[python] pin codecov/uploader==0.7.3 in codecov-action
#2827
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #2827 +/- ##
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Coverage 90.06% 90.06%
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Files 37 37
Lines 3937 3937
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Hits 3546 3546
Misses 391 391
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This was referenced Aug 2, 2024
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ryan-williams
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Aug 8, 2024
rm coverage/uploader pin added in #2827, per codecov/uploader#1673 (comment)
ryan-williams
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Aug 8, 2024
* 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
mojaveazure
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Aug 9, 2024
* [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>
eddelbuettel
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Aug 9, 2024
* [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>
eddelbuettel
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Aug 19, 2024
* [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>
eddelbuettel
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Aug 22, 2024
* [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>
mojaveazure
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Aug 26, 2024
* 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$tiledb_timestamp` Also plumb timestamps through for `write_soma()` in resume-mode * Timestamp range support for dataframe * (First half) new timestamp test for SOMADataFrame * Second half of new timestamp passing all but three reopen tests * Test can now use factor * Read and write DataFrame and {Dense,Sparse}Array under timestamps * Quieter warnings * Adapt one timestamped test * Pause one test predicate for collections * clang-format as obsessing over one whitespace char before a comment is added value * Micro-fix following code review More changes to follow in wider changeset * Update changelog Bump develop version --------- Co-authored-by: Paul Hoffman <mojaveazure@users.noreply.github.com> Co-authored-by: Ryan Williams <ryan.williams@tiledb.com> Co-authored-by: John Kerl <kerl.john.r@gmail.com> Co-authored-by: nguyenv <vivian@tiledb.com> Co-authored-by: Paul Hoffman <paul.hoffman@tiledb.com>
mojaveazure
added a commit
that referenced
this pull request
Aug 26, 2024
* [python] pin `pandas-stubs>=2` during pre-commit `mypy` hook (#2854) * pin `pandas-stubs>=2` during pre-commit `mypy` hook also simplify some `if TYPE_CHECKING` blocks fixes #2839 * add r-ci.yml exclusions * `actions{cache,checkout,setup-python}` upgrades (#2856) * CI: use `pip` directly (instead of `python -m pip`) * CI: checkout@v4, setup-python@v5 cache@v4 * disable setup-python cache for lint/pre-commit See actions/setup-python#919; setup-python cache likely doesn't help much here, as we only `pip install pre-commit`, and cache `~/.cache/pre-commit` separately using `actions/cache`. * bump to codecov-action@v4 rm coverage/uploader pin added in #2827, per codecov/uploader#1673 (comment) * `s/MacOS/macOS/ * fix typo from #2854 * [python] Offer better guidance on attribute names with `.` (#2864) * [python] Move `_update_column` into pybind11 (#2862) * [r] Expose `tiledb_timestamp` parameter to `$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>
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Issue and/or context: work-around for codecov/uploader#1673
uploader@0.8.0 was released 4h ago, and broke our invocations of codecov-action@v3 (example job that passed yesterday, and failed on re-run today)
Failures look like: