[python] `actions{cache,checkout,setup-python}` upgrades #2856

ryan-williams · 2024-08-08T17:35:15Z

Issue and/or context: some of this came from debugging actions/setup-python#919 on #2853. In particular, I wanted to test on latest setup-python (v5) there, though it turns out that issue seems to occur on both v4 and v5.

Changes:

Upgrade GHA versions:
- actions/checkout: v3 → v4
- actions/setup-python: v4 → v5
- actions/cache: v3 → v4
Use pip instead of python -m pip
- This is a no-op in all cases here, afaik
Bump codecov-action to v4 here (per uploader#1673 comment), and remove the v0.7.3 pin (added in #2827)

See actions/setup-python#919; setup-python cache likely doesn't help much here, as we only `pip install pre-commit`, and cache `~/.cache/pre-commit` separately using `actions/cache`.

rm coverage/uploader pin added in #2827, per codecov/uploader#1673 (comment)

codecov · 2024-08-08T17:44:58Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 90.19%. Comparing base (3fae283) to head (b9e97bf).

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2856      +/-   ##
==========================================
+ Coverage   90.04%   90.19%   +0.15%     
==========================================
  Files          37       37              
  Lines        3957     3957              
==========================================
+ Hits         3563     3569       +6     
+ Misses        394      388       -6

Flag	Coverage Δ
python	`90.19% <ø> (+0.15%)`	⬆️

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

Components	Coverage Δ
python_api	`90.19% <ø> (+0.15%)`	⬆️
libtiledbsoma	`∅ <ø> (∅)`

ryan-williams · 2024-08-08T20:33:50Z

r-ci.yml failure is the usual segfault. I broke it in a new way in #2854, without noticing, but have fixed that here. Everything else ✅, merging.

* [python] pin `pandas-stubs>=2` during pre-commit `mypy` hook (#2854) * pin `pandas-stubs>=2` during pre-commit `mypy` hook also simplify some `if TYPE_CHECKING` blocks fixes #2839 * add r-ci.yml exclusions * `actions{cache,checkout,setup-python}` upgrades (#2856) * CI: use `pip` directly (instead of `python -m pip`) * CI: checkout@v4, setup-python@v5 cache@v4 * disable setup-python cache for lint/pre-commit See actions/setup-python#919; setup-python cache likely doesn't help much here, as we only `pip install pre-commit`, and cache `~/.cache/pre-commit` separately using `actions/cache`. * bump to codecov-action@v4 rm coverage/uploader pin added in #2827, per codecov/uploader#1673 (comment) * `s/MacOS/macOS/ * fix typo from #2854 * [python] Offer better guidance on attribute names with `.` (#2864) * [python] Move `_update_column` into pybind11 (#2862) * [r] Expose `tiledb_timestamp` parameter to `$reopen()` Allow `$reopen()` to reopen at a particular timestamp; by default, the timestamp is set to `NULL` to reopen at the curren time. This is needed for compatibility between libtiledbsoma's timestamp handling and resume-mode [SC-52694](https://app.shortcut.com/tiledb-inc/story/52694/allow-reopen-to-take-a-timestamp-for-reopening) --------- Co-authored-by: Ryan Williams <ryan.williams@tiledb.com> Co-authored-by: John Kerl <kerl.john.r@gmail.com> Co-authored-by: nguyenv <vivian@tiledb.com>

* Timestamp range support for dataframe * Extended support * (First half) new timestamp test for SOMADataFrame * Second half of new timestamp passing all but three reopen tests * [r] Expose `tiledb_timestamp` parameter to `$reopen()` (#2866) * [python] pin `pandas-stubs>=2` during pre-commit `mypy` hook (#2854) * pin `pandas-stubs>=2` during pre-commit `mypy` hook also simplify some `if TYPE_CHECKING` blocks fixes #2839 * add r-ci.yml exclusions * `actions{cache,checkout,setup-python}` upgrades (#2856) * CI: use `pip` directly (instead of `python -m pip`) * CI: checkout@v4, setup-python@v5 cache@v4 * disable setup-python cache for lint/pre-commit See actions/setup-python#919; setup-python cache likely doesn't help much here, as we only `pip install pre-commit`, and cache `~/.cache/pre-commit` separately using `actions/cache`. * bump to codecov-action@v4 rm coverage/uploader pin added in #2827, per codecov/uploader#1673 (comment) * `s/MacOS/macOS/ * fix typo from #2854 * [python] Offer better guidance on attribute names with `.` (#2864) * [python] Move `_update_column` into pybind11 (#2862) * [r] Expose `tiledb_timestamp` parameter to `$reopen()` Allow `$reopen()` to reopen at a particular timestamp; by default, the timestamp is set to `NULL` to reopen at the curren time. This is needed for compatibility between libtiledbsoma's timestamp handling and resume-mode [SC-52694](https://app.shortcut.com/tiledb-inc/story/52694/allow-reopen-to-take-a-timestamp-for-reopening) --------- Co-authored-by: Ryan Williams <ryan.williams@tiledb.com> Co-authored-by: John Kerl <kerl.john.r@gmail.com> Co-authored-by: nguyenv <vivian@tiledb.com> * [r] [NO BACKPORT] Expose timestamps publicly and plumb through for resume-mode (#2871) Expose timestamps publicly through a new active binding; replace calls to `private$tiledb_timestamp` with `self$tiledb_timestamp` Also plumb timestamps through for `write_soma()` in resume-mode * Timestamp range support for dataframe * (First half) new timestamp test for SOMADataFrame * Second half of new timestamp passing all but three reopen tests * Test can now use factor * Read and write DataFrame and {Dense,Sparse}Array under timestamps * Quieter warnings * Adapt one timestamped test * Pause one test predicate for collections * clang-format as obsessing over one whitespace char before a comment is added value * Micro-fix following code review More changes to follow in wider changeset * Update changelog Bump develop version --------- Co-authored-by: Paul Hoffman <mojaveazure@users.noreply.github.com> Co-authored-by: Ryan Williams <ryan.williams@tiledb.com> Co-authored-by: John Kerl <kerl.john.r@gmail.com> Co-authored-by: nguyenv <vivian@tiledb.com> Co-authored-by: Paul Hoffman <paul.hoffman@tiledb.com>

