## libtiledb=2.18.2
cd /tmp/test-soma-copy/
rm -rf main/
python -c "import tiledbsoma; print(tiledbsoma.pytiledbsoma.version())"
## OSError: libtiledbsoma.so: cannot open shared object file: No such file or directory
pip uninstall --yes tiledbsoma

nguyenv · 2023-12-05T18:00:28Z

I'll go ahead and add to this PR copying libtiledb.so if built from source.

nguyenv · 2023-12-07T20:07:56Z

I made the changes but will need to follow up again tomorrow or early next week with tests so that the codecov/path CI test doesn't complain.

jdblischak · 2023-12-07T20:30:40Z

I made the changes but will need to follow up again tomorrow or early next week with tests

I'll also plan on re-running my tests. Thanks!

nguyenv · 2023-12-12T03:09:48Z

I made the changes but will need to follow up again tomorrow or early next week with tests so that the codecov/path CI test doesn't complain.

Alright got the codecov tests passing.

jdblischak · 2023-12-12T16:34:08Z

I tested this morning from the latest commit. libtiledb.so still wasn't copied

mkdir -p /tmp/test-soma-copy
cd /tmp/test-soma-copy

# install python dependencies
python -m venv ./venv-soma
conda deactivate
source ./venv-soma/bin/activate
pip install --prefer-binary cmake pybind11-global typeguard sparse wheel

# `pip install` copies libtiledbsoma.so but not libtiledb.so
git clone https://github.com/single-cell-data/TileDB-SOMA.git pip-install
cd pip-install
git checkout viviannguyen/do-not-cp-in-edit-mode
cd apis/python
pip install .
find $VIRTUAL_ENV -name 'libtiledb.so'
find $VIRTUAL_ENV -name 'libtiledbsoma.so'
## /tmp/test-soma-copy/venv-soma/lib/python3.10/site-packages/tiledbsoma/libtiledbsoma.so
find $VIRTUAL_ENV -name 'libtiledbsoma.so' | xargs ldd | grep libtiledb
## libtiledb.so.2.18 => /tmp/test-soma-copy/pip-install/dist/lib/libtiledb.so.2.18 (0x00007f83b0dda000)
python -c "import tiledbsoma; print(tiledbsoma.pytiledbsoma.version())"
## libtiledb=2.18.2
cd /tmp/test-soma-copy/
rm -rf pip-install/
python -c "import tiledbsoma; print(tiledbsoma.pytiledbsoma.version())"
## OSError: libtiledbsoma.so: cannot open shared object file: No such file or directory

nguyenv · 2023-12-13T18:25:47Z

Yeah I was only copying libtiledb.so.2.18 and not libtiledb.so. Have corrected that now.

jdblischak · 2023-12-13T19:19:07Z

Now libtiledb.so is being copied into the package, but libtiledbsoma.so is still linked against the version in the build directory

mkdir -p /tmp/test-soma-copy
cd /tmp/test-soma-copy

# install python dependencies
python -m venv ./venv-soma
conda deactivate
source ./venv-soma/bin/activate
pip install --prefer-binary cmake pybind11-global typeguard sparse wheel

# `pip install` copies libtiledbsoma.so and libtiledb.so but the linking is wrong
git clone https://github.com/single-cell-data/TileDB-SOMA.git pip-install
cd pip-install
git checkout viviannguyen/do-not-cp-in-edit-mode
cd apis/python
pip install .
find $VIRTUAL_ENV -name 'libtiledb.so*'
## /tmp/test-soma-copy/venv-soma/lib/python3.10/site-packages/tiledbsoma/libtiledb.so
## /tmp/test-soma-copy/venv-soma/lib/python3.10/site-packages/tiledbsoma/libtiledb.so.2.18
find $VIRTUAL_ENV -name 'libtiledbsoma.so*'
## /tmp/test-soma-copy/venv-soma/lib/python3.10/site-packages/tiledbsoma/libtiledbsoma.so
find $VIRTUAL_ENV -name 'libtiledbsoma.so*' | xargs ldd | grep libtiledb
## libtiledb.so.2.18 => /tmp/test-soma-copy/pip-install/dist/lib/libtiledb.so.2.18 (0x00007f0e9481c000)
python -c "import tiledbsoma; print(tiledbsoma.pytiledbsoma.version())"
## libtiledb=2.18.2
cd /tmp/test-soma-copy/
rm -rf pip-install/
python -c "import tiledbsoma; print(tiledbsoma.pytiledbsoma.version())"
## OSError: libtiledbsoma.so: cannot open shared object file: No such file or directory
find $VIRTUAL_ENV -name 'libtiledbsoma.so*' | xargs ldd | grep libtiledb
## libtiledb.so.2.18 => not found

