[python] pin pandas-stubs>=2 during pre-commit mypy hook
#2854
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also simplify some `if TYPE_CHECKING` blocks fixes #2839
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #2854 +/- ##
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+ Coverage 90.01% 90.19% +0.17%
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Files 37 37
Lines 3957 3957
==========================================
+ Hits 3562 3569 +7
+ Misses 395 388 -7
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* pin `pandas-stubs>=2` during pre-commit `mypy` hook also simplify some `if TYPE_CHECKING` blocks fixes #2839 * add r-ci.yml exclusions
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| - '!.pre-commit-config.yaml' | ||
| - '!apis/python/**' | ||
| - '!docs/**' | ||
| - '!LICENSE'' |
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typo here, fix in #2856
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* 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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* [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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* [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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* [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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* [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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* 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$tiledb_timestamp` Also plumb timestamps through for `write_soma()` in resume-mode * Timestamp range support for dataframe * (First half) new timestamp test for SOMADataFrame * Second half of new timestamp passing all but three reopen tests * Test can now use factor * Read and write DataFrame and {Dense,Sparse}Array under timestamps * Quieter warnings * Adapt one timestamped test * Pause one test predicate for collections * clang-format as obsessing over one whitespace char before a comment is added value * Micro-fix following code review More changes to follow in wider changeset * Update changelog Bump develop version --------- Co-authored-by: Paul Hoffman <mojaveazure@users.noreply.github.com> Co-authored-by: Ryan Williams <ryan.williams@tiledb.com> Co-authored-by: John Kerl <kerl.john.r@gmail.com> Co-authored-by: nguyenv <vivian@tiledb.com> Co-authored-by: Paul Hoffman <paul.hoffman@tiledb.com>
mojaveazure
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Aug 26, 2024
* [python] pin `pandas-stubs>=2` during pre-commit `mypy` hook (#2854) * pin `pandas-stubs>=2` during pre-commit `mypy` hook also simplify some `if TYPE_CHECKING` blocks fixes #2839 * add r-ci.yml exclusions * `actions{cache,checkout,setup-python}` upgrades (#2856) * CI: use `pip` directly (instead of `python -m pip`) * CI: checkout@v4, setup-python@v5 cache@v4 * disable setup-python cache for lint/pre-commit See actions/setup-python#919; setup-python cache likely doesn't help much here, as we only `pip install pre-commit`, and cache `~/.cache/pre-commit` separately using `actions/cache`. * bump to codecov-action@v4 rm coverage/uploader pin added in #2827, per codecov/uploader#1673 (comment) * `s/MacOS/macOS/ * fix typo from #2854 * [python] Offer better guidance on attribute names with `.` (#2864) * [python] Move `_update_column` into pybind11 (#2862) * [r] Expose `tiledb_timestamp` parameter to `$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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also simplify some
if TYPE_CHECKINGblocksIssue and/or context: #2839, #2853
The unpinned
pandas-stubsdep in.pre-commit-config.yamlallowed existing local environments (and old cachedsetup-pythonenvironments, which in some cases were being incorrectly used in our GHAs, per actions/setup-python#919) to run the pre-commitmypyhook usingpandas-stubs<2, wherepd.Seriesis the type, andpd.Series[Any]requires a# type: ignore[misc]annotation.With
pandas-stubs>=2(which new environments have been picking up),pd.Series[Any]is the correct type, and the# type: ignore[misc]annotation was flagged as "unused" (example).Pinning
pandas-stubs>=2, and using the correspondingpd.{Series,Index}[Any]annotations whenTYPE_CHECKING, should resolve this conflict, in both new and existing environments (in existing environments,pre-commitwill recognize the newpandas-stubs>=2pin, and create a new venv that incorporates it).