* [python] pin `pandas-stubs>=2` during pre-commit `mypy` hook (#2854) * pin `pandas-stubs>=2` during pre-commit `mypy` hook also simplify some `if TYPE_CHECKING` blocks fixes #2839 * add r-ci.yml exclusions * `actions{cache,checkout,setup-python}` upgrades (#2856) * CI: use `pip` directly (instead of `python -m pip`) * CI: checkout@v4, setup-python@v5 cache@v4 * disable setup-python cache for lint/pre-commit See actions/setup-python#919; setup-python cache likely doesn't help much here, as we only `pip install pre-commit`, and cache `~/.cache/pre-commit` separately using `actions/cache`. * bump to codecov-action@v4 rm coverage/uploader pin added in #2827, per codecov/uploader#1673 (comment) * `s/MacOS/macOS/ * fix typo from #2854 * [python] Offer better guidance on attribute names with `.` (#2864) * [python] Move `_update_column` into pybind11 (#2862) * [r] Expose `tiledb_timestamp` parameter to `$reopen()` Allow `$reopen()` to reopen at a particular timestamp; by default, the timestamp is set to `NULL` to reopen at the curren time. This is needed for compatibility between libtiledbsoma's timestamp handling and resume-mode [SC-52694](https://app.shortcut.com/tiledb-inc/story/52694/allow-reopen-to-take-a-timestamp-for-reopening) --------- Co-authored-by: Ryan Williams <ryan.williams@tiledb.com> Co-authored-by: John Kerl <kerl.john.r@gmail.com> Co-authored-by: nguyenv <vivian@tiledb.com>

ryan-williams added 4 commits August 8, 2024 13:22

CI: use pip directly (instead of python -m pip)

105def8

CI: checkout@v4, setup-python@v5 cache@v4

f0dcefb

disable setup-python cache for lint/pre-commit

81c0b30

See actions/setup-python#919; setup-python cache likely doesn't help much here, as we only `pip install pre-commit`, and cache `~/.cache/pre-commit` separately using `actions/cache`.

bump to codecov-action@v4

cdfb4d2

rm coverage/uploader pin added in #2827, per codecov/uploader#1673 (comment)

ryan-williams marked this pull request as ready for review August 8, 2024 18:50

ryan-williams requested review from johnkerl and jdblischak August 8, 2024 18:50

jdblischak approved these changes Aug 8, 2024

View reviewed changes

johnkerl approved these changes Aug 8, 2024

View reviewed changes

ryan-williams added 2 commits August 8, 2024 15:32

`s/MacOS/macOS/

98fd592

fix typo from #2854

b9e97bf

ryan-williams mentioned this pull request Aug 8, 2024

[python] pin pandas-stubs>=2 during pre-commit mypy hook #2854

Merged

ryan-williams merged commit 7742bff into main Aug 8, 2024
24 of 25 checks passed

ryan-williams deleted the rw/ci branch August 8, 2024 20:34

ryan-williams mentioned this pull request Aug 9, 2024

spawn Unknown system error -86 with uploader 0.8.0 (via codecov-action) codecov/uploader#1673

Closed

johnkerl changed the title ~~actions{cache,checkout,setup-python} upgrades~~ [python] actions{cache,checkout,setup-python} upgrades Sep 17, 2024

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[python] `actions{cache,checkout,setup-python}` upgrades #2856

[python] `actions{cache,checkout,setup-python}` upgrades #2856

ryan-williams commented Aug 8, 2024 •

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ryan-williams commented Aug 8, 2024

[python] actions{cache,checkout,setup-python} upgrades #2856

[python] actions{cache,checkout,setup-python} upgrades #2856

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ryan-williams commented Aug 8, 2024

[python] `actions{cache,checkout,setup-python}` upgrades #2856

[python] `actions{cache,checkout,setup-python}` upgrades #2856

ryan-williams commented Aug 8, 2024 •

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