jdblischak · 2023-12-13T19:22:39Z

@nguyenv given the complexity of this copying behavior, do you think it would be worthwhile for me to write a GitHub Actions workflow to confirm this copying behavior?

nguyenv · 2023-12-13T20:02:25Z

Yes I think that would be worthwhile. Thank you so much for doing that. I will see how to get libtiledbsoma to point to the correct libtiledb.

jdblischak · 2023-12-20T21:44:38Z

Sorry I haven't put the pipeline together yet. I have been busy working on VCF stuff. I see that this PR has been linked to other Issues, so I quickly re-ran my test above. According to ldd, libtiledbsoma.so still can't find libtiledb.so, but somehow now tiledbsoma.pytiledbsoma.version() returns the correct version. I also noticed that the cython shared object can't find libtiledbsoma.so. Do you understand how this is working?

mkdir -p /tmp/test-soma-copy
cd /tmp/test-soma-copy

# install python dependencies
python -m venv ./venv-soma
conda deactivate
source ./venv-soma/bin/activate
pip install --prefer-binary cmake pybind11-global typeguard sparse wheel

# `pip install` copies libtiledbsoma.so and libtiledb.so
git clone https://github.com/single-cell-data/TileDB-SOMA.git pip-install
cd pip-install
git checkout viviannguyen/do-not-cp-in-edit-mode
cd apis/python
pip install .
find $VIRTUAL_ENV -name 'libtiledb.so*'
## /tmp/test-soma-copy/venv-soma/lib/python3.10/site-packages/tiledbsoma/libtiledb.so
## /tmp/test-soma-copy/venv-soma/lib/python3.10/site-packages/tiledbsoma/libtiledb.so.2.18
find $VIRTUAL_ENV -name 'libtiledbsoma.so*'
## /tmp/test-soma-copy/venv-soma/lib/python3.10/site-packages/tiledbsoma/libtiledbsoma.so
find $VIRTUAL_ENV -name 'libtiledbsoma.so*' | xargs ldd | grep libtiledb
## libtiledb.so.2.18 => /tmp/test-soma-copy/pip-install/dist/lib/libtiledb.so.2.18 (0x00007f7498eec000)
python -c "import tiledbsoma; print(tiledbsoma.pytiledbsoma.version())"
## libtiledb=2.18.2
cd /tmp/test-soma-copy/
rm -rf pip-install/
python -c "import tiledbsoma; print(tiledbsoma.pytiledbsoma.version())"
## libtiledb=2.18.2
find $VIRTUAL_ENV -name 'libtiledbsoma.so*' | xargs ldd | grep libtiledb
## libtiledb.so.2.18 => not found
ldd $VIRTUAL_ENV/lib/python3.10/site-packages/tiledbsoma/pytiledbsoma.cpython-310-x86_64-linux-gnu.so | grep tile
## libtiledbsoma.so => not found

nguyenv · 2023-12-21T00:23:04Z

Yeah it's finding it via -Wl,-rpath

nguyenv · 2024-02-15T17:18:45Z

Thanks for approving @jdblischak. Looks like I need someone else to approve the PR before I can merge though.

jdblischak · 2024-02-19T17:07:39Z

Today I confirmed that the nightly builds in my centralized-tiledb-nightlies no longer create the unnecessary libtiledbsoma.so, and I added a strict test to fail if it is ever starts getting created again.

Also note that I started reporting the RPATH, which properly points to the location of the external libtiledb.so and libtiledbsoma.so:

readelf -d apis/python/src/tiledbsoma/pytiledbsoma.*.so  | grep R*PATH
## 0x000000000000001d (RUNPATH)            Library runpath: 
## [
## /opt/hostedtoolcache/Python/3.11.8/x64/lib:
## /home/runner/work/centralized-tiledb-nightlies/centralized-tiledb-nightlies/install-libtiledbsoma/lib:
## /home/runner/work/centralized-tiledb-nightlies/centralized-tiledb-nightlies/install-libtiledb/lib:
## /home/runner/work/centralized-tiledb-nightlies/centralized-tiledb-nightlies/install-libtiledbsoma/lib/x86_64-linux-gnu:
## /home/runner/work/centralized-tiledb-nightlies/centralized-tiledb-nightlies/install-libtiledbsoma/lib64:
## /home/runner/work/centralized-tiledb-nightlies/centralized-tiledb-nightlies/install-libtiledb/lib/x86_64-linux-gnu:
## /home/runner/work/centralized-tiledb-nightlies/centralized-tiledb-nightlies/install-libtiledb/lib64
## ]

…eady exists (#1937) * Do not copy libtiledbsoma.so into package_data if it already exists * Add except ImportError * Copy TileDB shared object library if built from source * Format * Move load lib into __init__.py * Imports * Ignore __imit__.py * Also install and copy `libtiledb.so` * Set TileDB Path Location in `bld` Script * Need to also load tiledb shared object * Rebase on main * Remove `libtiledb.so` load * Update with more descriptive names * Add workflow to test Python shared object copying --------- Co-authored-by: John Blischak <jdblischak@gmail.com>

…eady exists (#1937) (#2163) * Do not copy libtiledbsoma.so into package_data if it already exists * Add except ImportError * Copy TileDB shared object library if built from source * Format * Move load lib into __init__.py * Imports * Ignore __imit__.py * Also install and copy `libtiledb.so` * Set TileDB Path Location in `bld` Script * Need to also load tiledb shared object * Rebase on main * Remove `libtiledb.so` load * Update with more descriptive names * Add workflow to test Python shared object copying --------- Co-authored-by: nguyenv <vivian@tiledb.com> Co-authored-by: John Blischak <jdblischak@gmail.com>

nguyenv changed the title ~~Viviannguyen/do not cp in edit mode~~ [python] Do not copy libtiledbsoma.so into package_data if it already exists Nov 30, 2023

jdblischak approved these changes Nov 30, 2023

View reviewed changes

johnkerl changed the title ~~[python] Do not copy libtiledbsoma.so into package_data if it already exists~~ [python] Do not copy libtiledbsoma.so into package_data if it already exists Nov 30, 2023

johnkerl changed the title ~~[python] Do not copy libtiledbsoma.so into package_data if it already exists~~ [python] Do not copy libtiledbsoma.so into package_data if it already exists Dec 1, 2023

nguyenv requested a review from jdblischak December 4, 2023 14:29

jdblischak approved these changes Dec 4, 2023

View reviewed changes

nguyenv force-pushed the viviannguyen/do-not-cp-in-edit-mode branch 2 times, most recently from a39d3c6 to 8f8d1ec Compare December 7, 2023 18:29

nguyenv force-pushed the viviannguyen/do-not-cp-in-edit-mode branch 2 times, most recently from 450dfc1 to 4a2a06f Compare December 12, 2023 02:54

nguyenv force-pushed the viviannguyen/do-not-cp-in-edit-mode branch from 4a2a06f to 0e2e71c Compare December 13, 2023 18:25

nguyenv linked an issue Dec 19, 2023 that may be closed by this pull request

[python] pip install directly from GitHub not working #1991

Closed

This was referenced Dec 19, 2023

[misc] acceptance test GHA workflow chanzuckerberg/cellxgene-census#897

Merged

remove editable flag from full-unittest.yml workflow chanzuckerberg/cellxgene-census#907

Closed

nguyenv and others added 2 commits February 13, 2024 17:07

Update with more descriptive names

f9b507e

Add workflow to test Python shared object copying

453d03b

jdblischak approved these changes Feb 15, 2024

View reviewed changes

nguyenv requested review from eddelbuettel, johnkerl, thetorpedodog, gspowley and teo-tsirpanis February 15, 2024 17:16

johnkerl approved these changes Feb 16, 2024

View reviewed changes

johnkerl merged commit f4999d8 into main Feb 16, 2024
21 checks passed

johnkerl deleted the viviannguyen/do-not-cp-in-edit-mode branch February 16, 2024 15:09

johnkerl added the backport release-1.7 label Feb 22, 2024

github-actions bot mentioned this pull request Feb 22, 2024

[Backport release-1.7] [python] Do not copy libtiledbsoma.so into package_data if it already exists #2163

Merged

jdblischak mentioned this pull request Mar 1, 2024

tiledbsoma 1.8.0 pre-check TileDB-Inc/tiledbsoma-feedstock#91

Closed

This was referenced Mar 5, 2024

[ci] Updated hard-coded core version in another file #2207

Merged

[ci] Run python-so-copying.yml on Linux and Mac both [WIP] #2208

Closed

johnkerl added a commit that referenced this pull request Mar 5, 2024

[python] Revert #1937

e00d2e6

johnkerl mentioned this pull request Mar 5, 2024

[release-1.8] Revert #1937 #2209

Closed

johnkerl added a commit that referenced this pull request Mar 5, 2024

[release-1.7] Revert #1937

1139e99

jdblischak mentioned this pull request Mar 6, 2024

[ci] Add MacOS job to test shared object copying #2220

Merged

This was referenced Mar 6, 2024

[release-1.7] Revert #1937 #2211

Closed

[ci] dylib-copy logic appears to be broken on MacOS #2210

Closed

This was referenced Mar 6, 2024

[python] Fix and test setup.py flags to external shared objects #2221

Merged

[ci] Only run build tests when build files are modified #2229

Merged

This was referenced May 1, 2024

The new scikit-build-core setup copies external shared objects into Python wheel TileDB-Inc/TileDB-VCF#717

Open

[python/ci] Add CI job to test building wheel from sdist #2506

Merged

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

[python] Do not copy `libtiledbsoma.so` into `package_data` if it already exists #1937

[python] Do not copy `libtiledbsoma.so` into `package_data` if it already exists #1937

nguyenv commented Nov 30, 2023 •

edited

Loading

codecov-commenter commented Dec 1, 2023 •

edited by codecov bot

Loading

jdblischak commented Dec 1, 2023

nguyenv commented Dec 4, 2023

jdblischak commented Dec 4, 2023 •

edited

Loading

jdblischak commented Dec 4, 2023

nguyenv commented Dec 5, 2023

nguyenv commented Dec 7, 2023

jdblischak commented Dec 7, 2023

nguyenv commented Dec 12, 2023

jdblischak commented Dec 12, 2023

nguyenv commented Dec 13, 2023

jdblischak commented Dec 13, 2023 •

edited

Loading

jdblischak commented Dec 13, 2023

nguyenv commented Dec 13, 2023

jdblischak commented Dec 20, 2023

nguyenv commented Dec 21, 2023

nguyenv commented Feb 15, 2024

jdblischak commented Feb 19, 2024

[python] Do not copy libtiledbsoma.so into package_data if it already exists #1937

[python] Do not copy libtiledbsoma.so into package_data if it already exists #1937

Conversation

nguyenv commented Nov 30, 2023 • edited Loading

codecov-commenter commented Dec 1, 2023 • edited by codecov bot Loading

Codecov Report

jdblischak commented Dec 1, 2023

nguyenv commented Dec 4, 2023

jdblischak commented Dec 4, 2023 • edited Loading

jdblischak commented Dec 4, 2023

nguyenv commented Dec 5, 2023

nguyenv commented Dec 7, 2023

jdblischak commented Dec 7, 2023

nguyenv commented Dec 12, 2023

jdblischak commented Dec 12, 2023

nguyenv commented Dec 13, 2023

jdblischak commented Dec 13, 2023 • edited Loading

jdblischak commented Dec 13, 2023

nguyenv commented Dec 13, 2023

jdblischak commented Dec 20, 2023

nguyenv commented Dec 21, 2023

nguyenv commented Feb 15, 2024

jdblischak commented Feb 19, 2024

[python] Do not copy `libtiledbsoma.so` into `package_data` if it already exists #1937

[python] Do not copy `libtiledbsoma.so` into `package_data` if it already exists #1937

nguyenv commented Nov 30, 2023 •

edited

Loading

codecov-commenter commented Dec 1, 2023 •

edited by codecov bot

Loading

jdblischak commented Dec 4, 2023 •

edited

Loading

jdblischak commented Dec 13, 2023 •

edited

Loading